Host genetic by environment interactions in crop and wild plant microbiomes

Briana K. Whitaker, Mycotoxin Prevention & Applied Microbiology, USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Peoria, IL, Briana K. Whitaker, Qing Chai, Natalie S. Christian, Keith Clay and Heather L. Reynolds, Biology, Indiana University, Bloomington, IN, Briana K. Whitaker and Christine V. Hawkes, Plant and Microbial Biology, North Carolina State University, Raleigh, NC, Natalie S. Christian, Biology, University of Louisville, Louisville, KY, Keith Clay, Ecology and Evolutionary Biology, Tulane University, New Orleans, LA

Background/Question/Methods
The path to implementation of microbiome tools in agricultural and wild plant community settings will require an understanding of how microbiota both sort and function across plant genetic types (i.e., species, varieties) and also how that varies with environmental context. Our current work extends the traditional GxE approach to GxExM to examine the effects of host genetic type (G) and environment (E) on microbiome structure (M). Using three experiments, we manipulated host genetic type 1) within a single common garden and 2) across three environments in a reciprocal transplant design. 3) Lastly, we compared environmental and host trait drivers of a single crop species’ spanning several ecoregions from North Carolina. The common garden experiment consisted of 19 plant species from the Asteraceae family, representing three subfamilies and 17 genera. The reciprocal transplant experiment included three Midwestern sites representing the historic home for three varieties of Panicum virgatum (switchgrass), a native biofuel and foraging crop. For the NC experiment, we used generalized dissimilarity modeling to rank the geographic, abiotic, and biotic drivers of switchgrass mycobiomes from across four sites. Our work combines both culture-independent and culture-dependent approaches from across wild and agricultural host species.
Results/Conclusions
Overall, our studies provided contrasting results for genetic by environmental drivers of foliar mycobiome structure. At the spatial scale of a single common garden (field length 650m), we found that foliar mycobiomes were structured by field plot location and host species, but that phylogenetic distance between hosts was not a strong predictor of fungal community dissimilarity. By contrast, in the switchgrass reciprocal transplant experiment performed at a regional scale (site distances 350km), we did not find that foliar mycobiomes were significantly structured by host variety within a single plant species, however they were strongly structured by environment (42% variation explained). For the NC switchgrass (site distances 360km), generalized dissimilarity models explained 70.1% of the variation in foliar mycobiomes. Geographic space explained the most, with the largest community changes occurring over short distances (<120km), then plateauing. Interestingly, small to intermediate changes in plant height also drove increasing dissimilarity in the foliar mycobiome. Among abiotic drivers, foliar mycobiome dissimilarity increased linearly with increasing soil moisture dissimilarity, but for humidity only increased with the largest differences among samples. Our research demonstrates that the scale of sampling determines where and when environmental versus host genetic drivers are most important in the foliar mycobiome.