Seasonal activities of the phyllosphere microbiome of perennial crops

Adina Howe, Nejc Stopnisek, Shane K. Dooley, Fan Yang, Keara L. Grady and Ashley Shade ()
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Adina Howe: Iowa State University
Nejc Stopnisek: The Great Lakes Bioenergy Research Center, Michigan State University
Shane K. Dooley: Iowa State University
Fan Yang: Iowa State University
Keara L. Grady: The Great Lakes Bioenergy Research Center, Michigan State University
Ashley Shade: The Great Lakes Bioenergy Research Center, Michigan State University

Nature Communications, 2023, vol. 14, issue 1, 1-16

Abstract: Abstract 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.

Date: 2023
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DOI: 10.1038/s41467-023-36515-y

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