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Modeling bacterial interactions uncovers the importance of outliers in the coastal lignin-degrading consortium

Author

Listed:
  • Qiannan Peng

    (Shandong University)

  • Cheng Zhao

    (Chinese Academy of Agricultural Sciences)

  • Xiaopeng Wang

    (Ningbo University)

  • Kelin Cheng

    (Chinese Academy of Agricultural Sciences)

  • Congcong Wang

    (Chinese Academy of Agricultural Sciences)

  • Xihui Xu

    (Ministry of Agriculture and Rural Affairs)

  • Lu Lin

    (Shandong University
    Shandong University)

Abstract

Lignin, as the abundant carbon polymer, is essential for carbon cycle and biorefinery. Microorganisms interact to form communities for lignin biodegradation, yet it is a challenge to understand such complex interactions. Here, we develop a coastal lignin-degrading bacterial consortium (LD), through “top-down” enrichment. Sequencing and physiological analyses reveal that LD is dominated by the lignin degrader Pluralibacter gergoviae (>98%), with additional rare non-degraders. Interestingly, LD, cultured in lignin-MB medium, significantly enhances cell growth and lignin degradation as compared to P. gergoviae alone, implying a role of additional outliers. Using genome-scale metabolic models, metabolic profiling and culture experiments, modeling of inter-species interactions between P. gergoviae, Vibrio alginolyticus, Aeromonas hydrophila and Shewanella putrefaciens, unravels cross-feeding of amino acids, organic acids and alcohols between the degrader and non-degraders. Furthermore, the sub-population ratio is essential to enforce the synergy. Our study highlights the unrecognized role of outliers in lignin degradation.

Suggested Citation

  • Qiannan Peng & Cheng Zhao & Xiaopeng Wang & Kelin Cheng & Congcong Wang & Xihui Xu & Lu Lin, 2025. "Modeling bacterial interactions uncovers the importance of outliers in the coastal lignin-degrading consortium," Nature Communications, Nature, vol. 16(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-56012-8
    DOI: 10.1038/s41467-025-56012-8
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