@article{parnell_vintila_tang_wagner_kleiner_2023, title={Evaluation of ready-to-use freezer stocks of a synthetic microbial community for maize root colonization}, volume={12}, ISSN={["2165-0497"]}, url={https://doi.org/10.1128/spectrum.02401-23}, DOI={10.1128/spectrum.02401-23}, abstractNote={ABSTRACT Synthetic microbial communities (SynComs) are a valuable tool to study community assembly patterns, host–microbe interactions, and microbe–microbe interactions in a fully controllable setting. Constructing the SynCom inocula for plant–microbe experiments can be time-consuming and difficult because a large number of isolates with different medium requirements and growth rates are grown in parallel and mixed to appropriate titers. A potential workaround to assembling fresh SynCom inocula for every experiment could be to prepare and freeze SynComs on a large scale, creating ready-to-use inocula. The objective of this study was to compare the reproducibility, stability, and colonization ability of freshly prepared versus frozen SynCom inocula. We used a community of seven species known to colonize maize roots. The results from inoculation with the frozen SynCom were as consistent as those of standardized de novo construction of fresh SynCom. Our results indicate that creating frozen SynCom inocula for repeated use in experiments not only saves time but could also improve cross-experiment reproducibility. Although this approach was only validated with one SynCom, it demonstrates a principle that can be tested for improving approaches in constructing other SynComs. IMPORTANCE Synthetic communities (SynComs) are an invaluable tool to characterize and model plant–microbe interactions. Multimember SynComs approximate intricate real-world interactions between plants and their microbiome, but the complexity and time required for their construction increase enormously for each additional member added to the SynCom. Therefore, researchers who study a diversity of microbiomes using SynComs are looking for ways to simplify the use of SynComs. In this manuscript, we evaluate the feasibility of creating ready-to-use freezer stocks of a well-studied seven-member SynCom for maize roots. The frozen ready-to-use SynCom stocks work according to the principle of “just add buffer and apply to sterilized seeds or seedlings” and thus can save time applied in multiple days of laborious growing and combining of multiple microorganisms. We show that ready-to-use SynCom stocks provide comparable results to those of freshly constructed SynComs and thus allow for significant time savings when working with SynComs. Synthetic communities (SynComs) are an invaluable tool to characterize and model plant–microbe interactions. Multimember SynComs approximate intricate real-world interactions between plants and their microbiome, but the complexity and time required for their construction increase enormously for each additional member added to the SynCom. Therefore, researchers who study a diversity of microbiomes using SynComs are looking for ways to simplify the use of SynComs. In this manuscript, we evaluate the feasibility of creating ready-to-use freezer stocks of a well-studied seven-member SynCom for maize roots. The frozen ready-to-use SynCom stocks work according to the principle of “just add buffer and apply to sterilized seeds or seedlings” and thus can save time applied in multiple days of laborious growing and combining of multiple microorganisms. We show that ready-to-use SynCom stocks provide comparable results to those of freshly constructed SynComs and thus allow for significant time savings when working with SynComs.}, journal={MICROBIOLOGY SPECTRUM}, author={Parnell, J. Jacob and Vintila, Simina and Tang, Clara and Wagner, Maggie R. and Kleiner, Manuel}, editor={Hockett, Kevin LorenEditor}, year={2023}, month={Dec} }
 @article{wagner_tang_salvato_clouse_bartlett_vintila_phillips_sermons_hoffmann_balint-kurti_et al._2021, title={Microbe-dependent heterosis in maize}, volume={118}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/pnas.2021965118}, DOI={10.1073/pnas.2021965118}, abstractNote={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.}, number={30}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Wagner, Maggie R. and Tang, Clara and Salvato, Fernanda and Clouse, Kayla M. and Bartlett, Alexandria and Vintila, Simina and Phillips, Laura and Sermons, Shannon and Hoffmann, Mark and Balint-Kurti, Peter J. and et al.}, year={2021}, month={Jul} }
 @article{geml_wagner_2018, title={Out of sight, but no longer out of mind - towards an increased recognition of the role of soil microbes in plant speciation}, volume={217}, ISSN={["1469-8137"]}, DOI={10.1111/nph.14979}, abstractNote={This article is a Commentary on Osborne et al ., 217 : 1254–1266.}, number={3}, journal={NEW PHYTOLOGIST}, author={Geml, Jozsef and Wagner, Maggie R.}, year={2018}, month={Feb}, pages={965–967} }
 @article{anthony w. d'amato_orwig_foster_plotkin_schoonmaker_wagner_2017, title={Long-term structural and biomass dynamics of virgin Tsuga-canadensis-Pinus strobus forests after hurricane disturbance}, volume={98}, ISSN={["1939-9170"]}, DOI={10.1002/ecy.1684}, abstractNote={The development of old-growth forests in northeastern North America has largely been within the context of gap-scale disturbances given the rarity of stand-replacing disturbances. Using the 10-ha old-growth Harvard Tract and its associated 90-year history of measurements, including detailed surveys in 1989 and 2009, we document the long-term structural and biomass development of an old-growth Tsuga canadensis-Pinus strobus forest in southern New Hampshire, USA following a stand-replacing hurricane in 1938. Measurements of aboveground biomass pools were integrated with data from second- and old-growth T. canadensis forests to evaluate long-term patterns in biomass development following this disturbance. Ecosystem structure across the Tract prior to the hurricane exhibited a high degree of spatial heterogeneity with the greatest levels of live tree basal area (70-129 m2 /ha) on upper west-facing slopes where P. strobus was dominant and intermixed with T. canadensis. Live-tree biomass estimates for these stratified mixtures ranged from 159 to 503 Mg/ha at the localized, plot scale (100 m2 ) and averaged 367 Mg/ha across these portions of the landscape approaching the upper bounds for eastern forests. Live-tree biomass 71 years after the hurricane is more uniform and lower in magnitude, with T. canadensis currently the dominant overstory tree species throughout much of the landscape. Despite only one living P. strobus stem in the 2009 plots (and fewer than five stems known across the entire 10-ha area), the detrital legacy of this species is pronounced with localized accumulations of coarse woody debris exceeding 237.7-404.2 m3 /ha where this species once dominated the canopy. These patterns underscore the great sizes P. strobus attained in pre-European landscapes and its great decay resistance relative to its forest associates. Total aboveground biomass pools in this 71-year-old forest (255 Mg/ha) are comparable to those in modern old-growth ecosystems in the region that also lack abundant white pine. Results highlight the importance of disturbance legacies in affecting forest structural conditions over extended periods following stand-replacing events and underscore that post-disturbance salvage logging can alter ecosystem development for decades. Moreover, the dominant role of old-growth P. strobus in live and detrital biomass pools before and after the hurricane, respectively, demonstrate the disproportionate influence this species likely had on carbon storage at localized scales prior to the widespread, selective harvesting of large P. strobus across the region in the 18th and 19th centuries.}, number={3}, journal={ECOLOGY}, author={Anthony W. D'Amato and Orwig, David A. and Foster, David R. and Plotkin, Audrey Barker and Schoonmaker, Peter K. and Wagner, Maggie R.}, year={2017}, month={Mar}, pages={721–733} }
 @article{busby_soman_wagner_friesen_kremer_bennett_morsy_eisen_leach_dangl_2017, title={Research priorities for harnessing plant microbiomes in sustainable agriculture}, volume={15}, ISSN={["1545-7885"]}, DOI={10.1371/journal.pbio.2001793}, abstractNote={Feeding a growing world population amidst climate change requires optimizing the reliability, resource use, and environmental impacts of food production. One way to assist in achieving these goals is to integrate beneficial plant microbiomes—i.e., those enhancing plant growth, nutrient use efficiency, abiotic stress tolerance, and disease resistance—into agricultural production. This integration will require a large-scale effort among academic researchers, industry researchers, and farmers to understand and manage plant-microbiome interactions in the context of modern agricultural systems. Here, we identify priorities for research in this area: (1) develop model host–microbiome systems for crop plants and non-crop plants with associated microbial culture collections and reference genomes, (2) define core microbiomes and metagenomes in these model systems, (3) elucidate the rules of synthetic, functionally programmable microbiome assembly, (4) determine functional mechanisms of plant-microbiome interactions, and (5) characterize and refine plant genotype-by-environment-by-microbiome-by-management interactions. Meeting these goals should accelerate our ability to design and implement effective agricultural microbiome manipulations and management strategies, which, in turn, will pay dividends for both the consumers and producers of the world food supply.}, number={3}, journal={PLOS BIOLOGY}, author={Busby, Posy E. and Soman, Chinmay and Wagner, Maggie R. and Friesen, Maren L. and Kremer, James and Bennett, Alison and Morsy, Mustafa and Eisen, Jonathan A. and Leach, Jan E. and Dangl, Jeffery L.}, year={2017}, month={Mar} }
 @article{wagner_lundberg_rio_tringe_dangl_mitchell-olds_2016, title={Host genotype and age shape the leaf and root microbiomes of a wild perennial plant}, volume={7}, ISSN={["2041-1723"]}, DOI={10.1038/ncomms12151}, abstractNote={Abstract Bacteria living on and in leaves and roots influence many aspects of plant health, so the extent of a plant’s genetic control over its microbiota is of great interest to crop breeders and evolutionary biologists. Laboratory-based studies, because they poorly simulate true environmental heterogeneity, may misestimate or totally miss the influence of certain host genes on the microbiome. Here we report a large-scale field experiment to disentangle the effects of genotype, environment, age and year of harvest on bacterial communities associated with leaves and roots of Boechera stricta (Brassicaceae), a perennial wild mustard. Host genetic control of the microbiome is evident in leaves but not roots, and varies substantially among sites. Microbiome composition also shifts as plants age. Furthermore, a large proportion of leaf bacterial groups are shared with roots, suggesting inoculation from soil. Our results demonstrate how genotype-by-environment interactions contribute to the complexity of microbiome assembly in natural environments.}, journal={NATURE COMMUNICATIONS}, author={Wagner, Maggie R. and Lundberg, Derek S. and Rio, Tijana G. and Tringe, Susannah G. and Dangl, Jeffery L. and Mitchell-Olds, Thomas}, year={2016}, month={Jul} }