Harnessing deep-sea cold seep microbiomes for reductive dehalogenation: from culturomics and genomics insights

Deep-sea cold seeps harbor a rich and diverse repertoire of reductive dehalogenase-encoding genes (rdhA), yet their potential for reductive dehalogenation remains largely unexplored. In this study, we investigated the microbial debromination of 2,4,6-tribromophenol (TBP) in cold seep sediment microcosms. By optimizing culture conditions with different nutrient sources and substrate concentrations, we established a highly efficient debrominating microbial consortium capable of completely degrading 50 μM TBP within 72 hours. Metagenomic analysis revealed Bin3, a novel bacterium affiliated with Peptococcaceae, as a key dehalogenator harboring multiple rdhA genes. Microbial community analysis demonstrated that nutrient availability significantly influenced community composition but had no impact on alpha diversity. Through degradation kinetics, co-occurrence network analysis, normalized stochasticity ratio analysis, and metagenomic quantification, we found that supplementing lactate along with 0.05% yeast extract significantly enhanced TBP degradation efficiency and facilitated the targeted enrichment of key dehalogenating microbes (with relative abundance increasing from <1% to 32%). Comparative genomic analysis indicated that Bin3 has undergone species-specific adaptations, including gene families for pili formation, osmolyte transport, and motility, potentially enhancing its competitiveness in deep-sea cold seep environments. This study advances our understanding of deep-sea dehalogenating microbiomes and their adaptation to extreme environments, providing insights into their ecological significance and potential applications in pollutant bioremediation.