TY - JOUR TI - Rapid multilocus adaptation of clonal cabbage leaf curl virus populations to Arabidopsis thaliana AU - Hoyer, J. Steen AU - Wilkins, Olivia W. AU - Munshi, Aanandi AU - Wiese, Emma AU - Dubey, Divya AU - Renard, Savannah AU - Mortensen, Karoline Rosendal Hartø AU - Dye, Anna E. AU - Carbone, Ignazio AU - Duffy, Siobain AU - Ascencio-Ibáñez, José Trinidad AB - Abstract Cabbage leaf curl virus (CabLCV) has a bipartite single-stranded DNA genome and infects the model plant Arabidopsis thaliana . CabLCV serves as a model for the genus Begomovirus , members of which cause tremendous crop losses worldwide. We have used CabLCV as a model for within-plant virus evolution by inoculating individual plants with infectious clones of either a wild-type or mutagenized version of the CabLCV genome. Consistent with previous reports, detrimental substitutions in the Replication-associated gene (Rep) were readily compensated for by direct reversion and/or alternative mutations. A surprising number of common mutations were detected elsewhere in both viral segments (DNA-A and DNA-B) indicating convergent evolution and suggesting that CabLCV may not be as well adapted to A. thaliana as commonly presumed. Consistent with this idea, a spontaneous coat protein variant consistently rose to high allele frequency in susceptible accession Col-0, at a higher rate than in hypersusceptible accession Sei-0. Numerous high-frequency mutations were also detected in a candidate Rep binding site in DNA-B. Our results reinforce the fact that spontaneous mutation of this type of virus occurs rapidly and can change the majority consensus sequence of a within-plant virus population in weeks. DA - 2021/12/1/ PY - 2021/12/1/ DO - 10.1101/2021.11.29.468282 UR - https://doi.org/10.1101/2021.11.29.468282 ER - TY - JOUR TI - Lipid remodeling in response to low phosphate is modulated by inositol pyrophosphates AU - Cridland, Caitlin AU - Land, Eric AU - Williams, Phoebe AU - Hildreth, Sherry AU - Helm, Rich AU - Perera, Imara AU - Gillaspy, Glenda T2 - The FASEB Journal AB - Under changing environmental conditions, plants are able to modulate their lipids to respond to varying nutrient availability. Phosphate (Pi) is an essential nutrient for plants, required for plant growth and seed viability. Under Pi stress, plants undergo dynamic morphological and metabolism changes to leverage available Pi, including the modulation of lipids. Plants have been shown to “remodel” their lipid membrane profiles under phosphate starvation, degrading phospholipids in the cell membranes and utilizing the generated phosphorus for essential biological processes. By concomitantly inducing a phospholipid hydrolysis pathway and galactolipid biosynthetic pathway, membrane phospholipids are replaced by non-phosphorus containing galactolipids and sulfolipids. The inositol phosphate (InsP) signaling pathway is a crucial element of the plant's ability to respond to changing energy conditions. Inositol hexakisphosphate (InsP6) is the most abundant InsP signaling molecule and can be phosphorylated further by VIP kinases, resulting in inositol pyrophosphates (PP-InsPs). PP-InsPs have high energy bonds and have been linked to maintaining Pi and energy homeostasis in yeast and plants. Using liquid chromatography-mass spectrometry and tandem mass spectrometry, we have examined the lipid profiles of three Arabidopsis PP-InsP mutants, in response to Pi depletion, to address the role of PP-InsPs in Pi sensing. Our results suggest that PP-InsPs play a crucial role in Pi sensing and are involved in the regulation of lipid biosynthesis. Furthermore, the changes in the abundance of lipids suggest a possible direction for future seed oil engineering strategies. DA - 2021/5// PY - 2021/5// DO - 10.1096/fasebj.2021.35.s1.04115 UR - http://dx.doi.org/10.1096/fasebj.2021.35.s1.04115 ER - TY - JOUR TI - Tuning Gene Expression by Phosphate in the Methanogenic Archaeon Methanococcus maripaludis AU - Akinyemi, Taiwo S. AU - Shao, Nana AU - Lyu, Zhe AU - Drake, Ian J. AU - Liu, Yuchen AU - Whitman, William B. T2 - ACS Synthetic Biology AB - Methanococcus maripaludis is a rapidly growing, hydrogenotrophic, and genetically tractable methanogen with unique capabilities to convert formate and CO2 to CH4. The existence of genome-scale metabolic models and an established, robust system for both large-scale and continuous cultivation make it amenable for industrial applications. However, the lack of molecular tools for differential gene expression has hindered its application as a microbial cell factory to produce biocatalysts and biochemicals. In this study, a library of differentially regulated promoters was designed and characterized based on the pst promoter, which responds to the inorganic phosphate concentration in the growth medium. Gene expression increases by 4- to 6-fold when the medium phosphate drops to growth-limiting concentrations. Hence, this regulated system decouples growth from heterologous gene expression without the need for adding an inducer. The minimal pst promoter is identified and contains a conserved AT-rich region, a factor B recognition element, and a TATA box for phosphate-dependent regulation. Rational changes to the factor B recognition element and start codon had no significant impact on expression; however, changes to the transcription start site and the 5' untranslated region resulted in the differential protein production with regulation remaining intact. Compared to a previous expression system based upon the histone promoter, this regulated expression system resulted in significant improvements in the expression of a key methanogenic enzyme complex, methyl-coenzyme M reductase, and the potentially toxic arginine methyltransferase MmpX. DA - 2021/11/19/ PY - 2021/11/19/ DO - 10.1021/acssynbio.1c00322 VL - 10 IS - 11 SP - 3028-3039 UR - http://dx.doi.org/10.1021/acssynbio.1c00322 ER - TY - JOUR TI - Back to the Source: Molecular Identification of Methanogenic Archaea as Markers of Colonic Methane Production AU - Lyu, Zhe T2 - Digestive Diseases and Sciences DA - 2021/11// PY - 2021/11// DO - 10.1007/s10620-021-06839-0 VL - 66 IS - 11 SP - 3661-3664 UR - http://dx.doi.org/10.1007/s10620-021-06839-0 ER - TY - JOUR TI - Creation of a Cohort of Educational Research Practitioners: The TH!NK Researchers Program AU - Gallardo-Williams, Maria T. AU - Parks, Lisa D. AU - Carson, Susan T2 - The Journal of Faculty Development DA - 2021/// PY - 2021/// VL - 35 IS - 2 SP - 10–19 ER - TY - JOUR TI - The Role of Fire in the Dynamics of Piedmont Vegetation AU - Spooner, Joanna K. AU - Peet, Robert K. AU - Schafale, Michael P. AU - Weakley, Alan S. AU - Wentworth, Thomas R. T2 - FIRE ECOLOGY AND MANAGEMENT PAST, PRESENT, AND FUTURE OF US FORESTED ECOSYSTEMS AB - The Piedmont (PDMT) ecoregion of the USA stretches from New Jersey to Alabama, nestled between the Coastal Plain and Blue Ridge Mountain physiographic provinces. Many of the notable Piedmont plant communities, including the dominant oak-hickory forests of the region, are reliant upon fire to some degree. Before human settlement, most Piedmont vegetation burned relatively frequently and at low intensities, resulting in extensive closed canopy oak-hickory forests, studded with patches of open woodland and savanna largely defined by unusual soil conditions. Indigenous peoples of the Piedmont used fire as a land management tool for both agriculture and game production. Historical changes in land use throughout the region have altered fire regimes and changed forest dynamics dramatically over the past 400 years. Euro-American settlement led to widespread clearing of land for agriculture and logging; by the early twentieth century, very little old-growth forest remained in the Piedmont. During the mid-twentieth century, the decline of agriculture and the aggressive suppression and exclusion of wildfires brought about the growth of successional forests in the place of older, fire-mediated communities. The Piedmont region is currently experiencing a rapid expansion of the human population and land development, making restoration of the historical fire regime a challenge. However, land managers frequently do use prescribed fire to enhance timberland and restore rare plant communities. DA - 2021/// PY - 2021/// DO - 10.1007/978-3-030-73267-7_2 VL - 39 SP - 31-62 SN - 1568-1319 KW - Indigenous peoples KW - Land-use change KW - Mesophication KW - Oak-hickory forest KW - Oak-pine forest KW - Prescribed fire KW - Savanna KW - Ultisols KW - Heliophytes KW - Forest management KW - Forest structure KW - Oak regeneration KW - Restoration KW - Disturbance KW - Southeastern North America ER - TY - JOUR TI - The ALOG family members OsG1L1 and OsG1L2 regulate inflorescence branching in rice AU - Franchini, Emanuela AU - Beretta, Veronica M. AU - Din, Israr Ud AU - Lacchini, Elia AU - Broeck, Lisa Van AU - Sozzani, Rosangela AU - Orozco-Arroyo, Gregorio AU - Adam, Hélène AU - Jouannic, Stefan AU - Gregis, Veronica AU - Kater, Martin M. AB - ABSTRACT The architecture of the rice inflorescence is an important determinant of seed yield. The length of the inflorescence and the number of branches are among the key factors determining the amount of spikelets, and thus seeds, that will develop. Especially the timing of the identity transition from indeterminate branch meristem to determinate spikelet meristem regulates the complexity of the inflorescence. In this context, the ALOG gene TAWAWA1 ( TAW1 ) has been shown to delay the transition to determinate spikelet development in rice. Recently, by combining precise laser microdissection of inflorescence meristems with RNA-seq we observed that two ALOG genes, Oryza sativa OsG1-like 1 ( OsG1L1 ) and OsG1L2 , have an expression profile similar to TAW1 . Here we report that osg1l1 and osg1l2 loss-of-function CRISPR mutants have similar phenotypes as the taw1 mutant, suggesting that these genes might act on related pathways during inflorescence development. Transcriptome analysis of the osg1l2 mutant suggested interactions of OsG1L2 with other known inflorescence architecture regulators and the datasets were also used for the construction of a gene regulatory network (GRN) proposing interactions between genes potentially involved in controlling inflorescence development in rice. The spatio-temporal expression profiling and phenotypical analysis of CRISPR loss-of-function mutants of the homeodomain-leucine zipper transcription factor gene OsHOX14 suggest that the proposed GRN indeed serves as a valuable resource for the identification of new players involved in rice inflorescence development. One-sentence summary OsG1L1 and OsG1L2 control panicle architecture through delaying the transition from indeterminate branch- to determinate spikelet-meristem identity. DA - 2021/5/3/ PY - 2021/5/3/ DO - 10.1101/2021.05.03.442460 VL - 5 UR - https://doi.org/10.1101/2021.05.03.442460 ER - TY - JOUR TI - Gene regulatory networks for compatible versus incompatible grafts identify a role for SlWOX4 during junction formation AU - Thomas, Hannah AU - Broeck, Lisa Van AU - Spurney, Ryan AU - Sozzani, Rosangela AU - Frank, Margaret AB - Abstract Graft incompatibility is a poorly understood phenomenon that presents a serious agricultural challenge. Unlike immediate incompatibility that results in rapid death, delayed incompatibility can take months or even years to manifest, creating a significant economic burden for perennial crop production. To gain insight into the genetic mechanisms underlying this phenomenon, we developed a model system with Solanum lycopersicum ‘tomato’ and Capsicum annuum ‘pepper’ heterografting, which expresses signs of anatomical junction failure within the first week of grafting. By generating a detailed timeline for junction formation we were able to pinpoint the cellular basis for this delayed incompatibility. Furthermore, we infer gene regulatory networks for compatible self-grafts versus incompatible heterografts based on these key anatomical events, which predict core regulators for grafting. Finally, we delve into the role of vascular development in graft formation and validate SlWOX4 as a regulator for grafting in tomato. Notably, SlWOX4 is the first gene to be functionally implicated in vegetable crop grafting. DA - 2021/2/27/ PY - 2021/2/27/ DO - 10.1101/2021.02.26.433082 VL - 2 UR - https://doi.org/10.1101/2021.02.26.433082 ER - TY - JOUR TI - Tissue Regeneration with Hydrogel Encapsulation: A Review of Developments in Plants and Animals AU - Krishnamoorthy, Srikumar AU - Schwartz, Michael F. AU - Broeck, Lisa Van AU - Hunt, Aitch AU - Horn, Timothy J. AU - Sozzani, Rosangela T2 - BioDesign Research AB - Hydrogel encapsulation has been widely utilized in the study of fundamental cellular mechanisms and has been shown to provide a better representation of the complex in vivo microenvironment in natural biological conditions of mammalian cells. In this review, we provide a background into the adoption of hydrogel encapsulation methods in the study of mammalian cells, highlight some key findings that may aid with the adoption of similar methods for the study of plant cells, including the potential challenges and considerations, and discuss key findings of studies that have utilized these methods in plant sciences. DA - 2021/1// PY - 2021/1// DO - 10.34133/2021/9890319 UR - https://doi.org/10.34133/2021/9890319 ER - TY - JOUR TI - A non-adaptive demographic mechanism for genome expansion in Streptomyces AU - Choudoir, Mallory J AU - Järvenpää, Marko J AU - Marttinen, Pekka AU - Buckley, Daniel H AB - Abstract The evolution of microbial genome size is driven by gene acquisition and loss events that occur at scales from individual genomes to entire pangenomes. The equilibrium between gene gain and loss is shaped by evolutionary forces, including selection and drift, which are in turn influenced by population demographics. There is a well-known bias towards deletion in microbial genomes, which promotes genome streamlining. Less well described are mechanisms that promote genome expansion, giving rise to the many microbes, such as Streptomyces , that have unusually large genomes. We find evidence of genome expansion in Streptomyces sister-taxa, and we hypothesize that a recent demographic range expansion drove increases in genome size through a non-adaptive mechanism. These Streptomyces sister-taxa, NDR (northern-derived) and SDR (southern-derived), represent recently diverged lineages that occupy distinct geographic ranges. Relative to SDR genomes, NDR genomes are larger, have more genes, and their genomes are enriched in intermediate frequency genes. We also find evidence of relaxed selection in NDR genomes relative to SDR genomes. We hypothesize that geographic range expansion, coupled with relaxed selection, facilitated the introgression of non-adaptive horizontally acquired genes, which accumulated at intermediate frequencies through a mechanism known as genome surfing. We show that similar patterns of pangenome structure and genome expansion occur in a simulation that models the effects of population expansion on genome dynamics. We show that non-adaptive evolutionary phenomena can explain expansion of microbial genome size, and suggest that this mechanism might explain why some bacteria with large genomes can be found in soil. DA - 2021/1/11/ PY - 2021/1/11/ DO - 10.1101/2021.01.09.426074 VL - 1 UR - http://dx.doi.org/10.1101/2021.01.09.426074 ER - TY - JOUR TI - Introducing the Microbes and Social Equity Working Group: Considering the Microbial Components of Social, Environmental, and Health Justice AU - Ishaq, Suzanne L. AU - Parada, Francisco J. AU - Wolf, Patricia G. AU - Bonilla, Carla Y. AU - Carney, Megan A. AU - Benezra, Amber AU - Wissel, Emily AU - Friedman, Michael AU - DeAngelis, Kristen M. AU - Robinson, Jake M. AU - Fahimipour, Ashkaan K. AU - Manus, Melissa B. AU - Grieneisen, Laura AU - Dietz, Leslie G. AU - Pathak, Ashish AU - Chauhan, Ashvini AU - Kuthyar, Sahana AU - Stewart, Justin D. AU - Dasari, Mauna R. AU - Nonnamaker, Emily AU - Choudoir, Mallory AU - Horve, Patrick F. AU - Zimmerman, Naupaka B. AU - Kozik, Ariangela J. AU - Darling, Katherine Weatherford AU - Romero-Olivares, Adriana L. AU - Hariharan, Janani AU - Farmer, Nicole AU - Maki, Katherine A. AU - Collier, Jackie L. AU - O’Doherty, Kieran C. AU - Letourneau, Jeffrey AU - Kline, Jeff AU - Moses, Peter L. AU - Morar, Nicolae T2 - mSystems AB - Humans are inextricably linked to each other and our natural world, and microorganisms lie at the nexus of those interactions. Microorganisms form genetically flexible, taxonomically diverse, and biochemically rich communities, i.e., microbiomes that are integral to the health and development of macroorganisms, societies, and ecosystems. Yet engagement with beneficial microbiomes is dictated by access to public resources, such as nutritious food, clean water and air, safe shelter, social interactions, and effective medicine. In this way, microbiomes have sociopolitical contexts that must be considered. The Microbes and Social Equity (MSE) Working Group connects microbiology with social equity research, education, policy, and practice to understand the interplay of microorganisms, individuals, societies, and ecosystems. Here, we outline opportunities for integrating microbiology and social equity work through broadening education and training; diversifying research topics, methods, and perspectives; and advocating for evidence-based public policy that supports sustainable, equitable, and microbial wealth for all. DA - 2021/8/31/ PY - 2021/8/31/ DO - 10.1128/msystems.00471-21 VL - 6 IS - 4 UR - http://dx.doi.org/10.1128/msystems.00471-21 KW - biopolitics KW - health disparities KW - social determinants of health KW - structural determinants of health KW - integrated research KW - microbiomes ER - TY - JOUR TI - Broadening the impact of plant science through innovative, integrative, and inclusive outreach AU - Friesner, Joanna AU - Colon-Carmona, Adan AU - Schnoes, Alexandra M. AU - Stepanova, Anna AU - Mason, Grace Alex AU - Macintosh, Gustavo C. AU - Ullah, Hemayat AU - Baxter, Ivan AU - Callis, Judy AU - Sierra-Cajas, Kimberly AU - Elliott, Kiona AU - Haswell, Elizabeth S. AU - Zavala, Maria Elena AU - Wildermuth, Mary AU - Williams, Mary AU - Ayalew, Mentewab AU - Henkhaus, Natalie AU - Prunet, Nathanael AU - Lemaux, Peggy G. AU - Yadegari, Ramin AU - Amasino, Rick AU - Hangarter, Roger AU - Innes, Roger AU - Brady, Siobhan AU - Long, Terri AU - Woodford-Thomas, Terry AU - May, Victoria AU - Sun, Ying AU - Dinneny, Jose R. T2 - PLANT DIRECT AB - Abstract Population growth and climate change will impact food security and potentially exacerbate the environmental toll that agriculture has taken on our planet. These existential concerns demand that a passionate, interdisciplinary, and diverse community of plant science professionals is trained during the 21st century. Furthermore, societal trends that question the importance of science and expert knowledge highlight the need to better communicate the value of rigorous fundamental scientific exploration. Engaging students and the general public in the wonder of plants, and science in general, requires renewed efforts that take advantage of advances in technology and new models of funding and knowledge dissemination. In November 2018, funded by the National Science Foundation through the Arabidopsis Research and Training for the 21st century (ART 21) research coordination network, a symposium and workshop were held that included a diverse panel of students, scientists, educators, and administrators from across the US. The purpose of the workshop was to re‐envision how outreach programs are funded, evaluated, acknowledged, and shared within the plant science community. One key objective was to generate a roadmap for future efforts. We hope that this document will serve as such, by providing a comprehensive resource for students and young faculty interested in developing effective outreach programs. We also anticipate that this document will guide the formation of community partnerships to scale up currently successful outreach programs, and lead to the design of future programs that effectively engage with a more diverse student body and citizenry. DA - 2021/4// PY - 2021/4// DO - 10.1002/pld3.316 VL - 5 IS - 4 SP - SN - 2475-4455 UR - http://dx.doi.org/10.1002/pld3.316 ER - TY - JOUR TI - Cell-by-cell dissection of phloem development links a maturation gradient to cell specialization AU - Roszak, Pawel AU - Heo, Jung-Ok AU - Blob, Bernhard AU - Toyokura, Koichi AU - Sugiyama, Yuki AU - Balaguer, Maria Angels de Luis AU - Lau, Winnie W. Y. AU - Hamey, Fiona AU - Cirrone, Jacopo AU - Madej, Ewelina AU - Bouatta, Alida M. AU - Wang, Xin AU - Guichard, Marjorie AU - Ursache, Robertas AU - Tavares, Hugo AU - Verstaen, Kevin AU - Wendrich, Jos AU - Melnyk, Charles W. AU - Oda, Yoshihisa AU - Shasha, Dennis AU - Ahnert, Sebastian E. AU - Saeys, Yvan AU - De Rybel, Bert AU - Heidstra, Renze AU - Scheres, Ben AU - Grossmann, Guido AU - Mahonen, Ari Pekka AU - Denninger, Philipp AU - Gottgens, Berthold AU - Sozzani, Rosangela AU - Birnbaum, Kenneth D. AU - Helariutta, Yrjo T2 - SCIENCE AB - In the plant meristem, tissue-wide maturation gradients are coordinated with specialized cell networks to establish various developmental phases required for indeterminate growth. Here, we used single-cell transcriptomics to reconstruct the protophloem developmental trajectory from the birth of cell progenitors to terminal differentiation in the Arabidopsis thaliana root. PHLOEM EARLY DNA-BINDING-WITH-ONE-FINGER (PEAR) transcription factors mediate lineage bifurcation by activating guanosine triphosphatase signaling and prime a transcriptional differentiation program. This program is initially repressed by a meristem-wide gradient of PLETHORA transcription factors. Only the dissipation of PLETHORA gradient permits activation of the differentiation program that involves mutual inhibition of early versus late meristem regulators. Thus, for phloem development, broad maturation gradients interface with cell-type-specific transcriptional regulators to stage cellular differentiation. DA - 2021/12/24/ PY - 2021/12/24/ DO - 10.1126/science.aba5531 VL - 374 IS - 6575 SP - 1577-+ SN - 1095-9203 ER - TY - JOUR TI - Scientific Note: Capsule-Seed Allometric Relationships in Ludwigia ravenii (Onagraceae), a Critically Imperiled Wetland-Obligate AU - Lindelof, Kira AU - Krings, Alexander T2 - CASTANEA AB - Ludwigia ravenii is a critically imperiled tetraploid known historically from Virginia to Florida. There have been no published studies examining the number of seeds produced per capsule to guide researchers and conservationists in planning studies or collection efforts. Such data are important considering current guidelines by the Center for Plant Conservation recommend that no more than 10 percent of a population's seed production be collected in a single season. To fill this void, our objective was to examine and report on capsule-seed allometric relationships in the species. Our study is based on 25 capsules from six plants from the North Carolina Coastal Plain. Though admittedly limited in geographic scope, we focused on these wild plants to avoid destruction of herbarium specimens and as they were already the subject of a broader, permitted inquiry into seed germination. Consistent with prior, range-wide monographic study, measured capsule dimensions were: length 2.87–5.41 mm (mean=3.98, sd=0.64); broader facet width 1.95–3.67 mm (mean=2.94, sd=0.43); narrower facet width 1.88–3.27 mm (mean=2.70, sd=0.39). The mean number of seeds produced per capsule was 304.8 (sd=94.9). The mean number of seeds produced by capsules at least 4 mm long was 361 (sd=65.7), whereas the mean number of seeds produced by capsules less than 4 mm long was 233 (sd=77.8). In the absence of additional data from other populations, we preliminarily recommend that capsule collection efforts focus on capsules at least 4 mm long. DA - 2021/12// PY - 2021/12// DO - 10.2179/0008-7475.86.2.278 VL - 86 IS - 2 SP - 278-282 SN - 1938-4386 KW - Endangered KW - seedbox KW - infructescence KW - sect. Isnardia KW - G1 ER - TY - JOUR TI - A polyketide synthase gene cluster required for pathogenicity of Pseudocercospora fijiensis on banana AU - Thomas, Elizabeth AU - Noar, Roslyn D. AU - Daub, Margaret E. T2 - PLOS ONE AB - Pseudocercospora fijiensis is the causal agent of the highly destructive black Sigatoka disease of banana. Previous research has focused on polyketide synthase gene clusters in the fungus, given the importance of polyketide pathways in related plant pathogenic fungi. A time course study of expression of the previously identified PKS7-1, PKS8-2, and PKS10-2 gene clusters showed high expression of all three PKS genes and the associated clustered genes in infected banana plants from 2 weeks post-inoculation through 9 weeks. Engineered transformants silenced for PKS8-2 and PKS10-2 were developed and tested for pathogenicity. Inoculation of banana plants with silencing transformants for PKS10-2 showed significant reduction in disease symptoms and severity that correlated with the degree of silencing in the conidia used for inoculation, supporting a critical role for PKS10-2 in disease development. Unlike PKS10-2, a clear role for PKS8-2 could not be determined. Two of four PKS8-2 silencing transformants showed reduced disease development, but disease did not correlate with the degree of PKS8-2 silencing in the transformants. Overall, the degree of silencing obtained for the PKS8-2 transformants was less than that obtained for the PKS10-2 transformants, which may have limited the utility of the silencing strategy to identify a role for PKS8-2 in disease. Orthologous PKS10-2 clusters had previously been identified in the related banana pathogens Pseudocercospora musae and Pseudocercospora eumusae. Genome analysis identified orthologous gene clusters to that of PKS10-2 in the newly sequenced genomes of Pseudocercospora fuligena and Pseudocercospora cruenta, pathogens of tomato and cowpea, respectively. Our results support an important role for the PKS10-2 polyketide pathway in pathogenicity of Pseudocercospora fijiensis, and suggest a possible role for this pathway in disease development by other Pseudocercospora species. DA - 2021/10/27/ PY - 2021/10/27/ DO - 10.1371/journal.pone.0258981 VL - 16 IS - 10 SP - e0258981 J2 - PLoS ONE LA - en OP - SN - 1932-6203 UR - http://dx.doi.org/10.1371/journal.pone.0258981 DB - Crossref ER - TY - JOUR TI - A de novo regulation design shows an effectiveness in altering plant secondary metabolism AU - Li, Mingzhuo AU - He, Xianzhi AU - Hovary, Christophe La AU - Zhu, Yue AU - Dong, Yilun AU - Liu, Shibiao AU - Xing, Hucheng AU - Liu, Yajun AU - Jie, Yucheng AU - Ma, Dongming AU - Yuzuak, Seyit AU - Xie, De-Yu T2 - Journal of Advanced Research AB - Transcription factors (TFs) and cis-regulatory elements (CREs) control gene transcripts involved in various biological processes. We hypothesize that TFs and CREs can be effective molecular tools for De Novo regulation designs to engineer plants. We selected two Arabidopsis TF types and two tobacco CRE types to design a De Novo regulation and evaluated its effectiveness in plant engineering. G-box and MYB recognition elements (MREs) were identified in four Nicotiana tabacum JAZs (NtJAZs) promoters. MRE-like and G-box like elements were identified in one nicotine pathway gene promoter. TF screening led to select Arabidopsis Production of Anthocyanin Pigment 1 (PAP1/MYB) and Transparent Testa 8 (TT8/bHLH). Two NtJAZ and two nicotine pathway gene promoters were cloned from commercial Narrow Leaf Madole (NL) and KY171 (KY) tobacco cultivars. Electrophoretic mobility shift assay (EMSA), cross-linked chromatin immunoprecipitation (ChIP), and dual-luciferase assays were performed to test the promoter binding and activation by PAP1 (P), TT8 (T), PAP1/TT8 together, and the PAP1/TT8/Transparent Testa Glabra 1 (TTG1) complex. A DNA cassette was designed and then synthesized for stacking and expressing PAP1 and TT8 together. Three years of field trials were performed by following industrial and GMO protocols. Gene expression and metabolic profiling were completed to characterize plant secondary metabolism. PAP1, TT8, PAP1/TT8, and the PAP1/TT8/TTG1 complex bound to and activated NtJAZ promoters but did not bind to nicotine pathway gene promoters. The engineered red P + T plants significantly upregulated four NtJAZs but downregulated the tobacco alkaloid biosynthesis. Field trials showed significant reduction of five tobacco alkaloids and four carcinogenic tobacco specific nitrosamines in most or all cured leaves of engineered P + T and PAP1 genotypes. G-boxes, MREs, and two TF types are appropriate molecular tools for a De Novo regulation design to create a novel distant-pathway cross regulation for altering plant secondary metabolism. DA - 2021/6// PY - 2021/6// DO - 10.1016/j.jare.2021.06.017 VL - 6 UR - http://dx.doi.org/10.1016/j.jare.2021.06.017 KW - Arabidopsis KW - Alkaloid KW - Anthocyanin KW - Molecular tools KW - Tobacco KW - Transcription factor ER - TY - JOUR TI - Flavonols and dihydroflavonols inhibit the main protease activity of SARS-CoV-2 and the replication of human coronavirus 229E AU - Zhu, Yue AU - Scholle, Frank AU - Kisthardt, Samantha C. AU - Xie, De-Yu T2 - [] AB - Abstract Since December 2019, the deadly novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the current COVID-19 pandemic. To date, vaccines are available in the developed countries to prevent the infection of this virus, however, medicines are necessary to help control COVID-19. Human coronavirus 229E (HCoV-229E) causes the common cold. The main protease (M pro ) is an essential enzyme required for the multiplication of these two viruses in the host cells, and thus is an appropriate candidate to screen potential medicinal compounds. Flavonols and dihydroflavonols are two groups of plant flavonoids. In this study, we report docking simulation with two M pro enzymes and five flavonols and three dihydroflavonols, in vitro inhibition of the SARS-CoV-2 M pro , and in vitro inhibition of the HCoV 229E replication. The docking simulation results predicted that (+)-dihydrokaempferol, (+)-dihydroquercetin, (+)-dihydromyricetin, kaempferol, quercetin, myricentin, isoquercetin, and rutin could bind to at least two subsites (S1, S1’, S2, and S4) in the binding pocket and inhibit the activity of SARS-CoV-2 M pro . Their affinity scores ranged from −8.8 to −7.4. Likewise, these compounds were predicted to bind and inhibit the HCoV-229E M pro activity with affinity scores ranging from −7.1 to −7.8. In vitro inhibition assays showed that seven available compounds effectively inhibited the SARS-CoV-2 M pro activity and their IC50 values ranged from 0.125 to 12.9 µM. Five compounds inhibited the replication of HCoV-229E in Huh-7 cells. These findings indicate that these antioxidative flavonols and dihydroflavonols are promising candidates for curbing the two viruses. DA - 2021/7/2/ PY - 2021/7/2/ DO - 10.1101/2021.07.01.450756 VL - 7 UR - http://dx.doi.org/10.1101/2021.07.01.450756 ER - TY - JOUR TI - The Circadian-clock Regulates the Arabidopsis Gravitropic Response AU - Tolsma, Joseph S. AU - Ryan, Kaetlyn T. AU - Torres, Jacob J. AU - Richards, Jeffrey T. AU - Richardson, Zach AU - Land, Eric S. AU - Perera, Imara Y. AU - Doherty, Colleen J T2 - Gravitational and Space Research AB - Abstract For long-term space missions, it is necessary to understand how organisms respond to changes in gravity. Plant roots are positively gravitropic; the primary root grows parallel to gravity's pull even after being turned away from the direction of gravity. We examined if this gravitropic response varies depending on the time of day reorientation occurs. When plants were reoriented in relation to the gravity vector or placed in simulated microgravity, the magnitude of the root gravitropic response varied depending on the time of day the initial change in gravity occurred. The response was greatest when plants were reoriented at dusk, just before a period of rapid growth, and were minimal just before dawn as the plants entered a period of reduced root growth. We found that this variation in the magnitude of the gravitropic response persisted in constant light (CL) suggesting the variation is circadian-regulated. Gravitropic responses were disrupted in plants with disrupted circadian clocks, including plants overexpressing Circadian-clock Associated 1 (CCA1) and elf3 -2, in the reorientation assay and on a 2D clinostat. These findings indicate that circadian-regulated pathways modulate the gravitropic responses, thus, highlighting the importance of considering and recording the time of day gravitropic experiments are performed. DA - 2021/1/1/ PY - 2021/1/1/ DO - 10.2478/gsr-2021-0014 UR - https://doi.org/10.2478/gsr-2021-0014 ER - TY - JOUR TI - Species distribution models rarely predict the biology of real populations AU - A. Lee-Yaw, Julie AU - L. McCune, Jenny AU - Pironon, Samuel AU - N. Sheth, Seema T2 - ECOGRAPHY AB - Species distribution models (SDMs) are widely used in ecology. In theory, SDMs capture (at least part of) species' ecological niches and can be used to make inferences about the distribution of suitable habitat for species of interest. Because habitat suitability is expected to influence population demography, SDMs have been used to estimate a variety of population parameters, from occurrence to genetic diversity. However, a critical look at the ability of SDMs to predict independent data across different aspects of population biology is lacking. Here, we systematically reviewed the literature, retrieving 201 studies that tested predictions from SDMs against independent assessments of occurrence, abundance, population performance, and genetic diversity. Although there is some support for the ability of SDMs to predict occurrence (~53% of studies depending on how support was assessed), the predictive performance of these models declines progressively from occurrence to abundance, to population mean fitness, to genetic diversity. At the same time, we observed higher success among studies that evaluated performance for single versus multiple species, pointing to a possible publication bias. Thus, the limited accuracy of SDMs reported here may reflect the best‐case scenario. We discuss the limitations of these models and provide specific recommendations for their use for different applications going forward. However, we emphasize that predictions from SDMs, especially when used to inform conservation decisions, should be treated as hypotheses to be tested with independent data rather than as stand‐ins for the population parameters we seek to know. DA - 2021/12/21/ PY - 2021/12/21/ DO - 10.1111/ecog.05877 VL - 12 SP - SN - 1600-0587 KW - abundance KW - ecological niche KW - genetic diversity KW - habitat suitability KW - independent data KW - occurrence KW - performance KW - population growth ER - TY - JOUR TI - Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows AU - Bossche, Tim AU - Kunath, Benoit J. AU - Schallert, Kay AU - Schaepe, Stephanie S. AU - Abraham, Paul E. AU - Armengaud, Jean AU - Arntzen, Magnus O. AU - Bassignani, Ariane AU - Benndorf, Dirk AU - Fuchs, Stephan AU - Giannone, Richard J. AU - Griffin, Timothy J. AU - Hagen, Live H. AU - Halder, Rashi AU - Henry, Celine AU - Hettich, Robert L. AU - Heyer, Robert AU - Jagtap, Pratik AU - Jehmlich, Nico AU - Jensen, Marlene AU - Juste, Catherine AU - Kleiner, Manuel AU - Langella, Olivier AU - Lehmann, Theresa AU - Leith, Emma AU - May, Patrick AU - Mesuere, Bart AU - Miotello, Guylaine AU - Peters, Samantha L. AU - Pible, Olivier AU - Queiros, Pedro T. AU - Reichl, Udo AU - Renard, Bernhard Y. AU - Schiebenhoefer, Henning AU - Sczyrba, Alexander AU - Tanca, Alessandro AU - Trappe, Kathrin AU - Trezzi, Jean-Pierre AU - Uzzau, Sergio AU - Verschaffelt, Pieter AU - Bergen, Martin AU - Wilmes, Paul AU - Wolf, Maximilian AU - Martens, Lennart AU - Muth, Thilo T2 - NATURE COMMUNICATIONS AB - Metaproteomics has matured into a powerful tool to assess functional interactions in microbial communities. While many metaproteomic workflows are available, the impact of method choice on results remains unclear. Here, we carry out a community-driven, multi-laboratory comparison in metaproteomics: the critical assessment of metaproteome investigation study (CAMPI). Based on well-established workflows, we evaluate the effect of sample preparation, mass spectrometry, and bioinformatic analysis using two samples: a simplified, laboratory-assembled human intestinal model and a human fecal sample. We observe that variability at the peptide level is predominantly due to sample processing workflows, with a smaller contribution of bioinformatic pipelines. These peptide-level differences largely disappear at the protein group level. While differences are observed for predicted community composition, similar functional profiles are obtained across workflows. CAMPI demonstrates the robustness of present-day metaproteomics research, serves as a template for multi-laboratory studies in metaproteomics, and provides publicly available data sets for benchmarking future developments. DA - 2021/12/15/ PY - 2021/12/15/ DO - 10.1038/s41467-021-27542-8 VL - 12 IS - 1 SP - SN - 2041-1723 ER - TY - JOUR TI - To Fight or to Grow: The Balancing Role of Ethylene in Plant Abiotic Stress Responses AU - Chen, Hao AU - Bullock, David A., Jr. AU - Alonso, Jose M. AU - Stepanova, Anna N. T2 - Plants AB - Plants often live in adverse environmental conditions and are exposed to various stresses, such as heat, cold, heavy metals, salt, radiation, poor lighting, nutrient deficiency, drought, or flooding. To adapt to unfavorable environments, plants have evolved specialized molecular mechanisms that serve to balance the trade-off between abiotic stress responses and growth. These mechanisms enable plants to continue to develop and reproduce even under adverse conditions. Ethylene, as a key growth regulator, is leveraged by plants to mitigate the negative effects of some of these stresses on plant development and growth. By cooperating with other hormones, such as jasmonic acid (JA), abscisic acid (ABA), brassinosteroids (BR), auxin, gibberellic acid (GA), salicylic acid (SA), and cytokinin (CK), ethylene triggers defense and survival mechanisms thereby coordinating plant growth and development in response to abiotic stresses. This review describes the crosstalk between ethylene and other plant hormones in tipping the balance between plant growth and abiotic stress responses. DA - 2021/12/23/ PY - 2021/12/23/ DO - 10.3390/plants11010033 UR - https://doi.org/10.3390/plants11010033 KW - ethylene KW - abiotic stress KW - hormone crosstalk KW - growth and defense tradeoff ER - TY - JOUR TI - Exploratory analysis of Spirulina platensis LB 2340 growth in varied concentrations of anaerobically digested pig effluent (ADPE) AU - Baker, Matthew AU - Blackman, Sam AU - Cooper, Erin AU - Smartt, Kevin AU - Walser, David AU - Boland, Megan AU - Kolar, Praveen AU - Beck, Ashley E. AU - Chinn, Mari S. T2 - HELIYON AB - There is a significant interest in novel waste management solutions to treat wastewater from swine operations. Anaerobic digestion is a rising and prominent solution, but this technology still generates highly concentrated effluent that requires further remediation. Therefore, the aim of this study was to explore the feasibility of cultivating the cyanobacterium Spirulina platensis in swine effluent for future applications in biological waste treatment and value-added fermentation. To accomplish this goal, growth of S. platensis was characterized in varying proportions of ideal, synthetic Zarrouk medium and anaerobically digested pig effluent (ADPE) to obtain growth rate models. Results yielded a positive correlation between S. platensis growth rate and Zarrouk medium proportion, with the highest growth rate in 100% Zarrouk media but comparable growth in the 50/50% Zarrouk/ADPE mixture. This study demonstrates the potential for S. platensis to further improve the treatment efficacy of anaerobic digestion systems, and the exploratory analysis also highlights that further testing is required to investigate possible carbon availability, chemical inhibition, and overall nutrient reduction in ADPE. This research contributes important data toward the feasibility of producing value-added cyanobacterial biomass while simultaneously consuming excess nutrients to aid in agricultural wastewater management efforts and generate cost-effective products in a more sustainable manner. DA - 2021/9// PY - 2021/9// DO - 10.1016/j.heliyon.2021.e08065 VL - 7 IS - 9 SP - SN - 2405-8440 KW - Spirulina KW - Cyanobacteria KW - Swine effluent KW - Anaerobic digestion KW - Biomass production ER - TY - JOUR TI - Spatial variation in high temperature-regulated gene expression predicts evolution of plasticity with climate change in the scarlet monkeyflower AU - Preston, Jill C. AU - Wooliver, Rachel AU - Driscoll, Heather AU - Coughlin, Aeran AU - Sheth, Seema N. T2 - MOLECULAR ECOLOGY AB - Abstract A major way that organisms can adapt to changing environmental conditions is by evolving increased or decreased phenotypic plasticity. In the face of current global warming, more attention is being paid to the role of plasticity in maintaining fitness as abiotic conditions change over time. However, given that temporal data can be challenging to acquire, a major question is whether evolution in plasticity across space can predict adaptive plasticity across time. In growth chambers simulating two thermal regimes, we generated transcriptome data for western North American scarlet monkeyflowers ( Mimulus cardinalis ) collected from different latitudes and years (2010 and 2017) to test hypotheses about how plasticity in gene expression is responding to increases in temperature, and if this pattern is consistent across time and space. Supporting the genetic compensation hypothesis, individuals whose progenitors were collected from the warmer‐origin northern 2017 descendant cohort showed lower thermal plasticity in gene expression than their cooler‐origin northern 2010 ancestors. This was largely due to a change in response at the warmer (40°C) rather than cooler (20°C) treatment. A similar pattern of reduced plasticity, largely due to a change in response at 40°C, was also found for the cooler‐origin northern versus the warmer‐origin southern population from 2017. Our results demonstrate that reduced phenotypic plasticity can evolve with warming and that spatial and temporal changes in plasticity predict one another. DA - 2021/12/12/ PY - 2021/12/12/ DO - 10.1111/mec.16300 VL - 12 SP - SN - 1365-294X KW - climate change KW - differential gene expression KW - Mimulus cardinalis KW - phenotypic plasticity KW - space by time substitution KW - thermal adaptation ER - TY - JOUR TI - Comparative Phylogenomic Analysis Reveals Evolutionary Genomic Changes and Novel Toxin Families in Endophytic Liberibacter Pathogens AU - Tan, Yongjun AU - Wang, Cindy AU - Schneider, Theresa AU - Li, Huan AU - Souza, Robson Francisco AU - Tang, Xueming AU - Grimm, Kylie D. Swisher AU - Hsieh, Tzung-Fu AU - Wang, Xu AU - Li, Xu AU - Zhang, Dapeng T2 - MICROBIOLOGY SPECTRUM AB - Liberibacter pathogens are associated with several severe crop diseases, including citrus Huanglongbing, the most destructive disease to the citrus industry. Currently, no effective cure or treatments are available, and no resistant citrus variety has been found. DA - 2021/10// PY - 2021/10// DO - 10.1128/Spectrum.00509-21 VL - 9 IS - 2 SP - SN - 2165-0497 KW - Liberibacter pathogens KW - Huanglongbing KW - zebra chip KW - toxins KW - prophages KW - pathogenesis KW - evolution KW - comparative genomics ER - TY - JOUR TI - Evaluation of Sample Preservation and Storage Methods for Metaproteomics Analysis of Intestinal Microbiomes AU - Mordant, Angie AU - Kleiner, Manuel T2 - MICROBIOLOGY SPECTRUM AB - A critical step in studies of the intestinal microbiome using meta-omics approaches is the preservation of samples before analysis. Preservation is essential for approaches that measure gene expression, such as metaproteomics, which is used to identify and quantify proteins in microbiomes. Intestinal microbiome samples are typically stored by flash-freezing and storage at -80°C, but some experimental setups do not allow for immediate freezing of samples. In this study, we evaluated methods to preserve fecal microbiome samples for metaproteomics analyses when flash-freezing is not possible. We collected fecal samples from C57BL/6 mice and stored them for 1 and 4 weeks using the following methods: flash-freezing in liquid nitrogen, immersion in RNAlater, immersion in 95% ethanol, immersion in a RNAlater-like buffer, and combinations of these methods. After storage, we extracted protein and prepared peptides for liquid chromatography with tandem mass spectrometry (LC-MS/MS) analysis to identify and quantify peptides and proteins. All samples produced highly similar metaproteomes, except for ethanol-preserved samples that were distinct from all other samples in terms of protein identifications and protein abundance profiles. Flash-freezing and RNAlater (or RNAlater-like treatments) produced metaproteomes that differed only slightly, with less than 0.7% of identified proteins differing in abundance. In contrast, ethanol preservation resulted in an average of 9.5% of the identified proteins differing in abundance between ethanol and the other treatments. Our results suggest that preservation at room temperature in RNAlater or an RNAlater-like solution performs as well as freezing for the preservation of intestinal microbiome samples before metaproteomics analyses. IMPORTANCE Metaproteomics is a powerful tool to study the intestinal microbiome. By identifying and quantifying a large number of microbial, dietary, and host proteins in microbiome samples, metaproteomics provides direct evidence of the activities and functions of microbial community members. A critical step for metaproteomics workflows is preserving samples before analysis because protein profiles are susceptible to fast changes in response to changes in environmental conditions (air exposure, temperature changes, etc.). This study evaluated the effects of different preservation treatments on the metaproteomes of intestinal microbiome samples. In contrast to prior work on preservation of fecal samples for metaproteomics analyses, we ensured that all steps of sample preservation were identical so that all differences could be attributed to the preservation method. DA - 2021/12// PY - 2021/12// DO - 10.1128/Spectrum.01877-21 VL - 9 IS - 3 SP - SN - 2165-0497 UR - https://doi.org/10.1128/Spectrum.01877-21 KW - gut microbes KW - intestinal microbiome KW - LC-MS/MS KW - metaproteomics KW - microbiota KW - sample preservation KW - storage ER - TY - JOUR TI - Epigenetic modification associated with climate regulates betulin biosynthesis in birch AU - Wang, Jiang AU - Chen, Bowei AU - Ali, Shahid AU - Zhang, Tianxu AU - Wang, Yu AU - Zhang, He AU - Wang, Lishan AU - Zhang, Yonglan AU - Xie, Linan AU - Jiang, Tingbo AU - Yin, Jing AU - Sederoff, Heike W. AU - Zinta, Gaurav AU - Sederoff, Ronald R. AU - Li, Yuhua AU - Zhang, Qingzhu T2 - JOURNAL OF FORESTRY RESEARCH AB - Abstract The Betula genus contains pentacyclic triterpenoid betulin known for its environmental adaptation and medicinal properties. However, the mechanisms underlying betulin biosynthesis responding to climate change remain unclear. In this study, the role of epigenetic modification (DNA methylation) in betulin biosynthesis was examined and how climatic factors influence it. Whole-genome bisulfite sequencing was performed for greenhouse-grown Chinese white birch ( Betula platyphylla Sukaczev) treated with DNA methylation inhibitor zebularine (ZEB) and a natural birch population in Northeast China. ZEB treatment significantly affected the CHH methylation level of transposable elements and betulin content in a hormesis dose-dependent manner. The methylation and expression of bHLH9, a key transcriptional factor controlling betulin biosynthesis, were also consistently affected by ZEB treatment as a hormetic dose–response. In the natural population, there was a positive correlation between promoter methylation of bHLH9 and summer precipitation, while winter temperature was negatively correlated. Thus climate-dependent methylation of bHLH9 regulates the expression of downstream genes involved in betulin biosynthesis. This study highlights the role of environmental signals to induce epigenetic changes that result in betulin production, possibly helping to develop resilient plants to combat ongoing climate change and enhance secondary metabolite production. DA - 2021/12/4/ PY - 2021/12/4/ DO - 10.1007/s11676-021-01424-7 VL - 12 SP - SN - 1993-0607 KW - Epigenetics KW - DNA methylation KW - Betulin KW - bHLH9 transcription factor KW - Hormesis KW - Climate change KW - Secondary metabolite ER - TY - JOUR TI - Solving the puzzle of Fe homeostasis by integrating molecular, mathematical, and societal models AU - Hodgens, Charles AU - Akpa, Belinda S. AU - Long, Terri A. T2 - CURRENT OPINION IN PLANT BIOLOGY AB - To ensure optimal utilization and bioavailability, iron uptake, transport, subcellular localization, and assimilation are tightly regulated in plants. Herein, we examine recent advances in our understanding of cellular responses to Fe deficiency. We then use intracellular mechanisms of Fe homeostasis to discuss how formalizing cell biology knowledge via a mathematical model can advance discovery even when quantitative data is limited. Using simulation-based inference to identify plausible systems mechanisms that conform to known emergent phenotypes can yield novel, testable hypotheses to guide targeted experiments. However, this approach relies on the accurate encoding of domain-expert knowledge in exploratory mathematical models. We argue that this would be facilitated by fostering more "systems thinking" life scientists and that diversifying your research team may be a practical path to achieve that goal. DA - 2021/12// PY - 2021/12// DO - 10.1016/j.pbi.2021.102149 VL - 64 SP - SN - 1879-0356 UR - https://doi.org/10.1016/j.pbi.2021.102149 KW - Iron homeostasis KW - Simulation-based inference (SBI) KW - Inclusivity ER - TY - JOUR TI - Bioinformatic Teaching Resources - For Educators, by Educators - Using KBase, a Free, User-Friendly, Open Source Platform AU - Dow, Ellen G. AU - Wood-Charlson, Elisha M. AU - Biller, Steven J. AU - Paustian, Timothy AU - Schirmer, Aaron AU - Sheik, Cody S. AU - Whitham, Jason M. AU - Krebs, Rose AU - Goller, Carlos C. AU - Allen, Benjamin AU - Crockett, Zachary AU - Arkin, Adam P. T2 - FRONTIERS IN EDUCATION AB - Over the past year, biology educators and staff at the U.S. Department of Energy Systems Biology Knowledgebase (KBase) initiated a collaborative effort to develop a curriculum for bioinformatics education. KBase is a free web-based platform where anyone can conduct sophisticated and reproducible bioinformatic analyses via a graphical user interface. Here, we demonstrate the utility of KBase as a platform for bioinformatics education, and present a set of modular, adaptable, and customizable instructional units for teaching concepts in Genomics, Metagenomics, Pangenomics, and Phylogenetics. Each module contains teaching resources, publicly available data, analysis tools, and Markdown capability, enabling instructors to modify the lesson as appropriate for their specific course. We present initial student survey data on the effectiveness of using KBase for teaching bioinformatic concepts, provide an example case study, and detail the utility of the platform from an instructor’s perspective. Even as in-person teaching returns, KBase will continue to work with instructors, supporting the development of new active learning curriculum modules. For anyone utilizing the platform, the growing KBase Educators Organization provides an educators network, accompanied by community-sourced guidelines, instructional templates, and peer support, for instructors wishing to use KBase within a classroom at any educational level–whether virtual or in-person. DA - 2021/10/29/ PY - 2021/10/29/ DO - 10.3389/feduc.2021.711535 VL - 6 SP - SN - 2504-284X KW - computational biology KW - bioinformatics KW - data science KW - STEM education and learning KW - undergraduate education ER - TY - JOUR TI - Hydraulic segmentation does not protect stems from acute water loss during fire AU - Hoffmann, William A. AU - Rodrigues, Amanda C. AU - Uncles, Nicholas AU - Rossi, Lorenzo T2 - TREE PHYSIOLOGY AB - The heat plume associated with fire has been hypothesized to cause sufficient water loss from trees to induce embolism and hydraulic failure. However, it is unclear whether the water transport path remains sufficiently intact during scorching or burning of foliage to sustain high water loss. We measured water uptake by branches of Magnolia grandiflora while exposing them to a range of fire intensities and examined factors influencing continued water uptake after fire. Burning caused a 22-fold mean increase in water uptake, with greatest rates of water loss observed at burn intensities that caused complete consumption of leaves. Such rapid uptake is possible only with steep gradients in water potential, which would likely result in substantial cavitation of xylem and loss of conductivity in intact stems. Water uptake continued after burning was complete and was greatest following burn intensities that killed leaves but did not consume them. This post-fire uptake was mostly driven by rehydration of the remaining tissues, rather than evaporation from the tissues. Our results indicate that the fire plume hypothesis can be expanded to include a wide range of burning conditions experienced by plants. High rates of water loss are sustained during burning, even when leaves are killed or completely consumed. DA - 2021/10// PY - 2021/10// DO - 10.1093/treephys/tpab057 VL - 41 IS - 10 SP - 1785-1793 SN - 1758-4469 KW - burn KW - cavitation KW - combustion KW - heat plume KW - Magnolia grandiflora KW - scorch KW - water transport ER - TY - JOUR TI - Life in the Dark: Phylogenetic and Physiological Diversity of Chemosynthetic Symbioses AU - Maggie Sogin, E. AU - Kleiner, Manuel AU - Borowski, Christian AU - Gruber-Vodicka, Harald R. AU - Dubilier, Nicole T2 - ANNUAL REVIEW OF MICROBIOLOGY, VOL 75, 2021 AB - Possibly the last discovery of a previously unknown major ecosystem on Earth was made just over half a century ago, when researchers found teaming communities of animals flourishing two and a half kilometers below the ocean surface at hydrothermal vents. We now know that these highly productive ecosystems are based on nutritional symbioses between chemosynthetic bacteria and eukaryotes and that these chemosymbioses are ubiquitous in both deep-sea and shallow-water environments. The symbionts are primary producers that gain energy from the oxidation of reduced compounds, such as sulfide and methane, to fix carbon dioxide or methane into biomass to feed their hosts. This review outlines how the symbiotic partners have adapted to living together. We first focus on the phylogenetic and metabolic diversity of these symbioses and then highlight selected research directions that could advance our understanding of the processes that shaped the evolutionary and ecological success of these associations. DA - 2021/// PY - 2021/// DO - 10.1146/annurev-micro-051021-123130 VL - 75 SP - 695-718 SN - 1545-3251 KW - chemosymbiosis KW - host-microbe associations KW - nutritional interactions KW - adaptations to symbiosis KW - metabolism KW - thiotroph KW - methanotroph ER - TY - JOUR TI - Editorial overview: Toward deciphering the molecular basis of plant phenotypic plasticity AU - Qiao, Hong AU - Stepanova, Anna N. T2 - CURRENT OPINION IN PLANT BIOLOGY DA - 2021/10// PY - 2021/10// DO - 10.1016/j.pbi.2021.102107 VL - 63 SP - SN - 1879-0356 ER - TY - JOUR TI - Guided by Microbes: Applying Community Coalescence Principles for Predictive Microbiome Engineering AU - Rocca, Jennifer D. AU - Muscarella, Mario E. AU - Peralta, Ariane L. AU - Izabel-Shen, Dandan AU - Simonin, Marie T2 - MSYSTEMS AB - Every seed germinating in soils, wastewater treatment, and stream confluence exemplify microbial community coalescence-the blending of previously isolated communities. Here, we present theoretical and experimental knowledge on how separated microbial communities mix, with particular focus on managed ecosystems. We adopt the community coalescence framework, which integrates metacommunity theory and meta-ecosystem dynamics, and highlight the prevalence of these coalescence events within microbial systems. Specifically, we (i) describe fundamental types of community coalescences using naturally occurring and managed examples, (ii) offer ways forward to leverage community coalescence in managed systems, and (iii) emphasize the importance of microbial ecological theory to achieving desired coalescence outcomes. Further, considering the massive dispersal events of microbiomes and their coalescences is pivotal to better predict microbial community dynamics and responses to disturbances. We conclude our piece by highlighting some challenges and unanswered question yet to be tackled. DA - 2021/8// PY - 2021/8// DO - 10.1128/mSystems.00538-21 VL - 6 IS - 4 SP - SN - 2379-5077 KW - biostimulants KW - community coalescence KW - community inoculants KW - managed ecosystems KW - microbiome engineering ER - TY - JOUR TI - Enzyme Complexes of Ptr4CL and PtrHCT Modulate Co-enzyme A Ligation of Hydroxycinnamic Acids for Monolignol Biosynthesis in Populus trichocarpa AU - Lin, Chien-Yuan AU - Sun, Yi AU - Song, Jina AU - Chen, Hsi-Chuan AU - Shi, Rui AU - Yang, Chenmin AU - Liu, Jie AU - Tunlaya-Anukit, Sermsawat AU - Liu, Baoguang AU - Loziuk, Philip L. AU - Williams, Cranos M. AU - Muddiman, David C. AU - Lin, Ying-Chung Jimmy AU - Sederoff, Ronald R. AU - Wang, Jack P. AU - Chiang, Vincent L. T2 - FRONTIERS IN PLANT SCIENCE AB - Co-enzyme A (CoA) ligation of hydroxycinnamic acids by 4-coumaric acid:CoA ligase (4CL) is a critical step in the biosynthesis of monolignols. Perturbation of 4CL activity significantly impacts the lignin content of diverse plant species. In Populus trichocarpa , two well-studied xylem-specific Ptr4CLs (Ptr4CL3 and Ptr4CL5) catalyze the CoA ligation of 4-coumaric acid to 4-coumaroyl-CoA and caffeic acid to caffeoyl-CoA. Subsequently, two 4-hydroxycinnamoyl-CoA:shikimic acid hydroxycinnamoyl transferases (PtrHCT1 and PtrHCT6) mediate the conversion of 4-coumaroyl-CoA to caffeoyl-CoA. Here, we show that the CoA ligation of 4-coumaric and caffeic acids is modulated by Ptr4CL/PtrHCT protein complexes. Downregulation of PtrHCTs reduced Ptr4CL activities in the stem-differentiating xylem (SDX) of transgenic P. trichocarpa . The Ptr4CL/PtrHCT interactions were then validated in vivo using biomolecular fluorescence complementation (BiFC) and protein pull-down assays in P. trichocarpa SDX extracts. Enzyme activity assays using recombinant proteins of Ptr4CL and PtrHCT showed elevated CoA ligation activity for Ptr4CL when supplemented with PtrHCT. Numerical analyses based on an evolutionary computation of the CoA ligation activity estimated the stoichiometry of the protein complex to consist of one Ptr4CL and two PtrHCTs, which was experimentally confirmed by chemical cross-linking using SDX plant protein extracts and recombinant proteins. Based on these results, we propose that Ptr4CL/PtrHCT complexes modulate the metabolic flux of CoA ligation for monolignol biosynthesis during wood formation in P. trichocarpa . DA - 2021/10/6/ PY - 2021/10/6/ DO - 10.3389/fpls.2021.727932 VL - 12 SP - SN - 1664-462X KW - protein interaction KW - monolignol biosynthesis KW - wood formation KW - Populus trichocarpa KW - BiFC KW - metabolic flux ER - TY - JOUR TI - Plant Biology Research: What Is Next? AU - Stepanova, Anna N. T2 - FRONTIERS IN PLANT SCIENCE AB - SPECIALTY GRAND CHALLENGE article Front. Plant Sci., 30 September 2021 | https://doi.org/10.3389/fpls.2021.749104 DA - 2021/9/30/ PY - 2021/9/30/ DO - 10.3389/fpls.2021.749104 VL - 12 SP - SN - 1664-462X KW - plant biology KW - plant physiology KW - synthetic biology KW - translational research KW - data reproducibility ER - TY - JOUR TI - Fire and drought: Shifts in bark investment across a broad geographical scale for Neotropical savanna trees AU - Scalon, Marina Correa AU - Rossatto, Davi Rodrigo AU - Oliveras, Imma AU - Miatto, Raquel Carolina AU - Gray, Emma Fiona AU - Chaves Bicalho Domingos, Fabricius Maia AU - Brum, Fernanda Thiesen AU - Carlucci, Marcos Bergmann AU - Hoffmann, William Arthur AU - Marimon-Junior, Ben Hur AU - Marimon, Beatriz S. AU - Franco, Augusto Cesar T2 - BASIC AND APPLIED ECOLOGY AB - Savanna tree communities occurring in confluence zones with other biomes likely experience different environmental pressures, resulting in shifts in the selection of individual traits, the combinations of such traits, and species composition. In seasonally dry fire-prone environments, plant survival is presumably associated with adaptive changes in bark properties related to fire protection and water storage. Here, we integrated the multiple functions of the bark to investigate whether different selective pressures could influence patterns of variation in bark structure and allocation across species in a broad geographical range. We measured thickness, density, and water content of the inner and outer bark in branches and the main stem of the 51 most abundant species in three savanna communities differing in climatic aridity, one located at the core region of Cerrado in Central Brazil and the other two at its periphery, in the transition zones with Amazonia and Atlantic forest biomes. We found no difference in outer bark thickness but markedly difference in inner bark thickness between the three plant communities. In the central region, where dry season is long and fire is frequent, branches and main stem showed thicker inner bark. Contrastingly, in the south periphery region, where dry season is short, species showed thinner inner bark in both branches and main stem. Species from the north periphery region, where mean annual precipitation is higher, but fire is frequent and the dry season is also long, showed similar main stem inner bark thickness, but thinner branch inner bark compared to core region species. Our findings support the idea that investing in inner bark thickness and bark moisture may be the most advantageous strategy in plant communities that suffer from high evaporative demand during a long period and are at a high risk of fire. DA - 2021/11// PY - 2021/11// DO - 10.1016/j.baae.2021.06.011 VL - 56 SP - 110-121 SN - 1618-0089 KW - bark KW - biome transition KW - Cerrado KW - fire ecology KW - phellogen KW - water storage ER - TY - JOUR TI - Proteome and strain analysis of cyanobacterium Candidatus "Phormidium alkaliphilum" reveals traits for success in biotechnology AU - Ataeian, Maryam AU - Vadlamani, Agasteswar AU - Haines, Marianne AU - Mosier, Damon AU - Dong, Xiaoli AU - Kleiner, Manuel AU - Strous, Marc AU - Hawley, Alyse K. T2 - ISCIENCE AB - Cyanobacteria encompass a diverse group of photoautotrophic bacteria with important roles in nature and biotechnology. Here we characterized Candidatus "Phormidium alkaliphilum," an abundant member in alkaline soda lake microbial communities globally. The complete, circular whole-genome sequence of Ca. "P. alkaliphilum" was obtained using combined Nanopore and Illumina sequencing of a Ca. "P. alkaliphilum" consortium. Strain-level diversity of Ca. "P. alkaliphilum" was shown to contribute to photobioreactor robustness under different operational conditions. Comparative genomics of closely related species showed that adaptation to high pH was not attributed to specific genes. Proteomics at high and low pH showed only minimal changes in gene expression, but higher productivity in high pH. Diverse photosystem antennae proteins, and high-affinity terminal oxidase, compared with other soda lake cyanobacteria, appear to contribute to the success of Ca. "P. alkaliphilum" in photobioreactors and biotechnology applications. DA - 2021/12/17/ PY - 2021/12/17/ DO - 10.1016/j.isci.2021.103405 VL - 24 IS - 12 SP - SN - 2589-0042 UR - https://doi.org/10.1016/j.isci.2021.103405 ER - TY - JOUR TI - A New Type of Satellite Associated with Cassava Mosaic Begomoviruses AU - Aimone, Catherine D. AU - De Leon, Leandro AU - Dallas, Mary M. AU - Ndunguru, Joseph AU - Ascencio-Ibanez, Jose T. AU - Hanley-Bowdoin, Linda T2 - JOURNAL OF VIROLOGY AB - Cassava mosaic disease (CMD), which is caused by single-stranded DNA begomoviruses, severely limits cassava production across Africa. A previous study showed that CMD symptom severity and viral DNA accumulation increase in cassava in the presence of a DNA sequence designated SEGS-2 (sequence enhancing geminivirus symptoms). We report here that when SEGS-2 is coinoculated with African cassava mosaic virus (ACMV) onto Arabidopsis thaliana, viral symptoms increase. Transgenic Arabidopsis with an integrated copy of SEGS-2 inoculated with ACMV also display increased symptom severity and viral DNA levels. Moreover, SEGS-2 enables Cabbage leaf curl virus (CaLCuV) to infect a geminivirus-resistant Arabidopsis thaliana accession. Although SEGS-2 is related to cassava genomic sequences, an earlier study showed that it occurs as episomes and is packaged into virions in CMD-infected cassava and viruliferous whiteflies. We identified SEGS-2 episomes in SEGS-2 transgenic Arabidopsis. The episomes occur as both double-stranded and single-stranded DNA, with the single-stranded form packaged into virions. In addition, SEGS-2 episomes replicate in tobacco protoplasts in the presence, but not the absence, of ACMV DNA-A. SEGS-2 episomes contain a SEGS-2 derived promoter and an open reading frame with the potential to encode a 75-amino acid protein. An ATG mutation at the beginning of the SEGS-2 coding region does not enhance ACMV infection in A. thaliana. Together, the results established that SEGS-2 is a new type of begomovirus satellite that enhances viral disease through the action of an SEGS-2-encoded protein that may also be encoded by the cassava genome. IMPORTANCE Cassava is an important root crop in the developing world and a food and income crop for more than 300 million African farmers. Cassava is rising in global importance and trade as the demands for biofuels and commercial starch increase. More than half of the world's cassava is produced in Africa, where it is primarily grown by smallholder farmers, many of whom are from the poorest villages. Although cassava can grow under high temperature, drought, and poor soil conditions, its production is severely limited by viral diseases. Cassava mosaic disease (CMD) is one of the most important viral diseases of cassava and can cause up to 100% yield losses. We provide evidence that SEGS-2, which was originally isolated from cassava crops displaying severe and atypical CMD symptoms in Tanzanian fields, is a novel begomovirus satellite that can compromise the development of durable CMD resistance. DA - 2021/11// PY - 2021/11// DO - 10.1128/JVI.00432-21 VL - 95 IS - 21 SP - SN - 1098-5514 KW - Arabidopsis KW - begomovirus KW - cassava mosaic disease KW - SEGS ER - TY - JOUR TI - Activation of the Type VI Secretion System in the Squid Symbiont Vibrio fischeri Requires the Transcriptional Regulator TasR and the Structural Proteins TssM and TssA AU - Smith, Stephanie AU - Salvato, Fernanda AU - Garikipati, Aditi AU - Kleiner, Manuel AU - Septer, Alecia N. T2 - JOURNAL OF BACTERIOLOGY AB - Bacteria have evolved diverse strategies to compete for a niche, including the type VI secretion system (T6SS), a contact-dependent killing mechanism. T6SSs are common in bacterial pathogens, commensals, and beneficial symbionts, where they affect the diversity and spatial structure of host-associated microbial communities. Although T6SS gene clusters are often located on genomic islands (GIs), which may be transferred as a unit, the regulatory strategies that promote gene expression once the T6SS genes are transferred into a new cell are not known. We used the squid symbiont Vibrio fischeri to identify essential regulatory factors that control expression of a strain-specific T6SS encoded on a GI. We found that a transcriptional reporter for this T6SS is active only in strains that contain the T6SS-encoding GI, suggesting the GI encodes at least one essential regulator. A transposon screen identified seven mutants that could not activate the reporter. These mutations mapped exclusively to three genes on the T6SS-containing GI that encode two essential structural proteins (a TssA-like protein and TssM) and a transcriptional regulator (TasR). Using T6SS reporters, reverse transcription-PCR (RT-PCR), competition assays, and differential proteomics, we found that all three genes are required for expression of many T6SS components, except for the TssA-like protein and TssM, which are constitutively expressed. Based on these findings, we propose a model whereby T6SS expression requires conserved structural proteins, in addition to the essential regulator TasR, and this ability to self-regulate may be a strategy to activate T6SS expression upon transfer of T6SS-encoding elements into a new bacterial host. IMPORTANCE Interbacterial weapons like the T6SS are often located on mobile genetic elements, and their expression is highly regulated. We found that two conserved structural proteins are required for T6SS expression in Vibrio fischeri. These structural proteins also contain predicted GTPase and GTP binding domains, suggesting their role in promoting T6SS expression may involve sensing the energetic state of the cell. Such a mechanism would provide a direct link between T6SS activation and cellular energy levels, providing a "checkpoint" to ensure the cell has sufficient energy to build such a costly weapon. Because these regulatory factors are encoded within the T6SS gene cluster, they are predicted to move with the genetic element to activate T6SS expression in a new host cell. DA - 2021/11// PY - 2021/11// DO - 10.1128/JB.00399-21 VL - 203 IS - 21 SP - SN - 1098-5530 KW - type VI secretion systems KW - Aliivibrio fischeri KW - microbial interactions KW - genomic island KW - symbiosis ER - TY - JOUR TI - Evaluation of RNAlater as a Field-Compatible Preservation Method for Metaproteomic Analyses of Bacterium-Animal Symbioses AU - Jensen, Marlene AU - Wippler, Juliane AU - Kleiner, Manuel T2 - MICROBIOLOGY SPECTRUM AB - Field studies are central to environmental microbiology and microbial ecology, because they enable studies of natural microbial communities. Metaproteomics, the study of protein abundances in microbial communities, allows investigators to study these communities "in situ," which requires protein preservation directly in the field because protein abundance patterns can change rapidly after sampling. Ideally, a protein preservative for field deployment works rapidly and preserves the whole proteome, is stable in long-term storage, is nonhazardous and easy to transport, and is available at low cost. Although these requirements might be met by several protein preservatives, an assessment of their suitability under field conditions when targeted for metaproteomic analyses is currently lacking. Here, we compared the protein preservation performance of flash freezing and the preservation solution RNAlater using the marine gutless oligochaete Olavius algarvensis and its symbiotic microbes as a test case. In addition, we evaluated long-term RNAlater storage after 1 day, 1 week, and 4 weeks at room temperature (22°C to 23°C). We evaluated protein preservation using one-dimensional liquid chromatography-tandem mass spectrometry. We found that RNAlater and flash freezing preserved proteins equally well in terms of total numbers of identified proteins and relative abundances of individual proteins, and none of the test time points was altered, compared to time zero. Moreover, we did not find biases against specific taxonomic groups or proteins with particular biochemical properties. Based on our metaproteomic data and the logistical requirements for field deployment, we recommend RNAlater for protein preservation of field-collected samples targeted for metaproteomic analyses. IMPORTANCE Metaproteomics, the large-scale identification and quantification of proteins from microbial communities, provide direct insights into the phenotypes of microorganisms on the molecular level. To ensure the integrity of the metaproteomic data, samples need to be preserved immediately after sampling to avoid changes in protein abundance patterns. In laboratory setups, samples for proteomic analyses are most commonly preserved by flash freezing; however, liquid nitrogen or dry ice is often unavailable at remote field locations, due to their hazardous nature and transport restrictions. Our study shows that RNAlater can serve as a low-hazard, easy-to-transport alternative to flash freezing for field preservation of samples for metaproteomic analyses. We show that RNAlater preserves the metaproteome equally well, compared to flash freezing, and protein abundance patterns remain stable during long-term storage for at least 4 weeks at room temperature. DA - 2021/10// PY - 2021/10// DO - 10.1128/Spectrum.01429-21 VL - 9 IS - 2 SP - SN - 2165-0497 UR - https://doi.org/10.1128/Spectrum.01429-21 KW - mass spectrometry KW - 1D-LC-MS/MS KW - microbial communities KW - preservation methods KW - microbiome KW - field sampling KW - environmental microbiology ER - TY - JOUR TI - Integrated omics networks reveal the temporal signaling events of brassinosteroid response in Arabidopsis AU - Clark, Natalie M. AU - Nolan, Trevor M. AU - Wang, Ping AU - Song, Gaoyuan AU - Montes, Christian AU - Valentine, Conner T. AU - Guo, Hongqing AU - Sozzani, Rosangela AU - Yin, Yanhai AU - Walley, Justin W. T2 - NATURE COMMUNICATIONS AB - Brassinosteroids (BRs) are plant steroid hormones that regulate cell division and stress response. Here we use a systems biology approach to integrate multi-omic datasets and unravel the molecular signaling events of BR response in Arabidopsis. We profile the levels of 26,669 transcripts, 9,533 protein groups, and 26,617 phosphorylation sites from Arabidopsis seedlings treated with brassinolide (BL) for six different lengths of time. We then construct a network inference pipeline called Spatiotemporal Clustering and Inference of Omics Networks (SC-ION) to integrate these data. We use our network predictions to identify putative phosphorylation sites on BES1 and experimentally validate their importance. Additionally, we identify BRONTOSAURUS (BRON) as a transcription factor that regulates cell division, and we show that BRON expression is modulated by BR-responsive kinases and transcription factors. This work demonstrates the power of integrative network analysis applied to multi-omic data and provides fundamental insights into the molecular signaling events occurring during BR response. DA - 2021/10/6/ PY - 2021/10/6/ DO - 10.1038/s41467-021-26165-3 VL - 12 IS - 1 SP - SN - 2041-1723 ER - TY - JOUR TI - A calmodulin-binding transcription factor links calcium signaling to antiviral RNAi defense in plants AU - Wang, Yunjing AU - Gong, Qian AU - Wu, Yuyao AU - Huang, Fan AU - Ismayil, Asigul AU - Zhang, Danfeng AU - Li, Huangai AU - Gu, Hanqing AU - Ludman, Marta AU - Fatyol, Karoly AU - Qi, Yijun AU - Yoshioka, Keiko AU - Hanley-Bowdoin, Linda AU - Hong, Yiguo AU - Liu, Yule T2 - CELL HOST & MICROBE AB - RNA interference (RNAi) is an across-kingdom gene regulatory and defense mechanism. However, little is known about how organisms sense initial cues to mobilize RNAi. Here, we show that wounding to Nicotiana benthamiana cells during virus intrusion activates RNAi-related gene expression through calcium signaling. A rapid wound-induced elevation in calcium fluxes triggers calmodulin-dependent activation of calmodulin-binding transcription activator-3 (CAMTA3), which activates RNA-dependent RNA polymerase-6 and Bifunctional nuclease-2 (BN2) transcription. BN2 stabilizes mRNAs encoding key components of RNAi machinery, notably AGONAUTE1/2 and DICER-LIKE1, by degrading their cognate microRNAs. Consequently, multiple RNAi genes are primed for combating virus invasion. Calmodulin-, CAMTA3-, or BN2-knockdown/knockout plants show increased susceptibility to geminivirus, cucumovirus, and potyvirus. Notably, Geminivirus V2 protein can disrupt the calmodulin-CAMTA3 interaction to counteract RNAi defense. These findings link Ca2+ signaling to RNAi and reveal versatility of host antiviral defense and viral counter-defense. DA - 2021/9/8/ PY - 2021/9/8/ DO - 10.1016/j.chom.2021.07.003 VL - 29 IS - 9 SP - 1393-+ SN - 1934-6069 ER - TY - JOUR TI - Characterizing past fire occurrence in longleaf pine ecosystems with the Mid-Infrared Burn Index and a Random Forest classifier AU - Wall, Wade A. AU - Hohmann, Matthew G. AU - Just, Michael G. AU - Hoffmann, William A. T2 - FOREST ECOLOGY AND MANAGEMENT AB - Prior to European settlement the longleaf pine (Pinus palustris) ecosystem covered over 92 million hectares in the southeastern United States. Historically, fire was an important driver of species composition in the longleaf pine ecosystem, but fire exclusion since the early 20th century has led to the degradation of longleaf pine communities and has had a detrimental effect on the large number of rare and endemic species found within this system. Thus, accurate estimates of fire history are important for better informed management of longleaf pine communities. Recently, satellite imagery has been used to identify burned areas. However, results have been inconsistent across physiographic regions and vegetation types (e.g. wetlands under high canopy). We developed a model using Landsat satellite imagery, coupled with a Random Forest (RF) machine learning algorithm, to identify burned areas and estimate the fire history from 1991 to 2019 for Fort Bragg, NC, one of the largest contiguous areas of longleaf pine ecosystem remaining. We calculated six spectral indices from the Landsat band values, including the Mid-Infrared Burn Index (MIRBI) and the change in MIRBI through time (ΔMIRBI), and used them as predictors in our RF model. We used the developed RF model to estimate the fire history for all known populations of 24 rare upland and wetland plant species found on Fort Bragg. We compared our results to a recent continental U.S. fire occurrence dataset, as well as the prescribed fire records from Fort Bragg. The overall AUC (area under the curve) for our RF model (0.74) compared favorably to the continental U.S. dataset results for Fort Bragg (0.69), and was able to capture the reduced fire frequency in wetlands. The most important predictor in our RF model was ΔMIRBI. Depending on the model, individual plant species were estimated to have experienced significant differences in fire frequency relative to the prescribed fire records. For our RF model, we estimated that 50% of wetland and 25% of upland species experienced a lower fire frequency relative to that represented in the prescribed fire records. The burn probability and classification tool generated in this paper provides land managers in the southeastern U.S. with a novel approach for accurately identifying burned areas and estimating local fire frequency across landscapes. DA - 2021/11/15/ PY - 2021/11/15/ DO - 10.1016/j.foreco.2021.119635 VL - 500 SP - SN - 1872-7042 KW - Fire modeling KW - Prescribed fire KW - Pinus palustris KW - Pyrodiversity KW - Rare plant management KW - Threatened, endangered and at-risk species ER - TY - JOUR TI - Spatiotemporal Gene Expression Profiling and Network Inference: A Roadmap for Analysis, Visualization, and Key Gene Identification AU - Spurney, Ryan AU - Schwartz, Michael AU - Gobble, Mariah AU - Sozzani, Rosangela AU - Broeck, Lisa T2 - MODELING TRANSCRIPTIONAL REGULATION AB - Gene expression data analysis and the prediction of causal relationships within gene regulatory networks (GRNs) have guided the identification of key regulatory factors and unraveled the dynamic properties of biological systems. However, drawing accurate and unbiased conclusions requires a comprehensive understanding of relevant tools, computational methods, and their workflows. The topics covered in this chapter encompass the entire workflow for GRN inference including: (1) experimental design; (2) RNA sequencing data processing; (3) differentially expressed gene (DEG) selection; (4) clustering prior to inference; (5) network inference techniques; and (6) network visualization and analysis. Moreover, this chapter aims to present a workflow feasible and accessible for plant biologists without a bioinformatics or computer science background. To address this need, TuxNet, a user-friendly graphical user interface that integrates RNA sequencing data analysis with GRN inference, is chosen for the purpose of providing a detailed tutorial. DA - 2021/// PY - 2021/// DO - 10.1007/978-1-0716-1534-8_4 VL - 2328 SP - 47-65 SN - 1940-6029 KW - Gene regulatory network inference KW - RNA sequencing KW - Bioinformatics KW - Network visualization ER - TY - JOUR TI - Uncovering Transcriptional Responses to Fractional Gravity in Arabidopsis Roots AU - Sheppard, James AU - Land, Eric S. AU - Toennisson, Tiffany Aurora AU - Doherty, Colleen J. AU - Perera, Imara Y. T2 - LIFE-BASEL AB - Although many reports characterize the transcriptional response of Arabidopsis seedlings to microgravity, few investigate the effect of partial or fractional gravity on gene expression. Understanding plant responses to fractional gravity is relevant for plant growth on lunar and Martian surfaces. The plant signaling flight experiment utilized the European Modular Cultivation System (EMCS) onboard the International Space Station (ISS). The EMCS consisted of two rotors within a controlled chamber allowing for two experimental conditions, microgravity (stationary rotor) and simulated gravity in space. Seedlings were grown for 5 days under continuous light in seed cassettes. The arrangement of the seed cassettes within each experimental container results in a gradient of fractional g (in the spinning rotor). To investigate whether gene expression patterns are sensitive to fractional g, we carried out transcriptional profiling of root samples exposed to microgravity or partial g (ranging from 0.53 to 0.88 g). Data were analyzed using DESeq2 with fractional g as a continuous variable in the design model in order to query gene expression across the gravity continuum. We identified a subset of genes whose expression correlates with changes in fractional g. Interestingly, the most responsive genes include those encoding transcription factors, defense, and cell wall-related proteins and heat shock proteins. DA - 2021/10// PY - 2021/10// DO - 10.3390/life11101010 VL - 11 IS - 10 SP - SN - 2075-1729 UR - https://doi.org/10.3390/life11101010 KW - spaceflight KW - fractional gravity KW - RNA-seq KW - Arabidopsis KW - gene expression KW - heat shock proteins ER - TY - JOUR TI - Response of canola yields from marginal lands managed with tillage practices AU - Mayer, Michelle L. AU - Veal, Matthew W. AU - Godfrey, Edward E., III AU - Chinn, Mari S. T2 - JOURNAL OF AGRICULTURE AND FOOD RESEARCH AB - In recent years the discourse regarding the effective use of dwindling agricultural spaces for food, fiber, or fuel production has grown and it is becoming increasingly important to manage non-agricultural or marginal spaces that make them suitable for crop production. Highly eroded, highly compacted, low nutrient soils, similar to those found along highway rights-of-way (ROWs) offer unique field characteristics that can be used to study crop production potentials and land use decisions. This work evaluated the feasibility of maintaining a canola crop production system on the non-agricultural soils of highway ROWs across the humid subtropical climate within North Carolina, USA as a bioenergy feedstock for renewable fuels. Specific objectives included examination of (1) three different North Carolina geoclimatic conditions and (2) three levels of tillage (conventional (CT), minimum (MT), and no-till (NT)) on canola (Brassica napus L.) grain yields cultivated on ROW soils. Field experiments were conducted for two growing seasons in the Inner Coastal Plain, Piedmont, and Mountains regions and assessed main and interaction effects among tillage, site, and year of cultivation on crop productivity. After season 1, CT produced the highest average yield (1.24 Mg ha−1) followed by MT (0.93 Mg ha−1) and NT (0.86 Mg ha−1), respectively. In the second year, the comparative intensity of productive effects from CT was lower, and plots cultivated under MT resulted in the highest average yields (2.70 Mg ha−1), followed by CT (2.69 Mg ha−1) and NT (1.96 Mg ha−1), respectively. Yields observed were comparable to regional canola grain yields, and no significant difference was observed between yields under CT versus MT. These findings suggest that reduced levels of tillage on ROW soils in North Carolina hold the potential to produce yields comparable to those realized in traditional agricultural soils, and targeted tillage practices can support improved suitability of marginal crop production spaces. DA - 2021/6// PY - 2021/6// DO - 10.1016/j.jafr.2021.100133 VL - 4 SP - SN - 2666-1543 KW - Highway rights-of-way KW - Oil seed KW - Geoclimatic regions KW - Under-utilized space KW - Land management KW - Bio-energy crop ER - TY - JOUR TI - Molecular and Biochemical Characterization of Two 4-Coumarate: Coa Ligase Genes in Tea Plant (Camellia Sinensis) AU - Li, Mingzhuo AU - Guo, Lili AU - Wang, Yeru AU - Li, Yanzhi AU - Jiang, Xiaolan AU - Liu, Yajun AU - Xie, Deyu AU - Gao, Liping AU - Xia, Tao AB - Abstract Tea is rich in flavonoids benefiting human health. Lignin is essential for tea plant growth. Both flavonoids and lignin defend plants from stresses. The biosynthesis of lignin and flavonoids shares a key intermediate, p-coumaroyl-CoA, which is formed from p-coumaric acid catalyzed by p-coumaric acid: CoA ligase (4CL). Herein, we reported two 4CL paralogs from tea plant, Cs4CL1 and Cs4CL2 , which were a member of class I and II, respectively. Cs4CL1 was mainly expressed in roots and stems, while Cs4CL2 was mainly expressed in leaves. The promoter of Cs4CL1 had AC, light and stress-inducible (LSI), and meristem-specific elements, while that of Cs4CL2 had AC and LSI elements only. Moreover, the promoter of Cs4CL1 had two more stress-inducible elements than Cs4CL2 had and the two promoters had six different light-inducible elements. These features suggested their differences in their responses to environmental conditions. Three stress treatments indicated that the expression of Cs4CL1 was sensitive to mechanical wounding, while the expression of Cs4CL2 was UV-B-inducible. Enzymatic assay showed that both recombinant Cs4CL1 and Cs4CL2 transformed p-coumaric acid, ferulic acid and caffeic acid to their corresponding CoA ethers. Kinetic analysis indicated that the recombinant Cs4CL1 preferred to catalyze caffeic acid, while the recombinant Cs4CL2 favored to catalyze p-coumaric acid. The overexpression of both Cs4CL1 and Cs4CL2 increased the levels of chlorogenic acid and total lignin in transgenic tobacco seedlings. In addition, the overexpression of Cs4CL2 increased the levels of three flavonoid compounds. These findings indicate the differences of Cs4CL1 and Cs4CL2 in the phenylpropanoid metabolism. DA - 2021/9/21/ PY - 2021/9/21/ DO - 10.21203/rs.3.rs-897959/v1 UR - https://doi.org/10.21203/rs.3.rs-897959/v1 ER - TY - JOUR TI - Limited plasticity in thermally tolerant ectotherm populations: evidence for a trade-off AU - Barley, Jordanna M. AU - Cheng, Brian S. AU - Sasaki, Matthew AU - Gignoux-Wolfsohn, Sarah AU - Hays, Cynthia G. AU - Putnam, Alysha B. AU - Sheth, Seema AU - Villeneuve, Andrew R. AU - Kelly, Morgan T2 - PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES AB - Many species face extinction risks owing to climate change, and there is an urgent need to identify which species' populations will be most vulnerable. Plasticity in heat tolerance, which includes acclimation or hardening, occurs when prior exposure to a warmer temperature changes an organism's upper thermal limit. The capacity for thermal acclimation could provide protection against warming, but prior work has found few generalizable patterns to explain variation in this trait. Here, we report the results of, to our knowledge, the first meta-analysis to examine within-species variation in thermal plasticity, using results from 20 studies (19 species) that quantified thermal acclimation capacities across 78 populations. We used meta-regression to evaluate two leading hypotheses. The climate variability hypothesis predicts that populations from more thermally variable habitats will have greater plasticity, while the trade-off hypothesis predicts that populations with the lowest heat tolerance will have the greatest plasticity. Our analysis indicates strong support for the trade-off hypothesis because populations with greater thermal tolerance had reduced plasticity. These results advance our understanding of variation in populations' susceptibility to climate change and imply that populations with the highest thermal tolerance may have limited phenotypic plasticity to adjust to ongoing climate warming. DA - 2021/9/8/ PY - 2021/9/8/ DO - 10.1098/rspb.2021.0765 VL - 288 IS - 1958 SP - SN - 1471-2954 UR - https://doi.org/10.1098/rspb.2021.0765 KW - thermal acclimation KW - phenotypic plasticity KW - heat tolerance KW - trade-off hypothesis KW - climate change KW - local adaptation ER - TY - JOUR TI - A Role for Inositol Pyrophosphates in the Metabolic Adaptations to Low Phosphate in Arabidopsis AU - Land, Eric S. AU - Cridland, Caitlin A. AU - Craige, Branch AU - Dye, Anna AU - Hildreth, Sherry B. AU - Helm, Rich F. AU - Gillaspy, Glenda E. AU - Perera, Imara Y. T2 - METABOLITES AB - Phosphate is a major plant macronutrient and low phosphate availability severely limits global crop productivity. In Arabidopsis, a key regulator of the transcriptional response to low phosphate, phosphate starvation response 1 (PHR1), is modulated by a class of signaling molecules called inositol pyrophosphates (PP-InsPs). Two closely related diphosphoinositol pentakisphosphate enzymes (AtVIP1 and AtVIP2) are responsible for the synthesis and turnover of InsP8, the most implicated molecule. This study is focused on characterizing Arabidopsis vip1/vip2 double mutants and their response to low phosphate. We present evidence that both local and systemic responses to phosphate limitation are dampened in the vip1/vip2 mutants as compared to wild-type plants. Specifically, we demonstrate that under Pi-limiting conditions, the vip1/vip2 mutants have shorter root hairs and lateral roots, less accumulation of anthocyanin and less accumulation of sulfolipids and galactolipids. However, phosphate starvation response (PSR) gene expression is unaffected. Interestingly, many of these phenotypes are opposite to those exhibited by other mutants with defects in the PP-InsP synthesis pathway. Our results provide insight on the nexus between inositol phosphates and pyrophosphates involved in complex regulatory mechanisms underpinning phosphate homeostasis in plants. DA - 2021/9// PY - 2021/9// DO - 10.3390/metabo11090601 VL - 11 IS - 9 SP - SN - 2218-1989 UR - https://doi.org/10.3390/metabo11090601 KW - inositol pyrophosphates KW - phosphate starvation response KW - phosphate homeostasis KW - lipid remodeling KW - AtVIP1 KW - AtVIP2 ER - TY - JOUR TI - An Overview of the Practices and Management Methods for Enhancing Seed Production in Conifer Plantations for Commercial Use AU - Li, Yan AU - Li, Xiang AU - Zhao, Ming-Hui AU - Pang, Zhong-Yi AU - Wei, Jia-Tong AU - Tigabu, Mulualem AU - Chiang, Vincent L. AU - Sederoff, Heike AU - Sederoff, Ronald AU - Zhao, Xi-Yang T2 - HORTICULTURAE AB - Flowering, the beginning of the reproductive growth, is a significant stage in the growth and development of plants. Conifers are economically and ecologically important, characterized by straight trunks and a good wood quality and, thus, conifer plantations are widely distributed around the world. In addition, conifer species have a good tolerance to biotic and abiotic stress, and a stronger survival ability. Seeds of some conifer species, such as Pinus koraiensis, are rich in vitamins, amino acids, mineral elements and other nutrients, which are used for food and medicine. Although conifers are the largest (giant sequoia) and oldest living plants (bristlecone pine), their growth cycle is relatively long, and the seed yield is unstable. In the present work, we reviewed selected literature and provide a comprehensive overview on the most influential factors and on the methods and techniques that can be adopted in order to improve flowering and seed production in conifers species. The review revealed that flowering and seed yields in conifers are affected by a variety of factors, such as pollen, temperature, light, water availability, nutrients, etc., and a number of management techniques, including topping off, pruning, fertilization, hormone treatment, supplementary pollination, etc. has been developed for improving cone yields. Furthermore, several flowering-related genes (FT, Flowering locus T and MADS-box, MCMI, AGAMOUS, DEFICIENCES and SRF) that play a crucial role in flowering in coniferous trees were identified. The results of this study can be useful for forest managers and for enhancing seed yields in conifer plantations for commercial use. DA - 2021/8// PY - 2021/8// DO - 10.3390/horticulturae7080252 VL - 7 IS - 8 SP - SN - 2311-7524 KW - conifers KW - flowering KW - seed production KW - pollination KW - phytohormones KW - tree management KW - nutrient fertilization ER - TY - JOUR TI - Identification of Putative Biosynthetic Gene Clusters for Tolyporphins in Multiple Filamentous Cyanobacteria AU - Jin, Xiaohe AU - Zhang, Yunlong AU - Zhang, Ran AU - Nguyen, Kathy-Uyen AU - Lindsey, Jonathan S. AU - Miller, Eric S. T2 - LIFE-BASEL AB - Tolyporphins A–R are unusual tetrapyrrole macrocycles produced by the non-axenic filamentous cyanobacterium HT-58-2. A putative biosynthetic gene cluster for biosynthesis of tolyporphins (here termed BGC-1) was previously identified in the genome of HT-58-2. Here, homology searching of BGC-1 in HT-58-2 led to identification of similar BGCs in seven other filamentous cyanobacteria, including strains Nostoc sp. 106C, Nostoc sp. RF31YmG, Nostoc sp. FACHB-892, Brasilonema octagenarum UFV-OR1, Brasilonema octagenarum UFV-E1, Brasilonema sennae CENA114 and Oculatella sp. LEGE 06141, suggesting their potential for tolyporphins production. A similar gene cluster (BGC-2) also was identified unexpectedly in HT-58-2. Tolyporphins BGCs were not identified in unicellular cyanobacteria. Phylogenetic analysis based on 16S rRNA and a common component of the BGCs, TolD, points to a close evolutionary history between each strain and their respective tolyporphins BGC. Though identified with putative tolyporphins BGCs, examination of pigments extracted from three cyanobacteria has not revealed the presence of tolyporphins. Overall, the identification of BGCs and potential producers of tolyporphins presents a collection of candidate cyanobacteria for genetic and biochemical analysis pertaining to these unusual tetrapyrrole macrocycles. DA - 2021/8// PY - 2021/8// DO - 10.3390/life11080758 VL - 11 IS - 8 SP - SN - 2075-1729 KW - tolyporphins KW - tetrapyrroles KW - cyanobacteria KW - biosynthetic gene cluster KW - Brasilonema KW - Nostoc KW - Oculatella ER - TY - JOUR TI - Facilitation by isolated trees triggers woody encroachment and a biome shift at the savanna-forest transition AU - Abreu, Rodolfo C. R. AU - Durigan, Giselda AU - Melo, Antonio C. G. AU - Pilon, Natashi A. L. AU - Hoffmann, William A. T2 - JOURNAL OF APPLIED ECOLOGY AB - Abstract Woody encroachment into grassy biomes is a global phenomenon, often resulting in a nearly complete turnover of species, with savanna specialists being replaced by forest‐adapted species. Understanding the mechanisms involved in this change is important for devising strategies for managing savannas. We examined how isolated trees favour woody encroachment and species turnover by overcoming dispersal limitation and environmental filtering. In a savanna released from fire in south‐eastern Brazil (Cerrado), we sampled woody plants establishing under 40 tree canopies and in paired treeless plots. These trees comprised eight species selected for habitat preference (savanna or forest) and dispersal syndrome (bird dispersed or not). We recorded dimensions of each tree, dispersal syndrome and habitat preference of recruits, and quantified the physical environment within each plot, aiming at a mechanistic understanding of woody encroachment. We found clear evidence that isolated trees cause nucleation and drive changes in functional composition of savanna. Effectiveness as nucleator differed among species, but was unrelated to their functional guilds (habitat preference or dispersal syndrome). The density of saplings in nuclei was partially explained by soil moisture (+), daily temperature amplitude (−) and sum of bases (−). Our results indicate that isolated trees act first as perches, strongly favouring bird‐dispersed species. They then act as nurse trees, considerably changing the environment in favour of forest‐adapted recruits. In the long term, as the nuclei expand and merge, savanna specialists tend to disappear and the savanna turns into a low‐diversity forest. Synthesis and applications . Fire suppression has allowed the nucleation process and consequently the woody encroachment and fast replacement of savanna specialists by forest species in the Cerrado. By elucidating the mechanisms behind woody encroachment, we recommend using prescribed fires to burn forest seedlings and to reduce tree canopy size wherever the management goal is to maintain the typical savanna structure and composition. DA - 2021/8/28/ PY - 2021/8/28/ DO - 10.1111/1365-2664.13994 SP - SN - 1365-2664 KW - assembly rules KW - Cerrado vegetation KW - ecological filters KW - functional traits KW - nucleation KW - nurse trees KW - perches KW - savanna-forest mosaic ER - TY - JOUR TI - Local Plants, Not Soils, Are the Primary Source of Foliar Fungal Community Assembly in a C4 Grass AU - Whitaker, Briana K. AU - Giauque, Hannah AU - Timmerman, Corey AU - Birk, Nicolas AU - Hawkes, Christine V T2 - MICROBIAL ECOLOGY DA - 2021/8/18/ PY - 2021/8/18/ DO - 10.1007/s00248-021-01836-2 VL - 8 SP - SN - 1432-184X KW - Source-sink dynamics KW - Microbiome KW - Dispersal limitation KW - Turnover KW - Nestedness KW - Precipitation gradient ER - TY - JOUR TI - Epigenetic remodeling by DNA glycosylases during rice reproduction AU - Li, Mingzhuo AU - Cui, Qirui AU - Zhang, Xiang-Qian AU - Hsieh, Tzung-Fu T2 - MOLECULAR PLANT AB - Cytosine methylation is a covalent modification of DNA that regulates important processes in eukaryotic genomes, including gene transcription, transposon silencing, and genomic imprinting (Law and Jacobsen, 2010Law J.A. Jacobsen S.E. Establishing, maintaining and modifying DNA methylation patterns in plants and animals.Nat. Rev. Genet. 2010; 11: 204-220Crossref PubMed Scopus (2462) Google Scholar). DNA methylation patterns are faithfully duplicated upon cell division to ensure genome integrity and to maintain lineage-specific cell fate. However, DNA methylation also needs to be dynamically reprogramed or reconfigured during development to allow establishment of new cellular identity and transcriptional state, which plays a prominent role in animal development and reproduction, and is increasingly being appreciated for reproductive success in flowering plants (Walker et al., 2018Walker J. Gao H. Zhang J. Aldridge B. Vickers M. Higgins J.D. Feng X. Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis.Nat. Genet. 2018; 50: 130-137https://doi.org/10.1038/s41588-017-0008-5Crossref PubMed Scopus (99) Google Scholar; Ono and Kinoshita, 2021Ono A. Kinoshita T. Epigenetics and plant reproduction: multiple steps for responsibly handling succession.Curr. Opin. Plant Biol. 2021; 61: 102032https://doi.org/10.1016/j.pbi.2021.102032Crossref PubMed Scopus (6) Google Scholar). In mammals, germline cells and zygotes undergo genome-wide methylation resets to obtain cellular pluripotency. In flowering plants, multiple waves of localized smaller-scale epigenetic dynamics and remodeling have also been documented during reproduction (Gehring, 2019Gehring M. Epigenetic dynamics during flowering plant reproduction: evidence for reprogramming?.New Phytol. 2019; 224: 91-96https://doi.org/10.1111/nph.15856Crossref PubMed Scopus (41) Google Scholar). For example, before fertilization localized demethylation in vegetative and central cells (VC and CC, companion cells of sperm and egg) was found to be essential for seed viability (Gehring, 2019Gehring M. Epigenetic dynamics during flowering plant reproduction: evidence for reprogramming?.New Phytol. 2019; 224: 91-96https://doi.org/10.1111/nph.15856Crossref PubMed Scopus (41) Google Scholar). Upon fertilization, the genomes of endosperm and embryo undergo methylation reconfiguration in Arabidopsis, soybean, and rice (Park et al., 2016Park K. Kim M.Y. Vickers M. Park J.S. Hyun Y. Okamoto T. Zilberman D. Fischer R.L. Feng X. Choi Y. et al.DNA demethylation is initiated in the central cells of Arabidopsis and rice.Proc. Natl. Acad. Sci. U S A. 2016; 113: 15138-15143https://doi.org/10.1073/pnas.1619047114Crossref PubMed Scopus (104) Google Scholar; Kim et al., 2019Kim M.Y. Ono A. Scholten S. Kinoshita T. Zilberman D. Okamoto T. Fischer R.L. DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm.Proc. Natl. Acad. Sci. U S A. 2019; 116: 9652-9657https://doi.org/10.1073/pnas.1821435116Crossref PubMed Scopus (27) Google Scholar; Ono and Kinoshita, 2021Ono A. Kinoshita T. Epigenetics and plant reproduction: multiple steps for responsibly handling succession.Curr. Opin. Plant Biol. 2021; 61: 102032https://doi.org/10.1016/j.pbi.2021.102032Crossref PubMed Scopus (6) Google Scholar). Although DNA glycosylases and the de novo methylation pathways are implicated in some of these processes, many of their biological functions remain to be fully elucidated.Epigenome remodeling in gamete companion cells of Arabidopsis and riceIn Arabidopsis, the genome of the CC undergoes extensive demethylation at thousands of loci directed by the DEMETER (DME) glycosylase to establish parent-of-origin-specific expression of many imprinted genes in endosperm. DME also demethylates the genomes of VCs and the lack of DME activity in VCs resulted in CHH hypomethylation in corresponding loci in sperm (Ibarra et al., 2012Ibarra C.A. Feng X. Schoft V.K. Hsieh T.F. Uzawa R. Rodrigues J.A. Zemach A. Chumak N. Machlicova A. Nishimura T. et al.Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes.Science. 2012; 337: 1360-1364https://doi.org/10.1126/science.1224839Crossref PubMed Scopus (335) Google Scholar). Thus, the main functions of DME during Arabidopsis reproduction are to establish gene imprinting and to reinforce transgenerational TE silencing.Although no DME ortholog was detected in monocots, the rice ROS1a (DNG702) was shown to be the functional counterpart of DME in rice cultivar Nipponbare (Ono et al., 2012Ono A. Yamaguchi K. Fukada-Tanaka S. Terada R. Mitsui T. Iida S. A null mutation of ROS1a for DNA demethylation in rice is not transmittable to progeny.Plant J. 2012; 71: 564-574https://doi.org/10.1111/j.1365-313X.2012.05009.xCrossref PubMed Scopus (74) Google Scholar). Similar to the VC of Arabidopsis, the rice VC genome is also extensively hypomethylated compared with the sperm genome in a ROS1a-dependent manner (Kim et al., 2019Kim M.Y. Ono A. Scholten S. Kinoshita T. Zilberman D. Okamoto T. Fischer R.L. DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm.Proc. Natl. Acad. Sci. U S A. 2019; 116: 9652-9657https://doi.org/10.1073/pnas.1821435116Crossref PubMed Scopus (27) Google Scholar). In ROS1a/ros1a heterozygous plants, sperm CHH is hypomethylated at the loci where CG hypomethylation occurred in VCs, indicating that ROS1a activity in VCs is required for normal sperm CHH methylation. Furthermore, there is a large overlap between VC versus sperm and endosperm versus embryo hypomethylated DMRs, suggesting ROS1a also demethylates the rice CC genome (Kim et al., 2019Kim M.Y. Ono A. Scholten S. Kinoshita T. Zilberman D. Okamoto T. Fischer R.L. DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm.Proc. Natl. Acad. Sci. U S A. 2019; 116: 9652-9657https://doi.org/10.1073/pnas.1821435116Crossref PubMed Scopus (27) Google Scholar). Thus, gamete companion cells epigenetic remodeling by DNA glycosylases is an evolutionarily conserved phenomenon in rice and Arabidopsis; species that diverged more than 150 million years ago.Despite this conservation, many distinct features exist between rice and Arabidopsis. For example, DME’s expression is primarily restricted to the gamete companion cells of Arabidopsis, whereas ROS1a is broadly expressed throughout rice development. This suggests that the gamete companion cell function of ROS1a was delegated to DME in Arabidopsis and ROS1a might also play a role in rice gamete formation and seed development.Epigenome remodeling of gametes and zygote in riceRice has a persistent endosperm that serves as a staple food for humans and its genome contains more TEs than Arabidopsis (International Rice Genome Sequencing, 2005International Rice Genome Sequencing, PThe map-based sequence of the rice genome.Nature. 2005; 436: 793-800https://doi.org/10.1038/nature03895Crossref PubMed Scopus (2937) Google Scholar). Understanding its reproductive epigenetic mechanisms has direct relevance to food production and can complement the knowledge gained from research in Arabidopsis and other plant models. The Nipponbare reference genome encodes at least four DNA demethylases, DNG701–DNG704. Except for DNG702/ROS1a’s roles in gamete companion cells, functions of these DNA glycosylases in germline cells and zygote were not known until now. A new report published in Molecular Plants attempted to address this question by conducting a comprehensive DNA methylome study in rice gamete, zygote, and developing embryos in wild-type and dng mutants (cultivar Dongjing) (Zhou et al., 2021Zhou S. Li X. Liu Q. Zhao Y. Jiang W. Wu A. Zhou D.X. DNA demethylases remodel DNA methylation in rice gametes and zygote and are required for reproduction.Mol. Plant. 2021; https://doi.org/10.1016/j.molp.2021.06.006Abstract Full Text Full Text PDF Scopus (11) Google Scholar). In addition, this new study also revealed methylation dynamics among these cell types/tissues. In wild-type plants, there is a moderate difference in bulk methylation level between egg and sperm, which is likely due to differential maintenance and do novo DNA methylase activities during male and female gametogenesis, a phenomenon consistent with what was observed during male sex lineage development in Arabidopsis (Walker et al., 2018Walker J. Gao H. Zhang J. Aldridge B. Vickers M. Higgins J.D. Feng X. Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis.Nat. Genet. 2018; 50: 130-137https://doi.org/10.1038/s41588-017-0008-5Crossref PubMed Scopus (99) Google Scholar; Long et al., 2021Long J. Walker J. She W. Aldridge B. Gao H. Deans S. Vickers M. Feng X. Nurse cell-derived small RNAs define paternal epigenetic inheritance in Arabidopsis.Science. 2021; 373https://doi.org/10.1126/science.abh0556Crossref PubMed Scopus (27) Google Scholar). Inclusion of the unicellular zygote methylome (at 6.5 h after pollination) allowed for a direct interrogation into changes in parental genomes after they fused to form the zygote. Importantly, significant differential methylations were detected between zygote versus egg or sperm that were not a simple summation of the methylomes of the gametes, suggesting that the zygote epigenome is quickly reconfigured after fertilization. As the zygote develops, the globular embryo (GE) exhibited a slightly higher CG methylation but a lower CHH methylation level compared with the zygote. In the mature embryo, CHH methylation remains low as in GE, but CHG methylation showed a more significant decrease from GE. Taken together, these observations show that there is a substantial DNA methylation remodeling and reconfiguration during rice embryo development that is distinct from what was observed in Arabidopsis and soybean (Ono and Kinoshita, 2021Ono A. Kinoshita T. Epigenetics and plant reproduction: multiple steps for responsibly handling succession.Curr. Opin. Plant Biol. 2021; 61: 102032https://doi.org/10.1016/j.pbi.2021.102032Crossref PubMed Scopus (6) Google Scholar).To understand the contributions of gamete- and zygote-expressed glycosylases (DNG701, DNG702, and DNG704) to the rice epigenetic dynamics during reproduction, the authors generated loss-of-function mutations in these genes and profiled methylomes from mutant eggs, sperm, and zygotes. Self-pollination of homozygous dng702 plants can produce gametes but the zygotes failed to initiate embryogenesis. However, hybrid F1 seeds derived from reciprocal crosses between dng702 and wild-type plants produced viable embryos with defective endosperm. These observations showed that, for zygotes to initiate embryogenesis, at least one functional copy of DNG702 is needed; whereas for normal endosperm development, DNG702 activity is required in both the CC and sperm (Figure 1). This is intriguing as most known gametophytic-related endosperm failures are caused by CC defects (Huh et al., 2008Huh J.H. Bauer M.J. Hsieh T.-F. Fischer R.L. Cellular programming of plant gene imprinting.Cell. 2008; 132: 735-744Abstract Full Text Full Text PDF PubMed Scopus (123) Google Scholar). If validated, this would indicate DNG702 has a specific function in sperm that cannot be compensated by the wild-type CC genomes for endosperm development.For DNG701 and DNG704, reproductive defects were only observed in dng701/4 double mutants that produced 50% aborted, 35% normal, and 15% retarded seeds. This suggests that DNG701/4 also have a gamete formation function (see below) as well as a post-fertilization zygotic function that might be partially redundant with DNG702 (Figure 1). However, morphological phenotypes of F1 seeds derived from dng701/4 and wild-type reciprocal crosses were not presented, making it difficult to assess their functions accurately.Analysis of DMRs between mutant and wild-type gametes and zygotes enabled identification of loci targeted by each glycosylase. Interestingly, the DMRs of dng702 and dng701/704 versus wild-type egg and sperm are largely non-overlapping, indicating that DNG702 and DNG701/DNG704 have distinct targets in egg and sperm. Comparing targets of DNG701/4 in unicellular zygotes with those in eggs or sperm revealed that DNG701/4 have almost entirely new targets in zygotes, indicating that they have distinct functions before and after fertilization. Furthermore, loci demethylated by DNG702 in sperm or eggs are hypermethylated in wild-type zygotes, indicating that those gametic targets of DNG702 are quickly remethylated upon gamete fusion, presumably by the de novo methylation pathways. Likewise, DNG701/4 target sites in gametes were also remethylated in the unicellular zygotes.In conclusion, Zhou and colleagues provided a large amount of exciting new data that greatly enrich and extend our knowledge on the epigenetic dynamics during rice reproduction. Particularly, the generation of dng mutant plants and methylomes of gametes and zygotes provide the research community a rich epigenetic resource that will spark new discoveries and inspire motivations for deeper understanding of how these glycosylases function. This study strongly suggests that localized demethylation by these three DNG glycosylases in the sex cells likely serves to “prime” the gametes for successful fertilization and prepare the zygotes for rapid cellular division and differentiation during early embryogenesis. Once the gametes successfully fuse, parental imprints are quickly removed by de novo methylation and the glycosylases resume their zygotic functions by marking new target loci to ensure robust progression of embryogenesis. This notion is further supported by the transcriptomic analysis of zygote versus egg which revealed that the number of differentially expressed genes between zygote and egg is reduced by ∼50% in dng701/4, indicating that the zygotic function of DNG701/4 contributes substantially to the transcriptional state of the unicellular zygotes.FundingThis work is supported by the National Institute of Food and Agriculture ( Hatch-02413 ) and the National Science Foundation ( MCB-1715115 ). Cytosine methylation is a covalent modification of DNA that regulates important processes in eukaryotic genomes, including gene transcription, transposon silencing, and genomic imprinting (Law and Jacobsen, 2010Law J.A. Jacobsen S.E. Establishing, maintaining and modifying DNA methylation patterns in plants and animals.Nat. Rev. Genet. 2010; 11: 204-220Crossref PubMed Scopus (2462) Google Scholar). DNA methylation patterns are faithfully duplicated upon cell division to ensure genome integrity and to maintain lineage-specific cell fate. However, DNA methylation also needs to be dynamically reprogramed or reconfigured during development to allow establishment of new cellular identity and transcriptional state, which plays a prominent role in animal development and reproduction, and is increasingly being appreciated for reproductive success in flowering plants (Walker et al., 2018Walker J. Gao H. Zhang J. Aldridge B. Vickers M. Higgins J.D. Feng X. Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis.Nat. Genet. 2018; 50: 130-137https://doi.org/10.1038/s41588-017-0008-5Crossref PubMed Scopus (99) Google Scholar; Ono and Kinoshita, 2021Ono A. Kinoshita T. Epigenetics and plant reproduction: multiple steps for responsibly handling succession.Curr. Opin. Plant Biol. 2021; 61: 102032https://doi.org/10.1016/j.pbi.2021.102032Crossref PubMed Scopus (6) Google Scholar). In mammals, germline cells and zygotes undergo genome-wide methylation resets to obtain cellular pluripotency. In flowering plants, multiple waves of localized smaller-scale epigenetic dynamics and remodeling have also been documented during reproduction (Gehring, 2019Gehring M. Epigenetic dynamics during flowering plant reproduction: evidence for reprogramming?.New Phytol. 2019; 224: 91-96https://doi.org/10.1111/nph.15856Crossref PubMed Scopus (41) Google Scholar). For example, before fertilization localized demethylation in vegetative and central cells (VC and CC, companion cells of sperm and egg) was found to be essential for seed viability (Gehring, 2019Gehring M. Epigenetic dynamics during flowering plant reproduction: evidence for reprogramming?.New Phytol. 2019; 224: 91-96https://doi.org/10.1111/nph.15856Crossref PubMed Scopus (41) Google Scholar). Upon fertilization, the genomes of endosperm and embryo undergo methylation reconfiguration in Arabidopsis, soybean, and rice (Park et al., 2016Park K. Kim M.Y. Vickers M. Park J.S. Hyun Y. Okamoto T. Zilberman D. Fischer R.L. Feng X. Choi Y. et al.DNA demethylation is initiated in the central cells of Arabidopsis and rice.Proc. Natl. Acad. Sci. U S A. 2016; 113: 15138-15143https://doi.org/10.1073/pnas.1619047114Crossref PubMed Scopus (104) Google Scholar; Kim et al., 2019Kim M.Y. Ono A. Scholten S. Kinoshita T. Zilberman D. Okamoto T. Fischer R.L. DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm.Proc. Natl. Acad. Sci. U S A. 2019; 116: 9652-9657https://doi.org/10.1073/pnas.1821435116Crossref PubMed Scopus (27) Google Scholar; Ono and Kinoshita, 2021Ono A. Kinoshita T. Epigenetics and plant reproduction: multiple steps for responsibly handling succession.Curr. Opin. Plant Biol. 2021; 61: 102032https://doi.org/10.1016/j.pbi.2021.102032Crossref PubMed Scopus (6) Google Scholar). Although DNA glycosylases and the de novo methylation pathways are implicated in some of these processes, many of their biological functions remain to be fully elucidated. Epigenome remodeling in gamete companion cells of Arabidopsis and riceIn Arabidopsis, the genome of the CC undergoes extensive demethylation at thousands of loci directed by the DEMETER (DME) glycosylase to establish parent-of-origin-specific expression of many imprinted genes in endosperm. DME also demethylates the genomes of VCs and the lack of DME activity in VCs resulted in CHH hypomethylation in corresponding loci in sperm (Ibarra et al., 2012Ibarra C.A. Feng X. Schoft V.K. Hsieh T.F. Uzawa R. Rodrigues J.A. Zemach A. Chumak N. Machlicova A. Nishimura T. et al.Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes.Science. 2012; 337: 1360-1364https://doi.org/10.1126/science.1224839Crossref PubMed Scopus (335) Google Scholar). Thus, the main functions of DME during Arabidopsis reproduction are to establish gene imprinting and to reinforce transgenerational TE silencing.Although no DME ortholog was detected in monocots, the rice ROS1a (DNG702) was shown to be the functional counterpart of DME in rice cultivar Nipponbare (Ono et al., 2012Ono A. Yamaguchi K. Fukada-Tanaka S. Terada R. Mitsui T. Iida S. A null mutation of ROS1a for DNA demethylation in rice is not transmittable to progeny.Plant J. 2012; 71: 564-574https://doi.org/10.1111/j.1365-313X.2012.05009.xCrossref PubMed Scopus (74) Google Scholar). Similar to the VC of Arabidopsis, the rice VC genome is also extensively hypomethylated compared with the sperm genome in a ROS1a-dependent manner (Kim et al., 2019Kim M.Y. Ono A. Scholten S. Kinoshita T. Zilberman D. Okamoto T. Fischer R.L. DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm.Proc. Natl. Acad. Sci. U S A. 2019; 116: 9652-9657https://doi.org/10.1073/pnas.1821435116Crossref PubMed Scopus (27) Google Scholar). In ROS1a/ros1a heterozygous plants, sperm CHH is hypomethylated at the loci where CG hypomethylation occurred in VCs, indicating that ROS1a activity in VCs is required for normal sperm CHH methylation. Furthermore, there is a large overlap between VC versus sperm and endosperm versus embryo hypomethylated DMRs, suggesting ROS1a also demethylates the rice CC genome (Kim et al., 2019Kim M.Y. Ono A. Scholten S. Kinoshita T. Zilberman D. Okamoto T. Fischer R.L. DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm.Proc. Natl. Acad. Sci. U S A. 2019; 116: 9652-9657https://doi.org/10.1073/pnas.1821435116Crossref PubMed Scopus (27) Google Scholar). Thus, gamete companion cells epigenetic remodeling by DNA glycosylases is an evolutionarily conserved phenomenon in rice and Arabidopsis; species that diverged more than 150 million years ago.Despite this conservation, many distinct features exist between rice and Arabidopsis. For example, DME’s expression is primarily restricted to the gamete companion cells of Arabidopsis, whereas ROS1a is broadly expressed throughout rice development. This suggests that the gamete companion cell function of ROS1a was delegated to DME in Arabidopsis and ROS1a might also play a role in rice gamete formation and seed development. In Arabidopsis, the genome of the CC undergoes extensive demethylation at thousands of loci directed by the DEMETER (DME) glycosylase to establish parent-of-origin-specific expression of many imprinted genes in endosperm. DME also demethylates the genomes of VCs and the lack of DME activity in VCs resulted in CHH hypomethylation in corresponding loci in sperm (Ibarra et al., 2012Ibarra C.A. Feng X. Schoft V.K. Hsieh T.F. Uzawa R. Rodrigues J.A. Zemach A. Chumak N. Machlicova A. Nishimura T. et al.Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes.Science. 2012; 337: 1360-1364https://doi.org/10.1126/science.1224839Crossref PubMed Scopus (335) Google Scholar). Thus, the main functions of DME during Arabidopsis reproduction are to establish gene imprinting and to reinforce transgenerational TE silencing. Although no DME ortholog was detected in monocots, the rice ROS1a (DNG702) was shown to be the functional counterpart of DME in rice cultivar Nipponbare (Ono et al., 2012Ono A. Yamaguchi K. Fukada-Tanaka S. Terada R. Mitsui T. Iida S. A null mutation of ROS1a for DNA demethylation in rice is not transmittable to progeny.Plant J. 2012; 71: 564-574https://doi.org/10.1111/j.1365-313X.2012.05009.xCrossref PubMed Scopus (74) Google Scholar). Similar to the VC of Arabidopsis, the rice VC genome is also extensively hypomethylated compared with the sperm genome in a ROS1a-dependent manner (Kim et al., 2019Kim M.Y. Ono A. Scholten S. Kinoshita T. Zilberman D. Okamoto T. Fischer R.L. DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm.Proc. Natl. Acad. Sci. U S A. 2019; 116: 9652-9657https://doi.org/10.1073/pnas.1821435116Crossref PubMed Scopus (27) Google Scholar). In ROS1a/ros1a heterozygous plants, sperm CHH is hypomethylated at the loci where CG hypomethylation occurred in VCs, indicating that ROS1a activity in VCs is required for normal sperm CHH methylation. Furthermore, there is a large overlap between VC versus sperm and endosperm versus embryo hypomethylated DMRs, suggesting ROS1a also demethylates the rice CC genome (Kim et al., 2019Kim M.Y. Ono A. Scholten S. Kinoshita T. Zilberman D. Okamoto T. Fischer R.L. DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm.Proc. Natl. Acad. Sci. U S A. 2019; 116: 9652-9657https://doi.org/10.1073/pnas.1821435116Crossref PubMed Scopus (27) Google Scholar). Thus, gamete companion cells epigenetic remodeling by DNA glycosylases is an evolutionarily conserved phenomenon in rice and Arabidopsis; species that diverged more than 150 million years ago. Despite this conservation, many distinct features exist between rice and Arabidopsis. For example, DME’s expression is primarily restricted to the gamete companion cells of Arabidopsis, whereas ROS1a is broadly expressed throughout rice development. This suggests that the gamete companion cell function of ROS1a was delegated to DME in Arabidopsis and ROS1a might also play a role in rice gamete formation and seed development. Epigenome remodeling of gametes and zygote in riceRice has a persistent endosperm that serves as a staple food for humans and its genome contains more TEs than Arabidopsis (International Rice Genome Sequencing, 2005International Rice Genome Sequencing, PThe map-based sequence of the rice genome.Nature. 2005; 436: 793-800https://doi.org/10.1038/nature03895Crossref PubMed Scopus (2937) Google Scholar). Understanding its reproductive epigenetic mechanisms has direct relevance to food production and can complement the knowledge gained from research in Arabidopsis and other plant models. The Nipponbare reference genome encodes at least four DNA demethylases, DNG701–DNG704. Except for DNG702/ROS1a’s roles in gamete companion cells, functions of these DNA glycosylases in germline cells and zygote were not known until now. A new report published in Molecular Plants attempted to address this question by conducting a comprehensive DNA methylome study in rice gamete, zygote, and developing embryos in wild-type and dng mutants (cultivar Dongjing) (Zhou et al., 2021Zhou S. Li X. Liu Q. Zhao Y. Jiang W. Wu A. Zhou D.X. DNA demethylases remodel DNA methylation in rice gametes and zygote and are required for reproduction.Mol. Plant. 2021; https://doi.org/10.1016/j.molp.2021.06.006Abstract Full Text Full Text PDF Scopus (11) Google Scholar). In addition, this new study also revealed methylation dynamics among these cell types/tissues. In wild-type plants, there is a moderate difference in bulk methylation level between egg and sperm, which is likely due to differential maintenance and do novo DNA methylase activities during male and female gametogenesis, a phenomenon consistent with what was observed during male sex lineage development in Arabidopsis (Walker et al., 2018Walker J. Gao H. Zhang J. Aldridge B. Vickers M. Higgins J.D. Feng X. Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis.Nat. Genet. 2018; 50: 130-137https://doi.org/10.1038/s41588-017-0008-5Crossref PubMed Scopus (99) Google Scholar; Long et al., 2021Long J. Walker J. She W. Aldridge B. Gao H. Deans S. Vickers M. Feng X. Nurse cell-derived small RNAs define paternal epigenetic inheritance in Arabidopsis.Science. 2021; 373https://doi.org/10.1126/science.abh0556Crossref PubMed Scopus (27) Google Scholar). Inclusion of the unicellular zygote methylome (at 6.5 h after pollination) allowed for a direct interrogation into changes in parental genomes after they fused to form the zygote. Importantly, significant differential methylations were detected between zygote versus egg or sperm that were not a simple summation of the methylomes of the gametes, suggesting that the zygote epigenome is quickly reconfigured after fertilization. As the zygote develops, the globular embryo (GE) exhibited a slightly higher CG methylation but a lower CHH methylation level compared with the zygote. In the mature embryo, CHH methylation remains low as in GE, but CHG methylation showed a more significant decrease from GE. Taken together, these observations show that there is a substantial DNA methylation remodeling and reconfiguration during rice embryo development that is distinct from what was observed in Arabidopsis and soybean (Ono and Kinoshita, 2021Ono A. Kinoshita T. Epigenetics and plant reproduction: multiple steps for responsibly handling succession.Curr. Opin. Plant Biol. 2021; 61: 102032https://doi.org/10.1016/j.pbi.2021.102032Crossref PubMed Scopus (6) Google Scholar).To understand the contributions of gamete- and zygote-expressed glycosylases (DNG701, DNG702, and DNG704) to the rice epigenetic dynamics during reproduction, the authors generated loss-of-function mutations in these genes and profiled methylomes from mutant eggs, sperm, and zygotes. Self-pollination of homozygous dng702 plants can produce gametes but the zygotes failed to initiate embryogenesis. However, hybrid F1 seeds derived from reciprocal crosses between dng702 and wild-type plants produced viable embryos with defective endosperm. These observations showed that, for zygotes to initiate embryogenesis, at least one functional copy of DNG702 is needed; whereas for normal endosperm development, DNG702 activity is required in both the CC and sperm (Figure 1). This is intriguing as most known gametophytic-related endosperm failures are caused by CC defects (Huh et al., 2008Huh J.H. Bauer M.J. Hsieh T.-F. Fischer R.L. Cellular programming of plant gene imprinting.Cell. 2008; 132: 735-744Abstract Full Text Full Text PDF PubMed Scopus (123) Google Scholar). If validated, this would indicate DNG702 has a specific function in sperm that cannot be compensated by the wild-type CC genomes for endosperm development.For DNG701 and DNG704, reproductive defects were only observed in dng701/4 double mutants that produced 50% aborted, 35% normal, and 15% retarded seeds. This suggests that DNG701/4 also have a gamete formation function (see below) as well as a post-fertilization zygotic function that might be partially redundant with DNG702 (Figure 1). However, morphological phenotypes of F1 seeds derived from dng701/4 and wild-type reciprocal crosses were not presented, making it difficult to assess their functions accurately.Analysis of DMRs between mutant and wild-type gametes and zygotes enabled identification of loci targeted by each glycosylase. Interestingly, the DMRs of dng702 and dng701/704 versus wild-type egg and sperm are largely non-overlapping, indicating that DNG702 and DNG701/DNG704 have distinct targets in egg and sperm. Comparing targets of DNG701/4 in unicellular zygotes with those in eggs or sperm revealed that DNG701/4 have almost entirely new targets in zygotes, indicating that they have distinct functions before and after fertilization. Furthermore, loci demethylated by DNG702 in sperm or eggs are hypermethylated in wild-type zygotes, indicating that those gametic targets of DNG702 are quickly remethylated upon gamete fusion, presumably by the de novo methylation pathways. Likewise, DNG701/4 target sites in gametes were also remethylated in the unicellular zygotes.In conclusion, Zhou and colleagues provided a large amount of exciting new data that greatly enrich and extend our knowledge on the epigenetic dynamics during rice reproduction. Particularly, the generation of dng mutant plants and methylomes of gametes and zygotes provide the research community a rich epigenetic resource that will spark new discoveries and inspire motivations for deeper understanding of how these glycosylases function. This study strongly suggests that localized demethylation by these three DNG glycosylases in the sex cells likely serves to “prime” the gametes for successful fertilization and prepare the zygotes for rapid cellular division and differentiation during early embryogenesis. Once the gametes successfully fuse, parental imprints are quickly removed by de novo methylation and the glycosylases resume their zygotic functions by marking new target loci to ensure robust progression of embryogenesis. This notion is further supported by the transcriptomic analysis of zygote versus egg which revealed that the number of differentially expressed genes between zygote and egg is reduced by ∼50% in dng701/4, indicating that the zygotic function of DNG701/4 contributes substantially to the transcriptional state of the unicellular zygotes. Rice has a persistent endosperm that serves as a staple food for humans and its genome contains more TEs than Arabidopsis (International Rice Genome Sequencing, 2005International Rice Genome Sequencing, PThe map-based sequence of the rice genome.Nature. 2005; 436: 793-800https://doi.org/10.1038/nature03895Crossref PubMed Scopus (2937) Google Scholar). Understanding its reproductive epigenetic mechanisms has direct relevance to food production and can complement the knowledge gained from research in Arabidopsis and other plant models. The Nipponbare reference genome encodes at least four DNA demethylases, DNG701–DNG704. Except for DNG702/ROS1a’s roles in gamete companion cells, functions of these DNA glycosylases in germline cells and zygote were not known until now. A new report published in Molecular Plants attempted to address this question by conducting a comprehensive DNA methylome study in rice gamete, zygote, and developing embryos in wild-type and dng mutants (cultivar Dongjing) (Zhou et al., 2021Zhou S. Li X. Liu Q. Zhao Y. Jiang W. Wu A. Zhou D.X. DNA demethylases remodel DNA methylation in rice gametes and zygote and are required for reproduction.Mol. Plant. 2021; https://doi.org/10.1016/j.molp.2021.06.006Abstract Full Text Full Text PDF Scopus (11) Google Scholar). In addition, this new study also revealed methylation dynamics among these cell types/tissues. In wild-type plants, there is a moderate difference in bulk methylation level between egg and sperm, which is likely due to differential maintenance and do novo DNA methylase activities during male and female gametogenesis, a phenomenon consistent with what was observed during male sex lineage development in Arabidopsis (Walker et al., 2018Walker J. Gao H. Zhang J. Aldridge B. Vickers M. Higgins J.D. Feng X. Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis.Nat. Genet. 2018; 50: 130-137https://doi.org/10.1038/s41588-017-0008-5Crossref PubMed Scopus (99) Google Scholar; Long et al., 2021Long J. Walker J. She W. Aldridge B. Gao H. Deans S. Vickers M. Feng X. Nurse cell-derived small RNAs define paternal epigenetic inheritance in Arabidopsis.Science. 2021; 373https://doi.org/10.1126/science.abh0556Crossref PubMed Scopus (27) Google Scholar). Inclusion of the unicellular zygote methylome (at 6.5 h after pollination) allowed for a direct interrogation into changes in parental genomes after they fused to form the zygote. Importantly, significant differential methylations were detected between zygote versus egg or sperm that were not a simple summation of the methylomes of the gametes, suggesting that the zygote epigenome is quickly reconfigured after fertilization. As the zygote develops, the globular embryo (GE) exhibited a slightly higher CG methylation but a lower CHH methylation level compared with the zygote. In the mature embryo, CHH methylation remains low as in GE, but CHG methylation showed a more significant decrease from GE. Taken together, these observations show that there is a substantial DNA methylation remodeling and reconfiguration during rice embryo development that is distinct from what was observed in Arabidopsis and soybean (Ono and Kinoshita, 2021Ono A. Kinoshita T. Epigenetics and plant reproduction: multiple steps for responsibly handling succession.Curr. Opin. Plant Biol. 2021; 61: 102032https://doi.org/10.1016/j.pbi.2021.102032Crossref PubMed Scopus (6) Google Scholar). To understand the contributions of gamete- and zygote-expressed glycosylases (DNG701, DNG702, and DNG704) to the rice epigenetic dynamics during reproduction, the authors generated loss-of-function mutations in these genes and profiled methylomes from mutant eggs, sperm, and zygotes. Self-pollination of homozygous dng702 plants can produce gametes but the zygotes failed to initiate embryogenesis. However, hybrid F1 seeds derived from reciprocal crosses between dng702 and wild-type plants produced viable embryos with defective endosperm. These observations showed that, for zygotes to initiate embryogenesis, at least one functional copy of DNG702 is needed; whereas for normal endosperm development, DNG702 activity is required in both the CC and sperm (Figure 1). This is intriguing as most known gametophytic-related endosperm failures are caused by CC defects (Huh et al., 2008Huh J.H. Bauer M.J. Hsieh T.-F. Fischer R.L. Cellular programming of plant gene imprinting.Cell. 2008; 132: 735-744Abstract Full Text Full Text PDF PubMed Scopus (123) Google Scholar). If validated, this would indicate DNG702 has a specific function in sperm that cannot be compensated by the wild-type CC genomes for endosperm development. For DNG701 and DNG704, reproductive defects were only observed in dng701/4 double mutants that produced 50% aborted, 35% normal, and 15% retarded seeds. This suggests that DNG701/4 also have a gamete formation function (see below) as well as a post-fertilization zygotic function that might be partially redundant with DNG702 (Figure 1). However, morphological phenotypes of F1 seeds derived from dng701/4 and wild-type reciprocal crosses were not presented, making it difficult to assess their functions accurately. Analysis of DMRs between mutant and wild-type gametes and zygotes enabled identification of loci targeted by each glycosylase. Interestingly, the DMRs of dng702 and dng701/704 versus wild-type egg and sperm are largely non-overlapping, indicating that DNG702 and DNG701/DNG704 have distinct targets in egg and sperm. Comparing targets of DNG701/4 in unicellular zygotes with those in eggs or sperm revealed that DNG701/4 have almost entirely new targets in zygotes, indicating that they have distinct functions before and after fertilization. Furthermore, loci demethylated by DNG702 in sperm or eggs are hypermethylated in wild-type zygotes, indicating that those gametic targets of DNG702 are quickly remethylated upon gamete fusion, presumably by the de novo methylation pathways. Likewise, DNG701/4 target sites in gametes were also remethylated in the unicellular zygotes. In conclusion, Zhou and colleagues provided a large amount of exciting new data that greatly enrich and extend our knowledge on the epigenetic dynamics during rice reproduction. Particularly, the generation of dng mutant plants and methylomes of gametes and zygotes provide the research community a rich epigenetic resource that will spark new discoveries and inspire motivations for deeper understanding of how these glycosylases function. This study strongly suggests that localized demethylation by these three DNG glycosylases in the sex cells likely serves to “prime” the gametes for successful fertilization and prepare the zygotes for rapid cellular division and differentiation during early embryogenesis. Once the gametes successfully fuse, parental imprints are quickly removed by de novo methylation and the glycosylases resume their zygotic functions by marking new target loci to ensure robust progression of embryogenesis. This notion is further supported by the transcriptomic analysis of zygote versus egg which revealed that the number of differentially expressed genes between zygote and egg is reduced by ∼50% in dng701/4, indicating that the zygotic function of DNG701/4 contributes substantially to the transcriptional state of the unicellular zygotes. FundingThis work is supported by the National Institute of Food and Agriculture ( Hatch-02413 ) and the National Science Foundation ( MCB-1715115 ). This work is supported by the National Institute of Food and Agriculture ( Hatch-02413 ) and the National Science Foundation ( MCB-1715115 ). DA - 2021/9/6/ PY - 2021/9/6/ DO - 10.1016/j.molp.2021.07.009 VL - 14 IS - 9 SP - 1433-1435 SN - 1752-9867 UR - https://doi.org/10.1016/j.molp.2021.07.009 ER - TY - JOUR TI - Genetic basis of variation in cocaine and methamphetamine consumption in outbred populations of Drosophila melanogaster AU - Baker, Brandon M. AU - Carbone, Mary Anna AU - Huang, Wen AU - Anholt, Robert R. H. AU - Mackay, Trudy F. C. T2 - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA AB - Significance The use of cocaine and methamphetamine presents significant socioeconomic problems. However, identifying the genetic underpinnings that determine susceptibility to substance use is challenging in human populations. The fruit fly, Drosophila melanogaster , presents a powerful genetic model since we can control the genetic background and environment, 75% of disease-causing genes in humans have a fly counterpart, and flies—like humans—exhibit adverse effects upon cocaine and methamphetamine exposure. We showed that the genetic architecture underlying variation in voluntary cocaine and methamphetamine consumption differs between sexes and is dominated by variants in genes associated with connectivity and function of the nervous system. Results obtained from the Drosophila gene discovery model can guide studies on substance abuse susceptibility in human populations. DA - 2021/6/8/ PY - 2021/6/8/ DO - 10.1073/pnas.2104131118 VL - 118 IS - 23 SP - SN - 0027-8424 KW - extreme QTL genome-wide association mapping KW - Drosophila Genetic Reference Panel KW - RNA interference KW - advanced intercross population ER - TY - JOUR TI - PHENOTYPIC PLASTICITY MASKS RANGE-WIDE GENETIC DIFFERENTIATION FOR VEGETATIVE BUT NOT REPRODUCTIVE TRAITS IN A SHORT-LIVED PLANT AU - Villellas, Jesus AU - Ehrlen, Johan AU - Crone, Elizabeth E. AU - Csergo, Anna Maria AU - Garcia, Maria B. AU - Laine, Anna-Liisa AU - Roach, Deborah A. AU - Salguero-Gomez, Roberto AU - Wardle, Glenda M. AU - Childs, Dylan Z. AU - Elderd, Bret D. AU - Finn, Alain AU - Munne-Bosch, Sergi AU - Bachelot, Benedicte AU - Bodis, Judit AU - Bucharova, Anna AU - Caruso, Christina M. AU - Catford, Jane A. AU - Coghill, Matthew AU - Compagnoni, Aldo AU - Duncan, Richard P. AU - Dwyer, John M. AU - Ferguson, Aryana AU - Fraser, Lauchlan H. AU - Griffoul, Emily AU - Groenteman, Ronny AU - Hamre, Liv Norunn AU - Helm, Aveliina AU - Kelly, Ruth AU - Laanisto, Lauri AU - Lonati, Michele AU - Munzbergova, Zuzana AU - Nuche, Paloma AU - Olsen, Siri Lie AU - Oprea, Adrian AU - Partel, Meelis AU - Petry, William K. AU - Ramula, Satu AU - Rasmussen, Pil U. AU - Enri, Simone Ravetto AU - Roeder, Anna AU - Roscher, Christiane AU - Schultz, Cheryl AU - Skarpaas, Olav AU - Smith, Annabel L. AU - Tack, Ayco J. M. AU - Topper, Joachim Paul AU - Vesk, Peter A. AU - Vose, Gregory E. AU - Wandrag, Elizabeth AU - Wingler, Astrid AU - Buckley, Yvonne M. T2 - ECOLOGY LETTERS AB - Abstract Genetic differentiation and phenotypic plasticity jointly shape intraspecific trait variation, but their roles differ among traits. In short‐lived plants, reproductive traits may be more genetically determined due to their impact on fitness, whereas vegetative traits may show higher plasticity to buffer short‐term perturbations. Combining a multi‐treatment greenhouse experiment with observational field data throughout the range of a widespread short‐lived herb, Plantago lanceolata , we (1) disentangled genetic and plastic responses of functional traits to a set of environmental drivers and (2) assessed how genetic differentiation and plasticity shape observational trait–environment relationships. Reproductive traits showed distinct genetic differentiation that largely determined observational patterns, but only when correcting traits for differences in biomass. Vegetative traits showed higher plasticity and opposite genetic and plastic responses, masking the genetic component underlying field‐observed trait variation. Our study suggests that genetic differentiation may be inferred from observational data only for the traits most closely related to fitness. DA - 2021/8/5/ PY - 2021/8/5/ DO - 10.1111/ele.13858 VL - 8 SP - SN - 1461-0248 KW - biomass KW - common garden experiment KW - countergradient variation KW - fecundity KW - genotype by environment interaction KW - intraspecific trait variation KW - observational datasets KW - root KW - shoot ratio KW - specific leaf area KW - widespread species ER - TY - JOUR TI - Population diversity of cassava mosaic begomoviruses increases over the course of serial vegetative propagation AU - Aimone, Catherine D. AU - Lavington, Erik AU - Hoyer, J. Steen AU - Deppong, David O. AU - Mickelson-Young, Leigh AU - Jacobson, Alana AU - Kennedy, George G. AU - Carbone, Ignazio AU - Hanley-Bowdoin, Linda AU - Duffy, Siobain T2 - JOURNAL OF GENERAL VIROLOGY AB - Cassava mosaic disease (CMD) represents a serious threat to cassava, a major root crop for more than 300 million Africans. CMD is caused by single-stranded DNA begomoviruses that evolve rapidly, making it challenging to develop durable disease resistance. In addition to the evolutionary forces of mutation, recombination and reassortment, factors such as climate, agriculture practices and the presence of DNA satellites may impact viral diversity. To gain insight into the factors that alter and shape viral diversity in planta, we used high-throughput sequencing to characterize the accumulation of nucleotide diversity after inoculation of infectious clones corresponding to African cassava mosaic virus (ACMV) and East African cassava mosaic Cameroon virus (EACMCV) in the susceptible cassava landrace Kibandameno. We found that vegetative propagation had a significant effect on viral nucleotide diversity, while temperature and a satellite DNA did not have measurable impacts in our study. EACMCV diversity increased linearly with the number of vegetative propagation passages, while ACMV diversity increased for a time and then decreased in later passages. We observed a substitution bias toward C→T and G→A for mutations in the viral genomes consistent with field isolates. Non-coding regions excluding the promoter regions of genes showed the highest levels of nucleotide diversity for each genome component. Changes in the 5' intergenic region of DNA-A resembled the sequence of the cognate DNA-B sequence. The majority of nucleotide changes in coding regions were non-synonymous, most with predicted deleterious effects on protein structure, indicative of relaxed selection pressure over six vegetative passages. Overall, these results underscore the importance of knowing how cropping practices affect viral evolution and disease progression. DA - 2021/// PY - 2021/// DO - 10.1099/jgv.0.001622 VL - 102 IS - 7 SP - SN - 1465-2099 KW - cassava mosaic begomoviruses KW - vegetative propagation KW - viral diversity ER - TY - JOUR TI - Ultra-sensitive isotope probing to quantify activity and substrate assimilation in microbiomes AU - Kleiner, Manuel AU - Kouris, Angela AU - Jensen, Marlene AU - Grace, D’Angelo AU - Liu, Yihua AU - Korenek, Abigail AU - Tolić, Nikola AU - Sachsenberg, Timo AU - McCalder, Janine AU - Lipton, Mary S. AU - Strous, Marc AB - Abstract Stable isotope probing (SIP) approaches are a critical tool in microbiome research to determine associations between species and substrates. The application of these approaches ranges from studying microbial communities important for global biogeochemical cycling to host-microbiota interactions in the intestinal tract. Current SIP approaches, such as DNA-SIP or nanoSIMS, are limited in terms of sensitivity, resolution or throughput. Here we present an ultra-sensitive, high-throughput protein-based stable isotope probing approach (Protein-SIP), which cuts cost for labeled substrates by ∼90% as compared to other SIP and Protein-SIP approaches and thus enables isotope labeling experiments on much larger scales and with higher replication. It allows for the determination of isotope incorporation into microbiome members with species level resolution using standard metaproteomics LC-MS/MS measurements. The analysis has been implemented as an open-source application ( https://sourceforge.net/projects/calis-p/ ). We demonstrate sensitivity, precision and accuracy using bacterial cultures and mock communities with different labeling schemes. Furthermore, we benchmark our approach against two existing Protein-SIP approaches and show that in the low labeling range used our approach is the most sensitive and accurate. Finally, we measure translational activity using 18O heavy water labeling in a 63-species community derived from human fecal samples grown on media simulating two different diets. Activity could be quantified on average for 27 species per sample, with 9 species showing significantly higher activity on a high protein diet, as compared to a high fiber diet. Surprisingly, among the species with increased activity on high protein were several Bacteroides species known as fiber consumers. Apparently, protein supply is a critical consideration when assessing growth of intestinal microbes on fiber, including fiber based prebiotics. In summary, we demonstrate that our Protein-SIP approach allows for the ultra-sensitive (0.01% to 10% label) detection of stable isotopes of elements found in proteins, using standard metaproteomics data. DA - 2021/3/30/ PY - 2021/3/30/ DO - 10.1101/2021.03.29.437612 VL - 3 UR - https://doi.org/10.1101/2021.03.29.437612 ER - TY - JOUR TI - Highly variable fidelity drives symbiont community composition in an obligate symbiosis AU - Mankowski, Anna AU - Kleiner, Manuel AU - Erséus, Christer AU - Leisch, Nikolaus AU - Sato, Yui AU - Volland, Jean-Marie AU - Hüttel, Bruno AU - Wentrup, Cecilia AU - Woyke, Tanja AU - Wippler, Juliane AU - Dubilier, Nicole AU - Gruber-Vodicka, Harald AB - Abstract Many animals are obligately associated with microbial symbionts that provide essential services such as nutrition or protection against predators. It is assumed that in such obligate associations fidelity between the host and its symbionts must be high to ensure the evolutionary success of the symbiosis. We show here that this is not the case in marine oligochaete worms, despite the fact that they are so dependent on their bacterial symbionts for their nutrition and waste recycling that they have lost their digestive and excretory systems. Our metagenomic analyses of 64 gutless oligochaete species from around the world revealed highly variable levels of fidelity not only across symbiont lineages, but also within symbiont clades. We hypothesize that in gutless oligochaetes, selection within host species for locally adapted and temporally stable symbiont communities leads to varying levels of symbiont fidelity and shuffles the composition of symbiont assemblages across geographic and evolutionary scales. DA - 2021/4/28/ PY - 2021/4/28/ DO - 10.1101/2021.04.28.441735 VL - 4 UR - https://doi.org/10.1101/2021.04.28.441735 ER - TY - JOUR TI - Fidelity varies in the symbiosis between a gutless marine worm and its microbial consortium AU - Sato, Yui AU - Wippler, Juliane AU - Wentrup, Cecilia AU - Ansorge, Rebecca AU - Sadowski, Miriam AU - Gruber-Vodicka, Harald AU - Dubilier, Nicole AU - Kleiner, Manuel AB - Abstract In obligate symbioses, partner fidelity plays a central role in maintaining the association over evolutionary time. Fidelity has been well studied in hosts with only a few symbionts, but little is known about how fidelity is maintained in obligate associations with multiple co-occurring symbionts. Here, we show that partner fidelity varies from strict to absent in a gutless marine annelid and its consortium of co-occurring symbionts that provide it with nutrition. We sequenced the metagenomes of 80 Olavius algarvensis individuals from the Mediterranean, and compared host mitochondrial and symbiont phylogenies based on single nucleotide polymorphisms across genomes, using a low-coverage sequencing approach that has not yet been applied to microbial community analyses. Fidelity was strongest for the two chemoautotrophic, sulphur-oxidizing symbionts that dominated the microbial consortium in all host individuals. In contrast, fidelity was only intermediate to absent in the sulphate-reducing and spirochaetal symbionts, which occurred in lower abundance and were not always present in all host individuals. We propose that variable degrees of fidelity are advantageous for these hosts by allowing the faithful transmission of their nutritionally most important symbionts and flexibility in the acquisition of other symbionts that promote ecological plasticity in the acquisition of environmental resources. DA - 2021/1/30/ PY - 2021/1/30/ DO - 10.1101/2021.01.30.428904 VL - 1 UR - https://doi.org/10.1101/2021.01.30.428904 ER - TY - JOUR TI - Evaluation of RNAlater™ as a field-compatible preservation method for metaproteomic analyses of bacteria-animal symbioses AU - Jensen, Marlene AU - Wippler, Juliane AU - Kleiner, Manuel AB - Abstract Field studies are central to environmental microbiology and microbial ecology as they enable studies of natural microbial communities. Metaproteomics, the study of protein abundances in microbial communities, allows to study these communities ‘ in situ ’ which requires protein preservation directly in the field as protein abundance patterns can change rapidly after sampling. Ideally, a protein preservative for field deployment works rapidly and preserves the whole proteome, is stable in long-term storage, is non-hazardous and easy to transport, and is available at low cost. Although these requirements might be met by several protein preservatives, an assessment of their suitability in field conditions when targeted for metaproteomics is currently lacking. Here, we compared the protein preservation performance of flash freezing and the preservation solution RNA later ™ using the marine gutless oligochaete Olavius algarvensis and its symbiotic microbes as a test case. In addition, we evaluated long-term RNA later ™ storage after 1 day, 1 week and 4 weeks at room temperature (22-23 °C). We evaluated protein preservation using one dimensional liquid chromatography tandem mass spectrometry (1D-LC-MS/MS). We found that RNA later ™ and flash freezing preserved proteins equally well in terms of total number of identified proteins or relative abundances of individual proteins and none of the test time points were altered compared to t0. Moreover, we did not find biases against specific taxonomic groups or proteins with particular biochemical properties. Based on our metaproteomics data and the logistical requirements for field deployment we recommend RNA later ™ for protein preservation of field-collected samples when targeted for metaproteomcis. Importance Metaproteomics, the large-scale identification and quantification of proteins from microbial communities, provides direct insights into the phenotypes of microorganisms on the molecular level. To ensure the integrity of the metaproteomic data, samples need to be preserved immediately after sampling to avoid changes in protein abundance patterns. In laboratory set-ups samples for proteomic analyses are most commonly preserved by flash freezing; however, liquid nitrogen or dry ice is often unavailable at remote field locations due to its hazardous nature and transport restrictions. Our study shows that RNA later ™ can serve as a low hazard, easy to transport alternative to flash freezing for field preservation of samples for metaproteomics. We show that RNA later ™ preserves the metaproteome equally well as compared to flash freezing and protein abundance patterns remain stable during long-term storage for at least 4 weeks at room temperature. DA - 2021/6/17/ PY - 2021/6/17/ DO - 10.1101/2021.06.16.448770 VL - 6 UR - https://doi.org/10.1101/2021.06.16.448770 ER - TY - JOUR TI - Consistent declines in aquatic biodiversity across diverse domains of life in rivers impacted by surface coal mining AU - Simonin, Marie AU - Rocca, Jennifer D. AU - Gerson, Jacqueline R. AU - Moore, Eric AU - Brooks, Alexander C. AU - Czaplicki, Lauren AU - Ross, Matthew R. V. AU - Fierer, Noah AU - Craine, Joseph M. AU - Bernhardt, Emily S. T2 - ECOLOGICAL APPLICATIONS AB - Abstract The rivers of Appalachia (United States) are among the most biologically diverse freshwater ecosystems in the temperate zone and are home to numerous endemic aquatic organisms. Throughout the Central Appalachian ecoregion, extensive surface coal mines generate alkaline mine drainage that raises the pH, salinity, and trace element concentrations in downstream waters. Previous regional assessments have found significant declines in stream macroinvertebrate and fish communities after draining these mined areas. Here, we expand these assessments with a more comprehensive evaluation across a broad range of organisms (bacteria, algae, macroinvertebrates, all eukaryotes, and fish) using high‐throughput amplicon sequencing of environmental DNA (eDNA). We collected water samples from 93 streams in Central Appalachia (West Virginia, United States) spanning a gradient of mountaintop coal mining intensity and legacy to assess how this land use alters downstream water chemistry and affects aquatic biodiversity. For each group of organisms, we identified the sensitive and tolerant taxa along the gradient and calculated stream specific conductivity thresholds in which large synchronous declines in diversity were observed. Streams below mining operations had steep declines in diversity (−18 to −41%) and substantial shifts in community composition that were consistent across multiple taxonomic groups. Overall, large synchronous declines in bacterial, algal, and macroinvertebrate communities occurred even at low levels of mining impact at stream specific conductivity thresholds of 150–200 µS/cm that are substantially below the current U.S. Environmental Protection Agency aquatic life benchmark of 300 µS/cm for Central Appalachian streams. We show that extensive coal surface mining activities led to the extirpation of 40% of biodiversity from impacted rivers throughout the region and that current water quality criteria are likely not protective for many groups of aquatic organisms. DA - 2021/7/29/ PY - 2021/7/29/ DO - 10.1002/eap.2389 SP - SN - 1939-5582 KW - biodiversity loss KW - biomonitoring KW - community thresholds KW - environmental DNA KW - freshwater KW - indicator species KW - mountaintop mining KW - stream specific conductivity KW - surface coal mining KW - water quality criteria ER - TY - JOUR TI - Snow melt timing acts independently and in conjunction with temperature accumulation to drive subalpine plant phenology AU - Jerome, Diana K. AU - Petry, William K. AU - Mooney, Kailen A. AU - Iler, Amy M. T2 - GLOBAL CHANGE BIOLOGY AB - Organisms use environmental cues to align their phenology-the timing of life events-with sets of abiotic and biotic conditions that favor the successful completion of their life cycle. Climate change has altered the environmental cues organisms use to track climate, leading to shifts in phenology with the potential to affect a variety of ecological processes. Understanding the drivers of phenological shifts is critical to predicting future responses, but disentangling the effects of temperature from precipitation on phenology is often challenging because they tend to covary. We addressed this knowledge gap in a high-elevation environment where phenological shifts are associated with both the timing of spring snow melt and temperature. We factorially crossed early snow melt and passive warming treatments to (1) disentangle the effects of snow melt timing and warming on the phenology of flowering and fruiting and reproductive success in three subalpine plant species (Delphinium nuttallianum, Valeriana edulis, and Potentilla pulcherrima); and (2) assess whether snow melt acts via temperature accumulation or some other aspect of the environment (e.g., soil moisture) to affect phenological events. Both the timing and duration of flowering and fruiting responded to the climate treatments, but the effect of snow melt timing and warming varied among species and phenological stages. The combined effects of the treatments on phenology were always additive, and the snow melt treatment often affected phenology even when the warming treatment did not. Despite marked responses of phenology to climate manipulations, the species showed little change in reproductive success, with only one species producing fewer seeds in response to warming (Delphinium, -56%). We also found that snow melt timing can act both through temperature accumulation and as a distinct cue for phenology, and these effects are not mutually exclusive. Our results show that one environmental cue, here snow melt timing, may act through multiple mechanisms to shift phenology. DA - 2021/7/29/ PY - 2021/7/29/ DO - 10.1111/gcb.15803 VL - 7 SP - SN - 1365-2486 UR - https://doi.org/10.1111/gcb.15803 KW - climate change KW - flower duration KW - flower timing KW - fruit duration KW - fruit timing KW - growing degree days KW - passive warming KW - subalpine plant community ER - TY - JOUR TI - Extension of Plant Phenotypes by the Foliar Microbiome AU - Hawkes, Christine V. AU - Kjoller, Rasmus AU - Raaijmakers, Jos M. AU - Riber, Leise AU - Christensen, Svend AU - Rasmussen, Simon AU - Christensen, Jan H. AU - Dahl, Anders Bjorholm AU - Westergaard, Jesper Cairo AU - Nielsen, Mads AU - Brown-Guedira, Gina AU - Hansen, Lars Hestbjerg T2 - ANNUAL REVIEW OF PLANT BIOLOGY, VOL 72, 2021 AB - The foliar microbiome can extend the host plant phenotype by expanding its genomic and metabolic capabilities. Despite increasing recognition of the importance of the foliar microbiome for plant fitness, stress physiology, and yield, the diversity, function, and contribution of foliar microbiomes to plant phenotypic traits remain largely elusive. The recent adoption of high-throughput technologies is helping to unravel the diversityand spatiotemporal dynamics of foliar microbiomes, but we have yet to resolve their functional importance for plant growth, development, and ecology. Here, we focus on the processes that govern the assembly of the foliar microbiome and the potential mechanisms involved in extended plant phenotypes. We highlight knowledge gaps and provide suggestions for new research directions that can propel the field forward. These efforts will be instrumental in maximizing the functional potential of the foliar microbiome for sustainable crop production. DA - 2021/// PY - 2021/// DO - 10.1146/annurev-arplant-080620-114342 VL - 72 SP - 823-846 SN - 1545-2123 KW - phyllosphere KW - plant-microbe interactions KW - fungi KW - bacteria KW - phages KW - omics ER - TY - JOUR TI - Temperature and solvent exposure response of three fatty acid peroxygenase enzymes for application in industrial enzyme processes AU - Wapshott-Stehli, Hannah L. AU - Grunden, Amy M. T2 - BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS AB - Free fatty acids (FFAs) are a useful feedstock for a range of industrial chemical synthesis applications. However, efficiently converting FFAs to molecules for biofuel and other high-value chemicals requires more efficient and cost-effective catalysts. Cytochrome P450 fatty acid peroxygenases (CYP152) have a unique chemistry that allows use of the peroxide shunt pathway for biochemical conversion of FFAs. Known CYP152s are heat labile, however, requiring characterization of more thermotolerant versions for use in industrial applications. A fatty acid peroxygenase from Bacillus methanolicus (CYP152K6) was shown here to have a higher optimal reaction temperature than OleT (CYP152L1). CYP152K6 was stable up to 50 °C and showed great stability in 3% acetone and dimethylformamide. Stability in solvents helps the enzyme's substrates remain soluble in solution for more efficient catalysis, and heat stability allows enzymes to remain active longer during industrial processes. DA - 2021/9/24/ PY - 2021/9/24/ DO - 10.1016/j.bbrc.2021.07.052 VL - 571 SP - 60-65 SN - 1090-2104 UR - https://doi.org/10.1016/j.bbrc.2021.07.052 KW - Hydrogen peroxide KW - Cytochrome P450 (CYP450) KW - Peroxygenases KW - Biocatalysis KW - OleT KW - CYP152K6 ER - TY - JOUR TI - Microbe-dependent heterosis in maize AU - Wagner, Maggie R. AU - Tang, Clara AU - Salvato, Fernanda AU - Clouse, Kayla M. AU - Bartlett, Alexandria AU - Vintila, Simina AU - Phillips, Laura AU - Sermons, Shannon AU - Hoffmann, Mark AU - Balint-Kurti, Peter J. AU - Kleiner, Manuel T2 - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA AB - Hybrids account for nearly all commercially planted varieties of maize and many other crop plants because crosses between inbred lines of these species produce first-generation [F1] offspring that greatly outperform their parents. The mechanisms underlying this phenomenon, called heterosis or hybrid vigor, are not well understood despite over a century of intensive research. The leading hypotheses-which focus on quantitative genetic mechanisms (dominance, overdominance, and epistasis) and molecular mechanisms (gene dosage and transcriptional regulation)-have been able to explain some but not all of the observed patterns of heterosis. Abiotic stressors are known to impact the expression of heterosis; however, the potential role of microbes in heterosis has largely been ignored. Here, we show that heterosis of root biomass and other traits in maize is strongly dependent on the belowground microbial environment. We found that, in some cases, inbred lines perform as well by these criteria as their F1 offspring under sterile conditions but that heterosis can be restored by inoculation with a simple community of seven bacterial strains. We observed the same pattern for seedlings inoculated with autoclaved versus live soil slurries in a growth chamber and for plants grown in steamed or fumigated versus untreated soil in the field. In a different field site, however, soil steaming increased rather than decreased heterosis, indicating that the direction of the effect depends on community composition, environment, or both. Together, our results demonstrate an ecological phenomenon whereby soil microbes differentially impact the early growth of inbred and hybrid maize. DA - 2021/7/27/ PY - 2021/7/27/ DO - 10.1073/pnas.2021965118 VL - 118 IS - 30 SP - SN - 0027-8424 UR - https://doi.org/10.1073/pnas.2021965118 KW - hybrid vigor KW - microbiome KW - maize KW - endophytes KW - rhizosphere ER - TY - JOUR TI - Comprehending Cornales: phylogenetic reconstruction of the order using the Angiosperms353 probe set AU - Thomas, Shawn K. AU - Liu, Xiang AU - Du, Zhi-Yuan AU - Dong, Yibo AU - Cummings, Amanda AU - Pokorny, Lisa AU - Xiang, Qui-Yun AU - Leebens-Mack, James H. T2 - AMERICAN JOURNAL OF BOTANY AB - Premise Cornales is an order of flowering plants containing ecologically and horticulturally important families, including Cornaceae (dogwoods) and Hydrangeaceae (hydrangeas), among others. While many relationships in Cornales are strongly supported by previous studies, some uncertainty remains with regards to the placement of Hydrostachyaceae and to relationships among families in Cornales and within Cornaceae. Here we analyzed hundreds of nuclear loci to test published phylogenetic hypotheses and estimated a robust species tree for Cornales. Methods Using the Angiosperms353 probe set and existing data sets, we generated phylogenomic data for 158 samples, representing all families in the Cornales, with intensive sampling in the Cornaceae. Results We curated an average of 312 genes per sample, constructed maximum likelihood gene trees, and inferred a species tree using the summary approach implemented in ASTRAL‐III, a method statistically consistent with the multispecies coalescent model. Conclusions The species tree we constructed generally shows high support values and a high degree of concordance among individual nuclear gene trees. Relationships among families are largely congruent with previous molecular studies, except for the placement of the nyssoids and the Grubbiaceae‐Curtisiaceae clades. Furthermore, we were able to place Hydrostachyaceae within Cornales, and within Cornaceae, the monophyly of known morphogroups was well supported. However, patterns of gene tree discordance suggest potential ancient reticulation, gene flow, and/or ILS in the Hydrostachyaceae lineage and the early diversification of Cornus . Our findings reveal new insights into the diversification process across Cornales and demonstrate the utility of the Angiosperms353 probe set. DA - 2021/7/14/ PY - 2021/7/14/ DO - 10.1002/ajb2.1696 VL - 7 SP - SN - 1537-2197 UR - https://doi.org/10.1002/ajb2.1696 KW - ancient reticulation KW - Angiosperms353 KW - asterids KW - coalescence KW - Cornales KW - gene flow KW - incomplete lineage sorting KW - phylogenomics KW - species tree estimation KW - target capture ER - TY - JOUR TI - The role of morpho-physiological traits in frost tolerance of neotropical savanna trees AU - De Antonio, Ariadne C. AU - Hoffmann, William A. AU - Rossatto, Davi R. T2 - TREES-STRUCTURE AND FUNCTION DA - 2021/6/18/ PY - 2021/6/18/ DO - 10.1007/s00468-021-02150-7 SP - SN - 1432-2285 KW - Cerrado KW - Frost KW - Disturbance KW - Chlorophyll fluorescence ER - TY - JOUR TI - Precise transcriptional control of cellular quiescence by BRAVO/WOX5 complex in Arabidopsis roots AU - Betegon-Putze, Isabel AU - Mercadal, Josep AU - Bosch, Nadja AU - Planas-Riverola, Ainoa AU - Marques-Bueno, Mar AU - Vilarrasa-Blasi, Josep AU - Frigola, David AU - Burkart, Rebecca C. AU - Martinez, Cristina AU - Conesa, Ana AU - Sozzani, Rosangela AU - Stahl, Yvonne AU - Prat, Salome AU - Ibanes, Marta AU - Cano-Delgado, Ana I T2 - MOLECULAR SYSTEMS BIOLOGY AB - Understanding stem cell regulatory circuits is the next challenge in plant biology, as these cells are essential for tissue growth and organ regeneration in response to stress. In the Arabidopsis primary root apex, stem cell-specific transcription factors BRAVO and WOX5 co-localize in the quiescent centre (QC) cells, where they commonly repress cell division so that these cells can act as a reservoir to replenish surrounding stem cells, yet their molecular connection remains unknown. Genetic and biochemical analysis indicates that BRAVO and WOX5 form a transcription factor complex that modulates gene expression in the QC cells to preserve overall root growth and architecture. Furthermore, by using mathematical modelling we establish that BRAVO uses the WOX5/BRAVO complex to promote WOX5 activity in the stem cells. Our results unveil the importance of transcriptional regulatory circuits in plant stem cell development. DA - 2021/6// PY - 2021/6// DO - 10.15252/msb.20209864 VL - 17 IS - 6 SP - SN - 1744-4292 KW - BRAVO KW - mathematical modelling KW - quiescent centre KW - root growth KW - WOX5 ER - TY - JOUR TI - Leveraging synthetic biology approaches in plant hormone research AU - Zhao, Chengsong AU - Yaschenko, Anna AU - Alonso, Jose M. AU - Stepanova, Anna N. T2 - CURRENT OPINION IN PLANT BIOLOGY DA - 2021/4// PY - 2021/4// DO - 10.1016/j.pbi.2020.10998 VL - 60 SP - SN - 1879-0356 ER - TY - JOUR TI - Balancing crop production and energy harvesting in organic solar-powered greenhouses AU - Ravishankar, Eshwar AU - Charles, Melodi AU - Xiong, Yuan AU - Henry, Reece AU - Swift, Jennifer AU - Rech, Jeromy AU - Calero, John AU - Cho, Sam AU - Booth, Ronald E. AU - Kim, Taesoo AU - Balzer, Alex H. AU - Qin, Yunpeng AU - Ho, Carr Hoi Yi AU - So, Franky AU - Stingelin, Natalie AU - Amassian, Aram AU - Saravitz, Carole AU - You, Wei AU - Ade, Harald AU - Sederoff, Heike AU - Brendan T. O'Connor, T2 - CELL REPORTS PHYSICAL SCIENCE AB - Adding semitransparent organic solar cells (ST-OSCs) to a greenhouse structure enables simultaneous plant cultivation and electricity generation, thereby reducing the greenhouse energy demand. However, there is a need to establish the impact of such systems on plant growth and indoor climate and to optimize system tradeoffs. In this work, we consider plant growth under OSCs and system-relevant design. We evaluate the growth of red leaf lettuce under ST-OSC filters and compare the impact of three different OSC active layers that have unique transmittance. We find no significant differences in the fresh weight and chlorophyll content of the lettuce grown under these OSC filters. In addition, OSCs provide an opportunity for further light and thermal management of the greenhouse through device design and optical coatings. The OSCs can thus affect plant growth, power generation, and thermal load of the greenhouse, and this design trade space is reviewed and exemplified. DA - 2021/3/24/ PY - 2021/3/24/ DO - 10.1016/j.xcrp.2021.100381 VL - 2 IS - 3 SP - SN - 2666-3864 ER - TY - JOUR TI - Endocannabinoid System and Its Regulation by Polyunsaturated Fatty Acids and Full Spectrum Hemp Oils AU - Komarnytsky, Slavko AU - Rathinasabapathy, Thirumurugan AU - Wagner, Charles AU - Metzger, Brandon AU - Carlisle, Carolina AU - Panda, Chinmayee AU - Le Brun-Blashka, Sara AU - Troup, John P. AU - Varadharaj, Saradhadevi T2 - INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES AB - The endocannabinoid system (ECS) consists of endogenous cannabinoids, their receptors, and metabolic enzymes that play a critical homeostatic role in modulating polyunsaturated omega fatty acid (PUFA) signaling to maintain a balanced inflammatory and redox state. Whole food-based diets and dietary interventions linked to PUFAs of animal (fish, calamari, krill) or plant (hemp, flax, walnut, algae) origin, as well as full-spectrum hemp oils, are increasingly used to support the ECS tone, promote healthy metabolism, improve risk factors associated with cardiovascular disorders, encourage brain health and emotional well-being, and ameliorate inflammation. While hemp cannabinoids of THC and CBD groups show distinct but complementary actions through a variety of cannabinoid (CB1 and CB2), adenosine (A2A), and vanilloid (TRPV1) receptors, they also modulate PUFA metabolism within a wide variety of specialized lipid mediators that promote or resolve inflammation and oxidative stress. Clinical evidence reviewed in this study links PUFAs and cannabinoids to changes in ECS tone, immune function, metabolic and oxidative stress adaptation, and overall maintenance of a well-balanced systemic function of the body. Understanding how the body coordinates signals from the exogenous and endogenous ECS modulators is critical for discerning the underlying molecular mechanisms of the ECS tone in healthy and disease states. Nutritional and lifestyle interventions represent promising approaches to address chronic metabolic and inflammatory disorders that may overlap in the population at risk. Further investigation and validation of dietary interventions that modulate the ECS are required in order to devise clinically successful second-generation management strategies. DA - 2021/6// PY - 2021/6// DO - 10.3390/ijms22115479 VL - 22 IS - 11 SP - SN - 1422-0067 KW - ECS tone KW - phytocannabinoids KW - inflammation resolution KW - oxidative stress KW - systemic redox balance ER - TY - JOUR TI - The future of microbial ecological niche theory and modeling AU - Kivlin, Stephanie N. AU - Hawkes, Christine V. AU - Papeş, Monica AU - Treseder, Kathleen K. AU - Averill, Colin T2 - New Phytologist AB - This article is a Commentary on Davison et al . (2021), 231 : 763–776 . DA - 2021/7// PY - 2021/7// DO - 10.1111/nph.17373 VL - 231 IS - 2 SP - 508-511 UR - https://doi.org/10.1111/nph.17373 KW - ecological niche modeling KW - microbiome KW - mycorrhizal fungi KW - niche envelope KW - species distribution modeling ER - TY - JOUR TI - NASA GeneLab RNA-seq consensus pipeline: standardized processing of short-read RNA-seq data AU - Overbey, Eliah G. AU - Saravia-Butler, Amanda M. AU - Zhang, Zhe AU - Rathi, Komal S. AU - Fogle, Homer AU - Silveira, Willian A. AU - Barker, Richard J. AU - Bass, Joseph J. AU - Beheshti, Afshin AU - Berrios, Daniel C. AU - Blaber, Elizabeth A. AU - Cekanaviciute, Egle AU - Costa, Helio A. AU - Davin, Laurence B. AU - Fisch, Kathleen M. AU - Gebre, Samrawit G. AU - Geniza, Matthew AU - Gilbert, Rachel AU - Gilroy, Simon AU - Hardiman, Gary AU - Herranz, Raul AU - Kidane, Yared H. AU - Kruse, Colin P. S. AU - Lee, Michael D. AU - Liefeld, Ted AU - Lewis, Norman G. AU - McDonald, J. Tyson AU - Meller, Robert AU - Mishra, Tejaswini AU - Perera, Imara Y. AU - Ray, Shayoni AU - Reinsch, Sigrid S. AU - Rosenthal, Sara Brin AU - Strong, Michael AU - Szewczyk, Nathaniel J. AU - Tahimic, Candice G. T. AU - Taylor, Deanne M. AU - Vandenbrink, Joshua P. AU - Villacampa, Alicia AU - Weging, Silvio AU - Wolverton, Chris AU - Wyatt, Sarah E. AU - Zea, Luis AU - Costes, Sylvain V AU - Galazka, Jonathan M. T2 - ISCIENCE AB - With the development of transcriptomic technologies, we are able to quantify precise changes in gene expression profiles from astronauts and other organisms exposed to spaceflight. Members of NASA GeneLab and GeneLab-associated analysis working groups (AWGs) have developed a consensus pipeline for analyzing short-read RNA-sequencing data from spaceflight-associated experiments. The pipeline includes quality control, read trimming, mapping, and gene quantification steps, culminating in the detection of differentially expressed genes. This data analysis pipeline and the results of its execution using data submitted to GeneLab are now all publicly available through the GeneLab database. We present here the full details and rationale for the construction of this pipeline in order to promote transparency, reproducibility, and reusability of pipeline data; to provide a template for data processing of future spaceflight-relevant datasets; and to encourage cross-analysis of data from other databases with the data available in GeneLab. DA - 2021/4/23/ PY - 2021/4/23/ DO - 10.1016/j.isci.2021.102361 VL - 24 IS - 4 SP - SN - 2589-0042 ER - TY - JOUR TI - Mass spectrometry-based proteomic platforms for better understanding of SARS-CoV-2 induced pathogenesis and potential diagnostic approaches AU - Ahsan, Nagib AU - Rao, R. Shyama Prasad AU - Wilson, Rashaun S. AU - Punyamurtula, Ujwal AU - Salvato, Fernanda AU - Petersen, Max AU - Ahmed, Mohammad Kabir AU - Abid, M. Ruhul AU - Verburgt, Jacob C. AU - Kihara, Daisuke AU - Yang, Zhibo AU - Fornelli, Luca AU - Foster, Steven B. AU - Ramratnam, Bharat T2 - PROTEOMICS AB - Abstract While protein–protein interaction is the first step of the SARS‐CoV‐2 infection, recent comparative proteomic profiling enabled the identification of over 11,000 protein dynamics, thus providing a comprehensive reflection of the molecular mechanisms underlying the cellular system in response to viral infection. Here we summarize and rationalize the results obtained by various mass spectrometry (MS)‐based proteomic approaches applied to the functional characterization of proteins and pathways associated with SARS‐CoV‐2‐mediated infections in humans. Comparative analysis of cell‐lines versus tissue samples indicates that our knowledge in proteome profile alternation in response to SARS‐CoV‐2 infection is still incomplete and the tissue‐specific response to SARS‐CoV‐2 infection can probably not be recapitulated efficiently by in vitro experiments. However, regardless of the viral infection period, sample types, and experimental strategies, a thorough cross‐comparison of the recently published proteome, phosphoproteome, and interactome datasets led to the identification of a common set of proteins and kinases associated with PI3K‐Akt, EGFR, MAPK, Rap1, and AMPK signaling pathways. Ephrin receptor A2 (EPHA2) was identified by 11 studies including all proteomic platforms, suggesting it as a potential future target for SARS‐CoV‐2 infection mechanisms and the development of new therapeutic strategies. We further discuss the potentials of future proteomics strategies for identifying prognostic SARS‐CoV‐2 responsive age‐, gender‐dependent, tissue‐specific protein targets. DA - 2021/5// PY - 2021/5// DO - 10.1002/pmic.202000279 VL - 21 IS - 10 SP - SN - 1615-9861 KW - biomarkers KW - comparative proteomics KW - COVID‐ KW - 19 KW - kinase‐ KW - substrate signaling KW - post‐ KW - translational modifications KW - targeted proteomics KW - top‐ KW - down proteomics ER - TY - JOUR TI - Abundance of spring- and winter-active arthropods declines with warming AU - Fitzgerald, Jacquelyn L. AU - Stuble, Katharine L. AU - Nichols, Lauren M. AU - Diamond, Sarah E. AU - Wentworth, Thomas R. AU - Pelini, Shannon L. AU - Gotelli, Nicholas J. AU - Sanders, Nathan J. AU - Dunn, Robert R. AU - Penick, Clint A. T2 - ECOSPHERE AB - Abstract Because ectotherm activity and metabolism are sensitive to temperature, terrestrial arthropods may be especially responsive to ongoing climatic warming. Here, we quantified responses of arthropod abundance to two years of warming in an outdoor temperature manipulation experiment at Duke Forest, North Carolina, USA. Nine open‐top chambers were individually heated year‐round from 1.5° to 5.5°C above ambient temperature. From two years of monthly pitfall trapping, we collected and identified 4,468 arthropods representing 24 orders. We initially predicted that arthropods would experience the greatest negative effects of experimental warming during the summer months, when temperatures reach their yearly maximum and arthropods may be close to their maximum thermal tolerance limits. Instead, we found that the strongest negative effects on arthropod abundance occurred during the winter and spring, when ambient temperatures are relatively cooler, whereas the effects of experimental warming on abundance were not significant during the summer or fall. During the spring of 2012, the warmest spring on record for the southeastern USA, total arthropod abundance declined 20% per °C of experimental warming. Abundance declines were driven largely by flies (Diptera), which were the most abundant insect order, representing approximately a third of all arthropods collected. The most abundant arthropod family, Mycetophilidae (fungus gnats), declined 64% per °C of warming during the spring of 2012. Although previous research on climatic warming has focused on the impact of maximum yearly temperatures on organismal performance, our results are more consistent with the cool‐season sensitivity hypothesis, which posits that arthropods adapted for cooler conditions are likely to face the strongest negative effects of warming during the cooler seasons. DA - 2021/4// PY - 2021/4// DO - 10.1002/ecs2.3473 VL - 12 IS - 4 SP - SN - 2150-8925 KW - abundance declines KW - arthropods KW - climate change KW - global warming KW - insects KW - seasonality ER - TY - JOUR TI - Heat shock proteins and small nucleolar RNAs are dysregulated in a Drosophila model for feline hypertrophic cardiomyopathy AU - Tallo, Christian A. AU - Duncan, Laura H. AU - Yamamoto, Akihiko H. AU - Slaydon, Joshua D. AU - Arya, Gunjan H. AU - Turlapati, Lavanya AU - Mackay, Trudy F. C. AU - Carbone, Mary A. T2 - G3-GENES GENOMES GENETICS AB - In cats, mutations in myosin binding protein C (encoded by the MYBPC3 gene) have been associated with hypertrophic cardiomyopathy (HCM). However, the molecular mechanisms linking these mutations to HCM remain unknown. Here, we establish Drosophila melanogaster as a model to understand this connection by generating flies harboring MYBPC3 missense mutations (A31P and R820W) associated with feline HCM. The A31P and R820W flies displayed cardiovascular defects in their heart rates and exercise endurance. We used RNA-seq to determine which processes are misregulated in the presence of mutant MYBPC3 alleles. Transcriptome analysis revealed significant downregulation of genes encoding small nucleolar RNA (snoRNAs) in exercised female flies harboring the mutant alleles compared to flies that harbor the wild-type allele. Other processes that were affected included the unfolded protein response and immune/defense responses. These data show that mutant MYBPC3 proteins have widespread effects on the transcriptome of co-regulated genes. Transcriptionally differentially expressed genes are also candidate genes for future evaluation as genetic modifiers of HCM as well as candidate genes for genotype by exercise environment interaction effects on the manifestation of HCM; in cats as well as humans. DA - 2021/1// PY - 2021/1// DO - 10.1093/g3journal/jkaa014 VL - 11 IS - 1 SP - SN - 2160-1836 KW - MYBPC3 KW - cMyBP-C KW - Drosophila melanogaster KW - feline HCM KW - hypertrophic cardiomyopathy ER - TY - JOUR TI - Savannas are not old fields: Functional trajectories of forest expansion in a fire-suppressed Brazilian savanna are driven by habitat generalists AU - Flake, Samuel W. AU - Abreu, Rodolfo C. R. AU - Durigan, Giselda AU - Hoffmann, William A. T2 - FUNCTIONAL ECOLOGY AB - Abstract Under fire suppression, many tropical savannas transform into forests. Forest expansion entails changes in environmental variables and plant community structure. We hypothesized that forest expansion into savanna results in a shift in community‐weighted mean functional traits from stress tolerance to competitiveness, with generalist species having trait values intermediate between those of specialists of savanna and forest habitats. We studied 30 plots distributed over three savanna–forest boundaries undergoing forest expansion in the Brazilian Cerrado, capturing a gradient from open savanna to recently formed forest. We measured functional traits of 116 woody species of savanna specialist, generalist and forest specialist functional groups and quantified changes in species composition and mean traits across the basal area gradient. We identified two main axes of species traits. The first separated forest and generalist species from savanna specialists, with the latter possessing traits associated with resistance to disturbance and stress— such as thick leaves, thick bark, slower height growth and lower shade tolerance. Our second trait axis separated shrubs and understorey trees from pioneer species. Generalist species’ traits did not differ substantially from forest species, nor did they tend to have a typical pioneer strategy. Community‐weighted trait means changed linearly with forest development. There was a steady increase in traits associated with competitive dominance rather than stress tolerance and fire resistance, indicating a wholesale shift in the selective environment. Several of these patterns—for example, increasing height and decreasing light requirements—are common in old‐field succession. In contrast to old‐field succession, we found that SLA increased, leaf thickness decreased and wood density stayed constant. The assembly of forests appears to be shaped by environmental filters that contribute to a functional trajectory distinct from most other studied ecosystems. Our results highlight the importance of the functional composition of the early community and of the early colonizers of the open environment. Differences between savanna and forest specialists reflect the selective effects of the contrasting environments, while the traits of generalists—and their interaction with environmental filters—drive the dynamics of forest expansion. A free Plain Language Summary can be found within the Supporting Information of this article. DA - 2021/5/17/ PY - 2021/5/17/ DO - 10.1111/1365-2435.13818 SP - SN - 1365-2435 KW - cerrado KW - community-weighted mean KW - competition KW - environmental filtering KW - fire suppression KW - functional traits KW - savanna-forest transition KW - succession ER - TY - JOUR TI - Leveraging Pseudomonas Stress Response Mechanisms for Industrial Applications AU - Craig, Kelly AU - Johnson, Brant R. AU - Grunden, Amy T2 - FRONTIERS IN MICROBIOLOGY AB - Members of the genus Pseudomonas are metabolically versatile and capable of adapting to a wide variety of environments. Stress physiology of Pseudomonas strains has been extensively studied because of their biotechnological potential in agriculture as well as their medical importance with regards to pathogenicity and antibiotic resistance. This versatility and scientific relevance led to a substantial amount of information regarding the stress response of a diverse set of species such as Pseudomonas chlororaphis , P. fluorescens , P. putida , P. aeruginosa , and P. syringae . In this review, environmental and industrial stressors including desiccation, heat, and cold stress, are cataloged along with their corresponding mechanisms of survival in Pseudomonas . Mechanisms of survival are grouped by the type of inducing stress with a focus on adaptations such as synthesis of protective substances, biofilm formation, entering a non-culturable state, enlisting chaperones, transcription and translation regulation, and altering membrane composition. The strategies Pseudomonas strains utilize for survival can be leveraged during the development of beneficial strains to increase viability and product efficacy. DA - 2021/5/10/ PY - 2021/5/10/ DO - 10.3389/fmicb.2021.660134 VL - 12 SP - SN - 1664-302X KW - stress KW - Pseudomonas KW - formulation KW - heat KW - desiccation KW - cold KW - biofilm KW - chaperone ER - TY - JOUR TI - Draft Genome Sequences of Four Aerobic Isobutane-Metabolizing Bacteria AU - Chen, Weijue AU - Faulkner, Nicholas AU - Smith, Christy AU - Fruchte, Megan AU - Hyman, Michael T2 - MICROBIOLOGY RESOURCE ANNOUNCEMENTS AB - Here, we report the draft genome sequences of four aerobic gaseous alkane-oxidizing bacteria isolated from soil by enrichment culture using isobutane (2-methylpropane) as the sole carbon and energy source. The sequences all reveal microorganisms with multiple alkane-oxidizing monooxygenases, including soluble di-iron monooxygenases (SDIMOs), copper-containing monooxygenases (CuMMOs), and alkane hydroxylases (AHs). DA - 2021/5// PY - 2021/5// DO - 10.1128/MRA.01381-20 VL - 10 IS - 18 SP - SN - 2576-098X UR - https://doi.org/10.1128/MRA.01381-20 ER - TY - JOUR TI - A G protein-coupled receptor-like module regulates cellulose synthase secretion from the endomembrane system in Arabidopsis AU - McFarlane, Heather E. AU - Mutwil-Anderwald, Daniela AU - Verbancic, Jana AU - Picard, Kelsey L. AU - Gookin, Timothy E. AU - Froehlich, Anja AU - Chakravorty, David AU - Trindade, Luisa M. AU - Alonso, Jose M. AU - Assmann, Sarah M. AU - Persson, Staffan T2 - DEVELOPMENTAL CELL AB - Cellulose is produced at the plasma membrane of plant cells by cellulose synthase (CESA) complexes (CSCs). CSCs are assembled in the endomembrane system and then trafficked to the plasma membrane. Because CESAs are only active in the plasma membrane, control of CSC secretion regulates cellulose synthesis. We identified members of a family of seven transmembrane domain-containing proteins (7TMs) that are important for cellulose production during cell wall integrity stress. 7TMs are often associated with guanine nucleotide-binding (G) protein signaling and we found that mutants affecting the Gβγ dimer phenocopied the 7tm mutants. Unexpectedly, the 7TMs localized to the Golgi/trans-Golgi network where they interacted with G protein components. Here, the 7TMs and Gβγ regulated CESA trafficking but did not affect general protein secretion. Our results outline how a G protein-coupled module regulates CESA trafficking and reveal that defects in this process lead to exacerbated responses to cell wall integrity stress. DA - 2021/5/17/ PY - 2021/5/17/ DO - 10.1016/j.devcel.2021.03.031 VL - 56 IS - 10 SP - 1484-+ SN - 1878-1551 ER - TY - JOUR TI - The Switchgrass Microbiome: A Review of Structure, Function, and Taxonomic Distribution AU - Hestrin, Rachel AU - Lee, Marissa R. AU - Whitaker, Briana K. AU - Pett-Ridge, Jennifer T2 - PHYTOBIOMES JOURNAL AB - Switchgrass (Panicum virgatum L.) has been championed as a promising bioenergy crop due to its high productivity across a wide environmental range. The switchgrass microbiome—including bacteria, archaea, fungi, and other microbiota inhabiting soil and plant tissues—can influence plant function substantially. We conducted a review of the literature investigating switchgrass microbiome structure, key functional roles, and taxa isolated from field-grown plants. Although site conditions and plant compartment (i.e., location within shoots, roots, or root-influenced soil) appear to be the strongest drivers of switchgrass microbiome structure, the microbiome is also shaped by climate, season, and host genotype. Studies comparing across plant species show that the switchgrass microbiome is more similar to the microbiomes of other perennial plants than to the microbiomes of annual plants. Members of the switchgrass microbiome confer several benefits to their host. Most notably, mycorrhizal fungi can increase plant biomass many-fold, associative nitrogen-fixing bacteria can provide a substantial portion of the plant’s nitrogen demand, and fungal endophytes can improve plant tolerance to drought. Although the fungi and bacteria cultured from switchgrass represent only a portion of the microbiome, these serve as a valuable resource for researchers interested in investigating functional outcomes of the switchgrass microbiome. We highlight areas where additional research is necessary for a more comprehensive understanding of switchgrass microbiome structure, function, and potential to enhance sustainable bioenergy production. Key gaps include the role of understudied organisms (e.g., viruses, microeukaryotes, and nonmycorrhizal fungi), multitrophic relationships, mechanisms underpinning switchgrass–microbiome interactions, and field-scale validation of experimental findings. DA - 2021/// PY - 2021/// DO - 10.1094/PBIOMES-04-20-0029-FI VL - 5 IS - 1 SP - 14-28 SN - 2471-2906 KW - agriculture KW - bacteria KW - bioenergy KW - biofuel KW - endophyte KW - fungi KW - genomics KW - microbiome KW - mutualism KW - mycorrhizae KW - nutrient cycling KW - Panicum virgatum KW - perennial crop KW - plant-microbe interactions KW - plants KW - rhizosphere and phyllosphere KW - soil ecology KW - yield and crop productivity ER - TY - JOUR TI - Long-term cometabolic transformation of 1,1,1-trichloroethane and 1,4-dioxane by Rhodococcus rhodochrous ATCC 21198 grown on alcohols slowly produced by orthosilicates AU - Murnane, Riley A. AU - Chen, Weijue AU - Hyman, Michael AU - Semprini, Lewis T2 - JOURNAL OF CONTAMINANT HYDROLOGY AB - Long-term cometabolic transformation of 1,1,1-trichlorethane (1,1,1-TCA) and 1,4-dioxane (1,4-D) was achieved using slow release compounds (SRCs) as growth substrates for pure cultures of Rhodococcus rhodochrous ATCC 21198 (ATCC strain 21198). Resting cell transformation tests showed 1,4-D transformation occurred without a lag phase for cells grown on 2-butanol, while an induction period of several hours was required for 1-butanol grown cells. These observations were consistent with activity-based labeling patterns for monooxygenase hydroxylase components and specific rates of tetrahydrofuran (THF) degradation. 1,1,1-TCA and 1,4-D degradation rates for alcohol-grown cells were slower than those for cells grown on gaseous alkanes such as isobutane. Batch metabolism and degradation tests were performed, in the presence of 1,1,1-TCA and 1,4-D, with the growth of ATCC strain 21198 on alcohols produced by the hydrolysis of orthosilicates. Three orthosilicates were tested: tetrabutylorthosilicate (TBOS), tetra-s-butylorthosilicate (T2BOS), and tetraisopropoxysilane (T2POS). The measured rates of alcohol release in poisoned controls depended on the orthosilicate structure with TBOS, which produced a 1° alcohol (1-butanol), hydrolyzing more rapidly than T2POS and T2BOS, that produced the 2° alcohols 2-butanol and 2-propanol, respectively. The orthosilicates were added as light non-aqueous phase liquids (LNAPLs) with ATCC strain 21198 and formed dispersed droplets when continuously mixed. Continuous rates of oxygen (O2) consumption and carbon dioxide (CO2) production confirmed alcohol metabolism by ATCC strain 21198 was occurring. The rates of metabolism (TBOS > T2POS > T2BOS) were consistent with the rates of alcohol release via abiotic hydrolysis. 1,4-D and 1,1,1-TCA were continuously transformed in successive additions by ATCC strain 21198 over 125 days, with the rates highly correlated with the rates of metabolism. The metabolism of the alcohols was not inhibited by acetylene, while transformation of 1,4-D and 1,1,1-TCA was inhibited by this gas. As acetylene is a potent inactivator of diverse bacterial monooxygenases, these results suggest that monooxygenase activity was required for the observed cometabolic transformations but not for alcohol utilization. Alcohol concentrations in the biologically active reactors were maintained below the levels of detection, indicating they were metabolized rapidly after being produced. Much lower rates of O2 consumption were observed in the reactors containing T2BOS, which has benefits for in-situ bioremediation. The results illustrate the importance of the structure of the SRC when developing passive aerobic cometabolic treatment systems. DA - 2021/6// PY - 2021/6// DO - 10.1016/j.jconhyd.2021.103796 VL - 240 SP - SN - 1873-6009 KW - Cometabolism KW - Orthosilicates KW - Activity based labeling KW - Hydrolysis KW - 1,4-dioxane KW - 1,1,1-trichloroethane ER - TY - JOUR TI - Comparative phylogenomic analysis reveals evolutionary genomic changes and novel toxin families in endophytic Liberibacter pathogens AU - Tan, Yongjun AU - Wang, Cindy AU - Schneider, Theresa AU - Li, Huan AU - Souza, Robson Francisco AU - Tang, Xueming AU - Hsieh, Tzung-Fu AU - Wang, Xu AU - Li, Xu AU - Zhang, Dapeng AB - Abstract Liberibacter pathogens are the causative agents of several severe crop diseases worldwide, including citrus Huanglongbing and potato Zebra Chip. These bacteria are endophytic and non-culturable, which makes experimental approaches challenging and highlights the need for bioinformatic analysis in advancing our understanding about Liberibacter pathogenesis. Here, we performed an in-depth comparative phylogenomic analysis of the Liberibacter pathogens and their free-living, nonpathogenic, ancestral species, aiming to identify the major genomic changes and determinants associated with their evolutionary transitions in living habitats and pathogenicity. We found that prophage loci represent the most variable regions among Liberibacter genomes. Using gene neighborhood analysis and phylogenetic classification, we systematically recovered, annotated, and classified all prophage loci into four types, including one previously unrecognized group. We showed that these prophages originated through independent gene transfers at different evolutionary stages of Liberibacter and only the SC-type prophage was associated with the emergence of the pathogens. Using ortholog clustering, we vigorously identified two additional sets of genomic genes, which were either lost or gained in the ancestor of the pathogens. Consistent with the habitat change, the lost genes were enriched for biosynthesis of cellular building blocks. Importantly, among the gained genes, we uncovered several previously unrecognized toxins, including a novel class of polymorphic toxins, a YdjM phospholipase toxin, and a secreted EEP protein. Our results substantially extend the knowledge on the evolutionary events and potential determinants leading to the emergence of endophytic, pathogenic Liberibacter species and will facilitate the design of functional experiments and the development of new detection and blockage methods of these pathogens. Importance Liberibacter pathogens are associated with several severe crop diseases, including citrus Huanglongbing, the most destructive disease to the citrus industry. Currently, no effective cure or treatments are available, and no resistant citrus variety has been found. The fact that these obligate endophytic pathogens are not culturable has made it extremely challenging to experimentally uncover from the whole genome the genes/proteins important to Liberibacter pathogenesis. Further, earlier bioinformatics studies failed to identify the key genomic determinants, such as toxins and effector proteins, that underlie the pathogenicity of the bacteria. In this study, an in-depth comparative genomic analysis of Liberibacter pathogens together with their ancestral non-pathogenic species identified the prophage loci and several novel toxins that are evolutionarily associated with the emergence of the pathogens. These results shed new lights on the disease mechanism of Liberibacter pathogens and will facilitate the development of new detection and blockage methods targeting the toxins. DA - 2021/6/5/ PY - 2021/6/5/ DO - 10.1101/2021.06.02.446850 VL - 6 UR - https://doi.org/10.1101/2021.06.02.446850 ER - TY - JOUR TI - SnRK1: a versatile plant protein kinase that limits geminivirus infection AU - Shen, Wei AU - Hanley-Bowdoin, Linda T2 - CURRENT OPINION IN VIROLOGY AB - Geminiviruses are a family of single-stranded DNA viruses that infect many plant species and cause serious diseases in important crops. The plant protein kinase, SnRK1, has been implicated in host defenses against geminiviruses. Overexpression of SnRK1 makes plants more resistant to geminivirus infection, and knock-down of SnRK1 increases susceptibility to geminivirus infection. GRIK, the SnRK1 activating kinase, is upregulated by geminivirus infection, while the viral C2 protein inhibits the SnRK1 activity. SnRK1 also directly phosphorylates geminivirus proteins to reduce infection. These data suggest that SnRK1 is involved in the co-evolution of plant hosts and geminiviruses. DA - 2021/4// PY - 2021/4// DO - 10.1016/j.coviro.2020.12.002 VL - 47 SP - 18-24 SN - 1879-6265 ER - TY - JOUR TI - Natural Product Gene Clusters in the Filamentous Nostocales Cyanobacterium HT-58-2 AU - Jin, Xiaohe AU - Miller, Eric S. AU - Lindsey, Jonathan S. T2 - LIFE-BASEL AB - Cyanobacteria are known as rich repositories of natural products. One cyanobacterial-microbial consortium (isolate HT-58-2) is known to produce two fundamentally new classes of natural products: the tetrapyrrole pigments tolyporphins A–R, and the diterpenoid compounds tolypodiol, 6-deoxytolypodiol, and 11-hydroxytolypodiol. The genome (7.85 Mbp) of the Nostocales cyanobacterium HT-58-2 was annotated previously for tetrapyrrole biosynthesis genes, which led to the identification of a putative biosynthetic gene cluster (BGC) for tolyporphins. Here, bioinformatics tools have been employed to annotate the genome more broadly in an effort to identify pathways for the biosynthesis of tolypodiols as well as other natural products. A putative BGC (15 genes) for tolypodiols has been identified. Four BGCs have been identified for the biosynthesis of other natural products. Two BGCs related to nitrogen fixation may be relevant, given the association of nitrogen stress with production of tolyporphins. The results point to the rich biosynthetic capacity of the HT-58-2 cyanobacterium beyond the production of tolyporphins and tolypodiols. DA - 2021/4// PY - 2021/4// DO - 10.3390/life11040356 VL - 11 IS - 4 SP - SN - 2075-1729 KW - anatoxin-a KW - homoanatoxin-a KW - hapalosin KW - heterocyst glycolipids KW - natural products KW - secondary metabolites KW - shinorine KW - tolypodiols KW - tolyporphins ER - TY - JOUR TI - Divide and Conquer: The Initiation and Proliferation of Meristems AU - Schwartz, Michael F. AU - Peters, Rachel AU - Hunt, Aitch M. AU - Abdul-Matin, Abdul-Khaliq AU - Broeck, Lisa AU - Sozzani, Rosangela T2 - CRITICAL REVIEWS IN PLANT SCIENCES AB - In contrast to animals, which complete organogenesis early in their development, plants continuously produce organs, and structures throughout their entire lifecycle. Plants achieve the continuous growth of organs through the initiation and maintenance of meristems that populate the plant body. Plants contain two apical meristems, one at the shoot and one root, to produce the lateral organs of the shoot and the cell files of the root, respectively. Additional meristems within the plant produce branches while others produce the cell types within the vasculature system. Throughout development, plants must balance producing organs and maintaining their meristems, which requires tightly controlled regulations. This review focuses on the various plant meristems, how cells within these meristems maintain their identity, and particularly the molecular players that regulate stem cell maintenance. In addition, we summarize cell types which share molecular features with meristems, but do not follow the same rules regarding maintenance, including pericycle and rachis founder cells. Together, these populations of cells contribute to the entire organogenesis of plants. DA - 2021/3/4/ PY - 2021/3/4/ DO - 10.1080/07352689.2021.1915228 VL - 40 IS - 2 SP - 147-156 SN - 1549-7836 UR - http://dx.doi.org/10.1080/07352689.2021.1915228 KW - Founder cells KW - meristem initiation KW - meristem maintenance KW - procambium KW - root apical meristem KW - shoot apical meristem ER - TY - JOUR TI - Managing Plant Microbiomes for Sustainable Biofuel Production AU - Zhalnina, Kateryna AU - Hawkes, Christine AU - Shade, Ashley AU - Firestone, Mary K. AU - Pett-Ridge, Jennifer T2 - PHYTOBIOMES JOURNAL AB - The development of environmentally sustainable, economical, and reliable sources of energy is one of the great challenges of the 21st century. Large-scale cultivation of cellulosic feedstock crops (henceforth, bioenergy crops) is considered one of the most promising renewable sources for liquid transportation fuels. However, the mandate to develop a viable cellulosic bioenergy industry is accompanied by an equally urgent mandate to deliver not only cheap reliable biomass but also ecosystem benefits, including efficient use of water, nitrogen, and phosphorous; restored soil health; and net negative carbon emissions. Thus, sustainable bioenergy crop production may involve new agricultural practices or feedstocks and should be reliable, cost effective, and minimal input, without displacing crops currently grown for food production on fertile land. In this editorial perspective for the Phytobiomes Journal Focus Issue on Phytobiomes of Bioenergy Crops and Agroecosystems, we consider the microbiomes associated with bioenergy crops, the effects beneficial microbes have on their hosts, and potential ecosystem impacts of these interactions. We also address outstanding questions, major advances, and emerging biotechnological strategies to design and manipulate bioenergy crop microbiomes. This approach could simultaneously increase crop yields and provide important ecosystem services for a sustainable energy future. DA - 2021/// PY - 2021/// DO - 10.1094/PBIOMES-12-20-0090-E VL - 5 IS - 1 SP - 3-13 SN - 2471-2906 UR - https://doi.org/10.1094/PBIOMES-12-20-0090-E KW - agriculture KW - metabolomics KW - metagenomics KW - microbiome KW - nutrient cycling KW - rhizosphere and phyllosphere KW - soil ecology KW - yield and crop productivity ER - TY - JOUR TI - Metabolic source isotopic pair labeling and genome-wide association are complementary tools for the identification of metabolite-gene associations in plants AU - Simpson, Jeffrey P. AU - Wunderlich, Cole AU - Li, Xu AU - Svedin, Elizabeth AU - Dilkes, Brian AU - Chapple, Clint T2 - PLANT CELL AB - Abstract The optimal extraction of information from untargeted metabolomics analyses is a continuing challenge. Here, we describe an approach that combines stable isotope labeling, liquid chromatography– mass spectrometry (LC–MS), and a computational pipeline to automatically identify metabolites produced from a selected metabolic precursor. We identified the subset of the soluble metabolome generated from phenylalanine (Phe) in Arabidopsis thaliana, which we refer to as the Phe-derived metabolome (FDM) In addition to identifying Phe-derived metabolites present in a single wild-type reference accession, the FDM was established in nine enzymatic and regulatory mutants in the phenylpropanoid pathway. To identify genes associated with variation in Phe-derived metabolites in Arabidopsis, MS features collected by untargeted metabolite profiling of an Arabidopsis diversity panel were retrospectively annotated to the FDM and natural genetic variants responsible for differences in accumulation of FDM features were identified by genome-wide association. Large differences in Phe-derived metabolite accumulation and presence/absence variation of abundant metabolites were observed in the nine mutants as well as between accessions from the diversity panel. Many Phe-derived metabolites that accumulated in mutants also accumulated in non-Col-0 accessions and was associated to genes with known or suspected functions in the phenylpropanoid pathway as well as genes with no known functions. Overall, we show that cataloguing a biochemical pathway’s products through isotopic labeling across genetic variants can substantially contribute to the identification of metabolites and genes associated with their biosynthesis. DA - 2021/3// PY - 2021/3// DO - 10.1093/plcell/koaa046 VL - 33 IS - 3 SP - 492-510 SN - 1532-298X UR - https://doi.org/10.1093/plcell/koaa046 ER - TY - JOUR TI - Rcompadre and Rage - two R packages to facilitate the use of the COMPADRE and COMADRE databases and calculation of life history traits from matrix population models AU - Jones, Owen R. AU - Barks, Patrick AU - Stott, Iain AU - James, Tamora D. AU - Levin, Sam AU - Petry, William K. AU - Capdevila, Pol AU - Che-Castaldo, Judy AU - Jackson, John AU - Römer, Gesa AU - Schuette, Caroline AU - Thomas, Chelsea C. AU - Salguero-Gómez, Roberto AB - Summary Matrix population models (MPMs) are an important tool for biologists seeking to understand the causes and consequences of variation in vital rates (e.g., survival, reproduction) across life cycles. Empirical MPMs describe the age- or stage-structured demography of organisms and usually represent the life history of a population during a particular time frame at a specific geographic location. The COMPADRE Plant Matrix Database and COMADRE Animal Matrix Database are the most extensive resources for MPM data, collectively containing >12,000 individual projection matrices for >1,100 species globally. Although these databases represent an unparalleled resource for researchers, land managers, and educators, the current computational tools available to answer questions with MPMs impose significant barriers to potential COM(P)ADRE database users by requiring advanced knowledge to handle diverse data structures and program custom analysis functions. To close this knowledge gap, we present two interrelated R packages designed to (i) facilitate the use of these databases by providing functions to acquire, quality control, and manage both the MPM data contained in COMPADRE and COMADRE, and a user’s own MPM data ( Rcompadre ), and (ii) present a range of functions to calculate life history traits from MPMs in support of ecological and evolutionary analyses ( Rage ). We provide examples to illustrate the use of both. Rcompadre and Rage will facilitate demographic analyses using MPM data and contribute to the improved replicability of studies using these data. We hope that this new functionality will allow researchers, land managers, and educators to unlock the potential behind the thousands of MPMs and ancillary metadata stored in the COMPADRE and COMADRE matrix databases, and in their own MPM data. DA - 2021/4/26/ PY - 2021/4/26/ DO - 10.1101/2021.04.26.441330 VL - 4 UR - https://doi.org/10.1101/2021.04.26.441330 ER - TY - JOUR TI - Auxin Interactions with Other Hormones in Plant Development AU - Mazzoni-Putman, Serina M. AU - Brumos, Javier AU - Zhao, Chengsong AU - Alonso, Jose M. AU - Stepanova, Anna N. T2 - Cold Spring Harbor Perspectives in Biology AB - Auxin is a crucial growth regulator that governs plant development and responses to environmental perturbations. It functions at the heart of many developmental processes, from embryogenesis to organ senescence, and is key to plant interactions with the environment, including responses to biotic and abiotic stimuli. As remarkable as auxin is, it does not act alone, but rather solicits the help of, or is solicited by, other endogenous signals, including the plant hormones abscisic acid, brassinosteroids, cytokinins, ethylene, gibberellic acid, jasmonates, salicylic acid, and strigolactones. The interactions between auxin and other hormones occur at multiple levels: hormones regulate one another's synthesis, transport, and/or response; hormone-specific transcriptional regulators for different pathways physically interact and/or converge on common target genes; etc. However, our understanding of this crosstalk is still fragmentary, with only a few pieces of the gigantic puzzle firmly established. In this review, we provide a glimpse into the complexity of hormone interactions that involve auxin, underscoring how patchy our current understanding is. DA - 2021/4/26/ PY - 2021/4/26/ DO - 10.1101/cshperspect.a039990 VL - 13 IS - 10 SP - a039990 J2 - Cold Spring Harb Perspect Biol LA - en OP - SN - 1943-0264 UR - http://dx.doi.org/10.1101/cshperspect.a039990 DB - Crossref ER - TY - JOUR TI - Appropriate "marginal" farmlands for second-generation biofuel crops in North Carolina AU - Crozier, C. R. AU - Carvalho, H. D. R. AU - Johnson, A. AU - Chinn, M. AU - Heitman, J. L. T2 - AGRICULTURAL & ENVIRONMENTAL LETTERS AB - Abstract Current research on bioenergy crops shows that perennial grasses can yield substantial amounts of dry biomass with relatively low inputs of water and fertilizer. In order to minimize competition with food production, it has been suggested that bioenergy crops could be directed to land areas less suitable for commodity crops, commonly referred to as “marginal” lands. These are land units with inherent limitations to vegetative growth and production, which may be due to several factors (soil physical and chemical properties, climatic conditions, etc.). However the term “marginal” is an adjective with imprecise meaning, and objective criteria for determining “marginal” lands for siting bioenergy crops are necessary. Here we propose that such criteria may be based on soil survey classifications and realistic yield estimates, and we show an example of its use to justify site selection for bioenergy crops in different regions of North Carolina. DA - 2021/// PY - 2021/// DO - 10.1002/ael2.20041 VL - 6 IS - 1 SP - SN - 2471-9625 ER - TY - JOUR TI - Down-regulation of Fra a 1.02 in strawberry fruits causes transcriptomic and metabolic changes compatible with an altered defense response AU - Orozco-Navarrete, Begona AU - Song, Jina AU - Casanal, Ana AU - Sozzani, Rosangela AU - Flors, Victor AU - Sanchez-Sevilla, Jose F. AU - Trinkl, Johanna AU - Hoffmann, Thomas AU - Merchante, Catharina AU - Schwab, Wilfried AU - Valpuesta, Victoriano T2 - HORTICULTURE RESEARCH AB - Abstract The strawberry Fra a 1 proteins belong to the class 10 Pathogenesis-Related (PR-10) superfamily. In strawberry, a large number of members have been identified, but only a limited number is expressed in the fruits. In this organ, Fra a 1.01 and Fra a 1.02 are the most abundant Fra proteins in the green and red fruits, respectively, however, their function remains unknown. To know the function of Fra a 1.02 we have generated transgenic lines that silence this gene, and performed metabolomics, RNA-Seq, and hormonal assays. Previous studies associated Fra a 1.02 to strawberry fruit color, but the analysis of anthocyanins in the ripe fruits showed no diminution in their content in the silenced lines. Gene ontology (GO) analysis of the genes differentially expressed indicated that oxidation/reduction was the most represented biological process. Redox state was not apparently altered since no changes were found in ascorbic acid and glutathione (GSH) reduced/oxidized ratio, but GSH content was reduced in the silenced fruits. In addition, a number of glutathione-S-transferases (GST) were down-regulated as result of Fra a 1.02-silencing. Another highly represented GO category was transport which included a number of ABC and MATE transporters. Among the regulatory genes differentially expressed WRKY33.1 and WRKY33.2 were down-regulated, which had previously been assigned a role in strawberry plant defense. A reduced expression of the VQ23 gene and a diminished content of the hormones JA, SA, and IAA were also found. These data might indicate that Fra a 1.02 participates in the defense against pathogens in the ripe strawberry fruits. DA - 2021/3/10/ PY - 2021/3/10/ DO - 10.1038/s41438-021-00492-4 VL - 8 IS - 1 SP - SN - 2052-7276 ER - TY - JOUR TI - In situ H2O2 generation methods in the context of enzyme biocatalysis AU - Wapshott-Stehli, Hannah L. AU - Grunden, Amy M. T2 - ENZYME AND MICROBIAL TECHNOLOGY AB - Hydrogen peroxide is a versatile oxidant that has use in medical and biotechnology industries. Many enzymes require this oxidant as a reaction mediator in order to undergo their oxygenation chemistries. While there is a reliable method for generating hydrogen peroxide via an anthraquinone cycle, there are several advantages for generating hydrogen in situ. As highlighted in this review, this is particularly beneficial in the case of biocatalysts that require hydrogen peroxide as a reaction mediator because the exogenous addition of hydrogen peroxide can damage their reactive heme centers and render them inactive. In addition, generation of hydrogen peroxide in situ does not dilute the reaction mixture and cause solution parameters to change. The environment would also benefit from a hydrogen peroxide synthesis cycle that does not rely on nonrenewable chemicals obtained from fossil fuels. Generation of hydrogen peroxide in situ for biocatalysis using enzymes, bioelectrocatalyis, photocatalysis, and cold temperature plasmas are addressed. Particular emphasis is given to reaction processes that support high total turnover numbers (TTNs) of the hydrogen peroxide-requiring enzymes. Discussion of innovations in the use of hydrogen peroxide-producing enzyme cascades for antimicrobial activity, wastewater effluent treatment, and biosensors are also included. DA - 2021/4// PY - 2021/4// DO - 10.1016/j.enzmictec.2021.109744 VL - 145 SP - SN - 1879-0909 KW - Hydrogen peroxide KW - Peroxidases KW - Unspecific peroxygenases KW - Biocatalysis ER - TY - JOUR TI - A hybrid model connecting regulatory interactions with stem cell divisions in the root AU - Broeck, Lisa Van AU - Spurney, Ryan J. AU - Fisher, Adam P. AU - Schwartz, Michael AU - Clark, Natalie M. AU - Nguyen, Thomas T. AU - Madison, Imani AU - Gobble, Mariah AU - Long, Terri AU - Sozzani, Rosangela T2 - Quantitative Plant Biology AB - Stem cells give rise to the entirety of cells within an organ. Maintaining stem cell identity and coordinately regulating stem cell divisions is crucial for proper development. In plants, mobile proteins, such as WUSCHEL-RELATED HOMEOBOX 5 (WOX5) and SHORTROOT (SHR), regulate divisions in the root stem cell niche. However, how these proteins coordinately function to establish systemic behaviour is not well understood. We propose a non-cell autonomous role for WOX5 in the cortex endodermis initial (CEI) and identify a regulator, ANGUSTIFOLIA (AN3)/GRF-INTERACTING FACTOR 1, that coordinates CEI divisions. Here, we show with a multi-scale hybrid model integrating ordinary differential equations (ODEs) and agent-based modeling that quiescent center (QC) and CEI divisions have different dynamics. Specifically, by combining continuous models to describe regulatory networks and agent-based rules, we model systemic behaviour, which led us to predict cell-type-specific expression dynamics of SHR, SCARECROW, WOX5, AN3 and CYCLIND6;1, and experimentally validate CEI cell divisions. Conclusively, our results show an interdependency between CEI and QC divisions. DA - 2021/// PY - 2021/// DO - 10.1017/qpb.2021.1 VL - 2 UR - https://doi.org/10.1017/qpb.2021.1 ER - TY - JOUR TI - Remodeling hydrogen bond Interactions results in relaxed specificity of Caspase-3 AU - Yao, Liqi AU - Swartz, Paul AU - Hamilton, Paul T. AU - Clark, A. Clay T2 - BIOSCIENCE REPORTS AB - Caspase (or cysteinyl-aspartate specific proteases) enzymes play important roles in apoptosis and inflammation, and the non-identical but overlapping specificity profiles (that is, cleavage recognition sequence) direct cells to different fates. Although all caspases prefer aspartate at the P1 position of the substrate, the caspase-6 subfamily shows preference for valine at the P4 position, while caspase-3 shows preference for aspartate. In comparison with human caspases, caspase-3a from zebrafish has relaxed specificity and demonstrates equal selection for either valine or aspartate at the P4 position. In the context of the caspase-3 conformational landscape, we show that changes in hydrogen bonding near the S3 subsite affect selection of the P4 amino acid. Swapping specificity with caspase-6 requires accessing new conformational space, where each landscape results in optimal binding of DxxD (caspase-3) or VxxD (caspase-6) substrate and simultaneously disfavors binding of the other substrate. Within the context of the caspase-3 conformational landscape, substitutions near the active site result in nearly equal activity against DxxD and VxxD by disrupting a hydrogen bonding network in the substrate binding pocket. The converse substitutions in zebrafish caspase-3a result in increased selection for P4 aspartate over valine. Overall, the data show that the shift in specificity that results in a dual function protease, as in zebrafish caspase-3a, requires fewer amino acid substitutions compared with those required to access new conformational space for swapping substrate specificity, such as between caspases-3 and -6. DA - 2021/1// PY - 2021/1// DO - 10.1042/BSR20203495 VL - 41 IS - 1 SP - SN - 1573-4935 ER - TY - JOUR TI - Safety and Modulatory Effects of Humanized Galacto-Oligosaccharides on the Gut Microbiome AU - Arnold, Jason W. AU - Whittington, Hunter D. AU - Dagher, Suzanne F. AU - Roach, Jeffery AU - Azcarate-Peril, M. Andrea AU - Bruno-Barcena, Jose M. T2 - FRONTIERS IN NUTRITION AB - Complex dietary carbohydrate structures including β(1–4) galacto-oligosaccharides (GOS) are resistant to digestion in the upper gastrointestinal (GI) tract and arrive intact to the colon where they benefit the host by selectively stimulating microbial growth. Studies have reported the beneficial impact of GOS (alone or in combination with other prebiotics) by serving as metabolic substrates for modulating the assembly of the infant gut microbiome while reducing GI infections. N-Acetyl-D-lactosamine (LacNAc, Galβ1,4GlcNAc) is found in breast milk as a free disaccharide. This compound is also found as a component of human milk oligosaccharides (HMOs), which have repeating and variably branched lactose and/or LacNAc units, often attached to sialic acid and fucose monosaccharides. Human glycosyl-hydrolases do not degrade most HMOs, indicating that these structures have evolved as natural prebiotics to drive the proper assembly of the infant healthy gut microbiota. Here, we sought to develop a novel enzymatic method for generating LacNAc-enriched GOS, which we refer to as humanized GOS (hGOS). We showed that the membrane-bound β-hexosyl transferase (rBHT) from Hamamotoa (Sporobolomyces) singularis was able to generate GOS and hGOS from lactose and N-Acetyl-glucosamine (GlcNAc). The enzyme catalyzed the regio-selective, repeated addition of galactose from lactose to GlcNAc forming the β-galactosyl linkage at the 4-position of the GlcNAc and at the 1-position of D-galactose generating, in addition to GOS, LacNAc, and Galactosyl-LacNAc trisaccharides which were produced by two sequential transgalactosylations. Humanized GOS is chemically distinct from HMOs, and its effects in vivo have yet to be determined. Thus, we evaluated its safety and demonstrated the prebiotic's ability to modulate the gut microbiome in 6-week-old C57BL/6J mice. Longitudinal analysis of gut microbiome composition of stool samples collected from mice fed a diet containing hGOS for 5 weeks showed a transient reduction in alpha diversity. Differences in microbiome community composition mostly within the Firmicutes phylum were observed between hGOS and GOS, compared to control-fed animals. In sum, our study demonstrated the biological synthesis of hGOS, and signaled its safety and ability to modulate the gut microbiome in vivo , promoting the growth of beneficial microorganisms, including Bifidobacterium and Akkermansia . DA - 2021/4/7/ PY - 2021/4/7/ DO - 10.3389/fnut.2021.640100 VL - 8 SP - SN - 2296-861X UR - https://www.frontiersin.org/article/10.3389/fnut.2021.640100 KW - galactooligosaccharide (GOS) KW - N-Acetyl-D-lactosamine (LacNAc) KW - safety KW - human milk oligosaccharides (HMOs) KW - LacNAc synthesis KW - mouse models ER - TY - JOUR TI - Pioneers of Allelopathy: XVII. Udo Blum AU - Blum, Udo T2 - ALLELOPATHY JOURNAL AB - Udo Blum had a teaching and research career of 34 years. His primary role was teaching, advising, and mentoring undergraduate and graduate students. He authored or co-authored research publications on plant-plant allelopathic interactions, air pollution biology, and salt marsh biology. He retired in 2002 and has subsequently written a three-volume retrospective analysis of his research on plant-plant allelopathic interactions involving phenolic acids. His primary research goals were to understand: (i) how cinnamic and benzoic acids released from plants into the soil affect sensitive seedlings and soil and rhizosphere microorganisms, (ii) how phenolic acids are distributed and partitioned in seedling-microbe-soil-sand systems and (iii) how their effects on sensitive seedlings are modified by abiotic soil factors (soil pH, soil moisture, soil nutrients, presence of other organic compounds) and soil processes (microbial utilization and soil sorption) in laboratory and field model systems. In 1999 he received the Molisch Award from the International Allelopathic Society for his research contributions to our understanding of Plant-plant allelopathic interactions. DA - 2021/3// PY - 2021/3// DO - 10.26651/allelo.j/2021-52-2-1313 VL - 52 IS - 2 SP - 143-162 SN - 0973-5046 KW - cover crop residues KW - phenolic asids KW - seedling effects KW - soil processes KW - weeds ER - TY - JOUR TI - The effects of tree cover and soil nutrient addition on native herbaceous richness in a neotropical savanna AU - Massi, Klecia Gili AU - Orlando Eugenio, Chesterton Ulysses AU - Franco, Augusto Cesar AU - Hoffmann, William A. T2 - BIOTROPICA AB - Abstract Exotic grasses and high‐nutrient availability are common factors that may limit recovery of herbaceous diversity in derived savannas, while tree encroachment is a threat to diversity in old‐growth savannas. To understand the impacts of these factors on herbaceous communities, we studied the effect of nutrient addition, and the resulting increase in the exotic grass, Melinis minutiflora , at a savanna‐forest boundary in the Brazilian Cerrado. We inventoried richness of reproductive herbs, tree basal area and cover of the exotic grass, Melinis minutiflora , in each plot. Nutrient addition caused a large increase in Melinis and a large decrease in richness of flowering plants. Unexpectedly, structural equation model analysis suggests that the decline in herbaceous richness was a direct result of nutrient addition, rather than an indirect effect caused by the increase in Melinis . Tree density had a strong negative effect on both Melinis cover and herbaceous richness. Our results reveal that high‐nutrient availability imposes a barrier to the restoration of a diverse, native herbaceous layer in anthropogenic savannas, while tree encroachment is a threat to diversity in old‐growth savannas. Abstract in Portuguese is available with online material. DA - 2021/5// PY - 2021/5// DO - 10.1111/btp.12940 VL - 53 IS - 3 SP - 888-895 SN - 1744-7429 KW - Brazil KW - Cerrado KW - diversity KW - fertilization KW - Ground layer KW - shading ER - TY - JOUR TI - Decadal changes in fire frequencies shift tree communities and functional traits AU - Pellegrini, Adam F. A. AU - Refsland, Tyler AU - Averill, Colin AU - Terrer, Cesar AU - Staver, A. Carla AU - Brockway, Dale G. AU - Caprio, Anthony AU - Clatterbuck, Wayne AU - Coetsee, Corli AU - Haywood, James D. AU - Hobbie, Sarah E. AU - Hoffmann, William A. AU - Kush, John AU - Lewis, Tom AU - Moser, W. Keith AU - Overby, Steven T. AU - Patterson, William A., III AU - Peay, Kabir G. AU - Reich, Peter B. AU - Ryan, Casey AU - Sayer, Mary Anne S. AU - Scharenbroch, Bryant C. AU - Schoennagel, Tania AU - Smith, Gabriel Reuben AU - Stephan, Kirsten AU - Swanston, Chris AU - Turner, Monica G. AU - Varner, J. Morgan AU - Jackson, Robert B. T2 - NATURE ECOLOGY & EVOLUTION AB - Global change has resulted in chronic shifts in fire regimes. Variability in the sensitivity of tree communities to multi-decadal changes in fire regimes is critical to anticipating shifts in ecosystem structure and function, yet remains poorly understood. Here, we address the overall effects of fire on tree communities and the factors controlling their sensitivity in 29 sites that experienced multi-decadal alterations in fire frequencies in savanna and forest ecosystems across tropical and temperate regions. Fire had a strong overall effect on tree communities, with an average fire frequency (one fire every three years) reducing stem density by 48% and basal area by 53% after 50 years, relative to unburned plots. The largest changes occurred in savanna ecosystems and in sites with strong wet seasons or strong dry seasons, pointing to fire characteristics and species composition as important. Analyses of functional traits highlighted the impact of fire-driven changes in soil nutrients because frequent burning favoured trees with low biomass nitrogen and phosphorus content, and with more efficient nitrogen acquisition through ectomycorrhizal symbioses. Taken together, the response of trees to altered fire frequencies depends both on climatic and vegetation determinants of fire behaviour and tree growth, and the coupling between fire-driven nutrient losses and plant traits. Using tree community data from 29 tropical and temperate sites that have experienced multi-decadal alterations in fire frequency, the authors show repeated burning generally reduces stem density and basal area, with most pronounced effects in savanna ecosystems and in sites with strong wet seasons or strong dry seasons. DA - 2021/4// PY - 2021/4// DO - 10.1038/s41559-021-01401-7 VL - 5 IS - 4 SP - 504-+ SN - 2397-334X ER - TY - JOUR TI - The pleiotropic effects of prebiotic galacto-oligosaccharides on the aging gut (vol 9, 31, 2021) AU - Arnold, Jason W. AU - Roach, Jeffery AU - Fabela, Salvador AU - Moorfield, Emily AU - Ding, Shengli AU - Blue, Eric AU - Dagher, Suzanne AU - Magness, Scott AU - Tamayo, Rita AU - Bruno-Barcena, Jose M. AU - Azcarate-Peril, M. Andrea T2 - MICROBIOME AB - An amendment to this paper has been published and can be accessed via the original article. DA - 2021/2/26/ PY - 2021/2/26/ DO - 10.1186/s40168-021-01030-z VL - 9 IS - 1 SP - SN - 2049-2618 ER - TY - JOUR TI - Analysis of the transcriptomic, metabolomic, and gene regulatory responses to Puccinia sorghi in maize AU - Kim, Saet-Byul AU - Broeck, Lisa AU - Karre, Shailesh AU - Choi, Hoseong AU - Christensen, Shawn A. AU - Wang, Guan-Feng AU - Jo, Yeonhwa AU - Cho, Won Kyong AU - Balint-Kurti, Peter T2 - MOLECULAR PLANT PATHOLOGY AB - Abstract Common rust, caused by Puccinia sorghi , is a widespread and destructive disease of maize. The Rp1‐D gene confers resistance to the P. sorghi IN2 isolate, mediating a hypersensitive cell death response (HR). To identify differentially expressed genes (DEGs) and metabolites associated with the compatible (susceptible) interaction and with Rp1‐D ‐mediated resistance in maize, we performed transcriptomics and targeted metabolome analyses of P. sorghi IN2‐infected leaves from the near‐isogenic lines H95 and H95:Rp1‐D, which differed for the presence of Rp1‐D . We observed up‐regulation of genes involved in the defence response and secondary metabolism, including the phenylpropanoid, flavonoid, and terpenoid pathways. Metabolome analyses confirmed that intermediates from several transcriptionally up‐regulated pathways accumulated during the defence response. We identified a common response in H95:Rp1‐D and H95 with an additional H95:Rp1‐D‐specific resistance response observed at early time points at both transcriptional and metabolic levels. To better understand the mechanisms underlying Rp1‐D ‐mediated resistance, we inferred gene regulatory networks occurring in response to P. sorghi infection. A number of transcription factors including WRKY53, BHLH124, NKD1, BZIP84, and MYB100 were identified as potentially important signalling hubs in the resistance‐specific response. Overall, this study provides a novel and multifaceted understanding of the maize susceptible and resistance‐specific responses to P. sorghi . DA - 2021/4// PY - 2021/4// DO - 10.1111/mpp.13040 VL - 22 IS - 4 SP - 465-479 SN - 1364-3703 UR - https://doi.org/10.1111/mpp.13040 KW - common rust KW - gene regulatory network KW - maize KW - Puccinia sorghi KW - RNA‐ KW - Seq ER - TY - JOUR TI - Editorial: Integration of Hormonal Signals Shaping Root Growth, Development, and Architecture AU - Agusti, Javier AU - Ramireddy, Eswarayya AU - Brumos, Javier T2 - FRONTIERS IN PLANT SCIENCE AB - EDITORIAL article Front. Plant Sci., 12 February 2021 | https://doi.org/10.3389/fpls.2021.634066 DA - 2021/2/12/ PY - 2021/2/12/ DO - 10.3389/fpls.2021.634066 VL - 12 SP - SN - 1664-462X KW - development KW - root growth KW - plant hormones KW - regulation KW - crops KW - stress KW - auxin KW - ethylene ER - TY - JOUR TI - Structure, Function, and Thermal Adaptation of the Biotin Carboxylase Domain Dimer from Hydrogenobacter thermophilus 2-Oxoglutarate Carboxylase AU - Buhrman, Greg AU - Enriquez, Paul AU - Dillard, Lucas AU - Baer, Hayden AU - Truong, Vivian AU - Grunden, Amy M. AU - Rose, Robert B. T2 - BIOCHEMISTRY AB - 2-Oxoglutarate carboxylase (OGC), a unique member of the biotin-dependent carboxylase family from the order Aquificales, captures dissolved CO2 via the reductive tricarboxylic acid (rTCA) cycle. Structure and function studies of OGC may facilitate adaptation of the rTCA cycle to increase the level of carbon fixation for biofuel production. Here we compare the biotin carboxylase (BC) domain of Hydrogenobacter thermophilus OGC with the well-studied mesophilic homologues to identify features that may contribute to thermal stability and activity. We report three OGC BC X-ray structures, each bound to bicarbonate, ADP, or ADP-Mg2+, and propose that substrate binding at high temperatures is facilitated by interactions that stabilize the flexible subdomain B in a partially closed conformation. Kinetic measurements with varying ATP and biotin concentrations distinguish two temperature-dependent steps, consistent with biotin’s rate-limiting role in organizing the active site. Transition state thermodynamic values derived from the Eyring equation indicate a larger positive ΔH⧧ and a less negative ΔS⧧ compared to those of a previously reported mesophilic homologue. These thermodynamic values are explained by partially rate limiting product release. Phylogenetic analysis of BC domains suggests that OGC diverged prior to Aquificales evolution. The phylogenetic tree identifies mis-annotations of the Aquificales BC sequences, including the Aquifex aeolicus pyruvate carboxylase structure. Notably, our structural data reveal that the OGC BC dimer comprises a “wet” dimerization interface that is dominated by hydrophilic interactions and structural water molecules common to all BC domains and likely facilitates the conformational changes associated with the catalytic cycle. Mutations in the dimerization domain demonstrate that dimerization contributes to thermal stability. DA - 2021/2/2/ PY - 2021/2/2/ DO - 10.1021/acs.biochem.0c00815 VL - 60 IS - 4 SP - 324-345 SN - 0006-2960 ER - TY - JOUR TI - Five key aspects of metaproteomics as a tool to understand functional interactions in host-associated microbiomes AU - Salvato, Fernanda AU - Hettich, Robert L. AU - Kleiner, Manuel T2 - PLOS PATHOGENS DA - 2021/2// PY - 2021/2// DO - 10.1371/journal.ppat.1009245 VL - 17 IS - 2 SP - SN - 1553-7374 UR - https://doi.org/10.1371/journal.ppat.1009245 ER - TY - JOUR TI - The pleiotropic effects of prebiotic galacto-oligosaccharides on the aging gut AU - Arnold, Jason W. AU - Roach, Jeffery AU - Fabela, Salvador AU - Moorfield, Emily AU - Ding, Shengli AU - Blue, Eric AU - Dagher, Suzanne AU - Magness, Scott AU - Tamayo, Rita AU - Bruno-Barcena, Jose M. AU - Azcarate-Peril, M. Andrea T2 - MICROBIOME AB - Abstract Background Prebiotic galacto-oligosaccharides (GOS) have an extensively demonstrated beneficial impact on intestinal health. In this study, we determined the impact of GOS diets on hallmarks of gut aging: microbiome dysbiosis, inflammation, and intestinal barrier defects (“leaky gut”). We also evaluated if short-term GOS feeding influenced how the aging gut responded to antibiotic challenges in a mouse model of Clostridioides difficile infection. Finally, we assessed if colonic organoids could reproduce the GOS responder—non-responder phenotypes observed in vivo. Results Old animals had a distinct microbiome characterized by increased ratios of non-saccharolytic versus saccharolytic bacteria and, correspondingly, a lower abundance of β-galactosidases compared to young animals. GOS reduced the overall diversity, increased the abundance of specific saccharolytic bacteria (species of Bacteroides and Lactobacillus ), increased the abundance of β-galactosidases in young and old animals, and increased the non-saccharolytic organisms; however, a robust, homogeneous bifidogenic effect was not observed. GOS reduced age-associated increased intestinal permeability and increased MUC2 expression and mucus thickness in old mice. Clyndamicin reduced the abundance Bifidobacterium while increasing Akkermansia , Clostridium , Coprococcus , Bacillus , Bacteroides , and Ruminococcus in old mice. The antibiotics were more impactful than GOS on modulating serum markers of inflammation. Higher serum levels of IL-17 and IL-6 were observed in control and GOS diets in the antibiotic groups, and within those groups, levels of IL-6 were higher in the GOS groups, regardless of age, and higher in the old compared to young animals in the control diet groups. RTqPCR revealed significantly increased gene expression of TNFα in distal colon tissue of old mice, which was decreased by the GOS diet. Colon transcriptomics analysis of mice fed GOS showed increased expression of genes involved in small-molecule metabolic processes and specifically the respirasome in old animals, which could indicate an increased oxidative metabolism and energetic efficiency. In young mice, GOS induced the expression of binding-related genes. The galectin gene Lgals1 , a β-galactosyl-binding lectin that bridges molecules by their sugar moieties and is an important modulator of the immune response, and the PI3K-Akt and ECM-receptor interaction pathways were also induced in young mice. Stools from mice exhibiting variable bifidogenic response to GOS injected into colon organoids in the presence of prebiotics reproduced the response and non-response phenotypes observed in vivo suggesting that the composition and functionality of the microbiota are the main contributors to the phenotype. Conclusions Dietary GOS modulated homeostasis of the aging gut by promoting changes in microbiome composition and host gene expression, which was translated into decreased intestinal permeability and increased mucus production. Age was a determining factor on how prebiotics impacted the microbiome and expression of intestinal epithelial cells, especially apparent from the induction of galectin-1 in young but not old mice. DA - 2021/1/28/ PY - 2021/1/28/ DO - 10.1186/s40168-020-00980-0 VL - 9 IS - 1 SP - SN - 2049-2618 KW - Gut microbiome KW - Prebiotics KW - Bifidobacterium KW - Intestinal permeability KW - Host-microbiota interactions KW - Diet KW - Antibiotics KW - Metagenomics KW - Transcriptomics KW - Organoids ER - TY - JOUR TI - A review of clothing microbiology: the history of clothing and the role of microbes in textiles AU - Sanders, Deaja AU - Grunden, Amy AU - Dunn, Robert R. T2 - BIOLOGY LETTERS AB - Humans have worn clothing for thousands of years, and since its invention, clothing has evolved from its simple utilitarian function for survival to become an integral part of society. While much consideration has been given to the broad environmental impacts of the textile and laundering industries, little is known about the impact wearing clothing has had on the human microbiome, particularly that of the skin, despite our long history with clothing. This review discusses the history of clothing and the evolution of textiles, what is and is not known about microbial persistence on and degradation of various fibres, and what opportunities for the industrial and environmental application of clothing microbiology exist for the future. DA - 2021/// PY - 2021/// DO - 10.1098/rsbl.2020.0700 VL - 17 IS - 1 KW - clothing microbiology KW - textiles KW - fibres KW - degradation KW - microbes in clothing KW - microbiome ER - TY - JOUR TI - Plant-soil feedbacks and the introduction of Castanea (chestnut) hybrids to eastern North American forests AU - Coughlin, Erin M. AU - Shefferson, Richard P. AU - Clark, Stacy L. AU - Wurzburger, Nina T2 - RESTORATION ECOLOGY AB - The reintroduction of disease‐resistant hybrids is a commonly proposed solution to the introduction of pathogens and pests that weaken or eliminate native plant species. Plant interactions with soil biota result in plant–soil feedbacks (PSFs), which have consequences for individual plant growth and survival as well as broader community‐level processes, such as species diversity and coexistence. Because of their importance, species reintroduction should consider these interactions, yet little work has integrated this perspective. Here, we investigate the effects of hybrid Castanea (chestnut) reintroduction on PSFs and how these mechanisms may influence the recruitment of other species in contemporary forests. We also examine how blight‐resistant Castanea hybrids perform in the soil conditions of contemporary forests and we compare their belowground interactions with those of Castanea dentata . We conducted a reciprocal greenhouse experiment testing the effect of species‐specific soil inoculum on the growth and survival of C. dentata , Castanea hybrids, and other forest dominants. Our results suggest that C. dentata and hybrids had similar belowground interactions and were regulated by negative PSFs, meaning soil microbial communities reduced conspecific growth and survival. These negative PSFs may involve the presence of the non‐native pathogen Phytophthera cinnamomi . Soil inoculum of C. dentata and Castanea hybrids had similar effects on heterospecific growth, suggesting Castanea restoration will have neutral effects on natural regeneration in restoration plantings. We conclude that Castanea hybrids may fill a similar belowground niche to their parent species, and that site selection, screening for soil pathogens, and site planting density will be important to restoration. DA - 2021/3// PY - 2021/3// DO - 10.1111/rec.13326 VL - 29 IS - 3 SP - SN - 1526-100X KW - forest dominants KW - hybrid chestnut KW - microbial assemblage KW - negative plant-soil feedback KW - species reintroduction ER - TY - JOUR TI - Widespread co-occurrence of Sebacinales and arbuscular mycorrhizal fungi in switchgrass roots and soils has limited dependence on soil carbon or nutrients AU - Lee, Marissa R. AU - Hawkes, Christine V T2 - PLANTS PEOPLE PLANET AB - Societal Impact Statement This work addresses a novel group of Sebacinales mycorrhizal fungi being considered for development as inoculants in managed ecosystems because of their potential access to nutrients in soil organic matter. By comparing the diversity, distributions, and abundances of the Sebacinales with the more common arbuscular mycorrhizal fungi in switchgrass, a biofuel crop, we demonstrate that current suggestions for a Sebacinales revolution in agriculture should be tempered by their ecology. In particular, Sebacinales are rare compared to arbuscular mycorrhizal fungi, and are only weakly associated with soil carbon, suggesting that ideas about improved soil carbon cycling associated with Sebacinales need to be sufficiently studied across a range of environmental conditions prior to their consideration for broad‐spectrum soil inoculants. Summary Arbuscular mycorrhizal (AM) fungi are widespread and important root symbionts, but recent work suggests that Sebacinales fungi may play an equally important role in both plant success and ecosystem carbon and nutrient cycling based on their worldwide occurrence and putative access to organic matter. However, the ecological impacts of Sebacinales will depend on their abundance and distribution relative to AM fungi and environmental soil carbon and nutrient patterns, which remain unexplored. We characterized Glomeromycota and Sebacinales fungi in switchgrass ( Panicum virgatum L.) roots and soils across 14 sites with diverse soil conditions. We examined group richness differences, co‐occurrence patterns, and how the relative abundance of these fungi related to soil carbon, nutrient stoichiometry, and host size. Sebacinales were widespread, but less diverse, common, and abundant than Glomeromycota. Moreover, co‐occurrences were predominantly random, suggesting relatively few interactions between these groups. Sebacinales increased relative to Glomeromycota in soils with more carbon, but explanatory power was limited. Based on our findings, we suggest that Sebacinales are likely complementary to AM fungi in roots. Expectations that Sebacinales have large effects on soil carbon and nutrient cycling may need to be reconsidered, at least based on their limited abundances relative to AM fungi in switchgrass. This is an important consideration as Sebacinales are candidates for use as inoculants in managed ecosystems. DA - 2021/9// PY - 2021/9// DO - 10.1002/ppp3.10181 VL - 3 IS - 5 SP - 614-626 SN - 2572-2611 UR - https://doi.org/10.1002/ppp3.10181 KW - biofuel crop KW - co-occurrence KW - Glomeromycota KW - grass KW - Panicum virgatum KW - Sebacina KW - Serendipita ER - TY - JOUR TI - Bacterial valorization of pulp and paper industry process streams and waste AU - Brown, Dylan M. AU - Pawlak, Joel AU - Grunden, Amy M. T2 - APPLIED MICROBIOLOGY AND BIOTECHNOLOGY DA - 2021/2// PY - 2021/2// DO - 10.1007/s00253-021-11107-2 VL - 105 IS - 4 SP - 1345-1363 SN - 1432-0614 UR - https://doi.org/10.1007/s00253-021-11107-2 KW - Lignocellulose KW - Pulp and paper KW - Bacteria KW - Lignin KW - Cellulose KW - Hemicellulose ER - TY - JOUR TI - Leveraging synthetic biology approaches in plant hormone research AU - Zhao, Chengsong AU - Yaschenko, Anna AU - Alonso, Jose M AU - Stepanova, Anna N T2 - Current Opinion in Plant Biology AB - The study of plant hormones is critical to understanding development, physiology and interactions of plants with their environment. Synthetic biology holds promise to provide a new perspective and shed fresh light on the molecular mechanisms of plant hormone action and propel the design of novel biotechnologies. With the recent adoption of synthetic biology in plant sciences, exciting first examples of successful tool development and their applications in the area of plant hormone research are emerging, paving the way for new cadres to enter this promising field of science. DA - 2021/4// PY - 2021/4// DO - 10.1016/j.pbi.2020.101998 UR - https://doi.org/10.1016/j.pbi.2020.101998 ER - TY - JOUR TI - Bacterial symbiont subpopulations have different roles in a deep-sea symbiosis AU - Hinzke, Tjorven AU - Kleiner, Manuel AU - Meister, Mareike AU - Schlueter, Rabea AU - Hentschker, Christian AU - Pane-Farre, Jan AU - Hildebrandt, Petra AU - Felbeck, Horst AU - Sievert, Stefan M. AU - Bonn, Florian AU - Voelker, Uwe AU - Becher, Doerte AU - Schweder, Thomas AU - Markert, Stephanie T2 - ELIFE AB - The hydrothermal vent tubeworm Riftia pachyptila hosts a single 16S rRNA phylotype of intracellular sulfur-oxidizing symbionts, which vary considerably in cell morphology and exhibit a remarkable degree of physiological diversity and redundancy, even in the same host. To elucidate whether multiple metabolic routes are employed in the same cells or rather in distinct symbiont subpopulations, we enriched symbionts according to cell size by density gradient centrifugation. Metaproteomic analysis, microscopy, and flow cytometry strongly suggest that Riftia symbiont cells of different sizes represent metabolically dissimilar stages of a physiological differentiation process: While small symbionts actively divide and may establish cellular symbiont-host interaction, large symbionts apparently do not divide, but still replicate DNA, leading to DNA endoreduplication. Moreover, in large symbionts, carbon fixation and biomass production seem to be metabolic priorities. We propose that this division of labor between smaller and larger symbionts benefits the productivity of the symbiosis as a whole. DA - 2021/1/6/ PY - 2021/1/6/ DO - 10.7554/elife.58371 VL - 10 SP - SN - 2050-084X UR - https://europepmc.org/articles/PMC7787665 ER - TY - JOUR TI - Qu-2, a robust poplar suspension cell line for molecular biology AU - Liu, Caixia AU - Li, Kailong AU - Wang, Meng AU - Fan, Erqin AU - Yang, Chuanping AU - Wang, Junhui AU - Fu, Pengyue AU - Ge, Xiaolan AU - Sederoff, Heike W. AU - Sederoff, Ronald R. AU - Chiang, Vincent L. AU - Wang, Sui AU - Qu, Guanzheng T2 - JOURNAL OF FORESTRY RESEARCH AB - Abstract Populus spp. have long been used as model woody plant species for molecular biology research. However, tissues of poplar are often recalcitrant to experimental procedures for molecular studies. We generated a hormone autotrophic poplar suspension cell line from a hybrid of Populus alba × P. berolinensis ‘Yinzhong’, named Qu-2. Qu-2 cells are suitable as a model biological system for studying woody plants. Qu-2 cells have many advantages over suspension cell lines derived so far from any other woody plants. Qu-2 cells are very easy to cultivate and can grow on several common plant culture media without the addition of any plant hormone. They show exceptionally high growth rates, reaching an approximately 150-fold increase in biomass after one week of culturing. Another important unique characteristic of Qu-2 cells is that they can be cryopreserved and readily reactivated. Qu-2 cells are suitable for molecular manipulations such as protoplast production, transient transformation, and RNA-seq analysis. Therefore, Qu-2 cells have the great potential to be an excellent model cell line in tree molecular biological research, ranging from physiology to gene function. The Qu-2 cells will be made available to the plant community for research. DA - 2021/4// PY - 2021/4// DO - 10.1007/s11676-020-01266-9 VL - 32 IS - 2 SP - 733-740 SN - 1993-0607 KW - Qu-2 cell line KW - Suspension cell KW - Poplar KW - Protoplast isolation KW - Transient transformation ER - TY - JOUR TI - A protocol for genome-wide analysis of DNA replication timing in intact root tips AU - Mickelson-Young, Leigh AU - Wear, Emily E. AU - Song, Jawon AU - Zynda, Gregory J. AU - Hanley-Bowdoin, Linda AU - Thompson, William F. T2 - Methods in Molecular Biology series DA - 2021/// PY - 2021/// ER - TY - JOUR TI - Drought legacy affects microbial community trait distributions related to moisture along a savannah grassland precipitation gradient AU - Leizeaga, Ainara AU - Hicks, Lettice C. AU - Manoharan, Lokeshwaran AU - Hawkes, Christine V. AU - Rousk, Johannes T2 - JOURNAL OF ECOLOGY AB - Abstract Ecosystem models commonly use stable‐state assumptions to predict responses of soil microbial functions to environmental change. However, past climatic conditions can shape microbial functional responses resulting in a ‘legacy effect’. For instance, exposure to drier conditions in the field may shape how soil microbial communities respond to subsequent drought and drying and rewetting (DRW) events. We investigated microbial tolerance to low moisture levels (‘resistance’) and ability to recover after a DRW perturbation (‘resilience’) across a steep precipitation gradient in Texas, USA. Although differences in precipitation regime did not result in differences in resistance and resilience of soil microbes, microbial communities appeared to be generally resilient and resistant across the gradient, suggesting that frequent exposure to drought had characterised the trait distributions of microbial communities. Moreover, microbial communities from historically drier sites used carbon more efficiently during a DRW perturbation suggesting that long‐term drought history leaves a legacy effect on microbial functions. This may have been due to an indirect effect of drought caused via precipitation‐induced differences in primary productivity, influencing the availability of soil organic matter to microbes. Alternatively, different exposures to drought might have shaped the microbial ‘readiness’ to cope with the DRW disturbance. Microbial community composition was also linked to drought history, but was unrelated to variation in function. Synthesis . Exposure to drought can have both direct and indirect effects on soil microbial communities, which can result in lasting legacy effects on the functions they control. DA - 2021/9// PY - 2021/9// DO - 10.1111/1365-2745.13550 VL - 109 IS - 9 SP - 3195-3210 SN - 1365-2745 KW - carbon use efficiency KW - drought legacy KW - drying‐ KW - rewetting KW - microbial growth KW - resilience KW - resistance ER - TY - JOUR TI - Loss of Small-RNA-Directed DNA Methylation in the Plant Cell Cycle Promotes Germline Reprogramming and Somaclonal Variation AU - Borges, Filipe AU - Donoghue, Mark T. A. AU - LeBlanc, Chantal AU - Wear, Emily E. AU - Tanurdzic, Milos AU - Berube, Benjamin AU - Brooks, Ashley AU - Thompson, William F. AU - Hanley-Bowdoin, Linda AU - Martienssen, Robert A. T2 - CURRENT BIOLOGY AB - 5-methyl cytosine is widespread in plant genomes in both CG and non-CG contexts. During replication, hemi-methylation on parental DNA strands guides symmetric CG methylation on nascent strands, but non-CG methylation requires modified histones and small RNA guides. Here, we used immortalized Arabidopsis cell suspensions to sort replicating nuclei and determine genome-wide cytosine methylation dynamics during the plant cell cycle. We find that symmetric mCG and mCHG are selectively retained in actively dividing cells in culture, whereas mCHH is depleted. mCG becomes transiently asymmetric during S phase but is rapidly restored in G2, whereas mCHG remains asymmetric throughout the cell cycle. Hundreds of loci gain ectopic CHG methylation, as well as 24-nt small interfering RNAs (siRNAs) and histone H3 lysine dimethylation (H3K9me2), without gaining CHH methylation. This suggests that spontaneous epialleles that arise in plant cell cultures are stably maintained by siRNA and H3K9me2 independent of the canonical RNA-directed DNA methylation (RdDM) pathway. In contrast, loci that fail to produce siRNA may be targeted for demethylation when the cell cycle arrests. Comparative analysis with methylomes of various tissues and cell types suggests that loss of small-RNA-directed non-CG methylation during DNA replication promotes germline reprogramming and epigenetic variation in plants propagated as clones. DA - 2021/// PY - 2021/// DO - 10.1016/j.cub.2020.10.098 VL - 31 IS - 3 SP - 591-+ UR - https://doi.org/10.1016/j.cub.2020.10.098 ER - TY - JOUR TI - Plant and Soil Drivers of Whole-Plant Microbiomes: Variation in Switchgrass Fungi from Coastal to Mountain Sites AU - Lee, Marissa R. AU - Hawkes, Christine V T2 - PHYTOBIOMES JOURNAL AB - Plant-associated microbial diversity is regulated by dispersal from local and regional species pools, as well as filtering by the environment and plant host. However, few studies have simultaneously examined microbial community variation in multiple plant-associated habitats across multiple sites; thus, it is unclear what scales and filters are most important in shaping whole-plant microbiome diversity. To address this, we characterized fungal communities associated with switchgrass (Panicum virgatum L.) leaves, roots, and soils within and across 14 stands spanning mountain to coastal ecoregions of North Carolina. Niche differences at small scales (i.e., less than half a kilometer) best explained variation in fungal communities. However, the specific environmental drivers of fungal community composition differed for leaves, roots, and soils. Leaf and root fungi were both affected by plant height, whereas soil fungi were controlled by stand age. Different soil properties were important for fungi in all plant-associated habitats: K, P, and pH for leaves; clay, Mn, and pH for roots; and clay, dissolved organic carbon, total inorganic N, and Cu for soils. Climate and spatial variables were not significant, further supporting the key role of plant and soil properties. Advances such as these will help us explain, predict, and manipulate microbial assemblages that support plant growth in managed and natural systems. DA - 2021/// PY - 2021/// DO - 10.1094/PBIOMES-07-20-0056-FI VL - 5 IS - 1 SP - 69-79 SN - 2471-2906 UR - https://doi.org/10.1094/PBIOMES-07-20-0056-FI KW - community assembly KW - distance-decay KW - ecology KW - environmental filtering KW - fungi KW - leaf KW - microbiome KW - mycology KW - Panicum virgatum KW - rhizosphere and phyllosphere KW - root KW - soil KW - spatial scaling ER - TY - JOUR TI - Shade alters savanna grass layer structure and function along a gradient of canopy cover AU - Pilon, Natashi A. L. AU - Durigan, Giselda AU - Rickenback, Jess AU - Pennington, R. Toby AU - Dexter, Kyle G. AU - Hoffmann, William A. AU - Abreu, Rodolfo C. R. AU - Lehmann, Caroline E. R. T2 - JOURNAL OF VEGETATION SCIENCE AB - Abstract Aim In savannas, a grass‐dominated ground layer is key to ecosystem function via grass–fire feedbacks that maintain open ecosystems. With woody encroachment, tree density increases, thereby decreasing light in the ground layer and potentially altering ecosystem function. We investigated how light availability can filter individual grass species distributions and whether different functional traits are associated with response to a shade gradient in a landscape experiencing woody encroachment. Location Savanna–forest mosaic in the Cerrado domain, southeastern Brazil. Methods Along an encroachment gradient of increasing tree leaf area index (LAI) and shade, we determined how changing light availability alters grass diversity and ground layer structure relative to grass cover and grass functional traits (photosynthetic pathway, underground storage organs, bud protection and traits related to grass shape, size and leaf dimensions). Results Increasing shade led to a decrease in grass cover and grass species richness, and also compositional and functional changes. We found that where tree LAI reached 1, grass cover was reduced by 50% and species richness by 30%. While C 4 grass species abundances decreased with increasing shade, the opposite pattern was true for C 3 grasses. There were only small differences in light preferences among C 4 subtypes, with phosphoenolpyruvate carboxykinase (PCK) species tolerating slightly more shaded conditions. Persistence of some C 4 species under more shaded conditions was possible, likely due to an ability to store starch reserves via underground storage organs. Conclusions Woody encroachment changes diversity and structure of the grassy layer that is critical to the functioning of savanna ecosystems, highlighting the dependence of the diverse grass layer on open and sunny conditions. Our results suggest a threshold of tree cover close to LAI ≈ 1 as being critical to cerrado grassy layer conservation. DA - 2021/1// PY - 2021/1// DO - 10.1111/jvs.12959 VL - 32 IS - 1 SP - SN - 1654-1103 KW - cerrado conservation KW - functional traits KW - habitat filtering KW - photosynthetic pathway KW - shade tolerance KW - species co-occurrence KW - underground storage organs ER - TY - JOUR TI - Plasma agriculture: Review from the perspective of the plant and its ecosystem AU - Ranieri, Pietro AU - Sponsel, Nicholas AU - Kizer, Jon AU - Rojas‐Pierce, Marcela AU - Hernández, Ricardo AU - Gatiboni, Luciano AU - Grunden, Amy AU - Stapelmann, Katharina T2 - Plasma Processes and Polymers AB - Abstract Plasma agriculture details the role of nonthermal plasma in the development of plants from seeds to crops. Several publications reported enhanced plant growth, improved stress tolerance, and antimicrobial effects of plasma treatment and plasma‐treated water. In this review, we present an overview of the recent plasma agriculture literature and put it in the context of the plant needs and the effects on the plant ecosystem. We will discuss key developmental stages of plants and their needs, the different growth environments from hydroponics to soilless and soil substrates, and the plant microbiome. This review provides the context to design plasma‐based fertilization strategies to address the needs of plants and their ecosystem. DA - 2021/1// PY - 2021/1// DO - 10.1002/ppap.202000162 UR - https://doi.org/10.1002/ppap.202000162 KW - plant fertilizer KW - nonthermal plasma KW - plant development KW - seed germination KW - soil microbiome ER - TY - JOUR TI - The diversity of post-fire regeneration strategies in the cerrado ground layer AU - Pilon, Natashi A. L. AU - Cava, Mario G. B. AU - Hoffmann, William A. AU - Abreu, Rodolfo C. R. AU - Fidelis, Alessandra AU - Durigan, Giselda T2 - JOURNAL OF ECOLOGY AB - Abstract Disentangling species strategies that confer resilience to natural disturbances is key to conserving and restoring savanna ecosystems. Fire is a recurrent disturbance in savannas, and savanna vegetation is highly adapted to and often dependent on fire. However, although the woody component of tropical savannas is well studied, we still do not understand how ground‐layer plant communities respond to fire, limiting conservation and management actions. We investigated the effects of prescribed fire on community structure and composition, and evaluated which traits are involved in plant community regeneration after fire in the cerrado ground layer. We assessed traits related to species persistence and colonization capacity after fire, including resprouter type, underground structure, fire‐induced flowering, regeneration strategy and growth form. We searched for functional groups related to response to fire, to shed light on the main strategies of post‐fire recovery among species in the ground layer. Fire changed ground‐layer community structure and composition in the short term, leading to greater plant species richness, population densities and increasing bare soil, compared with unburned communities. Eight months after fire, species abundance did not differ from pre‐disturbance values for 86% of the species, demonstrating the resilience of this layer to fire. Only one ruderal species was disadvantaged by fire and 13% of the species benefited. Rapid recovery of soil cover by native vegetation in burned areas was driven by species with high capacity to resprout and spread vegetatively. Recovery of the savanna ground‐layer community, as a whole, resulted from a combination of different species traits. We summarized these traits into five large groups, encompassing key strategies involved in ground‐layer regeneration after fire. Synthesis . Fire dramatically changes the ground layer of savanna vegetation in the short term, but the system is highly resilient, quickly recovering the pre‐fire state. Recovery involves different strategies, which we categorized into five functional groups of plant species: grasses , seeders , bloomers , undergrounders and resprouters . Knowledge of these diverse strategies should be used as a tool to assess conservation and restoration status of fire‐resilient ecosystems in the cerrado. DA - 2021/1// PY - 2021/1// DO - 10.1111/1365-2745.13456 VL - 109 IS - 1 SP - 154-166 SN - 1365-2745 KW - below-ground bud bank KW - fire ecology KW - fire-prone ecosystems KW - fire response KW - functional traits KW - herbaceous species KW - neotropical savanna KW - underground structures ER - TY - JOUR TI - Rediscovery of the lost little dogwood Cornus wardiana (Cornaceae)-Its phylogenetic and morphological distinction and implication in the origin of the Arctic-Sino-Himalayan disjunction AU - Wahlsteen, Eric AU - Zhou, Wenbin AU - Xiang, Qiuyun AU - Rushforth, Keith T2 - JOURNAL OF SYSTEMATICS AND EVOLUTION AB - Abstract The dwarf dogwoods (subgenus Arctocrania ) have been widely known to consist of three circumboreal species Cornus suecica , Cornus canadensis , and Cornus unalaschkensis . A fourth putative species was discovered from the northern Myanmar in 1937, but it had never been formally reported on. Here, we formally report the species on the basis of phylogenetic and morphological evidence and name it Cornus wardiana Rushforth & Wahlsteen (sp. nov.). We conducted phylogenetic and morphometric analyses to determine its evolutionary relationship and differentiation from the existing relatives. We dated the phylogeny using molecular data and conducted a biogeographic analysis to gain insights into the evolution and biogeography of the Arctic‐Sino‐Himalayan disjunction. The phylogenetic analysis used sequences of the nrITS and plastid matK and rbcL genes and included all four dwarf dogwoods and 20 other species representing the three other major lineages of Cornus and the outgroup. The morphometric analyses included 60 populations and 102 specimens of dwarf dogwood, representing the entire range of the subgenus. The results showed that C. wardiana diverged first within subgenus Arctocrania in the Miocene, from a wide‐spread ancestor. Results from principal component analysis and discriminant analysis also showed that the Myanmar samples are well separated from the others. Taken together, these results suggest that the dwarf dogwood lineage split from the big‐bracted dogwoods in Asia or Asia‐western North America during the late Paleocene and spread widely to form a Eurasia‐North America distribution; the Arctic‐Sino‐Himalayan disjunction was the result of southward migration in the Miocene followed by extinction in the intervening highland areas. DA - 2021/3// PY - 2021/3// DO - 10.1111/jse.12576 VL - 59 IS - 2 SP - 405-416 SN - 1759-6831 KW - circumboreal-Himalayan disjunction KW - Cornus KW - morphometry KW - new species KW - phylogeny ER -