1. Ecology

Engineering multifunctional rhizosphere probiotics using consortia of Bacillus amyloliquefaciens transposon insertion mutants

  1. Jingxuan Li
  2. Chunlan Yang
  3. Alexandre Jousset
  4. Keming Yang
  5. Xiaofang Wang
  6. Zhihui Xu
  7. Tianjie Yang
  8. Xinlan Mei
  9. Zengtao Zhong
  10. Yangchun Xu
  11. Qirong Shen
  12. Ville-Petri Friman  Is a corresponding author
  13. Zhong Wei  Is a corresponding author
  1. Nanjing Agricultural University, China
  2. University of Helsinki, Finland
https://doi.org/10.7554/eLife.90726
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Cite this article
  1. Jingxuan Li
  2. Chunlan Yang
  3. Alexandre Jousset
  4. Keming Yang
  5. Xiaofang Wang
  6. Zhihui Xu
  7. Tianjie Yang
  8. Xinlan Mei
  9. Zengtao Zhong
  10. Yangchun Xu
  11. Qirong Shen
  12. Ville-Petri Friman
  13. Zhong Wei
(2023)
Engineering multifunctional rhizosphere probiotics using consortia of Bacillus amyloliquefaciens transposon insertion mutants
eLife 12:e90726.
https://doi.org/10.7554/eLife.90726
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Abstract

While bacterial diversity is beneficial for the functioning of rhizosphere microbiomes, multi-species bioinoculants often fail to promote plant growth. One potential reason for this is that competition between different species of inoculated consortia members creates conflicts for their survival and functioning. To circumvent this, we used transposon insertion mutagenesis to increase the functional diversity within Bacillus amyloliquefaciens bacterial species and tested if we could improve plant growth-promotion by assembling consortia of highly clonal but phenotypically dissimilar mutants. While most insertion mutations were harmful, some significantly improved B. amyloliquefaciens plant growth-promotion traits relative to the wild-type strain. Eight phenotypically distinct mutants were selected to test if their functioning could be improved by applying them as multifunctional consortia. We found that B. amyloliquefaciens consortium richness correlated positively with plant root colonization and protection from Ralstonia solanacearum phytopathogenic bacterium. Crucially, 8-mutant consortium consisting of phenotypically dissimilar mutants performed better than randomly assembled 8-mutant consortia, suggesting that improvements were likely driven by consortia multifunctionality instead of consortia richness. Together, our results suggest that increasing intra-species phenotypic diversity could be an effective way to improve probiotic consortium functioning and plant growth-promotion in agricultural systems.

Data availability

All data generated or analysed during this study are included in the manuscript and supporting file; Source Data files have been provided in Source data 1

Article and author information

Author details

  1. Jingxuan Li

    Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
    Competing interests
    The authors declare that no competing interests exist.

  2. Chunlan Yang

    Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
    Competing interests
    The authors declare that no competing interests exist.

  3. Alexandre Jousset

    Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
    Competing interests
    The authors declare that no competing interests exist.

  4. Keming Yang

    Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
    Competing interests
    The authors declare that no competing interests exist.

  5. Xiaofang Wang

    Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
    Competing interests
    The authors declare that no competing interests exist.

  6. Zhihui Xu

    Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3987-8836

  7. Tianjie Yang

    Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
    Competing interests
    The authors declare that no competing interests exist.

  8. Xinlan Mei

    Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
    Competing interests
    The authors declare that no competing interests exist.

  9. Zengtao Zhong

    Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
    Competing interests
    The authors declare that no competing interests exist.

  10. Yangchun Xu

    Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
    Competing interests
    The authors declare that no competing interests exist.

  11. Qirong Shen

    Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
    Competing interests
    The authors declare that no competing interests exist.

  12. Ville-Petri Friman

    Department of Microbiology, University of Helsinki, Helsinki, Finland
    For correspondence
    ville-petri.friman@helsinki.fi
    Competing interests
    The authors declare that no competing interests exist.

  13. Zhong Wei

    Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
    For correspondence
    weizhong@njau.edu.cn
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7967-4897

Funding

National Key Research and Development Program of China (2021YFD1900100)

  • Zhong Wei

Royal Society Research Grants (CHL\R1\180031)

  • Ville-Petri Friman

Strategic Priorities Fund Plant Bacterial Diseases programme (BB/T010606/1)

  • Ville-Petri Friman

National Key Research and Development Program of China (2022YFF1001804)

  • Xiaofang Wang

National Key Research and Development Program of China (2022YFD1500202)

  • Tianjie Yang

National Natural Science Foundation of China (42325704)

  • Zhong Wei

National Natural Science Foundation of China (42090064)

  • Qirong Shen

National Natural Science Foundation of China (41922053)

  • Zhong Wei

National Natural Science Foundation of China (31972504)

  • Yangchun Xu

Fundamental Research Funds for the Central Universities (KYT2023001)

  • Zhong Wei

Royal Society Research Grants (RSG\R1\180213)

  • Ville-Petri Friman

These funders supported study design, data collection and interpretation, and the decision to submit the work for publication.

Copyright

© 2023, Li et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Jingxuan Li
  2. Chunlan Yang
  3. Alexandre Jousset
  4. Keming Yang
  5. Xiaofang Wang
  6. Zhihui Xu
  7. Tianjie Yang
  8. Xinlan Mei
  9. Zengtao Zhong
  10. Yangchun Xu
  11. Qirong Shen
  12. Ville-Petri Friman
  13. Zhong Wei
(2023)
Engineering multifunctional rhizosphere probiotics using consortia of Bacillus amyloliquefaciens transposon insertion mutants
eLife 12:e90726.
https://doi.org/10.7554/eLife.90726

Share this article

https://doi.org/10.7554/eLife.90726

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