Distinct microbial communities within and on seep carbonates support long-term anaerobic oxidation of methane and divergent pMMO diversity
Creators
-
1.
California Institute of Technology
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2.
University of Nevada, Las Vegas
- 3. Geo-Ocean, Univ Brest, CNRS, Ifremer, UMR6538, Plouzané F-29280, France
Abstract
At methane seeps worldwide, syntrophic anaerobic methane-oxidizing archaea and sulfate-reducing bacteria promote carbonate precipitation and rock formation, acting as methane and carbon sinks. Although maintenance of anaerobic oxidation of methane (AOM) within seep carbonates has been documented, its reactivation upon methane exposure remains uncertain. Surface-associated microbes may metabolize sulfide from AOM, maintain carbonate anoxia, contribute to carbonate dissolution, and support higher trophic levels; however, these communities are poorly described. We provide insights into microbial diversity, metabolism, activity, and resiliency within and on seep carbonates through amplicon and metagenomic sequencing, incubations, and non-canonical amino acid tagging combined with fluorescence in situ hybridization (BONCAT-FISH). Ca. Methanophaga (ANME-1) dominated the carbonate interiors in active and low activity seeps, co-occurring with Ca. Desulfaltia as main sulfate reducer, potentially a new syntrophic partner in AOM. Single-cell BONCAT-FISH revealed variability in ANME-1 activity, suggesting potential dormancy in carbonates from low activity seep sites. However, incubations with carbonates from low activity seeps (≥24 months) showed exponential AOM reactivation (~44-day doubling), suggesting these carbonates retain the potential as long-term methane sinks under dynamic seepage conditions. Surface-associated microbial communities were heterogeneous and distinct from the carbonate interior and other seep habitats. Anaerobic methane-oxidizing biofilms and sulfide-oxidizing mats were associated with carbonates with high and intermediate AOM rates potentially influencing carbonate precipitation/dissolution. Shared aerobic methanotrophs between carbonate surfaces and invertebrates indicated carbonate surfaces may represent animal epibiont reservoirs. Recovered particulate methane monooxygenases included both aerobic methanotrophs and divergent forms associated with the Methylophagaceae, suggesting a new function in this group.
Copyright and License
Acknowledgement
We are grateful to the R/V Western Flyer crew (Monterey Bay Research Aquarium Institute), John Magyar, Rebecca Wipfler, Sujung Lim, and Shana Goffredi for sample retrieval. We thank Kriti Sharma for advice on rock work and BONCAT, Stefanie Imminger for advice on cell extraction, Dan Utter for advice on bioinformatics, and Lydia Varesio and the ecology reading group for their thoughtful comments on this manuscript. We acknowledge Makayla Betts, Alex Sessions, and the Resnick Sustainability Institute’s Water and Environment Lab at Caltech for isotope measurement support.
Funding
This research was supported by the National Science Foundation (OCE-2048666) to VJO and the Swiss National Science Foundation Postdoctoral Fellowship (P2EZP3_195375) to MJM. This work is further supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under Award Number DE-SC0022991 to VJO.
Data Availability
All raw reads generated in this study and selected high quality MAGs have been submitted to NCBI under project number PRJNA1196099. All MAGs are available from FigShare (10.6084/m9.figshare.28232936).
Ethics
This report was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor any agency thereof, nor any of their employees, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof.
Supplemental Material
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supplementary_figures_s1-s14_wraf153.pdf
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Additional details
Identifiers
- PMCID
- PMC12422003
- PMID
- 40910361
Related works
- Is supplemented by
- Dataset: 10.6084/m9.figshare.28232936 (DOI)
Funding
- National Science Foundation
- OCE-2048666
- Swiss National Science Foundation Postdoctoral Fellowship
- P2EZP3_195375
- United States Department of Energy
- DE-SC0022991
Dates
- Accepted
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2025-07-23
- Available
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2025-09-05Published
- Available
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2025-09-10Corrected and typeset