Genome-centric analyses of seasonal phyllosphere microbiome activities in perennial crops. phyllosphere metagenome

Plants and microbes form beneficial associations. It is expected that understanding these interactions will allow for microbiome management to enhance crop productivity and resilience to stress. Here, we apply a genome-centric approach to identify key leaf microbiome members on field-grown switchgrass and miscanthus and quantify their activities for switchgrass. We integrate metagenome and metatranscriptome sequencing from 192 leaf samples collected over key time points in crop phenology. We curated 41 metagenome-assembled-genomes (MAGs), and conservatively focus analysis on read recruitment to medium and high-quality MAGs that were 50% complete. Populations represented by these MAGs were actively transcribing genes and exhibited seasonal dynamics in key functions, including pyruvate metabolism and stress response. Notably, we detected enrichment in transcripts annotated to non-mevalonate isoprene biosynthesis in the late season, prior to and during host senescence, concurrent with when plants are expected to decrease their isoprene biosynthesis.