{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,20]],"date-time":"2026-07-20T08:02:07Z","timestamp":1784534527751,"version":"3.55.0"},"reference-count":101,"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\/501100001659","name":"German Research Foundation","doi-asserted-by":"publisher","award":["PE2147\/5-1"],"award-info":[{"award-number":["PE2147\/5-1"]}],"id":[{"id":"10.13039\/501100001659","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>Ammonia-oxidizing bacteria (AOB) catalyze the first and rate-limiting step of nitrification. They are essential for nitrogen cycling in engineered and natural environments, yet little is known about their viruses or the consequences of phage infection for host physiology. Here, we report the isolation and characterization of a novel lytic bacteriophage, vB_NeuP-Nir1 (DSM 111086), infecting the model AOB Nitrosomonas europaea. Phage Nir1 ceased ammonia oxidation within hours, and caused complete lysis of host populations even at multiplicities of infection as low as 10\u22126. Electron microscopy revealed drastic host cell remodeling during infection, including pronounced cell bloating and large-scale disintegration of intracytoplasmic membranes. Integrated transcriptomic and metabolomic analyses showed that loss of these ATP and reducing equivalent generating membrane systems was accompanied by signatures of compromised lipid homeostasis and collapse of autotrophic CO\u2082 fixation. In parallel, Nir1 infection induced metabolic rewiring of the host, including upregulation of uptake systems for nucleic acids, amino acids, and small organic compounds, increased expression of iron acquisition and putative iron-dependent respiratory components, as well as accumulation of metabolites associated with membrane breakdown and stabilization of viral DNA. Together, these results provide the first detailed mechanistic insight into phage-induced host modulation in a chemolithoautotrophic nitrifier. Our study establishes the Nir1\u2013N. europaea system as a model for investigating virus\u2013host interactions in AOB and lays the foundation for assessing the role of phages in shaping nitrification and nitrogen cycling in engineered and natural ecosystems.<\/jats:p>","DOI":"10.1093\/ismeco\/ycag170","type":"journal-article","created":{"date-parts":[[2026,6,16]],"date-time":"2026-06-16T12:29:29Z","timestamp":1781612969000},"source":"Crossref","is-referenced-by-count":0,"title":["Viral infection collapses intracytoplasmic membrane integrity and autotrophic metabolism in ammonia-oxidizing\n                    <i>Nitrosomonas europaea<\/i>"],"prefix":"10.1093","volume":"6","author":[{"given":"J\u00e1nos","family":"Papendorf","sequence":"first","affiliation":[{"name":"Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures , Inhoffenstra\u00dfe 7B, Braunschweig 38124 ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0442-4279","authenticated-orcid":false,"given":"David K","family":"Ngugi","sequence":"additional","affiliation":[{"name":"GEOMAR Helmholtz Centre for Ocean Research Kiel , Wischofstra\u00dfe 1-3, Kiel 24148 ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Petra","family":"B\u00fcsing","sequence":"additional","affiliation":[{"name":"Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures , Inhoffenstra\u00dfe 7B, Braunschweig 38124 ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicole","family":"Reimann","sequence":"additional","affiliation":[{"name":"Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures , Inhoffenstra\u00dfe 7B, Braunschweig 38124 ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7275-9927","authenticated-orcid":false,"given":"Johannes","family":"Wittmann","sequence":"additional","affiliation":[{"name":"Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures , Inhoffenstra\u00dfe 7B, Braunschweig 38124 ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephanie","family":"Peter","sequence":"additional","affiliation":[{"name":"Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures , Inhoffenstra\u00dfe 7B, Braunschweig 38124 ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1105-6363","authenticated-orcid":false,"given":"Richard L","family":"Hahnke","sequence":"additional","affiliation":[{"name":"Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures , Inhoffenstra\u00dfe 7B, Braunschweig 38124 ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-0692-9410","authenticated-orcid":false,"given":"Sarah","family":"Kirstein","sequence":"additional","affiliation":[{"name":"Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures , Inhoffenstra\u00dfe 7B, Braunschweig 38124 ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8420-8161","authenticated-orcid":false,"given":"Boyke","family":"Bunk","sequence":"additional","affiliation":[{"name":"Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures , Inhoffenstra\u00dfe 7B, Braunschweig 38124 ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0522-3580","authenticated-orcid":false,"given":"Manfred","family":"Rohde","sequence":"additional","affiliation":[{"name":"Central Facility for Microscopy, Helmholtz Centre for Infection Research , Inhoffenstra\u00dfe 7, Braunschweig 38124 ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mathias","family":"M\u00fcsken","sequence":"additional","affiliation":[{"name":"Central Facility for Microscopy, Helmholtz Centre for Infection Research , Inhoffenstra\u00dfe 7, Braunschweig 38124 ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1641-019X","authenticated-orcid":false,"given":"Meina","family":"Neumann-Schaal","sequence":"additional","affiliation":[{"name":"Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures , Inhoffenstra\u00dfe 7B, Braunschweig 38124 ,","place":["Germany"]},{"name":"Braunschweig Integrated Centre of Systems Biology (BRICS), TU Braunschweig , Rebenring 56, Braunschweig 38106 ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6296-4145","authenticated-orcid":false,"given":"Michael","family":"Pester","sequence":"additional","affiliation":[{"name":"Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures , Inhoffenstra\u00dfe 7B, Braunschweig 38124 ,","place":["Germany"]},{"name":"Chair of Microbial Physiology, Technical University of Munich , Emil-Ramann-Str. 4, Freising 85354 ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,6,18]]},"reference":[{"key":"2026072003063524100_ref1","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1038\/nrmicro.2018.9","article-title":"The microbial nitrogen-cycling network","volume":"16","author":"Kuypers","year":"2018","journal-title":"Nat Rev Microbiol"},{"key":"2026072003063524100_ref2","doi-asserted-by":"publisher","first-page":"303","DOI":"10.1080\/07352680600794232","article-title":"Scope and strategies for regulation of nitrification in agricultural systems\u2014challenges and opportunities","volume":"25","author":"Subbarao","year":"2006","journal-title":"Crit Rev Plant Sci"},{"key":"2026072003063524100_ref3","doi-asserted-by":"publisher","first-page":"405","DOI":"10.1128\/9781555817145.ch16","volume-title":"Nitrification","author":"Okabe","year":"2011"},{"key":"2026072003063524100_ref4","doi-asserted-by":"publisher","first-page":"6857","DOI":"10.1021\/acs.est.7b00392","article-title":"Growth of Nitrosococcus-related ammonia oxidizing bacteria coincides with extremely low pH values in wastewater with high ammonia content","volume":"51","author":"Fumasoli","year":"2017","journal-title":"Environ Sci Technol"},{"key":"2026072003063524100_ref5","doi-asserted-by":"publisher","first-page":"1067","DOI":"10.1038\/ismej.2010.191","article-title":"Ammonia concentration determines differential growth of ammonia-oxidising archaea and bacteria in soil microcosms","volume":"5","author":"Verhamme","year":"2011","journal-title":"ISME J"},{"key":"2026072003063524100_ref6","doi-asserted-by":"publisher","first-page":"524","DOI":"10.1038\/s41564-023-01593-7","article-title":"Ammonia-oxidizing bacteria and archaea exhibit differential nitrogen source preferences","volume":"9","author":"Qin","year":"2024","journal-title":"Nat Microbiol"},{"key":"2026072003063524100_ref7","doi-asserted-by":"publisher","first-page":"16771","DOI":"10.1073\/pnas.1106427108","article-title":"Thaumarchaeotes abundant in refinery nitrifying sludges express amoA but are not obligate autotrophic ammonia oxidizers","volume":"108","author":"Mu\u00dfmann","year":"2011","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026072003063524100_ref8","doi-asserted-by":"publisher","first-page":"778","DOI":"10.1007\/0-387-30745-1_36","volume-title":"The Prokaryotes: Volume 5: Proteobacteria: Alpha and Beta Subclasses","author":"Koops","year":"2006"},{"key":"2026072003063524100_ref9","doi-asserted-by":"publisher","first-page":"2931","DOI":"10.1111\/j.1462-2920.2008.01775.x","article-title":"Relative contributions of archaea and bacteria to aerobic ammonia oxidation in the environment","volume":"10","author":"Prosser","year":"2008","journal-title":"Environ Microbiol"},{"key":"2026072003063524100_ref10","doi-asserted-by":"publisher","first-page":"504","DOI":"10.1038\/nature16461","article-title":"Complete nitrification by Nitrospira bacteria","volume":"528","author":"Daims","year":"2015","journal-title":"Nature"},{"key":"2026072003063524100_ref11","doi-asserted-by":"publisher","first-page":"555","DOI":"10.1038\/nature16459","article-title":"Complete nitrification by a single microorganism","volume":"528","author":"van Kessel","year":"2015","journal-title":"Nature"},{"key":"2026072003063524100_ref12","doi-asserted-by":"publisher","first-page":"269","DOI":"10.1038\/nature23679","article-title":"Kinetic analysis of a complete nitrifier reveals an oligotrophic lifestyle","volume":"549","author":"Kits","year":"2017","journal-title":"Nature"},{"key":"2026072003063524100_ref13","doi-asserted-by":"publisher","DOI":"10.1128\/mSphere.00054-15","article-title":"Metagenomic evidence for the presence of Comammox Nitrospira-like bacteria in a drinking water system","volume":"1","author":"Pinto","year":"2016","journal-title":"mSphere"},{"key":"2026072003063524100_ref14","doi-asserted-by":"publisher","first-page":"332","DOI":"10.1016\/j.watres.2017.03.042","article-title":"Comammox in drinking water systems","volume":"116","author":"Wang","year":"2017","journal-title":"Water Res"},{"key":"2026072003063524100_ref15","doi-asserted-by":"publisher","first-page":"285","DOI":"10.1016\/j.biortech.2013.03.176","article-title":"Quantitative analyses of the composition and abundance of ammonia-oxidizing archaea and ammonia-oxidizing bacteria in eight full-scale biological wastewater treatment plants","volume":"138","author":"Gao","year":"2013","journal-title":"Bioresour Technol"},{"key":"2026072003063524100_ref16","doi-asserted-by":"publisher","first-page":"3694","DOI":"10.1016\/j.biortech.2010.11.085","article-title":"Abundance of amoA genes of ammonia-oxidizing archaea and bacteria in activated sludge of full-scale wastewater treatment plants","volume":"102","author":"Limpiyakorn","year":"2011","journal-title":"Bioresour Technol"},{"key":"2026072003063524100_ref17","doi-asserted-by":"publisher","first-page":"396","DOI":"10.1016\/j.watres.2019.03.060","article-title":"Comammox Nitrospira are the dominant ammonia oxidizers in a mainstream low dissolved oxygen nitrification reactor","volume":"157","author":"Roots","year":"2019","journal-title":"Water Res"},{"key":"2026072003063524100_ref18","doi-asserted-by":"publisher","first-page":"2589","DOI":"10.1111\/j.1462-2920.2012.02786.x","article-title":"Low-ammonia niche of ammonia-oxidizing archaea in rotating biological contactors of a municipal wastewater treatment plant","volume":"14","author":"Sauder","year":"2012","journal-title":"Environ Microbiol"},{"key":"2026072003063524100_ref19","doi-asserted-by":"publisher","first-page":"205","DOI":"10.1016\/j.femsec.2005.03.017","article-title":"Communities of ammonia-oxidizing bacteria in activated sludge of various sewage treatment plants in Tokyo","volume":"54","author":"Limpiyakorn","year":"2005","journal-title":"FEMS Microbiol Ecol"},{"key":"2026072003063524100_ref20","doi-asserted-by":"publisher","first-page":"8429145","DOI":"10.1155\/2018\/8429145","article-title":"Ammonia-oxidizing archaea (AOA) play with ammonia-oxidizing bacteria (AOB) in nitrogen removal from wastewater","volume":"2018","author":"Yin","year":"2018","journal-title":"Archaea"},{"key":"2026072003063524100_ref21","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1128\/9781555817145.ch2","volume-title":"Nitrification","author":"Sayavedra-Soto","year":"2011"},{"key":"2026072003063524100_ref22","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1016\/j.cbpa.2018.09.003","article-title":"Insights into the physiology of ammonia-oxidizing microorganisms","volume":"49","author":"Stein","year":"2019","journal-title":"Curr Opin Chem Biol"},{"key":"2026072003063524100_ref23","doi-asserted-by":"publisher","first-page":"1594","DOI":"10.1128\/jb.89.6.1594-1609.1965","article-title":"Structure of Nitrosocystis oceanus and comparison with Nitrosomonas and Nitrobacter","volume":"89","author":"Murray","year":"1965","journal-title":"J Bacteriol"},{"key":"2026072003063524100_ref24","doi-asserted-by":"publisher","first-page":"6809","DOI":"10.1128\/JB.185.23.6809-6814.2003","article-title":"Chemolithoorganotrophic growth of Nitrosomonas europaea on fructose","volume":"185","author":"Hommes","year":"2003","journal-title":"J Bacteriol"},{"key":"2026072003063524100_ref25","doi-asserted-by":"publisher","first-page":"296","DOI":"10.1038\/s41579-022-00811-z","article-title":"Soil viral diversity, ecology and climate change","volume":"21","author":"Jansson","year":"2023","journal-title":"Nat Rev Microbiol"},{"key":"2026072003063524100_ref26","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1007\/BF00166813","article-title":"The significance of viruses to mortality in aquatic microbial communities","volume":"28","author":"Suttle","year":"1994","journal-title":"Microb Ecol"},{"key":"2026072003063524100_ref27","doi-asserted-by":"publisher","first-page":"31","DOI":"10.4161\/bact.1.1.14942","article-title":"Phages in nature","volume":"1","author":"Clokie","year":"2011","journal-title":"Bacteriophage"},{"key":"2026072003063524100_ref28","doi-asserted-by":"publisher","first-page":"5398","DOI":"10.1038\/s41467-021-25678-1","article-title":"Prokaryotic viruses impact functional microorganisms in nutrient removal and carbon cycle in wastewater treatment plants","volume":"12","author":"Chen","year":"2021","journal-title":"Nat Commun"},{"key":"2026072003063524100_ref29","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1038\/s41579-019-0270-x","article-title":"Metabolic and biogeochemical consequences of viral infection in aquatic ecosystems","volume":"18","author":"Zimmerman","year":"2020","journal-title":"Nat Rev Microbiol"},{"key":"2026072003063524100_ref30","doi-asserted-by":"publisher","first-page":"209","DOI":"10.1007\/BF00166811","article-title":"Viruses and the microbial loop","volume":"28","author":"Bratbak","year":"1994","journal-title":"Microb Ecol"},{"key":"2026072003063524100_ref31","doi-asserted-by":"publisher","first-page":"781","DOI":"10.2307\/1313569","article-title":"Viruses and nutrient cycles in the sea viruses play critical roles in the structure and function of aquatic food webs","volume":"49","author":"Wilhelm","year":"1999","journal-title":"BioScience"},{"key":"2026072003063524100_ref32","doi-asserted-by":"publisher","first-page":"541","DOI":"10.1038\/21119","article-title":"Marine viruses and their biogeochemical and ecological effects","volume":"399","author":"Fuhrman","year":"1999","journal-title":"Nature"},{"key":"2026072003063524100_ref33","doi-asserted-by":"publisher","first-page":"52","DOI":"10.1016\/0922-338X(92)90268-Y","article-title":"Pure isolation of a new chemoautotrophic ammonia-oxidizing bacterium on gellan gum plate","volume":"74","author":"Takahashi","year":"1992","journal-title":"J Ferment Bioeng"},{"key":"2026072003063524100_ref34","doi-asserted-by":"publisher","DOI":"10.1093\/femsle\/fnac029","article-title":"Cultivation of ammonia-oxidising archaea on solid medium","volume":"369","author":"Klein","year":"2022","journal-title":"FEMS Microbiol Lett"},{"key":"2026072003063524100_ref35","doi-asserted-by":"publisher","first-page":"618","DOI":"10.1038\/s41396-018-0289-4","article-title":"Discovery of several novel, widespread, and ecologically distinct marine Thaumarchaeota viruses that encode amoC nitrification genes","volume":"13","author":"Ahlgren","year":"2019","journal-title":"ISME J"},{"key":"2026072003063524100_ref36","doi-asserted-by":"publisher","first-page":"1980","DOI":"10.1111\/1462-2920.14462","article-title":"Novel Caudovirales associated with marine group I Thaumarchaeota assembled from metagenomes","volume":"21","author":"Lopez-Perez","year":"2019","journal-title":"Environ Microbiol"},{"key":"2026072003063524100_ref37","doi-asserted-by":"publisher","first-page":"689","DOI":"10.1038\/nature19366","article-title":"Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses","volume":"537","author":"Roux","year":"2016","journal-title":"Nature"},{"key":"2026072003063524100_ref38","doi-asserted-by":"publisher","first-page":"15645","DOI":"10.1073\/pnas.1905682116","article-title":"Spindle-shaped viruses infect marine ammonia-oxidizing thaumarchaea","volume":"116","author":"Kim","year":"2019","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026072003063524100_ref39","doi-asserted-by":"publisher","first-page":"645","DOI":"10.1038\/s41396-023-01380-6","article-title":"Identification of a virulent phage infecting species of Nitrosomonas","volume":"17","author":"Quiros","year":"2023","journal-title":"ISME J"},{"key":"2026072003063524100_ref40","first-page":"87","article-title":"Contributions a la morphologie des organisms de la nitrification","volume":"1","author":"Winogradsky","year":"1892","journal-title":"Arkhiv Biologischeski Nauk (St Petersbourg)"},{"key":"2026072003063524100_ref41","doi-asserted-by":"publisher","first-page":"225","DOI":"10.1099\/00207713-30-1-225","article-title":"Approved lists of bacterial names","volume":"30","author":"Skerman","year":"1980","journal-title":"Int J Syst Evol Microbiol"},{"key":"2026072003063524100_ref42","doi-asserted-by":"publisher","first-page":"540","DOI":"10.1038\/s41587-019-0072-8","article-title":"Assembly of long, error-prone reads using repeat graphs","volume":"37","author":"Kolmogorov","year":"2019","journal-title":"Nat Biotechnol"},{"key":"2026072003063524100_ref43","doi-asserted-by":"publisher","first-page":"1103","DOI":"10.1038\/s41592-020-00971-x","article-title":"metaFlye: scalable long-read metagenome assembly using repeat graphs","volume":"17","author":"Kolmogorov","year":"2020","journal-title":"Nat Methods"},{"key":"2026072003063524100_ref44","author":"Bushnell","year":"2014"},{"key":"2026072003063524100_ref45","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":"2026072003063524100_ref46","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btac776","article-title":"Pharokka: a fast scalable bacteriophage annotation tool","volume":"39","author":"Bouras","year":"2023","journal-title":"Bioinformatics"},{"key":"2026072003063524100_ref47","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkaf1448","article-title":"Protein structure-informed bacteriophage genome annotation with Phold","volume":"54","author":"Bouras","year":"2026","journal-title":"Nucleic Acids Res"},{"key":"2026072003063524100_ref48","doi-asserted-by":"publisher","first-page":"2379","DOI":"10.1093\/bioinformatics\/btx157","article-title":"ViPTree: the viral proteomic tree server","volume":"33","author":"Nishimura","year":"2017","journal-title":"Bioinformatics"},{"key":"2026072003063524100_ref49","doi-asserted-by":"publisher","first-page":"685","DOI":"10.1093\/oxfordjournals.molbev.a025808","article-title":"BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data","volume":"14","author":"Gascuel","year":"1997","journal-title":"Mol Biol Evol"},{"key":"2026072003063524100_ref50","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1089\/phage.2024.0050","article-title":"taxMyPhage: automated taxonomy of dsDNA phage genomes at the genus and species level","volume":"6","author":"Millard","year":"2025","journal-title":"PHAGE"},{"key":"2026072003063524100_ref51","doi-asserted-by":"publisher","first-page":"1268","DOI":"10.3390\/v12111268","article-title":"VIRIDIC-A novel tool to calculate the intergenomic similarities of prokaryote-infecting viruses","volume":"12","author":"Moraru","year":"2020","journal-title":"Viruses"},{"key":"2026072003063524100_ref52","doi-asserted-by":"publisher","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol"},{"key":"2026072003063524100_ref53","doi-asserted-by":"publisher","first-page":"270","DOI":"10.1093\/gbe\/evy275","article-title":"Day and night: metabolic profiles and evolutionary relationships of six axenic non-marine cyanobacteria","volume":"11","author":"Will","year":"2019","journal-title":"Genome Biol Evol"},{"key":"2026072003063524100_ref54","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1186\/s12866-015-0614-2","article-title":"Time-resolved amino acid uptake of Clostridium difficile 630\u0394erm and concomitant fermentation product and toxin formation","volume":"15","author":"Neumann-Schaal","year":"2015","journal-title":"BMC Microbiol"},{"key":"2026072003063524100_ref55","doi-asserted-by":"publisher","first-page":"1970","DOI":"10.3389\/fmicb.2018.01970","article-title":"Metabolic reprogramming of Clostridioides difficile during the stationary phase with the induction of toxin production","volume":"9","author":"Hofmann","year":"2018","journal-title":"Front Microbiol"},{"key":"2026072003063524100_ref56","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":"2026072003063524100_ref57","doi-asserted-by":"publisher","first-page":"002111","DOI":"10.1099\/jgv.0.002111","article-title":"Summary of taxonomy changes ratified by the International Committee on Taxonomy of Viruses (ICTV) from the Bacterial Viruses Subcommittee, 2025","volume":"106","author":"Turner","year":"2025","journal-title":"J Gen Virol"},{"key":"2026072003063524100_ref58","doi-asserted-by":"publisher","DOI":"10.1093\/femsec\/fiab029","article-title":"The first sequenced Sphaerotilus natans bacteriophage- characterization and potential to control its filamentous bacterium host","volume":"97","author":"Ferreira","year":"2021","journal-title":"FEMS Microbiol Ecol"},{"key":"2026072003063524100_ref59","doi-asserted-by":"publisher","first-page":"506","DOI":"10.3390\/v13030506","article-title":"A roadmap for genome-based phage taxonomy","volume":"13","author":"Turner","year":"2021","journal-title":"Viruses"},{"key":"2026072003063524100_ref60","doi-asserted-by":"publisher","first-page":"1689","DOI":"10.1099\/00221287-137-7-1689","article-title":"Classification of eight new species of ammonia-oxidizing bacteria: Nitrosomonas communis sp. nov., Nitrosomonas ureae sp. nov., Nitrosomonas aestuarii sp. nov., Nitrosomonas marina sp. nov., Nitrosomonas nitrosa sp. nov., Nitrosomonas eutropha sp. nov., Nitrosomonas oligotropha sp. nov. and Nitrosomonas halophila sp. nov","volume":"137","author":"Koops","year":"1991","journal-title":"Microbiology"},{"key":"2026072003063524100_ref61","doi-asserted-by":"publisher","first-page":"2759","DOI":"10.1128\/JB.185.9.2759-2773.2003","article-title":"Complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea","volume":"185","author":"Chain","year":"2003","journal-title":"J Bacteriol"},{"key":"2026072003063524100_ref62","doi-asserted-by":"publisher","first-page":"1823","DOI":"10.1038\/ismej.2016.3","article-title":"High coverage metabolomics analysis reveals phage-specific alterations to Pseudomonas aeruginosa physiology during infection","volume":"10","author":"De Smet","year":"2016","journal-title":"ISME J"},{"key":"2026072003063524100_ref63","doi-asserted-by":"publisher","first-page":"E757","DOI":"10.1073\/pnas.1102164108","article-title":"Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism","volume":"108","author":"Thompson","year":"2011","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026072003063524100_ref64","doi-asserted-by":"publisher","first-page":"e1006134","DOI":"10.1371\/journal.pgen.1006134","article-title":"Next-generation \u201c-omics\u201d approaches reveal a massive alteration of host RNA metabolism during bacteriophage infection of Pseudomonas aeruginosa","volume":"12","author":"Chevallereau","year":"2016","journal-title":"PLoS Genet"},{"key":"2026072003063524100_ref65","doi-asserted-by":"publisher","first-page":"e02466","DOI":"10.1128\/mbio.02466-24","article-title":"Phage reprogramming of Pseudomonas aeruginosa amino acid metabolism drives efficient phage replication","volume":"16","author":"Fitzpatrick","year":"2025","journal-title":"mBio"},{"key":"2026072003063524100_ref66","doi-asserted-by":"publisher","first-page":"627","DOI":"10.1016\/S1001-0742(09)60155-8","article-title":"Community analysis of ammonia-oxidizing bacteria in activated sludge of eight wastewater treatment systems","volume":"22","author":"Wang","year":"2010","journal-title":"J Environ Sci"},{"key":"2026072003063524100_ref67","doi-asserted-by":"publisher","first-page":"250","DOI":"10.1007\/s00203-002-0452-0","article-title":"Molecular biology and biochemistry of ammonia oxidation by Nitrosomonas europaea","volume":"178","author":"Arp","year":"2002","journal-title":"Arch Microbiol"},{"key":"2026072003063524100_ref68","doi-asserted-by":"publisher","first-page":"366","DOI":"10.1128\/jb.99.2.366-370.1969","article-title":"Fatty acids in the lipids of marine and terrestrial nitrifying bacteria","volume":"99","author":"Blumer","year":"1969","journal-title":"J Bacteriol"},{"key":"2026072003063524100_ref69","doi-asserted-by":"publisher","first-page":"241","DOI":"10.1016\/0042-6822(69)90365-1","article-title":"A role for phospholipid hydrolysis in the lysis of Escherichia coli infected with bacteriophage T4","volume":"38","author":"Cronan","year":"1969","journal-title":"Virology"},{"key":"2026072003063524100_ref70","doi-asserted-by":"publisher","first-page":"977","DOI":"10.1016\/0042-6822(71)90101-2","article-title":"Phospholipid hydrolysis before the onset of lysis in T4-infected Escherichia coli","volume":"46","author":"Cronan","year":"1971","journal-title":"Virology"},{"key":"2026072003063524100_ref71","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1093\/femsre\/fuv008","article-title":"Bacterial membrane lipids: diversity in structures and pathways","volume":"40","author":"Sohlenkamp","year":"2015","journal-title":"FEMS Microbiol Rev"},{"key":"2026072003063524100_ref72","doi-asserted-by":"publisher","first-page":"222","DOI":"10.1038\/nrmicro1839","article-title":"Membrane lipid homeostasis in bacteria","volume":"6","author":"Zhang","year":"2008","journal-title":"Nat Rev Microbiol"},{"key":"2026072003063524100_ref73","doi-asserted-by":"publisher","first-page":"554","DOI":"10.1111\/1574-6976.12006","article-title":"Diversity in bacterial lysis systems: bacteriophages show the way","volume":"37","author":"Catal\u00e3o","year":"2013","journal-title":"FEMS Microbiol Rev"},{"key":"2026072003063524100_ref74","doi-asserted-by":"publisher","first-page":"243","DOI":"10.1007\/s12275-014-4087-z","article-title":"Phage lysis: three steps, three choices, one outcome","volume":"52","author":"Young","year":"2014","journal-title":"J Microbiol"},{"key":"2026072003063524100_ref75","doi-asserted-by":"publisher","first-page":"588","DOI":"10.1016\/0042-6822(89)90628-4","article-title":"Nucleotide sequence of the bacteriophage P22 gene 19 to 3 region: identification of a new gene required for lysis","volume":"171","author":"Casjens","year":"1989","journal-title":"Virology"},{"key":"2026072003063524100_ref76","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1016\/0022-2836(79)90262-6","article-title":"Transposition mutagenesis of bacteriophage lambda: a new gene affecting cell lysis","volume":"132","author":"Young","year":"1979","journal-title":"J Mol Biol"},{"key":"2026072003063524100_ref77","doi-asserted-by":"publisher","first-page":"1629","DOI":"10.1007\/s00253-009-2355-3","article-title":"Antibacterial free fatty acids: activities, mechanisms of action and biotechnological potential","volume":"85","author":"Desbois","year":"2010","journal-title":"Appl Microbiol Biotechnol"},{"key":"2026072003063524100_ref78","doi-asserted-by":"publisher","first-page":"346","DOI":"10.1016\/S0005-2728(00)00171-7","article-title":"Electron transfer during the oxidation of ammonia by the chemolithotrophic bacterium Nitrosomonas europaea","volume":"1459","author":"Whittaker","year":"2000","journal-title":"Biochim Biophys Acta"},{"key":"2026072003063524100_ref79","doi-asserted-by":"publisher","first-page":"1925","DOI":"10.1128\/AEM.02473-10","article-title":"Ecological aspects of the distribution of different autotrophic CO2 fixation pathways","volume":"77","author":"Berg","year":"2011","journal-title":"Appl Environ Microbiol"},{"key":"2026072003063524100_ref80","doi-asserted-by":"publisher","first-page":"22452","DOI":"10.1073\/pnas.2012288117","article-title":"Phosphoglycolate salvage in a chemolithoautotroph using the Calvin cycle","volume":"117","author":"Claassens","year":"2020","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026072003063524100_ref81","doi-asserted-by":"publisher","first-page":"e1009828","DOI":"10.1371\/journal.pcbi.1009828","article-title":"Flux balance analysis of the ammonia-oxidizing bacterium Nitrosomonas europaea ATCC19718 unravels specific metabolic activities while degrading toxic compounds","volume":"18","author":"Canto-Encalada","year":"2022","journal-title":"PLoS Comp Biol"},{"key":"2026072003063524100_ref82","doi-asserted-by":"publisher","first-page":"450","DOI":"10.1128\/mr.54.4.450-472.1990","article-title":"Occurrence, metabolism, metabolic role, and industrial uses of bacterial polyhydroxyalkanoates","volume":"54","author":"Anderson","year":"1990","journal-title":"Microbiol Rev"},{"key":"2026072003063524100_ref83","doi-asserted-by":"publisher","first-page":"18719","DOI":"10.1074\/jbc.TM118.003338","article-title":"Roles of polyamines in translation","volume":"293","author":"Dever","year":"2018","journal-title":"J Biol Chem"},{"key":"2026072003063524100_ref84","doi-asserted-by":"publisher","first-page":"1302","DOI":"10.1016\/j.bpj.2017.02.015","article-title":"A molecular view of the dynamics of dsDNA packing inside viral capsids in the presence of ions","volume":"112","author":"C\u00f3rdoba","year":"2017","journal-title":"Biophys J"},{"key":"2026072003063524100_ref85","doi-asserted-by":"publisher","first-page":"e2216430120","DOI":"10.1073\/pnas.2216430120","article-title":"Polyamines and linear DNA mediate bacterial threat assessment of bacteriophage infection","volume":"120","author":"de Mattos","year":"2023","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026072003063524100_ref86","doi-asserted-by":"publisher","first-page":"2238","DOI":"10.1128\/jb.173.7.2238-2243.1991","article-title":"Increase in spermine content coordinated with siderophore production in Paracoccus denitrificans","volume":"173","author":"Bergeron","year":"1991","journal-title":"J Bacteriol"},{"key":"2026072003063524100_ref87","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1111\/j.1365-2958.2008.06126.x","article-title":"A multifaceted role for polyamines in bacterial pathogens","volume":"68","author":"Shah","year":"2008","journal-title":"Mol Microbiol"},{"key":"2026072003063524100_ref88","doi-asserted-by":"publisher","first-page":"1437","DOI":"10.1038\/ismej.2015.210","article-title":"Transcriptome dynamics of a broad host-range cyanophage and its hosts","volume":"10","author":"Doron","year":"2016","journal-title":"ISME J"},{"key":"2026072003063524100_ref89","doi-asserted-by":"publisher","first-page":"881","DOI":"10.1038\/s41396-019-0580-z","article-title":"Phage-specific metabolic reprogramming of virocells","volume":"14","author":"Howard-Varona","year":"2020","journal-title":"ISME J"},{"key":"2026072003063524100_ref90","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1007\/s00203-006-0126-4","article-title":"Iron nutrition and physiological responses to iron stress in Nitrosomonas europaea","volume":"186","author":"Wei","year":"2006","journal-title":"Arch Microbiol"},{"key":"2026072003063524100_ref91","doi-asserted-by":"publisher","DOI":"10.1093\/femsle\/fny058","article-title":"Ammonia oxidation: ecology, physiology, biochemistry and why they must all come together","volume":"365","author":"Lehtovirta-Morley","year":"2018","journal-title":"FEMS Microbiol Lett"},{"key":"2026072003063524100_ref92","doi-asserted-by":"publisher","first-page":"10.1128\/jb.00771-17","DOI":"10.1128\/jb.00771-17","article-title":"Peptide transporter CstA imports pyruvate in Escherichia coli K-12","volume":"200","author":"Hwang","year":"2018","journal-title":"J Bacteriol"},{"key":"2026072003063524100_ref93","doi-asserted-by":"publisher","first-page":"367","DOI":"10.1128\/jb.91.1.367-373.1966","article-title":"Effect of mixed culture on Nitrosomonas europaea simulated by uptake and utilization of pyruvate","volume":"91","author":"Clark","year":"1966","journal-title":"J Bacteriol"},{"key":"2026072003063524100_ref94","doi-asserted-by":"publisher","first-page":"1302","DOI":"10.1128\/jb.93.4.1302-1308.1967","article-title":"Growth response of Nitrosomonas europaea to amino acids","volume":"93","author":"Clark","year":"1967","journal-title":"J Bacteriol"},{"key":"2026072003063524100_ref95","doi-asserted-by":"publisher","first-page":"1309","DOI":"10.1128\/jb.93.4.1309-1315.1967","article-title":"Uptake and utilization of amino acids by resting cells of Nitrosomonas europaea","volume":"93","author":"Clark","year":"1967","journal-title":"J Bacteriol"},{"key":"2026072003063524100_ref96","doi-asserted-by":"publisher","first-page":"860","DOI":"10.1111\/j.1365-2958.2011.07647.x","article-title":"Two steps away from novelty--principles of bacterial DNA uptake","volume":"80","author":"Kruger","year":"2011","journal-title":"Mol Microbiol"},{"key":"2026072003063524100_ref97","doi-asserted-by":"publisher","first-page":"9389","DOI":"10.1074\/jbc.M111.319475","article-title":"Crystal structure of urea carboxylase provides insights into the carboxyltransfer reaction*","volume":"287","author":"Fan","year":"2012","journal-title":"J Biol Chem"},{"key":"2026072003063524100_ref98","doi-asserted-by":"publisher","first-page":"1089","DOI":"10.1038\/ismej.2013.216","article-title":"Phage infection of an environmentally relevant marine bacterium alters host metabolism and lysate composition","volume":"8","author":"Ankrah","year":"2013","journal-title":"ISME J"},{"key":"2026072003063524100_ref99","doi-asserted-by":"publisher","first-page":"646","DOI":"10.1038\/s41586-024-07832-z","article-title":"Growth of complete ammonia oxidizers on guanidine","volume":"633","author":"Palatinszky","year":"2024","journal-title":"Nature"},{"key":"2026072003063524100_ref100","doi-asserted-by":"publisher","first-page":"116728","DOI":"10.1016\/j.watres.2020.116728","article-title":"N2O and NOy production by the comammox bacterium Nitrospira inopinata in comparison with canonical ammonia oxidizers","volume":"190","author":"Han","year":"2021","journal-title":"Water Res"},{"key":"2026072003063524100_ref101","doi-asserted-by":"publisher","first-page":"641","DOI":"10.1038\/294641a0","article-title":"Production of NO and N2O by soil nitrifying bacteria","volume":"294","author":"Lipschultz","year":"1981","journal-title":"Nature"}],"container-title":["ISME Communications"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/ismecommun\/advance-article-pdf\/doi\/10.1093\/ismeco\/ycag170\/68555167\/ycag170.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/ismecommun\/article-pdf\/6\/1\/ycag170\/68555167\/ycag170.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/ismecommun\/article-pdf\/6\/1\/ycag170\/68555167\/ycag170.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,20]],"date-time":"2026-07-20T07:06:43Z","timestamp":1784531203000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/ismecommun\/article\/doi\/10.1093\/ismeco\/ycag170\/8711258"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1]]},"references-count":101,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2026,1,14]]}},"URL":"https:\/\/doi.org\/10.1093\/ismeco\/ycag170","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":"ycag170"}}