{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T10:58:14Z","timestamp":1790852294330,"version":"4.1.0"},"reference-count":70,"publisher":"MDPI AG","issue":"19","license":[{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100006769","name":"Russian Science Foundation","doi-asserted-by":"publisher","award":["25-14-00062"],"award-info":[{"award-number":["25-14-00062"]}],"id":[{"id":"10.13039\/501100006769","id-type":"DOI","asserted-by":"publisher"}]},{"award":["25-14-00062"],"award-info":[{"award-number":["25-14-00062"]}],"id":[{"id":"https:\/\/ror.org\/03y2gwe85","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Int. J. Mol. Sci.","IJMS"],"abstract":"<jats:p>The family Gallionellaceae includes neutrophilic, aerobic, iron-oxidizing bacteria, many of which remain uncultured and known only from metagenomic data. In this study, two high-quality Gallionellaceae genomes were assembled from a ferruginous spring in the Voronezh region, Russia. Phylogenetic analysis based on 120 concatenated proteins, ANI (average nucleotide identity), and AAI (average amino acid identity) indicates that BG-057 belongs to the genus Gallionella and BG-364 to the genus 39-52-133. We propose the names \u201cCandidatus Gallionella aquifuscii\u201d sp. nov. for BG-057 and \u201cCandidatus Dubininella ochracea\u201d gen. nov., sp. nov. for BG-364. Both genomes encode genes for the Calvin-Benson-Bassham (CBB) cycle. Both are potentially capable of aerobic respiration due to the presence of electron transfer chain components. Both genomes encode the iron oxidase Cyc2, and BG-057 also encodes MtoA. BG-057 is potentially capable of lithotrophic growth in the presence of H2 and H2S. BG-364 is potentially capable of growth via Mn (II) oxidation; arsenite oxidation; the direct oxidation of thiosulfate; H2S, elemental sulfur, and sulfite oxidation. BG-364 encodes denitrification genes (narGHI, nirS, norBC). BG-057 possesses systems for the biosynthesis and export of siderophores, while BG-364 lacks these systems but retains Ton-dependent receptors, suggesting the use of exogenous siderophores.<\/jats:p>","DOI":"10.3390\/ijms27198801","type":"journal-article","created":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T10:25:44Z","timestamp":1790850344000},"page":"8801","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["The Genomic Characterization of a Novel Candidatus Genus of the Family Gallionellaceae, a Novel Candidatus Species of the Genus Gallionella and Their Metabolic Potential for Iron Oxidation"],"prefix":"10.3390","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1456-1832","authenticated-orcid":false,"given":"Nikolai V.","family":"Ravin","sequence":"first","affiliation":[{"name":"Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Prosp., Bld. 33-2, 119071 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4887-794X","authenticated-orcid":false,"given":"Maria V.","family":"Gureeva","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya Pl., 1, 394018 Voronezh, Russia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7611-2354","authenticated-orcid":false,"given":"Alexey V.","family":"Beletsky","sequence":"additional","affiliation":[{"name":"Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Prosp., Bld. 33-2, 119071 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7877-3829","authenticated-orcid":false,"given":"Margarita Y.","family":"Grabovich","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya Pl., 1, 394018 Voronezh, Russia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"}]}],"member":"1968","published-online":{"date-parts":[[2026,10,1]]},"reference":[{"key":"ref_1","first-page":"13","article-title":"Vorlaufige Mitteilung iiber das wirkliche Vorkommen fossiler Infusorien und ihre grosse Verbreitung","volume":"38","author":"Ehrenberg","year":"1836","journal-title":"Ann. Phys."},{"key":"ref_2","first-page":"262","article-title":"\u00dcber Eisenbakterien","volume":"46","author":"Winogradsky","year":"1888","journal-title":"Bot. Ztg."},{"key":"ref_3","first-page":"1","article-title":"Eisenbakterien als Anorgoxydanten","volume":"57","author":"Winogradsky","year":"1922","journal-title":"Zentralblatt F\u00fcr Bakteriol. Parasitenkd. Und Infekt."},{"key":"ref_4","unstructured":"Whitman, W.B. (2015). Gallionella. Bergey\u2019s Manual of Systematics of Archaea and Bacteria, Wiley."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"126306","DOI":"10.1016\/j.syapm.2022.126306","article-title":"\u2018Candidatus ferrigenium straubiae\u2019 sp. nov., \u2018Candidatus ferrigenium bremense\u2019 sp. nov., \u2018Candidatus ferrigenium altingense\u2019 sp. nov., are autotrophic Fe(II)-oxidizing bacteria of the family Gallionellaceae","volume":"45","author":"Huang","year":"2022","journal-title":"Syst. Appl. Microbiol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"717","DOI":"10.1038\/ismej.2010.173","article-title":"Lithotrophic iron-oxidizing bacteria produce organic stalks to control mineral growth: Implications for biosignature formation","volume":"5","author":"Chan","year":"2011","journal-title":"ISME J."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"e0003823","DOI":"10.1128\/msystems.00038-23","article-title":"Gallionellaceae pangenomic analysis reveals insight into phylogeny, metabolic flexibility, and iron oxidation mechanisms","volume":"8","author":"Hoover","year":"2023","journal-title":"mSystems"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"e0049621","DOI":"10.1128\/AEM.00496-21","article-title":"Meta-omics reveal Gallionellaceae and Rhodanobacter species as interdependent key players for Fe(II) oxidation and nitrate reduction in the autotrophic enrichment culture KS","volume":"87","author":"Huang","year":"2021","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"fiaf051","DOI":"10.1093\/femsec\/fiaf051","article-title":"Custom-made medium approach for effective enrichment and isolation of chemolithotrophic iron-oxidizing bacteria","volume":"101","author":"Uchijima","year":"2025","journal-title":"FEMS Microbiol. Ecol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1038\/nbt.4229","article-title":"A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life","volume":"36","author":"Parks","year":"2018","journal-title":"Nat. Biotechnol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"2587","DOI":"10.1099\/ijsem.0.002882","article-title":"Ferrigenium kumadai gen. nov., sp. nov., a microaerophilic iron-oxidizing bacterium isolated from a paddy field soil","volume":"68","author":"Khalifa","year":"2018","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Emerson, D., Rentz, J.A., Lilburn, T.G., Davis, R.E., Aldrich, H., Chan, C., and Moyer, C.L. (2007). A novel lineage of proteobacteria involved in formation of marine Fe-oxidizing microbial mat communities. PLoS ONE, 2.","DOI":"10.1371\/journal.pone.0000667"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1139\/m68-061","article-title":"Isolation of Gallionella ferruginea by use of formalin","volume":"14","author":"Nunley","year":"1968","journal-title":"Can. J. Microbiol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"4784","DOI":"10.1128\/aem.63.12.4784-4792.1997","article-title":"Isolation and characterization of novel iron-oxidizing bacteria that grow at circumneutral pH","volume":"63","author":"Emerson","year":"1997","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"921","DOI":"10.1099\/ijs.0.058487-0","article-title":"Ferriphaselus amnicola gen. nov., sp. nov., a neutrophilic, stalk-forming, iron-oxidizing bacterium isolated from an iron-rich groundwater seep","volume":"64","author":"Kato","year":"2014","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1134\/S002626171604010X","article-title":"A novel uncultured bacterium of the family Gallionellaceae: Description and genome reconstruction based on the metagenomic analysis of microbial community in acid mine drainage","volume":"85","author":"Kadnikov","year":"2016","journal-title":"Microbiology"},{"key":"ref_17","first-page":"131","article-title":"Bromine and iodine-bromine mineral waters of the Voronezh region","volume":"4","author":"Zhiskar","year":"2022","journal-title":"Vestn. Voronezhskogo Gos. Univ. Seriya Geogr. Geoekologiya"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"948","DOI":"10.1038\/s41587-025-02738-1","article-title":"Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper","volume":"44","author":"Woodcroft","year":"2026","journal-title":"Nat. Biotechnol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"2567","DOI":"10.1073\/pnas.0409727102","article-title":"Genomic insights that advance the species definition for prokaryotes","volume":"102","author":"Konstantinidis","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"2399","DOI":"10.1038\/ismej.2017.113","article-title":"Uncultivated microbes in need of their own taxonomy","volume":"11","author":"Konstantinidis","year":"2017","journal-title":"ISME J."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"006300","DOI":"10.1099\/ijsem.0.006300","article-title":"Update on the proposed minimal standards for the use of genome data for the taxonomy of prokaryotes","volume":"74","author":"Riesco","year":"2024","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"17443","DOI":"10.1021\/acs.est.2c05142","article-title":"Biological oxidation of Fe(II)-bearing smectite by microaerophilic iron oxidizer Sideroxydans lithotrophicus using dual Mto and Cyc2 iron oxidation pathways","volume":"56","author":"Zhou","year":"2022","journal-title":"Environ. Sci. Technol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"e0186524","DOI":"10.1128\/aem.01865-24","article-title":"Microbial magnetite oxidation via MtoAB porin-multiheme cytochrome complex in Sideroxydans lithotrophicus ES-1","volume":"91","author":"Keffer","year":"2025","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"e0107421","DOI":"10.1128\/mBio.01074-21","article-title":"Iron oxidation by a fused cytochrome-porin common to diverse iron-oxidizing bacteria","volume":"12","author":"Keffer","year":"2021","journal-title":"mBio"},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"He, S., Barco, R.A., Emerson, D., and Roden, E.E. (2017). Comparative genomic analysis of neutrophilic iron(II) oxidizer genomes for candidate genes in extracellular electron transfer. Front. Microbiol., 21.","DOI":"10.3389\/fmicb.2017.01584"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"27758","DOI":"10.1074\/jbc.M302582200","article-title":"Characterization of the Shewanella oneidensis MR-1 decaheme cytochrome MtrA: Expression in Escherichia coli confers the ability to reduce soluble Fe(III) chelates","volume":"278","author":"Pitts","year":"2003","journal-title":"J. Biol. Chem."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Liu, J., Wang, Z., Belchik, S.M., Edwards, M.J., Liu, C., Kennedy, D.W., Merkley, E.D., Lipton, M.S., Butt, J.N., and Richardson, D.J. (2012). Identification and characterization of MtoA: A decaheme C-type cytochrome of the neutrophilic Fe(II)-oxidizing bacterium Sideroxydans lithotrophicus ES-1. Front. Microbiol., 3.","DOI":"10.3389\/fmicb.2012.00037"},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Ross, D.E., Flynn, J.M., Baron, D.B., Gralnick, J.A., and Bond, D.R. (2011). Towards electrosynthesis in Shewanella: Energetics of reversing the Mtr pathway for reductive metabolism. PLoS ONE, 6.","DOI":"10.1371\/journal.pone.0016649"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"001240","DOI":"10.1099\/mic.0.001240","article-title":"Reconstructing electron transfer components from an Fe(II)-oxidizing bacterium","volume":"168","author":"Jain","year":"2022","journal-title":"Microbiology"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"4944","DOI":"10.1128\/JB.01518-06","article-title":"Specific bonds between an iron oxide surface and outer membrane cytochromes MtrC and OmcA from Shewanella oneidensis MR-1","volume":"189","author":"Lower","year":"2007","journal-title":"J. Bacteriol."},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Shi, L., Fredrickson, J.K., and Zachara, J.M. (2014). Genomic analyses of bacterial porin-cytochrome gene clusters. Front. Microbiol., 5.","DOI":"10.3389\/fmicb.2014.00657"},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Garber, A.I., Nealson, K.H., Okamoto, A., McAllister, S.M., Chan, C.S., Barco, R.A., and Merino, N. (2020). FeGenie: A comprehensive tool for the identification of iron genes and iron gene neighborhoods in genome and metagenome assemblies. Front. Microbiol., 11.","DOI":"10.3389\/fmicb.2020.00037"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1007\/s12104-024-10180-8","article-title":"Resonance assignments of cytochrome MtoD from the extracellular electron uptake pathway of Sideroxydans lithotrophicus ES-1","volume":"18","author":"Coelho","year":"2024","journal-title":"Biomol. NMR Assign."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"752","DOI":"10.1038\/nrmicro1490","article-title":"Microorganisms pumping iron: Anaerobic microbial iron oxidation and reduction","volume":"4","author":"Weber","year":"2006","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1139\/O10-141","article-title":"TonB or not TonB: Is that the question?","volume":"89","author":"Krewulak","year":"2011","journal-title":"Biochem Cell Biol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1080\/10409238.2018.1476449","article-title":"Ironing out siderophore biosynthesis: A review of non-ribosomal peptide synthetase (NRPS)-independent siderophore synthetases","volume":"53","author":"Carroll","year":"2018","journal-title":"Crit. Rev. Biochem Mol. Biol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1016\/j.cbpa.2013.12.014","article-title":"Heme uptake in bacterial pathogens","volume":"19","author":"Contreras","year":"2014","journal-title":"Curr. Opin. Chem. Biol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"e00097-18","DOI":"10.1128\/AAC.00097-18","article-title":"TonB-Dependent receptor repertoire of Pseudomonas aeruginosa for uptake of siderophore-drug conjugates","volume":"62","author":"Luscher","year":"2018","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Emerson, D., Field, E.K., Chertkov, O., Davenport, K.W., Goodwin, L., Munk, C., Nolan, M., and Woyke, T. (2013). Comparative genomics of freshwater Fe-oxidizing bacteria: Implications for physiology, ecology, and systematics. Front. Microbiol., 4.","DOI":"10.3389\/fmicb.2013.00254"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1007\/s00775-016-1336-0","article-title":"Ferritins: Furnishing proteins with iron","volume":"21","author":"Bradley","year":"2016","journal-title":"J. Biol. Inorg. Chem."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"151530","DOI":"10.1016\/j.ijbiomac.2026.151530","article-title":"Heterologous expression, purification and characteristics of a high molecular weight manganese oxidase McoA from Pseudomonas sp. AN-1","volume":"355","author":"Guo","year":"2026","journal-title":"Int. J. Biol. Macromol."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1007\/s11434-012-5541-0","article-title":"Research progress of heavy metal pollution in China: Sources, analytical methods, status, and toxicity","volume":"58","author":"He","year":"2013","journal-title":"Chin. Sci. Bull."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1007\/s00294-018-0894-9","article-title":"Genetic mechanisms of arsenic detoxification and metabolism in bacteria","volume":"65","author":"Yan","year":"2019","journal-title":"Curr. Genet"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"1081","DOI":"10.1128\/JB.188.3.1081-1088.2006","article-title":"Complex regulation of arsenite oxidation in Agrobacterium tumefaciens","volume":"188","author":"Kashyap","year":"2006","journal-title":"J. Bacteriol."},{"key":"ref_45","doi-asserted-by":"crossref","unstructured":"Koechler, S., Cleiss-Arnold, J., Proux, C., Sismeiro, O., Dillies, M.A., Goulhen-Chollet, F., Hommais, F., Li\u00e8vremont, D., Ars\u00e8ne-Ploetze, F., and Copp\u00e9e, J.Y. (2010). Multiple controls affect arsenite oxidase gene expression in Herminiimonas arsenicoxydans. BMC Microbiol., 10, Erratum in BMC Microbiol 2017 28, 74. https:\/\/doi.org\/10.1186\/s12866-017-0976-8.","DOI":"10.1186\/1471-2180-10-53"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1007\/400_2006_027","article-title":"Hydrogenases and H+-reduction in primary energy conservation","volume":"45","author":"Vignais","year":"2008","journal-title":"Results Probl. Cell Differ."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"e0033522","DOI":"10.1128\/msystems.00335-22","article-title":"Compositional and metabolic responses of autotrophic microbial community to salinity in lacustrine environments","volume":"7","author":"Fang","year":"2022","journal-title":"mSystems"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"819","DOI":"10.1089\/ars.2011.4051","article-title":"Bacterial adaptation of respiration from oxic to microoxic and anoxic conditions: Redox control","volume":"16","author":"Bueno","year":"2012","journal-title":"Antioxid. Redox Signal"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"755","DOI":"10.1099\/00221287-142-4-755","article-title":"The cytochrome bd quinol oxidase in Escherichia coli has an extremely high oxygen affinity and two oxygen-binding haems: Implications for regulation of activity in vivo by oxygen inhibition","volume":"142","author":"Hill","year":"1996","journal-title":"Microbiology"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"514","DOI":"10.1038\/nature11182","article-title":"Structural insights into electron transfer in caa3-type cytochrome oxidase","volume":"487","author":"Lyons","year":"2012","journal-title":"Nature"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"1562","DOI":"10.1046\/j.1365-2958.2001.02343.x","article-title":"How does oxygen inhibit central metabolism in the obligate anaerobe Bacteroides thetaiotaomicron","volume":"39","author":"Pan","year":"2001","journal-title":"Mol. Microbiol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"e71339","DOI":"10.7554\/eLife.71339","article-title":"Pyruvate:Ferredoxin oxidoreductase and low abundant ferredoxins support aerobic photomixotrophic growth in cyanobacteria","volume":"11","author":"Wang","year":"2022","journal-title":"Elife"},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"10","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads","volume":"17","author":"Martin","year":"2011","journal-title":"EMBnet. J."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"2957","DOI":"10.1093\/bioinformatics\/btr507","article-title":"FLASH: Fast length adjustment of short reads to improve genome assemblies","volume":"27","author":"Salzberg","year":"2011","journal-title":"Bioinformatics"},{"key":"ref_55","doi-asserted-by":"crossref","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":"ref_56","doi-asserted-by":"crossref","first-page":"e7359","DOI":"10.7717\/peerj.7359","article-title":"MetaBAT 2: An adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies","volume":"7","author":"Kang","year":"2019","journal-title":"PeerJ"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1038\/s41467-023-44290-z","article-title":"Effective binning of metagenomic contigs using contrastive multi-view representation learning","volume":"15","author":"Wang","year":"2024","journal-title":"Nat. Commun."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"1144","DOI":"10.1038\/nmeth.3103","article-title":"Binning metagenomic contigs by coverage and composition","volume":"11","author":"Alneberg","year":"2014","journal-title":"Nat. Methods"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1093\/bioinformatics\/btv638","article-title":"MaxBin 2.0: An automated binning algorithm to recover genomes from multiple metagenomic datasets","volume":"32","author":"Wu","year":"2016","journal-title":"Bioinformatics"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"836","DOI":"10.1038\/s41564-018-0171-1","article-title":"Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy","volume":"3","author":"Sieber","year":"2018","journal-title":"Nat. Microbiol."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"1203","DOI":"10.1038\/s41592-023-01940-w","article-title":"CheckM2: A rapid, scalable and accurate tool for assessing microbial genome quality using machine learning","volume":"20","author":"Chklovski","year":"2023","journal-title":"Nat. Methods"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"5315","DOI":"10.1093\/bioinformatics\/btac672","article-title":"GTDB-Tk v2: Memory friendly classification with the genome taxonomy database","volume":"38","author":"Chaumeil","year":"2022","journal-title":"Bioinformatics"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"8365","DOI":"10.1038\/srep08365","article-title":"RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes","volume":"5","author":"Brettin","year":"2015","journal-title":"Sci. Rep."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"420","DOI":"10.1038\/s41587-019-0036-z","article-title":"SignalP 5.0 improves signal peptide predictions using deep neural networks","volume":"37","author":"Tsirigos","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1006\/jmbi.2000.4315","article-title":"Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes","volume":"305","author":"Krogh","year":"2001","journal-title":"J. Mol. Biol."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1093\/sysbio\/syq010","article-title":"New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0","volume":"59","author":"Guindon","year":"2010","journal-title":"Syst. Biol."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"685","DOI":"10.1093\/sysbio\/syr041","article-title":"Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes","volume":"60","author":"Anisimova","year":"2011","journal-title":"Syst. Biol."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"2657","DOI":"10.1099\/00221287-137-11-2657","article-title":"Autotrophic and mixotrophic growth of Gallionella ferruginea","volume":"137","author":"Hallbeck","year":"1991","journal-title":"J. General. Microbiol."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"e0039525","DOI":"10.1128\/aem.00395-25","article-title":"An organotrophic Sideroxydans reveals potential iron oxidation marker genes","volume":"91","author":"Hoover","year":"2025","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"fiac156","DOI":"10.1093\/femsec\/fiac156","article-title":"Mixotrophy broadens the ecological niche range of the iron oxidizer Sideroxydans sp. CL21 isolated from an iron-rich peatland","volume":"99","author":"Cooper","year":"2023","journal-title":"FEMS Microbiol. Ecol."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/19\/8801\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T10:26:34Z","timestamp":1790850394000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/19\/8801"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,10,1]]},"references-count":70,"journal-issue":{"issue":"19","published-online":{"date-parts":[[2026,10]]}},"alternative-id":["ijms27198801"],"URL":"https:\/\/doi.org\/10.3390\/ijms27198801","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,10,1]]}}}