{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T23:29:18Z","timestamp":1787009358506,"version":"build-2736575974"},"reference-count":85,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2026,1,7]],"date-time":"2026-01-07T00:00:00Z","timestamp":1767744000000},"content-version":"vor","delay-in-days":2,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","award":["692637"],"award-info":[{"award-number":["692637"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["DFG 446072859"],"award-info":[{"award-number":["DFG 446072859"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100020618","name":"University of Bayreuth","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100020618","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Magnetotactic bacteria produce membrane-bound organelles known as magnetosomes, which consist of chains of magnetite crystals and function as sensors for orientation within the Earth\u2019s magnetic field. Magnetosome biosynthesis is a complex, multistep process that depends on iron availability and suboxic conditions. However, the expression of the ca. 30 core magnetosome biosynthetic genes has previously been described as constitutive and largely unaffected by environmental conditions.<\/jats:p>\n                  <jats:p>A recent study by Pang et\u00a0al., published in this journal, reported the identification of a transcriptional regulator, NsrRMg, which was proposed to activate magnetosome biosynthesis in Magnetospirillum gryphiswaldense in response to the endogenous signaling molecule nitric oxide (NO). Furthermore, the study suggested that NO also regulates a putative, previously unrecognized nitrification pathway that presumably supports endogenous NO production via denitrification, even in the absence of extracellular nitrate.<\/jats:p>\n                  <jats:p>Here, we present results of genetic and transcriptional analyses demonstrating that, contrary to the findings of Pang et\u00a0al., NsrRMg is not required for magnetosome biosynthesis. We also refute the existence of the proposed nitrification pathway and conclude that there is no compelling evidence supporting a role of NsrRMg as a key regulator of magnetosome formation in M. gryphiswaldense.<\/jats:p>","DOI":"10.1093\/nar\/gkaf1422","type":"journal-article","created":{"date-parts":[[2025,12,5]],"date-time":"2025-12-05T13:37:25Z","timestamp":1764941845000},"source":"Crossref","is-referenced-by-count":2,"title":["No evidence for the putative nitric oxide sensor NsrR as a key regulator of magnetosome formation in\n                    <i>Magnetospirillum gryphiswaldense<\/i>"],"prefix":"10.1093","volume":"54","author":[{"ORCID":"https:\/\/orcid.org\/0009-0007-6314-8079","authenticated-orcid":false,"given":"Alexandra","family":"Woller","sequence":"first","affiliation":[{"name":"Department of Microbiology, University of Bayreuth , Bayreuth 95447 ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ren\u00e9","family":"Uebe","sequence":"additional","affiliation":[{"name":"Department of Microbiology, University of Bayreuth , Bayreuth 95447 ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dirk","family":"Sch\u00fcler","sequence":"additional","affiliation":[{"name":"Department of Microbiology, University of Bayreuth , Bayreuth 95447 ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,1,6]]},"reference":[{"key":"2026010622411265400_B1","doi-asserted-by":"publisher","first-page":"114995","DOI":"10.1016\/j.celrep.2024.114995","article-title":"Biomineralization in magnetotactic bacteria: from diversity to molecular discovery-based applications","volume":"43","author":"Wan","year":"2024","journal-title":"Cell Rep"},{"key":"2026010622411265400_B2","doi-asserted-by":"publisher","first-page":"e1008499","DOI":"10.1371\/journal.pgen.1008499","article-title":"Magnetic genes: studying the genetics of biomineralization in magnetotactic bacteria","volume":"16","author":"McCausland","year":"2020","journal-title":"PLoS Genet"},{"key":"2026010622411265400_B3","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-025-01234-2","article-title":"Biosynthesis and function of magnetic organelles in magnetotactic bacteria","author":"Sch\u00fcler","year":"2025","journal-title":"Nat Rev Micro"},{"key":"2026010622411265400_B4","doi-asserted-by":"publisher","first-page":"379","DOI":"10.1016\/S0723-2020(11)80313-9","article-title":"The genus Magnetospirillum gen. nov. Description of Magnetospirillum gryphiswaldense sp. nov. and transfer of Aquaspirillum magnetotacticum to Magnetospirillum magnetotacticum comb","volume":"14","author":"Schleifer","year":"1991","journal-title":"Syst Appl Microbiol"},{"key":"2026010622411265400_B5","first-page":"150","article-title":"The isolation of a new magnetic spirillum","volume":"147","author":"Sch\u00fcler","year":"1992","journal-title":"Z Mikrobiol"},{"key":"2026010622411265400_B6","doi-asserted-by":"publisher","first-page":"102614","DOI":"10.1016\/j.mib.2025.102614","article-title":"Organizing organelles: bacterial strategies for localizing intracellular compartments","volume":"86","author":"Ra","year":"2025","journal-title":"Curr Opin Microbiol"},{"key":"2026010622411265400_B7","first-page":"100052","article-title":"Current view of iron biomineralization in magnetotactic bacteria","volume":"5","author":"Ben-Shimon","year":"2021","journal-title":"J Struct Biol X"},{"key":"2026010622411265400_B8","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1038\/s41522-022-00304-0","article-title":"Magnetotactic bacteria and magnetofossils: ecology, evolution and environmental implications","volume":"8","author":"Goswami","year":"2022","journal-title":"npj Biofilms Microbiomes"},{"key":"2026010622411265400_B9","doi-asserted-by":"publisher","first-page":"070902","DOI":"10.1063\/5.0018036","article-title":"Magnetotactic bacteria for cancer therapy","volume":"128","author":"Fdez-Gubieda","year":"2020","journal-title":"J Appl Phys"},{"key":"2026010622411265400_B10","first-page":"5","article-title":"Applications of magnetosomes synthesized by magnetotactic bacteria in medicine","volume":"2","author":"Alphand\u00e9ry","year":"2014","journal-title":"Front Bioeng Biotechnol"},{"key":"2026010622411265400_B11","doi-asserted-by":"publisher","first-page":"2438","DOI":"10.3390\/molecules23102438","article-title":"Applications of magnetotactic bacteria, magnetosomes and magnetosome crystals in biotechnology and nanotechnology: mini-review","volume":"23","author":"Vargas","year":"2018","journal-title":"Molecules"},{"key":"2026010622411265400_B12","doi-asserted-by":"publisher","first-page":"351","DOI":"10.1146\/annurev.biochem.74.082803.133444","article-title":"Molecular mechanisms of magnetosome formation","volume":"76","author":"Komeili","year":"2007","journal-title":"Annu Rev Biochem"},{"key":"2026010622411265400_B13","doi-asserted-by":"publisher","first-page":"228","DOI":"10.1111\/1348-0421.13062","article-title":"Recent advances in studies on magnetosome-associated proteins composing the bacterial geomagnetic sensor organelle","volume":"67","author":"Taoka","year":"2023","journal-title":"Microbiol Immunol"},{"key":"2026010622411265400_B14","doi-asserted-by":"publisher","first-page":"115","DOI":"10.1038\/s41565-023-01500-5","article-title":"Exploring the host range for genetic transfer of magnetic organelle biosynthesis","volume":"19","author":"Dziuba","year":"2023","journal-title":"Nat Nanotechnol"},{"key":"2026010622411265400_B15","doi-asserted-by":"publisher","first-page":"e00565","DOI":"10.1128\/mSystems.00565-20","article-title":"Genome-wide identification of essential and auxiliary gene sets for magnetosome biosynthesis in Magnetospirillum gryphiswaldense","volume":"5","author":"Silva","year":"2020","journal-title":"Msystems"},{"key":"2026010622411265400_B16","doi-asserted-by":"publisher","first-page":"53","DOI":"10.1080\/01490458509385920","article-title":"Microaerobic conditions are required for magnetite formation within Aquaspirillum magnetotacticum","volume":"4","author":"Blakemore","year":"1985","journal-title":"Geomicrobiol J"},{"key":"2026010622411265400_B17","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1128\/JB.180.1.159-162.1998","article-title":"Dynamics of iron uptake and Fe3 O4 biomineralization during aerobic and microaerobic growth of Magnetospirillum gryphiswaldense","volume":"180","author":"Sch\u00fcler","year":"1998","journal-title":"J Bacteriol"},{"key":"2026010622411265400_B18","doi-asserted-by":"publisher","first-page":"536","DOI":"10.1007\/s00253-002-1219-x","article-title":"Growth and magnetosome formation by microaerophilic Magnetospirillum strains in an oxygen-controlled fermentor","volume":"61","author":"Heyen","year":"2003","journal-title":"Appl Microbiol Biotechnol"},{"key":"2026010622411265400_B19","doi-asserted-by":"crossref","first-page":"206","DOI":"10.1186\/s12934-020-01469-z","article-title":"An automated oxystat fermentation regime for microoxic cultivation of Magnetospirillum gryphiswaldense","volume":"19","author":"Riese","year":"2020","journal-title":"Microb Cell Fact"},{"key":"2026010622411265400_B20","doi-asserted-by":"publisher","first-page":"699","DOI":"10.1186\/s12864-022-08913-x","article-title":"The transcriptomic landscape of Magnetospirillum gryphiswaldense during magnetosome biomineralization","volume":"23","author":"Riese","year":"2022","journal-title":"Bmc Genomics [Electronic Resource]"},{"key":"2026010622411265400_B21","doi-asserted-by":"publisher","first-page":"371","DOI":"10.1111\/1758-2229.12395","article-title":"Transcriptome analysis reveals physiological characteristics required for magnetosome formation in Magnetospirillum gryphiswaldense MSR-1","volume":"8","author":"Wang","year":"2016","journal-title":"Environ Microbiol Rep"},{"key":"2026010622411265400_B22","doi-asserted-by":"crossref","first-page":"2800","DOI":"10.1038\/s41598-017-03012-4","article-title":"Physiological characteristics of Magnetospirillum gryphiswaldense MSR-1 that control cell growth under high-iron and low-oxygen conditions","volume":"7","author":"Wang","year":"2017","journal-title":"Sci Rep"},{"key":"2026010622411265400_B23","doi-asserted-by":"publisher","first-page":"e1006101","DOI":"10.1371\/journal.pgen.1006101","article-title":"Genetic and ultrastructural analysis reveals the key players and initial steps of bacterial magnetosome membrane biogenesis","volume":"12","author":"Raschdorf","year":"2016","journal-title":"PLoS Genet"},{"key":"2026010622411265400_B24","doi-asserted-by":"crossref","first-page":"5757","DOI":"10.1128\/AEM.00201-06","article-title":"Transcriptional organization and regulation of magnetosome operons in Magnetospirillum gryphiswaldense","volume":"72","author":"Sch\u00fcbbe","year":"2006","journal-title":"Appl Environ Microb"},{"key":"2026010622411265400_B25","first-page":"533","article-title":"Cell biology and molecular basis of denitrification","volume":"61","author":"Zumft","year":"1997","journal-title":"Microbiol Mol Biol Rev"},{"key":"2026010622411265400_B26","doi-asserted-by":"publisher","first-page":"4847","DOI":"10.1128\/JB.00903-12","article-title":"The periplasmic nitrate reductase nap is required for anaerobic growth and involved in redox control of magnetite biomineralization in Magnetospirillum gryphiswaldense","volume":"194","author":"Li","year":"2012","journal-title":"J Bacteriol"},{"key":"2026010622411265400_B27","doi-asserted-by":"publisher","first-page":"4297","DOI":"10.1128\/JB.00686-13","article-title":"Cytochrome cd1 nitrite reductase NirS is involved in anaerobic magnetite biomineralization in Magnetospirillum gryphiswaldense and requires NirN for proper d1 heme assembly","volume":"195","author":"Li","year":"2013","journal-title":"J Bacteriol"},{"key":"2026010622411265400_B28","doi-asserted-by":"publisher","first-page":"2552","DOI":"10.1128\/JB.01652-14","article-title":"Terminal oxidase cbb3 functions in redox control of magnetite biomineralization in Magnetospirillum gryphiswaldense","volume":"196","author":"Li","year":"2014","journal-title":"J Bacteriol"},{"key":"2026010622411265400_B29","doi-asserted-by":"crossref","first-page":"1830","DOI":"10.1089\/ars.2017.7365","article-title":"Reassessing the structure and function relationship of the O2sensing transcription factor FNR","volume":"29","author":"Mettert","year":"2018","journal-title":"Antioxid Redox Signal"},{"key":"2026010622411265400_B30","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/S0065-2911(01)44010-0","article-title":"Functional versatility in the CRP-FNR superfamily of transcription factors: FNR and FLP","volume":"44","author":"Green","year":"2001","journal-title":"Adv Microb Physiol"},{"key":"2026010622411265400_B31","first-page":"208","article-title":"The disruption of an OxyR-like protein impairs intracellular magnetite biomineralization in Magnetospirillum gryphiswaldense MSR-1","volume":"8","author":"Zhang","year":"2017","journal-title":"Front Microbiol"},{"key":"2026010622411265400_B32","doi-asserted-by":"publisher","first-page":"272","DOI":"10.1016\/j.freeradbiomed.2020.10.015","article-title":"OxyR controls magnetosome formation by regulating magnetosome island (MAI) genes, iron metabolism, and redox state","volume":"161","author":"Niu","year":"2020","journal-title":"Free Radical Biol Med"},{"key":"2026010622411265400_B33","doi-asserted-by":"publisher","first-page":"8044","DOI":"10.1128\/AEM.02585-15","article-title":"Iron response regulator protein IrrB in Magnetospirillum gryphiswaldense MSR-1 helps control the iron\/oxygen balance, oxidative stress tolerance, and magnetosome formation","volume":"81","author":"Wang","year":"2015","journal-title":"Appl Environ Microb"},{"key":"2026010622411265400_B34","doi-asserted-by":"publisher","first-page":"4192","DOI":"10.1128\/JB.00319-10","article-title":"Deletion of a fur-like gene affects iron homeostasis and magnetosome formation in Magnetospirillum gryphiswaldense","volume":"192","author":"Uebe","year":"2010","journal-title":"J Bacteriol"},{"key":"2026010622411265400_B35","doi-asserted-by":"publisher","first-page":"e29572","DOI":"10.1371\/journal.pone.0029572","article-title":"Fur in Magnetospirillum gryphiswaldense influences magnetosomes formation and directly regulates the genes involved in iron and oxygen metabolism","volume":"7","author":"Qi","year":"2012","journal-title":"PLoS One"},{"key":"2026010622411265400_B36","doi-asserted-by":"publisher","first-page":"2924","DOI":"10.1093\/nar\/gkad1230","article-title":"Nitric oxide sensor NsrR is the key direct regulator of magnetosome formation and nitrogen metabolism in Magnetospirillum","volume":"52","author":"Pang","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"2026010622411265400_B37","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1016\/j.tim.2009.12.009","article-title":"There\u2019s NO stopping NsrR, a global regulator of the bacterial NO stress response","volume":"18","author":"Tucker","year":"2010","journal-title":"Trends Microbiol"},{"key":"2026010622411265400_B38","doi-asserted-by":"publisher","first-page":"5878","DOI":"10.1128\/JB.00486-06","article-title":"The nitric oxide-responsive regulator NsrR controls ResDE-dependent gene expression","volume":"188","author":"Nakano","year":"2066","journal-title":"J Bacteriol"},{"key":"2026010622411265400_B39","doi-asserted-by":"publisher","first-page":"148","DOI":"10.1111\/j.1365-2958.2004.04248.x","article-title":"Expression of nitrite reductase in Nitrosomonas europaea involves NsrR, a novel nitrite-sensitive transcription repressor","volume":"54","author":"Beaumont","year":"2004","journal-title":"Mol Microbiol"},{"key":"2026010622411265400_B40","doi-asserted-by":"publisher","first-page":"102543","DOI":"10.1016\/j.mib.2024.102543","article-title":"Iron\u2013sulfur Rrf2 transcription factors: an emerging versatile platform for sensing stress","volume":"82","author":"Banerjee","year":"2024","journal-title":"Curr Opin Microbiol"},{"key":"2026010622411265400_B41","doi-asserted-by":"publisher","first-page":"2488","DOI":"10.1128\/JB.01869-07","article-title":"The nitric oxide (NO)-sensing repressor NsrR of Neisseria meningitidis has a compact regulon of genes involved in NO synthesis and detoxification","volume":"190","author":"Heurlier","year":"2008","journal-title":"J Bacteriol"},{"key":"2026010622411265400_B42","doi-asserted-by":"publisher","first-page":"1138","DOI":"10.1128\/JB.01368-06","article-title":"Regulation of denitrification genes in Neisseria meningitidis by nitric oxide and the repressor NsrR","volume":"189","author":"Rock","year":"2007","journal-title":"J Bacteriol"},{"key":"2026010622411265400_B43","doi-asserted-by":"crossref","first-page":"e70079","DOI":"10.1111\/1462-2920.70079","article-title":"The flavohemoglobin Hmp and nitric oxide reductase restrict initial nir expression in the Bet-Hedging denitrifier Paracoccus denitrificans by curtailing hypoxic no signalling","volume":"27","author":"Kellermann","year":"2025","journal-title":"Environ Microbiol"},{"key":"2026010622411265400_B44","doi-asserted-by":"publisher","first-page":"4410","DOI":"10.1128\/JB.00080-07","article-title":"The NsrR regulon of Escherichia coli K-12 includes genes encoding the hybrid cluster protein and the periplasmic, respiratory nitrite reductase","volume":"189","author":"Filenko","year":"2007","journal-title":"J Bacteriol"},{"key":"2026010622411265400_B45","doi-asserted-by":"publisher","first-page":"13084","DOI":"10.1021\/bi801342x","article-title":"Transcription factor NsrR from Bacillus subtilis senses nitric oxide with a 4Fe-4S cluster","volume":"47","author":"Yukl","year":"2008","journal-title":"Biochemistry"},{"key":"2026010622411265400_B46","doi-asserted-by":"publisher","first-page":"e00309","DOI":"10.1128\/genomeA.00309-18","article-title":"Reevaluation of the complete genome sequence of Magnetospirillum gryphiswaldense MSR-1 with single-molecule real-time sequencing data","volume":"6","author":"Uebe","year":"2018","journal-title":"Genome Announc"},{"key":"2026010622411265400_B47","doi-asserted-by":"publisher","first-page":"4323","DOI":"10.1128\/AEM.00588-14","article-title":"A tailored galK counterselection system for efficient markerless gene deletion and chromosomal tagging in Magnetospirillum gryphiswaldense","volume":"80","author":"Raschdorf","year":"2014","journal-title":"Appl Environ Microb"},{"key":"2026010622411265400_B48","doi-asserted-by":"publisher","first-page":"641","DOI":"10.1128\/AAC.38.4.641","article-title":"Purification and characterization of aminoglycoside 3\u2019-phosphotransferase type IIa and kinetic comparison with a new mutant enzyme","volume":"38","author":"Siregar","year":"1994","journal-title":"Antimicrob Agents Chemother"},{"key":"2026010622411265400_B49","first-page":"151","article-title":"Galactokinase gene fusion in the study of gene regulation in E. coli, Streptomyces, yeast, and higher cell systems","volume":"8","author":"Rosenberg","year":"1986","journal-title":"Genet Eng (N Y)"},{"key":"2026010622411265400_B50","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1016\/S0378-1119(96)00546-X","article-title":"Positive-negative KG cassettes for construction of multi-gene deletions using a single drug marker","volume":"183","author":"Ueki","year":"1996","journal-title":"Gene"},{"key":"2026010622411265400_B51","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1111\/j.1574-6968.1995.tb07823.x","article-title":"A simple light scattering method to assay magnetism in Magnetospirillum gryphiswaldense","volume":"132","author":"Sch\u00fcler","year":"1995","journal-title":"FEMS Microbiol Lett"},{"key":"2026010622411265400_B52","first-page":"36","article-title":"Image processing with ImageJ","volume":"11","author":"Abr\u00e0moff","year":"2004","journal-title":"Biophotonics Int"},{"key":"2026010622411265400_B53","doi-asserted-by":"publisher","first-page":"2237","DOI":"10.1016\/j.jmb.2017.12.007","article-title":"A completely reimplemented MPI bioinformatics toolkit with a new HHpred server at its core","volume":"430","author":"Zimmermann","year":"2018","journal-title":"J Mol Biol"},{"key":"2026010622411265400_B54","doi-asserted-by":"publisher","first-page":"3702","DOI":"10.1093\/bioinformatics\/bth444","article-title":"CLANS: a Java application for visualizing protein families based on pairwise similarity","volume":"20","author":"Frickey","year":"2004","journal-title":"Bioinformatics"},{"key":"2026010622411265400_B55","doi-asserted-by":"publisher","first-page":"10657","DOI":"10.1038\/s41467-024-55121-0","article-title":"MamF-like proteins are distant Tic20 homologs involved in organelle assembly in bacteria","volume":"15","author":"Paulus","year":"2024","journal-title":"Nat Commun"},{"key":"2026010622411265400_B56","doi-asserted-by":"publisher","first-page":"1160","DOI":"10.1093\/bib\/bbx108","article-title":"MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization","volume":"20","author":"Katoh","year":"2019","journal-title":"Briefings Bioinf"},{"key":"2026010622411265400_B57","doi-asserted-by":"publisher","first-page":"1972","DOI":"10.1093\/bioinformatics\/btp348","article-title":"trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses","volume":"25","author":"Capella-Guti\u00e9rrez","year":"2009","journal-title":"Bioinformatics"},{"key":"2026010622411265400_B58","doi-asserted-by":"publisher","first-page":"W232","DOI":"10.1093\/nar\/gkw256","article-title":"W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis","volume":"44","author":"Trifinopoulos","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2026010622411265400_B59","doi-asserted-by":"publisher","first-page":"587","DOI":"10.1038\/nmeth.4285","article-title":"ModelFinder: fast model selection for accurate phylogenetic estimates","volume":"14","author":"Kalyaanamoorthy","year":"2017","journal-title":"Nat Methods"},{"key":"2026010622411265400_B60","doi-asserted-by":"publisher","first-page":"W78","DOI":"10.1093\/nar\/gkae268","article-title":"Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool","volume":"52","author":"Letunic","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"2026010622411265400_B61","doi-asserted-by":"crossref","first-page":"e1005944","DOI":"10.1371\/journal.pcbi.1005944","article-title":"MUMmer4: a fast and versatile genome alignment system","volume":"14","author":"Mar\u00e7ais","year":"2018","journal-title":"PLoS Comput Biol"},{"key":"2026010622411265400_B62","doi-asserted-by":"publisher","first-page":"5114","DOI":"10.1038\/s41467-018-07641-9","article-title":"High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries","volume":"9","author":"Jain","year":"2018","journal-title":"Nat Commun"},{"key":"2026010622411265400_B63","doi-asserted-by":"crossref","first-page":"W83","DOI":"10.1093\/nar\/gkae410","article-title":"The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update","volume":"52","author":"The Galaxy Community","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"2026010622411265400_B64","doi-asserted-by":"publisher","first-page":"1394","DOI":"10.1101\/gr.2289704","article-title":"Mauve: multiple alignment of conserved genomic sequence with rearrangements","volume":"14","author":"Darling","year":"2004","journal-title":"Genome Res"},{"key":"2026010622411265400_B65","doi-asserted-by":"publisher","first-page":"1639","DOI":"10.1101\/gr.092759.109","article-title":"Circos: an information aesthetic for comparative genomics","volume":"19","author":"Krzywinski","year":"2009","journal-title":"Genome Res"},{"key":"2026010622411265400_B66","doi-asserted-by":"crossref","DOI":"10.32614\/R.manuals","article-title":"R: a language and environment for statistical computing","author":"R Core Team","year":"2025"},{"key":"2026010622411265400_B67","first-page":"e00171","article-title":"Complete genome sequence of Magnetospirillum gryphiswaldense MSR-1","volume":"2","author":"Wang","year":"2014","journal-title":"Genome Announc"},{"key":"2026010622411265400_B68","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1186\/s12866-021-02124-2","article-title":"Identification and elimination of genomic regions irrelevant for magnetosome biosynthesis by large-scale deletion in Magnetospirillum gryphiswaldense","volume":"21","author":"Zwiener","year":"2021","journal-title":"BMC Microbiol"},{"key":"2026010622411265400_B69","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1186\/1471-2180-14-153","article-title":"The oxygen sensor MgFnr controls magnetite biomineralization by regulation of denitrification in Magnetospirillum gryphiswaldense","volume":"14","author":"Li","year":"2014","journal-title":"BMC Microbiol"},{"key":"2026010622411265400_B70","doi-asserted-by":"publisher","first-page":"e0089321","DOI":"10.1128\/msystems.00893-21","article-title":"The complex transcriptional landscape of magnetosome gene clusters in Magnetospirillum gryphiswaldense","volume":"6","author":"Dziuba","year":"2021","journal-title":"Msystems"},{"key":"2026010622411265400_B71","doi-asserted-by":"publisher","first-page":"7501","DOI":"10.1128\/AEM.01960-12","article-title":"Diversity, physiology, and niche differentiation of ammonia-oxidizing archaea","volume":"78","author":"Hatzenpichler","year":"2012","journal-title":"Appl Environ Microb"},{"key":"2026010622411265400_B72","doi-asserted-by":"publisher","first-page":"503","DOI":"10.1146\/annurev.micro.61.080706.093449","article-title":"The impact of genome analyses on our understanding of ammonia-oxidizing bacteria","volume":"61","author":"Arp","year":"2007","journal-title":"Annu Rev Microbiol"},{"key":"2026010622411265400_B73","doi-asserted-by":"publisher","first-page":"e2417993121","DOI":"10.1073\/pnas.2417993121","article-title":"Structures of methane and ammonia monooxygenases in native membranes","volume":"122","author":"Tucci","year":"2025","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026010622411265400_B74","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1016\/j.joule.2018.01.018","article-title":"Alternative bioenergy: updates to and challenges in nitrification metalloenzymology","volume":"2","author":"Lancaster","year":"2018","journal-title":"Joule"},{"key":"2026010622411265400_B75","doi-asserted-by":"publisher","first-page":"wrae174","DOI":"10.1093\/ismejo\/wrae174","article-title":"Heterotrophic nitrification by Alcaligenes faecalis links organic and inorganic nitrogen metabolism","volume":"18","author":"Qin","year":"2024","journal-title":"ISME J"},{"key":"2026010622411265400_B76","doi-asserted-by":"publisher","first-page":"3805","DOI":"10.1016\/j.febslet.2007.07.005","article-title":"An octaheme c-type cytochrome from Shewanella oneidensis can reduce nitrite and hydroxylamine","volume":"581","author":"Atkinson","year":"2007","journal-title":"FEBS Lett"},{"key":"2026010622411265400_B77","doi-asserted-by":"publisher","first-page":"693","DOI":"10.1038\/nbt.2280","article-title":"Hybrid error correction and de novo assembly of single-molecule sequencing reads","volume":"30","author":"Koren","year":"2012","journal-title":"Nat Biotechnol"},{"key":"2026010622411265400_B78","doi-asserted-by":"publisher","first-page":"260","DOI":"10.1038\/nrmicro2319","article-title":"Antibiotic resistance and its cost: is it possible to reverse resistance?","volume":"8","author":"Andersson","year":"2010","journal-title":"Nat Rev Micro"},{"key":"2026010622411265400_B79","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1186\/s12934-021-01517-2","article-title":"Towards a \u2018chassis\u2019 for bacterial magnetosome biosynthesis: genome streamlining of Magnetospirillum gryphiswaldense by multiple deletions","volume":"20","author":"Zwiener","year":"2021","journal-title":"Microb Cell Fact"},{"key":"2026010622411265400_B80","doi-asserted-by":"publisher","first-page":"5328","DOI":"10.1128\/JB.05491-11","article-title":"Frequent mutations within the genomic magnetosome island of Magnetospirillum gryphiswaldense are mediated by RecA","volume":"193","author":"Kolinko","year":"2011","journal-title":"J Bacteriol"},{"key":"2026010622411265400_B81","doi-asserted-by":"publisher","first-page":"7176","DOI":"10.1128\/JB.187.21.7176-7184.2005","article-title":"A hypervariable 130-kilobase genomic region of Magnetospirillum gryphiswaldense comprises a magnetosome island which undergoes frequent rearrangements during stationary growth","volume":"187","author":"Ullrich","year":"2005","journal-title":"J Bacteriol"},{"key":"2026010622411265400_B82","doi-asserted-by":"crossref","first-page":"5779","DOI":"10.1128\/JB.185.19.5779-5790.2003","article-title":"Characterization of a spontaneous nonmagnetic mutant of Magnetospirillum gryphiswaldense reveals a large deletion comprising a putative magnetosome island","volume":"185","author":"Sch\u00fcbbe","year":"2003","journal-title":"J Bacteriol"},{"key":"2026010622411265400_B83","doi-asserted-by":"publisher","first-page":"665","DOI":"10.1111\/j.1432-1033.1995.665_2.x","article-title":"Nitrite reductase from the magnetotactic bacterium Magnetospirillum magnetotacticum: a novel cytochrome cd1 with Fe (II): nitrite oxidoreductase activity","volume":"233","author":"Yamazaki","year":"1995","journal-title":"Eur J Biochem"},{"key":"2026010622411265400_B84","doi-asserted-by":"publisher","first-page":"581283","DOI":"10.3389\/fmicb.2020.581283","article-title":"Comparison of novel and established nitrification inhibitors relevant to agriculture on soil ammonia- and nitrite-oxidizing isolates","volume":"11","author":"Papadopoulou","year":"2020","journal-title":"Front Microbiol"},{"key":"2026010622411265400_B85","doi-asserted-by":"publisher","DOI":"10.26434\/chemrxiv-2025-0tr1r","article-title":"Potential risks of the nitrification inhibitors nitrapyrin and DMPP: a review on non-target effects on microorganisms and environmental fate in agricultural soil","author":"Horstmann","year":"2025"}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/54\/1\/gkaf1422\/66284908\/gkaf1422.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/54\/1\/gkaf1422\/66284908\/gkaf1422.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,7]],"date-time":"2026-01-07T03:41:32Z","timestamp":1767757292000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/doi\/10.1093\/nar\/gkaf1422\/8415818"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1,5]]},"references-count":85,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2026,1,5]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkaf1422","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,1,13]]},"published":{"date-parts":[[2026,1,5]]},"article-number":"gkaf1422"}}