Life on the leaf: Seasonal activities of the phyllosphere microbiome of perennial crops

Abstract

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 <15.5% contaminated, >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.

Diversity and pathobiology of an ilarvirus unexpectedly detected in diverse host plants and in global sequencing data

“…Based on the results of this study, it is thus hypothesized that contamination by SnIV1infected pollen might be one of the reasons (if not the most probable) for the identification of SnIV1 in different sequencing datasets. Detection of SnIV1 sequences in 39 datasets of leaf surface or epiphyte RNA sequencing from two Poaceae species (Panicum and Miscanthus) (Howe et al 2022) fits well with such a hypothesis of surface contamination by SnIV1. Thus, it is postulated that infected nearby crop or non-crop plants (most probably Solanaceae) could be a source of SnIV1-infected pollen that could make its way, passively or assisted by arthropod vectors, to neighboring plants.…”

The search for Schizosaccharomyces fission yeasts in environmental metatranscriptomes

“…In the next group, 'soil', 99% of the reads came from the BioProject PRJNA621679, which surveyed soil microbial communities from a watershed in Colorado, USA. Similarly, over 99% of the reads from the 'trees/plants' group were from the Bio-Projects PRJNA572120, PRJNA571995 and PRJNA572130, which all surveyed switchgrass phyllosphere microbial communities in Michigan, USA (Howe et al, 2021).…”