Abstract
Actively venting high temperature deep-sea hydrothermal vent deposits along tectonic spreading centers and in backarc basins harbor a rich diversity of thermophilic Bacteria and Archaea, many of which have no representatives in cultivation nor any genomic representation in databases. Here, in order to produce a global-scale time series metagenomic resource for studying the microbial functional and genomic diversity in these high temperature ecosystems, we obtained 70 metagenomes from collections across spatial and temporal gradients from 21 different vent fields spanning 16 years (1993–2009). The dataset (Deep-Sea Hydrothermal Vent dataset (DSV70)) includes 3.56 Tbp of raw DNA sequence reads, that have been assembled to produce 7,422 medium- to high-quality (based on CheckM2) metagenome-assembled genomes (MAGs) of Bacteria (6,063 MAGs) and Archaea (1,359 MAGs). Collectively, this DSV70 dataset and the published 40 metagenomes from more recent deep-sea collections (2004 to 2018), represent a valuable resource for exploring the functional and phylogenomic diversity of the deep-sea hydrothermal microbiomes, and provide many reference genomes for studies in the taxonomy and systematics of poorly studied microbial lineages. Further, with the interest in mining the mineral resources at deep-sea vents, the DSV70 provides a genomic legacy for monitoring impacts on the microbial communities in these systems.
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Data availability
The primary metagenome sequences and the MAGs of ≥90% completion have been deposited in GenBank and the NCBI Sequence Read Archive (SRA), respectively, under PRJNA1244896 and SRP575724. Primary metagenome sequences, metagenome assemblies and all medium- to high-quality MAGs are available in the European Bioinformatics Institute BioStudies repository (accession number S-BSST2227).
Code availability
All of the bioinformatic tools presented in this analysis are publicly available, and version numbers and parameters are described in detail in the Methods. Custom scripts for calculating normalized MAG coverage are available at https://github.com/ALR-Lab/MAG-coverage.
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Acknowledgements
Thank-you to the crews of the R/V Atlantis, R/V Knorr, R/V Le Nadir, R/V Melville, R/V Roger Revelle, R/V Thomas G. Thompson, R/V Western Flyer, R/V Yokosuka, DSV Alvin, DSV Nautile, DSV Shinkai 6500, ROV Jason I, Jason II and ROV Tiburon for their help with sample collection. Our thanks to Jennifer Meneghin for her assistance in developing coverage-related scripts. This work was funded by the US-National Science Foundation grant DEB-2409507 to A.-L. Reysenbach. The US-National Science Foundation grants OCE-1558795, 1235432, 0937404, 0752469, 0728391, 0242038, 0118240, 9714302 provided funding for the many collections.
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E.S.J. extracted and quantified DNA, conducted the metagenome trimming, quality control, assembly, read mapping and binning, phylogenomic tree construction and figure generation, collected metadata and helped write the manuscript. A.L.R. designed the study, collected the samples, helped analyze the data and wrote the manuscript. Both authors approved the final version of the manuscript.
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St. John, E., Reysenbach, AL. Global deep-sea hydrothermal deposit metagenomes and metagenome-assembled genomes over time and space. Sci Data (2026). https://doi.org/10.1038/s41597-026-06612-w
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DOI: https://doi.org/10.1038/s41597-026-06612-w
