ArticleNature communications2023
Evolutionary ecology of microbial populations inhabiting deep sea sediments associated with cold seeps.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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37 citing papers in PubMed, 61 citations in OpenAlex.
- Widespread horizontal transfer and strong selection enhance microbial adaptation in Antarctic soils.Nature communications · 2026Article
- Multi-omics and cultivation reveal laminarin-degrading PVC bacteria in the deep sea.Nature communications · 2026Article
- The patterns of microbial community distribution and co-occurrence in water columns and sediments of Haima cold seep.Microbiology spectrum · 2026Article
- Viral modulation of sulfur-oxidizing bacteria drives organic carbon sink formation during primary succession in deglaciating ecosystems.Nature communications · 2026Article
- Depth-associated selection and drift shape persistent microbial populations in Holocene lake sediments.mSystems · 2026Article
- Diversification in ANME-1 archaea is associated with the presence of highly variable genomic hotspots.Nature communications · 2026Article
- Microbial drivers of ammonium accumulation in Holocene sediments of the Pearl River Delta.Nature communications · 2026Article
- Carbon, nitrogen, and sulfur cycling unveil deep-sea microbial niches in the Atacama Trench.Nature communications · 2026Article
- Structure and Spatial Heterogeneity of Chemosynthesis-Based Deep-Sea Archaeal and Bacterial Communities in Western South Atlantic.Ecology and evolution · 2026Article
- Molecular Phylogeny of "Chemosensory Proteins" in Bacteria and Arthropods: CSP as an Extremely Ancient Gene.Journal of molecular evolution · 2026Article
- Phylogenetic assembly of methanogenesis regulates methane yield in food-waste anaerobic digestion.The ISME journal · 2026Article
- Host-linked virome assembly and turnover predict bacterial community structure in wastewater treatment systems.The ISME journal · 2026Article
- Co-occurrence of diverse defense systems shapes complex microbe-virus relationships in deep-sea cold seeps.Nature communications · 2026Article
- Surface sediment microbial communities remain viable, culturable, and metabolically active during sequential heating.Frontiers in microbiology · 2026Article
- Microbial population structure along the water columns and sediments in the Diamantina and Kermadec trenches.BMC biology · 2025Article
- Methane dynamics in gas chimneys linking geochemical and microbial methane cycling in the Ulleung basin.BMC microbiology · 2025Article
- Capturing the spatial structure of the benthic microbiome under an intensive aquaculture scenario in Chilean Patagonia.BMC microbiology · 2025Article
- Exploring the Biosynthetic Potential of Microorganisms from the South China Sea Cold Seep Using Culture-Dependent and Culture-Independent Approaches.Marine drugs · 2025Article
- Evidence of microbial reductive dehalogenation in deep-sea cold seeps and its implications for biogeochemical cycles.Microbiome · 2025Article
- Identification of key steps in the evolution of anaerobic methanotrophy inScience advances · 2025Article
Corrections and comments
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Authors and funding
12 authors at 8 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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