ORIGINAL RESEARCH article
Front. Microbiol.
Sec. Extreme Microbiology
This article is part of the Research TopicMicrobial Bioremediation of Oil Contaminated SitesView all articles
Top-Down Enrichment of Oil-Degrading Microbial Consortia Reveals Functional Streamlining and Novel Degraders
Provisionally accepted
- 1CNPC research institute of safety and environment technology Co Ltd, Beijing, China
- 2China University of Geosciences college of materials science and engineering, Beijing, China
- 3Chinese Academy of Sciences Research Centre for Eco-Environmental Sciences, Beijing, China
- 4Nanjing Tech University College of Biotechnology and Pharmaceutical Engineering, Nanjing, China
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Top-down microbial enrichment is a reliable approach for understanding and designing microbiomes for crude oil remediation. Environmental variables serve as valuable determinants for selecting desired microbiomes with superior performance. However, the linkages between selection methods and the structure and function of desired microbiomes remain unclear. This study integrated substrate concentration gradients, cultivation patterns, and microbial metagenomics to investigate how selection pressures shape top-down enriched crude oil-degrading consortia. The top-down process led to a significant reduction in phylogenetic diversity but a notable increase in the potential for xenobiotic degradation and metabolic. The final consortia, GT4, achieved a 55.72% degradation rate of crude oil at an initial concentration of 5 g/L within 7 days. Metagenomic analysis identified Microbacterium, Mesorhizobium and Ralstonia as dominant genera harboring key enzymes for the degradation of alkane, cyclohexane and aromatic compounds. Co-occurrence network analysis revealed Mesorhizobium as a keystone genus, showing positive associations with multiple diazotrophic bacteria and hydrocarbon-degrading bacteria. Nine bacterial strains were isolated from the consortium. Among them, Microbacterium sp. WS3 and Cellulosimicrobium sp. WS9 exhibited high degradation efficiencies (57.85% and 58.60%, respectively). To the best of our knowledge, this study provides the first experimental evidence for crude oil degradation by Paracandidimonas and Caulobacter, with degradation rates of 51.19% and 40.90%, respectively. These findings highlight the effectiveness of top-down enrichment strategy in generating functionally streamlined consortia and uncover novel oil-degrading microbes with potential for bioremediation applications.
Keywords: top-down enrichment strategy, Microbial Consortia, Petroleum hydrocarbon, bioremediation, correlation network
Received: 02 Jul 2025; Accepted: 18 Nov 2025.
Copyright: © 2025 Wu, Du, Zheng, Li, Song, Yan, Ma, Xu and Li. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Jufeng Li, lijufeng69@163.com
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