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

Abstract

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 beta diversity (community composition) but had only a minor effect 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 specific adaptations through expansion of gene families involved in pili formation, cell motility, nutrient acquisition, and diverse metabolic pathways, 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.