@article{sullivan_kitzmiller_tran_choudoir_simoes_dayarathne_deangelis_2023, title={Complete genome sequence of Bacillus thuringiensis strain RC340, isolated from a temperate forest soil sample in New England}, volume={10}, ISSN={["2576-098X"]}, url={https://doi.org/10.1128/MRA.00607-23}, DOI={10.1128/MRA.00607-23}, abstractNote={ABSTRACT The complete genome sequence of Bacillus thuringiensis strain RC340, isolated from an environmental microbiology experiment soil sample is presented here. B. thuringiensis strain RC340 sequenced by GridION consists of a single genome consisting of 5.86 million bases, 8,152 predicted genes, and 0.23% contamination.}, journal={MICROBIOLOGY RESOURCE ANNOUNCEMENTS}, author={Sullivan, Brendan and Kitzmiller, Claire E. and Tran, Wyatt C. and Choudoir, Mallory and Simoes, Rachel and Dayarathne, Nipuni and DeAngelis, Kristen M.}, editor={Rasko, DavidEditor}, year={2023}, month={Oct} }
@article{tran_sullivan_kitzmiller_choudoir_simoes_dayarathne_deangelis_2023, title={Draft genome sequence of Paenibacillus sp. strain RC67, an isolate from a long-term forest soil warming experiment in Petersham, Massachusetts}, volume={10}, ISSN={["2576-098X"]}, DOI={10.1128/MRA.00373-23}, abstractNote={ABSTRACT Paenibacillus sp. strain RC67 was isolated from the Harvard Forest long-term soil warming experiment. The assembled genome is a single contig with 7,963,753 bp and 99.4% completion. Genome annotation suggests that the isolate is of a novel bacterial species.}, journal={MICROBIOLOGY RESOURCE ANNOUNCEMENTS}, author={Tran, Wyatt C. and Sullivan, Brendan and Kitzmiller, Claire E. and Choudoir, Mallory and Simoes, Rachel and Dayarathne, Nipuni and Deangelis, Kristen M.}, year={2023}, month={Oct} }
@article{kitzmiller_tran_sullivan_cortez_choudoir_simoes_dayarathne_deangelis_2023, title={High-quality genomes of Paenibacillus spp. RC334 and RC343, isolated from a long-term forest soil warming experiment}, volume={8}, ISSN={["2576-098X"]}, url={https://doi.org/10.1128/MRA.00371-23}, DOI={10.1128/MRA.00371-23}, abstractNote={ABSTRACT Paenibacillus spp. RC334 and RC343 were isolated from heated soil in a long-term soil warming experiment. Both genomes were 5.98 Mb and assembled as a single contig. We describe the assembly and annotation of the two high-quality draft genomes for these isolates here.}, journal={MICROBIOLOGY RESOURCE ANNOUNCEMENTS}, author={Kitzmiller, Claire E. and Tran, Wyatt C. and Sullivan, Brendan and Cortez, Florencia and Choudoir, Mallory and Simoes, Rachel and Dayarathne, Nipuni and Deangelis, Kristen M.}, editor={Baltrus, David A.Editor}, year={2023}, month={Aug} }
@article{choudoir_narayanan_rodriguez-ramos_simoes_efroni_sondrini_deangelis_2023, title={Pangenomes reveal genomic signatures of microbial adaptation to experimental soil warming}, url={https://doi.org/10.1101/2023.03.16.532972}, DOI={10.1101/2023.03.16.532972}, abstractNote={Below-ground carbon transformations represent a natural climate change mitigation solution, but newly-acquired traits adaptive to climate stress may alter microbial climate feedback mechanisms. To better define microbial evolutionary responses to long-term climate warming, we study microorganisms from an ongoing in situ soil warming experiment at the Harvard Forest Long-term Ecological Research (LTER) site where, for over three decades, soils are continuously heated 5 °C above ambient temperatures. We hypothesize that across generations of chronic warming, genomic signatures within diverse bacterial lineages reflect trait-based adaptations related to growth and carbon utilization. From our culture collection of soil bacteria isolated from experimental heated and control plots, we sequenced genomes representing taxa dominant in soil communities and sensitive to warming, including independent lineages of Alphaproteobacteria, Actinobacteria, and Betaproteobacteria. We investigated differences in genomic attributes and patterns of functional gene content to identify genetic signatures of adaptation. Comparative pangenomics revealed differently abundant gene clusters with functional annotations related to carbon and nitrogen metabolism. We also observed differences in global codon usage bias between heated and control genomes, suggesting potential adaptive traits related to growth or growth efficiency. This effect was more varied for organisms with fewer 16S rrn operons, suggesting that these organisms experience different selective pressures on growth efficiency. Together, these data illustrate the emergence of lineage-specific traits as well as common ecological-evolutionary microbial responses to climate change.}, author={Choudoir, Mallory J. and Narayanan, Achala and Rodriguez-Ramos, Damayanti and Simoes, Rachel and Efroni, Alon and Sondrini, Abigail and DeAngelis, Kristen M.}, year={2023}, month={Mar} }
@article{choudoir_deangelis_2022, title={A framework for integrating microbial dispersal modes into soil ecosystem ecology}, volume={25}, url={http://dx.doi.org/10.1016/j.isci.2022.103887}, DOI={10.1016/j.isci.2022.103887}, abstractNote={Dispersal is a fundamental community assembly process that maintains soil microbial biodiversity across spatial and temporal scales, yet the impact of dispersal on ecosystem function is largely unpredictable. Dispersal is unique in that it contributes to both ecological and evolutionary processes and is shaped by both deterministic and stochastic forces. The ecosystem-level ramifications of dispersal outcomes are further compounded by microbial dormancy dynamics and environmental selection. Here we review the knowledge gaps and challenges that remain in defining how dispersal, environmental filtering, and microbial dormancy interact to influence the relationship between microbial community structure and function in soils. We propose the classification of microbial dispersal into three categories, through vegetative or active cells, through dormant cells, and through acellular dispersal, each with unique spatiotemporal dynamics and microbial trait associations. This conceptual framework should improve the integration of dispersal in defining soil microbial community structure-function relationships.}, number={3}, journal={iScience}, publisher={Elsevier BV}, author={Choudoir, Mallory J. and DeAngelis, Kristen M.}, year={2022}, month={Mar}, pages={103887} }
@article{schaal_choudoir_diwanji_stoffolano_deangelis_2022, title={Chitosan diet alters the microbiome of adult house flies}, url={https://doi.org/10.1101/2022.08.31.502951}, DOI={10.1101/2022.08.31.502951}, abstractNote={House flies are disease vectors, carrying human pathogens which include Escherichia coli and Vibrio cholera. To explore the use of chitosan as a bioinsecticide, we evaluated the effects of a chitosan-amended diet on Musca domestica (house fly). We first conducted longevity experiments to understand the impact of chitosan on house fly longevity. We confirmed that chitosan diet amendment is associated with reduced longevity and that this is not due to starvation. We then extracted fly microbiome DNA and used 16S ribosomal RNA gene amplicon sequencing and quantitative PCR to assess the composition and load of the microbiome for flies fed chitosan-amended diets compared to controls. Diversity of the chitosan-fed fly microbiomes was lower than the control, with significant dissimilarities in community composition. Chitosan-fed flies showed lower Ralstonia relative abundance but increased relative abundance of Serratia. Both control and chitosan-fed flies had highly uneven communities, but the control flies were dominated by genera Ralstonia and Providencia, while the chitosan-fed flies were dominated by genera Serratia, Kosakonia, and Providencia. Contrary to our expected results, chitosan-fed flies also contained 56% more bacteria compared to controls. Gut microbiome changes appear to result from chitinolytic bacteria becoming more relatively abundant, and our results suggest that chitosan-amended diet alters the house fly microbiome resulting in higher fly mortality.}, author={Schaal, Hila and Choudoir, Mallory J. and Diwanji, Vedang and Stoffolano, John, Jr. and DeAngelis, Kristen M.}, year={2022}, month={Aug} }
@article{choudoir_eggleston_2022, title={Reciprocal Inclusion of Microbiomes and Environmental Justice Contributes Solutions to Global Environmental Health Challenges}, volume={7}, url={http://dx.doi.org/10.1128/msystems.01462-21}, DOI={10.1128/msystems.01462-21}, abstractNote={Generations of colonialism, industrialization, intensive agriculture, and anthropogenic climate change have radically altered global ecosystems and by extension, their environmental microbiomes. The environmental consequences of global change disproportionately burden racialized communities, those with lower socioeconomic status, and other systematically underserved populations. ABSTRACT Generations of colonialism, industrialization, intensive agriculture, and anthropogenic climate change have radically altered global ecosystems and by extension, their environmental microbiomes. The environmental consequences of global change disproportionately burden racialized communities, those with lower socioeconomic status, and other systematically underserved populations. Environmental justice seeks to balance the relationships between environmental burden, beneficial ecosystem functions, and local communities. Given their direct links to human and ecosystem health, microbes are embedded within social and environmental justice. Considering scientific and technological advances is becoming an important step in developing actionable solutions to global equity challenges. Here we identify areas where inclusion of microbial knowledge and research can support planetary health goals. We offer guidelines for strengthening a reciprocal integration of environmental justice into environmental microbiology research. Microbes form intimate relationships with the environment and society, thus microbiologists have numerous and unique opportunities to incorporate equity into their research, teaching, and community engagement.}, number={3}, journal={mSystems}, publisher={American Society for Microbiology}, author={Choudoir, Mallory J. and Eggleston, Erin M.}, editor={Ishaq, Suzanne LynnEditor}, year={2022}, month={Jun} }
@article{hariharan_choudoir_diebold_panke-buisse_buckley_2022, title={Streptomyces apricus sp. nov., isolated from soil}, volume={72}, url={https://doi.org/10.1099/ijsem.0.005178}, DOI={10.1099/ijsem.0.005178}, abstractNote={A novel Streptomyces strain, SUN51T, was isolated from soils sampled in Wisconsin, USA, as part of a Streptomyces biogeography survey. Genome sequencing revealed that this strain had less than 90 % average nucleotide identity (ANI) to type species of Streptomyces: SUN51T was most closely related to Streptomyces dioscori A217T (99.5 % 16S rRNA gene identity, 89.4 % ANI). Genome size was estimated at 8.81 Mb, and the genome DNA G+C content was 72 mol%. The strain possessed the cellular fatty acids anteiso-C15 : 0, iso-C16 : 0, 16 : 1 ω7c, anteiso-C17 : 0, iso-C14 : 0 and C16 : 0. The predominant menaquinones were MK-9 H4, MK-9 H6 and MK-9 H8. Strain SUN51T contained the polar lipids phosphatidic acid, phosphatidyl ethanolamine, phosphatidyl glycerol and diphosphatidyl glycerol. The cell wall contained ll-diaminopimelic acid. The strain could grow on a broad range of carbon sources and tolerate temperatures of up to 40 °C. The results of the polyphasic study confirmed that this isolate represents a novel species of the genus Streptomyces, for which the name Streptomyces apricus sp. nov. is proposed. The type strain of this species is SUN51T (=NRRL B-65543T=JCM 33736T).}, number={1}, journal={International Journal of Systematic and Evolutionary Microbiology}, publisher={Microbiology Society}, author={Hariharan, Janani and Choudoir, Mallory J. and Diebold, Peter and Panke-Buisse, Kevin and Buckley, Daniel H.}, year={2022}, month={Jan} }
@article{choudoir_järvenpää_marttinen_buckley_2021, title={A non-adaptive demographic mechanism for genome expansion in Streptomyces}, volume={1}, url={http://dx.doi.org/10.1101/2021.01.09.426074}, DOI={10.1101/2021.01.09.426074}, abstractNote={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 so many bacteria with large genomes can be found in soil. Importance Most bacterial genomes are small, but some are quite large, and differences in genome size are ultimately driven by the interplay of gene gain and loss dynamics operating at the population level. The evolutionary forces that favor genome size reduction are well known, but less understood are the forces that drive genome expansion. It is generally assumed that large genomes are adaptive because they favor metabolic versatility. However, we find evidence in Streptomyces for a non-adaptive mechanism of genome expansion driven by horizontal gene transfer. We hypothesize that historical range expansion decreased the strength of selection acting these genomes. Relaxed selection allowed many newly acquired genes (which would normally be lost to deletion) to accumulate, leading to increased genome size. Streptomyces have large genomes that contain a remarkable diversity of antibiotic producing gene clusters, and genome expansion has likely contributed to the evolution of these traits.}, publisher={Cold Spring Harbor Laboratory}, author={Choudoir, Mallory J and Järvenpää, Marko J and Marttinen, Pekka and Buckley, Daniel H}, year={2021}, month={Jan} }
@article{ishaq_parada_wolf_bonilla_carney_benezra_wissel_friedman_deangelis_robinson_et al._2021, title={Introducing the Microbes and Social Equity Working Group: Considering the Microbial Components of Social, Environmental, and Health Justice}, volume={6}, url={http://dx.doi.org/10.1128/msystems.00471-21}, DOI={10.1128/msystems.00471-21}, abstractNote={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. ABSTRACT 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.}, number={4}, journal={mSystems}, publisher={American Society for Microbiology}, author={Ishaq, Suzanne L. and Parada, Francisco J. and Wolf, Patricia G. and Bonilla, Carla Y. and Carney, Megan A. and Benezra, Amber and Wissel, Emily and Friedman, Michael and DeAngelis, Kristen M. and Robinson, Jake M. and et al.}, editor={Gilbert, Jack A.Editor}, year={2021}, month={Aug} }
@article{mcbride_choudoir_fierer_strickland_2020, title={Volatile organic compounds from leaf litter decomposition alter soil microbial communities and carbon dynamics}, url={https://doi.org/10.1002/ecy.3130}, DOI={10.1002/ecy.3130}, abstractNote={Investigations into the transfer of carbon from plant litter to underlying soil horizons has primarily focused on the leaching of soluble carbon from litter belowground or the mixing of litter directly into soil. However, previous work has largely ignored the role of volatile organic compounds (VOCs) released during litter decomposition. Unlike most leaf carbon, these litter-derived VOCs are able to diffuse directly into the soil matrix. Here, we used a 99-day microcosm experiment to track VOCs produced during microbial decomposition of 13 C-labeled leaf litter into soil carbon fractions where the decomposing litters were only sharing headspace with the soil samples, thus preventing direct contact and aqueous movement of litter carbon. We also determined the effects of these litter-derived VOCs on soil microbial community structure. We demonstrated that the litter VOCs contributed to all measured soil carbon pools. Specifically, VOC derived carbon accounted for 2.0, 0.61, 0.18, and 0.08% of carbon in the microbial biomass, dissolved organic matter, mineral associated organic matter, and particulate organic matter pools, respectively. We also show that litter-derived VOCs can affect soil bacterial and fungal community diversity and composition. These findings highlight the importance of an underappreciated pathway where VOCs alter soil microbial communities and carbon dynamics.}, journal={Ecology}, author={McBride, Steven G. and Choudoir, Mallory and Fierer, Noah and Strickland, Michael S.}, year={2020}, month={Oct} }
@article{choudoir_rossabi_gebert_helmig_fierer_2019, title={A Phylogenetic and Functional Perspective on Volatile Organic Compound Production by Actinobacteria}, volume={4}, url={https://doi.org/10.1128/mSystems.00295-18}, DOI={10.1128/mSystems.00295-18}, abstractNote={Soil microbes produce a diverse array of natural products, including volatile organic compounds (VOCs). Volatile compounds are important molecules in soil habitats, where they mediate interactions between bacteria, fungi, insects, plants, and animals. We measured the VOCs produced by a broad diversity of soil- and dust-dwelling Actinobacteria in vitro. We detected a total of 126 unique volatile compounds, and each strain produced a unique combination of VOCs. While some of the compounds were produced by many strains, most were strain specific. Importantly, VOC profiles were more similar between closely related strains, indicating that evolutionary and ecological processes generate predictable patterns of VOC production. Finally, we observed that actinobacterial VOCs had both stimulatory and inhibitory effects on the growth of bacteria that represent a plant-beneficial symbiont and a plant-pathogenic strain, information that may lead to the development of novel strategies for plant disease prevention. ABSTRACT Soil microbes produce an immense diversity of metabolites, including volatile organic compounds (VOCs), which can shape the structure and function of microbial communities. VOCs mediate a multitude of microbe-microbe interactions, including antagonism. Despite their importance, the diversity and functional relevance of most microbial volatiles remain uncharacterized. We assembled a taxonomically diverse collection of 48 Actinobacteria isolated from soil and airborne dust and surveyed the VOCs produced by these strains on two different medium types in vitro using gas chromatography-mass spectrometry (GC-MS). We detected 126 distinct VOCs and structurally identified approximately 20% of these compounds, which were predominately C1 to C5 hetero-VOCs, including (oxygenated) alcohols, ketones, esters, and nitrogen- and sulfur-containing compounds. Each strain produced a unique VOC profile. While the most common VOCs were likely by-products of primary metabolism, most of the VOCs were strain specific. We observed a strong taxonomic and phylogenetic signal for VOC profiles, suggesting their role in finer-scale patterns of ecological diversity. Finally, we investigated the functional potential of these VOCs by assessing their effects on growth rates of both pathogenic and nonpathogenic pseudomonad strains. We identified sets of VOCs that correlated with growth inhibition and stimulation, information that may facilitate the development of microbial VOC-based pathogen control strategies. IMPORTANCE Soil microbes produce a diverse array of natural products, including volatile organic compounds (VOCs). Volatile compounds are important molecules in soil habitats, where they mediate interactions between bacteria, fungi, insects, plants, and animals. We measured the VOCs produced by a broad diversity of soil- and dust-dwelling Actinobacteria in vitro. We detected a total of 126 unique volatile compounds, and each strain produced a unique combination of VOCs. While some of the compounds were produced by many strains, most were strain specific. Importantly, VOC profiles were more similar between closely related strains, indicating that evolutionary and ecological processes generate predictable patterns of VOC production. Finally, we observed that actinobacterial VOCs had both stimulatory and inhibitory effects on the growth of bacteria that represent a plant-beneficial symbiont and a plant-pathogenic strain, information that may lead to the development of novel strategies for plant disease prevention.}, number={2}, journal={mSystems}, publisher={American Society for Microbiology}, author={Choudoir, Mallory and Rossabi, Sam and Gebert, Matthew and Helmig, Detlev and Fierer, Noah}, editor={Whiteson, Katrine L.Editor}, year={2019}, month={Apr} }
@article{choudoir_pepe-ranney_buckley_2018, title={Diversification of Secondary Metabolite Biosynthetic Gene Clusters Coincides with Lineage Divergence in Streptomyces}, volume={7}, url={http://www.mdpi.com/2079-6382/7/1/12}, DOI={10.3390/antibiotics7010012}, abstractNote={We have identified Streptomyces sister-taxa which share a recent common ancestor and nearly identical small subunit (SSU) rRNA gene sequences, but inhabit distinct geographic ranges demarcated by latitude and have sufficient genomic divergence to represent distinct species. Here, we explore the evolutionary dynamics of secondary metabolite biosynthetic gene clusters (SMGCs) following lineage divergence of these sister-taxa. These sister-taxa strains contained 310 distinct SMGCs belonging to 22 different gene cluster classes. While there was broad conservation of these 22 gene cluster classes among the genomes analyzed, each individual genome harbored a different number of gene clusters within each class. A total of nine SMGCs were conserved across nearly all strains, but the majority (57%) of SMGCs were strain-specific. We show that while each individual genome has a unique combination of SMGCs, this diversity displays lineage-level modularity. Overall, the northern-derived (NDR) clade had more SMGCs than the southern-derived (SDR) clade (40.7 ± 3.9 and 33.8 ± 3.9, mean and S.D., respectively). This difference in SMGC content corresponded with differences in the number of predicted open reading frames (ORFs) per genome (7775 ± 196 and 7093 ± 205, mean and S.D., respectively) such that the ratio of SMGC:ORF did not differ between sister-taxa genomes. We show that changes in SMGC diversity between the sister-taxa were driven primarily by gene acquisition and deletion events, and these changes were associated with an overall change in genome size which accompanied lineage divergence.}, number={1}, journal={Antibiotics}, publisher={MDPI AG}, author={Choudoir, Mallory and Pepe-Ranney, Charles and Buckley, Daniel}, year={2018}, month={Feb}, pages={12} }
@article{choudoir_buckley_2018, title={Phylogenetic conservatism of thermal traits explains dispersal limitation and genomic differentiation of Streptomyces sister-taxa}, volume={12}, url={http://dx.doi.org/10.1038/s41396-018-0180-3}, DOI={10.1038/s41396-018-0180-3}, abstractNote={The latitudinal diversity gradient is a pattern of biogeography observed broadly in plants and animals but largely undocumented in terrestrial microbial systems. Although patterns of microbial biogeography across broad taxonomic scales have been described in a range of contexts, the mechanisms that generate biogeographic patterns between closely related taxa remain incompletely characterized. Adaptive processes are a major driver of microbial biogeography, but there is less understanding of how microbial biogeography and diversification are shaped by dispersal limitation and drift. We recently described a latitudinal diversity gradient of species richness and intraspecific genetic diversity in Streptomyces by using a geographically explicit culture collection. Within this geographically explicit culture collection, we have identified Streptomyces sister-taxa whose geographic distribution is delimited by latitude. These sister-taxa differ in geographic distribution, genomic diversity, and ecological traits despite having nearly identical SSU rRNA gene sequences. Comparative genomic analysis reveals genomic differentiation of these sister-taxa consistent with restricted gene flow across latitude. Furthermore, we show phylogenetic conservatism of thermal traits between the sister-taxa suggesting that thermal trait adaptation limits dispersal and gene flow across climate regimes as defined by latitude. Such phylogenetic conservatism of thermal traits is commonly associated with latitudinal diversity gradients for plants and animals. These data provide further support for the hypothesis that the Streptomyces latitudinal diversity gradient was formed as a result of historical demographic processes defined by dispersal limitation and driven by paleoclimate dynamics.}, number={9}, journal={The ISME Journal}, publisher={Springer Science and Business Media LLC}, author={Choudoir, Mallory J. and Buckley, Daniel H.}, year={2018}, month={Sep}, pages={2176–2186} }
@article{choudoir_barberan_menninger_dunn_fierer_2018, title={Variation in range size and dispersal capabilities of microbial taxa}, volume={99}, ISSN={["1939-9170"]}, url={https://doi.org/10.1002/ecy.2094}, DOI={10.1002/ecy.2094}, abstractNote={Abstract}, number={2}, journal={ECOLOGY}, publisher={Wiley}, author={Choudoir, Mallory J. and Barberan, Albert and Menninger, Holly L. and Dunn, Rob R. and Fierer, Noah}, year={2018}, month={Feb}, pages={322–334} }
@article{rossabi_choudoir_helmig_hueber_fierer_2018, title={Volatile Organic Compound Emissions From Soil Following Wetting Events}, url={https://doi.org/10.1029/2018JG004514}, DOI={10.1029/2018JG004514}, abstractNote={Dynamics of carbon dioxide (CO2) emissions following the wetting of dry soil have been widely studied in field and laboratory settings. Nonmethane volatile organic compounds (VOCs) are also emitted from soil following a rain event and are evident from the characteristic smell of wet soil. Few studies have documented VOC emissions before and after soil rewetting. Soil emissions were studied using a dynamic flux chamber system purged with VOC‐free air, with identification and quantification of emissions performed by gas chromatography/mass spectrometry. All soils exhibited a rewetting‐induced pulse of VOC emissions, with VOC emissions 14 times higher (on average) in the few hours after rewetting compared to moist soils 2 days after rewetting. This VOC rewetting pulse mirrored the CO2 rewetting pulse (the so‐called “Birch Effect”) but was shorter in duration. Average VOC emissions were 5.0 ± 2.0% of CO2 emissions (molar C equivalent) and increased with increasing soil organic matter content (ρ = 0.40, ρ = 0.99 with one soil excluded). The amounts and types of VOCs varied with time since rewetting and across the five studied soil types, though acetone and small hydrocarbons were the dominant compounds emitted from all soils. Some of the VOCs emitted are likely important mediators of microbial activities and relevant to atmospheric chemical dynamics. Soil VOC emissions, similar to CO2 emissions, are strongly affected by rewetting events, and it is important to consider these rewetting dynamics when modeling soil and ecosystem VOC emissions and understand their relevance to terrestrial ecosystem functioning and atmospheric processes.}, journal={Journal of Geophysical Research: Biogeosciences}, author={Rossabi, Sam and Choudoir, Mallory and Helmig, Detlev and Hueber, Jacques and Fierer, Noah}, year={2018}, month={Jun} }
@article{choudoir_panke-buisse_andam_buckley_2017, title={Genome Surfing As Driver of Microbial Genomic Diversity}, volume={25}, url={http://dx.doi.org/10.1016/j.tim.2017.02.006}, DOI={10.1016/j.tim.2017.02.006}, abstractNote={Microbial genomic diversity is often explained by invoking selection acting on large populations at demographic equilibrium. However, historical fluctuations in population size can produce nonadaptive changes in genomic diversity due to drift. Gene surfing can explain patterns of genomic diversity in diverse species of plants and animals as a consequence of postglacial range expansion driven by historical climate change during the Pleistocene. We propose that genome surfing can result when the demographic mechanisms which produce gene surfing act on microbial populations capable of horizontal gene transfer (HGT). Patterns of genetic diversity and gene flow within Streptomyces are indicative of postglacial demographic range expansion. Genome surfing provides a mechanism to explain ancestral patterns of horizontal gene exchange and current patterns of genomic diversity observed within Streptomyces. Historical changes in population size, such as those caused by demographic range expansions, can produce nonadaptive changes in genomic diversity through mechanisms such as gene surfing. We propose that demographic range expansion of a microbial population capable of horizontal gene exchange can result in genome surfing, a mechanism that can cause widespread increase in the pan-genome frequency of genes acquired by horizontal gene exchange. We explain that patterns of genetic diversity within Streptomyces are consistent with genome surfing, and we describe several predictions for testing this hypothesis both in Streptomyces and in other microorganisms. Historical changes in population size, such as those caused by demographic range expansions, can produce nonadaptive changes in genomic diversity through mechanisms such as gene surfing. We propose that demographic range expansion of a microbial population capable of horizontal gene exchange can result in genome surfing, a mechanism that can cause widespread increase in the pan-genome frequency of genes acquired by horizontal gene exchange. We explain that patterns of genetic diversity within Streptomyces are consistent with genome surfing, and we describe several predictions for testing this hypothesis both in Streptomyces and in other microorganisms. a severe reduction in a population size. the number of individuals of an idealized population needed to capture the genetic diversity of the actual population. the moving boundary of a range expansion. a reduction in genetic diversity caused when a small number of individuals founds a population. a genetic consequence of range expansion driven by neutral variations in gene frequencies that occur at an expansion edge. an evolutionary mechanism whereby allele or gene frequencies change as a result of random sampling effects. contemporaneous introgression of many horizontally acquired genes into a pan-genome as a consequence of gene surfing. the permanent incorporation of genes from one pan-genome into a second pan-genome of a divergent lineage. a mechanism that causes spatial gradients of genetic diversity when dispersal limitation allows the local accumulation of genetic variation. a radial pattern of genetic discontinuity produced during range expansions. a population characterized by unlimited gene flow. the physical co-occurrence of items in space and time. an event that occurs when a population colonizes a geographic region which it did not previously occupy, and which may or may not already be occupied by other populations, as facilitated by dispersal. an evolutionary mechanism whereby allele or gene frequencies change in response to fitness effects. a loss of genetic variation resulting from a rapid fixation of a beneficial allele or gene.}, number={8}, journal={Trends in Microbiology}, publisher={Elsevier BV}, author={Choudoir, Mallory J. and Panke-Buisse, Kevin and Andam, Cheryl P. and Buckley, Daniel H.}, year={2017}, month={Aug}, pages={624–636} }
@article{andam_doroghazi_campbell_kelly_choudoir_buckley_2016, title={A Latitudinal Diversity Gradient in Terrestrial Bacteria of the Genus Streptomyces}, volume={7}, number={2}, journal={mBio}, publisher={Am Soc Microbiol}, author={Andam, Cheryl P and Doroghazi, James R and Campbell, Ashley N and Kelly, Peter J and Choudoir, Mallory J and Buckley, Daniel H}, year={2016}, pages={e02200–15} }
@article{andam_choudoir_nguyen_park_buckley_2016, title={Contributions of ancestral inter-species recombination to the genetic diversity of extant Streptomyces lineages}, journal={The ISME journal}, publisher={Nature Publishing Group}, author={Andam, Cheryl P and Choudoir, Mallory J and Nguyen, Anh Vinh and Park, Han Sol and Buckley, Daniel H}, year={2016} }
@article{choudoir_doroghazi_d.h._2016, title={Latitude delineates patterns of biogeography in terrestrial Streptomyces}, volume={18}, DOI={10.1111/1462-2920.13420}, abstractNote={Summary The biogeography of Streptomyces was examined at regional spatial scales to identify factors that govern patterns of microbial diversity. Streptomyces are spore forming filamentous bacteria which are widespread in soil. Streptomyces strains were isolated from perennial grass habitats sampled across a spatial scale of more than 6000 km. Previous analysis of this geographically explicit culture collection provided evidence for a latitudinal diversity gradient in Streptomyces species. Here the hypothesis that this latitudinal diversity gradient is a result of evolutionary dynamics associated with historical demographic processes was evaluated. Historical demographic phenomena have genetic consequences that can be evaluated through analysis of population genetics. Population genetic approaches were applied to analyze population structure in six of the most numerically abundant and geographically widespread Streptomyces phylogroups from our culture collection. Streptomyces population structure varied at regional spatial scales, and allelic diversity correlated with geographic distance. In addition, allelic diversity and gene flow are partitioned by latitude. Finally, it was found that nucleotide diversity within phylogroups was negatively correlated with latitude. These results indicate that phylogroup diversification is constrained by dispersal limitation at regional spatial scales, and they are consistent with the hypothesis that historical demographic processes have influenced the contemporary biogeography of Streptomyces .}, journal={Environmental Microbiology}, author={Choudoir, M.J. and Doroghazi, Buckley, JR and D.H.}, year={2016}, pages={4931–4945} }
@article{choudoir_campbell_buckley_2012, title={Grappling with Proteus: population level approaches to understanding microbial diversity}, volume={3}, journal={Frontiers in microbiology}, publisher={Frontiers}, author={Choudoir, Mallory J and Campbell, Ashley N and Buckley, Daniel H}, year={2012}, pages={336} }
@article{raphael_choudoir_lúquez_fernández_maslanka_2010, title={Sequence diversity of genes encoding botulinum neurotoxin type F}, volume={76}, number={14}, journal={Applied and environmental microbiology}, publisher={Am Soc Microbiol}, author={Raphael, Brian H and Choudoir, Mallory J and Lúquez, Carolina and Fernández, Rafael and Maslanka, Susan E}, year={2010}, pages={4805–4812} }
@article{kramer_choudoir_wielgus_bhaskar_jiang_2009, title={Correlation between transcript abundance of the RB gene and the level of the RB-mediated late blight resistance in potato}, volume={22}, number={4}, journal={Molecular Plant-Microbe Interactions}, publisher={Am Phytopath Society}, author={Kramer, Lara C and Choudoir, Mallory J and Wielgus, Susan M and Bhaskar, Pudota B and Jiang, Jiming}, year={2009}, pages={447–455} }