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

Qiannan Peng, Cheng Zhao, Xiaopeng Wang, Kelin Cheng, Congcong Wang, Xihui Xu and Lu Lin ()
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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

Nature Communications, 2025, vol. 16, issue 1, 1-13

Abstract: 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.

Date: 2025
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DOI: 10.1038/s41467-025-56012-8

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