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PreprintCited by 4Bacteriophages and microbial interactionsMicrobial Community Ecology and PhysiologyPlant and Fungal Interactions Research

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Co-occurrence of diverse defense systems shapes complex microbe-virus relationships in deep-sea cold seeps

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Han, Yingchun, Liao, Jing, Li, Chengpeng, Xing, Fengmin, Peng, Jiaxue, Liu, Xinyue, Xie, Wentao, Wu, Fabai, Jian, Huahua, Cheng, Rui, Dong, Xiyang·2024·Nature Communications
DOI 10.1101/2024.09.26.614923PMC PMC12881386

Preprint — published as 10.1038/s41467-025-68174-6

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Abstract

Cold seeps host diverse microbes and viruses with numerous unexplored defense and anti-defense systems. Analysis of 3,813 microbial and 13,336 viral genomes from 191 metagenomes across 17 cold seep sites reveals extensive microbial defense repertoires, with over 60% representing candidate systems. Experimental validation confirms that several candidates protect against viral infection. These defense systems frequently co-occur, suggesting potential synergistic interactions, and are broadly distributed across sediments. In response, viruses have evolved diverse anti-defense genes, and the concurrent presence of multiple viral and microbial systems highlights intricate coevolution. Functionally critical lineages, such as anaerobic methanotrophic archaea, sulfate-reducing bacteria, and diazotrophs, appear to modify their defensive strategies under ecological and environmental pressures; for example, sulfate-reducing bacteria harbor multiple Gabija systems while corresponding viruses carry anti-Gabija genes, illustrating specific coevolutionary adaptations. Overall, these findings underscore the critical role of virus-microbe interactions in shaping microbial metabolic functions and environmental adaptation in deep-sea ecosystems.

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Metadata

Authors
Han, Y., Liao, J., Li, C., Xing, F., Peng, J., Liu, X., Xie, W., Wu, F., Jian, H., Cheng, R., & Dong, X.
Affiliations
  • Ministry of Natural Resources (CN)
  • Chinese Academy of Sciences (CN)
  • Zhejiang University (CN)
  • Dalian Maritime University (CN)
  • Shanghai Jiao Tong University (CN)
  • Eastern Institute of Technology, Ningbo (CN)
  • Huazhong Agricultural University (CN)
Corresponding author
  • Cheng, Rui
  • Dong, Xiyang
ORCID
Venue
Nature Communications
Publisher
openRxiv
Published
2024-09-26
Volume
17
Issue
1
Pages
1427-1427
ISSN
2041-1723 (ISSN-L)
DOI
10.1101/2024.09.26.614923
PMC
PMC12881386
OpenAlex
W7119537043
Cited by
4
References
1
Citations by year
2026: 1 · 2025: 2 · 2024: 1
FWCI
3.48
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by-nc-nd)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • PubMed Central (publishedVersion, cc-by-nc-nd)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Topics
  • Life Sciences › Immunology and Microbiology › Virology › Bacteriophages and microbial interactions
  • Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
  • Life Sciences › Immunology and Microbiology › Virology › Plant and Fungal Interactions Research
Keywords
cold seeps, deep-sea sediments, coevolution, sulfate-reducing bacteria, anaerobic methanotrophic archaea, nitrogen-fixing bacteria, virome, microbial metagenome
MeSH terms
Archaea, Bacteria, Cold Temperature, Phylogeny, Seawater, Viruses, Genome, Viral, Ecosystem, Geologic Sediments, Metagenome

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