@article{whitaker_giauque_timmerman_birk_hawkes_2021, title={Local Plants, Not Soils, Are the Primary Source of Foliar Fungal Community Assembly in a C4 Grass}, volume={8}, ISSN={["1432-184X"]}, url={https://doi.org/10.1007/s00248-021-01836-2}, DOI={10.1007/s00248-021-01836-2}, abstractNote={Microbial communities, like their macro-organismal counterparts, assemble from multiple source populations and by processes acting at multiple spatial scales. However, the relative importance of different sources to the plant microbiome and the spatial scale at which assembly occurs remains debated. In this study, we analyzed how source contributions to the foliar fungal microbiome of a C4 grass differed between locally abundant plants and soils across an abiotic gradient at different spatial scales. Specifically, we used source-sink analysis to assess the likelihood that fungi in leaves from Panicum hallii came from three putative sources: two plant functional groups (C4 grasses and dicots) and soil. We expected that physiologically similar C4 grasses would be more important sources to P. hallii than dicots. We tested this at ten sites in central Texas spanning a steep precipitation gradient. We also examined source contributions at three spatial scales: individual sites (local), local plus adjacent sites (regional), or all sites (gradient-wide). We found that plants were substantially more important sources than soils, but contributions from the two plant functional groups were similar. Plant contributions overall declined and unexplained variation increased as mean annual precipitation increased. This source-sink analysis, combined with partitioning of beta-diversity into nestedness and turnover components, indicated high dispersal limitation and/or strong environmental filtering. Overall, our results suggest that the source-sink dynamics of foliar fungi are primarily local, that foliar fungi spread from plant-to-plant, and that the abiotic environment may affect fungal community sourcing both directly and via changes to host plant communities.}, journal={MICROBIAL ECOLOGY}, publisher={Springer Science and Business Media LLC}, author={Whitaker, Briana K. and Giauque, Hannah and Timmerman, Corey and Birk, Nicolas and Hawkes, Christine V}, year={2021}, month={Aug} }
 @misc{hestrin_lee_whitaker_pett-ridge_2021, title={The Switchgrass Microbiome: A Review of Structure, Function, and Taxonomic Distribution}, volume={5}, ISSN={["2471-2906"]}, DOI={10.1094/PBIOMES-04-20-0029-FI}, abstractNote={ 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. }, number={1}, journal={PHYTOBIOMES JOURNAL}, author={Hestrin, Rachel and Lee, Marissa R. and Whitaker, Briana K. and Pett-Ridge, Jennifer}, year={2021}, pages={14–28} }
 @article{whitaker_bakker_2019, title={Bacterial endophyte antagonism toward a fungal pathogen in vitro does not predict protection in live plant tissue}, volume={95}, ISSN={["1574-6941"]}, DOI={10.1093/femsec/fiy237}, abstractNote={&NA; Endophytic microbiota are potentially useful plant symbionts for conferring biotic or abiotic stress tolerance. Common approaches to identify putatively beneficial functions of endophytes rely on lab‐based assays. However, if functional roles are context‐dependent, lab‐based assessments may not accurately represent functional outcomes under variable field conditions. Our objective was to test whether antagonism by bacterial endophytes towards a plant pathogen in vitro would be predictive of disease outcomes in live plant tissue. We challenged Fusarium graminearum, a fungal pathogen of wheat, against bacterial endophytes isolated from wheat plants in two in vitro assays. A subset of isolates, with in vitro antagonistic activity ranging from weak to strong, was selected for testing in live plant tissue (detached wheat heads). Assays were performed under different temperature and/or carbon dioxide conditions to test environmental dependency in the plant‐endophyte‐pathogen interactions. The two in vitro assays produced contrasting measures of pathogen inhibition, and neither predicted pathogen load reductions in the detached wheat head assay. Additionally, outcomes were environment‐dependent and varied among bacterial isolates. Thus, endophytic impacts on plant performance cannot be easily inferred from simplified in vitro assays, and environmental gradients should be incorporated into future testing of microbial interactions in plant hosts. &NA; Graphical Abstract Figure. Investigators tested whether lab‐based measurements accurately predicted bacterial antagonism of a wheat fungal pathogen in plants using a series of increasingly realistic experimental assays.}, number={2}, journal={FEMS MICROBIOLOGY ECOLOGY}, author={Whitaker, Briana K. and Bakker, Matthew G.}, year={2019}, month={Feb} }
 @article{laforest-lapointe_whitaker_2019, title={Decrypting the phyllosphere microbiota: progress and challenges}, volume={106}, ISSN={["1537-2197"]}, DOI={10.1002/ajb2.1229}, abstractNote={As global change accelerates, terrestrial ecosystems will face an increasing rate of abiotic (e.g., extreme events, temperature increases, droughts) and biotic perturbations (e.g., invasive species, emerging diseases), that will alter inter-kingdom community assembly and species interactions. The majority of global change research has focused on the interactions among macroorganisms and their influence on ecosystem productivity, diversity, and resilience, leaving much to be known about the impact of perturbations on microscopic life. Importantly, research in the past two decades has shown that microbial communities can play a critical role in driving plant-host fitness and productivity and, consequently, ecosystem dynamics. However, to date the majority of plant–microbe research has focused on belowground (i.e., rhizosphere) versus aboveground (i.e., the phyllosphere) microbiota. In this essay, we provide an overview of current knowledge in plant phyllosphere microbiota research and discuss the challenges that must be tackled to move beyond domain-specific, static, and correlational perspectives and better integrate the microscopic world of leaves with questions of ecosystem functioning. The phyllosphere (i.e., aerial photosynthetic tissues of plants) represents one of the most extensive habitats in the world, estimated to measure up to 4 × 108 km2 in area globally (Morris et al., 2002). This habitat is oligotrophic and experiences rapid fluctuations in physicochemical conditions (i.e., temperature, humidity, radiation; Lindow and Brandl, 2003). The phyllosphere, one of our planet's most diverse ecosystems (Lindow and Leveau, 2002), is colonized by bacteria, archaea, viruses, protists, and fungi that live on (i.e., epiphytic) and inside (i.e., endophytic) aboveground plant tissues. Leaf-colonizing bacteria have been shown to influence plant-host fitness through several mechanisms, including by (1) contributing to plant defense against pathogens and abiotic stressors (Fitzpatrick et al., 2018), (2) influencing plant ecosystem functions (Laforest-Lapointe et al., 2017), (3) degrading environmental pollutants (Zheng et al., 2018), and (4) synthesizing phytohormones such as indole-3-acetic acid (Glickmann et al., 1998) and cytokinins (Brandl and Lindow, 1998) that contribute to plant productivity. To date, most research on plant–microbe interactions has focused on a single microbial kingdom, generally bacteria, due to the traditional focus within the discipline of microbiology and prohibitive costs associated with sequencing multiple genetic markers (but see our discussion of all-inclusive metagenomic techniques below). However, phyllosphere fungal colonizers, like their bacterial counterparts, are incredibly diverse (U'Ren et al., 2012), can mediate host health (Christian et al., 2017), and produce metabolites with important consequences for host physiology (e.g., Strobel et al., 2004). Yet phyllosphere fungi and bacteria are still rarely studied in tandem. Similarly, the roles of bacteriophages (Koskella and Parr, 2015) and mycoviruses as symbionts in the phyllosphere, as well as plant viruses themselves, remain to be better integrated into studies of community dynamics. At the ecosystem level, phyllosphere microbiota have been suggested to contribute considerably to both carbon cycling, by exploiting plant-produced methanol (Jo et al., 2015), and nitrogen cycling, by fixing nitrogen in situ (Furnkranz et al., 2008). Recent studies have also suggested that phyllosphere diversity is positively linked to plant productivity (Laforest-Lapointe et al., 2017) and that phyllosphere microbiota can potentially mediate plant species coexistence via conspecific negative-density dependence (Whitaker et al., 2017). Taken together, these findings suggest an underappreciated role for phyllosphere microbiota in driving ecosystem function and plant community dynamics. Before the work of Yang et al. (2001) with denaturating gradient gel electrophoresis (DGGE) with 16S rDNA primers, research in phyllosphere microbial ecology was limited to culture-dependent methods that underestimated microbial population sizes and biodiversity. However, improvements in culture-independent sequencing technologies have greatly enhanced our assessments of phyllosphere community diversity and structure (see Vorholt et al., 2017 for a perspective). Although high-throughput sequencing techniques have allowed for unprecedented detection of nonculturable communities across many microbial systems (Martin et al., 2011), sequencing short marker genes (i.e., 16S, 18S, ITS) does not distinguish between inactive (i.e., dormant) and active microbes. Therefore, the structure of microbial communities obtained through this technology may reflect the past (inactive), actual (active), and potential future (dormant) members combined. Similarly, short marker genes provide very little information on the functional profiles of microbial communities. Taxonomic classification using short marker genes is still limited in resolution to the level of genus, yet many recent studies have revealed that host–microbe and microbe–microbe functional outcomes occur at the level of intraspecific variants (Costea et al., 2017). Research groups have recently started using whole-genome shotgun sequencing and metagenomics to provide a more accurate and “all inclusive” portrayal of the phyllosphere taxa and function (Finkel et al., 2016). Pairing culture-independent and culture-dependent approaches with whole-genome sequencing will be crucial to gain a better understanding gained from short marker genes and improve the description of leaf microbiota currently possible in phyllosphere research (Fig. 1). Culture-dependent techniques (i.e., phenotypic and genotypic fingerprinting analyses) can provide a mechanistic understanding of the feedbacks between microbes on host and ecosystem functions, allowing researchers to go beyond correlational studies. Similarly, incorporating technologies such as multilocus sequencing techniques on cultured microbiota may offer researchers the ability to identify population-genetic and functional differences among isolates across broad geographic regions (Barge et al., Oregon State University, personal communication). Similarly, metagenomic and metaproteomic analyses of phyllosphere microbial communities (Muller et al., 2016) offer researchers the potential to combine observational (i.e., “What's there?”) with functional knowledge (i.e., “What are they doing?”) for all microbiota, and not just one group (i.e., bacteria only or fungi only). We now know that the assembly of microbial communities is determined by a combination of intrinsic (e.g., intraspecific competition, autoregulation, density-dependence) and extrinsic (e.g., host genetics, abiotic conditions, dispersal) factors, which are modulated by stochastic and deterministic processes (Vorholt, 2012; Vorholt et al., 2017). Thus, plant–microbe studies should be designed to provide a more integrated and mechanistic understanding of microbial communities by linking the taxonomic structure (one dimension) to functional profiles (two dimensions), in the context of spatial (three dimensions) and temporal heterogeneities (four dimensions) (Shade et al., 2018). Our increased ability to characterize these microbial communities must now be balanced by a greater emphasis on their mechanistic roles in driving ecosystem functions such as plant resilience to global change stressors (e.g., extreme events, urban pressures, invasive species) and plant resistance to pathogens. Research on phyllosphere microbiota has great potential for applications in the domains of commercial plant productivity (e.g., agriculture, viticulture, forestry), biofuels, and even human health. Yet, experimental studies are required to improve our understanding of the dynamics at play. In view of our current knowledge, future studies should aim to (1) provide a more inclusive portrait of inter-kingdom microbial interactions and their feedbacks on host and ecosystem functions, (2) improve the taxonomic and functional resolution of high-throughput DNA sequencing data by including culture-dependent techniques and widening our library of complete microbial genomes, and (3) incorporate spatial and temporal drivers into the study of phyllosphere community assembly and diversity (Fig. 1). Future research on phyllosphere microbiota holds great promise to understand the challenges that global warming will place on terrestrial ecosystem functioning and may allow us to design reliable microbial tools (e.g., synthetic microbial communities) that will support the resilience of our world's plant ecosystems to abiotic stresses and pathogens. We thank the reviewers for providing very useful comments and advice that improved the quality of this article. We also thank Vincent Gaudet for the creation of the figure.}, number={2}, journal={AMERICAN JOURNAL OF BOTANY}, author={Laforest-Lapointe, Isabelle and Whitaker, Briana K.}, year={2019}, month={Feb}, pages={171–173} }
 @article{whitaker_reynolds_clay_2018, title={Foliar fungal endophyte communities are structured by environment but not host ecotype in Panicum virgatum (switchgrass)}, volume={99}, ISSN={["1939-9170"]}, DOI={10.1002/ecy.2543}, abstractNote={Abstract}, number={12}, journal={ECOLOGY}, author={Whitaker, Briana K. and Reynolds, Heather L. and Clay, Keith}, year={2018}, month={Dec}, pages={2703–2711} }