Abstract
Aquatic environments absorb ~2.5 gigatonnes of atmospheric carbon each year1, more than the carbon stored in the atmosphere, soils, and all biomass combined. Primary producers transform this dissolved inorganic carbon into biomass that can subsequently flow into other trophic levels, or be released back into the environment through viral lysis. While there is substantial knowledge about the diversity and activity of viruses infecting photoautotrophic primary producers and the ecosystem impact, little is known about viruses infecting chemoautotrophs, representing a gap in our understanding of key processes driving microbial carbon cycling. Here, we combine metagenomics with quantitative 12/13C stable isotopic probing (qSIP) mesocosm experiments in a marine-derived meromictic pond to quantify population-specific isotopic enrichment, identify key chemoautotrophic primary producers, and virus-host dynamics. Isotopically enriched carbon is tracked from the genomes of chemoautotrophs to putative viruses, showing that active populations of hydrogen/sulfur-oxidizing chemoautotrophs (Thiomicrorhabdus, Hydrogenovibrio, Sulfurimonas, Sulfurovum) are targeted by viruses. This work provides the foundation for revealing the diversity and activity of viruses infecting globally-widespread chemoautotrophs. Our study sheds light on trophic interactions that impact microbial carbon cycling in aphotic environments and builds toward biogeochemical models that incorporate viral impacts on chemoautotrophic microbial communities.
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Data availability
Raw sequence data for this project is available on NCBI under Bioproject PRJNA1390687. Source data are provided with this paper. All other data is provided with the paper or appended as supplementary data. Source data are provided with this paper.
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Acknowledgements
We would like to acknowledge Gretta Serres, Alex Worden, Matthew Johnson, Sabrina Elkassas, Cynthia Becker, and Amy Apprill for discussions and/or methodology relevant to this manuscript. The data generation, analyses, and manuscript were supported by the University of North Carolina at Charlotte (startup funds to E.L.), the Hypothesis Fund (to E.L.), and the National Science Foundation (OCE-2513189 to E.L.). Wet lab analyses were supported by the Woods Hole Oceanographic Institution (Weston Howland Jr. Postdoctoral Fellowship to E.L.), the National Oceanic and Atmospheric Administration (NA19OAR4320072 subaward 0007525/102212019 to J.A.H.), and the National Science Foundation (OCE-1947776 to J.A.H.). B.E.B. was supported by the National Science Foundation (PRFB2010963). JJV was supported by the Simons Foundation (549941FY22). G.T. was supported by the US Department of Energy (SCW1632) and was conducted under Contract DE-AC52-07NA27344.
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E.L. conceptualized, supervised, and acquired funding for the study with input from J.A.H.; E.L. and B.E.B. collected the samples with help from JV and JAH. EL conducted experiments and wet lab analyses with input from G.T. and J.A.H.; N.P., T.J.R., M.M.S., J.J.V., and E.L. conducted the data analyses. E.L. wrote the manuscript with input from all co-authors. Correspondence and requests for materials should be addressed to elaine.luo@charlotte.edu.
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Luo, E., Pham, N.D., Rogers, T.J. et al. Quantitative stable isotope probing (qSIP)-informed metagenomics identifies viruses infecting chemoautotrophs. Nat Commun (2026). https://doi.org/10.1038/s41467-026-71833-x
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DOI: https://doi.org/10.1038/s41467-026-71833-x
