Evolutionary ecology of microbial populations inhabiting deep sea sediments associated with cold seeps

Xiyang Dong (), Yongyi Peng, Muhua Wang, Laura Woods, Wenxue Wu, Yong Wang, Xi Xiao, Jiwei Li, Kuntong Jia, Chris Greening, Zongze Shao () and Casey R. J. Hubert
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Xiyang Dong: Ministry of Natural Resources
Yongyi Peng: Ministry of Natural Resources
Muhua Wang: Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)
Laura Woods: Monash University
Wenxue Wu: Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)
Yong Wang: Tsinghua University
Xi Xiao: China Geological Survey
Jiwei Li: Chinese Academy of Sciences
Kuntong Jia: Sun Yat-Sen University
Chris Greening: Monash University
Zongze Shao: Ministry of Natural Resources
Casey R. J. Hubert: University of Calgary

Nature Communications, 2023, vol. 14, issue 1, 1-13

Abstract: Abstract Deep sea cold seep sediments host abundant and diverse microbial populations that significantly influence biogeochemical cycles. While numerous studies have revealed their community structure and functional capabilities, little is known about genetic heterogeneity within species. Here, we examine intraspecies diversity patterns of 39 abundant species identified in sediment layers down to 430 cm below the sea floor across six cold seep sites. These populations are grouped as aerobic methane-oxidizing bacteria, anaerobic methanotrophic archaea and sulfate-reducing bacteria. Different evolutionary trajectories are observed at the genomic level among these physiologically and phylogenetically diverse populations, with generally low rates of homologous recombination and strong purifying selection. Functional genes related to methane (pmoA and mcrA) and sulfate (dsrA) metabolisms are under strong purifying selection in most species investigated. These genes differ in evolutionary trajectories across phylogenetic clades but are functionally conserved across sites. Intrapopulation diversification of genomes and their mcrA and dsrA genes is depth-dependent and subject to different selection pressure throughout the sediment column redox zones at different sites. These results highlight the interplay between ecological processes and the evolution of key bacteria and archaea in deep sea cold seep extreme environments, shedding light on microbial adaptation in the subseafloor biosphere.

Date: 2023
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DOI: 10.1038/s41467-023-36877-3

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