Environment and plant genetics shape barley rhizosphere microbiome structure across contrasting locations

AbstractSoil microorganisms are crucial for plant survival and productivity, but factors governing rhizosphere recruitment across diverse regions remain unclear. This study investigated the rhizosphere microbiome of barley, using elite cultivars across seven location-year trials to evaluate the effects of environmental factors and crop genotype on bacterial and fungal community composition. Three locations were in the US northern Great Plains, and Hawaii was used as a contrasting environment. A greenhouse reciprocal transplant study determined the relative contributions of soil physicochemical factors and soil inoculum to rhizosphere community structure. Using 16S and ITS2 amplicon sequencing, the study characterized bacterial and fungal microbiomes and assessed the contribution of environment, soil chemistry, and barley genetics to microbial community assembly. In locations within the adapted range of barley, Actinobacteriota was the dominant phylum, while Proteobacteria was dominant in Hawaii. Variance partitioning showed that 73% of bacterial and 80% of fungal genera were associated with location-year effects while 53% of bacterial and 36% of fungal genera were responsive to soil factors. Enrichment analysis found 21.6% of bacterial and 51.4% of fungal ASVs were unique to specific barley genetic subpopulations. Results from the reciprocal transplant study validated field observations by demonstrating that 20.7% of the variation in community structure was explained by soil while 18.2% was explained by inoculum source. These findings demonstrate that environmental variation is the dominant constraint on rhizosphere community composition but within these constraints, barley genotype drives recruitment of distinct bacterial and fungal taxa. ImportanceThese findings underscore the complex interplay between plant genotype, environment, and microbial community assembly, providing insights into how barley recruits distinct microbial communities in the rhizosphere across different environments. These insights have the potential to be leveraged for management and plant breeding strategies to optimize plant-microbe interactions for enhancing agricultural sustainability.