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Bacterial genome size and gene functional diversity negatively correlate with taxonomic diversity along a pH gradient

Author

Listed:
  • Cong Wang

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Qing-Yi Yu

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Niu-Niu Ji

    (Chinese Academy of Sciences
    University of Illinois Urbana-Champaign)

  • Yong Zheng

    (Chinese Academy of Sciences
    Fujian Normal University)

  • John W. Taylor

    (University of California)

  • Liang-Dong Guo

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Cheng Gao

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

Abstract

Bacterial gene repertoires reflect adaptive strategies, contribute to ecosystem functioning and are limited by genome size. However, gene functional diversity does not necessarily correlate with taxonomic diversity because average genome size may vary by community. Here, we analyse gene functional diversity (by shotgun metagenomics) and taxonomic diversity (by 16S rRNA gene amplicon sequencing) to investigate soil bacterial communities along a natural pH gradient in 12 tropical, subtropical, and temperate forests. We find that bacterial average genome size and gene functional diversity decrease, whereas taxonomic diversity increases, as soil pH rises from acid to neutral; as a result, bacterial taxonomic and functional diversity are negatively correlated. The gene repertoire of acid-adapted oligotrophs is enriched in functions of signal transduction, cell motility, secretion system, and degradation of complex compounds, while that of neutral pH-adapted copiotrophs is enriched in functions of energy metabolism and membrane transport. Our results indicate that a mismatch between taxonomic and functional diversity can arise when environmental factors (such as pH) select for adaptive strategies that affect genome size distributions.

Suggested Citation

  • Cong Wang & Qing-Yi Yu & Niu-Niu Ji & Yong Zheng & John W. Taylor & Liang-Dong Guo & Cheng Gao, 2023. "Bacterial genome size and gene functional diversity negatively correlate with taxonomic diversity along a pH gradient," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-43297-w
    DOI: 10.1038/s41467-023-43297-w
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    2. Ernest D. Osburn & Steven G. McBride & Mohammad Bahram & Michael S. Strickland, 2024. "Global patterns in the growth potential of soil bacterial communities," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
    3. Zhenghu Zhou & Chuankuan Wang & Xinyu Cha & Tao Zhou & Xuesen Pang & Fazhu Zhao & Xinhui Han & Gaihe Yang & Gehong Wei & Chengjie Ren, 2024. "The biogeography of soil microbiome potential growth rates," Nature Communications, Nature, vol. 15(1), pages 1-9, December.

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