Articles | Volume 22, issue 19
https://doi.org/10.5194/bg-22-5173-2025
© Author(s) 2025. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/bg-22-5173-2025
© Author(s) 2025. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Adaptation of methane-oxidizing bacteria to environmental changes: implications for coastal methane dynamics
Tim R. de Groot
NIOZ Royal Netherlands Institute for Sea Research, Texel, the Netherlands
Julia C. Engelmann
CORRESPONDING AUTHOR
NIOZ Royal Netherlands Institute for Sea Research, Texel, the Netherlands
Pierre Ramond
NIOZ Royal Netherlands Institute for Sea Research, Texel, the Netherlands
Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Barcelona, Catalunya, Spain
Julia Dorigo
NIOZ Royal Netherlands Institute for Sea Research, Texel, the Netherlands
Judith van Bleijswijk
NIOZ Royal Netherlands Institute for Sea Research, Texel, the Netherlands
NIOZ Royal Netherlands Institute for Sea Research, Texel, the Netherlands
Department of Earth Sciences, Utrecht University, Utrecht, the Netherlands
Department of Geosciences, CAGE – Centre of Arctic Gas Hydrate, Environment and Climate, UiT the Arctic University of Norway, Tromsø, Norway
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This paper is a step towards understanding the basal peat ecosystem beneath the North Sea. Plant remains followed parallel sequences. Methane concentrations were low with local exceptions, with the source likely being trapped pockets of millennia-old methane. Microbial community structure indicated the absence of a biofilter and was diverse across sites. Large carbon stores in the presence of methanogens and in the absence of methanotrophs have the potential to be metabolized into methane.
Cited articles
Abdala Asbun, A., Besseling, M. A., Balzano, S., Van Bleijswijk, J. D. L., Witte, H. J., Villanueva, L., and Engelmann, J. C.: Cascabel: A Scalable and Versatile Amplicon Sequence Data Analysis Pipeline Delivering Reproducible and Documented Results, Front. Genet., 11, 489357, https://doi.org/10.3389/fgene.2020.489357, 2020.
Bodelier, P. L. and Laanbroek, H. J.: Nitrogen as a regulatory factor of methane oxidation in soils and sediments, FEMS Microbiol. Ecol., 47, 265–277, https://doi.org/10.1016/S0168-6496(03)00304-0, 2004.
Bodelier, P. L. E., Meima-Franke, M., Hordijk, C. A., Steenbergh, A. K., Hefting, M. M., Bodrossy, L., Von Bergen, M., and Seifert, J.: Microbial minorities modulate methane consumption through niche partitioning, ISME J., 7, 2214–2228, 2013.
Bodelier, P. L. E., Pérez, G., Veraart, A. J., and Krause, S. M. B.: Methanotroph Ecology, Environmental Distribution and Functioning, in: Methanotrophs: Microbiology Fundamentals and Biotechnological Applications, edited by: Lee, E. Y., Springer International Publishing, 1–38, https://doi.org/10.1007/978-3-030-23261-0_1, 2019.
Broman, E., Olsson, M., Maciute, A., Donald, D., Humborg, C., Norkko, A., Jilbert, T., Bonaglia, S., and Nascimento, F. J. A.: Biotic interactions between benthic infauna and aerobic methanotrophs mediate methane fluxes from coastal sediments, ISME J., 18, https://doi.org/10.1093/ismejo/wrae013, 2024.
Callahan, B. J., Mcmurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J. A., and Holmes, S. P.: DADA2: High-resolution sample inference from Illumina amplicon data, Nat. Methods, 13, 581–583, 2016.
Calvo-Díaz, A., Díaz-Pérez, L., Suárez, L.Á., Morán, X.a.G., Teira, E., and Marañón, E.: Decrease in the Autotrophic-to-Heterotrophic Biomass Ratio of Picoplankton in Oligotrophic Marine Waters Due to Bottle Enclosure, Appl. Environ. Microb., 77, 5739–5746, 2011.
Collins, M., Sutherland, M., Bouwer, L., Cheong, S.-M., Frolicher, T., Descombes, H. J., Roxy, M. K., Losada, I., Mcinnes, K., and Ratter, B.: Extremes, abrupt changes and managing risk, in: IPCC Special Report on the Ocean and Cryosphere in a Changing Climate eddited by: Pörtner, H.-O., Roberts, D. C., Masson-Delmotte, V., Zhai, P., Tignor, M., Poloczanska, E., Mintenbeck, K., Alegría, A., Nicolai, M., Okem, A., Petzold, J., Rama, B., and Weyer, N. M., Cambridge University Press, Cambridge, UK and New York, NY, USA, https://doi.org/10.1017/9781009157964.001, 2019.
Crespo-Medina, M., Meile, C. D., Hunter, K. S., Diercks, A. R., Asper, V. L., Orphan, V. J., Tavormina, P. L., Nigro, L. M., Battles, J. J., Chanton, J. P., Shiller, A. M., Joung, D. J., Amon, R. M. W., Bracco, A., Montoya, J. P., Villareal, T. A., Wood, A. M., and Joye, S. B.: The rise and fall of methanotrophy following a deepwater oil-well blowout, Nat. Geosci., 7, 423–427, 2014.
Debray, R., Herbert, R. A., Jaffe, A. L., Crits-Christoph, A., Power, M. E., and Koskella, B.: Priority effects in microbiome assembly, Nat. Rev. Microbiol., 20, 109–121, https://doi.org/10.1038/s41579-021-00604-w, 2022.
Dedysh, S. N. and Knief, C.: Diversity and Phylogeny of Described Aerobic Methanotrophs, in: Methane Biocatalysis: Paving the Way to Sustainability, edited by: Kalyuzhnaya, M. G. and Xing, X.-H., Springer International Publishing, https://doi.org/10.1007/978-3-319-74866-5_2, 2018.
de Groot, T. R., Mol, A. M., Mesdag, K., Ramond, P., Ndhlovu, R., Engelmann, J. C., Röckmann, T., and Niemann, H.: Diel and seasonal methane dynamics in the shallow and turbulent Wadden Sea, Biogeosciences, 20, 3857–3872, https://doi.org/10.5194/bg-20-3857-2023, 2023.
de Groot, T. R., Menoud, M., van Bleijswijk, J., van Leeuwen, S. M., van der Molen, J., Hernando-Morales, V., Czerski, H., Maazallahi, H., Walter, S., Rush, D., Röckmann, T., and Niemann, H.: Tidal and seasonal influence on cold seep activity and methanotroph efficiency in the North Sea, Commun. Earth Environ., 5, 368, https://doi.org/10.1038/s43247-024-01483-8, 2024.
Dixon, P.: VEGAN, a package of R functions for community ecology, J. Veg. Sci., 14, 927–930, 2003.
Ettwig, K. F., Alen, T. V., Pas-Schoonen, K. T. V. D., Jetten, M. S. M., and Strous, M.: Enrichment and Molecular Detection of Denitrifying Methanotrophic Bacteria of the NC10 Phylum, Appl. Environ. Microb., 75, 3656–3662, 2009.
Etminan, M., Myhre, G., Highwood, E. J., and Shine, K. P.: Radiative forcing of carbon dioxide, methane, and nitrous oxide: A significant revision of the methane radiative forcing, Geophys. Res. Lett., 43, 12614–12623, https://doi.org/10.1002/2016gl071930, 2016.
Ettwig, K. F., Butler, M. K., Paslier, D. L., Pelletier, E., Mangenot, S., Kuypers, M. M. M., Schreiber, F., Dutilh, B. E., Zedelius, J., Beer, D. de, Gloerich, J., Wessels, H., Alen, T. van, Luesken, F., Wu, M. L., Pas-Schoonen, K. T. van de, Camp, H. den, Janssen-Megens, E. M., Francoijs, K. J., Stunnenberg, H., Weissenbach, J., Jetten, M. S. M., and Strous, M.: Nitrite-driven anaerobic methane oxidation by oxygenic bacteria, Nature, 464, 543–548, https://doi.org/10.1038/nature08883, 2010.
Ghashghavi, M., Jetten, M. S. M., and Lüke, C.: Survey of methanotrophic diversity in various ecosystems by degenerate methane monooxygenase gene primers, AMB Express 7, 162, https://doi.org/10.1186/s13568-017-0466-2, 2017.
Greenwood, N., Parker, E. R., Fernand, L., Sivyer, D. B., Weston, K., Painting, S. J., Kröger, S., Forster, R. M., Lees, H. E., Mills, D. K., and Laane, R. W. P. M.: Detection of low bottom water oxygen concentrations in the North Sea; implications for monitoring and assessment of ecosystem health, Biogeosciences, 7, 1357–1373, https://doi.org/10.5194/bg-7-1357-2010, 2010.
Gründger, F., Probandt, D., Knittel, K., Carrier, V., Kalenitchenko, D., Silyakova, A., Serov, P., Ferré, B., Svenning, M. M., and Niemann, H.: Seasonal shifts of microbial methane oxidation in Arctic shelf waters above gas seeps, Limnol. Oceanogr., 66, 1896–1914, 2021.
Hammes, F., Vital, M., and Egli, T.: Critical Evaluation of the Volumetric “Bottle Effect” on Microbial Batch Growth. Appl. Environ. Microb. 76, 1278–1281, 2010.
Hanson, R. S. and Hanson, T. E.: Methanotrophic Bacteria, Microbiol. Rev., 60, https://doi.org/10.1128/mr.60.2.439-471.1996 1996.
Haque, M. F. U., Xu, H.-J., Murrell, J. C., and Crombie, A.: Facultative methanotrophs – diversity, genetics, molecular ecology and biotechnological potential: a mini-review, Microbiology, 166, 894–908, 2020.
Haro-Moreno, J. M., Rodriguez-Valera, F., and López-Pérez, M.: Prokaryotic Population Dynamics and Viral Predation in a Marine Succession Experiment Using Metagenomics, Front. Microbiol., 10, https://doi.org/10.3389/fmicb.2019.02926, 2019.
He, R., Wooller, M. J., Pohlman, J. W., Quensen, J., Tiedje, J. M., and Leigh, M. B.: Shifts in Identity and Activity of Methanotrophs in Arctic Lake Sediments in Response to Temperature Changes. Appl. Environ. Microb., 78, 4715–4723, 2012.
Henckel, T., Jäckel, U., Schnell, S., and Conrad, R.: Molecular analyses of novel methanotrophic communities in forest soil that oxidize atmospheric methane, Appl. Environ. Microb., 66, 1801–1808, 2000.
Herlemann, D. P. R., Markert, S., Meeske, C., Andersson, A. F., Bruijn, I. de, Hentschker, C., Unfried, F., Becher, D., Jürgens, K., and Schweder, T.: Individual Physiological Adaptations Enable Selected Bacterial Taxa To Prevail during Long-Term Incubations, Appl. Environ. Microb., 85, https://doi.org/10.1128/aem.00825-19, 2019.
Hirayama, H., Takaki, Y., Abe, M., Imachi, H., Ikuta, T., Miyazaki, J., Tasumi, E., Uematsu, K., Tame, A., Tsuda, M., Tanaka, K., Matsui, Y., Watanabe, H. K., Yamamoto, H., and Takai, K.: Multispecies Populations of Methanotrophic Methyloprofundus and Cultivation of a Likely Dominant Species from the Iheya North Deep-Sea Hydrothermal Field, Appl. Environ. Microb., 88, doi.org/10.1128/aem.00758-21 2022.
Ho, A., De Roy, K., Thas, O., De Neve, J., Hoefman, S., Vandamme, P., Heylen, K., and Boon, N.: The more, the merrier: heterotroph richness stimulates methanotrophic activity, ISME J., 8, 1945–1948, 2014.
Ho, A., Mo, Y., Lee, H. J., Sauheitl, L., Jia, Z., and Horn, M. A.: Effect of salt stress on aerobic methane oxidation and associated methanotrophs; a microcosm study of a natural community from a non-saline environment, Soil Biol. Biochem., 125, 210–214, 2018.
James, R.H., Bousquet, P., Bussmann, I., Haeckel, M., Kipfer, R., Leifer, I., Niemann, H., Ostrovsky, I., Piskozub, J., Rehder, G., Treude, T., Vielstädte, L., and Greinert, J.: Effects of climate change on methane emissions from seafloor sediments in the Arctic Ocean: A review, Limnol. Oceanogr., 61, https://doi.org/10.1002/lno.10307, 2016.
Jensen, S., Neufeld, J. D., Birkeland, N.-K., Hovland, M., and Murrell, J. C.: Methane assimilation and trophic interactions with marine Methylomicrobium in deep-water coral reef sediment off the coast of Norway, FEMS Microbiol. Ecol., 66, 320–330, 2008.
Kalenitchenko, D., Peru, E., and Galand, P. E.: Historical contingency impacts on community assembly and ecosystem function in chemosynthetic marine ecosystems, Sci. Rep., 11, 13994, https://doi.org/10.1038/s41598-021-92613-1, 2021.
Kalyuzhnaya, M. G., Gomez, O. A., and Murrell, J. C.: The Methane-Oxidizing Bacteria (Methanotrophs), in: Taxonomy, Genomics and Ecophysiology of Hydrocarbon-Degrading Microbes, edited by: Mcgenity, T. J., Springer International Publishing, 245–278, ISBN 978-3-319-60053-6, https://doi.org/10.1007/978-3-319-60053-6_10-1, 2019.
Kessler, J. D., Valentine, D. L., Redmond, M. C., Du, M., Chan, E. W., Mendes, S. D., Quiroz, E. W., Villanueva, C. J., Shusta, S. S., Werra, L. M., Yvon-Lewis, S. A., and Weber, T. C.: A Persistent Oxygen Anomaly Reveals the Fate of Spilled Methane in the Deep Gulf of Mexico, Science, 331, 312–315, 2011.
Knief, C.: Diversity and Habitat Preferences of Cultivated and Uncultivated Aerobic Methanotrophic Bacteria Evaluated Based on pmoA as Molecular Marker, Front. Microbiol., 6, https://doi.org/10.3389/fmicb.2015.01346, 2015.
Knief, C. and Dunfield, P. F.: Response and adaptation of different methanotrophic bacteria to low methane mixing ratios, Environ. Microbiol., 7, 1307–1317, https://doi.org/10.1111/j.1462-2920.2005.00814.x, 2005.
Kox, M. A. R., Haque, M. F. U., Alen, T. A. V., Crombie, A. T., Jetten, M. S. M., Camp, H. J. M. O. D., Dedysh, S. N., Kessel, M. A. H. J. V., and Murrell, J. C.: Complete Genome Sequence of the Aerobic Facultative Methanotroph Methylocella tundrae Strain T4, Microbiol. Resour. Announc., 8, https://doi.org/10.1128/mra.00286-19, 2019.
Leray, M. and Knowlton, N.: Random sampling causes the low reproducibility of rare eukaryotic OTUs in Illumina COI metabarcoding, PeerJ, 5, https://doi.org/10.7717/peerj.3006, 2017.
Li, J., Liu, C., He, X., Santosh, M., Hu, G., Sun, Z., Li, Y., Meng, Q., and Ning, F.: Aerobic microbial oxidation of hydrocarbon gases: Implications for oil and gas exploration, Mar. Petrol. Geol., 103, 76–86, 2019.
Li, J., Xu, X., Liu, C., Wu, N., Sun, Z., He, X., and Chen, Y.: Active Methanotrophs and Their Response to Temperature in Marine Environments: An Experimental Study, J. Mar. Sci. Eng., 9, https://doi.org/10.3390/jmse9111261, 2021.
Love, M. I., Huber, W., and Anders, S.: Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol., 15, https://doi.org/10.1186/s13059-014-0550-8, 2014.
Macalady, J. L., Mcmillan, A. M., Dickens, A. F., Tyler, S. C., and Scow, K. M.: Population dynamics of type I and II methanotrophic bacteria in rice soils, Environ. Microbiol., 4, 148–157, 2002.
Mao, S.-H., Zhang, H.-H., Zhuang, G.-C., Li, X.-J., Liu, Q., Zhou, Z., Wang, W.-L., Li, C.-Y., Lu, K.-Y., Liu, X.-T., Montgomery, A., Joye, S. B., Zhang, Y.-Z., and Yang, G.-P.: Aerobic oxidation of methane significantly reduces global diffusive methane emissions from shallow marine waters, Nat. Commun., 13, https://doi.org/10.1038/s41467-022-35082-y, 2022.
Masson-Delmotte, V., Zhai, P., Pirani, A., Connors, S. L., Péan, C., Berger, S., Caud, N., Chen, Y., Goldfarb, L., Gomis, M. I., Huang, M., Leitzell, K., Lonnoy, E., Matthews, J. B. R., Maycock, T. K., Waterfield, T., Yelekçi, O., Yu, R., Zhou, B.: IPCC, 2021: Climate Change 2021: The Physical Science Basis. Contribution of Working Group I to the Sixth Assessment Report of the Intergovernmental Panel on Climate Change, Cambridge University press, 2391 pp., https://doi.org/10.1017/9781009157896, 2021.
Mau, S., Blees, J., Helmke, E., Niemann, H., and Damm, E.: Vertical distribution of methane oxidation and methanotrophic response to elevated methane concentrations in stratified waters of the Arctic fjord Storfjorden (Svalbard, Norway), Biogeosciences, 10, 6267–6278, https://doi.org/10.5194/bg-10-6267-2013, 2013.
Mau, S., Tu, T.-H., Becker, M., Dos Santos Ferreira, C., Chen, J.-N., Lin, L.-H., Wang, P.-L., Lin, S., and Bohrmann, G.: Methane Seeps and Independent Methane Plumes in the South China Sea Offshore Taiwan, Front. Mar. Sci., 7, https://doi.org/10.3389/fmars.2020.00543, 2020.
Murrell, J. C.: The Aerobic Methane Oxidizing Bacteria (Methanotrophs), in: Handbook of Hydrocarbon and Lipid Microbiology, eddited by: Timmis, K. N., Springer, Berlin, 4699 pp., https://doi.org/10.1007/978-3-540-77587-4_143, 2010.
Niemann, H. and Engelmann, J.: Adaptation of methane oxidising bacteria to environmental changes: implications for coastal methane dynamics – data and scripts, V1, NIOZ [data set] and [code], https://doi.org/10.25850/nioz/7b.b.6h, 2025.
Niemann, H., Steinle, L., Blees, J., Bussmann, I., Treude, T., Krause, S., Elvert, M., and Lehmann, M. F.: Toxic effects of lab-grade butyl rubber stoppers on aerobic methane oxidation, Limnology Oceanogr Methods, 13, 40–52, https://doi.org/10.1002/lom3.10005, 2015.
Pol, A., Heijmans, K., Harhangi, H. R., Tedesco, D., Jetten, M. S. M., and Op Den Camp, H. J. M.: Methanotrophy below pH 1 by a new Verrucomicrobia species, Nature, 450, 874–878, 2007.
Parada, A. E., Needham, D. M., and Fuhrman, J. A.: Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples, Environ. Microbiol., 18, 1403–1414, https://doi.org/10.1111/1462-2920.13023, 2016.
Quince, C., Lanzen, A., Davenport, R. J., and Turnbaugh, P. J.: Removing noise from pyrosequenced amplicons, BMC Bioinformatics, 12, doi.org/10.1186/1471-2105-12-38, 2011.
Ramond, P., Galand, P. E., and Logares, R.: Microbial functional diversity and redundancy: moving forward, FEMS Microbiol. Rev., https://doi.org/10.1093/femsre/fuae031, 2024.
Reeburgh, W. S.: Oceanic Methane Biogeochemistry, Chem. Rev., 107, 486–513, 2007.
Saunois, M., Martinez, A., Poulter, B., Zhang, Z., Raymond, P. A., Regnier, P., Canadell, J. G., Jackson, R. B., Patra, P. K., Bousquet, P., Ciais, P., Dlugokencky, E. J., Lan, X., Allen, G. H., Bastviken, D., Beerling, D. J., Belikov, D. A., Blake, D. R., Castaldi, S., Crippa, M., Deemer, B. R., Dennison, F., Etiope, G., Gedney, N., Höglund-Isaksson, L., Holgerson, M. A., Hopcroft, P. O., Hugelius, G., Ito, A., Jain, A. K., Janardanan, R., Johnson, M. S., Kleinen, T., Krummel, P. B., Lauerwald, R., Li, T., Liu, X., McDonald, K. C., Melton, J. R., Mühle, J., Müller, J., Murguia-Flores, F., Niwa, Y., Noce, S., Pan, S., Parker, R. J., Peng, C., Ramonet, M., Riley, W. J., Rocher-Ros, G., Rosentreter, J. A., Sasakawa, M., Segers, A., Smith, S. J., Stanley, E. H., Thanwerdas, J., Tian, H., Tsuruta, A., Tubiello, F. N., Weber, T. S., Werf, G. R. van der, Worthy, D. E. J., Xi, Y., Yoshida, Y., Zhang, W., Zheng, B., Zhu, Q., Zhu, Q., and Zhuang, Q.: Global Methane Budget 2000–2020, Earth Syst. Sci. Data, 17, 1873–1958, https://doi.org/10.5194/essd-17-1873-2025, 2025.
Sert, M. F., Schweitzer, H. D., De Groot, T. R., Kekäläinen, T., Jänis, J., Bernstein, H. C., Ferré, B., Gründger, F., Kalenitchenko, D., and Niemann, H.: Elevated methane alters dissolved organic matter composition in the Arctic Ocean cold seeps, Front. Earth Sci., 11, https://doi.org/10.3389/feart.2023.1290882, 2023.
Sherry, A., Osborne, K. A., Sidgwick, F. R., Gray, N. D., and Talbot, H. M.: A temperate river estuary is a sink for methanotrophs adapted to extremes of pH, temperature and salinity, Env. Microbiol. Rep., 8, 122–131, 2016.
Shirazi, S., Meyer, R. S., and Shapiro, B.: Revisiting the effect of PCR replication and sequencing depth on biodiversity metrics in environmental DNA metabarcoding, Ecol. Evol., 11, 15766–15779, https://doi.org/10.1002/ece3.8239, 2021.
Steinle, L., Graves, C. A., Treude, T., Ferre, B., Biastoch, A., Bussmann, I., Berndt, C., Krastel, S., James, R. H., Behrens, E., Boning, C. W., Greinert, J., Sapart, C.-J., Scheinert, M., Sommer, S., Lehmann, M. F., and Niemann, H.: Water column methanotrophy controlled by a rapid oceanographic switch, Nat. Geosci., 8, 378–382, https://doi.org/10.1038/ngeo2420, 2015.
Steinle, L., Schmidt, M., Bryant, L., Haeckel, M., Linke, P., Sommer, S., Zopfi, J., Lehmann, M. F., Treude, T., and Niemannn, H.: Linked sediment and water-column methanotrophy at a man-made gas blowout in the North Sea: Implications for methane budgeting in seasonally stratified shallow seas, Limnol. Oceanogr., 61, 367–386, 2016.
Stephens, M.: False discovery rates: a new deal, Biostat. (Oxf., Engl.), 18, 275–294, https://doi.org/10.1093/biostatistics/kxw041, 2017.
Takeuchi, M., Ozaki, H., Hiraoka, S., Kamagata, Y., Sakata, S., Yoshioka, H., and Iwasaki, W.: Possible cross-feeding pathway of facultative methylotroph Methyloceanibacter caenitepidi Gela4 on methanotroph Methylocaldum marinum S8, PloS One, 14, https://doi.org/10.1371/journal.pone.0213535, 2019.
Takeuchi, M., Ozaki, H., Hiraoka, S., Kamagata, Y., Sakata, S., Yoshioka, H., and Iwasaki, W.: Correction: Possible cross-feeding pathway of facultative methylotroph Methyloceanibacter caenitepidi Gela4 on methanotroph Methylocaldum marinum S8, PloS One, 16, https://doi.org/10.1371/journal.pone.0251538, 2021.
Tavormina, P. L., Orphan, V. J., Kalyuzhnaya, M. G., Jetten, M. S., and Klotz, M. G.: A novel family of functional operons encoding methane/ammonia monooxygenase-related proteins in gammaproteobacterial methanotrophs, Env. Microbiol. Rep., 3, https://doi.org/10.1111/j.1758-2229.2010.00192.x, 2011.
Tavormina, P. L., Hatzenpichler, R., McGlynn, S., Chadwick, G., Dawson, K. S., Connon, S. A., and Orphan, V. J.: Methyloprofundus sedimenti gen. nov., sp. nov., an obligate methanotroph from ocean sediment belonging to the `deep sea-1' clade of marine methanotrophs, Int. J. Syst. Evol. Microbiol., 65, 251–259, https://doi.org/10.1099/ijs.0.062927-0, 2015.
Vaksmaa, A., Knittel, K., Abdala Asbun, A., Goudriaan, M., Ellrott, A., Witte, H. J., Vollmer, I., Meirer, F., Lott, C., Weber, M., Engelmann, J. C., and Niemann, H.: Microbial Communities on Plastic Polymers in the Mediterranean Sea, Front. Microbiol., 12, https://doi.org/10.3389/fmicb.2021.673553, 2021.
Vekeman, B., Kerckhof, F.-M., Cremers, G., De Vos, P., Vandamme, P., Boon, N., Op Den Camp, H. J. M., and Heylen, K.: New Methyloceanibacter diversity from North Sea sediments includes methanotroph containing solely the soluble methane monooxygenase, Environ. Microbiol., 18, 4523–4536, 2016.
Weber, T., Wiseman, N. A., and Kock, A.: Global ocean methane emissions dominated by shallow coastal waters, Nat. Commun., 10, https://doi.org/10.1038/s41467-019-12541-7, 2019.
Yao, X., Wang, J., and Hu, B.: How methanotrophs respond to pH: A review of ecophysiology, Front. Microbiol., 13, https://doi.org/10.3389/fmicb.2022.1034164, 2022.
Yu, W.-J., Lee, J.-W., Nguyen, N.-L., Rhee, S.-K., and Park, S.-J.: The characteristics and comparative analysis of methanotrophs reveal genomic insights into Methylomicrobium sp. enriched from marine sediments, Syst. Appl. Microbiol., 41, 415–426, 2018.
Zhang, S., Yan, L., Cao, J., Wang, K., Luo, Y., Hu, H., Wang, L., Yu, R., Pan, B., Yu, K., Zhao, J., and Bao, Z.: Salinity significantly affects methane oxidation and methanotrophic community in Inner Mongolia lake sediments, Front. Microbiol., 13, https://doi.org/10.3389/fmicb.2022.1067017, 2023
Zobell, C. E.: The effect of solid surfaces upon bacterial activity, J. Bacteriol., 46, 39–56, 1943.
Short summary
In the ocean, the potent greenhouse gas methane is largely produced – but also consumed – in coastal systems before reaching the atmosphere. Rising temperatures and shifting precipitation patterns will likely impact the community composition of aerobic methanotrophic bacteria (MOBs). Experiments with North Sea and Wadden Sea water showed that methane availability increased MOB abundance but that different MOB types could thrive under drastically changed environmental conditions.
In the ocean, the potent greenhouse gas methane is largely produced – but also consumed – in...
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