Seasonal activities of the phyllosphere microbiome of perennial crops

• Published in: Nature communications 2023-02, Vol.14 (1), p.1039-1039, Article 1039
• Main Authors: Howe, Adina, Stopnisek, Nejc, Dooley, Shane K., Yang, Fan, Grady, Keara L., Shade, Ashley
• Format: Article
• Language: English
• Subjects: 45/22; 45/23; 45/90; 45/91; 631/158/855; 631/326/2565/2134; 631/326/2565/2142; 631/449/2676; Agricultural sciences; Bacteria - genetics; BASIC BIOLOGICAL SCIENCES; Biodiversity and Ecology; Crop production; Crops; Ecology, environment; Environmental Sciences; Genomes; Growing season; Humanities and Social Sciences; Leaves; Life Sciences; Metagenome; Metagenomics; Microbial ecology; Microbiology and Parasitology; Microbiome; Microbiomes; Microbiota - genetics; Microorganisms; Molybdopterin; multidisciplinary; Oxidoreductase; Panicum; Panicum virgatum; Perennial crops; Phyllosphere; Plant symbiosis; Plants (botany); Productivity; Resilience; Science; Science (multidisciplinary); Seasons; Symbiosis; Terpenes
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-023-36515-y

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. Understanding the interactions between plants and microorganisms can inform microbiome management to enhance crop productivity and resilience to stress. Here, Howe et al. use metagenomics and metatranscriptomics to study changes in the leaf microbiome of perennial crops over two growing seasons.