Microbially-mediated halogenation and dehalogenation cycling of organohalides in the ocean

Na Zhou, Qihao Li, Zhiwei Liang, Ke Yu, Chunfang Zhang, Huijuan Wang, Pengcheng Li, Zhili He and Shanquan Wang ()
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Na Zhou: Sun Yat-Sen University, Environmental Microbiomics Research Center, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Environmental Science and Engineering
Qihao Li: Sun Yat-Sen University, Environmental Microbiomics Research Center, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Environmental Science and Engineering
Zhiwei Liang: Sun Yat-Sen University, Environmental Microbiomics Research Center, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Environmental Science and Engineering
Ke Yu: Shenzhen Graduate School, School of Environment and Energy, Peking University
Chunfang Zhang: Zhejiang University, Institute of Marine Biology and Pharmacology, Ocean College
Huijuan Wang: Anhui Normal University, School of Geography and Tourism
Pengcheng Li: Great Bay University, Department of Mathematics, School of Sciences
Zhili He: Sun Yat-Sen University, Environmental Microbiomics Research Center, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Environmental Science and Engineering
Shanquan Wang: Sun Yat-Sen University, Environmental Microbiomics Research Center, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Environmental Science and Engineering

Nature Communications, 2025, vol. 16, issue 1, 1-15

Abstract: Abstract Microbially mediated organohalide cycling in the ocean has profound implications for global biogeochemical cycles and climate, but the geographic distribution and diversity of the halogenation-dehalogenation cycling microorganisms remain unknown. Here, we constructed an organohalide-cycling gene database (HaloCycDB) to explore the global atlas of halogenation-dehalogenation cycling microorganisms and genes from 1473 marine metagenomes. Strikingly, 6204 out of 15,252 metagenome-assembled genomes (MAGs) carry organohalide-cycling genes, of which 84.30% are dehalogenating populations. Microorganisms of Pseudomonadota with even spatial distribution dominate both halogenation and dehalogenation potentials in the ocean, in contrast to lineages of Asgardarchaeota and Thermoproteota solely mediating dehalogenation in the Northern hemisphere. Notably, 80.91% of reductive dehalogenase (RDase) genes and 91.35% of RDase-containing prokaryotes represent uncharacterized lineages, substantially expanding known dehalogenation diversity. Further integration of microbial cultivation, protein structure prediction, and molecular docking revealed four unique “microorganism-RDase-organohalide” patterns for marine dehalogenation and its coupling with carbon/sulfur cycles, being distinctively different from their terrestrial patterns. These results advance our understanding of microbial organohalide cycling by providing insights into the halogenation-dehalogenation microbiomes in the ocean.

Date: 2025
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DOI: 10.1038/s41467-025-65696-x

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