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Seasonal activities of the phyllosphere microbiome of perennial crops

Author

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  • Adina Howe

    (Iowa State University
    Iowa State University
    Center for Advanced Bioenergy and Bioproducts Innovation)

  • Nejc Stopnisek

    (The Great Lakes Bioenergy Research Center, Michigan State University
    Michigan State University
    Michigan State University)

  • Shane K. Dooley

    (Iowa State University
    Iowa State University)

  • Fan Yang

    (Iowa State University)

  • Keara L. Grady

    (The Great Lakes Bioenergy Research Center, Michigan State University
    Michigan State University)

  • Ashley Shade

    (The Great Lakes Bioenergy Research Center, Michigan State University
    Michigan State University
    Michigan State University
    Michigan State University)

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.

Suggested Citation

  • Adina Howe & Nejc Stopnisek & Shane K. Dooley & Fan Yang & Keara L. Grady & Ashley Shade, 2023. "Seasonal activities of the phyllosphere microbiome of perennial crops," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-36515-y
    DOI: 10.1038/s41467-023-36515-y
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    References listed on IDEAS

    as
    1. Tao Chen & Kinya Nomura & Xiaolin Wang & Reza Sohrabi & Jin Xu & Lingya Yao & Bradley C. Paasch & Li Ma & James Kremer & Yuti Cheng & Li Zhang & Nian Wang & Ertao Wang & Xiu-Fang Xin & Sheng Yang He, 2020. "A plant genetic network for preventing dysbiosis in the phyllosphere," Nature, Nature, vol. 580(7805), pages 653-657, April.
    2. Keara L. Grady & Jackson W. Sorensen & Nejc Stopnisek & John Guittar & Ashley Shade, 2019. "Assembly and seasonality of core phyllosphere microbiota on perennial biofuel crops," Nature Communications, Nature, vol. 10(1), pages 1-10, December.
    3. Stephen Nayfach & Zhou Jason Shi & Rekha Seshadri & Katherine S. Pollard & Nikos C. Kyrpides, 2019. "New insights from uncultivated genomes of the global human gut microbiome," Nature, Nature, vol. 568(7753), pages 505-510, April.
    4. Davide Bulgarelli & Matthias Rott & Klaus Schlaeppi & Emiel Ver Loren van Themaat & Nahal Ahmadinejad & Federica Assenza & Philipp Rauf & Bruno Huettel & Richard Reinhardt & Elmon Schmelzer & Joerg Pe, 2012. "Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota," Nature, Nature, vol. 488(7409), pages 91-95, August.
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    Cited by:

    1. Xiaolong Lyu & Ping Li & Liang Jin & Feng Yang & Boas Pucker & Chenhao Wang & Linye Liu & Meng Zhao & Lu Shi & Yutong Zhang & Qinrong Yang & Kuangtian Xu & Xiao Li & Zhongyuan Hu & Jinghua Yang & Jing, 2024. "Tracing the evolutionary and genetic footprints of atmospheric tillandsioids transition from land to air," Nature Communications, Nature, vol. 15(1), pages 1-23, December.
    2. Sun, Xiaolei & Yang, Xiaosong & Hu, Zhengyi & Liu, Fulai & Xie, Zijian & Li, Songyan & Wang, Guoxi & Li, Meng & Sun, Zheng & Bol, Roland, 2024. "Biochar effects on soil nitrogen retention, leaching and yield of perennial citron daylily under three irrigation regimes," Agricultural Water Management, Elsevier, vol. 296(C).

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