Impact of drought severity on assembly of rhizosphere microbial communities in two plant species

Mitigating the effects of climate-related 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 a greenhouse experiment aimed to understand rhizobiome member responses to drought across two plant species (switchgrass, common bean), the impact of drought severity on rhizobiome recruitment, and the direct versus plant-mediated consequences of drought on the rhizobiome. We collected field rhizosphere soils from switchgrass and common bean, divided them into planted and unplanted treatments, and exposed them to a gradient of drought severity over time. 16S-V4 rRNA gene amplicon sequencing of the active community revealed differences in the rhizobiome composition of bean and switchgrass. Within each crop, there were differences in rhizobiome community structure and rhizosphere soil metabolite profiles between drought and well-watered, and planted and unplanted treatments. Actinobacteria and Alphaproteobacteria were enriched with drought severity in bean. Furano-diterpenes were enriched in drought-treated switchgrass roots and in drought-treated planted soils. In bean, active communities recruited during drought trended towards increasing dissimilarity to pre-drought condition over time; whereas, in switchgrass, they trended towards a stabilizing effect. Major differences in physiology, ecology, development and root morphology between bean and switchgrass could largely explain why switchgrass could be less reliant on beneficial support from the plant microbiome, whereas common bean could potentially benefit from directed manipulation of microbiome during short-term drought.