Methanogen-mediated dolomite precipitation in an early Permian lake in northwestern China
Published version of a preprint
Abstract
Microbes are known to mediate dolomite precipitation in laboratory experiments; however, the linkage of specific microbes to ancient dolomites remains poorly constrained due to scarce diagnostic biogeochemical signatures and mineralized microbial relics in the rock record. Here, we report the occurrence of methanogen-mediated dolomite in the Lower Permian lacustrine Lucaogou Formation in northwestern China. The clumped isotope (Δ47) temperature provides direct evidence of a low-temperature origin (typically <40 °C). The extremely positive δ26MgDSM3 (up to +0.44‰) and δ13CVPDB (up to +19‰) values in the dolomite indicate authigenic precipitation in methanogenic lake sediments. Micron-sized spheroidal bodies and filamentous and sheetlike structures are interpreted as mineralized coccoid methanogenic archaea and extracellular polymeric substances (EPSs), respectively. Dolomite nanoglobules (primarily 40–100 nm in diameter) are interpreted as mineralized viruses attached to the archaea and EPSs and between the cells. A combination of geochemical and microscale evidence confirms the microbial origin of the dolomite induced by methanogens and their associated bacteriophages. Furthermore, dolomite nanoglobules initially nucleated on the surfaces of methanogen cells, EPSs, and viruses and then merged into larger aggregates. The formation of microbial dolomite is characterized by a metabolic incubation, heterogeneous nucleation, and aggregative growth pathway. These findings provide valuable clues to decipher the biosignatures of these particular ancient dolomites.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Flemming, H.-C., & Wingender, J. (2010) · Nature Reviews Microbiology · doi:10.1038/nrmicro2415 · Cited by 10,137 · see citing works
Whiticar, M. J., Faber, E., & Schoell, M. (1986) · Geochimica et Cosmochimica Acta · doi:10.1016/0016-7037(86)90346-7 · Cited by 1,931 · see citing works
Isotopic evidence for source of diagenetic carbonates formed during burial of organic-rich sediments
Irwin, H., Curtis, C. D., & Coleman, M. L. (1977) · Nature · doi:10.1038/269209a0 · Cited by 1,349 · see citing works
<i>Metabolic, Phylogenetic, and Ecological Diversity of the Methanogenic Archaea</i>
Liu, Y., & Whitman, W. B. (2008) · Annals of the New York Academy of Sciences · doi:10.1196/annals.1419.019 · Cited by 1,346 · see citing works
Microbial mediation as a possible mechanism for natural dolomite formation at low temperatures
Vasconcelos, C., McKenzie, J. A., Bernasconi, S., Grujic, D., & Tiens, A. J. (1995) · Nature · doi:10.1038/377220a0 · Cited by 745 · see citing works
Defining an absolute reference frame for ‘clumped’ isotope studies of CO2
Dennis, K. J., Affek, H. P., Passey, B. H., Schrag, D. P., & Eiler, J. M. (2011) · Geochimica et Cosmochimica Acta · doi:10.1016/j.gca.2011.09.025 · Cited by 627 · see citing works
Vasconcelos, C., & McKenzie, J. A. (1997) · Journal of Sedimentary Research · doi:10.1306/d4268577-2b26-11d7-8648000102c1865d · Cited by 620 · see citing works
Gregg, J. M., Bish, D. L., Kaczmarek, S. E., & Machel, H. G. (2015) · Sedimentology · doi:10.1111/sed.12202 · Cited by 480 · see citing works
Dolomite formation within microbial mats in the coastal sabkha of Abu Dhabi (United Arab Emirates)
BONTOGNALI, T. R. R., VASCONCELOS, C., WARTHMANN, R. J., BERNASCONI, S. M., DUPRAZ, C., STROHMENGER, C. J., & McKENZIE, J. A. (2010) · Sedimentology · doi:10.1111/j.1365-3091.2009.01121.x · Cited by 360 · see citing works
Vasconcelos, C., McKenzie, J. A., Warthmann, R., & Bernasconi, S. M. (2005) · Geology · doi:10.1130/g20992.1 · Cited by 354 · see citing works
Microbially catalyzed dolomite formation: From near-surface to burial
Petrash, D. A., Bialik, O. M., Bontognali, T. R. R., Vasconcelos, C., Roberts, J. A., McKenzie, J. A., & Konhauser, K. O. (2017) · Earth-Science Reviews · doi:10.1016/j.earscirev.2017.06.015 · Cited by 338 · see citing works
Anderson, N. T., Kelson, J. R., Kele, S., Daëron, M., Bonifacie, M., Horita, J., Mackey, T. J., John, C. M., Kluge, T., Petschnig, P., et al. (2021) · Geophysical Research Letters · doi:10.1029/2020gl092069 · Cited by 323 · see citing works
Wright, D. T. (1999) · Sedimentary Geology · doi:10.1016/s0037-0738(99)00037-8 · Cited by 314 · see citing works
Aerobic microbial dolomite at the nanometer scale: implications for the geologic record
Sánchez-Román, M., Vasconcelos, C., Schmid, T., Dittrich, M., McKenzie, J. A., Zenobi, R., & Rivadeneyra, M. A. (2008) · Geology · doi:10.1130/g25013a.1 · Cited by 280 · see citing works
PALEOMAP PALEOATLAS FOR GPLATES AND THE PALEODATAPLOTTER PROGRAM
PALEOMAP Project, & Scotese, C. (2016) · Abstracts with programs - Geological Society of America · doi:10.1130/abs/2016nc-275387 · Cited by 274 · see citing works
Microbial precipitation of dolomite in methanogenic groundwater
Roberts, J. A., Bennett, P. C., González, L. A., Macpherson, G. L., & Milliken, K. L. (2004) · Geology · doi:10.1130/g20246.2 · Cited by 269 · see citing works
John, C. M., & Bowen, D. (2016) · Rapid Communications in Mass Spectrometry · doi:10.1002/rcm.7720 · Cited by 247 · see citing works
Surface chemistry allows for abiotic precipitation of dolomite at low temperature
Roberts, J. A., Kenward, P. A., Fowle, D. A., Goldstein, R. H., González, L. A., & Moore, D. S. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1305403110 · Cited by 246 · see citing works
Some hydrothermal syntheses of dolomite and protodolomite
Graf, D. L., & Goldsmith, J. R. (1956) · The Journal of Geology · doi:10.1086/626332 · Cited by 225 · see citing works
Microbes produce nanobacteria-like structures, avoiding cell entombment
Bontognali, T. R. R., Vasconcelos, C., Warthmann, R. J., Dupraz, C., Bernasconi, S. M., & McKenzie, J. A. (2008) · Geology · doi:10.1130/g24755a.1 · Cited by 198 · see citing works
Nucleation of calcium carbonate on bacterial nanoglobules
Aloisi, G., Gloter, A., Krüger, M., Wallmann, K., Guyot, F., & Zuddas, P. (2006) · Geology · doi:10.1130/g22986a.1 · Cited by 183 · see citing works
Upper Permian lacustrine organic facies evolution, Southern Junggar Basin, NW China
Carroll, A. R. (1998) · Organic Geochemistry · doi:10.1016/s0146-6380(98)00040-0 · Cited by 181 · see citing works
KENWARD, P. A., GOLDSTEIN, R. H., GONZÁLEZ, L. A., & ROBERTS, J. A. (2009) · Geobiology · doi:10.1111/j.1472-4669.2009.00210.x · Cited by 175 · see citing works
The magnesium isotope (δ26Mg) signature of dolomites
Geske, A., Goldstein, R. H., Mavromatis, V., Richter, D. K., Buhl, D., Kluge, T., John, C. M., & Immenhauser, A. (2014) · Geochimica et Cosmochimica Acta · doi:10.1016/j.gca.2014.11.003 · Cited by 171 · see citing works
Upper Permian Lacustrine Oil Shales, Southern Junggar Basin, Northwest China
Carroll, A. R., Brassell, S. C., & Graham, S. A. (1992) · AAPG Bulletin · doi:10.1306/bdff8b0a-1718-11d7-8645000102c1865d · Cited by 171 · see citing works
Zhang, F., Xu, H., Konishi, H., Shelobolina, E. S., & Roden, E. E. (2012) · American Mineralogist · doi:10.2138/am.2012.3979 · Cited by 170 · see citing works
Mg and Ca isotope signatures of authigenic dolomite in siliceous deep-sea sediments
Blättler, C. L., Miller, N. R., & Higgins, J. A. (2015) · Earth and Planetary Science Letters · doi:10.1016/j.epsl.2015.03.006 · Cited by 162 · see citing works
Extreme carbon-isotope enrichments in evaporating brines
Stiller, M., Rounick, J. S., & Shasha, S. (1985) · Nature · doi:10.1038/316434a0 · Cited by 162 · see citing works
A route for the direct crystallization of dolomite
Rodriguez-Blanco, J. D., Shaw, S., & Benning, L. G. (2015) · American Mineralogist · doi:10.2138/am-2015-4963 · Cited by 161 · see citing works
Li, W., Beard, B. L., Li, C., Xu, H., & Johnson, C. M. (2015) · Geochimica et Cosmochimica Acta · doi:10.1016/j.gca.2015.02.024 · Cited by 158 · see citing works
Perri, E., Tucker, M. E., Słowakiewicz, M., Whitaker, F., Bowen, L., & Perrotta, I. D. (2017) · Sedimentology · doi:10.1111/sed.12419 · Cited by 156 · see citing works
Dual clumped isotope thermometry resolves kinetic biases in carbonate formation temperatures
Bajnai, D., Guo, W., Spötl, C., Coplen, T. B., Methner, K., Löffler, N., Krsnik, E., Gischler, E., Hansen, M., Henkel, D., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-17501-0 · Cited by 147 · see citing works
Liu, D., Xu, Y., Papineau, D., Yu, N., Fan, Q., Qiu, X., & Wang, H. (2019) · Geochimica et Cosmochimica Acta · doi:10.1016/j.gca.2018.12.036 · Cited by 141 · see citing works
Bacterial fossils and microbial dolomite in Triassic stromatolites
Perri, E., & Tucker, M. (2007) · Geology · doi:10.1130/g23354a.1 · Cited by 140 · see citing works
Schulz, S., Matsuyama, H., & Conrad, R. (2006) · FEMS Microbiology Ecology · doi:10.1111/j.1574-6941.1997.tb00372.x · Cited by 139 · see citing works
Dale, A., John, C. M., Mozley, P. S., Smalley, P. C., & Muggeridge, A. H. (2014) · Earth and Planetary Science Letters · doi:10.1016/j.epsl.2014.03.004 · Cited by 123 · see citing works
Mavromatis, V., Meister, P. H., & Oelkers, É. H. (2014) · Chemical Geology · doi:10.1016/j.chemgeo.2014.07.019 · Cited by 105 · see citing works
High salinity facilitates dolomite precipitation mediated by Haloferax volcanii DS52
Qiu, X., Wang, H., Yao, Y., & Duan, Y. (2017) · Earth and Planetary Science Letters · doi:10.1016/j.epsl.2017.05.018 · Cited by 102 · see citing works
Loyd, S. J., Corsetti, F. A., Eiler, J. M., & Tripati, A. (2012) · Journal of Sedimentary Research · doi:10.2110/jsr.2012.85 · Cited by 96 · see citing works
Viruses as new agents of organomineralization in the geological record
Pacton, M., Wacey, D., Corinaldesi, C., Tangherlini, M., Kilburn, M. R., Gorin, G., Danovaro, R., & Vásconcelos, C. (2014) · Nature Communications · doi:10.1038/ncomms5298 · Cited by 82 · see citing works
Sustained and intensified lacustrine methane cycling during Early Permian climate warming
Sun, F., Hu, W., Cao, J., Wang, X., Zhang, Z., Ramezani, J., & Shen, S. (2022) · Nature Communications · doi:10.1038/s41467-022-32438-2 · Cited by 79 · see citing works
Self-citationInitial Reports of the Deep Sea Drilling Project, 59
Kroenke, L. W., Scott, R. J., & al., E. (1981) · U.S. Government Printing Office eBooks · doi:10.2973/dsdp.proc.59.1981 · Cited by 71 · see citing works
Dissolved silica-catalyzed disordered dolomite precipitation
Fang, Y., & Xu, H. (2022) · American Mineralogist · doi:10.2138/am-2021-7474 · Cited by 69 · see citing works
The dolomite problem; an outstanding controversy
Judith, A. M. (1991) · Pages · Cited by 68 · see citing works
Hu, Z., Hu, W., Wang, X., Lu, Y., Wang, L., Liao, Z., & Li, W. (2017) · Geochimica et Cosmochimica Acta · doi:10.1016/j.gca.2017.03.026 · Cited by 68 · see citing works
Self-citationLiu, D., Yu, N., Papineau, D., Fan, Q., Wang, H., Qiu, X., She, Z., & Luo, G. (2019) · Geochimica et Cosmochimica Acta · doi:10.1016/j.gca.2019.07.056 · Cited by 61 · see citing works
Methanogen microfossils and methanogenesis in Permian lake deposits
Sun, F., Hu, W., Wang, X., Cao, J., Fu, B., Wu, H., & Yang, S. (2020) · Geology · doi:10.1130/g47857.1 · Cited by 58 · see citing works
Self-citationGao, Y., Huang, H., Tao, H., Carroll, A. R., Qin, J., Chen, J., Yuan, X., & Wang, C. (2019) · Journal of Asian Earth Sciences · doi:10.1016/j.jseaes.2019.104222 · Cited by 57 · see citing works
You, X., Sun, S., Zhu, J., Li, Q., Hu, W., & Dong, H. (2013) · Terra Nova · doi:10.1111/ter.12048 · Cited by 54 · see citing works
Self-citationFang, Y., Wu, C., Wang, Y., Hou, K., & Guo, Z. (2019) · Gondwana Research · doi:10.1016/j.gr.2019.03.020 · Cited by 54 · see citing works
Formation of ordered dolomite in anaerobic photosynthetic biofilms
Daye, M., Higgins, J. A., & Bosak, T. (2019) · Geology · doi:10.1130/g45821.1 · Cited by 52 · see citing works
Guo, Y., Deng, W., & Wei, G. (2019) · Geochimica et Cosmochimica Acta · doi:10.1016/j.gca.2019.01.012 · Cited by 50 · see citing works
Self-citationBiogeochemical reappraisal of the freshwater–seawater mixing‐zone diagenetic model
Petrash, D. A., Bialik, O. M., Staudigel, P. T., Konhauser, K. O., & Budd, D. A. (2021) · Sedimentology · doi:10.1111/sed.12849 · Cited by 39 · see citing works
Bojanowski, M. J. (2014) · Marine and Petroleum Geology · doi:10.1016/j.marpetgeo.2013.12.001 · Cited by 36 · see citing works
Zhu, Z., Chen, J., & Zeng, Y. (2012) · Quaternary International · doi:10.1016/j.quaint.2012.06.004 · Cited by 34 · see citing works
Zhang, F., Xu, H., Shelobolina, E. S., Konishi, H., & Roden, E. E. (2021) · American Mineralogist · doi:10.2138/am-2020-7381 · Cited by 30 · see citing works
Perri, E., Słowakiewicz, M., Perrotta, I. D., & Tucker, M. E. (2021) · Sedimentology · doi:10.1111/sed.12932 · Cited by 29 · see citing works
Zhao, Y., Wei, X., Han, Z., Han, C., Gao, X. P., Meng, R., Wang, Q., Tucker, M. E., Li, M., & Sánchez‐Román, M. (2023) · Chemical Geology · doi:10.1016/j.chemgeo.2023.121376 · Cited by 27 · see citing works
Anoxygenic phototrophs and the forgotten art of making dolomite
Bontognali, T. R. R. (2019) · Geology · doi:10.1130/focus062019.1 · Cited by 24 · see citing works
No biological effect on magnesium isotope fractionation during stromatolite growth
Hu, Z., Hohl, S. V., Viehmann, S., Meister, P. H., & Tepe, N. (2023) · Geochimica et Cosmochimica Acta · doi:10.1016/j.gca.2023.07.022 · Cited by 22 · see citing works
Self-citationSłowakiewicz, M., Borkowski, A., Syczewski, M. D., Perrotta, I., Owczarek, F., Sikora, A., Detman, A., Perri, E., & Tucker, M. E. (2020) · Geochimica et Cosmochimica Acta · doi:10.1016/j.gca.2020.10.012 · Cited by 21 · see citing works
Jiao, X., Liu, Y., Yang, W., Li, H., Meng, Z., Zhao, M., & Li, Z. (2022) · Sedimentology · doi:10.1111/sed.13031 · Cited by 21 · see citing works
An Early Holocene Primary Dolomite Layer of Abiotic Origin in Lake Sayram, Central Asia
Cheng, J., Meng, X., Zhang, E., Jiang, Q., Ni, Z., & Ji, J. (2021) · Geophysical Research Letters · doi:10.1029/2021gl096309 · Cited by 20 · see citing works
You, X., Sun, S., & Zhu, J. (2014) · Science China Earth Sciences · doi:10.1007/s11430-014-4935-z · Cited by 19 · see citing works
Wang, Y., Wu, C., Fang, Y., Ma, J., Shen, B., Huang, F., Li, L., Ning, M., Zhai, L., & Zhang, W. (2020) · Chemical Geology · doi:10.1016/j.chemgeo.2020.119569 · Cited by 18 · see citing works
Wu, A., Cao, J., Zhang, J., Wu, T., & Wang, Y. (2022) · Sedimentary Geology · doi:10.1016/j.sedgeo.2022.106260 · Cited by 17 · see citing works
Oligocene syndepositional lacustrine dolomite: A study from the southern Junggar Basin, NW China
Li, Q., Zhang, Y., Dong, L., & Guo, Z. (2018) · Palaeogeography Palaeoclimatology Palaeoecology · doi:10.1016/j.palaeo.2018.04.004 · Cited by 15 · see citing works
Viruses participate in the organomineralization of travertines
Słowakiewicz, M., Perri, E., Taglıasacchı, E., Działak, P., Borkowski, A., Gradziński, M., Kele, S., & Tucker, M. E. (2023) · Scientific Reports · doi:10.1038/s41598-023-38873-5 · Cited by 14 · see citing works
Orbitally Forced Organic Matter Accumulation Recorded in an Early Permian Mid-Latitude Palaeolake
Huang, W., Wu, H., Fang, Q., Zhang, S., Yang, T., Li, H., & Shi, M. (2022) · Palaeogeography Palaeoclimatology Palaeoecology · doi:10.1016/j.palaeo.2022.111259 · Cited by 12 · see citing works
Self-citationHydrothermal-sedimentary dolomite — a case from the Middle Permian in eastern Junggar Basin, China
Zhang, S., Liu, Y., Li, H., Jiao, X., & Zhou, D. (2020) · Journal of Palaeogeography · doi:10.1186/s42501-020-00070-0 · Cited by 11 · see citing works
Geovirology: viruses and their roles in geological history
Xie, S., Zhu, X., Algeo, T. J., & Qiu, X. (2023) · 中国科学通报：英文版 · doi:10.1016/j.scib.2023.02.001 · Cited by 6 · see citing works
Diagenetic replacement controlled by force of crystallization
Maliva, R. G., & Siever, R. (1988) · Geology · doi:10.1130/0091-7613(1988)016
Flagged first, then by citations
1 of the 73 references couldn’t be matched to a known paper.
Cited by
Sorted by citations
A non-classical crystallization mechanism of microbially-induced disordered dolomite
Liu, D., Chen, T., Dai, Z., Papineau, D., Qiu, X., Wang, H., & Benzerara, K. (2024) · Geochimica et Cosmochimica Acta · doi:10.1016/j.gca.2024.05.005 · Cited by 29 · see citing works
Zhang, K., Liu, Z., Xu, Z., Chang, Q., Fathy, D., Liu, R., & Bai, E. (2024) · Sedimentary Geology · doi:10.1016/j.sedgeo.2024.106739 · Cited by 19 · see citing works
Methane fueled lake pelagic food webs in a Cretaceous greenhouse world
Sun, F., Luo, G., Pancost, R. D., Dong, Z., Li, Z., Wang, H., Chen, Z., & Xie, S. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2411413121 · Cited by 12 · see citing works
Self-citationLiu, G., Wang, G., Li, N., He, H.-L., Lu, N.-N., Lei, Q., & Wang, Z.-A. (2024) · Journal of Palaeogeography · doi:10.1016/j.jop.2024.08.008 · Cited by 6 · see citing works
Petrash, D. A., Roeser, P. A., Křı́bek, B., Staudigel, P. T., Bernecker, M., Jačková, I., Čejková, B., Kochergina, Y. V. E., Koubová, M., Křížová, Š., et al. (2025) · Geochimica et Cosmochimica Acta · doi:10.1016/j.gca.2025.08.025 · Cited by 5 · see citing works
Hydrocarbon Generation Recrystallization of Carbonate Rocks and Its Geological Significance
Zhong, M., Huang, H., & Zhang, H. (2025) · SPE Journal · doi:10.2118/228420-pa
Navarro, G. M., López-Doncel, R. A., Castillo-Rivera, F., Iñiguez, E., Ramírez, M. J., & Magaña, H. O. (2026) · npj Heritage Science · doi:10.1038/s40494-026-02382-1
Xinyu, C., Jin, S., Yang, L., Zhangsun, H., Guangquan, Y., Xuan, Q., Deng, L., & Hongmei, W. (2026) · Earth Science-Journal of China University of Geosciences · doi:10.3799/dqkx.2026.179
- Authors
- Sun, F., Hu, W., Wang, X., Hu, Z., Wu, H., Guo, Y., & Wei, G.
- Affiliations
- China University of Geosciences (CN)
- Nanjing University (CN)
- Northeast Petroleum University (CN)
- Chinese Academy of Sciences (CN)
- Venue
- Geological Society of America Bulletin
- Publisher
- Geological Society of America
- Published
- 2023-11-01
- Volume
- 136
- Issue
- 7-8
- Pages
- 2637-2645
- ISSN
- 0016-7606 (ISSN-L)
- 1943-2674
- OpenAlex
- W4388125671
- Cited by
- 8
- References
- 73
- Citations by year
- 2026: 2 · 2025: 2 · 2024: 4
- FWCI
- 1.62
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Geological Society of America Bulletin (publishedVersion)
- Topics
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Paleontology and Stratigraphy of Fossils
- Physical Sciences › Engineering › Mechanics of Materials › Hydrocarbon exploration and reservoir analysis
- Physical Sciences › Earth and Planetary Sciences › Geochemistry and Petrology › Geochemistry and Elemental Analysis
- Keywords
- methanogenic archaea, extracellular polymeric substances, bacteriophages, authigenic dolomite, magnesium isotopes, carbon isotopes, heterogeneous nucleation, Lucaogou Formation
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
