{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,20]],"date-time":"2026-07-20T08:02:08Z","timestamp":1784534528531,"version":"3.55.0"},"reference-count":98,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2026,6,18]],"date-time":"2026-06-18T00:00:00Z","timestamp":1781740800000},"content-version":"vor","delay-in-days":168,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["42125603"],"award-info":[{"award-number":["42125603"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2023YFF0805002"],"award-info":[{"award-number":["2023YFF0805002"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"NSFC","doi-asserted-by":"publisher","award":["42430404"],"award-info":[{"award-number":["42430404"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,14]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Following the ubiquitous autotrophic ammonia-oxidizing archaea (AOA), heterotrophic representatives of the marine Nitrososphaerota (HMN) form the second most abundant group within this archaeal phylum. However, their eco-evolutionary strategies remain poorly understood. Previous studies have reported a consistent co-occurrence of HMN with marine AOA (MAOA), prompting a detailed investigation into their potential interaction. Through large-scale (meta)genomic and metatranscriptomic analyses, we reveal that HMN possess ultra-streamlined genomes and globally co-occur with marine AOA. The absence of most B vitamin biosynthesis pathways, incomplete citrate cycle and glycolysis, along with the essential requirement for exogenous amino acids, suggest their potential metabolic dependency on AOA. Meanwhile, catalyzed reporter deposition fluorescence in situ hybridization supports a close physical association between HMN and AOA. The nearly synchronous origins of HMN and AOA after oxygen rise, coupled with HMN\u2019s dispersive microhabitats (evidenced by dense, shallow subclades) and extensive horizontal gene transfer between these groups, further support their close relationship\u2014although HMN likely acquired heterotrophic capabilities from bacteria. This study reveals a previously unrecognized association between HMN and AOA, implying a tight coupling between autotrophic and heterotrophic processes in deep-sea habitats.<\/jats:p>","DOI":"10.1093\/ismeco\/ycag173","type":"journal-article","created":{"date-parts":[[2026,6,16]],"date-time":"2026-06-16T12:29:32Z","timestamp":1781612972000},"source":"Crossref","is-referenced-by-count":0,"title":["Close spatial and metabolic association between heterotrophic and ammonia-oxidizing marine Nitrososphaerota"],"prefix":"10.1093","volume":"6","author":[{"given":"Qian","family":"Li","sequence":"first","affiliation":[{"name":"State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University , Xiamen, Fujian 361102 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mingming","family":"Chen","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University , Xiamen, Fujian 361102 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ye","family":"Lu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University , Xiamen, Fujian 361102 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cheng","family":"Xu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University , Xiamen, Fujian 361102 ,","place":["China"]},{"name":"Advanced Institute for Marine Studies, Fujian Ocean Innovation Center , Xiamen, Fujian 361102 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yue","family":"Zheng","sequence":"additional","affiliation":[{"name":"College of the Environment and Ecology, Xiamen University , Xiamen, Fujian 361102 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhirui","family":"Zeng","sequence":"additional","affiliation":[{"name":"Department of Ocean Science and Engineering, Southern University of Science and Technology , Shenzhen, Guangdong 518055 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dapeng","family":"Xu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University , Xiamen, Fujian 361102 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0895-0126","authenticated-orcid":false,"given":"Wei","family":"Qin","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign , Urbana, IL 61801 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1211-4745","authenticated-orcid":false,"given":"Yao","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University , Xiamen, Fujian 361102 ,","place":["China"]},{"name":"Advanced Institute for Marine Studies, Fujian Ocean Innovation Center , Xiamen, Fujian 361102 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,6,18]]},"reference":[{"key":"2026072003064318100_ref1","doi-asserted-by":"publisher","first-page":"938","DOI":"10.1038\/ismej.2013.193","article-title":"Niche specialization of novel Thaumarchaeota to oxic and hypoxic acidic geothermal springs of Yellowstone National Park","volume":"8","author":"Beam","year":"2013","journal-title":"ISME J"},{"key":"2026072003064318100_ref2","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3389\/fmicb.2020.608832","article-title":"Genomic insights of \u201cCandidatus Nitrosocaldaceae\u201d based on nine new metagenome-assembled genomes, including \u201cCandidatus Nitrosothermus\u201d gen nov. and two new species of \u201cCandidatus Nitrosocaldus\u201d","volume":"11","author":"Luo","year":"2021","journal-title":"Front Microbiol"},{"key":"2026072003064318100_ref3","doi-asserted-by":"publisher","first-page":"2131","DOI":"10.5194\/bg-11-2131-2014","article-title":"Diversity and distribution of amoA-type nitrifying and nirS-type denitrifying microbial communities in the Yangtze River estuary","volume":"11","author":"Zhang","year":"2014","journal-title":"Biogeosciences"},{"key":"2026072003064318100_ref4","doi-asserted-by":"publisher","first-page":"5169","DOI":"10.5194\/bg-15-5169-2018","article-title":"Niche differentiation of ammonia and nitrite oxidizers along a salinity gradient from the Pearl River estuary to the South China Sea","volume":"15","author":"Hou","year":"2018","journal-title":"Biogeosciences"},{"key":"2026072003064318100_ref5","doi-asserted-by":"publisher","first-page":"3757","DOI":"10.5194\/bg-19-3757-2022","article-title":"Potential contributions of nitrifiers and denitrifiers to nitrous oxide sources and sinks in China's estuarine and coastal areas","volume":"19","author":"Dai","year":"2022","journal-title":"Biogeosciences"},{"key":"2026072003064318100_ref6","doi-asserted-by":"publisher","first-page":"507","DOI":"10.1038\/35054051","article-title":"Archaeal dominance in the mesopelagic zone of the Pacific Ocean","volume":"409","author":"Karner","year":"2001","journal-title":"Nature"},{"key":"2026072003064318100_ref7","doi-asserted-by":"publisher","first-page":"543","DOI":"10.1038\/nature03911","article-title":"Isolation of an autotrophic ammonia-oxidizing marine archaeon","volume":"437","author":"K\u00f6nneke","year":"2005","journal-title":"Nature"},{"key":"2026072003064318100_ref8","doi-asserted-by":"publisher","first-page":"496","DOI":"10.1126\/science.1120250","article-title":"Community genomics among stratified microbial assemblages in the ocean's interior","volume":"311","author":"DeLong","year":"2006","journal-title":"Science"},{"key":"2026072003064318100_ref9","doi-asserted-by":"publisher","first-page":"9188","DOI":"10.1073\/pnas.93.17.9188","article-title":"Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences","volume":"93","author":"Barns","year":"1996","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2026072003064318100_ref10","doi-asserted-by":"publisher","first-page":"e00415","DOI":"10.1128\/msystems.00415-20","article-title":"Heterotrophic Thaumarchaea with small genomes are widespread in the dark ocean","volume":"5","author":"Aylward","year":"2020","journal-title":"mSystems"},{"key":"2026072003064318100_ref11","doi-asserted-by":"publisher","first-page":"788","DOI":"10.1038\/nature07535","article-title":"Major gradients in putatively nitrifying and non-nitrifying archaea in the deep North Atlantic","volume":"456","author":"Agogu\u00e9","year":"2008","journal-title":"Nature"},{"key":"2026072003064318100_ref12","doi-asserted-by":"publisher","first-page":"595","DOI":"10.1111\/j.1751-7915.2010.00186.x","article-title":"Genomic signatures of fifth autotrophic carbon assimilation pathway in bathypelagic Crenarchaeota","volume":"3","author":"La Cono","year":"2010","journal-title":"Microb Biotechnol"},{"key":"2026072003064318100_ref13","doi-asserted-by":"publisher","first-page":"679","DOI":"10.1111\/j.1462-2920.2009.02108.x","article-title":"Abundances of crenarchaeal amoA genes and transcripts in the Pacific Ocean","volume":"12","author":"Church","year":"2010","journal-title":"Environ Microbiol"},{"key":"2026072003064318100_ref14","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3389\/fmicb.2013.00072","article-title":"An analysis of Thaumarchaeota populations from the northern Gulf of Mexico","volume":"4","author":"Tolar","year":"2013","journal-title":"Front Microbiol"},{"key":"2026072003064318100_ref15","doi-asserted-by":"publisher","first-page":"2041","DOI":"10.1002\/lno.11436","article-title":"Time series assessment of Thaumarchaeota ecotypes in Monterey Bay reveals the importance of water column position in predicting distribution\u2013environment relationships","volume":"65","author":"Tolar","year":"2020","journal-title":"Limnol Oceanogr"},{"key":"2026072003064318100_ref16","doi-asserted-by":"publisher","first-page":"2105","DOI":"10.1038\/s41396-020-0675-6","article-title":"Metagenome-assembled genomes reveal unique metabolic adaptations of a basal marine Thaumarchaeota lineage","volume":"14","author":"Reji","year":"2020","journal-title":"ISME J"},{"key":"2026072003064318100_ref17","doi-asserted-by":"publisher","first-page":"1162","DOI":"10.1111\/j.1462-2920.2007.01239.x","article-title":"Quantitative distribution of presumptive archaeal and bacterial nitrifiers in Monterey Bay and the North Pacific subtropical gyre","volume":"9","author":"Mincer","year":"2007","journal-title":"Environ Microbiol"},{"key":"2026072003064318100_ref18","doi-asserted-by":"publisher","first-page":"549","DOI":"10.1007\/s00248-011-9866-z","article-title":"Community structure and function of planktonic Crenarchaeota: changes with depth in the South China Sea","volume":"62","author":"Hu","year":"2011","journal-title":"Microb Ecol"},{"key":"2026072003064318100_ref19","doi-asserted-by":"publisher","first-page":"50","DOI":"10.1128\/aem.63.1.50-56.1997","article-title":"Vertical distribution and phylogenetic characterization of marine planktonic archaea in the Santa Barbara Channel","volume":"63","author":"Massana","year":"1997","journal-title":"Appl Environ Microbiol"},{"key":"2026072003064318100_ref20","doi-asserted-by":"publisher","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"Fastp: an ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"2026072003064318100_ref21","doi-asserted-by":"publisher","first-page":"1674","DOI":"10.1093\/bioinformatics\/btv033","article-title":"MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph","volume":"31","author":"Li","year":"2015","journal-title":"Bioinformatics"},{"key":"2026072003064318100_ref22","doi-asserted-by":"publisher","first-page":"2864","DOI":"10.1038\/ismej.2017.126","article-title":"dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication","volume":"11","author":"Olm","year":"2017","journal-title":"ISME J"},{"key":"2026072003064318100_ref23","doi-asserted-by":"publisher","first-page":"1043","DOI":"10.1101\/gr.186072.114","article-title":"CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes","volume":"25","author":"Parks","year":"2015","journal-title":"Genome Res"},{"key":"2026072003064318100_ref24","doi-asserted-by":"publisher","first-page":"1925","DOI":"10.1093\/bioinformatics\/btz848","article-title":"GTDB-Tk: a toolkit to classify genomes with the genome taxonomy database","volume":"36","author":"Chaumeil","year":"2020","journal-title":"Bioinformatics"},{"key":"2026072003064318100_ref25","doi-asserted-by":"publisher","first-page":"3211","DOI":"10.1093\/bioinformatics\/bts611","article-title":"SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data","volume":"28","author":"Kopylova","year":"2012","journal-title":"Bioinformatics"},{"key":"2026072003064318100_ref26","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat Methods"},{"key":"2026072003064318100_ref27","doi-asserted-by":"publisher","first-page":"1367","DOI":"10.1038\/s41564-017-0008-3","article-title":"Environmental drivers of a microbial genomic transition zone in the ocean\u2019s interior","volume":"2","author":"Mende","year":"2017","journal-title":"Nat Microbiol"},{"key":"2026072003064318100_ref28","doi-asserted-by":"publisher","first-page":"238","DOI":"10.1186\/s13059-019-1832-y","article-title":"OrthoFinder: phylogenetic orthology inference for comparative genomics","volume":"20","author":"Emms","year":"2019","journal-title":"Genome Biol"},{"key":"2026072003064318100_ref29","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"KEGG: Kyoto Encyclopedia of genes and genomes","volume":"28","author":"Kanehisa","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"2026072003064318100_ref30","doi-asserted-by":"publisher","first-page":"818","DOI":"10.3390\/life5010818","article-title":"Archaeal clusters of orthologous genes (arCOGs): an update and application for analysis of shared features between Thermococcales, Methanococcales, and Methanobacteriales","volume":"5","author":"Makarova","year":"2015","journal-title":"Life"},{"key":"2026072003064318100_ref31","doi-asserted-by":"publisher","first-page":"W445","DOI":"10.1093\/nar\/gks479","article-title":"dbCAN: a web resource for automated carbohydrate-active enzyme annotation","volume":"40","author":"Yin","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2026072003064318100_ref32","doi-asserted-by":"publisher","first-page":"D624","DOI":"10.1093\/nar\/gkx1134","article-title":"The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database","volume":"46","author":"Rawlings","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2026072003064318100_ref33","doi-asserted-by":"publisher","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","article-title":"IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era","volume":"37","author":"Minh","year":"2020","journal-title":"Mol Biol Evol"},{"key":"2026072003064318100_ref34","doi-asserted-by":"publisher","first-page":"3939","DOI":"10.1038\/s41467-020-17408-w","article-title":"Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution","volume":"11","author":"Dombrowski","year":"2020","journal-title":"Nat Commun"},{"key":"2026072003064318100_ref35","doi-asserted-by":"publisher","first-page":"1586","DOI":"10.1093\/molbev\/msm088","article-title":"PAML 4: phylogenetic analysis by maximum likelihood","volume":"24","author":"Yang","year":"2007","journal-title":"Mol Biol Evol"},{"key":"2026072003064318100_ref36","doi-asserted-by":"publisher","first-page":"1910","DOI":"10.1093\/bioinformatics\/btq315","article-title":"Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood","volume":"26","author":"Cs\u0171\u00f6s","year":"2010","journal-title":"Bioinformatics"},{"key":"2026072003064318100_ref37","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1038\/nmeth.3176","article-title":"Fast and sensitive protein alignment using DIAMOND","volume":"12","author":"Buchfink","year":"2015","journal-title":"Nat Methods"},{"key":"2026072003064318100_ref38","doi-asserted-by":"publisher","first-page":"1283","DOI":"10.1126\/science.1123061","article-title":"Toward automatic reconstruction of a highly resolved tree of life","volume":"311","author":"Ciccarelli","year":"2006","journal-title":"Science"},{"key":"2026072003064318100_ref39","doi-asserted-by":"publisher","first-page":"5825","DOI":"10.1093\/molbev\/msab293","article-title":"eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale","volume":"38","author":"Cantalapiedra","year":"2021","journal-title":"Mol Biol Evol"},{"key":"2026072003064318100_ref40","doi-asserted-by":"publisher","first-page":"9658","DOI":"10.1073\/pnas.1632870100","article-title":"Horizontal gene transfer: a critical view","volume":"100","author":"Kurland","year":"2003","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2026072003064318100_ref41","doi-asserted-by":"publisher","first-page":"717","DOI":"10.1186\/1471-2164-15-717","article-title":"HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene transfers","volume":"15","author":"Zhu","year":"2014","journal-title":"BMC Genomics"},{"key":"2026072003064318100_ref42","doi-asserted-by":"publisher","first-page":"1261359","DOI":"10.1126\/science.1261359","article-title":"Structure and function of the global ocean microbiome","volume":"348","author":"Sunagawa","year":"2015","journal-title":"Science"},{"key":"2026072003064318100_ref43","doi-asserted-by":"publisher","first-page":"e108173","DOI":"10.1371\/journal.pone.0108173","article-title":"Ammonium uptake by phytoplankton regulates nitrification in the sunlit ocean","volume":"9","author":"Smith","year":"2014","journal-title":"PLoS One"},{"key":"2026072003064318100_ref44","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3389\/fmars.2019.00739","article-title":"Processes and microorganisms involved in the marine nitrogen cycle: knowledge and gaps","volume":"6","author":"Pajares","year":"2019","journal-title":"Front Mar Sci"},{"key":"2026072003064318100_ref45","doi-asserted-by":"publisher","first-page":"1771","DOI":"10.1111\/j.1462-2920.2008.01598.x","article-title":"The small genome of an abundant coastal ocean methylotroph","volume":"10","author":"Giovannoni","year":"2008","journal-title":"Environ Microbiol"},{"key":"2026072003064318100_ref46","doi-asserted-by":"publisher","first-page":"305","DOI":"10.1146\/annurev-marine-120308-081034","article-title":"Prochlorococcus: advantages and limits of minimalism","volume":"2","author":"Partensky","year":"2010","journal-title":"Annu Rev Mar Sci"},{"key":"2026072003064318100_ref47","doi-asserted-by":"publisher","first-page":"231","DOI":"10.1146\/annurev-marine-010814-015934","article-title":"SAR11 bacteria: the most abundant plankton in the oceans","volume":"9","author":"Giovannoni","year":"2017","journal-title":"Annu Rev Mar Sci"},{"key":"2026072003064318100_ref48","doi-asserted-by":"publisher","first-page":"2595","DOI":"10.1038\/s41396-020-0710-7","article-title":"Alternative strategies of nutrient acquisition and energy conservation map to the biogeography of marine ammonia-oxidizing archaea","volume":"14","author":"Qin","year":"2020","journal-title":"ISME J"},{"key":"2026072003064318100_ref49","doi-asserted-by":"publisher","first-page":"1136","DOI":"10.1111\/1462-2920.16348","article-title":"Single-amplified genomes reveal most streamlined free-living marine bacteria","volume":"25","author":"Roda-Garcia","year":"2023","journal-title":"Environ Microbiol"},{"key":"2026072003064318100_ref50","doi-asserted-by":"publisher","first-page":"629","DOI":"10.1038\/s41579-018-0076-2","article-title":"Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations","volume":"16","author":"Castelle","year":"2018","journal-title":"Nat Rev Microbiol"},{"key":"2026072003064318100_ref51","doi-asserted-by":"publisher","first-page":"e00602","DOI":"10.1128\/msystems.00602-21","article-title":"Comparative genomics provides insights into the genetic diversity and evolution of the DPANN superphylum","volume":"6","author":"Li","year":"2021","journal-title":"mSystems"},{"key":"2026072003064318100_ref52","doi-asserted-by":"publisher","first-page":"58","DOI":"10.1038\/nrg1504","article-title":"Archaeal genetics \u2014 the third way","volume":"6","author":"Allers","year":"2005","journal-title":"Nat Rev Genet"},{"key":"2026072003064318100_ref53","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1186\/s13062-015-0085-2","article-title":"Pan-genomic analysis to redefine species and subspecies based on quantum discontinuous variation: the klebsiella paradigm","volume":"10","author":"Caputo","year":"2015","journal-title":"Biol Direct"},{"key":"2026072003064318100_ref54","doi-asserted-by":"publisher","first-page":"1247","DOI":"10.1038\/s41396-020-0600-z","article-title":"Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity","volume":"14","author":"Maistrenko","year":"2020","journal-title":"ISME J"},{"key":"2026072003064318100_ref55","doi-asserted-by":"publisher","first-page":"1606","DOI":"10.1073\/pnas.56.5.1606","article-title":"The conversion of serine at the active site of subtilisin to cysteine: a \"chemical mutation\"","volume":"56","author":"Neet","year":"1966","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2026072003064318100_ref56","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1002\/jobm.201100067","article-title":"GC content-independent amino acid patterns in bacteria and archaea","volume":"52","author":"Schmidt","year":"2012","journal-title":"J Basic Microbiol"},{"key":"2026072003064318100_ref57","doi-asserted-by":"publisher","first-page":"2150","DOI":"10.1038\/s41396-019-0418-8","article-title":"Phylogenomics suggests oxygen availability as a driving force in Thaumarchaeota evolution","volume":"13","author":"Ren","year":"2019","journal-title":"ISME J"},{"key":"2026072003064318100_ref58","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1016\/j.orggeochem.2018.08.004","article-title":"Dissolved organic carbon compounds in deep-sea hydrothermal vent fluids from the East Pacific rise at 9\u00b050\u2032N","volume":"125","author":"Longnecker","year":"2018","journal-title":"Org Geochem"},{"key":"2026072003064318100_ref59","doi-asserted-by":"publisher","first-page":"144","DOI":"10.1038\/178144a0","article-title":"Soil as a habitat of vitamin-requiring bacteria","volume":"178","author":"Lochhead","year":"1956","journal-title":"Nature"},{"key":"2026072003064318100_ref60","doi-asserted-by":"publisher","first-page":"1242","DOI":"10.1126\/science.1114057","article-title":"Genome streamlining in a cosmopolitan oceanic bacterium","volume":"309","author":"Giovannoni","year":"2005","journal-title":"Science"},{"key":"2026072003064318100_ref61","doi-asserted-by":"publisher","first-page":"1506","DOI":"10.1038\/s41396-019-0365-4","article-title":"Co-culture and biogeography of Prochlorococcus and SAR11","volume":"13","author":"Becker","year":"2019","journal-title":"ISME J"},{"key":"2026072003064318100_ref62","doi-asserted-by":"publisher","first-page":"461","DOI":"10.1038\/ismej.2014.142","article-title":"Aquatic metagenomes implicate Thaumarchaeota in global cobalamin production","volume":"9","author":"Doxey","year":"2015","journal-title":"ISME J"},{"key":"2026072003064318100_ref63","doi-asserted-by":"publisher","first-page":"364","DOI":"10.1073\/pnas.1608462114","article-title":"Two distinct pools of B12 analogs reveal community interdependencies in the ocean","volume":"114","author":"Heal","year":"2017","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2026072003064318100_ref64","doi-asserted-by":"publisher","first-page":"4062","DOI":"10.1111\/1462-2920.14755","article-title":"Ammonia-oxidizing archaea release a suite of organic compounds potentially fueling prokaryotic heterotrophy in the ocean","volume":"21","author":"Bayer","year":"2019","journal-title":"Environ Microbiol"},{"key":"2026072003064318100_ref65","doi-asserted-by":"publisher","first-page":"14041","DOI":"10.1073\/pnas.1208755109","article-title":"Multiple B-vitamin depletion in large areas of the coastal ocean","volume":"109","author":"Sa\u00f1udo-Wilhelmy","year":"2012","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2026072003064318100_ref66","doi-asserted-by":"publisher","first-page":"wrae172","DOI":"10.1093\/ismejo\/wrae172","article-title":"Metabolite release by nitrifiers facilitates metabolic interactions in the ocean","volume":"18","author":"Bayer","year":"2024","journal-title":"ISME J"},{"key":"2026072003064318100_ref67","doi-asserted-by":"publisher","first-page":"53","DOI":"10.1007\/BF00428345","article-title":"Pyruvate dehydrogenase complex, pyruvate: ferredoxin oxidoreductase and lipoic acid content in microorganisms","volume":"102","author":"Bothe","year":"1975","journal-title":"Arch Microbiol"},{"key":"2026072003064318100_ref68","doi-asserted-by":"publisher","first-page":"227","DOI":"10.1016\/0891-5849(95)00017-R","article-title":"Alpha-lipoic acid as a biological antioxidant","volume":"19","author":"Packer","year":"1995","journal-title":"Free Radic Biol Med"},{"key":"2026072003064318100_ref69","doi-asserted-by":"publisher","first-page":"463","DOI":"10.1016\/S0981-9428(02)01407-9","article-title":"Lipoic acid: a unique antioxidant in the detoxification of activated oxygen species","volume":"40","author":"Navari-Izzo","year":"2002","journal-title":"Plant Physiol Biochem"},{"key":"2026072003064318100_ref70","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3389\/fmars.2016.00237","article-title":"Ammonia oxidation in the ocean can be inhibited by nanomolar concentrations of hydrogen peroxide","volume":"3","author":"Tolar","year":"2016","journal-title":"Front Mar Sci"},{"key":"2026072003064318100_ref71","doi-asserted-by":"publisher","first-page":"7888","DOI":"10.1073\/pnas.1605501113","article-title":"Hydrogen peroxide detoxification is a key mechanism for growth of ammonia-oxidizing archaea","volume":"113","author":"Kim","year":"2016","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2026072003064318100_ref72","doi-asserted-by":"publisher","first-page":"119734","DOI":"10.1016\/j.watres.2023.119734","article-title":"An overlooked influence of reactive oxygen species on ammonia-oxidizing microbial communities in redox-fluctuating aquifers","volume":"233","author":"Wang","year":"2023","journal-title":"Water Res"},{"key":"2026072003064318100_ref73","doi-asserted-by":"publisher","first-page":"250","DOI":"10.1111\/1758-2229.12525","article-title":"Influence of oxygen availability on the activities of ammonia-oxidizing archaea","volume":"9","author":"Qin","year":"2017","journal-title":"Environ Microbiol Rep"},{"key":"2026072003064318100_ref74","doi-asserted-by":"publisher","first-page":"e2123193119","DOI":"10.1073\/pnas.2123193119","article-title":"Archaeal lipids trace ecology and evolution of marine ammonia-oxidizing archaea","volume":"119","author":"Rattanasriampaipong","year":"2022","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2026072003064318100_ref75","doi-asserted-by":"publisher","first-page":"4829","DOI":"10.1128\/AEM.66.11.4829-4833.2000","article-title":"Marine planktonic archaea take up amino acids","volume":"66","author":"Ouverney","year":"2000","journal-title":"Appl Environ Microbiol"},{"key":"2026072003064318100_ref76","doi-asserted-by":"publisher","first-page":"65","DOI":"10.3354\/ame01324","article-title":"Role of mesoscale cyclonic eddies in the distribution and activity of archaea and bacteria in the South China Sea","volume":"56","author":"Zhang","year":"2009","journal-title":"Aquat Microb Ecol"},{"key":"2026072003064318100_ref77","doi-asserted-by":"publisher","first-page":"60","DOI":"10.4319\/lo.2006.51.1.0060","article-title":"Archaeal uptake of enantiomeric amino acids in the meso- and bathypelagic waters of the North Atlantic","volume":"51","author":"Teira","year":"2006","journal-title":"Limnol Oceanogr"},{"key":"2026072003064318100_ref78","doi-asserted-by":"publisher","first-page":"3926","DOI":"10.1073\/pnas.062043799","article-title":"Ammonium\/methylammonium transport (amt) proteins facilitate diffusion of NH3 bidirectionally","volume":"99","author":"Soupene","year":"2002","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2026072003064318100_ref79","doi-asserted-by":"publisher","first-page":"eaaf3883","DOI":"10.1126\/science.aaf3883","article-title":"Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life","volume":"357","author":"Spang","year":"2017","journal-title":"Science"},{"key":"2026072003064318100_ref80","doi-asserted-by":"publisher","first-page":"395","DOI":"10.1007\/s00203-008-0402-6","article-title":"Ignicoccus hospitalis and Nanoarchaeum equitans: ultrastructure, cell\u2013cell interaction, and 3D reconstruction from serial sections of freeze-substituted cells and by electron cryotomography","volume":"190","author":"Junglas","year":"2008","journal-title":"Arch Microbiol"},{"key":"2026072003064318100_ref81","doi-asserted-by":"publisher","first-page":"1072","DOI":"10.3389\/fmicb.2017.01072","article-title":"A complex endomembrane system in the archaeon Ignicoccus hospitalis tapped by Nanoarchaeum equitans","volume":"8","author":"Heimerl","year":"2017","journal-title":"Front Microbiol"},{"key":"2026072003064318100_ref82","doi-asserted-by":"publisher","first-page":"3637","DOI":"10.1093\/molbev\/msab129","article-title":"The evolution pathway of ammonia-oxidizing archaea shaped by major geological events","volume":"38","author":"Yang","year":"2021","journal-title":"Mol Biol Evol"},{"key":"2026072003064318100_ref83","doi-asserted-by":"publisher","first-page":"26","DOI":"10.1016\/j.earscirev.2011.09.004","article-title":"The Neoproterozoic oxygenation event: environmental perturbations and biogeochemical cycling","volume":"110","author":"Och","year":"2012","journal-title":"Earth-Sci Rev"},{"key":"2026072003064318100_ref84","doi-asserted-by":"publisher","first-page":"2465","DOI":"10.1038\/s41396-019-0447-3","article-title":"Isolation and characterization of a thermophilic sulfur- and iron-reducing thaumarchaeote from a terrestrial acidic hot spring","volume":"13","author":"Kato","year":"2019","journal-title":"ISME J"},{"key":"2026072003064318100_ref85","doi-asserted-by":"publisher","first-page":"1545","DOI":"10.1093\/molbev\/msg167","article-title":"Increased rates of sequence evolution in endosymbiotic bacteria and fungi with small effective population sizes","volume":"20","author":"Woolfit","year":"2003","journal-title":"Mol Biol Evol"},{"key":"2026072003064318100_ref86","doi-asserted-by":"publisher","first-page":"16","DOI":"10.1111\/nyas.12740","article-title":"Endosymbiont evolution: predictions from theory and surprises from genomes","volume":"1360","author":"Wernegreen","year":"2015","journal-title":"Ann N Y Acad Sci"},{"key":"2026072003064318100_ref87","doi-asserted-by":"publisher","first-page":"486","DOI":"10.1038\/ngeo889","article-title":"Spatial variability in oceanic redox structure 1.8\u2009billion years ago","volume":"3","author":"Poulton","year":"2010","journal-title":"Nat Geosci"},{"key":"2026072003064318100_ref88","doi-asserted-by":"publisher","first-page":"e00036","DOI":"10.1128\/mbio.00036-12","article-title":"The black queen hypothesis: evolution of dependencies through adaptive gene loss","volume":"3","author":"Morris","year":"2012","journal-title":"mBio"},{"key":"2026072003064318100_ref89","doi-asserted-by":"publisher","first-page":"492","DOI":"10.1038\/nrmicro.2017.41","article-title":"Mechanisms of gene flow in archaea","volume":"15","author":"Wagner","year":"2017","journal-title":"Nat Rev Microbiol"},{"key":"2026072003064318100_ref90","doi-asserted-by":"publisher","first-page":"481","DOI":"10.1146\/annurev-micro-040820-124627","article-title":"Horizontal gene transfer in archaea\u2014from mechanisms to genome evolution","volume":"76","author":"Gophna","year":"2022","journal-title":"Ann Rev Microbiol"},{"key":"2026072003064318100_ref91","doi-asserted-by":"publisher","first-page":"447","DOI":"10.1038\/nrmicro3485","article-title":"Bacterial gene import and mesophilic adaptation in archaea","volume":"13","author":"L\u00f3pez-Garc\u00eda","year":"2015","journal-title":"Nat Rev Microbiol"},{"key":"2026072003064318100_ref92","doi-asserted-by":"publisher","first-page":"R158","DOI":"10.1186\/gb-2008-9-11-r158","article-title":"A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans","volume":"9","author":"Podar","year":"2008","journal-title":"Genome Biol"},{"key":"2026072003064318100_ref93","doi-asserted-by":"publisher","first-page":"1384","DOI":"10.1038\/s41467-023-36988-x","article-title":"Abiotic selection of microbial genome size in the global ocean","volume":"14","author":"Ngugi","year":"2023","journal-title":"Nat Commun"},{"key":"2026072003064318100_ref94","doi-asserted-by":"publisher","first-page":"6241","DOI":"10.1073\/pnas.93.13.6241","article-title":"A psychrophilic crenarchaeon inhabits a marine sponge: Cenarchaeum symbiosum gen. Nov., sp. nov","volume":"93","author":"Preston","year":"1996","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2026072003064318100_ref95","doi-asserted-by":"publisher","first-page":"18296","DOI":"10.1073\/pnas.0608549103","article-title":"Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum","volume":"103","author":"Hallam","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2026072003064318100_ref96","doi-asserted-by":"publisher","first-page":"699","DOI":"10.1111\/1574-6941.12427","article-title":"Symbiotic archaea in marine sponges show stability and host specificity in community structure and ammonia oxidation functionality","volume":"90","author":"Zhang","year":"2014","journal-title":"FEMS Microbiol Ecol"},{"key":"2026072003064318100_ref97","doi-asserted-by":"publisher","first-page":"4823","DOI":"10.1073\/pnas.1912367117","article-title":"Nitrifier adaptation to low energy flux controls inventory of reduced nitrogen in the dark ocean","volume":"117","author":"Zhang","year":"2020","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2026072003064318100_ref98","doi-asserted-by":"publisher","first-page":"5039","DOI":"10.5194\/essd-15-5039-2023","article-title":"Database of nitrification and nitrifiers in the global ocean","volume":"15","author":"Tang","year":"2023","journal-title":"Earth Syst Sci Data"}],"container-title":["ISME Communications"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/ismecommun\/advance-article-pdf\/doi\/10.1093\/ismeco\/ycag173\/68555174\/ycag173.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/ismecommun\/article-pdf\/6\/1\/ycag173\/68555174\/ycag173.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/ismecommun\/article-pdf\/6\/1\/ycag173\/68555174\/ycag173.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,20]],"date-time":"2026-07-20T07:06:55Z","timestamp":1784531215000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/ismecommun\/article\/doi\/10.1093\/ismeco\/ycag173\/8711259"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1]]},"references-count":98,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2026,1,14]]}},"URL":"https:\/\/doi.org\/10.1093\/ismeco\/ycag173","relation":{},"ISSN":["2730-6151"],"issn-type":[{"value":"2730-6151","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,1]]},"published":{"date-parts":[[2026,1]]},"article-number":"ycag173"}}