Effects of Drought Stress on the Panicum hallii Microbiome Over a Growth Cycle

Forecasted increases in drought events resulting from climate change pose a serious threat to bioenergy crop yields, and improving the resilience of crops against water stress is essential to bioenergy development. Many plants exhibit a conserved drought response that is partially mediated by their associated microbiomes. Panicum hallii, a close relative of the promising bioenergy crop switchgrass, is a model organism for this grass due to its genetic tractability and short generation time. Nevertheless, little is known regarding the effects of drought on its associated microbiome. A comprehensive analysis of bacterial and archaeal microbiomes of drought-exposed P. hallii combining 16S rRNA amplicon and shotgun metagenomic data supports a drought response similar to that observed in other crops and offers new insights. Over the course of one growth cycle, exposure of P. hallii to drought led to a decrease in bacterial diversity in the rhizosphere-associated microbiome, corresponding with a decrease in Proteobacteria (Pseudomonadota) and Bacteroidota, and an increase in Actinobacteriota (Actinomycetota). Genome-resolved metagenomic analysis further revealed an enrichment in Patescibacteria and specific Bacteroidota under drought. Functional analysis linked the changes in community structure with increased capacities for complex carbohydrate metabolism, molecular salvaging, chemotaxis, and antioxidant accumulation. By confirming that drought stress effects similar changes to the P. hallii rhizosphere microbiome as observed in switchgrass and other plants, we reinforce the strength of P. hallii as a model organism for crop improvement studies, and emphasize the value of a dual amplicon and shotgun-based analysis for a comprehensive interpretation of community composition.