{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,30]],"date-time":"2026-04-30T08:27:16Z","timestamp":1777537636969,"version":"3.51.4"},"reference-count":50,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2019,9,24]],"date-time":"2019-09-24T00:00:00Z","timestamp":1569283200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0221574","type":"journal-article","created":{"date-parts":[[2019,9,24]],"date-time":"2019-09-24T17:25:39Z","timestamp":1569345939000},"page":"e0221574","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":35,"title":["The genome of Alcaligenes aquatilis strain BU33N: Insights into hydrocarbon degradation capacity"],"prefix":"10.1371","volume":"14","author":[{"given":"Mouna","family":"Mahjoubi","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Habibu","family":"Aliyu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Simone","family":"Cappello","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mohamed","family":"Naifer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yasmine","family":"Souissi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Don A.","family":"Cowan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0474-1530","authenticated-orcid":true,"given":"Ameur","family":"Cherif","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2019,9,24]]},"reference":[{"issue":"1","key":"pone.0221574.ref001","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1016\/j.chnaes.2009.12.002","article-title":"Advance in the toxic effects of petroleum water accommodated fraction on marine plankton","volume":"30","author":"Z Jiang","year":"2010","journal-title":"Acta Ecologica Sinica"},{"issue":"1","key":"pone.0221574.ref002","first-page":"67","article-title":"Isolation and characterization of diesel-degrading Pseudomonas strains from diesel-contaminated soils in Iran (Fars province)","volume":"2","author":"Z Niazy","year":"2016","journal-title":"Pollution"},{"issue":"4","key":"pone.0221574.ref003","doi-asserted-by":"crossref","first-page":"1317","DOI":"10.1590\/S1517-83822014000400023","article-title":"Quick stimulation of Alcanivorax sp. by bioemulsificant EPS2003 on microcosm oil spill simulation","volume":"45","author":"S Cappello","year":"2014","journal-title":"Brazilian Journal of Microbiology"},{"issue":"1\u20132","key":"pone.0221574.ref004","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1016\/j.marpolbul.2016.03.017","article-title":"Bioremediation technologies for polluted seawater sampled after an oil-spill in Taranto Gulf (Italy): A comparison of biostimulation, bioaugmentation and use of a washing agent in microcosm studies","volume":"106","author":"F Crisafi","year":"2016","journal-title":"Marine pollution bulletin"},{"key":"pone.0221574.ref005","doi-asserted-by":"crossref","first-page":"162","DOI":"10.3389\/fmicb.2014.00162","article-title":"Effective bioremediation strategy for rapid in situ cleanup of anoxic marine sediments in mesocosm oil spill simulation","volume":"5","author":"M Genovese","year":"2014","journal-title":"Frontiers in microbiology"},{"issue":"3","key":"pone.0221574.ref006","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1038\/nrmicro1348","article-title":"Marine microorganisms make a meal of oil","volume":"4","author":"IM Head","year":"2006","journal-title":"Nature Reviews Microbiology"},{"issue":"16","key":"pone.0221574.ref007","doi-asserted-by":"crossref","first-page":"3029","DOI":"10.1016\/j.watres.2006.06.021","article-title":"Piggery wastewater treatment using Alcaligenes faecalis strain No. 4 with heterotrophic nitrification and aerobic denitrification","volume":"40","author":"H-S Joo","year":"2006","journal-title":"Water Research"},{"key":"pone.0221574.ref008","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1016\/j.jbiotec.2015.12.001","article-title":"The complete genome sequence of Alcaligenes faecalis ZD02, a novel potential bionematocide","volume":"218","author":"S Ju","year":"2016","journal-title":"Journal of biotechnology"},{"issue":"3","key":"pone.0221574.ref009","first-page":"830","article-title":"Subspecies Names Automatically Created by Rule 46","volume":"46","author":"J. Euzeby","year":"1996","journal-title":"International Journal of Systematic and Evolutionary Microbiology"},{"issue":"1","key":"pone.0221574.ref010","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1078\/0723-2020-00001","article-title":"Alcaligenes faecalis subsp. parafaecalis subsp. nov., a Bacterium Accumulating Poly-\u03b2-hydroxybutyrate from Acetone-butanol Bioprocess Residues","volume":"24","author":"G Schroll","year":"2001","journal-title":"Systematic and applied microbiology"},{"issue":"5","key":"pone.0221574.ref011","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1016\/j.syapm.2005.03.003","article-title":"Alcaligenes faecalis subsp. phenolicus subsp. nov. a phenol-degrading, denitrifying bacterium isolated from a graywater bioprocessor","volume":"28","author":"M Rehfuss","year":"2005","journal-title":"Systematic and applied microbiology"},{"issue":"6","key":"pone.0221574.ref012","doi-asserted-by":"crossref","first-page":"2571","DOI":"10.1099\/ijs.0.63849-0","article-title":"Alcaligenes aquatilis sp. nov., a novel bacterium from sediments of the Weser Estuary, Germany, and a salt marsh on Shem Creek in Charleston Harbor, USA","volume":"55","author":"S Van Trappen","year":"2005","journal-title":"International journal of systematic and evolutionary microbiology"},{"issue":"4","key":"pone.0221574.ref013","doi-asserted-by":"crossref","first-page":"939","DOI":"10.1099\/ijsem.0.001719","article-title":"Alcaligenes endophyticus sp. nov., isolated from roots of Ammodendron bifolium","volume":"67","author":"C-Y Lu","year":"2017","journal-title":"International journal of systematic and evolutionary microbiology"},{"issue":"4","key":"pone.0221574.ref014","doi-asserted-by":"crossref","first-page":"859","DOI":"10.1007\/s10482-015-0540-1","article-title":"A heavy-metal tolerant novel bacterium, Alcaligenes pakistanensis sp. nov., isolated from industrial effluent in Pakistan","volume":"108","author":"S Abbas","year":"2015","journal-title":"Antonie Van Leeuwenhoek"},{"issue":"2","key":"pone.0221574.ref015","first-page":"e00222","article-title":"The genome sequence of Alcaligenes faecalis NBIB-017 contains genes with potentially high activities against Erwinia carotovora","volume":"4","author":"X Liu","year":"2016","journal-title":"Genome announcements"},{"issue":"1","key":"pone.0221574.ref016","doi-asserted-by":"crossref","first-page":"23","DOI":"10.4265\/bio.19.23","article-title":"Development of a PCR-based method for monitoring the status of Alcaligenes species in the agricultural environment","volume":"19","author":"M Nakano","year":"2014","journal-title":"Biocontrol science"},{"key":"pone.0221574.ref017","doi-asserted-by":"crossref","first-page":"21332","DOI":"10.1038\/srep21332","article-title":"Biodegradation of DDT by Stenotrophomonas sp. DDT-1: characterization and genome functional analysis","volume":"6","author":"X Pan","year":"2016","journal-title":"Scientific reports"},{"issue":"10","key":"pone.0221574.ref018","first-page":"3697","article-title":"Cationic dispersant immobilized matrix for sequestering Cr (III) from contaminated soil","volume":"3","author":"CJ Magthalin","year":"2016","journal-title":"Materials Today: Proceedings"},{"issue":"5","key":"pone.0221574.ref019","doi-asserted-by":"crossref","first-page":"e01664","DOI":"10.1128\/MRA.01664-18","article-title":"Complete Genome Sequence of the Marine Hydrocarbon Degrader Alcaligenes aquatilis QD168, Isolated from Crude Oil-Polluted Sediment of Quintero Bay, Central Chile","volume":"8","author":"RE Dur\u00e1n","year":"2019","journal-title":"Microbiology Resource Announcements"},{"key":"pone.0221574.ref020","doi-asserted-by":"crossref","first-page":"528","DOI":"10.3389\/fmicb.2019.00528","article-title":"Genomic and Physiological Traits of the Marine Bacterium Alcaligenes aquatilis QD168 Isolated From Quintero Bay, Central Chile, Reveal a Robust Adaptive Response to Environmental Stressors","volume":"10","author":"RE Dur\u00e1n","year":"2019","journal-title":"Frontiers in microbiology"},{"issue":"2","key":"pone.0221574.ref021","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1590\/S1517-838246120131276","article-title":"Biodegradation of crude oil by individual bacterial strains and a mixed bacterial consortium","volume":"46","author":"S Santisi","year":"2015","journal-title":"Brazilian Journal of Microbiology"},{"key":"pone.0221574.ref022","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1016\/j.marenvres.2013.12.010","article-title":"Bioremediation (bioaugmentation\/biostimulation) trials of oil polluted seawater: a mesocosm simulation study","volume":"95","author":"M Hassanshahian","year":"2014","journal-title":"Marine environmental research"},{"issue":"5","key":"pone.0221574.ref023","doi-asserted-by":"crossref","first-page":"975","DOI":"10.1007\/s00253-009-1896-9","article-title":"Analysis of rhamnolipid biosurfactants by methylene blue complexation","volume":"82","author":"NM Pinzon","year":"2009","journal-title":"Applied microbiology and biotechnology"},{"issue":"3","key":"pone.0221574.ref024","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1016\/j.mimet.2003.11.001","article-title":"Comparison of methods to detect biosurfactant production by diverse microorganisms","volume":"56","author":"NH Youssef","year":"2004","journal-title":"Journal of microbiological methods"},{"issue":"6","key":"pone.0221574.ref025","doi-asserted-by":"crossref","first-page":"723","DOI":"10.1016\/j.nbt.2013.03.004","article-title":"Hydrocarbonoclastic bacteria isolated from petroleum contaminated sites in Tunisia: isolation, identification and characterization of the biotechnological potential","volume":"30","author":"M Mahjoubi","year":"2013","journal-title":"New biotechnology"},{"key":"pone.0221574.ref026","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1016\/j.sajb.2013.01.007","article-title":"An evaluation of the endophytic colonies present in pathogenic and non-pathogenic Vanguerieae using electron microscopy","volume":"86","author":"S Stanton","year":"2013","journal-title":"South African journal of botany"},{"issue":"4","key":"pone.0221574.ref027","doi-asserted-by":"crossref","first-page":"1131","DOI":"10.1128\/AEM.59.4.1131-1137.1993","article-title":"Cloning of a novel cryIC-type gene from a strain of Bacillus thuringiensis subsp. galleriae","volume":"59","author":"S Kalman","year":"1993","journal-title":"Appl Environ Microbiol"},{"issue":"5","key":"pone.0221574.ref028","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"A Bankevich","year":"2012","journal-title":"Journal of computational biology"},{"issue":"9","key":"pone.0221574.ref029","doi-asserted-by":"crossref","first-page":"3100","DOI":"10.1093\/nar\/gkm160","article-title":"RNAmmer: consistent and rapid annotation of ribosomal RNA genes","volume":"35","author":"K Lagesen","year":"2007","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"pone.0221574.ref030","doi-asserted-by":"crossref","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":"S-H Yoon","year":"2017","journal-title":"International journal of systematic and evolutionary microbiology"},{"key":"pone.0221574.ref031","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1007\/978-1-62703-646-7_8","volume-title":"Multiple Sequence Alignment Methods","author":"K Katoh","year":"2014"},{"issue":"15","key":"pone.0221574.ref032","doi-asserted-by":"crossref","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":"JM Silla-Mart\u00ednez","year":"2009","journal-title":"Bioinformatics"},{"issue":"1","key":"pone.0221574.ref033","first-page":"1","article-title":"Genome sequence-based species delimitation with confidence intervals and improved distance functions","volume":"14","author":"JP Meier-Kolthoff","year":"2013","journal-title":"BMC Bioinformatics"},{"issue":"2","key":"pone.0221574.ref034","doi-asserted-by":"crossref","first-page":"1100","DOI":"10.1099\/ijsem.0.000760","article-title":"OrthoANI: An improved algorithm and software for calculating average nucleotide identity","volume":"66","author":"I Lee","year":"2016","journal-title":"Int J Syst Evol Microbiol"},{"issue":"1","key":"pone.0221574.ref035","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1186\/1471-2164-9-75","article-title":"The RAST Server: rapid annotations using subsystems technology","volume":"9","author":"RK Aziz","year":"2008","journal-title":"BMC genomics"},{"issue":"suppl_2","key":"pone.0221574.ref036","doi-asserted-by":"crossref","first-page":"W181","DOI":"10.1093\/nar\/gkn179","article-title":"The CGView Server: a comparative genomics tool for circular genomes","volume":"36","author":"JR Grant","year":"2008","journal-title":"Nucleic acids research"},{"issue":"14","key":"pone.0221574.ref037","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation","volume":"30","author":"T. Seemann","year":"2014","journal-title":"Bioinformatics"},{"issue":"W1","key":"pone.0221574.ref038","doi-asserted-by":"crossref","first-page":"W3","DOI":"10.1093\/nar\/gkw343","article-title":"The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update","volume":"44","author":"E Afgan","year":"2016","journal-title":"Nucleic acids research"},{"issue":"7","key":"pone.0221574.ref039","doi-asserted-by":"crossref","first-page":"1009","DOI":"10.1093\/bioinformatics\/btr039","article-title":"Easyfig: a genome comparison visualizer","volume":"27","author":"MJ Sullivan","year":"2011","journal-title":"Bioinformatics"},{"key":"pone.0221574.ref040","first-page":"31","article-title":"Isolation and identification of three-rings polyaromatic hydrocarbons (anthracene and phenanthrene) degrading bacteria","volume":"5","author":"HE Abd-Elsalam","year":"2009","journal-title":"Am Eurasian J Agric Environ Sci"},{"issue":"48","key":"pone.0221574.ref041","doi-asserted-by":"crossref","first-page":"e01346","DOI":"10.1128\/genomeA.01346-17","article-title":"Draft Genome Sequence of Alcaligenes faecalis BDB4, a Polyaromatic Hydrocarbon-Degrading Bacterium Isolated from Crude Oil-Contaminated Soil","volume":"5","author":"LP Singha","year":"2017","journal-title":"Genome announcements"},{"issue":"5\u20136","key":"pone.0221574.ref042","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1016\/j.ygeno.2017.06.002","article-title":"Genome analysis of crude oil degrading Franconibacter pulveris strain DJ34 revealed its genetic basis for hydrocarbon degradation and survival in oil contaminated environment","volume":"109","author":"S Pal","year":"2017","journal-title":"Genomics"},{"issue":"2","key":"pone.0221574.ref043","doi-asserted-by":"crossref","first-page":"e15","DOI":"10.1371\/journal.pgen.0010015","article-title":"Comparative and evolutionary analysis of the bacterial homologous recombination systems","volume":"1","author":"EP Rocha","year":"2005","journal-title":"PLoS genetics"},{"issue":"1","key":"pone.0221574.ref044","doi-asserted-by":"crossref","first-page":"e0115516","DOI":"10.1371\/journal.pone.0115516","article-title":"Comparative Genomic and Phylogenetic Analyses of Gammaproteobacterial glg Genes Traced the Origin of the Escherichia coli Glycogen glgBXCAP Operon to the Last Common Ancestor of the Sister Orders Enterobacteriales and Pasteurellales","volume":"10","author":"G Almagro","year":"2015","journal-title":"PLOS ONE"},{"issue":"1","key":"pone.0221574.ref045","doi-asserted-by":"crossref","first-page":"e84000","DOI":"10.1371\/journal.pone.0084000","article-title":"Pseudomonas putida CSV86: a candidate genome for genetic bioaugmentation","volume":"9","author":"V Paliwal","year":"2014","journal-title":"PLoS One"},{"key":"pone.0221574.ref046","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/j.margen.2017.02.005","article-title":"Genomic potential of Marinobacter salinus Hb8 T as sulfur oxidizing and aromatic hydrocarbon degrading bacterium","volume":"34","author":"S Rani","year":"2017","journal-title":"Marine Genomics"},{"issue":"1","key":"pone.0221574.ref047","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1007\/s11274-017-2391-6","article-title":"Insights into the genome and proteome of Sphingomonas paucimobilis strain 20006FA involved in the regulation of polycyclic aromatic hydrocarbon degradation","volume":"34","author":"M Macchi","year":"2018","journal-title":"World Journal of Microbiology and Biotechnology"},{"issue":"1","key":"pone.0221574.ref048","doi-asserted-by":"crossref","first-page":"278","DOI":"10.3390\/ijerph6010278","article-title":"Bacterial degradation of aromatic compounds","volume":"6","author":"J-S Seo","year":"2009","journal-title":"International journal of environmental research and public health"},{"issue":"5","key":"pone.0221574.ref049","doi-asserted-by":"crossref","first-page":"830","DOI":"10.1080\/09168451.2014.993915","article-title":"In vitro reconstitution of the catabolic reactions catalyzed by PcaHG, PcaB, and PcaL: the protocatechuate branch of the \u03b2-ketoadipate pathway in Rhodococcus jostii RHA1","volume":"79","author":"T Yamanashi","year":"2015","journal-title":"Bioscience, biotechnology, and biochemistry"},{"issue":"1","key":"pone.0221574.ref050","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1186\/s40793-017-0252-4","article-title":"First draft genome sequence of a strain from the genus Fusibacter isolated from Salar de Ascot\u00e1n in Northern Chile","volume":"12","author":"AE Serrano","year":"2017","journal-title":"Standards in genomic sciences"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0221574","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,1,23]],"date-time":"2021-01-23T01:48:44Z","timestamp":1611366524000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0221574"}},"subtitle":[],"editor":[{"given":"Paula V.","family":"Morais","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2019,9,24]]},"references-count":50,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2019,9,24]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0221574","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,9,24]]}}}