Long-read nanopore sequencing reveals genotype-dependent microbiome shifts and host-microbe interactions in the barley rhizosphere

Background Barley ( Hordeum vulgare L.) provides a suitable model for studying domestication-driven plant-microbiome interactions. Although wild, landrace, and modern genotypes host distinct rhizosphere communities, the extent to which roots and microbes reciprocally influence each other remains unclear. Here, we applied an integrated multi-omics approach combining long-read metagenomics, root transcriptomics, and plant genomics to understand genotype-specific host-microbiome coordination. Results Oxford Nanopore whole metagenome sequencing (WMS) revealed clear genotype-dependent shifts in rhizosphere communities across seasons. Functional profiling showed a conserved metabolic backbone including amino acid metabolism, energy production, and secondary metabolite biosynthesis accompanied by genotype-specific differences in carbohydrate metabolism and transport-associated pathways. Genome-resolved analysis through metagenome-assembled genomes (MAGs) further detailed the taxonomic and functional architecture of key rhizosphere lineages. Root transcriptomics identified extensive differential expression linked to microbial perception, signaling, defense, and metabolic reprogramming. Integrating host and microbiome data revealed coordinated molecular responses, indicating that barley genotypes not only shape microbial assembly but also program their transcriptional activity in response to microbial cues. Conclusions These findings demonstrate that domestication has shaped a bidirectional interaction network in which barley genotypes and their rhizosphere microbiomes jointly modulate microbial community structure and host transcriptional regulation. The coordinated exchange provides new insights into the evolutionary tuning of plant-microbiome relationships and highlights opportunities for microbiome-informed crop improvement.