Modeling bacterial interactions uncovers the importance of outliers in the coastal lignin-degrading consortium
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),...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-01-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-56012-8 |
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| _version_ | 1832594604683165696 |
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| author | Qiannan Peng Cheng Zhao Xiaopeng Wang Kelin Cheng Congcong Wang Xihui Xu Lu Lin |
| author_facet | Qiannan Peng Cheng Zhao Xiaopeng Wang Kelin Cheng Congcong Wang Xihui Xu Lu Lin |
| author_sort | Qiannan Peng |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-205c1ce37961453288f2e9f6851d65b7 |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-205c1ce37961453288f2e9f6851d65b72025-01-19T12:30:05ZengNature PortfolioNature Communications2041-17232025-01-0116111310.1038/s41467-025-56012-8Modeling bacterial interactions uncovers the importance of outliers in the coastal lignin-degrading consortiumQiannan Peng0Cheng Zhao1Xiaopeng Wang2Kelin Cheng3Congcong Wang4Xihui Xu5Lu Lin6Institute of Marine Science and Technology, Shandong UniversityShenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesKey Laboratory of Aquacultral Biotechnology, Chinese Ministry of Education, Ningbo UniversityShenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesDepartment of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural AffairsInstitute of Marine Science and Technology, Shandong UniversityAbstract 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.https://doi.org/10.1038/s41467-025-56012-8 |
| spellingShingle | Qiannan Peng Cheng Zhao Xiaopeng Wang Kelin Cheng Congcong Wang Xihui Xu Lu Lin Modeling bacterial interactions uncovers the importance of outliers in the coastal lignin-degrading consortium Nature Communications |
| title | Modeling bacterial interactions uncovers the importance of outliers in the coastal lignin-degrading consortium |
| title_full | Modeling bacterial interactions uncovers the importance of outliers in the coastal lignin-degrading consortium |
| title_fullStr | Modeling bacterial interactions uncovers the importance of outliers in the coastal lignin-degrading consortium |
| title_full_unstemmed | Modeling bacterial interactions uncovers the importance of outliers in the coastal lignin-degrading consortium |
| title_short | Modeling bacterial interactions uncovers the importance of outliers in the coastal lignin-degrading consortium |
| title_sort | modeling bacterial interactions uncovers the importance of outliers in the coastal lignin degrading consortium |
| url | https://doi.org/10.1038/s41467-025-56012-8 |
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