Disentangling plant- and environment-mediated drivers of active rhizosphere bacterial community dynamics during short-term drought
This work is a preprint
Bandopadhay, S., X Li, AW Bowsher, RL Last and A Shade. 2023. Disentangling plant- and environment- mediated drivers of active rhizosphere bacterial community dynamics during short-term drought. bioRXiv. V1. https://doi.org/10.1101/2023.06.06.543716
Raw sequence data are also deposited to NCBI Sequence Read Archive under BioProject number PRJNA862978
Mitigating the effects of climate stress on crops is important for global food security. The microbiome associated with plant roots, henceforth, the rhizobiome, can harbor beneficial microbes that alleviate impacts of stress. However, the factors influencing the recruitment of the rhizobiome during stress are not clear. We conducted an experiment to understand bacterial rhizobiome responses to short-term drought for two crop species: switchgrass and common bean. We used 16S rRNA and rRNA gene sequencing to investigate the impact of drought severity on active rhizobiome recruitment. We included planted and unplanted conditions to further distinguish the environment- versus plant-mediated outcomes for the rhizobiome. Though each crop had a distinct rhizobiome, for each there were differences in the active microbiome structure between drought and watered, and between planted and unplanted treatments. Overall, the microbiome dynamics were similar across the two crops despite their different community structures. However, in bean, the presence of a plant more strongly explained the microbiome variation (17%) than in switchgrass (3%), with a significant effect of drought only observed for the bean microbiome. The lack of an observed interaction between planted and drought factors in switchgrass suggests a relatively more stable microbiome associated to switchgrass than to bean. Switchgrass microbiome stability was in spite of strong differences in the rhizosphere metabolite profiles between planted and unplanted treatments. Specifically, saponins and terpenes were enriched in droughted, planted switchgrass soils. We conclude that microbiome benefits to resist short-term drought are crop-specific, with the possibility of decoupling of exudation and microbiome responses as we observed in switchgrass. We propose bacterial taxa that uniquely associated with common bean during drought that could be further tested for directed manipulation of microbiome during short-term drought
This work was supported by the National Science Foundation Award Number MCB 1817377 to AS, by the Great Lakes Bioenergy Research Center, U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under Award Number DE-SC0018409, and by the National Science Foundation Long-term Ecological Research Program (DEB 1832042) at the Kellogg Biological Station. AS acknowledges support from the USDA National Institute of Food and Agriculture and Michigan State University AgBioResearch.