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Metagenomic-based discovery and comparison of the lignin degrading potential of microbiomes in aquatic and terrestrial ecosystems via the LCdb database.
- Source :
-
Molecular ecology resources [Mol Ecol Resour] 2024 Jul; Vol. 24 (5), pp. e13950. Date of Electronic Publication: 2024 Apr 03. - Publication Year :
- 2024
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Abstract
- Lignin, as an abundant organic carbon, plays a vital role in the global carbon cycle. However, our understanding of the global lignin-degrading microbiome remains elusive. The greatest barrier has been absence of a comprehensive and accurate functional gene database. Here, we first developed a curated functional gene database (LCdb) for metagenomic profiling of lignin degrading microbial consortia. Via the LCdb, we draw a clear picture describing the global biogeography of communities with lignin-degrading potential. They exhibit clear niche differentiation at the levels of taxonomy and functional traits. The terrestrial microbiomes showed the highest diversity, yet the lowest correlations. In particular, there were few correlations between genes involved in aerobic and anaerobic degradation pathways, showing a clear functional redundancy property. In contrast, enhanced correlations, especially closer inter-connections between anaerobic and aerobic groups, were observed in aquatic consortia in response to the lower diversity. Specifically, dypB and dypA, are widespread on Earth, indicating their essential roles in lignin depolymerization. Estuarine and marine consortia featured the laccase and mnsod genes, respectively. Notably, the roles of archaea in lignin degradation were revealed in marine ecosystems. Environmental factors strongly influenced functional traits, but weakly shaped taxonomic groups. Null mode analysis further verified that composition of functional traits was deterministic, while taxonomic composition was highly stochastic, demonstrating that the environment selects functional genes rather than taxonomic groups. Our study not only develops a useful tool to study lignin degrading microbial communities via metagenome sequencing but also advances our understanding of ecological traits of these global microbiomes.<br /> (© 2024 John Wiley & Sons Ltd.)
- Subjects :
- Archaea genetics
Archaea classification
Archaea metabolism
Bacteria classification
Bacteria genetics
Bacteria metabolism
Bacteria isolation & purification
Microbial Consortia genetics
Microbial Consortia physiology
Metagenome
Lignin metabolism
Microbiota genetics
Microbiota physiology
Metagenomics methods
Ecosystem
Subjects
Details
- Language :
- English
- ISSN :
- 1755-0998
- Volume :
- 24
- Issue :
- 5
- Database :
- MEDLINE
- Journal :
- Molecular ecology resources
- Publication Type :
- Academic Journal
- Accession number :
- 38567644
- Full Text :
- https://doi.org/10.1111/1755-0998.13950