{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,29]],"date-time":"2026-07-29T07:09:57Z","timestamp":1785308997564,"version":"3.55.0"},"reference-count":69,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,11,3]],"date-time":"2025-11-03T00:00:00Z","timestamp":1762128000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2025,11,3]],"date-time":"2025-11-03T00:00:00Z","timestamp":1762128000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"DOI":"10.13039\/100004457","name":"The World Academy of Sciences","doi-asserted-by":"publisher","award":["TWAS-Sida Scholarship"],"award-info":[{"award-number":["TWAS-Sida Scholarship"]}],"id":[{"id":"10.13039\/100004457","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000277","name":"Department for Environment, Food and Rural Affairs, UK Government","doi-asserted-by":"publisher","award":["OCPP"],"award-info":[{"award-number":["OCPP"]}],"id":[{"id":"10.13039\/501100000277","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100011054","name":"Danish International Development Agency","doi-asserted-by":"publisher","award":["21-01-KU"],"award-info":[{"award-number":["21-01-KU"]}],"id":[{"id":"10.13039\/501100011054","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"DOI":"10.1038\/s41598-025-22768-8","type":"journal-article","created":{"date-parts":[[2025,11,3]],"date-time":"2025-11-03T15:52:46Z","timestamp":1762185166000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Identification of microbial groups and functional genes associated with greenhouse gas emissions in prawn farms"],"prefix":"10.1038","volume":"15","author":[{"given":"Abul","family":"Bashar","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amaru Miranda","family":"Djurhuus","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patrick Denis","family":"Browne","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Raju","family":"Podduturi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Md. Zahid","family":"Hasan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abdullah","family":"Al Rakib","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chantelle","family":"Hooper","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Morena","family":"Santi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"H. M. Rakibul","family":"Islam","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Neaz A","family":"Hasan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muhammad Tofazzal","family":"Hossain","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M. M. R.","family":"Jahangir","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Bass","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Md Ismail","family":"Hossain","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Niels O. G.","family":"J\u00f8rgensen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lars Hestbjerg","family":"Hansen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohammad Mahfujul","family":"Haque","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,11,3]]},"reference":[{"key":"22768_CR1","doi-asserted-by":"crossref","first-page":"738","DOI":"10.1111\/raq.12754","volume":"15","author":"C Hooper","year":"2023","unstructured":"Hooper, C. et al. Diseases of the giant river Prawn macrobrachium rosenbergii: A review for a growing industry. Rev. Aquac. 15, 738\u2013758 (2023).","journal-title":"Rev. Aquac"},{"key":"22768_CR2","doi-asserted-by":"crossref","first-page":"2017","DOI":"10.1002\/fsn3.1031","volume":"7","author":"TMT Nguyen","year":"2019","unstructured":"Nguyen, T. M. T., Chen, T. Y., Shiau, C. Y., Cheng, Y. T. & Chang, Y. W. Study on biochemical divergences of the meat and egg of freshwater prawns (Macrobrachium rosenbergii). Food Sci. Nutr. 7, 2017\u20132023 (2019).","journal-title":"Food Sci. Nutr."},{"key":"22768_CR3","doi-asserted-by":"crossref","first-page":"3806","DOI":"10.1016\/j.jclepro.2017.06.110","volume":"172","author":"N Ahmed","year":"2018","unstructured":"Ahmed, N., Thompson, S. & Glaser, M. Transforming organic Prawn farming in bangladesh: potentials and challenges. J. Clean. Prod. 172, 3806\u20133816 (2018).","journal-title":"J. Clean. Prod."},{"key":"22768_CR4","doi-asserted-by":"crossref","first-page":"3769","DOI":"10.1111\/are.13844","volume":"49","author":"FS David","year":"2018","unstructured":"David, F. S., Fonseca, T., Wolff Bueno, G. & Valenti, W. C. Economic feasibility of intensification of macrobrachium Rosenbergii hatchery. Aquac Res. 49, 3769\u20133776 (2018).","journal-title":"Aquac Res."},{"key":"22768_CR5","doi-asserted-by":"crossref","first-page":"100853","DOI":"10.1016\/j.ecocom.2020.100853","volume":"43","author":"H Bergland","year":"2020","unstructured":"Bergland, H., Burlakov, E., Pedersen, P. A. & Wyller, J. Aquaculture, pollution and fishery - dynamics of marine industrial interactions. Ecol. Complex. 43, 100853 (2020).","journal-title":"Ecol. Complex."},{"key":"22768_CR6","doi-asserted-by":"crossref","first-page":"548","DOI":"10.1038\/s43016-024-01005-x","volume":"5","author":"DL Ar\u00e9valo-Mart\u00ednez","year":"2024","unstructured":"Ar\u00e9valo-Mart\u00ednez, D. L. Offshore aquaculture greenhouse gas emissions based on ocean net primary productivity. Nat. Food. 5, 548\u2013549 (2024).","journal-title":"Nat. Food"},{"key":"22768_CR7","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1007\/s10533-015-0099-y","volume":"124","author":"MA Holgerson","year":"2015","unstructured":"Holgerson, M. A. Drivers of carbon dioxide and methane supersaturation in small, temporary ponds on JSTOR. Biogeochemistry 124, 305\u2013318 (2015).","journal-title":"Biogeochemistry"},{"key":"22768_CR8","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1016\/j.atmosenv.2015.05.067","volume":"115","author":"P Yang","year":"2015","unstructured":"Yang, P., He, Q., Huang, J. & Tong, C. Fluxes of greenhouse gases at two different aquaculture ponds in the coastal zone of southeastern China. Atmos. Environ. 115, 269\u2013277 (2015).","journal-title":"Atmos. Environ."},{"key":"22768_CR9","doi-asserted-by":"crossref","unstructured":"MacLeod, M. J., Hasan, M. R., Robb, D. H. F. & Mamun-Ur-Rashid, M. Quantifying greenhouse gas emissions from global aquaculture. Sci. Rep. 10, 1\u20138 (2020).","DOI":"10.1038\/s41598-020-68231-8"},{"key":"22768_CR10","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1002\/fee.1482","volume":"15","author":"J Boone Kauffman","year":"2017","unstructured":"Boone Kauffman, J. et al. The Jumbo carbon footprint of a shrimp: carbon losses from Mangrove deforestation. Front. Ecol. Environ. 15, 183\u2013188 (2017).","journal-title":"Front. Ecol. Environ."},{"key":"22768_CR11","doi-asserted-by":"publisher","unstructured":"Zhang, H. et al. Editorial: microbial ecology and function of the aquatic systems. Front Microbiol 13, 1109221 (2023). https:\/\/doi.org\/10.3389\/fmicb.2022.1109221","DOI":"10.3389\/fmicb.2022.1109221"},{"key":"22768_CR12","doi-asserted-by":"crossref","first-page":"672","DOI":"10.1038\/s41597-024-03528-1","volume":"11","author":"N Pechlivanis","year":"2024","unstructured":"Pechlivanis, N. et al. Microbial co-occurrence network demonstrates Spatial and Climatic trends for global soil diversity. Sci. Data. 11, 672 (2024).","journal-title":"Sci. Data"},{"key":"22768_CR13","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1111\/1462-2920.16161","volume":"25","author":"Y Ahn","year":"2023","unstructured":"Ahn, Y., Lee, J. A., Choi, K. R., Bang, J. & Lee, S. Y. Can microbes be Harnessed to reduce atmospheric loads of greenhouse gases? Environ. Microbiol. 25, 17\u201325 (2023).","journal-title":"Environ. Microbiol."},{"key":"22768_CR14","doi-asserted-by":"crossref","first-page":"172108","DOI":"10.1016\/j.scitotenv.2024.172108","volume":"926","author":"M Deng","year":"2024","unstructured":"Deng, M. et al. Greenhouse gases emissions from aquaculture ponds: different emission patterns and key microbial processes affected by increased nitrogen loading. Sci. Total Environ. 926, 172108 (2024).","journal-title":"Sci. Total Environ."},{"key":"22768_CR15","doi-asserted-by":"crossref","first-page":"118520","DOI":"10.1016\/j.watres.2022.118520","volume":"218","author":"G Lin","year":"2022","unstructured":"Lin, G. & Lin, X. Bait input altered microbial community structure and increased greenhouse gases production in coastal wetland sediment. Water Res. 218, 118520 (2022).","journal-title":"Water Res."},{"key":"22768_CR16","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1038\/s41558-017-0063-z","volume":"8","author":"TA Davidson","year":"2018","unstructured":"Davidson, T. A. et al. Synergy between nutrients and warming enhances methane ebullition from experimental lakes. Nat. Clim. Chang. 8, 156\u2013160 (2018).","journal-title":"Nat. Clim. Chang."},{"key":"22768_CR17","doi-asserted-by":"crossref","first-page":"569","DOI":"10.1038\/s41579-019-0222-5","volume":"17","author":"R Cavicchioli","year":"2019","unstructured":"Cavicchioli, R. et al. Scientists\u2019 warning to humanity: microorganisms and climate change. Nat. Rev. Microbiol. 17, 569\u2013586 (2019).","journal-title":"Nat. Rev. Microbiol."},{"key":"22768_CR18","first-page":"1046","volume":"358","author":"MG Pachiadaki","year":"2017","unstructured":"Pachiadaki, M. G. et al. Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation. Sci. (1979). 358, 1046\u20131051 (2017).","journal-title":"Sci. (1979)"},{"key":"22768_CR19","doi-asserted-by":"crossref","first-page":"120943","DOI":"10.1016\/j.watres.2023.120943","volume":"249","author":"P Yang","year":"2024","unstructured":"Yang, P. et al. Significant inter-annual fluctuation in CO2 and CH4 diffusive fluxes from subtropical aquaculture ponds: implications for climate change and carbon emission evaluations. Water Res. 249, 120943 (2024).","journal-title":"Water Res."},{"key":"22768_CR20","doi-asserted-by":"crossref","first-page":"20200184","DOI":"10.1098\/rspb.2020.0184","volume":"287","author":"WB Perry","year":"2020","unstructured":"Perry, W. B., Lindsay, E., Payne, C. J., Brodie, C. & Kazlauskaite, R. The role of the gut Microbiome in sustainable teleost aquaculture. Proc. Royal Soc. B: Biol. Sci. 287, 20200184 (2020).","journal-title":"Proc. Royal Soc. B: Biol. Sci."},{"key":"22768_CR21","doi-asserted-by":"publisher","unstructured":"Gao, Y. & Wu, M. Accounting for 16S rRNA copy number prediction uncertainty and its implications in bacterial diversity analyses. ISME Communications 3, 59 (2023). https:\/\/doi.org\/10.1038\/s43705-023-00266-0","DOI":"10.1038\/s43705-023-00266-0"},{"key":"22768_CR22","doi-asserted-by":"crossref","first-page":"2743","DOI":"10.1038\/s41598-023-27816-9","volume":"13","author":"BLDU Pushpakumara","year":"2023","unstructured":"Pushpakumara, B. L. D. U., Tandon, K., Willis, A. & Verbruggen, H. Unravelling microalgal-bacterial interactions in aquatic ecosystems through 16S rRNA gene-based co-occurrence networks. Sci. Rep. 13, 2743 (2023).","journal-title":"Sci. Rep."},{"key":"22768_CR23","first-page":"001203","volume":"10","author":"MS Matchado","year":"2024","unstructured":"Matchado, M. S. et al. On the limits of 16S rRNA gene-based metagenome prediction and functional profiling. Microb. Genom. 10, 001203 (2024).","journal-title":"Microb. Genom"},{"key":"22768_CR24","doi-asserted-by":"crossref","first-page":"1279041","DOI":"10.3389\/fmicb.2023.1279041","volume":"14","author":"X Han","year":"2023","unstructured":"Han, X. et al. Synthetic oligonucleotides as quantitative PCR standards for quantifying microbial genes. Front. Microbiol. 14, 1279041 (2023).","journal-title":"Front. Microbiol."},{"key":"22768_CR25","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1016\/j.soilbio.2019.02.006","volume":"132","author":"S Turner","year":"2019","unstructured":"Turner, S., Mikutta, R., Guggenberger, G., Schaarschmidt, F. & Schippers, A. Distinct pattern of nitrogen functional gene abundances in top- and subsoils along a 120,000-year ecosystem development gradient. Soil. Biol. Biochem. 132, 111\u2013119 (2019).","journal-title":"Soil. Biol. Biochem."},{"key":"22768_CR26","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1111\/1751-7915.12094","volume":"7","author":"R Morris","year":"2014","unstructured":"Morris, R. et al. Methyl coenzyme M reductase (mcrA) gene abundance correlates with activity measurements of methanogenic H\u2082 \/CO\u2082 -enriched anaerobic biomass. Microb. Biotechnol. 7, 77\u201384 (2014).","journal-title":"Microb. Biotechnol."},{"key":"22768_CR27","doi-asserted-by":"publisher","unstructured":"Lynes, M. M. et al. Diversity and function of methyl-coenzyme M reductase-encoding archaea in Yellowstone hot springs revealed by metagenomics and mesocosm experiments. ISME Communications 3, 22 (2023). https:\/\/doi.org\/10.1038\/s43705-023-00225-9","DOI":"10.1038\/s43705-023-00225-9"},{"key":"22768_CR28","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1016\/j.jenvman.2012.07.021","volume":"111","author":"D Traversi","year":"2012","unstructured":"Traversi, D., Villa, S., Lorenzi, E., Degan, R. & Gilli, G. Application of a real-time qPCR method to measure the methanogen concentration during anaerobic digestion as an indicator of biogas production capacity. J. Environ. Manage. 111, 173\u2013177 (2012).","journal-title":"J. Environ. Manage."},{"key":"22768_CR29","doi-asserted-by":"crossref","first-page":"1020","DOI":"10.1038\/ismej.2013.226","volume":"8","author":"T Watsuji","year":"2014","unstructured":"Watsuji, T. et al. Diversity and methane oxidation of active epibiotic methanotrophs on live Shinkaia crosnieri. ISME J. 8, 1020\u20131031 (2014).","journal-title":"ISME J."},{"key":"22768_CR30","doi-asserted-by":"crossref","first-page":"1160","DOI":"10.1038\/s41598-021-04486-z","volume":"12","author":"I Altshuler","year":"2022","unstructured":"Altshuler, I. et al. Unique high Arctic methane metabolizing community revealed through in situ 13CH4-DNA-SIP enrichment in concert with genome Binning. Sci. Rep. 12, 1160 (2022).","journal-title":"Sci. Rep."},{"key":"22768_CR31","doi-asserted-by":"crossref","first-page":"392","DOI":"10.1111\/1758-2229.13155","volume":"15","author":"R Shinjo","year":"2023","unstructured":"Shinjo, R. et al. Type-specific quantification of particulate methane monooxygenase gene of methane-oxidizing bacteria at the oxic-anoxic interface of a surface paddy soil by digital PCR. Environ. Microbiol. Rep. 15, 392\u2013403 (2023).","journal-title":"Environ. Microbiol. Rep."},{"key":"22768_CR32","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1128\/AEM.02654-14","volume":"81","author":"J Li","year":"2015","unstructured":"Li, J. et al. AmoA gene abundances and nitrification potential rates suggest that benthic Ammonia-Oxidizing bacteria and not archaea dominate N cycling in the Colne Estuary, united Kingdom. Appl. Environ. Microbiol. 81, 159\u2013165 (2015).","journal-title":"Appl. Environ. Microbiol."},{"key":"22768_CR33","doi-asserted-by":"crossref","first-page":"43283","DOI":"10.1038\/srep43283","volume":"7","author":"L Yang","year":"2017","unstructured":"Yang, L., Zhang, X. & Ju, X. Linkage between N2O emission and functional gene abundance in an intensively managed calcareous fluvo-aquic soil. Sci. Rep. 7, 43283 (2017).","journal-title":"Sci. Rep."},{"key":"22768_CR34","doi-asserted-by":"publisher","unstructured":"Yoon, S. et al. Suggested role of NosZ in preventing N2O inhibition of dissimilatory nitrite reduction to ammonium. mBio 14, e01540-23 (2023). https:\/\/doi.org\/10.1128\/mbio.01540-23","DOI":"10.1128\/mbio.01540-23"},{"key":"22768_CR35","doi-asserted-by":"crossref","first-page":"805","DOI":"10.1038\/ismej.2008.58","volume":"2","author":"RD Bardgett","year":"2008","unstructured":"Bardgett, R. D., Freeman, C. & Ostle, N. J. Microbial contributions to climate change through carbon cycle feedbacks. ISME J. 2, 805\u2013814 (2008).","journal-title":"ISME J."},{"key":"22768_CR36","doi-asserted-by":"crossref","first-page":"2361","DOI":"10.3390\/pr10112361","volume":"10","author":"H Wang","year":"2022","unstructured":"Wang, H. et al. Microbial-Mediated emissions of greenhouse gas from farmland soils: A review. Processes 10, 2361 (2022).","journal-title":"Processes"},{"key":"22768_CR37","doi-asserted-by":"publisher","unstructured":"Muhammad, I. et al. Regulation of soil microbial community structure and biomass to mitigate soil greenhouse gas emission. Front Microbiol 13, 868862 (2022). https:\/\/doi.org\/10.3389\/fmicb.2022.868862","DOI":"10.3389\/fmicb.2022.868862"},{"key":"22768_CR38","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1016\/j.scitotenv.2018.05.040","volume":"637\u2013638","author":"Y Ma","year":"2018","unstructured":"Ma, Y. et al. A comparison of methane and nitrous oxide emissions from inland mixed-fish and crab aquaculture ponds. Sci. Total Environ. 637\u2013638, 517\u2013523 (2018).","journal-title":"Sci. Total Environ."},{"key":"22768_CR39","doi-asserted-by":"crossref","first-page":"1025","DOI":"10.1016\/j.scitotenv.2018.04.102","volume":"635","author":"P Yang","year":"2018","unstructured":"Yang, P. et al. Fluxes of carbon dioxide and methane across the water\u2013atmosphere interface of aquaculture shrimp ponds in two subtropical estuaries: the effect of temperature, substrate, salinity and nitrate. Sci. Total Environ. 635, 1025\u20131035 (2018).","journal-title":"Sci. Total Environ."},{"key":"22768_CR40","doi-asserted-by":"crossref","first-page":"737229","DOI":"10.1016\/j.aquaculture.2021.737229","volume":"545","author":"C Tong","year":"2021","unstructured":"Tong, C. et al. Annual CO2 and CH4 fluxes in coastal earthen ponds with Litopenaeus vannamei in southeastern China. Aquaculture 545, 737229 (2021).","journal-title":"Aquaculture"},{"key":"22768_CR41","doi-asserted-by":"crossref","first-page":"6470","DOI":"10.1021\/es300110x","volume":"46","author":"Z Hu","year":"2012","unstructured":"Hu, Z., Lee, J. W., Chandran, K., Kim, S. & Khanal, S. K. Nitrous oxide (N2O) emission from aquaculture: A review. Environ. Sci. Technol. 46, 6470\u20136480 (2012).","journal-title":"Environ. Sci. Technol."},{"key":"22768_CR42","doi-asserted-by":"crossref","first-page":"108029","DOI":"10.1016\/j.agee.2022.108029","volume":"336","author":"W Ye","year":"2022","unstructured":"Ye, W. et al. Greenhouse gas emissions from fed mollusk mariculture: A case study of a sinonovacula constricta farming system. Agric. Ecosyst. Environ. 336, 108029 (2022).","journal-title":"Agric. Ecosyst. Environ."},{"key":"22768_CR43","doi-asserted-by":"crossref","first-page":"318","DOI":"10.1038\/s41558-019-0425-9","volume":"9","author":"J Yuan","year":"2019","unstructured":"Yuan, J. et al. Rapid growth in greenhouse gas emissions from the adoption of industrial-scale aquaculture. Nat. Clim. Chang. 9, 318\u2013322 (2019).","journal-title":"Nat. Clim. Chang."},{"key":"22768_CR44","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1016\/S0144-8609(99)00024-2","volume":"21","author":"LE Meijer","year":"1999","unstructured":"Meijer, L. E. & Avnimelech, Y. On the use of micro-electrodes in fish pond sediments. Aquac Eng. 21, 71\u201383 (1999).","journal-title":"Aquac Eng."},{"key":"22768_CR45","doi-asserted-by":"crossref","first-page":"1274","DOI":"10.3390\/agronomy11071274","volume":"11","author":"KH Chen","year":"2021","unstructured":"Chen, K. H., Longley, R., Bonito, G. & Liao, H. L. A Two-Step PCR protocol enabling flexible primer choice and high sequencing yield for illumina miseq Meta-Barcoding. Agronomy 11, 1274 (2021).","journal-title":"Agronomy"},{"key":"22768_CR46","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1111\/1758-2229.12251","volume":"7","author":"M Hugoni","year":"2015","unstructured":"Hugoni, M. et al. Temporal dynamics of active archaea in oxygen-depleted zones of two deep lakes. Environ. Microbiol. Rep. 7, 321\u2013329 (2015).","journal-title":"Environ. Microbiol. Rep."},{"key":"22768_CR47","doi-asserted-by":"publisher","unstructured":"Pausan, M. R. et al. Exploring the archaeome: detection of archaeal signatures in the human body. Front Microbiol 10, 2796 (2019). https:\/\/doi.org\/10.3389\/fmicb.2019.02796","DOI":"10.3389\/fmicb.2019.02796"},{"key":"22768_CR48","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1038\/s41587-019-0209-9","volume":"37","author":"E Bolyen","year":"2019","unstructured":"Bolyen, E. et al. Reproducible, interactive, scalable and extensible Microbiome data science using QIIME 2. Nat. Biotechnol. 37, 852\u2013857 (2019).","journal-title":"Nat. Biotechnol."},{"key":"22768_CR49","doi-asserted-by":"crossref","first-page":"W293","DOI":"10.1093\/nar\/gkab301","volume":"49","author":"I Letunic","year":"2021","unstructured":"Letunic, I. & Bork, P. Interactive tree of life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 49, W293\u2013W296 (2021).","journal-title":"Nucleic Acids Res."},{"key":"22768_CR50","doi-asserted-by":"publisher","unstructured":"Bashar, A. et al. Optimized cloning protocol for standard curve generation in qPCR of environmental functional genes. Protocols.io (2024). https:\/\/doi.org\/10.17504\/protocols.io.5qpvok2odl4o\/v1","DOI":"10.17504\/protocols.io.5qpvok2odl4o\/v1"},{"key":"22768_CR51","doi-asserted-by":"crossref","first-page":"4435","DOI":"10.1128\/AEM.02858-08","volume":"75","author":"LM Steinberg","year":"2009","unstructured":"Steinberg, L. M. & Regan, J. M. mcrA-Targeted Real-Time quantitative PCR method to examine methanogen communities. Appl. Environ. Microbiol. 75, 4435\u20134442 (2009).","journal-title":"Appl. Environ. Microbiol."},{"key":"22768_CR52","doi-asserted-by":"publisher","unstructured":"Bashar, A., Djurhuus, A. M., J\u00f8rgensen, N. O. G., Hansen, L. H. & Haque, M. M. Scripts for GHG-Microbes consortium publication. Zenodo (2024). https:\/\/doi.org\/10.5281\/zenodo.13214257","DOI":"10.5281\/zenodo.13214257"},{"key":"22768_CR53","doi-asserted-by":"crossref","first-page":"2385","DOI":"10.1038\/s41467-024-46792-w","volume":"15","author":"MA Anthony","year":"2024","unstructured":"Anthony, M. A. et al. Fungal community composition predicts forest carbon storage at a continental scale. Nat. Commun. 15, 2385 (2024).","journal-title":"Nat. Commun."},{"key":"22768_CR54","first-page":"987","volume":"360","author":"J Poore","year":"2018","unstructured":"Poore, J. & Nemecek, T. Reducing food\u2019s environmental impacts through producers and consumers. Sci. (1979). 360, 987\u2013992 (2018).","journal-title":"Sci. (1979)"},{"key":"22768_CR55","doi-asserted-by":"crossref","first-page":"5489","DOI":"10.1128\/jb.174.17.5489-5495.1992","volume":"174","author":"JG Ferry","year":"1992","unstructured":"Ferry, J. G. Methane from acetate. J. Bacteriol. 174, 5489\u20135495 (1992).","journal-title":"J. Bacteriol."},{"key":"22768_CR56","doi-asserted-by":"crossref","first-page":"330","DOI":"10.1038\/ismej.2017.150","volume":"12","author":"SA Carr","year":"2018","unstructured":"Carr, S. A. et al. Acetoclastic Methanosaeta are dominant methanogens in organic-rich Antarctic marine sediments. ISME J. 12, 330\u2013342 (2018).","journal-title":"ISME J."},{"key":"22768_CR57","doi-asserted-by":"crossref","first-page":"408","DOI":"10.1039\/C3EE42189A","volume":"7","author":"AE Rotaru","year":"2014","unstructured":"Rotaru, A. E. et al. A new model for electron flow during anaerobic digestion: direct interspecies electron transfer to Methanosaeta for the reduction of carbon dioxide to methane. Energy Environ. Sci. 7, 408\u2013415 (2014).","journal-title":"Energy Environ. Sci."},{"key":"22768_CR58","doi-asserted-by":"crossref","first-page":"340","DOI":"10.1111\/1462-2920.15316","volume":"23","author":"LA Zinke","year":"2021","unstructured":"Zinke, L. A. et al. Evidence for non-methanogenic metabolisms in globally distributed archaeal clades basal to the methanomassiliicoccales. Environ. Microbiol. 23, 340\u2013357 (2021).","journal-title":"Environ. Microbiol."},{"key":"22768_CR59","doi-asserted-by":"crossref","first-page":"1428","DOI":"10.1038\/ncomms2432","volume":"4","author":"M Poulsen","year":"2013","unstructured":"Poulsen, M. et al. Methylotrophic methanogenic thermoplasmata implicated in reduced methane emissions from bovine rumen. Nat. Commun. 4, 1428 (2013).","journal-title":"Nat. Commun."},{"key":"22768_CR60","doi-asserted-by":"crossref","first-page":"6967","DOI":"10.1128\/JB.01829-12","volume":"194","author":"G Guti\u00e9rrez","year":"2012","unstructured":"Guti\u00e9rrez, G. Draft genome sequence of methanobacterium formicicum DSM 3637, an Archaebacterium isolated from the methane producer amoeba pelomyxa palustris. J. Bacteriol. 194, 6967\u20136968 (2012).","journal-title":"J. Bacteriol."},{"key":"22768_CR61","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1038\/ismej.2017.173","volume":"12","author":"Z Lyu","year":"2018","unstructured":"Lyu, Z. & Lu, Y. Metabolic shift at the class level sheds light on adaptation of methanogens to oxidative environments. ISME J. 12, 411\u2013423 (2018).","journal-title":"ISME J."},{"key":"22768_CR62","doi-asserted-by":"crossref","first-page":"287","DOI":"10.2478\/s11756-019-00190-6","volume":"74","author":"M Kumar","year":"2019","unstructured":"Kumar, M. et al. Biodiversity of Methylotrophic microbial communities and their potential role in mitigation of abiotic stresses in plants. Biol. (Bratisl). 74, 287\u2013308 (2019).","journal-title":"Biol. (Bratisl)"},{"key":"22768_CR63","doi-asserted-by":"crossref","first-page":"1477","DOI":"10.1038\/s41467-024-45758-2","volume":"15","author":"HT Ouboter","year":"2024","unstructured":"Ouboter, H. T. et al. Mechanisms of extracellular electron transfer in anaerobic methanotrophic archaea. Nat. Commun. 15, 1477 (2024).","journal-title":"Nat. Commun."},{"key":"22768_CR64","first-page":"3195","volume":"14","author":"P Li","year":"2022","unstructured":"Li, P., Peng, Y., Wang, S. & Liu, Y. N2O emission from partial nitrification and full nitrification in domestic wastewater treatment process. Water (Basel). 14, 3195 (2022).","journal-title":"Water (Basel)"},{"key":"22768_CR65","doi-asserted-by":"crossref","first-page":"5350","DOI":"10.1038\/ncomms6350","volume":"5","author":"MJ Bogard","year":"2014","unstructured":"Bogard, M. J. et al. Oxic water column methanogenesis as a major component of aquatic CH4 fluxes. Nat. Commun. 5, 5350 (2014).","journal-title":"Nat. Commun."},{"key":"22768_CR66","doi-asserted-by":"crossref","first-page":"19657","DOI":"10.1073\/pnas.1110716108","volume":"108","author":"HP Grossart","year":"2011","unstructured":"Grossart, H. P., Frindte, K., Dziallas, C., Eckert, W. & Tang, K. W. Microbial methane production in oxygenated water column of an oligotrophic lake. Proc. Natl. Acad. Sci. 108, 19657\u201319661 (2011).","journal-title":"Proc. Natl. Acad. Sci."},{"key":"22768_CR67","doi-asserted-by":"crossref","unstructured":"Preston, C. M., Wu, K. Y., Molinski, T. F. & DeLong, E. F. A psychrophilic crenarchaeon inhabits a marine sponge: Cenarchaeum symbiosum gen. nov., sp. nov. Proc. Natl. Acad. Sci. 93, 6241\u20136246 (1996).","DOI":"10.1073\/pnas.93.13.6241"},{"key":"22768_CR68","doi-asserted-by":"crossref","first-page":"1460","DOI":"10.1016\/j.biotechadv.2014.09.004","volume":"32","author":"X Ge","year":"2014","unstructured":"Ge, X., Yang, L., Sheets, J. P., Yu, Z. & Li, Y. Biological conversion of methane to liquid fuels: status and opportunities. Biotechnol. Adv. 32, 1460\u20131475 (2014).","journal-title":"Biotechnol. Adv."},{"key":"22768_CR69","doi-asserted-by":"crossref","first-page":"1799","DOI":"10.1038\/ismej.2017.51","volume":"11","author":"HK Marchant","year":"2017","unstructured":"Marchant, H. K. et al. Denitrifying community in coastal sediments performs aerobic and anaerobic respiration simultaneously. ISME J. 11, 1799\u20131812 (2017).","journal-title":"ISME J."}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41598-025-22768-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-025-22768-8","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-025-22768-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,12,30]],"date-time":"2025-12-30T01:02:58Z","timestamp":1767056578000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41598-025-22768-8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,11,3]]},"references-count":69,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["22768"],"URL":"https:\/\/doi.org\/10.1038\/s41598-025-22768-8","relation":{},"ISSN":["2045-2322"],"issn-type":[{"value":"2045-2322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,11,3]]},"assertion":[{"value":"5 June 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"30 September 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"3 November 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no competing interests.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}},{"value":"Ethical approval for this study was received from the Ethical Standard of Research Committee of Bangladesh Agricultural University (Reference No: 977\/BAURES\/ESRC\/FISH\/31; Date: September 10, 2023).","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}}],"article-number":"38450"}}