Plants, as sessile organisms, cannot escape environmental stress, but evidence suggests their adaptation is aided by their close association with soil microbes. These associations are increasingly important under climate change, but also may enable us to cultivate non-food crops, such as biofuels, on marginal lands. These areas often experience low nutrient availability and/or periods of water stress—factors which have been previously shown to drive dramatic shifts in microbial communities. However, the molecular mechanisms responsible for these shifts are largely unknown. To explore microbial traits associated with drought stress, we employed 16S amplicon sequencing, genome-resolved metagenomics, and comparative genomics to the rhizosphere of the biofuel crop, Sorghum bicolor. We also explore the underlying ecological forces shaping rhizosphere assembly (both composition and function) across the growing season using a null-based assembly model.
Results/Conclusions
Our analysis of 16S amplicons, metagenome assembled contigs, and metagenome-assembled genomes (MAGs) revealed that the sorghum rhizosphere is dominated by Proteobacteria and Actinobacteria. We found that overall microbial diversity dramatically decreased midway through the growing season regardless of treatment. This decrease in alpha diversity coincided with an increase in Actinobacterial taxa, which nearly doubled under drought. Shotgun metagenomic data revealed that these drought-induced shifts in taxonomy correlated with shifts in community-wide functional capacity. We found that drought enriched for several genes related to carbohydrate, secondary metabolite, and amino acid transport and metabolism which agree with the small number of existing studies on the sorghum rhizosphere. Comparative analysis of over 60 unique MAGs from these samples showed that this enrichment was specific to select Actinobacteria and Proteobacteria with the capacity for complex sugar breakdown and oxidative stress responses. Our assembly analysis confirmed that while early assembly of the rhizosphere is stochastic, later assembly of select plant-beneficial functions is deterministic (especially under drought). Overall, our results suggest that under drought stress, sorghum can recruit beneficial bacteria to their rhizosphere and that microbial assembly plays a critical role in plant resilience.
