{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,4]],"date-time":"2026-08-04T18:01:22Z","timestamp":1785866482345,"version":"3.56.0"},"reference-count":111,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2024,5,28]],"date-time":"2024-05-28T00:00:00Z","timestamp":1716854400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004837","name":"Spanish Ministry of Science and Innovation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004837","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003359","name":"Generalitat Valenciana","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003359","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>Prokaryotes dominate global oceans and shape biogeochemical cycles, yet most taxa remain uncultured and uncharacterized as of today. Here we present the characterization of 26 novel marine bacterial strains from a large isolate collection obtained from Blanes Bay (NW Mediterranean) microcosm experiments made in the four seasons. Morphological, cultural, biochemical, physiological, nutritional, genomic, and phylogenomic analyses were used to characterize and phylogenetically place the novel isolates. The strains represent 23 novel bacterial species and six novel genera: three novel species pertaining to class <jats:italic>Alphaproteobacteria<\/jats:italic> (families <jats:italic>Rhodobacteraceae<\/jats:italic> and <jats:italic>Sphingomonadaceae<\/jats:italic>), six novel species and three new genera from class <jats:italic>Gammaproteobacteria<\/jats:italic> (families <jats:italic>Algiphilaceae<\/jats:italic>, <jats:italic>Salinispheraceae<\/jats:italic>, and <jats:italic>Alteromonadaceae<\/jats:italic>), 13 novel species and three novel genera from class <jats:italic>Bacteroidia<\/jats:italic> (family <jats:italic>Flavobacteriaceae<\/jats:italic>), and one new species from class <jats:italic>Rhodothermia<\/jats:italic> (family <jats:italic>Rubricoccaceae<\/jats:italic>). The bacteria described here have potentially relevant roles in the cycles of carbon (e.g., carbon fixation or energy production via proteorhodopsin), nitrogen (e.g., denitrification or use of urea), sulfur (oxidation of sulfur compounds), phosphorus (acquisition and use of different forms of phosphorus and remodeling of membrane phospholipids), and hydrogen (oxidation of hydrogen to obtain energy). We mapped the genomes of the presented strains to the Tara Oceans metagenomes to reveal that these strains were globally distributed, with those of the family <jats:italic>Flavobacteriaceae<\/jats:italic> being the most widespread and abundant, while <jats:italic>Rhodothermia<\/jats:italic> being the rarest and most localized. While molecular-only approaches are also important, our study stresses the importance of culturing as a powerful tool to further understand the functioning of marine bacterial communities.<\/jats:p>","DOI":"10.3389\/fmicb.2024.1407904","type":"journal-article","created":{"date-parts":[[2024,5,28]],"date-time":"2024-05-28T11:11:13Z","timestamp":1716894673000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":16,"title":["Genomic and phenotypic characterization of 26 novel marine bacterial strains with relevant biogeochemical roles and widespread presence across the global ocean"],"prefix":"10.3389","volume":"15","author":[{"given":"Xavier","family":"Rey-Velasco","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Teresa","family":"Lucena","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana","family":"Belda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Josep M.","family":"Gasol","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olga","family":"S\u00e1nchez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David R.","family":"Arahal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mar\u00eda J.","family":"Pujalte","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2024,5,28]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3389\/fmicb.2020.00465","article-title":"Transcriptional patterns of biogeochemically relevant marker genes by temperate marine Bacteria","volume":"11","author":"Alonso-S\u00e1ez","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"1465","DOI":"10.1111\/1462-2920.16367","article-title":"Seasonality of biogeochemically relevant microbial genes in a coastal ocean microbiome","volume":"25","author":"Auladell","year":"2023","journal-title":"Environ. Microbiol."},{"key":"ref4","doi-asserted-by":"publisher","first-page":"257","DOI":"10.3354\/meps010257","article-title":"The ecological role of water-column microbes in the sea","volume":"10","author":"Azam","year":"1983","journal-title":"Mar. Ecol. Prog. Ser."},{"key":"ref5","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2164-9-75","article-title":"The RAST server: rapid annotations using subsystems technology","volume":"9","author":"Aziz","year":"2008","journal-title":"BMC Genomics"},{"key":"ref6","author":"Bache","year":"2022"},{"key":"ref7","doi-asserted-by":"publisher","first-page":"2185","DOI":"10.1099\/ijs.0.64330-0","article-title":"Glaciecola nitratireducens sp. nov., isolated from seawater","volume":"56","author":"Baik","year":"2006","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref8","doi-asserted-by":"publisher","first-page":"1451","DOI":"10.1016\/j.cell.2019.11.018","article-title":"The biomass composition of the oceans: a blueprint of our blue planet","volume":"179","author":"Bar-On","year":"2019","journal-title":"Cell"},{"key":"ref9","first-page":"1302","article-title":"The marine gram-negative eubacteria: genera Photobacterium, Beneckea, Alteromonas, Pseudomonas and Alcaligenes","volume-title":"The prokaryotes","author":"Baumann","year":"1981"},{"key":"ref10","volume-title":"Package \u201cmapdata\u201d - Extra Map Databases","author":"Becker","year":"2022"},{"key":"ref11","volume-title":"Package \u201cmaps\u201d: Draw geographical maps","author":"Becker","year":"2023"},{"key":"ref12","doi-asserted-by":"publisher","first-page":"1902","DOI":"10.1126\/science.289.5486.1902","article-title":"Bacterial rhodopsin: evidence for a new type of phototrophy in the sea","volume":"289","author":"Beja","year":"2000","journal-title":"Science"},{"key":"ref13","doi-asserted-by":"publisher","first-page":"1049","DOI":"10.1099\/ijs.0.02136-0.02136","article-title":"Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and Jean-franc by the members of the subcommittee on the taxonomy of Flavobacterium and Cytophaga -like bacteria of the international committee on systematics of","volume":"52","author":"Bernadet","year":"2002","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref14","first-page":"1213","article-title":"Glaciecola punicea gen. Nov., sp. nov. and Glaciecola pallidula gen. Nov., sp. nov.: psychrophilic bacteria from Antarctic Sea-ice habitats","volume-title":"Int. J. Syst. Bacteriol.","author":"Bowman","year":"1998"},{"key":"ref15","doi-asserted-by":"publisher","first-page":"366","DOI":"10.1038\/s41592-021-01101-x","article-title":"Sensitive protein alignments at tree-of-life scale using DIAMOND","volume":"18","author":"Buchfink","year":"2021","journal-title":"Nat. Methods"},{"key":"ref16","first-page":"1","article-title":"BBMap: a fast, accurate, splice-aware aligner","volume-title":"BMC Bioinformatics","author":"Bushnell","year":"2012"},{"key":"ref17","doi-asserted-by":"publisher","first-page":"5825","DOI":"10.1093\/molbev\/msab293","article-title":"eggNOG-mapper v2: functional annotation, Orthology assignments, and domain prediction at the metagenomic scale","volume":"38","author":"Cantalapiedra","year":"2021","journal-title":"Mol. Biol. Evol."},{"key":"ref18","doi-asserted-by":"publisher","first-page":"1925","DOI":"10.1093\/bioinformatics\/btz848","article-title":"GTDB-Tk: a toolkit to classify genomes with the genome taxonomy database","volume":"36","author":"Chaumeil","year":"2020","journal-title":"Bioinformatics"},{"key":"ref19","doi-asserted-by":"publisher","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":"ref20","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1099\/ijsem.0.005472","article-title":"Croceicoccus hydrothermalis sp. nov., isolated from shallow-sea hydrothermal system off Kueishantao Island","volume":"72","author":"Chen","year":"2022","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref21","doi-asserted-by":"publisher","first-page":"2857","DOI":"10.1099\/ijs.0.018945-0","article-title":"Stakelama pacifica gen. Nov., sp. nov., a new member of the family Sphingomonadaceae isolated from the Pacific Ocean","volume":"60","author":"Chen","year":"2010","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"D633","DOI":"10.1093\/nar\/gkt1244","article-title":"Ribosomal database project: data and tools for high throughput rRNA analysis","volume":"42","author":"Cole","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"ref23","doi-asserted-by":"publisher","first-page":"2868","DOI":"10.1038\/s41396-019-0479-8","article-title":"Atmospheric carbon monoxide oxidation is a widespread mechanism supporting microbial survival","volume":"13","author":"Cordero","year":"2019","journal-title":"ISME J."},{"key":"ref24","doi-asserted-by":"publisher","first-page":"379","DOI":"10.1038\/nature01165","article-title":"Respiration in the open ocean","volume":"420","author":"Del Giorgio","year":"2002","journal-title":"Nature"},{"key":"ref25","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1002\/lob.10008","article-title":"Seafaring in the 21st century: the Malaspina 2010 circumnavigation expedition","volume":"24","author":"Duarte","year":"2015","journal-title":"Limnol. Oceanogr. Bull."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"276","DOI":"10.1038\/s41587-020-0439-x","article-title":"The nf-core framework for community-curated bioinformatics pipelines","volume":"38","author":"Ewels","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"ref27","doi-asserted-by":"publisher","first-page":"1034","DOI":"10.1126\/science.1153213","article-title":"The microbial engines that drive earth\u2019s biogeochemical cycles","volume":"320","author":"Falkowski","year":"2008","journal-title":"Science"},{"key":"ref28","doi-asserted-by":"publisher","first-page":"694","DOI":"10.1126\/science.280.5364.694","article-title":"Microbial control of oceanic carbon flux: the plot thickens","volume":"280","author":"Farooq","year":"1998","journal-title":"Science"},{"key":"ref29","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1016\/j.jembe.2008.07.013","article-title":"The microbial loop - 25 years later","volume":"366","author":"Fenchel","year":"2008","journal-title":"J. Exp. Mar. Biol. Ecol."},{"key":"ref30","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1016\/j.mib.2015.03.007","article-title":"Prokaryotic functional gene diversity in the sunlit ocean: stumbling in the dark","volume":"25","author":"Ferrera","year":"2015","journal-title":"Curr. Opin. Microbiol."},{"key":"ref31","doi-asserted-by":"publisher","first-page":"4130","DOI":"10.1099\/ijsem.0.004256","article-title":"Ningiella ruwaisensis gen. Nov., sp. nov., a member of the family Alteromonadaceae isolated from marine water of the Arabian gulf","volume":"70","author":"Fotedar","year":"2020","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref32","volume-title":"Microbial ecology of the oceans","author":"Gasol","year":"2018"},{"key":"ref33","doi-asserted-by":"publisher","first-page":"820","DOI":"10.1038\/nrmicro1752","article-title":"The importance of culturing bacterioplankton in the \u201comics\u201d age","volume":"5","author":"Giovannoni","year":"2007","journal-title":"Nat. Rev. Microbiol."},{"key":"ref34","doi-asserted-by":"publisher","first-page":"e1000358","DOI":"10.1371\/journal.pbio.1000358","article-title":"Proteorhodopsin phototrophy promotes survival of marine bacteria during starvation","volume":"8","author":"G\u00f3mez-Consarnau","year":"2010","journal-title":"PLoS Biol."},{"key":"ref35","doi-asserted-by":"publisher","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","article-title":"QUAST: quality assessment tool for genome assemblies","volume":"29","author":"Gurevich","year":"2013","journal-title":"Bioinformatics"},{"key":"ref36","doi-asserted-by":"publisher","first-page":"2743","DOI":"10.1099\/ijs.0.033324-0","article-title":"Algiphilus aromaticivorans gen. Nov., sp. nov., an aromatic hydrocarbon-degrading bacterium isolated from a culture of the marine dinoflagellate Lingulodinium polyedrum, and proposal of Algiphilaceae fam. Nov","volume":"62","author":"Gutierrez","year":"2012","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref37","doi-asserted-by":"publisher","first-page":"388","DOI":"10.1099\/ijs.0.65822-0","article-title":"Tropicimonas isoalkanivorans gen. Nov., sp. nov., a branched-alkane-degrading bacterium isolated from Semarang port in Indonesia","volume":"59","author":"Harwati","year":"2009","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref38","doi-asserted-by":"publisher","first-page":"308","DOI":"10.4319\/lom.2006.4.308","article-title":"Expression of glutamine synthetase and glutamate dehydrogenase by marine bacterioplankton: assay optimizations and efficacy for assessing nitrogen to carbon metabolic balance in situ","volume":"4","author":"Hoch","year":"2006","journal-title":"Limnol. Oceanogr. Methods"},{"key":"ref39","doi-asserted-by":"publisher","first-page":"D309","DOI":"10.1093\/nar\/gky1085","article-title":"EggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses","volume":"47","author":"Huerta-Cepas","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref40","doi-asserted-by":"publisher","first-page":"519","DOI":"10.1038\/s41586-019-1916-6","article-title":"Isolation of an archaeon at the prokaryote\u2013eukaryote interface","volume":"577","author":"Imachi","year":"2020","journal-title":"Nature"},{"key":"ref41","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":"ref42","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2105-15-182","article-title":"Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads","volume":"15","author":"Jiang","year":"2014","journal-title":"BMC Bioinformatics"},{"key":"ref43","doi-asserted-by":"publisher","first-page":"e4820","DOI":"10.1002\/pro.4820","article-title":"KEGG tools for classification and analysis of viral proteins","volume":"32","author":"Jin","year":"2023","journal-title":"Protein Sci."},{"key":"ref44","doi-asserted-by":"publisher","first-page":"4119","DOI":"10.1099\/ijsem.0.004254","article-title":"Patiriisocius marinistellae gen. Nov., sp. nov., isolated from the starfish Patiria pectinifera, and reclassification of Ulvibacter marinus as a member of the genus Patiriisocius comb. nov","volume":"70","author":"Kawano","year":"2020","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref45","doi-asserted-by":"publisher","first-page":"1647","DOI":"10.1093\/bioinformatics\/bts199","article-title":"Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data","volume":"28","author":"Kearse","year":"2012","journal-title":"Bioinformatics"},{"key":"ref46","doi-asserted-by":"publisher","first-page":"609","DOI":"10.1007\/s12275-021-1231-4","article-title":"UBCG2: up-to-date bacterial core genes and pipeline for phylogenomic analysis","volume":"59","author":"Kim","year":"2021","journal-title":"J. Microbiol."},{"key":"ref47","doi-asserted-by":"publisher","first-page":"476","DOI":"10.1007\/s12275-021-1154-0","article-title":"Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity","volume":"59","author":"Kim","year":"2021","journal-title":"J. Microbiol."},{"key":"ref48","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1038\/s41564-023-01322-0","article-title":"Molecular hydrogen in seawater supports growth of diverse marine bacteria","volume":"8","author":"Lappan","year":"2023","journal-title":"Nat. Microbiol."},{"key":"ref49","doi-asserted-by":"publisher","first-page":"2505","DOI":"10.1099\/ijs.0.65697-0","article-title":"Description of Croceitalea gen. Nov. in the family Flavobacteriaceae with two species, Croceitalea eckloniae sp. nov. and Croceitalea dokdonensis sp. nov., isolated from the rhizosphere of the marine alga Ecklonia kurome","volume":"58","author":"Lee","year":"2008","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref50","doi-asserted-by":"publisher","first-page":"6535","DOI":"10.1128\/jb.181.20.6535-6539.1999","article-title":"Genetic analysis of nif regulatory genes by utilizing the yeast two- hybrid system detected formation of a NifL-NifA complex that is implicated in regulated expression of nif genes","volume":"181","author":"Lei","year":"1999","journal-title":"J. Bacteriol."},{"key":"ref51","doi-asserted-by":"publisher","first-page":"W293","DOI":"10.1093\/nar\/gkab301","article-title":"Interactive tree of life (iTOL) v5: an online tool for phylogenetic tree display and annotation","volume":"49","author":"Letunic","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref52","author":"Li","year":"2013"},{"key":"ref53","doi-asserted-by":"publisher","first-page":"5970","DOI":"10.1073\/pnas.1521291113","article-title":"Scaling laws predict global microbial diversity","volume":"113","author":"Locey","year":"2016","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref54","doi-asserted-by":"publisher","first-page":"2198","DOI":"10.1038\/s41396-022-01266-z","article-title":"Global and seasonal variation of marine phosphonate metabolism","volume":"16","author":"Lockwood","year":"2022","journal-title":"ISME J."},{"key":"ref55","doi-asserted-by":"publisher","first-page":"21219","DOI":"10.1073\/pnas.0907586106","article-title":"Subcellular localization of marine bacterial alkaline phosphatases","volume":"106","author":"Luo","year":"2009","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref56","doi-asserted-by":"publisher","first-page":"1573","DOI":"10.1093\/jxb\/38.9.1573","article-title":"Isolation and analysis of the cell walls of brown algae: Fucus spiralis, F. ceranoides, F. vesiculosus, F. serratus, Bifurcaria bifurcata and Laminaria digitata","volume":"38","author":"Mabeau","year":"1987","journal-title":"J. Exp. Bot."},{"key":"ref57","doi-asserted-by":"publisher","first-page":"1293","DOI":"10.1007\/s00203-020-02131-3","article-title":"Pseudidiomarina piscicola sp. nov., isolated from cultured European seabass, Dicenthrarchus labrax","volume":"203","author":"Maci\u00e1n","year":"2021","journal-title":"Arch. Microbiol."},{"key":"ref58","doi-asserted-by":"publisher","first-page":"1363","DOI":"10.1111\/j.1462-2920.2011.02612.x","article-title":"Phosphite utilization by the marine picocyanobacterium Prochlorococcus MIT9301","volume":"14","author":"Mart\u00ednez","year":"2012","journal-title":"Environ. Microbiol."},{"key":"ref59","doi-asserted-by":"publisher","first-page":"2125","DOI":"10.1038\/s41396-019-0410-3","article-title":"High proportions of bacteria are culturable across major biomes","volume":"13","author":"Martiny","year":"2019","journal-title":"ISME J."},{"key":"ref60","doi-asserted-by":"publisher","first-page":"1055","DOI":"10.1099\/00207713-50-3-1055","article-title":"Taxonomy of Antarctic Flavobacterium species: description of Flavobacterium gillisiae sp. nov., Flavobacterium tegetincola sp. nov., and Flavobacterium xanthum sp. nov., nom. Rev","volume":"50","author":"McCammon","year":"2000","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref61","doi-asserted-by":"publisher","first-page":"60","DOI":"10.1186\/1471-2105-14-60","article-title":"Genome sequence-based species delimitation with confidence intervals and improved distance functions","volume":"14","author":"Meier-Kolthoff","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"ref62","doi-asserted-by":"publisher","first-page":"2182","DOI":"10.1038\/s41467-019-10210-3","article-title":"TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy","volume":"10","author":"Meier-Kolthoff","year":"2019","journal-title":"Nat. Commun."},{"key":"ref63","doi-asserted-by":"publisher","first-page":"2957","DOI":"10.1111\/j.1462-2920.2007.01407.x","article-title":"Molecular analysis of the distribution and phylogeny of the soxB gene among sulfur-oxidizing bacteria - evolution of the sox sulfur oxidation enzyme system","volume":"9","author":"Meyer","year":"2007","journal-title":"Environ. Microbiol."},{"key":"ref64","doi-asserted-by":"publisher","first-page":"D412","DOI":"10.1093\/nar\/gkaa913","article-title":"Pfam: the protein families database in 2021","volume":"49","author":"Mistry","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref65","doi-asserted-by":"publisher","first-page":"523","DOI":"10.1146\/annurev-marine-120710-100827","article-title":"Genomic insights into bacterial DMSP transformations","volume":"4","author":"Moran","year":"2012","journal-title":"Annu. Rev. Mar. Sci."},{"key":"ref66","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1099\/ijs.0.63307-0","article-title":"Winogradskyella thalassocola gen. Nov., sp. nov., Winogradskyella epiphytica sp. nov. and Winogradskyella eximia sp. nov., marine bacteria of the family Flavobacteriaceae","volume":"55","author":"Nedashkovskaya","year":"2005","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref67","doi-asserted-by":"publisher","first-page":"1465","DOI":"10.1099\/ijs.0.005421-0","article-title":"Winogradskyella echinorum sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from the sea urchin Strongylocentrotus intermedius","volume":"59","author":"Nedashkovskaya","year":"2009","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref68","doi-asserted-by":"publisher","first-page":"784","DOI":"10.1038\/ismej.2009.150","article-title":"Genome characteristics of a generalist marine bacterial lineage","volume":"4","author":"Newton","year":"2010","journal-title":"ISME J."},{"key":"ref69","doi-asserted-by":"publisher","first-page":"4432","DOI":"10.1099\/ijsem.0.003935","article-title":"Division of the genus Chryseobacterium: observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. Nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical speciments","volume":"70","author":"Nicholson","year":"2020","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref70","doi-asserted-by":"publisher","first-page":"2400","DOI":"10.1111\/j.1462-2920.2009.01968.x","article-title":"Molecular analysis of the phosphorus starvation response in Trichodesmium spp","volume":"11","author":"Orchard","year":"2009","journal-title":"Environ. Microbiol."},{"key":"ref71","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1128\/AEM.70.11.6542","article-title":"Representative freshwater Bacterioplankton isolated from crater Lake, Oregon","volume":"70","author":"Page","year":"2005","journal-title":"Appl. Environ. Microbiol."},{"key":"ref72","doi-asserted-by":"publisher","first-page":"1877","DOI":"10.1099\/ijs.0.028647-0","article-title":"Salinisphaera orenii sp. nov., isolated from a solar saltern","volume":"62","author":"Park","year":"2012","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref73","doi-asserted-by":"publisher","first-page":"1321","DOI":"10.1099\/ijsem.0.002671","article-title":"Thalassotalea insulae sp. nov., isolated from tidal flat sediment","volume":"68","author":"Park","year":"2018","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref74","doi-asserted-by":"publisher","first-page":"2229","DOI":"10.1099\/ijs.0.046318-0","article-title":"Rubrivirga marina gen. Nov., sp. nov., a member of the family Rhodothermaceae isolated from deep seawater","volume":"63","author":"Park","year":"2013","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref75","doi-asserted-by":"publisher","first-page":"S1","DOI":"10.1099\/ijsem.0.000778","article-title":"International code of nomenclature of prokaryotes","volume":"69","author":"Parker","year":"2019","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref76","doi-asserted-by":"publisher","first-page":"D785","DOI":"10.1093\/nar\/gkab776","article-title":"GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy","volume":"50","author":"Parks","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"ref77","doi-asserted-by":"publisher","first-page":"1043","DOI":"10.1101\/gr.186072.114","article-title":"CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes","volume":"25","author":"Parks","year":"2015","journal-title":"Genome Res."},{"key":"ref78","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.5289278","article-title":"nf-core\/bacass: v2.0.0 nf-core\/bacass: \u201cNavy Steel Swordfish.\u201d","author":"Peltzer","year":"2021","journal-title":"Zenodo"},{"key":"ref79","doi-asserted-by":"publisher","first-page":"150023","DOI":"10.1038\/sdata.2015.23","article-title":"Open science resources for the discovery and analysis of Tara oceans data","volume":"2","author":"Pesant","year":"2015","journal-title":"Sci. Data"},{"key":"ref80","doi-asserted-by":"publisher","first-page":"1823","DOI":"10.1093\/bioinformatics\/bts252","article-title":"SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes","volume":"28","author":"Pruesse","year":"2012","journal-title":"Bioinformatics"},{"key":"ref81","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3389\/fmicb.2017.02645","article-title":"Comparative genomics of Thalassobius including the description of Thalassobius activus sp. nov., and Thalassobius autumnalis sp. nov","volume":"8","author":"Pujalte","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref82","doi-asserted-by":"publisher","first-page":"e0089023","DOI":"10.1128\/spectrum.00890-23","article-title":"Expanding success in the isolation of abundant marine bacteria after reduction in grazing and viral pressure and increase in nutrient availability","volume":"11","author":"Rey-Velasco","year":"2023","journal-title":"Microbiol. Spectr."},{"key":"ref83","volume-title":"Qdap: Quantitative discourse analysis package. 2.4.2.","author":"Rinker","year":"2020"},{"key":"ref84","doi-asserted-by":"publisher","first-page":"e1900v1","DOI":"10.7287\/peerj.preprints.1900v1","article-title":"The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes","volume":"4","author":"Rodriguez-R","year":"2016","journal-title":"PeerJ Prepr."},{"key":"ref85","doi-asserted-by":"publisher","first-page":"19773","DOI":"10.1038\/s41598-020-76590-5","article-title":"Seasonal impact of grazing, viral mortality, resource availability and light on the group-specific growth rates of coastal Mediterranean bacterioplankton","volume":"10","author":"S\u00e1nchez","year":"2020","journal-title":"Sci. Rep."},{"key":"ref86","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3389\/fmars.2017.00253","article-title":"Patterns of bacterial and archaeal gene expression through the lower Amazon River","volume":"4","author":"Satinsky","year":"2017","journal-title":"Front. Mar. Sci."},{"key":"ref87","doi-asserted-by":"publisher","first-page":"563","DOI":"10.1038\/ismej.2009.10","article-title":"The alkaline phosphatase PhoX is more widely distributed in marine bacteria than the classical PhoA","volume":"3","author":"Sebastian","year":"2009","journal-title":"ISME J."},{"key":"ref88","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"ref89","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1371\/journal.pone.0163962","article-title":"SeqKit: a cross-platform and ultrafast toolkit for FASTA\/Q file manipulation","volume":"11","author":"Shen","year":"2016","journal-title":"PLoS One"},{"key":"ref90","doi-asserted-by":"publisher","first-page":"2424","DOI":"10.1099\/ijs.0.037929-0","article-title":"Tropicimonas sediminicola sp. nov., isolated from marine sediment","volume":"62","author":"Shin","year":"2012","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref91","doi-asserted-by":"publisher","first-page":"1751","DOI":"10.1099\/ijsem.0.003966","article-title":"Urechidicola croceus gen. Nov., sp. nov., a member of the family Flavobacteriaceae","volume":"70","author":"Shin","year":"2020","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref92","doi-asserted-by":"publisher","first-page":"3253","DOI":"10.1099\/ijsem.0.001182","article-title":"Rubrivirga profundi sp. nov., isolated from deep-sea water, and emended description of the genus Rubrivirga","volume":"66","author":"Song","year":"2016","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref93","doi-asserted-by":"publisher","first-page":"3126","DOI":"10.1038\/s41396-019-0484-y","article-title":"High proportions of bacteria and archaea across most biomes remain uncultured","volume":"13","author":"Steen","year":"2019","journal-title":"ISME J."},{"key":"ref94","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.1493841","article-title":"nf-core\/ampliseq: Ampliseq Version 2.7.1","author":"Straub","year":"2023","journal-title":"Zenodo"},{"key":"ref95","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1099\/ijsem.0.005321","article-title":"Algiphilus acroporae sp. nov. and Coraliihabitans acroporae gen. Nov. sp. nov., isolated from scleractinian coral Acropora digitifera","volume":"72","author":"Sun","year":"2022","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref96","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1093\/nar\/28.1.33","article-title":"The COG database: a tool for genome-scale analysis of protein functions and evolution","volume":"28","author":"Tatusov","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"ref97","volume-title":"R: A language and environment for statistical computing","year":"2022"},{"key":"ref98","volume-title":"RStudio: Integrated development environment for R","year":"2020"},{"key":"ref99","doi-asserted-by":"publisher","first-page":"608","DOI":"10.1126\/science.1218344","article-title":"Substrate-controlled succession of marine bacterioplankton populations induced by a phytoplankton bloom","volume":"336","author":"Teeling","year":"2012","journal-title":"Science"},{"key":"ref100","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1099\/ijsem.0.005902","article-title":"Stakelama marina sp. nov., isolated from seawater of the Tangyin hydrothermal field in the Okinawa trough","volume":"73","author":"Wang","year":"2023","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref101","doi-asserted-by":"publisher","first-page":"6578","DOI":"10.1073\/pnas.95.12.6578","article-title":"Prokaryotes: the unseen majority","volume":"95","author":"Whitman","year":"1998","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref102","doi-asserted-by":"publisher","first-page":"e1005595","DOI":"10.1371\/journal.pcbi.1005595","article-title":"Unicycler: resolving bacterial genome assemblies from short and long sequencing reads","volume":"13","author":"Wick","year":"2017","journal-title":"PLoS Comput. Biol."},{"key":"ref103","doi-asserted-by":"publisher","first-page":"1686","DOI":"10.21105\/joss.01686","article-title":"Welcome to the Tidyverse","volume":"4","author":"Wickham","year":"2019","journal-title":"J. Open Source Softw."},{"key":"ref104","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1146\/annurev.micro.54.1.289","article-title":"Alginate lyase: review of major sources and enzyme characteristics, structure-function analysis, biological roles, and applications","volume":"54","author":"Wong","year":"2000","journal-title":"Ann. Rev. Microbiol."},{"key":"ref105","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1186\/s13059-019-1891-0","article-title":"Improved metagenomic analysis with kraken 2","volume":"20","author":"Wood","year":"2019","journal-title":"Genome Biol."},{"key":"ref106","doi-asserted-by":"publisher","first-page":"2247","DOI":"10.1099\/ijs.0.004267-0","article-title":"Croceicoccus marinus gen. Nov., sp. nov., a yellow-pigmented bacterium from deep-sea sediment, and emended description of the family Erythrobacteraceae","volume":"59","author":"Xu","year":"2009","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref107","doi-asserted-by":"publisher","first-page":"1613","DOI":"10.1099\/ijsem.0.001755","article-title":"Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies","volume":"67","author":"Yoon","year":"2017","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref108","doi-asserted-by":"publisher","first-page":"6732","DOI":"10.1073\/pnas.1403051111","article-title":"Functional characterization of flavobacteria rhodopsins reveals a unique class of light-driven chloride pump in bacteria","volume":"111","author":"Yoshizawa","year":"2014","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref109","doi-asserted-by":"publisher","first-page":"2218","DOI":"10.1099\/ijs.0.037515-0","article-title":"Pricia Antarctica gen. Nov., sp. nov., a member of the family Flavobacteriaceae, isolated from antarctic intertidal sediment","volume":"62","author":"Yu","year":"2012","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref110","doi-asserted-by":"publisher","first-page":"2174","DOI":"10.1099\/ijs.0.035584-0","article-title":"Salinisphaera halophila sp. nov., a moderately halophilic bacterium isolated from brine of a salt well","volume":"62","author":"Zhang","year":"2012","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref111","doi-asserted-by":"publisher","first-page":"1223","DOI":"10.1099\/ijs.0.055913-0","article-title":"Description of Thalassotalea piscium gen. Nov., sp. nov., isolated from flounder (Paralichthys olivaceus), reclassification of four species of the genus Thalassomonas as members of the genus Thalassotalea gen. Nov. and emended description of the genus Tha","volume":"64","author":"Zhang","year":"2014","journal-title":"Int. J. Syst. Evol. Microbiol."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2024.1407904\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,5,28]],"date-time":"2024-05-28T11:11:41Z","timestamp":1716894701000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2024.1407904\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,5,28]]},"references-count":111,"alternative-id":["10.3389\/fmicb.2024.1407904"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2024.1407904","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,5,28]]},"article-number":"1407904"}}