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Green manure-induced shifts in nematode communities associated with soil bacterial and fungal biomes

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Abstract

Green manures are widely used to enhance soil health and suppress plant-parasitic nematodes, and their effects on the broader soil food web have been studied. Beyond direct suppression, the role of green manures in supporting and sustaining soil food webs has attracted increasing attention. In this study, we evaluated the use of DNA sequencing to identify various nematode genera and their microbial associates in a field trial using oat (Avena sativa) and hairy vetch (Vicia villosa) as green manures. Nematode index analysis revealed that the oat treatment promoted a structured nematode community. Furthermore, the nematode community structure observed in the oat treatment was linked to specific bacterial and fungal genera. Several beneficial fungi were identified, indicating that oats, used as a green manure, actively enhanced the microbiome. Our results showed that enriching the micro-food web through organic fertilizers can help in the detection of beneficial microorganisms, with the nematode index serving as a potential indicator.

Data availability

Sequence data that support the findings of this study have been deposited in the National Center for Biotechnology Information with the BioSample IDs: SAMN48745011, SAMN48745012, and SAMN48745013.

Code availability

Not applicable.

Materials availability

Not applicable.

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Acknowledgements

We thank the former students in our laboratory (Tanioka K., Sawada H., Senoo Y., Nezu Y., Ueda K., Hayashi D., Matsumoto R., Iwamoto N., Tanaka T., Hashimoto T., Hashimoto M., Onishi F., Sato A., Watanabe R. and Yoshimoto T.) for their dedicated efforts in both fieldwork and laboratory work, particularly in handling soil samples. We are grateful to Dr. Wang, KH. at the University of Hawaii for critical reading of this manuscript. This research was supported by a grant (2021-2022) from the Research Institute for Food and Agriculture, Ryukoku University.

Funding

This research was supported by a grant (2021–2022) from the Research Institute for Food and Agriculture, Ryukoku University.

Author information

Authors and Affiliations

  1. Department of Life Sciences, Faculty of Agriculture, Ryukoku University, 1-5 Yokotani Seta Oe-cho, Otsu, 520-2194, Shiga, Japan

    Atsuya Sudo & Erika Asamizu

  2. Department of Agricultural Sciences, Faculty of Agriculture, Ryukoku University, 1-5 Yokotani Seta Oe-cho, Otsu, 520-2194, Shiga, Japan

    Daisuke Yoshimura & Hiroyuki Daimon

  3. Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-857, Miyagi, Japan

    Shusei Sato

Authors

  1. Atsuya Sudo
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  2. Daisuke Yoshimura
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  3. Hiroyuki Daimon
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  4. Shusei Sato
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  5. Erika Asamizu
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Contributions

E.A. conceived the conception of this study, performed analyses, wrote the manuscript. A.S. and D.Y. performed field practices, acquired data. H.D. and S.S. designed the methodology and interpreted the results. All authors read and approved the manuscript.

Corresponding author

Correspondence to
Erika Asamizu.

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Sudo, A., Yoshimura, D., Daimon, H. et al. Green manure-induced shifts in nematode communities associated with soil bacterial and fungal biomes.
Sci Rep (2025). https://doi.org/10.1038/s41598-025-31442-y

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  • DOI: https://doi.org/10.1038/s41598-025-31442-y

Keywords

  • Green manure
  • Nematode index
  • Oat (Avena sativa)
  • rRNA amplicon sequence
  • Soil bacteria
  • Soil fungi

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