Comparative metagenomics reveals the metabolic flexibility of coastal prokaryotic microbiomes contributing to lignin degradation
Abstract Coastal wetlands are rich in terrestrial organic carbon. Recent studies suggest that microbial consortia play a role in lignin degradation in coastal wetlands, where lignin turnover rates are likely underestimated. However, the metabolic potentials of these consortia remain elusive. This gr...
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2025-01-01
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| Series: | Biotechnology for Biofuels and Bioproducts |
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| Online Access: | https://doi.org/10.1186/s13068-025-02605-w |
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| author | Qiannan Peng Lu Lin |
| author_facet | Qiannan Peng Lu Lin |
| author_sort | Qiannan Peng |
| collection | DOAJ |
| description | Abstract Coastal wetlands are rich in terrestrial organic carbon. Recent studies suggest that microbial consortia play a role in lignin degradation in coastal wetlands, where lignin turnover rates are likely underestimated. However, the metabolic potentials of these consortia remain elusive. This greatly hinders our understanding of the global carbon cycle and the “bottom-up” design of synthetic consortia to enhance lignin conversion. Here, we developed two groups of lignin degrading consortia, L6 and L18, through the 6- and 18-month in situ lignin enrichments in the coastal East China Sea, respectively. Lignin degradation by L18 was 3.6-fold higher than L6. Using read-based analysis, 16S rRNA amplicon and metagenomic sequencing suggested that these consortia possessed varied taxonomic compositions, yet similar functional traits. Further comparative metagenomic analysis, based on metagenomic assembly, revealed that L18 harbored abundant metagenome-assembled genomes (MAGs) that encoded diverse and unique lignin degradation gene clusters (LDGCs). Importantly, anaerobic MAGs were significantly enriched in L18, highlighting the role of anaerobic lignin degradation. Furthermore, the generalist taxa, which possess metabolic flexibility, increased during the extended enrichment period, indicating the advantage of generalists in adapting to heterogenous resources. This study advances our understanding of the metabolic strategies of coastal prokaryotic consortia and lays a foundation for the design of synthetic communities for sustainable lignocellulose biorefining. |
| format | Article |
| id | doaj-art-645d97a9645d434fb0bb6763f34d12ca |
| institution | Kabale University |
| issn | 2731-3654 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
| record_format | Article |
| series | Biotechnology for Biofuels and Bioproducts |
| spelling | doaj-art-645d97a9645d434fb0bb6763f34d12ca2025-01-19T12:13:44ZengBMCBiotechnology for Biofuels and Bioproducts2731-36542025-01-0118111610.1186/s13068-025-02605-wComparative metagenomics reveals the metabolic flexibility of coastal prokaryotic microbiomes contributing to lignin degradationQiannan Peng0Lu Lin1Institute of Marine Science and Technology, Shandong UniversityInstitute of Marine Science and Technology, Shandong UniversityAbstract Coastal wetlands are rich in terrestrial organic carbon. Recent studies suggest that microbial consortia play a role in lignin degradation in coastal wetlands, where lignin turnover rates are likely underestimated. However, the metabolic potentials of these consortia remain elusive. This greatly hinders our understanding of the global carbon cycle and the “bottom-up” design of synthetic consortia to enhance lignin conversion. Here, we developed two groups of lignin degrading consortia, L6 and L18, through the 6- and 18-month in situ lignin enrichments in the coastal East China Sea, respectively. Lignin degradation by L18 was 3.6-fold higher than L6. Using read-based analysis, 16S rRNA amplicon and metagenomic sequencing suggested that these consortia possessed varied taxonomic compositions, yet similar functional traits. Further comparative metagenomic analysis, based on metagenomic assembly, revealed that L18 harbored abundant metagenome-assembled genomes (MAGs) that encoded diverse and unique lignin degradation gene clusters (LDGCs). Importantly, anaerobic MAGs were significantly enriched in L18, highlighting the role of anaerobic lignin degradation. Furthermore, the generalist taxa, which possess metabolic flexibility, increased during the extended enrichment period, indicating the advantage of generalists in adapting to heterogenous resources. This study advances our understanding of the metabolic strategies of coastal prokaryotic consortia and lays a foundation for the design of synthetic communities for sustainable lignocellulose biorefining.https://doi.org/10.1186/s13068-025-02605-wLignin degradationMetagenome-assembled genomesLignin degradation gene clustersProkaryotic consortiaCoastal wetlands |
| spellingShingle | Qiannan Peng Lu Lin Comparative metagenomics reveals the metabolic flexibility of coastal prokaryotic microbiomes contributing to lignin degradation Biotechnology for Biofuels and Bioproducts Lignin degradation Metagenome-assembled genomes Lignin degradation gene clusters Prokaryotic consortia Coastal wetlands |
| title | Comparative metagenomics reveals the metabolic flexibility of coastal prokaryotic microbiomes contributing to lignin degradation |
| title_full | Comparative metagenomics reveals the metabolic flexibility of coastal prokaryotic microbiomes contributing to lignin degradation |
| title_fullStr | Comparative metagenomics reveals the metabolic flexibility of coastal prokaryotic microbiomes contributing to lignin degradation |
| title_full_unstemmed | Comparative metagenomics reveals the metabolic flexibility of coastal prokaryotic microbiomes contributing to lignin degradation |
| title_short | Comparative metagenomics reveals the metabolic flexibility of coastal prokaryotic microbiomes contributing to lignin degradation |
| title_sort | comparative metagenomics reveals the metabolic flexibility of coastal prokaryotic microbiomes contributing to lignin degradation |
| topic | Lignin degradation Metagenome-assembled genomes Lignin degradation gene clusters Prokaryotic consortia Coastal wetlands |
| url | https://doi.org/10.1186/s13068-025-02605-w |
| work_keys_str_mv | AT qiannanpeng comparativemetagenomicsrevealsthemetabolicflexibilityofcoastalprokaryoticmicrobiomescontributingtolignindegradation AT lulin comparativemetagenomicsrevealsthemetabolicflexibilityofcoastalprokaryoticmicrobiomescontributingtolignindegradation |