{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,14]],"date-time":"2026-07-14T17:39:35Z","timestamp":1784050775010,"version":"3.55.0"},"reference-count":96,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2024,11,20]],"date-time":"2024-11-20T00:00:00Z","timestamp":1732060800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Ministry of Science and Higher Education of the Russian Federation","award":["075-15-2024-646"],"award-info":[{"award-number":["075-15-2024-646"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>The negative ecological impact of industrialization, which involves the use of petroleum products and dyes in the environment, has prompted research into effective, sustainable, and economically beneficial green technologies. For green remediation primarily based on active microbial metabolites, these microbes are typically from relevant sources. Active microbial metabolite production and genetic systems involved in xenobiotic degradation provide these microbes with the advantage of survival and proliferation in polluted ecological niches. In this study, we evaluated the ability of wheat root-associated L. fusiformis MGMM7 to degrade xenobiotic contaminants such as crude oil, phenol, and azo dyes. We sequenced the whole genome of MGMM7 and provided insights into the genomic structure of related strains isolated from contaminated sources. The results revealed that influenced by its isolation source, L. fusiformis MGMM7 demonstrated remediation and plant growth-promoting abilities in soil polluted with crude oil. Lysinibacillus fusiformis MGMM7 degraded up to 44.55 \u00b1 5.47% crude oil and reduced its toxicity in contaminated soil experiments with garden cress (Lepidium sativum L.). Additionally, L. fusiformis MGMM7 demonstrated a significant ability to degrade Congo Red azo dye (200 mg\/L), reducing its concentration by over 60% under both static and shaking cultivation conditions. However, the highest degradation efficiency was observed under shaking conditions. Genomic comparison among L. fusiformis strains revealed almost identical genomic profiles associated with xenobiotic assimilation. Genomic relatedness using Average Nucleotide Identity (ANI) and digital DNA\u2013DNA hybridization (DDH) revealed that MGMM7 is distantly related to TZA38, Cu-15, and HJ.T1. Furthermore, subsystem distribution and pangenome analysis emphasized the distinctive features of MGMM7, including functional genes in its chromosome and plasmid, as well as the presence of unique genes involved in PAH assimilation, such as phnC\/T\/E, which is involved in phosphonate biodegradation, and nemA, which is involved in benzoate degradation and reductive degradation of N-ethylmaleimide. These findings highlight the potential properties of petroleum-degrading microorganisms isolated from non-contaminated rhizospheres and offer genomic insights into their functional diversity for xenobiotic remediation.<\/jats:p>","DOI":"10.3390\/microorganisms12112377","type":"journal-article","created":{"date-parts":[[2024,11,20]],"date-time":"2024-11-20T09:14:38Z","timestamp":1732094078000},"page":"2377","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Genomic Insights of Wheat Root-Associated Lysinibacillus fusiformis Reveal Its Related Functional Traits for Bioremediation of Soil Contaminated with Petroleum Products"],"prefix":"10.3390","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8876-8270","authenticated-orcid":false,"given":"Roderic Gilles Claret","family":"Diabankana","sequence":"first","affiliation":[{"name":"Laboratory of Molecular Genetics and Microbiology Methods, Kazan Scientific Center, Russian Academy of Sciences, 420111 Kazan, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8077-5361","authenticated-orcid":false,"given":"Akerke Altaikyzy","family":"Zhamalbekova","sequence":"additional","affiliation":[{"name":"Kazakh Scientific Research Institute of Plant Protection and Quarantine Named After Zh. Zhiembayev, Timiryazev 45, Almaty 050040, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-7036-331X","authenticated-orcid":false,"given":"Aigerim Erbolkyzy","family":"Shakirova","sequence":"additional","affiliation":[{"name":"Kazakh Scientific Research Institute of Plant Protection and Quarantine Named After Zh. Zhiembayev, Timiryazev 45, Almaty 050040, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Valeriia Igorevna","family":"Vasiuk","sequence":"additional","affiliation":[{"name":"Laboratory of Molecular Genetics and Microbiology Methods, Kazan Scientific Center, Russian Academy of Sciences, 420111 Kazan, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria Nikolaevna","family":"Filimonova","sequence":"additional","affiliation":[{"name":"Academic and Research Centre, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9441-409X","authenticated-orcid":false,"given":"Shamil Zavdatovich","family":"Validov","sequence":"additional","affiliation":[{"name":"Laboratory of Molecular Genetics and Microbiology Methods, Kazan Scientific Center, Russian Academy of Sciences, 420111 Kazan, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Radik Ilyasovich","family":"Safin","sequence":"additional","affiliation":[{"name":"Centre of Agroecological Research, Kazan State Agrarian University, 420015 Kazan, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0494-3693","authenticated-orcid":false,"given":"Daniel Mawuena","family":"Afordanyi","sequence":"additional","affiliation":[{"name":"Laboratory of Molecular Genetics and Microbiology Methods, Kazan Scientific Center, Russian Academy of Sciences, 420111 Kazan, Russia"},{"name":"Tatar Research Institute of Agriculture, Kazan Scientific Center, Russian Academy of Sciences, 420111 Kazan, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2024,11,20]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1016\/j.scitotenv.2018.11.483","article-title":"Impact of upstream oil extraction and environmental public health: A review of the evidence","volume":"657","author":"Johnston","year":"2019","journal-title":"Sci. Total Environ."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"123019","DOI":"10.1016\/j.jhazmat.2020.123019","article-title":"Assessing the impact of industrial waste on environment and mitigation strategies: A comprehensive review","volume":"398","author":"Gaur","year":"2020","journal-title":"J. Hazard. Mater."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1504\/IJEWM.2021.112947","article-title":"The threatening effects of open dumping on soil at waste disposal sites of Akure city, Nigeria","volume":"27","author":"Ajibade","year":"2021","journal-title":"Int. J. Environ. Waste Manag."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1016\/j.envpol.2023.122215","article-title":"Underpinning the ecological response of mixed chlorinated volatile organic compounds (CVOCs) associated with contaminated and bioremediated groundwaters: A potential nexus of microbial community structure and function for strategizing efficient bioremediation","volume":"334","author":"Hussain","year":"2023","journal-title":"Environ. Pollut."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1016\/0273-2300(91)90040-3","article-title":"Estimating human exposure through multiple pathways from air, water, and soil","volume":"13","author":"McKone","year":"1991","journal-title":"Regul. Toxicol. Pharmacol."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Malik, A., and Grohmann, E. (2012). Dyes\u2014Environmental Impact and Remediation. Environmental Protection Strategies for Sustainable Development. Strategies for Sustainability, Springer.","DOI":"10.1007\/978-94-007-1591-2"},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Marcomini, A.L., Suter, G., and Critto, A. (2009). Contaminated land: A multi-dimensional problem. Decision Support Systems for Risk-Based Management of Contaminated Sites, Springer.","DOI":"10.1007\/978-0-387-09722-0"},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Meuser, H. (2010). Contaminated Urban Soils, Springer Science & Business Media.","DOI":"10.1007\/978-90-481-9328-8"},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Liu, H., Xu, J., Liang, R., and Liu, J. (2014). Characterization of the medium-and long-chain n-alkanes degrading Pseudomonas aeruginosa strain SJTD-1 and its alkane hydroxylase genes. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0105506"},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Azubuike, C.C., Chikere, C.B., and Okpokwasili, G.C. (2016). Bioremediation techniques\u2013classification based on site of application: Principles, advantages, limitations and prospects. World J. Microbiol. Biotechnol., 32.","DOI":"10.1007\/s11274-016-2137-x"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Xu, X., Liu, W., Tian, S., Wang, W., Qi, Q., Jiang, P., and Yu, H. (2018). Petroleum hydrocarbon-degrading bacteria for the remediation of oil pollution under aerobic conditions: A perspective analysis. Front. Microbiol., 9.","DOI":"10.3389\/fmicb.2018.02885"},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Ngo, A.C.R., and Tischler, D. (2022). Microbial Degradation of Azo Dyes: Approaches and Prospects for a Hazard-Free Conversion by Microorganisms. Int. J. Environ. Res. Public Health, 19.","DOI":"10.3390\/ijerph19084740"},{"key":"ref_13","first-page":"1090","article-title":"Azo dye removal technologies","volume":"5","author":"Shah","year":"2018","journal-title":"Adv. Res. Appl."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Ali, G.A.M., and Makhlouf, A.S.H. (2022). Role of Microorganisms in Biodegradation of Pollutants. Handbook of Biodegradable Materials, Springer.","DOI":"10.1007\/978-3-030-83783-9"},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Xiang, W., Hong, S., Xue, Y., and Ma, Y. (2023). Functional Analysis of Novel alkB Genes Encoding Long-Chain n-Alkane Hydroxylases in Rhodococcus sp. Strain CH91. Microorganisms, 11.","DOI":"10.3390\/microorganisms11061537"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1016\/j.bcab.2017.09.007","article-title":"Purification, immobilization and kinetic characterization of GxSxG esterase with short chain fatty acid specificity from Lysinibacillus fusiformis AU01","volume":"12","author":"Divakar","year":"2017","journal-title":"Biocatal. Agric. Biotechnol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1505","DOI":"10.1007\/s10529-005-1466-x","article-title":"Biotransformation of Isoeugenol to Vanillin by a Novel Strain of Bacillus fusiformis","volume":"27","author":"Zhao","year":"2005","journal-title":"Biotechnol. Lett."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"682","DOI":"10.1016\/j.jhazmat.2010.09.072","article-title":"Characterization and Genomic Analysis of a Highly Chromate Resistant and Reducing Bacterial Strain Lysinibacillus fusiformis ZC1","volume":"185","author":"He","year":"2011","journal-title":"J. Hazard Mater."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"771","DOI":"10.1016\/j.jhazmat.2010.06.101","article-title":"Biodegradation of Naphthalene by Strain Bacillus fusiformis (BFN)","volume":"182","author":"Lin","year":"2010","journal-title":"J. Hazard. Mater."},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Passera, A., Rossato, M., Oliver, J.S., Battelli, G., Shahzad, G.I.R., Cosentino, E., Sage, J.M., Toffolatti, S.L., Lopatriello, G., and Davis, J.R. (2021). Characterization of Lysinibacillus fusiformis strain S4C11: In Vitro, in Planta, and in Silico Analyses Reveal a Plant-Beneficial Microbe. Microbiol. Res., 244.","DOI":"10.1016\/j.micres.2020.126665"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"103","DOI":"10.7831\/ras.9.0_103","article-title":"Lysinibacillus Species: Their Potential as Effective Bioremediation, Biostimulant, and Biocontrol Agents","volume":"9","author":"Ahsan","year":"2021","journal-title":"Rev. Agric. Sci."},{"key":"ref_22","first-page":"243","article-title":"Assessment of different screening methods for selecting biosurfactant producing marine bacteria","volume":"37","author":"Satpute","year":"2008","journal-title":"Indian J. Mar. Sci."},{"key":"ref_23","first-page":"1314","article-title":"Isolation and identification of petroleum hydrocarbon degrading microorganisms from oil contaminated environment","volume":"3","author":"Panda","year":"2013","journal-title":"Int. J. Environ. Sci."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1234","DOI":"10.2134\/jeq2003.1234","article-title":"Effect of nutrient amendments on indigenous hydrocarbon biodegradation in oil-contaminated beach sediments","volume":"32","author":"Xu","year":"2003","journal-title":"J. Environ. Qual."},{"key":"ref_25","first-page":"63","article-title":"An assessment of toxic in urban soils using garden cress (Lepidium sativum) in Vasileostrovsky Ostrov and Elagin Ostrov, Saint Petersburg, Russia","volume":"5","author":"Gyekye","year":"2013","journal-title":"J. Geogr. Geol."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Mahgoub, S.A., Qattan, S.Y., Salem, S.S., Abdelbasit, H.M., Raafat, M., Ashkan, M.F., Al-Quwaie, D.A., Motwali, E.A., Alqahtani, F.S., and Abd El-Fattah, H.I. (2023). Characterization and biodegradation of phenol by Pseudomonas aeruginosa and Klebsiella variicola strains isolated from sewage sludge and their effect on soybean seeds germination. Molecules, 28.","DOI":"10.3390\/molecules28031203"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"6580","DOI":"10.1016\/j.biortech.2010.03.067","article-title":"Decolorization of water-soluble azo dyes by bacterial cultures, isolated from dye house effluent","volume":"101","author":"Modi","year":"2010","journal-title":"Bioresour. Technol."},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Asses, N., Ayed, L., Hkiri, N., and Hamdi, M. (2018). Congo red decolorization and detoxification by Aspergillus niger: Removal mechanisms and dye degradation pathway. BioMed Res. Int., 1.","DOI":"10.1155\/2018\/3049686"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"pdb-prot4455","DOI":"10.1101\/pdb.prot4455","article-title":"Purification of nucleic acids by extraction with phenol: Chloroform","volume":"1","author":"Sambrook","year":"2006","journal-title":"Cold Spring Harb. Protoc."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: A flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"Fastp: An ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_32","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":"Bankevich","year":"2012","journal-title":"Comput. Biol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1093\/bioinformatics\/btx543","article-title":"A contig scaffolding tool using algebraic rearrangements","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"3380","DOI":"10.1093\/bioinformatics\/btw493","article-title":"PlasmidSPAdes: Assembly of plasmids from whole-genome sequencing data","volume":"32","author":"Antipov","year":"2016","journal-title":"Bioinformatics"},{"key":"ref_35","first-page":"e000206","article-title":"MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies","volume":"4","author":"Robertson","year":"2018","journal-title":"Microb. Genom."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"6614","DOI":"10.1093\/nar\/gkw569","article-title":"NCBI prokaryotic genome annotation pipeline","volume":"44","author":"Tatusova","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_37","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_38","doi-asserted-by":"crossref","first-page":"472","DOI":"10.1016\/j.ecoenv.2019.06.036","article-title":"Microbial characterization of heavy metal-resistant bacterial strains isolated from an electroplating wastewater treatment plant","volume":"181","author":"Cai","year":"2019","journal-title":"Ecotoxicol. Environ. Saf."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"W566","DOI":"10.1093\/nar\/gkv468","article-title":"ClustVis: A web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap","volume":"43","author":"Metsalu","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"726","DOI":"10.1016\/j.jmb.2015.11.006","article-title":"BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences","volume":"428","author":"Kanehisa","year":"2016","journal-title":"J. Mol. Biol."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"W46","DOI":"10.1093\/nar\/gkad344","article-title":"antiSMASH 7.0: New and improved predictions for detection, regulation, chemical structures and visualisation","volume":"51","author":"Blin","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"W30","DOI":"10.1093\/nar\/gkx343","article-title":"IslandViewer 4: Expanded prediction of genomic islands for larger-scale datasets","volume":"45","author":"Bertelli","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref_43","doi-asserted-by":"crossref","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":"ref_44","doi-asserted-by":"crossref","first-page":"3691","DOI":"10.1093\/bioinformatics\/btv421","article-title":"Roary: Rapid large-scale prokaryote pangenome analysis","volume":"31","author":"Page","year":"2015","journal-title":"Bioinformatics"},{"key":"ref_45","doi-asserted-by":"crossref","unstructured":"Oberto, J. (2013). SyntTax: A web server linking synteny to prokaryotic taxonomy. BMC Bioinform., 14.","DOI":"10.1186\/1471-2105-14-4"},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Aziz, R.K., Bartels, D., Best, A.A., DeJongh, M., Disz, T., Edwards, R.A., and Zagnitko, O. (2008). The RAST Server: Rapid annotations using subsystems technology. BMC Genom., 9.","DOI":"10.1186\/1471-2164-9-75"},{"key":"ref_47","doi-asserted-by":"crossref","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":"ref_48","doi-asserted-by":"crossref","unstructured":"Filip, J., Cajthaml, T., Najmanov\u00e1, P., \u010cern\u00edk, M., and Zbo\u0159il, R. (2020). Modern bioremediation approaches: Use of biosurfactant, emulsifiers, enzymes, GMOs. Advanced Nano-Bio Technologies for Water and Soil Treatment, Springer. Applied Environmental Science and Engineering for a Sustainable Future.","DOI":"10.1007\/978-3-030-29840-1"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"663","DOI":"10.1007\/s42770-021-00432-3","article-title":"Evaluation of biosurfactant production potential of Lysinibacillus fusiformis MK559526 isolated from automobile-mechanic-workshop soil","volume":"52","author":"John","year":"2021","journal-title":"Braz. J. Microbiol."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"2982","DOI":"10.1039\/C5RA25128A","article-title":"Biodegradation of polyethylene waste by simultaneous use of two bacteria: Bacillus licheniformis for production of bio-surfactant and Lysinibacillus fusiformis for biodegradation","volume":"6","author":"Mukherjee","year":"2016","journal-title":"RSC Adv."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"372","DOI":"10.1080\/01490451.2023.2176573","article-title":"Hydrocarbon- utilizing and metal-tolerant bacteria simultaneously degrade hydrocarbons and detoxify metals in petroleum contaminated soil","volume":"40","author":"Wani","year":"2023","journal-title":"Geomicrobiol. J."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1016\/j.chemosphere.2012.08.020","article-title":"The primary biodegradation of dispersed crude oil in the sea","volume":"90","author":"Prince","year":"2013","journal-title":"Chemosphere"},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.seppur.2016.11.072","article-title":"A versatile and efficient approach to separate both surfactant-stabilized water-in-oil and oil-in-water emulsions","volume":"176","author":"Li","year":"2017","journal-title":"Separ. Purif. Technol."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"e03249-16","DOI":"10.1128\/AEM.03249-16","article-title":"Transcriptomic analyses elucidate adaptive differences of closely related strains of Pseudomonas aeruginosa in fuel","volume":"83","author":"Gunasekera","year":"2017","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1007\/BF00056425","article-title":"Screening of bacteria, isolated from PAH-contaminated soils, for production of biosurfactants and bioemulsifiers","volume":"7","author":"Willumsen","year":"1996","journal-title":"Biodegradation"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1016\/j.petlm.2018.03.007","article-title":"Role of biosurfactants in bioremediation of oil pollution\u2014A review","volume":"4","author":"Karlapudi","year":"2018","journal-title":"Petroleum"},{"key":"ref_57","doi-asserted-by":"crossref","unstructured":"Zhou, T., Cai, P., Li, J., Li, Z., Dan, X., Huang, X., and Zhang, X. (2024). Whole genome analysis of intestinal source Bacillus and its effect on the prevention and control of hybrid snakehead (Channa maculata\u2640\u00d7 Channa argus\u2642) nocardiosis. Front. Mar. Sci., 11.","DOI":"10.3389\/fmars.2024.1254806"},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1128\/mBio.02079-18","article-title":"Petrobactin protects against oxidative stress and enhances sporulation efficiency in Bacillus anthracis Sterne","volume":"9","author":"Hagan","year":"2018","journal-title":"MBio"},{"key":"ref_59","first-page":"494","article-title":"Optimization of degradation of petroleum crude oil by Lysinibacillus sp. SS1 in seawater by response surface methodology","volume":"9","author":"Goveas","year":"2022","journal-title":"J. Appl. Biotechnol. Rep."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"110250","DOI":"10.1016\/j.ecoenv.2020.110250","article-title":"Transcriptome profiling reveals the molecular processes for survival of Lysinibacillus fusiformis strain 15-4 in petroleum environments","volume":"192","author":"Li","year":"2020","journal-title":"Ecotoxicol. Environ. Saf."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1007\/s00792-024-01332-8","article-title":"A novel alkane monooxygenase evolved from a broken piece of ribonucleotide reductase in Geobacillus kaustophilus HTA426 isolated from Mariana Trench","volume":"28","author":"Nithimethachoke","year":"2024","journal-title":"Extremophiles"},{"key":"ref_62","first-page":"291","article-title":"Pathways for the degradation of fatty acids in bacteria","volume":"Volume 10","author":"Rojo","year":"2017","journal-title":"Aerobic Utilization of Hydrocarbons, Oils and Lipids"},{"key":"ref_63","doi-asserted-by":"crossref","unstructured":"Su, H., and Lin, J. (2023). Biosynthesis pathways of expanding carbon chains for producing advanced biofuels. Biotechnol. Biofuels Bioprod., 16.","DOI":"10.1186\/s13068-023-02340-0"},{"key":"ref_64","doi-asserted-by":"crossref","unstructured":"Ahn, J.H., Jung, K.H., Lim, E.S., Kim, S.M., Han, S.O., and Um, Y. (2023). Recent advances in microbial production of medium- chain fatty acid from renewable carbon resources: A comprehensive review. Bioresour. Technol., 381.","DOI":"10.1016\/j.biortech.2023.129147"},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"202","DOI":"10.1016\/j.envexpbot.2017.12.016","article-title":"Rhizoremediation of petroleum hydrocarbon-contaminated soils: Improvement opportunities and field applications","volume":"147","author":"Hussain","year":"2018","journal-title":"Environ. Exp. Bot."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1016\/j.ibiod.2013.06.005","article-title":"Biodegradation of phenol in hypersaline conditions by Halomonas sp. strain PH2-2 isolated from saline soil","volume":"85","author":"Haddadi","year":"2013","journal-title":"Int. Biodeter Biodegr."},{"key":"ref_67","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":"Rehfuss","year":"2005","journal-title":"Syst. Appl. Microbiol."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"781","DOI":"10.1016\/S1004-9541(08)60002-6","article-title":"Proteome analysis of the adaptation of a phenol-degrading bacterium Acinetobacter sp. EDP3 to the variation of phenol loadings","volume":"15","author":"Anli","year":"2007","journal-title":"Chin. J. Chem. Eng."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"312","DOI":"10.1007\/s12088-011-0123-4","article-title":"Purification and characterization of catechol 1, 2-dioxygenase from Acinetobacter sp. DS002 and cloning, sequencing of partial catA gene","volume":"51","author":"Pandeeti","year":"2011","journal-title":"Indian J. Microbiol."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1146\/annurev.mi.46.100192.001425","article-title":"The electron-transport proteins of hydroxylating bacterial dioxygenases","volume":"46","author":"Mason","year":"1992","journal-title":"Annu. Rev. Microbiol."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"4232","DOI":"10.1016\/j.biortech.2010.12.067","article-title":"Analysis of bacterial degradation pathways for long-chain alkylphenols involving phenol hydroxylase, alkylphenol monooxygenase and catechol dioxygenase genes","volume":"102","author":"Tuan","year":"2011","journal-title":"Bioresour. Technol."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"568","DOI":"10.2741\/e400","article-title":"Toxicological significance of azo dye metabolism by human intestinal microbiota","volume":"4","author":"Feng","year":"2012","journal-title":"Front. Biosci. Elite Ed."},{"key":"ref_73","doi-asserted-by":"crossref","unstructured":"Srinivasan, S., Parameswari, K., and Nagaraj, S. (2020). Chapter 12-Latest innovations in bacterial degradation of textile azo dyes. Emerging Technologies in Environmental Bioremediation, Elsevier.","DOI":"10.1016\/B978-0-12-819860-5.00012-2"},{"key":"ref_74","doi-asserted-by":"crossref","unstructured":"Zafar, S., Bukhari, D.A., and Rehman, A. (2022). Azo dyes degradation by microorganisms\u2013An efficient and sustainable approach. Saudi J. Biol. Sci., 29.","DOI":"10.1016\/j.sjbs.2022.103437"},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1016\/j.jtice.2010.06.006","article-title":"Bacterial Decolorization and Degradation of Azo Dyes: A Review","volume":"42","author":"Saratale","year":"2011","journal-title":"J. Taiwan Inst. Chem. Eng."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1016\/j.chemosphere.2004.02.012","article-title":"Two stage biological treatment of a diazo reactive textile dye and the fate of the dye metabolites","volume":"56","author":"Libra","year":"2004","journal-title":"Chemosphere"},{"key":"ref_77","doi-asserted-by":"crossref","unstructured":"Fass, R., Flashner, Y., and Reuveny, S. (1999). Mineralization of Azo Dyes under Integrated Anaerobic\/Aerobic Conditions. Novel Approaches for Bioremediation of Organic Pollution, Springer.","DOI":"10.1007\/978-1-4615-4749-5"},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"956","DOI":"10.1080\/09593330.2013.856957","article-title":"Study of biodegradation and bio-decolourization of azo dye by Enterobacter sp. SXCR","volume":"35","author":"Prasad","year":"2014","journal-title":"Environ. Technol."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1016\/S0143-7208(03)00064-0","article-title":"The removal of colour from textile wastewater using whole bacterial cells: A review","volume":"58","author":"Pearce","year":"2003","journal-title":"Dyes Pigm."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"190152","DOI":"10.1098\/rsos.190152","article-title":"Comparative static and shaking culture of metabolite derived from methyl red degradation by Lysinibacillus fusiformis strain W1B6","volume":"6","author":"Sari","year":"2019","journal-title":"R. Soc. Open Sci."},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"5267","DOI":"10.1007\/s12010-023-04425-w","article-title":"Biodegradation of Congo red dye using Lysinibacillus species in a moving bed biofilm reactor: Continuous study and kinetic evaluation","volume":"195","author":"Maurya","year":"2023","journal-title":"Appl. Biochem. Biotechnol."},{"key":"ref_82","doi-asserted-by":"crossref","unstructured":"Santhanarajan, A.E., Rhee, C., Sul, W.J., Yoo, K., Seong, H.J., Kim, H.G., and Koh, S.C. (2022). Transcriptomic analysis of degradative pathways for azo dye acid blue 113 in Sphingomonas melonis B-2 from the dye wastewater treatment process. Microorganisms, 10.","DOI":"10.3390\/microorganisms10020438"},{"key":"ref_83","doi-asserted-by":"crossref","unstructured":"Meier-Kolthoff, J.P., Auch, A.F., Klenk, H.P., and G\u00f6ker, M. (2013). Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform., 14.","DOI":"10.1186\/1471-2105-14-60"},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1099\/ijs.0.64483-0","article-title":"DNA-DNA hybridization values and their relationship to whole genome sequence similarities","volume":"57","author":"Goris","year":"2007","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"576","DOI":"10.3390\/genes3040576","article-title":"Genome Sequence of Azospirillum brasilense CBG497 and comparative analyses of Azospirillum core and accessory genomes provide insight into niche adaptation","volume":"3","author":"Lozano","year":"2012","journal-title":"Genes"},{"key":"ref_86","doi-asserted-by":"crossref","unstructured":"Ku, Y.S., Wang, Z., Duan, S., and Lam, H.M. (2021). Rhizospheric communication through mobile genetic element transfers for the regulation of microbe\u2013plant interactions. Biology, 10.","DOI":"10.3390\/biology10060477"},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"e00162-16","DOI":"10.1128\/mSystems.00162-16","article-title":"Balance trees reveal microbial niche differentiation","volume":"2","author":"Morton","year":"2017","journal-title":"MSystems"},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"1653","DOI":"10.1038\/ismej.2012.22","article-title":"Stochastic and deterministic assembly processes in subsurface microbial communities","volume":"6","author":"Stegen","year":"2012","journal-title":"ISME J."},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"2855","DOI":"10.1128\/JB.184.11.2855-2856.2002","article-title":"Evolving insights: Symbiosis islands and horizontal gene transfer","volume":"184","author":"Finan","year":"2002","journal-title":"J. Bacteriol."},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"1251","DOI":"10.1111\/j.1600-0706.2011.19964.x","article-title":"The importance of plant\u2013soil interactions, soil nutrients, and plant life history traits for the temporal dynamics of Jacobaea vulgaris in a chronosequence of old-fields","volume":"121","author":"Bezemer","year":"2012","journal-title":"Oikos"},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1002\/ecy.1670","article-title":"Low- abundant soil bacteria can be metabolically versatile and fast growing","volume":"98","author":"Kurm","year":"2017","journal-title":"Ecology"},{"key":"ref_92","doi-asserted-by":"crossref","unstructured":"Meena, V., Mishra, P., Bisht, J., and Pattanayak, A. (2017). Horizontal gene transfer in soil and the rhizosphere: Impact on ecological fitness of bacteria. Agriculturally Important Microbes for Sustainable Agriculture, Springer.","DOI":"10.1007\/978-981-10-5343-6"},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1016\/j.tig.2011.01.005","article-title":"Horizontal gene transfer between bacteria and animals","volume":"27","author":"Hotopp","year":"2011","journal-title":"Trends Genet."},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"12112","DOI":"10.1073\/pnas.0503654102","article-title":"Bacterial genome size reduction by experimental evolution","volume":"102","author":"Nilsson","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_95","doi-asserted-by":"crossref","unstructured":"Koskiniemi, S., Sun, S., Berg, O.G., and Andersson, D.I. (2012). Selection-driven gene loss in bacteria. PLoS Genet., 8.","DOI":"10.1371\/journal.pgen.1002787"},{"key":"ref_96","doi-asserted-by":"crossref","unstructured":"Dufresne, A., Garczarek, L., and Partensky, F. (2005). Accelerated evolution associated with genome reduction in free-living prokaryote. Genome Biol., 6.","DOI":"10.1186\/gb-2005-6-2-r14"}],"container-title":["Microorganisms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2607\/12\/11\/2377\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T16:36:05Z","timestamp":1760114165000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2607\/12\/11\/2377"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,11,20]]},"references-count":96,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2024,11]]}},"alternative-id":["microorganisms12112377"],"URL":"https:\/\/doi.org\/10.3390\/microorganisms12112377","relation":{},"ISSN":["2076-2607"],"issn-type":[{"value":"2076-2607","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,11,20]]}}}