ADS Chen M., Xu P., Zeng G., Yang C., Huang D., Zhang J. ISSN 1476-4687 (online) JLS1 for enhanced degradation of C16 alkane. Development of a duplex droplet digital PCR assay for absolute quantitative detection of "Candidatus Liberibacter asiaticus". However, oil contaminated environment is enriched with microorganisms that can utilize petroleum oil and use hydrocarbon for their growth, nutrition and metabolic activities. Extended Data Fig. Yakimov M. M., Timmis K. N., Golyshin P. N. (2007). Jiang C. Y., Dong L., Zhao J. K., Hu X., Shen C., Qiao Y., et al. Biodegradation of marine oil spill residues using aboriginal bacterial consortium based on Penglai 19-3 oil spill accident. Effects of rhamnolipid on the biodegradation of n-hexadecane by microorganism and the cell surface hydrophobicity. A., Makarov S. O., Cunningham C. J., et al. Supplementary Figs. Synergistic degradation of pyrene by five culturable bacteria in a mangrove sediment-derived bacterial consortium. Tao et al. 6, 579591 (2008). ISME J. Provided by the Springer Nature SharedIt content-sharing initiative. 47, W256W259 (2019). Numbers in parenthesis indicate the number of acrA/mcrA sequences detected in the different metagenomes. & Ralf, R. in The Prokaryotes: Ecophysiology and Biochemistry Vol. Heipieper H. J., Neumann G., Cornelissen S., Meinhardt F. (2007). Prodigal: prokaryotic gene recognition and translation initiation site identification. Oil spill problems and sustainable response strategies through new technologies. (2015b). Microbial degradation of resins fractionated from Arabian light crude oil. Mayumi, D. et al. 16 and the legends for Supplementary Tables 113. Methanoliparia. and M.L. However, recent culture-independent . PubMed the contents by NLM or the National Institutes of Health. Most petroleum hydrocarbons encountered in the environment are ultimately degraded or metabolized by indigenous bacteria because of their energetic and carbon needs for growth and reproduction, as well as the requirement to relieve physiological stress caused by the presence of petroleum hydrocarbons in the microbial bulk environment (Hazen et al . Article PDF New Way to Implement Hydrocarbon degradation in Soil Through Bioremediation The asterisk (*) marking Ca. Liu S., Guo C., Liang X., Wu F., Dang Z. Methanoliparum. N. Y. Acad. Alkane degradation under anoxic conditions by a nitrate-reducing bacterium with possible involvement of the electron acceptor in substrate activation. (PDF) Microbial Degradation of Hydrocarbons - ResearchGate Bacosa H. P., Erdner D. L., Rosenheim B. E., Shetty P., Seitz K. W., Baker B. J., et al. Genome Res. For aerobic degradation processes, using oxygen as an electron acceptor is quite important, but it is usually not adequate in petroleum oil-contaminated environments because of the limited air permeability. & Amann, R. Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria. A Comprehensive Review of Aliphatic Hydrocarbon Biodegradation by Bacteria LH-1 and the study on its metabolisms and fermentation kinetics. 7 Identification of coenzyme M derivatives in cultures by HPLC-MS/MS based on the corresponding retention times. Cosmochim. Funding. Reconstructing metabolic pathways of hydrocarbon-degrading bacteria from the Deepwater Horizon oil spill. b, Genome based average Amino Acid Identity (AAI). Fate of a heavy oil in the marine environment. Aydin, O. Labud et al. Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper. Rev. Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. DQ12-45-1b utilizes n-alkanes (C6C40) and other compounds as the sole carbon sources (Wang et al., 2011) and Achromobacter xylosoxidans DN002 works well on a variety of monoaromatic and polyaromatic hydrocarbons (Ma et al., 2015), almost no bacteria can degrade the entire petroleum hydrocarbon fraction. Extended Data Fig. Article Novel alkane hydroxylase gene (alkB) diversity in sediments associated with hydrocarbon seeps in the Timor Sea. A bacterial consortium composed of five culturable bacteria has been constructed by Wanapaisan et al. Methanoliparum clusters and phylogenetic analysis of their AcrA and McrA protein sequences. 4, e1000069 (2008). Bioremediation approaches for organic pollutants: a critical perspective. Bacterial hydrocarbon contaminants degradation: A cleaner perspective PLoSComput. (2017). b, Annotations and Locus tag for the corresponding genes shown in panel a that are found in the representative MAG of Ca. Environ. 77, 52125219 (2011). Letunic, I. By comparing R 2, it was found that the petroleum hydrocarbon degradation process was more in line with the second-order kinetic model, and the R 2 value . By submitting a comment you agree to abide by our Terms and Community Guidelines. Am. The efficacy of the two-hydrocarbon degradation by the isolates bacterial was determined at a temperature of 25 C and 37 C and pH of 5.0 and 9.0. (2007). Fowler, S. J., Dong, X., Sensen, C. W., Suflita, J. M. & Gieg, L. M. Methanogenic toluene metabolism: community structure and intermediates. Reconstructing metabolic pathways of hydrocarbon-degrading bacteria 1b1d. The sources of the code and programs used for analyses are mentioned in theMethods, and are also available at GitHub (https://github.com/liupfskygre/Methanoliparum_MS_code/tree/main). Destruction and production of high molecular weight non-hydrocarbon species and destruction of aromatic hydrocarbons during progressive in-reservoir biodegradation. Google Scholar. 67, 503549 (2003). Polycyclic aromatic hydrocarbon degradation by a new marine bacterium. RAG-1, with C16 alkane as the carbon source and beneficial to bacterial adherence, assimilation hydrophobic substrates and their metabolic activity (Rosenberg and Rosenberg, 1985). However, petroleum use results in environmental deterioration (Xue et al., 2015). Oldenburg, T. B. P. et al. However, indigenous bacteria form very large aggregates, and each species has its own function. In marine animals, the oil spills and other exposure to petroleum hydrocarbons causes fluctuations in body temperature, blindness, dehydration, hypothermia, impaired digestion, liver and lung disorder (Bostrm et al., 2002, Korashy and El-Kadi, 2006; EPA, 2013; Raju and Scalvenzi, 2017 ). Bioremediation of soils contaminated with polycyclic aromatic hydrocarbons, petroleum, pesticides, chlorophenols and heavy metals by composting: applications, microbes and future research needs. Wang Y., Liang J., Wang J., Gao S. (2018). Szulc A., Ambroewicz D., Sydow M., awniczak ., Piotrowska-Cyplik A., Marecik R.et al. Nurk, S., Meleshko, D., Korobeynikov, A. & Yassikaya, M. Y. Validity and reliability analysis of the plotdigitizer software program for data extraction from single-case graphs. Science 354, 222225 (2016). designed CARD-FISH probes, and R.L.-P. performed CARD-FISH and cell visualization. This review covers an overview of common hydrocarbon pollutants, microbes known as hydrocarbon degraders, major pathways and enzymes involved therein, factors affecting hydrocarbon. III. Petroleum hydrocarbons are one of the most alarming pollutants due to their high toxicity to human and environmental health. 10, 1822 (2019). (2013). d, Identity based on the percentage of conserved proteins (POCP). Bioinformatics 25, 20782079 (2009). Solvent-tolerant bacteria for biotransformations in two-phase fermentation systems. Hazen T. C., Dubinsky E. A., DeSantis T. Z., Andersen G. L., Piceno Y. M., Singh N., et al. We thank LetPub (www.letpub.com) for its linguistic assistance during the preparation of this manuscript. Moreover, they found that the decline in richness and phylogenetic diversity was linked to the disruption of the nitrogen cycle, with species and functional genes involved in nitrification being significantly reduced (van Dorst et al., 2014). (2013). Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi. Microbiol. A large amount of bacterial species with petroleum hydrocarbon-degrading ability have been exploited and applied in bioremediation. (2018) found that an aboriginal bacterial consortium based on the Penglai 19-3 oil spill accident (China) had higher oil degradation efficiency compared to individual bacteria and demonstrated that this indigenous consortium had the potential for bioremediating crude oil dispersed in the marine ecosystem. Microbiol. Thauer, R. K. Methyl (alkyl)-coenzyme M reductases: nickel F-430-containing enzymes involved in anaerobic methane formation and in anaerobic oxidation of methane or of short chain alkanes. Mago, T. & Salzberg, S. L. FLASH: fast length adjustment of short reads to improve genome assemblies. 48, 88838900 (2020). Nat. PLoS ONE 13, e0197184 (2018). No use, distribution or reproduction is permitted which does not comply with these terms. Although some bacteria have been reported to mineralize petroleum hydrocarbons completely within several days, or even less than 1 day under culture conditions, the degradation efficiency of these bacteria makes it difficult to meet the expected effects in practical usage (Chen et al., 2017; Zheng et al., 2018). Liu, Y.-F. et al. Wiley Interdiscip. & Minh, B. Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Geochem. a, Identities of the 16S rRNA gene. In inoculated media at 37 C, Rhodococcus. WL, ST, WW, QQ, PJ, XG, FL, and HL contributed to the collection of literatures and summarization. 3 Altmetric Metrics Abstract Thirty-six bacteria that degraded long-chain hydrocarbons were isolated from natural environments using long-chain hydrocarbons (waste car engine oil, base oil or the c -alkane fraction of base oil) as the sole carbon and energy source. Methanoliparia MAGs based on the concatenated alignments of 16 ribosomal proteins67. Biodegradation of naphthalene, BTEX, and aliphatic hydrocarbons by The advantages of microbial communities are presented because there are a variety of catabolic genes in a bacterial consortium, and the synergistic effects of these genes are beneficial to achieving the purification of pollutants (Gurav et al., 2017). Van Hamme, J. D., Singh, A. Download .nbib Dez S., Jover E., Bayona J. M., Albaigs J. Uptake and trans-membrane transport of petroleum hydrocarbons by microorganisms. Aquatic Chemistry: Chemical Equilibria and Rates in Natural Waters (Wiley, 1996). Ayed et al. You are using a browser version with limited support for CSS. Ma Y. L., Lu W., Wan L. L., Luo N. (2015). Chen Y. J., Wang H. Q., Wang R., Yun Y. Biodegradation of crude oil by nitrogen fixing marine bacteria. Methods 7, 335336 (2010). Details of all copies are included in Supplementary Table 7. a and b, hexadecyl-CoM and the corresponding 3 characterized fragments (in blue) in cell extracts from cultures with hexadecane (C16H34) addition. Microbiol. Remediation of petroleum hydrocarbon-contaminated groundwater by
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