Investigating GERMs: how genotype, environment, and rhizosphere microbiome interactions underlie heat response in maize and sorghum.

Plant responses to heat stress emerge from interactions among host genotype, environment, and the rhizosphere microbiome, yet most studies examine these components in isolation. We applied the Genotype × Environment × Rhizosphere Microbiomes (GERMs) framework to test how host-microbe coordination contributes to heat tolerance in cereal crops Zea mays and Sorghum bicolor. We analyzed maize and sorghum grown under optimal and heat-stressed conditions across contrasting soil treatments using integrated plant-microbial metatranscriptomics. Host and microbial gene expression profiles were jointly analyzed alongside microbiome composition and plant phenotypes and compared with amplicon-based profiling. Metatranscriptomics captured microbial community structure comparable to amplicon sequencing while providing enhanced functional and taxonomic resolution. Host genotype and temperature jointly shaped microbial functional profiles. Conserved plant orthologs across maize and sorghum were linked to microbial pathways, specifically microbial d-amino acid metabolism was associated with plant heat tolerance. These findings indicate the rhizosphere microbiome actively participates in plant heat stress responses through coordinated transcriptional interactions with the host. Integrating host and microbial transcriptomes reveals mechanistic insights into plant adaptation and establishes a framework for dissecting plant-microbiome interactions under environmental stress.