B., Kuyukina M. S., Krivoruchko A. V., Elkin A. and L.C. Antonie Van Leeuwenhoek 110, 12811286 (2017). From rare to dominant: a fine-tuned soil bacterial bloom during petroleum hydrocarbon bioremediation. How microorganisms use hydrophobicity and what does this mean for human needs? Using dispersants after oil spills: impacts on the composition and activity of microbial communities. 23, 530541 (2020). was funded by DFG under Germanys Excellence Strategy-EXC-2077-390741603 and the Max Planck Society. J. Clin. (2015). Methanolliviera. Prestige oil spill. Mago, T. & Salzberg, S. L. FLASH: fast length adjustment of short reads to improve genome assemblies. Therefore, it is necessary to establish a database of petroleum hydrocarbon pollutants and bioemulsifier-producing bacteria which is conducive to the targeted selection of suitable bacteria to treat with petroleum hydrocarbons. performed oil analysis. A. et al. Sci. 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 . Petroleum hydrocarbon-degrading bacteria and their preferred degradation substrates. contributed to high biodegradation efficiency (89%) in a 365-day treatment of diesel oil-contaminated soil (Szulc et al., 2014). Moreover, petroleum hydrocarbons are completely mineralized into carbon dioxide and water under the action of various microbes, although bioremediation is time-consuming. Methanoliparum. 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). Wang X. Reconstructing metabolic pathways of hydrocarbon-degrading bacteria Abbasian F., Lockington R., Mallavarapu M., Naidu R. (2015). Biodegradation of hydrocarbons from contaminated soils by microbial Further details are provided in Supplementary Table 13. Download .nbib (2018). FOIA CAS Ivshina I. Bioinform. 2015 ). Bioinformatics 30, 21142120 (2014). Open Access articles citing this article. Unfortunately, the releasing of hydrocarbon contaminants into the soil naturally or anthropologically affects both biotic and abiotic components of ecosystems [ 1 ]. Methanoliparum thrives not only on a variety of long-chain alkanes, but also on n-alkylcyclohexanes and n-alkylbenzenes with long n-alkyl (C13) moieties. Borrel, G. et al. Chemical dispersants enhance the activity of oil-and gas condensate-degrading marine bacteria. Branched hydrocarbons and cyclic hydrocarbons are also degraded by bacteria. Nat. Lastly, assembled metagenomes assign the degradation potential to . For example, the Deep Water Horizon oil spill accident in the Gulf of Mexico produced a profound impact on the economy and environmental safety, which is still the focus of peoples attention (Xue et al., 2015). official website and that any information you provide is encrypted Aydin, O. Preprint at https://arxiv.org/abs/1303.3997 (2013). 2 Epifluorescence micrographs of different community members of the oily sludge. Characterization of the phenanthrene degradation-related genes and degrading ability of a newly isolated copper-tolerant bacterium. 8, 494 (2017). 10281049 (Springer, 2006). Appl. Ma, T.-T. et al. A new look on factors affecting microbial degradation of petroleum hydrocarbon pollutants. Supplementary Figs. Proc. Rling W. F., Milner M. G., Jones D. M., Fratepietro F., Swannell R. P., Daniel F., et al. open access Abstract Oil contamination is a worldwide concern now. Chaumeil, P.-A., Mussig, A. J., Hugenholtz, P. & Parks, D. H. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. (1983) investigated the toxicity of naphthalene, 1-methylnaphthalene, and 2-methylnaphthalene as well as their oxygenated derivatives to bacterial cells of Agmenellum quadruplicatum, and found that these compounds produced no significant inhibitory effects on bacterial growth. In addition, there is no time to screen for indigenous bacteria or flora in contaminated accident zones, and the application of exogenous bacteria requires scientific assessment, government approval, etc., all of which will consume time (Ivshina et al., 2015). Hydrocarbon Degradation Samina Siddiqui & Asghari Bano Chapter First Online: 09 February 2019 1197 Accesses 2 Citations Abstract Bioremediation involved the use of microbes to degrade petroleum hydrocarbons. Systematic adsorption process of petroleum hydrocarbon by immobilised Gunter Wegener, Meng Li or Lei Cheng. Obuekwe C. O., Al-Jadi Z. K., Al-Saleh E. S. (2009). Several studies have also reported that certain metabolic intermediates with relatively high solubility produced from the degradation of petroleum hydrocarbons by bacteria may have higher cytotoxicity than the parent molecules and therefore damage the bacteria (Hou et al., 2018). 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). Progressive degradation of crude oil n-alkanes coupled to methane production under mesophilic and thermophilic conditions. The key components of bacterial degradation of petroleum hydrocarbons are various specific enzymes (Wasmund et al., 2009; Varjani, 2017). Provided by the Springer Nature SharedIt content-sharing initiative. Novel alkane hydroxylase gene (alkB) diversity in sediments associated with hydrocarbon seeps in the Timor Sea. Microbiol. Biodegradation of crude oil by nitrogen fixing marine bacteria. DQ12-45-1b and its team role with alkw1 in alkane degradation. Bioremediation potential of hydrocarbon-utilizing fungi from select Anaerobic hydrocarbon degradation in candidate phylum Atribacteria (JS1) inferred from genomics. 20 October 2022, Access Nature and 54 other Nature Portfolio journals, Get Nature+, our best-value online-access subscription, Receive 51 print issues and online access, Get just this article for as long as you need it, Prices may be subject to local taxes which are calculated during checkout. Ron and Rosenberg (2014) found that adherence of hydrophobic pollutants to bacterial cells is mainly related to hydrophobic fimbriae, fibrils, outer-membrane proteins and lipids, as well as certain small molecules present in cell surfaces such as gramicidin S and prodigiosin. Wickham, H. ggplot2. Bacosa H. P., Erdner D. L., Rosenheim B. E., Shetty P., Seitz K. W., Baker B. J., et al. Biotechnol. Margesin R., Labb D., Schinner F., Greer C. W., Whyte L. G. (2003). Liu S., Guo C., Liang X., Wu F., Dang Z. L.C. Synergistic ex-situ biodegradation of crude oil by halotolerant bacterial consortium of indigenous strains isolated from on shore sites of Gujarat. Wang C. et al. 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. This can be attributed to the fact that different indigenous bacteria have different catalytic enzymes; thus, their roles in oil-contaminated sites also vary widely. Extended Data Fig. 114, 5780 (2017). Nat. JCYJ20200109105010363), the Fundamental Research Funds for the Central Universities (LZUJBKY-2021-KB16), the Central Public-interest Scientific Institution Basal Research Fund (Y2021PT02, Y2021XK06). 56, 19191925 (1990). Biotechnol. Chen M., Xu P., Zeng G., Yang C., Huang D., Zhang J. Contribution of the hydrophobic effect to microbial infection. Oldenburg, T. B. P. et al. Mukherjee A. K., Bhagowati P., Biswa B. Aquatic Chemistry: Chemical Equilibria and Rates in Natural Waters (Wiley, 1996). 5 Gene clusters associated with the alkane degradation and methanogenesis pathways detected in the representative MAGs of the four Ca. 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. 4, e1000069 (2008). The site is secure. PDF New Way to Implement Hydrocarbon degradation in Soil Through Bioremediation It is concluded as follows: (1) Continue the theoretical basis of the interfacial interaction mechanism between bacteria and petroleum hydrocarbons in order to overcome barriers for microbial uptake of petroleum hydrocarbons, (2) develop novel biocompatible surfactants to enhance contact between bacteria and petroleum hydrocarbons, (3) explore undiscovered resources of petroleum hydrocarbon-degrading bacteria via new biotechnology, such as a high-throughput screening method to increase and enrich functional bacterial resources, (4) further optimize the strategy of artificial microbial consortia, such as by way of the metagenome enrichment approach to enrich and develop preferable consortia, (5) explore the novel functional genes controlling the pathway of hydrocarbon degradation to provide new looks on the molecular mechanism and microbial remediation, and (6) construct genetically engineered bacteria by using synthetic biology technology to give them more ability for petroleum hydrocarbon degradation. 1Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China, 2Hinggan League Academy of Agriculture and Animal Husbandry, Ulanhot, China, 3School of Life Science and Technology, Changchun University of Science and Technology, Changchun, China. A case study of bioremediation of petroleum-hydrocarbon contaminated soil at a crude oil spill site. (2021). In diesel exposure experiments, researchers found that the primary effects of diesel fuel toxicity were reductions in species richness, evenness and phylogenetic diversity, with the resulting community being heavily dominated by a few species, principally Pseudomonas. Overholt W. A., Marks K. P., Romero I. C., Hollander D. J., Snell T. W., Kostka J. E. (2015). and transmitted securely. 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). Methanoliparum MAGs retrieved in the present studied. Soluble and non-soluble nutrients suffer from problems in the actual remediation, leading to low bioremediation efficiencies (Ron and Rosenberg, 2014). Petroleum degradation Coastal wetlands Oil sludge Sulfate-reducing bacteria Denitrifying bacteria Metal-reducing bacteria 1. Anaerobic degradation of paraffins by thermophilic Actinobacteria under methanogenic conditions. Google Scholar. Numbers in parenthesis indicate the number of acrA/mcrA sequences detected in the different metagenomes. Mol. This paper provides an overview of the recent literature referring to the usage of bacteria as biodegraders, discusses barriers regarding the implementation of this microbial technology, and provides suggestions for further developments. This also implies that the remediation of petroleum hydrocarbon contamination requires the joint action of multiple functional bacteria to achieve the best environmental purification effect (Dombrowski et al., 2016). Sci. All three bacteria were able to use petroleum hydrocarbons as the sole carbon source during in vitro degradation assays. Microbial degradation of resins fractionated from Arabian light crude oil. Jones, D. M. et al. 2020KCXTD023) and the Shenzhen Science and Technology Program (no. It is well known that the growth of bacteria requires sufficient carbon, hydrogen, oxygen, nitrogen, sulfur, phosphorus, and various trace elements. Laso-Prez, R. et al. Extremely high levels of petroleum hydrocarbons strongly inhibit bacterial growth, resulting in poor biodegradation efficiency and even death of the bacteria (Ma et al., 2015). & Amann, R. Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria. Microbiol. Funding. CAS Methanoliparum with the general archaeal probe and the specific DC06-660Mlp probe. Characterization of bacterial isolates from industrial wastewater according to probable modes of hexadecane uptake. Ma Y. L., Lu W., Wan L. L., Luo N. (2015). Evol. Google Scholar. Mechanisms of membrane toxicity of hydrocarbons. Google Scholar. Article However, recent culture-independent studies have suggested that the archaeon Candidatus Methanoliparum alone can combine the degradation of long-chain alkanes with methanogenesis4,5. Methanoliparum cultures at 55C. Influence of adhesion on aerobic biodegradation and bioremediation of liquid hydrocarbons. Abbasnezhad H., Gray M., Foght J. M. (2011). Trees were constructed by using IQ-TREE with the parameters -m WAG, -bb 1000, with bootstrap values >0.95 shown in grey dots. Methanoliparum (green) and archaea (red). Mendler, K. et al. 14, 754764 (2012). While in the substrate mixtures, toluene and benzene enhance the biodegradation of phenol; however, phenol inhibits the biodegradation of benzene and toluene (Abuhamed et al., 2004). and L.-p.B. Fuentes S., Barra B., Caporaso J. G., Seeger M. (2015). nov., a novel hydrocarbonoclastic marine bacterium isolated from Antarctic coastal sea water. Indeed, whether various biosurfactants stimulate or inhibit the bioremediation of pollutants is dependent on the physico-chemical properties of the surfactants, types of pollutants and physiological characteristics of the functional microorganisms (Hua and Wang, 2014). R.L.-P. was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germanys Excellence Strategy (EXC-2077-390741603) via Excellence Chair Victoria Orphan. Hydrocarbon degrading bacteria exhibit a species specific response to dispersed oil while moderating ecotoxicity. A Comprehensive Review of Aliphatic Hydrocarbon Biodegradation by Bacteria Wanapaisan P., Laothamteep N., Vejarano F., Chakraborty J., Shintani M., Muangchinda C., et al. mBio 10, e01814-19 (2019). CAS Combining stable carbon isotope analysis and petroleum-fingerprinting to evaluate petroleum contamination in the Yanchang oilfield located on loess plateau in China. (2017). Microbial biodegradation Non-syntrophic methanogenic hydrocarbon degradation by an archaeal species. d-i, QE Plus-Orbitrap MS analyses of cultures supplemented with a mixture of n-docosane (C22H46), n-hexadecyl benzene (C22H38) and n-hexadecyl cyclohexane (C22H44) as substrates, and detection of d and e docosyl-CoM (C24H49S2O3, m/z=449.31134) with the fragment C22H45S (m/z=341.32495); of f and g n-hexadecyl benzene coenzyme M (C24H41S2O3, m/z=441.25064) with the predicted fragment C22H37S (m/z=333.26212) and of h and i n-hexadecyl cyclohexane CoM (C24H47S2O3, m/z=447.29730) with the fragment C22H43S (m/z=339.30939). 7 Identification of coenzyme M derivatives in cultures by HPLC-MS/MS based on the corresponding retention times. Although bacterial adherence can enhance the biodegradation of hydrophobic hydrocarbons, it is not necessary to attach bacterial cells to targeted substrates (Abbasnezhad et al., 2011). Appl Environ . (2018). Gurav R., Lyu H., Ma J., Tang J., Liu Q., Zhang H. (2017). Nurk, S., Meleshko, D., Korobeynikov, A. 8600 Rockville Pike These species are called hydrocarbonoclastic bacteria (HCB), and they play a key role in the removal of hydrocarbons from polluted and non-polluted environments ( Harayama et al., 2004; Head et al., 2006; Yakimov et al., 2007; Wang et al., 2010a, b ). Kasai Y., Kishira H., Harayama S. (2002). Kleindienst S., Paul J. H., Joye S. B. Edited by: Mariusz Cyco, Medical University of Silesia, Poland, Reviewed by: Eric D. van Hullebusch, UMR7154 Institut de Physique du Globe de Paris (IPGP), France; Kazuhiro Mori, University of Yamanashi, Japan, This article was submitted to Microbiotechnology, Ecotoxicology and Bioremediation, a section of the journal Frontiers in Microbiology. Bacterial community dynamics and hydrocarbon degradation during a field-scale evaluation of bioremediation on a mudflat beach contaminated with buried oil. During petroleum production, storage and transportation, refining and processing, as well as spills and discharges of petroleum hydrocarbons often occur as a result of blowout accidents during oilfield development, leakage from oil pipelines and storage tanks, oil tanker and tanker leakage accidents, oil well waxing, and during overhauls of refineries and petrochemical production equipment (Chaerun et al., 2004; Chen et al., 2015; Wang C. et al., 2018). Sarkar P., Roy A., Pal S., Mohapatra B., Kazy S. K., Maiti M. K., et al. (2003). Biofuels 10, 207 (2017). Langmead, B. Geochem. Article Bacteria with such functions are often screened for use as environmental remediation agents, accelerating the removal of petroleum hydrocarbon pollutants from the environment (Kaczorek et al., 2012; Krasowska and Sigler, 2014). However, the phenolic and quinonic naphthalene derivatives inhibited bacterial growth. PLoSComput. PubMed 32, 13631371 (2004). Reconstructing metabolic pathways of hydrocarbon-degrading bacteria from the Deepwater Horizon oil spill. b and c, Abundance of 16S rRNA gene of Ca. Dombrowski N., Donaho J. Bathyarchaeota set as outgroup. Factors Affecting the Hydrocarbon Degradation by Microorganisms References The structure of hydrocarbon (HC) compounds consists of hydrogen and carbon. A., Poolman B. Methanoliparum contains and overexpresses genes encoding alkyl-coenzyme M reductases and methyl-coenzyme M reductases, the marker genes for archaeal multicarbon alkane and methane metabolism. 196, 22102215 (2014). Biol. Bioremediation potential of hydrocarbon degrading bacteria: isolation Egland, P. G., Pelletier, D. A., Dispensa, M., Gibson, J. To enhance the bioavailability of petroleum hydrocarbons, one promising approach is the application of surfactants (Kleindienst et al., 2015a), which may enhance dissolution or desorption rates leading to the solubilization or emulsification of petroleum hydrocarbon pollutants (Varjani and Upasani, 2017). Open Access Diversity, ecology and evolution of Archaea. Borrel, G. et al. 4 was the fitting result. Anaerobic degradation of non-methane alkanes by Candidatus Methanoliparia in hydrocarbon seeps of the Gulf of Mexico. A large amount of bacterial species with petroleum hydrocarbon-degrading ability have been exploited and applied in bioremediation. (2007). J. Biochem. Kanehisa, M., Sato, Y. Cheng, L. et al. Nature 431, 291294 (2004). Methanoliparum species. Hedlund B. P., Geiselbrecht A. D., Bair T. J., Staley J. T. (1999). (2007) reported that petroleum hydrocarbons inhibited microbial biomass, and that the greatest negative effects were observed in the gasoline-polluted sandy soil. Biodegradation of petroleum hydrocarbons by oleophilic strain of. Accordingly, it is difficult to reproduce laboratory results in practical applications. Wang Y., Liang J., Wang J., Gao S. (2018). (2013). However, various problems that slow down biodegradation effects have been found during the process of practical application. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. PLoS ONE 8, e66784 (2013). Destruction and production of high molecular weight non-hydrocarbon species and destruction of aromatic hydrocarbons during progressive in-reservoir biodegradation. Marine microorganisms make a meal of oil. Grey cells indicate that the corresponding genes were not found in the MAGs. Methanoliparum (red) with the genes involved in benzoyl-CoA degradation in the model organisms Thauera aromatica (green) and Rhodopseudomonas palustris (blue). (1995). Boyd, J. 1. The degradation rate of petroleum hydrocarbon in the actual environment is the result of these factors acting on the petroleum hydrocarbon-degradation bacteria, which has led to most microbial remediation technologies taking a long time, especially when compared to physico-chemical remediation techniques. For instance, some bacteria can metabolize specific alkanes, while others break down aromatic or resin fractions of hydrocarbons. (2017). Researchers found that these five bacteria showed synergistic pyrene degradation due to the following aspects: (1) The Bacillus strain enhanced the bioavailability of the pyrene by producing biosurfactant, (2) two Mycobacterium strains contributed to the initiation of pyrene degradation, and (3) Novosphingobium and Ochrobactrum efficiently degraded the intermediates of pyrene. Hence, the present study aimed at harnessing the potential of fungi isolated from three marine niches of India, towards efficient hydrocarbon degradation and detoxification. 13, 12691279 (2019). Cerniglia C. E., Freeman J. P., Althaus J. R., van Baalen C. (1983). Given the complexity of the petroleum components, construction of the minimal functional bacterial consortium or genetic engineering bacteria for bioremediation of petroleum oil has become a trend in this field (Dvok et al., 2017). A field study showed that bioaugmentation with an artificial consortium containing Aeromonas hydrophila, Alcaligenes xylosoxidans, Gordonia sp., Pseudomonas fluorescens, Pseudomonas putida, Rhodococcus equi, S. maltophilia, and Xanthomonas sp. Nucleic Acids Res. Appl. 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 ). Here we cultured Ca. ISME J. However, recent culture-independent . Frontiers | Hydrocarbon-Degrading Bacteria Alcanivorax and Marinobacter

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