@article{jenny_shapiro_davis_davies_pierce_meineke_2023, title={Herbarium specimens reveal herbivory patterns across the genus Cucurbita}, ISSN={["1537-2197"]}, DOI={10.1002/ajb2.16126}, abstractNote={AbstractPremiseQuantifying how closely related plant species differ in susceptibility to insect herbivory is important for understanding the variation in evolutionary pressures on plant functional traits. However, empirically measuring in situ variation in herbivory spanning the geographic range of a plant–insect complex is logistically difficult. Recently, new methods have been developed using herbarium specimens to investigate patterns in plant–insect symbioses across large geographic scales. Such investigations provide insights into how accelerated anthropogenic changes may impact plant–insect interactions that are of ecological or agricultural importance.MethodsHere, we analyze 274 pressed herbarium samples to investigate variation in herbivory damage in 13 different species of the economically important plant genus Cucurbita (Cucurbitaceae). This collection is composed of specimens of wild, undomesticated Cucurbita that were collected from across their native range, and Cucurbita cultivars collected from both within their native range and from locations where they have been introduced for agriculture in temperate North America.ResultsHerbivory is common on individuals of all Cucurbita species collected throughout their geographic ranges. However, estimates of herbivory varied considerably among individuals, with mesophytic species accruing more insect damage than xerophytic species, and wild specimens having more herbivory than specimens collected from human‐managed habitats.ConclusionsOur study suggests that long‐term evolutionary changes in habitat from xeric to mesic climates and wild to human‐managed habitats may mediate the levels of herbivory pressure from coevolved herbivores. Future investigations into the potential factors that contribute to herbivory may inform the management of domesticated crop plants and their insect herbivores.}, journal={AMERICAN JOURNAL OF BOTANY}, author={Jenny, Laura A. A. and Shapiro, Lori R. R. and Davis, Charles C. C. and Davies, T. Jonathan and Pierce, Naomi E. E. and Meineke, Emily}, year={2023}, month={Feb} }
 @article{landis_oliverio_mckenney_nichols_kfoury_biango-daniels_shell_madden_shapiro_sakunala_et al._2021, title={The diversity and function of sourdough starter microbiomes}, volume={10}, ISSN={2050-084X}, url={http://dx.doi.org/10.7554/eLife.61644}, DOI={10.7554/eLife.61644}, abstractNote={Humans have relied on sourdough starter microbial communities to make leavened bread for thousands of years, but only a small fraction of global sourdough biodiversity has been characterized. Working with a community-scientist network of bread bakers, we determined the microbial diversity of 500 sourdough starters from four continents. In sharp contrast with widespread assumptions, we found little evidence for biogeographic patterns in starter communities. Strong co-occurrence patterns observed in situ and recreated in vitro demonstrate that microbial interactions shape sourdough community structure. Variation in dough rise rates and aromas were largely explained by acetic acid bacteria, a mostly overlooked group of sourdough microbes. Our study reveals the extent of microbial diversity in an ancient fermented food across diverse cultural and geographic backgrounds.}, journal={eLife}, publisher={eLife Sciences Publications, Ltd}, author={Landis, Elizabeth A and Oliverio, Angela M and McKenney, Erin A and Nichols, Lauren M and Kfoury, Nicole and Biango-Daniels, Megan and Shell, Leonora K and Madden, Anne A and Shapiro, Lori and Sakunala, Shravya and et al.}, year={2021}, month={Jan} }
 @article{chase_zhaxybayeva_rocha_cosgrove_shapiro_2020, title={Global cellulose biomass, horizontal gene transfers and domain fusions drive microbial expansin evolution}, volume={226}, ISSN={["1469-8137"]}, DOI={10.1111/nph.16428}, abstractNote={Summary


Plants must rearrange the network of complex carbohydrates in their cell walls during normal growth and development. To accomplish this, all plants depend on proteins called expansins that nonenzymatically loosen noncovalent bonding between cellulose microfibrils.

Surprisingly, expansin genes have more recently been found in some bacteria and microbial eukaryotes, where their biological functions are largely unknown.

Here, we reconstruct a comprehensive phylogeny of microbial expansin genes. We find these genes in all eukaryotic microorganisms that have structural cell wall cellulose, suggesting expansins evolved in ancient marine microorganisms long before the evolution of land plants. We also find expansins in an unexpectedly high diversity of bacteria and fungi that do not have cellulosic cell walls. These bacteria and fungi inhabit varied ecological contexts, mirroring the diversity of terrestrial and aquatic niches where plant and/or algal cellulosic cell walls are present.

The microbial expansin phylogeny shows evidence of multiple horizontal gene transfer events within and between bacterial and eukaryotic microbial lineages, which may in part underlie their unusually broad phylogenetic distribution. Overall, expansins are unexpectedly widespread in bacteria and eukaryotes, and the contribution of these genes to microbial ecological interactions with plants and algae has probbaly been underappreciated.

}, number={3}, journal={NEW PHYTOLOGIST}, author={Chase, William R. and Zhaxybayeva, Olga and Rocha, Jorge and Cosgrove, Daniel J. and Shapiro, Lori R.}, year={2020}, month={May}, pages={921–938} }
 @article{shapiro_paulson_arnold_scully_zhaxybayeva_pierce_rocha_klepac-ceraj_holton_kolter_2018, title={An Introduced Crop Plant Is Driving Diversification of the Virulent Bacterial Pathogen Erwinia tracheiphila}, volume={9}, ISSN={["2150-7511"]}, DOI={10.1128/mBio.01307-18}, abstractNote={
            Erwinia tracheiphila
            is a virulent phytopathogen that infects two genera of cucurbit crop plants,
            Cucurbita
            spp. (pumpkin and squash) and
            Cucumis
            spp. (muskmelon and cucumber). One of the unusual ecological traits of this pathogen is that it is limited to temperate eastern North America. Here, we complete the first large-scale sequencing of an
            E. tracheiphila
            isolate collection. From phylogenomic, comparative genomic, and empirical analyses, we find that introduced
            Cucumis
            spp. crop plants are driving the diversification of
            E. tracheiphila
            into multiple lineages. Together, the results from this study show that locally unique biotic (plant population) and abiotic (climate) conditions can drive the evolutionary trajectories of locally endemic pathogens in unexpected ways.
          }, number={5}, journal={MBIO}, author={Shapiro, Lori R. and Paulson, Joseph N. and Arnold, Brian J. and Scully, Erin D. and Zhaxybayeva, Olga and Pierce, Naomi E. and Rocha, Jorge and Klepac-Ceraj, Vanja and Holton, Kristina and Kolter, Roberto}, year={2018} }
 @article{andrade-dominguez_kolte_shapiro_2018, title={Complete Genome Sequence of EtG, the First Phage Sequenced from Erwinia tracheiphila}, volume={6}, ISSN={["2169-8287"]}, DOI={10.1128/genomeA.00127-18}, abstractNote={ABSTRACT
          
            Erwinia tracheiphila
            is the causal agent of bacterial wilt of cucurbits. Here, we report the genome sequence of the temperate phage EtG, which was isolated from an
            E. tracheiphila
            -infected cucumber plant. Phage EtG has a linear 30,413-bp double-stranded DNA genome with cohesive ends and 45 predicted open reading frames.
          }, number={8}, journal={GENOME ANNOUNCEMENTS}, author={Andrade-Dominguez, Andres and Kolte, Roberto and Shapiro, Lori R.}, year={2018}, month={Feb} }
 @article{shapiro_andrade_scully_rocha_paulson_kolter_2018, title={Draft Genome Sequence of an Erwinia tracheiphila Isolate from an Infected Muskmelon (Cucumis melo)}, volume={7}, ISSN={["2576-098X"]}, DOI={10.1128/MRA.01058-18}, abstractNote={
            Erwinia tracheiphila
            is a bacterial plant pathogen emerging in eastern North America. To aid in understanding genetic variation within
            E. tracheiphila
            , here we sequence the first reference genome of an infected muskmelon (
            Cucumis melo
            ).
          }, number={17}, journal={MICROBIOLOGY RESOURCE ANNOUNCEMENTS}, author={Shapiro, Lori R. and Andrade, Andres and Scully, Erin D. and Rocha, Jorge and Paulson, Joseph N. and Kolter, Roberto}, year={2018}, month={Nov} }
 @article{mauck_chesnais_shapiro_2018, title={Evolutionary Determinants of Host and Vector Manipulation by Plant Viruses}, volume={101}, ISSN={["0065-3527"]}, DOI={10.1016/bs.aivir.2018.02.007}, abstractNote={Plant viruses possess adaptations for facilitating acquisition, retention, and inoculation by vectors. Until recently, it was hypothesized that these adaptations are limited to virus proteins that enable virions to bind to vector mouthparts or invade their internal tissues. However, increasing evidence suggests that viruses can also manipulate host plant phenotypes and vector behaviors in ways that enhance their own transmission. Manipulation of vector–host interactions occurs through virus effects on host cues that mediate vector orientation, feeding, and dispersal behaviors, and thereby, the probability of virus transmission. Effects on host phenotypes vary by pathosystem but show a remarkable degree of convergence among unrelated viruses whose transmission is favored by the same vector behaviors. Convergence based on transmission mechanism, rather than phylogeny, supports the hypothesis that virus effects are adaptive and not just by-products of infection. Based on this, it has been proposed that viruses manipulate hosts through multifunctional proteins that facilitate exploitation of host resources and elicitation of specific changes in host phenotypes. But this proposition is rarely discussed in the context of the numerous constraints on virus evolution imposed by molecular and environmental factors, which figure prominently in research on virus–host interactions not dealing with host manipulation. To explore the implications of this oversight, we synthesized available literature to identify patterns in virus effects among pathogens with shared transmission mechanisms and discussed the results of this synthesis in the context of molecular and environmental constraints on virus evolution, limitations of existing studies, and prospects for future research.}, journal={ENVIRONMENTAL VIROLOGY AND VIRUS ECOLOGY}, author={Mauck, Kerry E. and Chesnais, Quentin and Shapiro, Lori R.}, year={2018}, pages={189–250} }
 @article{haney_wiesmann_shapiro_melnyk_lucy r. o'sullivan_khorasani_xiao_han_bush_carrillo_et al._2018, title={Rhizosphere-associated Pseudomonas induce systemic resistance to herbivores at the cost of susceptibility to bacterial pathogens}, volume={27}, ISSN={["1365-294X"]}, DOI={10.1111/mec.14400}, abstractNote={AbstractPlant‐associated soil microbes are important mediators of plant defence responses to diverse above‐ground pathogen and insect challengers. For example, closely related strains of beneficial rhizosphere Pseudomonas spp. can induce systemic resistance (ISR), systemic susceptibility (ISS) or neither against the bacterial foliar pathogen Pseudomonas syringae pv. tomato DC3000 (Pto DC3000). Using a model system composed of root‐associated Pseudomonas spp. strains, the foliar pathogen Pto DC3000 and the herbivore Trichoplusia ni (cabbage looper), we found that rhizosphere‐associated Pseudomonas spp. that induce either ISS and ISR against Pto DC3000 all increased resistance to herbivory by T. ni. We found that resistance to T. ni and resistance to Pto DC3000 are quantitative metrics of the jasmonic acid (JA)/salicylic acid (SA) trade‐off and distinct strains of rhizosphere‐associated Pseudomonas spp. have distinct effects on the JA/SA trade‐off. Using genetic analysis and transcriptional profiling, we provide evidence that treatment of Arabidopsis with Pseudomonas sp. CH267, which induces ISS against bacterial pathogens, tips the JA/SA trade‐off towards JA‐dependent defences against herbivores at the cost of a subset of SA‐mediated defences against bacterial pathogens. In contrast, treatment of Arabidopsis with the ISR strain Pseudomonas sp. WCS417 disrupts JA/SA antagonism and simultaneously primes plants for both JA‐ and SA‐mediated defences. Our findings show that ISS against the bacterial foliar pathogens triggered by Pseudomonas sp. CH267, which is a seemingly deleterious phenotype, may in fact be an adaptive consequence of increased resistance to herbivory. Our work shows that pleiotropic effects of microbiome modulation of plant defences are important to consider when using microbes to modify plant traits in agriculture.}, number={8}, journal={MOLECULAR ECOLOGY}, author={Haney, Cara H. and Wiesmann, Christina L. and Shapiro, Lori R. and Melnyk, Ryan A. and Lucy R. O'Sullivan and Khorasani, Sophie and Xiao, Li and Han, Jiatong and Bush, Jenifer and Carrillo, Juli and et al.}, year={2018}, month={Apr}, pages={1833–1847} }