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

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 and quantify their activities on field-grown switchgrass and miscanthus. We integrate metagenome and metatranscriptome sequencing from 237 leaf samples collected over key time points in crop phenology. We curate metagenome-assembled-genomes (MAGs), and conservatively focus analysis on the highest quality MAGs that were 70% complete, and detected in a minimum of 10% of samples for each crop. Populations represented by these MAGs were actively transcribing genes, and exhibited seasonal dynamics in key functions, including pyruvate metabolism, threonine, homoserine and serine biosynthesis, and stress response. Notably, we detected enrichment in transcripts annotated to nonmavalonate isoprene biosynthesis in the late season, prior to and during host senescence, concurrent with when plants are expected to decrease their isoprene biosynthesis. We also detected groups of MAGs that had coherent transcript dynamics in thioredoxin reductase, which suggests a response to reactive oxygen species, potentially released by plant hosts experiencing abiotic stress. Overall, this study overcame laboratory and bioinformatic challenges associated with field-based leaf metatranscriptomes analysis to direct to some of the key activities of phyllosphere bacteria. These activities collectively support that leaf-associated bacterial populations can be seasonally dynamic, responsive to host cues, and, likely, interactively engage in feedbacks with the plant.