Seasonal Activities of the Phyllosphere Microbiome of Perennial Crops

Themes: Sustainability

Keywords: Biomass Analytics, Field Data, Genomics

Citation

Howe, A.Stopnisek, N., Dooley, S.K., Yang, F., Grady, K.L, Shade, A. Feb. 23, 2023. “Seasonal Activities of the Phyllosphere Microbiome of Perennial Crops.” Nature Communications 14, 1039. DOI: 10.1038/s41467-023-36515-y. 

Overview

2016 (green, circle) and 2017 (blue, triangle) switchgrass leaf transcript dynamics associated with terpene metabolism. Volatile terpenes engage in indirect and complex feedback with methane and nitrous oxide greenhouse gases. They also help protect leaf photosynthesis against short episodes of high temperature.

Understanding the interactions between plants and microorganisms can inform microbiome management to enhance crop productivity and resilience to stress. Here, we apply a genome-centric approach to identify ecologically important leaf microbiome members on replicated plots of field-grown switchgrass and miscanthus, and to quantify their activities over two growing seasons for switchgrass. We use metagenome and metatranscriptome sequencing and curate 40 medium- and high-quality metagenome-assembled-genomes (MAGs). We find that classes represented by these MAGs (Actinomycetia, Alpha- and Gamma- Proteobacteria, and Bacteroidota) are active in the late season, and upregulate transcripts for short-chain dehydrogenase, molybdopterin oxidoreductase, and polyketide cyclase. Stress-associated pathways are expressed for most MAGs, suggesting engagement with the host environment. We also detect seasonally activated biosynthetic pathways for terpenes and various non-ribosomal peptide pathways that are poorly annotated. Our findings support that leaf-associated bacterial populations are seasonally dynamic and responsive to host cues.

Data

JGI Genome Portal

NIH BioProject

Github Repository

Zenodo — Conditionally Rare Taxa scripts

Download (3.6MB) includes:

  • Metatranscriptomes and Metagenomes
  • Transcript Dynamics
  • MAGs Taxonomy
  • Key Gene Pathways