Exploitation of Potential Extremophiles for Bioremediation of Xenobiotics Compounds: A Biotechnological Approach

Author(s): Awadhesh Kumar Shukla*, Amit Kishore Singh

Journal Name: Current Genomics

Volume 21 , Issue 3 , 2020

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Graphical Abstract:


Microorganisms that are capable of live and adapt in hostile habitats of different environmental factors such as extremes temperature, salinity, nutrient availability and pressure are known as extremophiles. Exposure to xenobiotic compounds is global concern influencing the world population as a health hazard. Hence their removal is warranted using biological means that is very sustainable, potentially cost-effective and eco-friendly. Due to adaptation in extreme environments and unique defense mechanisms, they are receiving more attention for the bioremediation of the xenobiotic compounds. They possess robust enzymatic and biocatalytic systems that make them suitable for the effective removal of pollutants from the contaminated environment. Additionally, the extremophiles act as microfactories having specific genetic and biotechnological potential for the production of biomolecules. This mini review will provide an overview of microbial degradation metabolic pathways for bioremediation along with the molecular and physiological properties of diverse extremophiles from variety of habitats. Furthermore, the factors affecting the bioremediation process is also summarized.

Keywords: Extremophiles, xenobiotics, biodegradation, pollutants, extremozymes, metabolic pathway.

Torsvik, V.; Sorheim, R.; Goksoyr, J. Total bacterial diversity in soil and sediment communities: a review. J. Ind. Microbiol. Biotechnol., 1996, 17, 170-178.
McCaig, A.E.; Grayston, S.J.; Prosser, J.I.; Glover, L.A. Impact of cultivation on characterisation of species composition of soil bacterial communities. FEMS Microbiol. Ecol., 2001, 35(1), 37-48.
[http://dx.doi.org/10.1111/j.1574-6941.2001.tb00786.x] [PMID: 11248388]
Arulazhagan, P.; Mnif, S.; Banu, J.R.; Huda, Q.; Jalal, M.A.B. Biodegradation of hydrocarbons by extremophiles.In:Biodegradation and bioconversion of hydrocarbons, environmental footprints and eco-design of products and processes; Heimann, K., Ed.; Springer Science, Business Media Singapore, 2017.
Nikolaki, S.; Tsiamis, G. Microbial diversity in the era of omic technologies. BioMed Res. Int., 2013, 2013, 15.
Rawat, N.; Joshi, G.K. Bacterial community structure analysis of a hot spring soil by next generation sequencing of ribosomal RNA. Genomics, 2019, 111(5), 1053-1058.
[http://dx.doi.org/10.1016/j.ygeno.2018.06.008] [PMID: 31533897]
Saxena, R.; Dhakan, D.B.; Mittal, P.; Waiker, P.; Chowdhury, A.; Ghatak, A.; Sharma, V.K. Metagenomic analysis of hot springs in Central India reveals hydrocarbon degrading thermophiles and pathways essential for survival in extreme environments. Front. Microbiol., 2017, 7, 2123.
[http://dx.doi.org/10.3389/fmicb.2016.02123] [PMID: 28105025]
Rekadwad, B.; Gonzalez, J.M. New generation DNA sequencing (NGS): mining for genes and the potential of extremophiles.Microbial Applications;; V.C, Kalia.; P, Kumar., Eds.; Springer International Publishing AG. , 2017.
Burg, D.; Ng, C.; Ting, L.; Cavicchioli, R. Proteomics of extremophiles. Environ. Microbiol., 2011, 13(8), 1934-1955.
[http://dx.doi.org/10.1111/j.1462-2920.2011.02484.x] [PMID: 21518215]
Kumar, A.; Alam, A.; Tripathi, D.; Rani, M.; Khatoon, H.; Pandey, S.; Ehtesham, N.Z.; Hasnain, S.E. Protein adaptations in extremophiles: An insight into extremophilic connection of mycobacterial proteome. Semin. Cell Dev. Biol., 2018, 84, 147-157.
[http://dx.doi.org/10.1016/j.semcdb.2018.01.003] [PMID: 29331642]
Stan-Lotter, H.; Fendrihan, S. Adaption of microbial life to environmental extremes: novel research results and applications; Wien, Newyork, 2012, p. 2.
Yadav, M.; Shukla, A.K.; Srivastva, N.; Upadhyay, S.N.; Dubey, S.K. Utilization of microbial community potential for removal of chlorpyrifos: a review. Crit. Rev. Biotechnol., 2016, 36(4), 727-742.
[PMID: 25782532]
Shukla, A.K.; Upadhyay, S.N.; Dubey, S.K. Current trends in trichloroethylene biodegradation: a review. Crit. Rev. Biotechnol., 2014, 34(2), 101-114.
[http://dx.doi.org/10.3109/07388551.2012.727080] [PMID: 23057686]
Le Borgne, S.; Paniagua, D.; Vazquez-Duhalt, R. Biodegradation of organic pollutants by halophilic bacteria and archaea. J. Mol. Microbiol. Biotechnol., 2008, 15(2-3), 74-92.
[http://dx.doi.org/10.1159/000121323] [PMID: 18685264]
Hedlund, B.P.; Geiselbrecht, A.D.; Staley, J.T. Marinobacter strain NCE312 has a Pseudomonas-like naphthalene dioxygenase. FEMS Microbiol. Lett., 2001, 201(1), 47-51.
[http://dx.doi.org/10.1111/j.1574-6968.2001.tb10731.x] [PMID: 11445166]
Peeples, T.L. Bioremediation using extremophiles. Microbial Biodegradation and Bioremediation; Elsevier Inc., 2014.
Bargar, J.R.; Bernier-Latmani, R.; Giammar, D.E.; Tebo, B.M. Biogenic uraninite nanoparticles and their importance for uranium remediation. Elements, 2008, 4, 407-412.
Marques, C.R. Extremophilic microfactories: applications in metal and radionuclide bioremediation. Front. Microbiol., 2018, 9, 1191.
[http://dx.doi.org/10.3389/fmicb.2018.01191] [PMID: 29910794]
Parrilli, E.; Papa, R.; Tutino, M.L.; Sannia, G. Engineering of a psychrophilic bacterium for the bioremediation of aromatic compounds. Bioeng. Bugs, 2010, 1(3), 213-216.
[http://dx.doi.org/10.4161/bbug.1.3.11439] [PMID: 21326928]
Bertoni, G.; Bolognese, F.; Galli, E.; Barbieri, P. Cloning of the genes for and characterization of the early stages of toluene and o-xylene catabolism in Pseudomonas stutzeri OX1. Appl. Environ. Microbiol., 1996, 62(10), 3704-3711.
[http://dx.doi.org/10.1128/AEM.62.10.3704-3711.1996] [PMID: 8837426]
Siani, L.; Papa, R.; Di Donato, A.; Sannia, G. Recombinant expression of Toluene o-Xylene Monooxygenase (ToMO) from Pseudomonas stutzeri OX1 in the marine Antarctic bacterium Pseudoalteromonas haloplanktis TAC125. J. Biotechnol., 2006, 126(3), 334-341.
[http://dx.doi.org/10.1016/j.jbiotec.2006.04.027] [PMID: 16730836]
Anderson, R.T.; Vrionis, H.A.; Ortiz-Bernad, I.; Resch, C.T.; Long, P.E.; Dayvault, R.; Karp, K.; Marutzky, S.; Metzler, D.R.; Peacock, A.; White, D.C.; Lowe, M.; Lovley, D.R. Stimulating the in situ activity of Geobacter species to remove uranium from the groundwater of a uranium-contaminated aquifer. Appl. Environ. Microbiol., 2003, 69(10), 5884-5891.
[http://dx.doi.org/10.1128/AEM.69.10.5884-5891.2003] [PMID: 14532040]
Fuentes, S.; Méndez, V.; Aguila, P.; Seeger, M. Bioremediation of petroleum hydrocarbons: catabolic genes, microbial communities, and applications. Appl. Microbiol. Biotechnol., 2014, 98(11), 4781-4794.
[http://dx.doi.org/10.1007/s00253-014-5684-9] [PMID: 24691868]
Lu, X.Y.; Zhang, T.; Fang, H.H. Bacteria-mediated PAH degradation in soil and sediment. Appl. Microbiol. Biotechnol., 2011, 89(5), 1357-1371.
[http://dx.doi.org/10.1007/s00253-010-3072-7] [PMID: 21210104]
Kumar, M.; Vladimir, L.; de Sistro Materano, A.; Ilzins, O.A. A halotolerant and thermotolerant Bacillus sp. degrades hydrocarbons and produces tension active emulsifying agent. World J. Microbiol. Biotechnol., 2007, 23, 211-220.
Kuznetsov, V.D.; Zaitseva, T.A.; Vakulenko, L.V.; Filippova, S.N. Streptomyces albiaxialis sp. Nov. A new petroleum hydrocarbon degrading species of thermo and halotolerant Streptomyces. Microbiology, 1992, 61, 62-67.
Emerson, D.; Chauchan, S.; Oriel, P.; Breznak, J.A. Haloferax sp. D1227, a halophilic archaeon capable of growth on aromatic compounds. Arch. Microbiol., 1994, 161, 445-452.
Palumbo, J.; Zhou, J. Amazing Microbes., 1996.www.ornl.gov
Zvyagintseva, I.S.; Poglasova, M.N.; Gotoeva, M.T.; Belyaev, S.S. Effect of the medium salinity on oil degradation by nocardioform bacteria. Microbiology, 2001, 70, 652-656.
Piedad Díaz, M.; Grigson, S.J.W.; Peppiatt, C.J.; Burgess, J.G. Isolation and characterization of novel hydrocarbon-degrading euryhaline consortia from crude oil and mangrove sediments. Mar. Biotechnol. (NY), 2000, 2(6), 522-532.
[http://dx.doi.org/10.1007/s101260000037] [PMID: 14961176]
Díaz, M.P.; Boyd, K.G.; Grigson, S.J.W.; Burgess, J.G. Biodegradation of crude oil across a wide range of salinities by an extremely halotolerant bacterial consortium MPD-M, immobilized onto polypropylene fibers. Biotechnol. Bioeng., 2002, 79(2), 145-153.
[http://dx.doi.org/10.1002/bit.10318] [PMID: 12115430]
Fairley, D.J.; Boyd, D.R.; Sharma, N.D.; Allen, C.C.; Morgan, P.; Larkin, M.J. Aerobic metabolism of 4-hydroxybenzoic acid in Archaea via an unusual pathway involving an intramolecular migration (NIH shift). Appl. Environ. Microbiol., 2002, 68(12), 6246-6255.
[http://dx.doi.org/10.1128/AEM.68.12.6246-6255.2002] [PMID: 12450849]
Riis, V.; Kleinsteuber, S.; Babel, W. Influence of high salinities on the degradation of diesel fuel by bacterial consortia. Can. J. Microbiol., 2003, 49(11), 713-721.
[http://dx.doi.org/10.1139/w03-083] [PMID: 14735221]
Alva, V.A.; Peyton, B.M. Phenol and catechol biodegradation by the haloalkaliphile Halomonas campisalis: influence of pH and salinity. Environ. Sci. Technol., 2003, 37(19), 4397-4402.
[http://dx.doi.org/10.1021/es0341844] [PMID: 14572091]
García, M.T.; Mellado, E.; Ostos, J.C.; Ventosa, A. Halomonas organivorans sp. nov., a moderate halophile able to degrade aromatic compounds. Int. J. Syst. Evol. Microbiol., 2004, 54(Pt 5), 1723-1728.
[http://dx.doi.org/10.1099/ijs.0.63114-0] [PMID: 15388735]
Gu, J.; Cai, H.; Yu, S.L.; Qu, R.; Yin, B.; Guo, Y.F.; Zhao, J.Y.; Wu, X.L. Marinobacter gudaonensis sp. nov., isolated from an oil-polluted saline soil in a Chinese oilfield. Int. J. Syst. Evol. Microbiol., 2007, 57(Pt 2), 250-254.
[http://dx.doi.org/10.1099/ijs.0.64522-0] [PMID: 17267959]
Abdelkafi, S.; Sayadi, S.; Ben Ali Gam, Z.; Casalot, L.; Labat, M. Bioconversion of ferulic acid to vanillic acid by Halomonas elongata isolated from table-olive fermentation. FEMS Microbiol. Lett., 2006, 262(1), 115-120.
[http://dx.doi.org/10.1111/j.1574-6968.2006.00381.x] [PMID: 16907747]
Sorokin, D.Y.; van Pelt, S.; Tourova, T.P.; Takaichi, S.; Muyzer, G. Acetonitrile degradation under haloalkaline conditions by Natronocella acetinitrilica gen. nov., sp. nov. Microbiology, 2007, 153(Pt 4), 1157-1164.
[http://dx.doi.org/10.1099/mic.0.2006/004150-0] [PMID: 17379725]
Arulazhagan, P.; Vasudevan, N. Role of nutrients in the utilization of PAHs by halotolerant bacterial strain. J. Environ. Sci. (China), 2011, 23, 282-287.
[http://dx.doi.org/10.1016/S1001-0742(10)60404-4] [PMID: 21517002]
Fatajeva, E.; Gailiūtė, I.; Paliulis, D.; Grigiškis, S. The use of Acinetobacter sp. for oil hydrocarbon degradation in saline waters. Biologija (Vilnius), 2014, 60(3), 126-133.
Hidayat, A.; Tachibana, S. Biodegradation of aliphatic hydrocarbon in three types of crude oil by Fusarium sp. F092 under stress with artificial sea water. J. Environ. Sci. Technol., 2012, 5, 64-73.
Behnood, M.; Nasernejad, B.; Nikazar, M. Biodegradation of crude oil from saline wastewater using white rot fungus Phanerochaete chrysosporium. J. Ind. Eng. Chem., 2014, 20, 1879-1885.
Engel, A.S.; Johnson, L.R.; Porter, M.L. Arsenite oxidase gene diversity among chloroflexi and proteobacteria from El tatio geyser field, Chile. FEMS Microbiol. Ecol., 2013, 83(3), 745-756.
[http://dx.doi.org/10.1111/1574-6941.12030] [PMID: 23066664]
Orellana, R.; Macaya, C.; Bravo, G.; Dorochesi, F.; Cumsille, A.; Valencia, R.; Rojas, C.; Seeger, M. Living at the frontiers of life: extremophiles in Chile and their potential for bioremediation. Front. Microbiol., 2018, 9, 2309.
[http://dx.doi.org/10.3389/fmicb.2018.02309] [PMID: 30425685]
Dennett, G.V.; Blamey, J.M. A new thermophilic nitrilase from an antarctic hyperthermophilic microorganism. Front. Bioeng. Biotechnol., 2016, 4, 5.
[http://dx.doi.org/10.3389/fbioe.2016.00005] [PMID: 26973832]
Dumorné, K.; Córdova, D.C.; Astorga-Eló, M.; Renganathan, P. Extremozymes: a potential source for industrial applications. J. Microbiol. Biotechnol., 2017, 27(4), 649-659.
[http://dx.doi.org/10.4014/jmb.1611.11006] [PMID: 28104900]
Adams, M.W.W.; Kelly, R.M. Enzymes isolated from microorganisms that grow in extreme environments. Chem. Eng. News, 1995, 73(51), 32-42.
da Fonseca, F.S.; Angolini, C.F.; Arruda, M.A.; Junior, C.A.; Santos, C.A.; Saraiva, A.M.; Pilau, E.; Souza, A.P.; Laborda, P.R.; de Oliveira, P.F.; de Oliveira, V.M.; Reis, F.A.; Marsaioli, A.J. Identification of oxidoreductases from the petroleum Bacillus safensis strain. Biotechnol. Rep. (Amst.), 2015, 8, 152-159.
[http://dx.doi.org/10.1016/j.btre.2015.09.001] [PMID: 28352585]
Saito, A.; Iwabuchi, T.; Harayama, S. A novel phenanthrene dioxygenase from Nocardioides sp. Strain KP7: expression in Escherichia coli. J. Bacteriol., 2000, 182(8), 2134-2141.
[http://dx.doi.org/10.1128/JB.182.8.2134-2141.2000] [PMID: 10735855]
Wang, L.; Wang, W.; Lai, Q.; Shao, Z. Gene diversity of CYP153A and AlkB alkane hydroxylases in oil-degrading bacteria isolated from the Atlantic Ocean. Environ. Microbiol., 2010, 12(5), 1230-1242.
[http://dx.doi.org/10.1111/j.1462-2920.2010.02165.x] [PMID: 20148932]
Di Donato, P.; Buono, A.; Poli, A.; Finore, I.; Abbamondi, G.R.; Nicolaus, B.; Lama, L. Exploring marine environments for the identification of extremophiles and their enzymes for sustainable and green bioprocesses. Sustainability, 2019, 11, 149.

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Article Details

Year: 2020
Published on: 22 April, 2020
Page: [161 - 167]
Pages: 7
DOI: 10.2174/1389202921999200422122253
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