{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T09:48:52Z","timestamp":1792057732283,"version":"4.4.0"},"reference-count":96,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,7,16]],"date-time":"2026-07-16T00:00:00Z","timestamp":1784160000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T00:00:00Z","timestamp":1791763200000},"content-version":"vor","delay-in-days":88,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Biol"],"DOI":"10.1186\/s12915-026-02685-6","type":"journal-article","created":{"date-parts":[[2026,7,16]],"date-time":"2026-07-16T08:34:39Z","timestamp":1784190879000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Diversity and potential ecological roles of viruses in Pleistocene permafrost"],"prefix":"10.1186","volume":"24","author":[{"given":"Changhua","family":"He","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuntong","family":"Du","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karen G.","family":"Lloyd","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tatiana A.","family":"Vishnivetskaya","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elizaveta M.","family":"Rivkina","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hongchen","family":"Jiang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Renxing","family":"Liang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,7,16]]},"reference":[{"issue":"3-4","key":"2685_CR1","doi-asserted-by":"publisher","first-page":"158","DOI":"10.1016\/j.earscirev.2011.06.007","volume":"108","author":"W Dobinski","year":"2011","unstructured":"Dobinski W. Permafrost. Earth-Sci Rev. 2011;108(3\u20134):158\u201369.","journal-title":"Earth-Sci Rev"},{"issue":"2","key":"2685_CR2","doi-asserted-by":"publisher","DOI":"10.1093\/femsec\/fiaa260","volume":"97","author":"A Abramov","year":"2021","unstructured":"Abramov A, Vishnivetskaya T, Rivkina E. Are permafrost microorganisms as old as permafrost? FEMS Microbiol Ecol. 2021;97(2):fiaa260.","journal-title":"FEMS Microbiol Ecol"},{"issue":"17","key":"2685_CR3","doi-asserted-by":"publisher","first-page":"5007","DOI":"10.1111\/gcb.16231","volume":"28","author":"JG Ernakovich","year":"2022","unstructured":"Ernakovich JG, Barbato RA, Rich VI, Sch\u00e4del C, Hewitt RE, Doherty SJ, et al. Microbiome assembly in thawing permafrost and its feedbacks to climate. Glob Change Biol. 2022;28(17):5007\u201326.","journal-title":"Glob Change Biol"},{"key":"2685_CR4","doi-asserted-by":"publisher","DOI":"10.1093\/femsml\/uqac003","author":"S Rigou","year":"2022","unstructured":"Rigou S, Christo-Foroux E, Santini S, Goncharov A, Strauss J, Grosse G, et al. Metagenomic survey of the microbiome of ancient Siberian permafrost and modern Kamchatkan cryosols. MicroLife. 2022. https:\/\/doi.org\/10.1093\/femsml\/uqac003.","journal-title":"MicroLife"},{"issue":"6","key":"2685_CR5","doi-asserted-by":"publisher","first-page":"1252","DOI":"10.1002\/edn3.446","volume":"5","author":"A Perfumo","year":"2023","unstructured":"Perfumo A, \u00c7abuk U, Schulte L, Courtin J, Harms L, Stoof\u2010Leichsenring KR, et al. Paleometagenomics reveals environmental microbiome response to vegetation changes in northern Siberia over the millennia. Environ DNA. 2023;5(6):1252\u201364.","journal-title":"Environ DNA"},{"key":"2685_CR6","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2019.01442","volume":"10","author":"BM Tripathi","year":"2019","unstructured":"Tripathi BM, Kim HM, Jung JY, Nam S, Ju HT, Kim M, et al. Distinct taxonomic and functional profiles of the microbiome associated with different soil horizons of a moist tussock tundra in Alaska. Front Microbiol. 2019;10:1442.","journal-title":"Front Microbiol"},{"issue":"3","key":"2685_CR7","doi-asserted-by":"publisher","DOI":"10.1093\/femsec\/fiab008","volume":"97","author":"M Varsadiya","year":"2021","unstructured":"Varsadiya M, Urich T, Hugelius G, B\u00e1rta J. Microbiome structure and functional potential in permafrost soils of the Western Canadian Arctic. FEMS Microbiol Ecol. 2021;97(3):fiab008.","journal-title":"FEMS Microbiol Ecol"},{"issue":"1","key":"2685_CR8","doi-asserted-by":"publisher","first-page":"208","DOI":"10.1186\/s40168-021-01154-2","volume":"9","author":"G Trubl","year":"2021","unstructured":"Trubl G, Kimbrel JA, Liquet-Gonzalez J, Nuccio EE, Weber PK, Pett-Ridge J, et al. Active virus-host interactions at sub-freezing temperatures in Arctic peat soil. Microbiome. 2021;9(1):208.","journal-title":"Microbiome"},{"issue":"1","key":"2685_CR9","doi-asserted-by":"publisher","first-page":"5853","DOI":"10.1038\/s41467-022-33633-x","volume":"13","author":"S Rigou","year":"2022","unstructured":"Rigou S, Santini S, Abergel C, Claverie JM, Legendre M. Past and present giant viruses diversity explored through permafrost metagenomics. Nat Commun. 2022;13(1):5853.","journal-title":"Nat Commun"},{"issue":"6","key":"2685_CR10","doi-asserted-by":"publisher","DOI":"10.1128\/msystems.00582-22","volume":"7","author":"R Wu","year":"2022","unstructured":"Wu R, Bottos EM, Danna VG, Stegen JC, Jansson JK, Davison MR. RNA viruses linked to eukaryotic hosts in thawed permafrost. mSystems. 2022;7(6):e00582-22.","journal-title":"mSystems"},{"issue":"8","key":"2685_CR11","doi-asserted-by":"publisher","first-page":"870","DOI":"10.1038\/s41564-018-0190-y","volume":"3","author":"JB Emerson","year":"2018","unstructured":"Emerson JB, Roux S, Brum JR, Bolduc B, Woodcroft BJ, Jang HB, et al. Host-linked soil viral ecology along a permafrost thaw gradient. Nat Microbiol. 2018;3(8):870\u201380.","journal-title":"Nat Microbiol"},{"issue":"38","key":"2685_CR12","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1510795112","volume":"112","author":"M Legendre","year":"2015","unstructured":"Legendre M, Lartigue A, Bertaux L, Jeudy S, Bartoli J, Lescot M, et al. In-depth study of Mollivirus sibericum, a new 30,000-y-old giant virus infecting Acanthamoeba. Proc Natl Acad Sci U S A. 2015;112(38):E5327-35.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"2","key":"2685_CR13","doi-asserted-by":"publisher","DOI":"10.1128\/mbio.03009-22","volume":"14","author":"M Ji","year":"2023","unstructured":"Ji M, Fan X, Cornell CR, Zhang Y, Yuan MM, Tian Z, et al. Tundra soil viruses mediate responses of microbial communities to climate warming. MBio. 2023;14(2):e03009-22.","journal-title":"MBio"},{"key":"2685_CR14","unstructured":"Davison MR, Wu R, Danna VG, Godinez IG. Uncovering novel RNA viruses in permafrost. Richland, WA, US; Pacific Northwest National Lab.(PNNL); 2020."},{"key":"2685_CR15","doi-asserted-by":"publisher","DOI":"10.1128\/msystems.00076-18","author":"G Trubl","year":"2018","unstructured":"Trubl G, Jang HB, Roux S, Emerson JB, Solonenko N, Vik DR, et al. Soil viruses are underexplored players in ecosystem carbon processing. mSystems. 2018. https:\/\/doi.org\/10.1128\/msystems.00076-18.","journal-title":"mSystems"},{"issue":"7546","key":"2685_CR16","doi-asserted-by":"publisher","first-page":"171","DOI":"10.1038\/nature14338","volume":"520","author":"EAG Schuur","year":"2015","unstructured":"Schuur EAG, McGuire AD, Sch\u00e4del C, Grosse G, Harden JW, Hayes DJ, et al. Climate change and the permafrost carbon feedback. Nature. 2015;520(7546):171\u20139.","journal-title":"Nature"},{"issue":"21","key":"2685_CR17","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2100163118","volume":"118","author":"SM Natali","year":"2021","unstructured":"Natali SM, Holdren JP, Rogers BM, Treharne R, Duffy PB, Pomerance R, et al. Permafrost carbon feedbacks threaten global climate goals. Proc Natl Acad Sci U S A. 2021;118(21):e2100163118.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2685_CR18","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1016\/j.mib.2022.102229","volume":"70","author":"TL Brown","year":"2022","unstructured":"Brown TL, Charity OJ, Adriaenssens EM. Ecological and functional roles of bacteriophages in contrasting environments: marine, terrestrial and human gut. Curr Opin Microbiol. 2022;70:70.","journal-title":"Curr Opin Microbiol"},{"issue":"7","key":"2685_CR19","doi-asserted-by":"publisher","first-page":"519","DOI":"10.1038\/nrmicro3289","volume":"12","author":"LF Jover","year":"2014","unstructured":"Jover LF, Effler TC, Buchan A, Wilhelm SW, Weitz JS. The elemental composition of virus particles: implications for marine biogeochemical cycles. Nat Rev Microbiol. 2014;12(7):519\u201328.","journal-title":"Nat Rev Microbiol"},{"issue":"1","key":"2685_CR20","doi-asserted-by":"publisher","first-page":"41","DOI":"10.3354\/ame01553","volume":"66","author":"EJ Shelford","year":"2012","unstructured":"Shelford EJ, Middelboe M, M\u00f8ller EF, Suttle CA. Virus-driven nitrogen cycling enhances phytoplankton growth. Aquat Microb Ecol. 2012;66(1):41\u20136.","journal-title":"Aquat Microb Ecol"},{"issue":"39","key":"2685_CR21","doi-asserted-by":"publisher","first-page":"E757","DOI":"10.1073\/pnas.1102164108","volume":"108","author":"LR Thompson","year":"2011","unstructured":"Thompson LR, Zeng Q, Kelly L, Huang KH, Singer AU, Stubbe J, et al. Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism. Proc Natl Acad Sci U S A. 2011;108(39):E757\u201364.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2685_CR22","doi-asserted-by":"publisher","first-page":"219","DOI":"10.1016\/j.virol.2016.09.016","volume":"499","author":"LT Crummett","year":"2016","unstructured":"Crummett LT, Puxty RJ, Weihe C, Marston MF, Martiny JB. The genomic content and context of auxiliary metabolic genes in marine cyanomyoviruses. Virology. 2016;499:219\u201329.","journal-title":"Virology"},{"issue":"4","key":"2685_CR23","doi-asserted-by":"publisher","DOI":"10.3390\/atmos13040532","volume":"13","author":"BA Revich","year":"2022","unstructured":"Revich BA, Eliseev DO, Shaposhnikov DA. Risks for public health and social infrastructure in Russian Arctic under climate change and permafrost degradation. Atmosphere. 2022;13(4):532.","journal-title":"Atmosphere"},{"issue":"2","key":"2685_CR24","doi-asserted-by":"publisher","first-page":"564","DOI":"10.3390\/v15020564","volume":"15","author":"JM Alempic","year":"2023","unstructured":"Alempic JM, Lartigue A, Goncharov AE, Grosse G, Strauss J, Tikhonov AN, et al. An update on Eukaryotic viruses revived from ancient permafrost. Viruses. 2023;15(2):564.","journal-title":"Viruses"},{"issue":"4","key":"2685_CR25","doi-asserted-by":"publisher","first-page":"351","DOI":"10.1016\/j.oneear.2022.03.010","volume":"5","author":"R Wu","year":"2022","unstructured":"Wu R, Trubl G, Ta\u015f N, Jansson JK. Permafrost as a potential pathogen reservoir. One Earth. 2022;5(4):351\u201360.","journal-title":"One Earth"},{"issue":"10","key":"2685_CR26","doi-asserted-by":"publisher","first-page":"809","DOI":"10.1038\/s41558-021-01162-y","volume":"11","author":"KR Miner","year":"2021","unstructured":"Miner KR, D\u2019Andrilli J, Mackelprang R, Edwards A, Malaska MJ, Waldrop MP, et al. Emergent biogeochemical risks from Arctic permafrost degradation. Nat Clim Change. 2021;11(10):809\u201319.","journal-title":"Nat Clim Change"},{"key":"2685_CR27","doi-asserted-by":"publisher","DOI":"10.1128\/jvi.01997-19","author":"E Christo-Foroux","year":"2020","unstructured":"Christo-Foroux E, Alempic J-M, Lartigue A, Santini S, Labadie K, Legendre M, et al. Characterization of Mollivirus kamchatka, the first modern representative of the proposed Molliviridae family of giant viruses. J Virol. 2020. https:\/\/doi.org\/10.1128\/jvi.01997-19.","journal-title":"J Virol"},{"issue":"1","key":"2685_CR28","doi-asserted-by":"publisher","first-page":"136","DOI":"10.1186\/s40168-024-01851-8","volume":"12","author":"JL Liang","year":"2024","unstructured":"Liang JL, Feng SW, Jia P, Lu JL, Yi X, Gao SM, et al. Unraveling the habitat preferences, ecological drivers, potential hosts, and auxiliary metabolism of soil giant viruses across China. Microbiome. 2024;12(1):136.","journal-title":"Microbiome"},{"key":"2685_CR29","doi-asserted-by":"publisher","DOI":"10.1016\/j.scitotenv.2024.172829","volume":"932","author":"Q Wen","year":"2024","unstructured":"Wen Q, Yin X, Moming A, Liu G, Jiang B, Wang J, et al. Viral communities locked in high elevation permafrost up to 100 m in depth on the Tibetan Plateau. Sci Total Environ. 2024;932:172829.","journal-title":"Sci Total Environ"},{"issue":"1","key":"2685_CR30","doi-asserted-by":"publisher","first-page":"110","DOI":"10.1186\/s40168-021-01057-2","volume":"9","author":"R Liang","year":"2021","unstructured":"Liang R, Li Z, Lau Vetter MCY, Vishnivetskaya TA, Zanina OG, Lloyd KG, et al. Genomic reconstruction of fossil and living microorganisms in ancient Siberian permafrost. Microbiome. 2021;9(1):110.","journal-title":"Microbiome"},{"issue":"1","key":"2685_CR31","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1186\/s40793-023-00487-9","volume":"18","author":"X Wu","year":"2023","unstructured":"Wu X, Almatari AL, Cyr WA, Williams DE, Pfiffner SM, Rivkina EM, et al. Microbial life in 25-m-deep boreholes in ancient permafrost illuminated by metagenomics. Environ Microbiome. 2023;18(1):33.","journal-title":"Environ Microbiome"},{"key":"2685_CR32","doi-asserted-by":"crossref","unstructured":"Benko M, Aoki K, Arnberg N, Davison AJ, Echavarria M, Hess M, et al. ICTV virus taxonomy profile: Adenoviridae 2022. J Gen Virol. 2022;103(3):001721.","DOI":"10.1099\/jgv.0.001721"},{"key":"2685_CR33","doi-asserted-by":"crossref","unstructured":"Fiallo-Olive E, Lett JM, Martin DP, Roumagnac P, Varsani A, Zerbini FM, et al. ICTV virus taxonomy profile: Geminiviridae 2021. J Gen Virol. 2021;102(12):001696.","DOI":"10.1099\/jgv.0.001696"},{"issue":"1","key":"2685_CR34","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1146\/annurev-virology-100114-055036","volume":"3","author":"JE Oliver","year":"2016","unstructured":"Oliver JE, Whitfield AE. The genus Tospovirus: emerging bunyaviruses that threaten food security. Annu Rev Virol. 2016;3(1):101\u201324.","journal-title":"Annu Rev Virol"},{"issue":"9","key":"2685_CR35","doi-asserted-by":"publisher","first-page":"1185","DOI":"10.1099\/jgv.0.001107","volume":"99","author":"RL Harrison","year":"2018","unstructured":"Harrison RL, Herniou EA, Jehle JA, Theilmann DA, Burand JP, Becnel JJ, et al. ICTV virus taxonomy profile: Baculoviridae. J Gen Virol. 2018;99(9):1185\u20136.","journal-title":"J Gen Virol"},{"issue":"1","key":"2685_CR36","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1099\/jgv.0.001381","volume":"101","author":"RL Harrison","year":"2020","unstructured":"Harrison RL, Herniou EA, Bezier A, Jehle JA, Burand JP, Theilmann DA, et al. ICTV Virus taxonomy profile: Nudiviridae. J Gen Virol. 2020;101(1):3\u20134.","journal-title":"J Gen Virol"},{"key":"2685_CR37","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2019.01407","volume":"10","author":"M Herrmann","year":"2019","unstructured":"Herrmann M, Wegner CE, Taubert M, Geesink P, Lehmann K, Yan L, et al. Predominance of Cand. Patescibacteria in groundwater is caused by their preferential mobilization from soils and flourishing under oligotrophic conditions. Front Microbiol. 2019;10:1407.","journal-title":"Front Microbiol"},{"issue":"7","key":"2685_CR38","doi-asserted-by":"publisher","first-page":"1450","DOI":"10.1016\/j.soilbio.2011.03.012","volume":"43","author":"GT Bergmann","year":"2011","unstructured":"Bergmann GT, Bates ST, Eilers KG, Lauber CL, Caporaso JG, Walters WA, et al. The under-recognized dominance of Verrucomicrobia in soil bacterial communities. Soil Biol Biochem. 2011;43(7):1450\u20135.","journal-title":"Soil Biol Biochem"},{"key":"2685_CR39","doi-asserted-by":"publisher","first-page":"987","DOI":"10.3389\/fmicb.2018.00987","volume":"9","author":"D Hu","year":"2018","unstructured":"Hu D, Cha G, Gao B. A phylogenomic and molecular markers based Analysis of the class Acidimicrobiia. Front Microbiol. 2018;9:987.","journal-title":"Front Microbiol"},{"issue":"6","key":"2685_CR40","doi-asserted-by":"publisher","first-page":"1989","DOI":"10.1111\/1462-2920.14487","volume":"21","author":"Y Zhao","year":"2019","unstructured":"Zhao Y, Qin F, Zhang R, Giovannoni SJ, Zhang Z, Sun J, et al. Pelagiphages in the Podoviridae family integrate into host genomes. Environ Microbiol. 2019;21(6):1989\u20132001.","journal-title":"Environ Microbiol"},{"issue":"1","key":"2685_CR41","doi-asserted-by":"publisher","first-page":"1816","DOI":"10.1038\/s41467-019-09747-0","volume":"10","author":"X Dong","year":"2019","unstructured":"Dong X, Greening C, Rattray JE, Chakraborty A, Chuvochina M, Mayumi D, et al. Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments. Nat Commun. 2019;10(1):1816.","journal-title":"Nat Commun"},{"issue":"3","key":"2685_CR42","doi-asserted-by":"publisher","first-page":"750","DOI":"10.1038\/s41396-021-01111-9","volume":"16","author":"YJ Chen","year":"2022","unstructured":"Chen YJ, Leung PM, Cook PLM, Wong WW, Hutchinson T, Eate V, et al. Hydrodynamic disturbance controls microbial community assembly and biogeochemical processes in coastal sediments. ISME J. 2022;16(3):750\u201363.","journal-title":"ISME J"},{"issue":"6259","key":"2685_CR43","doi-asserted-by":"publisher","first-page":"434","DOI":"10.1126\/science.aac7745","volume":"350","author":"PN Evans","year":"2015","unstructured":"Evans PN, Parks DH, Chadwick GL, Robbins SJ, Orphan VJ, Golding SD, et al. Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics. Science. 2015;350(6259):434\u20138.","journal-title":"Science"},{"issue":"1","key":"2685_CR44","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-023-01628-5","volume":"11","author":"E Magnuson","year":"2023","unstructured":"Magnuson E, Altshuler I, Freyria NJ, Leveille RJ, Whyte LG. Sulfur-cycling chemolithoautotrophic microbial community dominates a cold, anoxic, hypersaline Arctic spring. Microbiome. 2023;11(1):203.","journal-title":"Microbiome"},{"key":"2685_CR45","doi-asserted-by":"publisher","first-page":"1479","DOI":"10.1007\/s00705-002-0822-6","volume":"147","author":"J Van Etten","year":"2002","unstructured":"Van Etten J, Graves M, M\u00fcller D, Boland W, Delaroque N. Phycodnaviridae\u2013large DNA algal viruses. Arch Virol. 2002;147:1479\u2013516.","journal-title":"Arch Virol"},{"issue":"10","key":"2685_CR46","doi-asserted-by":"publisher","first-page":"1751","DOI":"10.1007\/s11274-013-1358-5","volume":"29","author":"SA Jassim","year":"2013","unstructured":"Jassim SA, Limoges RG. Impact of external forces on cyanophage\u2013host interactions in aquatic ecosystems. World J Microbiol Biotechnol. 2013;29(10):1751\u201362.","journal-title":"World J Microbiol Biotechnol"},{"key":"2685_CR47","doi-asserted-by":"publisher","DOI":"10.1038\/srep03337","volume":"3","author":"Y Tomaru","year":"2013","unstructured":"Tomaru Y, Toyoda K, Suzuki H, Nagumo T, Kimura K, Takao Y. New single-stranded DNA virus with a unique genomic structure that infects marine diatom Chaetoceros setoensis. Sci Rep. 2013;3:3337.","journal-title":"Sci Rep"},{"issue":"2","key":"2685_CR48","doi-asserted-by":"publisher","first-page":"178","DOI":"10.1016\/j.resmic.2004.09.004","volume":"156","author":"RP Maharjan","year":"2005","unstructured":"Maharjan RP, Yu P-L, Seeto S, Ferenci T. The role of isocitrate lyase and the glyoxylate cycle in Escherichia coli growing under glucose limitation. Res Microbiol. 2005;156(2):178\u201383.","journal-title":"Res Microbiol"},{"issue":"1","key":"2685_CR49","doi-asserted-by":"publisher","first-page":"1857","DOI":"10.1038\/s41467-024-46109-x","volume":"15","author":"ZP Zhong","year":"2024","unstructured":"Zhong ZP, Du J, Kostlbacher S, Pjevac P, Orlic S, Sullivan MB. Viral potential to modulate microbial methane metabolism varies by habitat. Nat Commun. 2024;15(1):1857.","journal-title":"Nat Commun"},{"issue":"20","key":"2685_CR50","doi-asserted-by":"publisher","first-page":"3805","DOI":"10.1016\/j.febslet.2007.07.005","volume":"581","author":"SJ Atkinson","year":"2007","unstructured":"Atkinson SJ, Mowat CG, Reid GA, Chapman SK. An octaheme c-type cytochrome from Shewanella oneidensis can reduce nitrite and hydroxylamine. FEBS Lett. 2007;581(20):3805\u20138.","journal-title":"FEBS Lett"},{"issue":"1","key":"2685_CR51","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1111\/j.1574-6968.1998.tb13211.x","volume":"167","author":"L Sayavedra-Soto","year":"1998","unstructured":"Sayavedra-Soto L, Hommes N, Alzerreca J, Arp D, Norton JM, Klotz M. Transcription of the amoC, amoA and amoB genes in Nitrosomonas europaea and Nitrosospira sp. NpAV. FEMS Microbiol Lett. 1998;167(1):81\u20138.","journal-title":"FEMS Microbiol Lett"},{"issue":"3","key":"2685_CR52","doi-asserted-by":"publisher","first-page":"618","DOI":"10.1038\/s41396-018-0289-4","volume":"13","author":"NA Ahlgren","year":"2019","unstructured":"Ahlgren NA, Fuchsman CA, Rocap G, Fuhrman JA. Discovery of several novel, widespread, and ecologically distinct marine Thaumarchaeota viruses that encode amoC nitrification genes. ISME J. 2019;13(3):618\u201331.","journal-title":"ISME J"},{"issue":"5","key":"2685_CR53","doi-asserted-by":"publisher","first-page":"2096","DOI":"10.1128\/AEM.66.5.2096-2104.2000","volume":"66","author":"G Braker","year":"2000","unstructured":"Braker G, Zhou J, Wu L, Devol AH, Tiedje JM. Nitrite reductase genes (nirK and nirS) as functional markers to investigate diversity of denitrifying bacteria in Pacific Northwest marine sediment communities. Appl Environ Microbiol. 2000;66(5):2096\u2013104.","journal-title":"Appl Environ Microbiol"},{"issue":"20","key":"2685_CR54","doi-asserted-by":"publisher","first-page":"2418","DOI":"10.1016\/j.scib.2023.09.007","volume":"68","author":"Y Liu","year":"2023","unstructured":"Liu Y, Jiao N, Xu Zhong K, Zang L, Zhang R, Xiao X, et al. Diversity and function of mountain and polar supraglacial DNA viruses. Sci Bull. 2023;68(20):2418\u201333.","journal-title":"Sci Bull"},{"issue":"8","key":"2685_CR55","doi-asserted-by":"publisher","first-page":"4638","DOI":"10.1074\/jbc.M512736200","volume":"281","author":"J Panadero","year":"2006","unstructured":"Panadero J, Pallotti C, Rodriguez-Vargas S, Randez-Gil F, Prieto JA. A downshift in temperature activates the high osmolarity glycerol (HOG) pathway, which determines freeze tolerance in Saccharomyces cerevisiae. J Biol Chem. 2006;281(8):4638\u201345.","journal-title":"J Biol Chem"},{"issue":"1","key":"2685_CR56","doi-asserted-by":"publisher","first-page":"196","DOI":"10.1074\/jbc.272.1.196","volume":"272","author":"W Jiang","year":"1997","unstructured":"Jiang W, Hou Y, Inouye M. CspA, the major cold-shock protein of Escherichia coli, is an RNA chaperone. J Biol Chem. 1997;272(1):196\u2013202.","journal-title":"J Biol Chem"},{"issue":"237","key":"2685_CR57","doi-asserted-by":"publisher","first-page":"pe26","DOI":"10.1126\/stke.2372004pe26","volume":"2004","author":"M Inouye","year":"2004","unstructured":"Inouye M, Phadtare S. Cold shock response and adaptation at near-freezing temperature in microorganisms. Sci STKE. 2004;2004(237):pe26-pe.","journal-title":"Sci STKE"},{"key":"2685_CR58","doi-asserted-by":"publisher","unstructured":"Bird JT, Tague ED, Zinke L, Schmidt JM, Steen AD, Reese B, et al. Uncultured microbial phyla suggest mechanisms for multi-thousand-year subsistence in Baltic Sea sediments. mBio. 2019;10(2). https:\/\/doi.org\/10.1128\/mbio.02376-18.","DOI":"10.1128\/mbio.02376-18"},{"key":"2685_CR59","first-page":"122","volume":"2","author":"R Cavicchioli","year":"2009","unstructured":"Cavicchioli R, Saunders N, Thomas T. Cold-shock response in microorganisms. Extremophiles. 2009;2:122\u201343.","journal-title":"Extremophiles"},{"issue":"1","key":"2685_CR60","doi-asserted-by":"publisher","first-page":"222","DOI":"10.1128\/MMBR.70.1.222-252.2006","volume":"70","author":"RM Morgan-Kiss","year":"2006","unstructured":"Morgan-Kiss RM, Priscu JC, Pocock T, Gudynaite-Savitch L, Huner NP. Adaptation and acclimation of photosynthetic microorganisms to permanently cold environments. Microbiol Mol Biol Rev. 2006;70(1):222\u201352.","journal-title":"Microbiol Mol Biol Rev"},{"issue":"3","key":"2685_CR61","doi-asserted-by":"publisher","DOI":"10.1111\/1462-2920.70277","volume":"28","author":"R Liang","year":"2026","unstructured":"Liang R, Vishnivetskaya T, Avc\u0131 B, Rivkina EM, Lloyd KG. Promethearchaeota persistence in marine sediments frozen for over 100 kyr. Environ Microbiol. 2026;28(3):e70277.","journal-title":"Environ Microbiol"},{"issue":"15","key":"2685_CR62","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","volume":"30","author":"AM Bolger","year":"2014","unstructured":"Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114\u201320.","journal-title":"Bioinformatics"},{"key":"2685_CR63","unstructured":"Bushnell B. BBMap: a fast, accurate, splice-aware aligner. 2014."},{"issue":"10","key":"2685_CR64","doi-asserted-by":"publisher","first-page":"1674","DOI":"10.1093\/bioinformatics\/btv033","volume":"31","author":"D Li","year":"2015","unstructured":"Li D, Liu C-M, Luo R, Sadakane K, Lam T-W. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics. 2015;31(10):1674\u20136.","journal-title":"Bioinformatics"},{"issue":"4","key":"2685_CR65","doi-asserted-by":"publisher","first-page":"605","DOI":"10.1093\/bioinformatics\/btv638","volume":"32","author":"Y-W Wu","year":"2016","unstructured":"Wu Y-W, Simmons BA, Singer SW. MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics. 2016;32(4):605\u20137.","journal-title":"Bioinformatics"},{"key":"2685_CR66","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.7359","volume":"7","author":"DD Kang","year":"2019","unstructured":"Kang DD, Li F, Kirton E, Thomas A, Egan R, An H, et al. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ. 2019;7:e7359.","journal-title":"PeerJ"},{"key":"2685_CR67","doi-asserted-by":"publisher","first-page":"i21","DOI":"10.1093\/bioinformatics\/btad209","volume":"39","author":"S Pan","year":"2023","unstructured":"Pan S, Zhao X-M, Coelho LP. SemiBin2: self-supervised contrastive learning leads to better MAGs for short-and long-read sequencing. Bioinformatics. 2023;39:i21\u20139.","journal-title":"Bioinformatics"},{"issue":"5","key":"2685_CR68","doi-asserted-by":"publisher","first-page":"555","DOI":"10.1038\/s41587-020-00777-4","volume":"39","author":"JN Nissen","year":"2021","unstructured":"Nissen JN, Johansen J, Alles\u00f8e RL, S\u00f8nderby CK, Armenteros JJA, Gr\u00f8nbech CH, et al. Improved metagenome binning and assembly using deep variational autoencoders. Nat Biotechnol. 2021;39(5):555\u201360.","journal-title":"Nat Biotechnol"},{"issue":"12","key":"2685_CR69","doi-asserted-by":"publisher","first-page":"2864","DOI":"10.1038\/ismej.2017.126","volume":"11","author":"MR Olm","year":"2017","unstructured":"Olm MR, Brown CT, Brooks B, Banfield JF. dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J. 2017;11(12):2864\u20138.","journal-title":"ISME J"},{"issue":"7","key":"2685_CR70","doi-asserted-by":"publisher","first-page":"836","DOI":"10.1038\/s41564-018-0171-1","volume":"3","author":"CM Sieber","year":"2018","unstructured":"Sieber CM, Probst AJ, Sharrar A, Thomas BC, Hess M, Tringe SG, et al. Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy. Nat Microbiol. 2018;3(7):836\u201343.","journal-title":"Nat Microbiol"},{"key":"2685_CR71","first-page":"1925","volume-title":"GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database","author":"P-A Chaumeil","year":"2020","unstructured":"Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Oxford University Press; 2020. p. 1925\u20137."},{"key":"2685_CR72","doi-asserted-by":"crossref","unstructured":"Camargo AP, Roux S, Schulz F, Babinski M, Xu Y, Hu B, et al. Identification of mobile genetic elements with geNomad. Nat Biotechnol. 2024;42(8):1303\u201312.","DOI":"10.1038\/s41587-023-01953-y"},{"issue":"1","key":"2685_CR73","doi-asserted-by":"publisher","first-page":"64","DOI":"10.1007\/s40484-019-0187-4","volume":"8","author":"J Ren","year":"2020","unstructured":"Ren J, Song K, Deng C, Ahlgren NA, Fuhrman JA, Li Y, et al. Identifying viruses from metagenomic data using deep learning. Quant Biol. 2020;8(1):64\u201377.","journal-title":"Quant Biol"},{"key":"2685_CR74","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s40168-020-00867-0","volume":"8","author":"K Kieft","year":"2020","unstructured":"Kieft K, Zhou Z, Anantharaman K. VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences. Microbiome. 2020;8:1\u201323.","journal-title":"Microbiome"},{"key":"2685_CR75","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s40168-017-0283-5","volume":"5","author":"J Ren","year":"2017","unstructured":"Ren J, Ahlgren NA, Lu YY, Fuhrman JA, Sun F. VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data. Microbiome. 2017;5:1\u201320.","journal-title":"Microbiome"},{"key":"2685_CR76","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s40168-020-00990-y","volume":"9","author":"J Guo","year":"2021","unstructured":"Guo J, Bolduc B, Zayed AA, Varsani A, Dominguez-Huerta G, Delmont TO, et al. VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses. Microbiome. 2021;9:1\u201313.","journal-title":"Microbiome"},{"issue":"5","key":"2685_CR77","doi-asserted-by":"publisher","first-page":"578","DOI":"10.1038\/s41587-020-00774-7","volume":"39","author":"S Nayfach","year":"2021","unstructured":"Nayfach S, Camargo AP, Schulz F, Eloe-Fadrosh E, Roux S, Kyrpides NC. CheckV assesses the quality and completeness of metagenome-assembled viral genomes. Nat Biotechnol. 2021;39(5):578\u201385.","journal-title":"Nat Biotechnol"},{"issue":"1","key":"2685_CR78","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1186\/1471-2105-11-119","volume":"11","author":"D Hyatt","year":"2010","unstructured":"Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11(1):119.","journal-title":"BMC Bioinformatics"},{"key":"2685_CR79","doi-asserted-by":"crossref","unstructured":"Trgovec-Greif L, Hellinger H-J, Mainguy J, Pfundner A, Frishman D, Kiening M, et al. VOGDB-database of virus orthologous groups. 2024.","DOI":"10.20944\/preprints202407.0238.v1"},{"issue":"4","key":"2685_CR80","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btaf147","volume":"41","author":"STN Aroney","year":"2025","unstructured":"Aroney STN, Newell RJP, Nissen JN, Camargo AP, Tyson GW, Woodcroft BJ. CoverM: read alignment statistics for metagenomics. Bioinformatics. 2025;41(4):btaf147.","journal-title":"Bioinformatics"},{"issue":"18","key":"2685_CR81","doi-asserted-by":"publisher","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","volume":"34","author":"H Li","year":"2018","unstructured":"Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018;34(18):3094\u2013100.","journal-title":"Bioinformatics"},{"issue":"1","key":"2685_CR82","doi-asserted-by":"publisher","first-page":"5114","DOI":"10.1038\/s41467-018-07641-9","volume":"9","author":"C Jain","year":"2018","unstructured":"Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun. 2018;9(1):5114.","journal-title":"Nat Commun"},{"issue":"1","key":"2685_CR83","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbac505","volume":"24","author":"J-Z Jiang","year":"2023","unstructured":"Jiang J-Z, Yuan W-G, Shang J, Shi Y-H, Yang L-L, Liu M, et al. Virus classification for viral genomic fragments using PhaGCN2. Brief Bioinform. 2023;24(1):bbac505.","journal-title":"Brief Bioinform"},{"issue":"16","key":"2685_CR84","doi-asserted-by":"publisher","first-page":"8883","DOI":"10.1093\/nar\/gkaa621","volume":"48","author":"M Shaffer","year":"2020","unstructured":"Shaffer M, Borton MA, McGivern BB, Zayed AA, La Rosa SL, Solden LM, et al. DRAM for distilling microbial metabolism to automate the curation of microbiome function. Nucleic Acids Res. 2020;48(16):8883\u2013900.","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"2685_CR85","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1145\/3068335","volume":"42","author":"E Schubert","year":"2017","unstructured":"Schubert E, Sander J, Ester M, Kriegel HP, Xu X. DBSCAN revisited, revisited: why and how you should (still) use DBSCAN. ACM Transactions on Database Systems (TODS). 2017;42(3):1\u201321.","journal-title":"ACM Transactions on Database Systems (TODS)"},{"issue":"1","key":"2685_CR86","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1093\/nar\/28.1.27","volume":"28","author":"M Kanehisa","year":"2000","unstructured":"Kanehisa M, Goto S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 2000;28(1):27\u201330.","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"2685_CR87","doi-asserted-by":"publisher","first-page":"D412","DOI":"10.1093\/nar\/gkaa913","volume":"49","author":"J Mistry","year":"2021","unstructured":"Mistry J, Chuguransky S, Williams L, Qureshi M, Salazar GA, Sonnhammer EL, et al. Pfam: the protein families database in 2021. Nucleic Acids Res. 2021;49(D1):D412\u20139.","journal-title":"Nucleic Acids Res"},{"issue":"7","key":"2685_CR88","doi-asserted-by":"publisher","first-page":"1009","DOI":"10.1093\/bioinformatics\/btr039","volume":"27","author":"MJ Sullivan","year":"2011","unstructured":"Sullivan MJ, Petty NK, Beatson SA. Easyfig: a genome comparison visualizer. Bioinformatics. 2011;27(7):1009\u201310.","journal-title":"Bioinformatics"},{"issue":"Database issue","key":"2685_CR89","doi-asserted-by":"publisher","first-page":"D233","DOI":"10.1093\/nar\/gkn663","volume":"37","author":"BL Cantarel","year":"2009","unstructured":"Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, Henrissat B. The Carbohydrate-active enzymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res. 2009;37(Database issue):D233-8.","journal-title":"Nucleic Acids Res"},{"issue":"12","key":"2685_CR90","doi-asserted-by":"publisher","first-page":"5825","DOI":"10.1093\/molbev\/msab293","volume":"38","author":"CP Cantalapiedra","year":"2021","unstructured":"Cantalapiedra CP, Hernandez-Plaza A, Letunic I, Bork P, Huerta-Cepas J. eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol Biol Evol. 2021;38(12):5825\u20139.","journal-title":"Mol Biol Evol"},{"issue":"D1","key":"2685_CR91","doi-asserted-by":"publisher","first-page":"D309","DOI":"10.1093\/nar\/gky1085","volume":"47","author":"J Huerta-Cepas","year":"2019","unstructured":"Huerta-Cepas J, Szklarczyk D, Heller D, Hernandez-Plaza A, Forslund SK, Cook H, et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res. 2019;47(D1):D309\u201314.","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"2685_CR92","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.3002083","volume":"21","author":"S Roux","year":"2023","unstructured":"Roux S, Camargo AP, Coutinho FH, Dabdoub SM, Dutilh BE, Nayfach S, et al. iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria. PLoS Biol. 2023;21(4):e3002083.","journal-title":"PLoS Biol"},{"issue":"1","key":"2685_CR93","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1186\/s40168-024-01796-y","volume":"12","author":"L Perini","year":"2024","unstructured":"Perini L, Sipes K, Zervas A, Bellas C, Lutz S, Moniruzzaman M, et al. Giant viral signatures on the Greenland ice sheet. Microbiome. 2024;12(1):91.","journal-title":"Microbiome"},{"issue":"4","key":"2685_CR94","doi-asserted-by":"publisher","first-page":"366","DOI":"10.1038\/s41592-021-01101-x","volume":"18","author":"B Buchfink","year":"2021","unstructured":"Buchfink B, Reuter K, Drost HG. Sensitive protein alignments at tree-of-life scale using DIAMOND. Nat Methods. 2021;18(4):366\u20138.","journal-title":"Nat Methods"},{"issue":"1","key":"2685_CR95","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1093\/molbev\/msu300","volume":"32","author":"L-T Nguyen","year":"2015","unstructured":"Nguyen L-T, Schmidt HA, Von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015;32(1):268\u201374.","journal-title":"Mol Biol Evol"},{"issue":"2","key":"2685_CR96","doi-asserted-by":"publisher","first-page":"511","DOI":"10.1093\/nar\/gki198","volume":"33","author":"K Katoh","year":"2005","unstructured":"Katoh K, Kuma K-i, Toh H, Miyata T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 2005;33(2):511\u20138.","journal-title":"Nucleic Acids Res"}],"container-title":["BMC Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12915-026-02685-6","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12915-026-02685-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12915-026-02685-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T09:23:52Z","timestamp":1792056232000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12915-026-02685-6"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,16]]},"references-count":96,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["2685"],"URL":"https:\/\/doi.org\/10.1186\/s12915-026-02685-6","relation":{},"ISSN":["1741-7007"],"issn-type":[{"value":"1741-7007","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,16]]},"assertion":[{"value":"5 November 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 July 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 July 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","label":"Ethics approval and\u00a0consent to participate","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","label":"Consent for publication","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no competing interests.","order":3,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Declarations"}}],"article-number":"215"}}