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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. (2010). Bioremediation of soils contaminated with polycyclic aromatic hydrocarbons, petroleum, pesticides, chlorophenols and heavy metals by composting: applications, microbes and future research needs. Genome Biol. (2017) utilized a defined co-culture of an indigenous bacterial consortium and exogenous Bacillus subtilis to effectively accelerate the degradation of crude oil. Phylogenetic analysis of long-chain hydrocarbon-degrading bacteria and Petroleum oil is an important strategic resource for which all countries compete fiercely (Sun, 2009). Asgard archaea capable of anaerobic hydrocarbon cycling. Nature 601, 257262 (2022). The mass error for all mass peaks shown here are < 5 p.p.m. Effect of hydrocarbon pollution on the microbial properties of a sandy and a clay soil. Megharaj M., Ramakrishnan B., Venkateswarlu K., Sethunathan N., Naidu R. (2011). petroleum hydrocarbon-degrading bacteria, petroleum oil, bioremediation, bacterial consortia, environmental factors, enzymes. 3 Phylogenetic analyses of MAGs and 16S rRNA gene sequences of Ca. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Letunic, I. For MAG- derived sequences source information is given: i.e., T55 indicates temperature of the culture (55C) and after the MAGs (bin) number the substrate used is indicated (e.g., n-hexadecane). Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Rabus, R. et al. Dez S., Jover E., Bayona J. M., Albaigs J. PubMed Central Diversity, ecology and evolution of Archaea. Hyatt, D. et al. designed research. Appl. (2007). 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). Wasmund K., Burns K. A., Kurtbke D. I., Bourne D. G. (2009). (2017). Mol. Asphaltenes biodegradation under shaking and static conditions. Biotechnol. 11, 28642868 (2017). A large amount of bacterial species with petroleum hydrocarbon-degrading ability have been exploited and applied in bioremediation. 4, 603613 (2019). Open Access Curr. Provided by the Springer Nature SharedIt content-sharing initiative. and M.L. Preferential degradation of long-chain alkyl substituted hydrocarbons in heavy oil under methanogenic conditions. (2003) reported that up to 75% of the hydrocarbon contaminants were degraded within 1 year in field tests by controlling and regulating aeration. Characterization of cyclohexane and hexane degradation by Rhodococcus sp. Introduction The demand and utilization of petroleum-derived hydrocarbon products lead to the contamination of environments such as air, water, and soil. Introduction Global daily oil consumption was over 100 million barrels in 2019, with large amounts of accidental leakage petroleum entering the environment ( Bamgbose and Anderson, 2020, Fahd et al., 2020 ). Behav. High efficiency degradation of alkanes and crude oil by a salt-tolerant bacterium Dietzia species CN-3. Microbiol. From rare to dominant: a fine-tuned soil bacterial bloom during petroleum hydrocarbon bioremediation. Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper. Reconstructing metabolic pathways of hydrocarbon-degrading bacteria from the Deepwater Horizon oil spill. A large-scale evaluation of algorithms to calculate average nucleotide identity. Sign up for the Nature Briefing newsletter what matters in science, free to your inbox daily. Head, I. M., Jones, D. M. & Rling, W. F. M. Marine microorganisms make a meal of oil. Syst. 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). Inakollu S., Hung H. C., Shreve G. S. (2004). PubMedGoogle Scholar. Google Scholar. In a laboratory study, the petroleum hydrocarbons phenanthrene and dibenzothiophenes were well degraded, but similar degradation effects did not occur in a field experiment, which could be attributed to the temperature range during the study (Rling et al., 2002, 2004). Evol. Nature 568, 108111 (2019). This review covers an overview of common hydrocarbon pollutants, microbes known as hydrocarbon degraders, major pathways and enzymes involved therein, factors affecting hydrocarbon. ADS PubMed Central Nucleic Acids Res. Federal government websites often end in .gov or .mil. Aydin, O. Wickham, H. ggplot2. The estimates of reported methane production rates base on the time interval for the formation of 5% and 90% of the maximum methane formation. 7 Identification of coenzyme M derivatives in cultures by HPLC-MS/MS based on the corresponding retention times. Uptake and trans-membrane transport of petroleum hydrocarbons by microorganisms. Enzymes and genes involved in aerobic alkane degradation Eur. Although people are becoming increasingly concerned about the toxic effects of oil pollution on humans and animals in affected areas, (Dez et al., 2007; Mason et al., 2012), the strong toxic impacts of petroleum hydrocarbons on affected microbial communities are often overlooked (Rivers et al., 2013; Overholt et al., 2015). Systematic adsorption process of petroleum hydrocarbon by immobilised (2015) constructed a halotolerant Hydrocarbon Utilizing Bacterial Consortium (HUBC) consisting of the bacterial isolates Ochrobactrum sp., Stenotrophomonas maltophilia and Pseudomonas aeruginosa that was found to be good at degrading crude oil (3% v/v), with a degradation percentage as high as 83.49%. PeerJ 7, e7359 (2019). 10281049 (Springer, 2006). Biol. Cheng, L. et al. Standard appears in black primary anions and second anions (produced by fragmentation) detected in hexadecane and eicosane cultures showed the same retention time as the synthetic standards of hexadecyl-CoM and eicosyl-CoM, respectively. 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). Appl Environ . A variety of hydrocarbon-degrading consortia were obtained from hydrothermal samples collected at the aforementioned sites after low-temperature enrichment under high hydrostatic pressures, and. PubMed J. Mol. Wang C., Liu X., Guo J., Lv Y., Li Y. Chaerun S. K., Tazaki K., Asada R., Kogure K. (2004). & Minh, B. Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Breese, K., Boll, M., AltMrbe, J., Schgger, H. & Fuchs, G. Genes coding for the benzoylCoA pathway of anaerobic aromatic metabolism in the bacterium Thauera aromatica. Biodegradation of marine oil spill residues using aboriginal bacterial consortium based on Penglai 19-3 oil spill accident. Bryant, M. Commentary on the Hungate technique for culture of anaerobic bacteria. Factors Affecting the Hydrocarbon Degradation by Microorganisms References The structure of hydrocarbon (HC) compounds consists of hydrogen and carbon. Bioremediation of polycyclic aromatic hydrocarbons by. M. whitmanii; Cluster 4 (C4): Ca. Margesin R., Labb D., Schinner F., Greer C. W., Whyte L. G. (2003). CAS 5, 887900 (2020). Non-syntrophic methanogenic hydrocarbon degradation by an - Nature This study was supported by National Natural Science Foundation of China (nos 92051108, 91851105, 41802179, 31970066, 31570009 and 31970105), Agricultural Science and Technology Innovation Project of the Chinese Academy of Agriculture Science (no. J. Bacteriol. ASM. Anaerobic hydrocarbon degradation in candidate phylum Atribacteria (JS1) inferred from genomics. Although some bacteria have been reported to have a broad spectrum of petroleum hydrocarbon degradation ability, Dietzia sp. Incubation experiments with different substrates and mass spectrometric detection of coenzyme-M-bound intermediates confirm that Ca. Due to the hydrophobicities and low water solubilities of most petroleum hydrocarbons, the biodegradation rate is generally limited in the environment. (2002). Current state of knowledge in microbial degradation of polycyclic aromatic hydrocarbons (PAHs): a review. Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea. (2012). Other indicates the sum of groups with relative abundance < 1%. Many environmental factors such as temperature, nutrients, electron acceptors and substrates play vital roles in bioremediation and influence biodegradation reactions (Varjani and Upasani, 2017). As a library, NLM provides access to scientific literature. Front. Cheng, L. et al. Zhukov D. V., Murygina V. P., Kalyuzhnyi S. V. (2007). The vast majority of indoor studies are focused on the degradation of a single substrate, but in nature the components of petroleum hydrocarbon pollutants are extremely complex. In the meantime, to ensure continued support, we are displaying the site without styles d, Relative abundance of main archaeal groups determined by 16S rRNA gene sequencing with archaeal primer set Arch519F/Arch915R. WL, ST, WW, QQ, PJ, XG, FL, and HL contributed to the collection of literatures and summarization. PLoS ONE 13, e0197184 (2018). Seitz, K. W. et al. Nucleic Acids Res. There is no full clarity though on what, in the absence of petroleum, their natural niches are. Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill. Biodegradation of selected hydrocarbons by novel bacterial - Nature Taken together, these studies indicate that improving the biodegradation potential via the application of bacterial consortia possessing multiple catabolic genes is a reasonable and feasible strategy for accelerating the removal efficiency of petroleum hydrocarbons from contaminated environments. 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., 2010; Kleindienst et al., 2015a). M. widdelii; Cluster 3 (C3): Ca. Head I. M., Jones D. M., Rling W. F. (2006). Environ. Laso Prez, R. et al. 25, 13241328 (1972). Bacterial community dynamics and hydrocarbon degradation during a field-scale evaluation of bioremediation on a mudflat beach contaminated with buried oil. Indeed, most bacteria can only effectively degrade or utilize certain petroleum hydrocarbon components, while others are completely unavailable (Chaerun et al., 2004; Varjani, 2017). 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. Here we cultured Ca. Z.Z. 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. 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. The addition of fertilizers containing bioavailable nitrogen and phosphorus has been successfully applied to stimulate petroleum oil biodegradation on a number of different shorelines and sandy beaches (Rling et al., 2002; Hazen et al., 2016). Mendler, K. et al. A novel method for the synergistic remediation of oil-water mixtures using nanoparticles and oil-degrading bacteria. HHS Vulnerability Disclosure, Help (2017). A., Gutierrez T., Seitz K. W., Teske A. P., Baker B. J. 38, 10791086 (2020). Biodegradation of phenanthrene by biodemulsifier-producing strain Achromobacter sp. mBio 11, e00600-20 (2020). The residual R- describes a methyl-, cyclohexane- or aromatic unit with an alkyl chain CnH2n+1 for n 13. They are the major source of energy for transportation, industries, and household purposes. Many isolated bacteria possess the ability to mineralize chemically simple petroleum hydrocarbons completely, such as linear alkanes, as long as these bacteria possess all of the enzymes for the targeted substrate (Head et al., 2006; Seth-Smith, 2010; Margesin et al., 2013). 41, D590D596 (2012). Scale bars in all images are 10 m. However, bacteria have evolved countermeasures against petroleum contaminants, such as improving the adhesion ability of cells by altering their surface components and secreting bioemulsifier to enhance their access to target hydrocarbon substrates. Yoon, S. H., Ha, S. M., Lim, J., Kwon, S. & Chun, J. 26, 528 (2016). (2007). Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. van Dorst J., Siciliano S. D., Winsley T., Snape I., Ferrari B. C. (2014). Google Scholar. Ayed H. B., Jemil N., Maalej H., Bayoudh A., Hmidet N., Nasri M. (2015). Methane production from coal by a single methanogen. d-f, Visualization of Ca. The core element of bioremediation is functional microorganisms that need sufficient nutrients and suitable environmental conditions. (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. A Comprehensive Review of Aliphatic Hydrocarbon Biodegradation by Bacteria Langmead, B. Microbiol. Nat. Labud et al. Hug, L. A. et al. Two samples were taken for cultures with n-hexadecane addition (Hex.) Characterization of bacterial isolates from industrial wastewater according to probable modes of hexadecane uptake. https://doi.org/10.1038/s41586-021-04235-2, DOI: https://doi.org/10.1038/s41586-021-04235-2. Fimbriae present on bacterial surfaces were confirmed to be necessary for the growth of Acinetobacter sp. Microbial biodegradation is the use of bioremediation and biotransformation methods to harness the naturally occurring ability of microbial xenobiotic metabolism to degrade, transform or accumulate environmental pollutants, including hydrocarbons (e.g. Nature 431, 291294 (2004). 2015 ). Geochem. CAS Tao et al. In order to effectively control petroleum hydrocarbon pollution by immobilisation technology, it is necessary to understanding the degradation pathways of petroleum hydrocarbon in immobilised petroleum-degradation bacteria system. The https:// ensures that you are connecting to the PubMed Central This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). Ludwig, W. et al. Tremblay J., Yergeau E., Fortin N., Cobanli S., Elias M., King T. L., et al. BMC Bioinform. It is estimated that approximately 150 g of nitrogen and 30 g of phosphorous are consumed to convert 1 kg of hydrocarbons in bacterial cells (Ron and Rosenberg, 2014). PubMed Central Jahromi H., Fazaelipoor M. H., Ayatollahi S., Niazi A. Google Scholar. Biodegradation by natural populations of microorganisms represents one of the primary mechanisms by which petroleum and other hydrocarbon pollutants can be removed from the environment [ 6] and is cheaper than other remediation technologies [ 7 ]. Nature thanks Guillaume Borrel, Rudolph Thauer and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. The letters for candidate genes of Ca. Characterization of a CYP153 alkane hydroxylase gene in a gram-positive Dietzia sp. (2016). Rling W. F., Milner M. G., Jones D. M., Lee K., Daniel F., Swannell R. J., et al. ADS The aerobic bacteria use different types of oxygenases, including monooxygenase, cytochrome-dependent oxygenase and dioxygenase, to insert one or two atoms of oxygen into their targets. 10, 1822 (2019). Appl. Kopylova, E., No, L. & Touzet, H. SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Extensive laboratory and field studies have been devoted to solving this problem. (2008). Nine natural PAHs-degrading bacteria were obtained from polluted areas.
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