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Cited by 3Genomics and Phylogenetic StudiesMicrobial Community Ecology and PhysiologyProtist diversity and phylogeny

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New groups of highly divergent proteins in families as old as cellular life with important biological functions in the ocean

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Sussfeld, Duncan, Lannes, Romain, Corel, Eduardo, Bernard, Guillaume, Martin, Pierre, Bapteste, Eric, Pelletier, Eric, Lopez, Philippe·2025·Environmental Microbiome
DOI 10.1186/s40793-025-00697-3PMC PMC12153180

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Abstract

Background: Metagenomics has considerably broadened our knowledge of microbial diversity, unravelling fascinating adaptations and characterising multiple novel major taxonomic groups, e.g. CPR bacteria, DPANN and Asgard archaea, and novel viruses. Such findings profoundly reshaped the structure of the known Tree of Life and emphasised the central role of investigating uncultured organisms. However, despite significant progresses, a large portion of proteins predicted from metagenomes remain today unannotated, both taxonomically and functionally, across many biomes and in particular in oceanic waters. Results: Here, we used an iterative, network-based approach for remote homology detection, to probe a dataset of 40 million ORFs predicted in marine environments. We assessed the environmental diversity of 53 core gene families broadly distributed across the Tree of Life, with essential functions including translational, replication and trafficking processes. For nearly half of them, we identified clusters of remote environmental homologues that showed divergence from the known genetic diversity comparable to the divergence between Archaea and Bacteria, with representatives distributed across all the oceans. In particular, we report the detection of environmental clades with new structural variants of essential SMC (Structural Maintenance of Chromosomes) genes, divergent polymerase subunits forming deep-branching clades in the polymerase tree, and variant DNA recombinases in Bacteria as well as viruses. Conclusions: These results indicate that significant environmental diversity may yet be unravelled even in strongly conserved gene families. Protein sequence similarity network approaches, in particular, appear well-suited to highlight potential sources of biological novelty and make better sense of microbial dark matter across taxonomical scales.

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Metadata

Authors
Sussfeld, D., Lannes, R., Corel, E., Bernard, G., Martin, P., Bapteste, E., Pelletier, E., & Lopez, P.
Affiliations
Centre National de la Recherche Scientifique (FR)
Corresponding author
Sussfeld, Duncan
ORCID
Venue
Environmental Microbiome
Publisher
Springer Science and Business Media LLC
Published
2025-06-11
Volume
20
Issue
1
Pages
65-65
ISSN
2524-6372 (ISSN-L)
DOI
10.1186/s40793-025-00697-3
PMC
PMC12153180
OpenAlex
W4411214362
Cited by
3
References
5
Citations by year
2026: 2 · 2025: 1
FWCI
0.90
Type
journal article
Language
en
Open access
Licence
Locations
  • Environmental Microbiome (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • HAL AMU (submittedVersion, cc-by)
  • HAL (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
European Research Council (615274)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
  • Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Protist diversity and phylogeny
Keywords
remote homology detection, marine metagenomes, microbial dark matter, unculturable microorganisms, protein divergence

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