Abstract
Non-degradable pollutants have emerged as a consequence of industrialization, population increment, and changing lifestyles, endangering human well-being and the environment. Biological techniques based on microorganisms are gaining popularity as an environmentally beneficial and cost-effective way to reduce pollution. Microorganisms may thrive in a variety of environments and create metabolites that degrade and change contaminants, allowing contaminated places to be organically revived. For a greater knowledge of biological and life sciences, multiple technologies have begun to be integrated into metagenomics. Technology such as metagenomics is now being used to develop strategies for studying the ecology and variety of microbes, as well as its application in the environment. Metagenomics is a novel and rapidly expanding discipline of environmental biology that provides a strong tool for accessing information on the genomes of environmental microorganisms and entire microbial communities. The application of metagenomics in environmental surveying and bioremediation is becoming more usual. In recent years, a number of functional metagenomics techniques have been used to investigate a wide range of resistant microbial degradation mechanisms. In a metagenomic investigation, it is critical to identify and screen metagenomes from the polluted location. These procedures are well-known for their effectiveness in eliminating many types of contaminants. These strategies may change rapidly as technology develops, but the once that focus on the best ways to improve bioremediation of the contaminated places will be the most successful. Culture-independent molecular approaches, on the other hand, can disclose very relevant information on the metagenome of environmental microorganisms, which play a key role in biogeochemical cycles and the breakdown and detoxification of environmental pollutants. These high-throughput studies would assist in the discovery of novel species for bioremediation, as well as providing new and interesting insights into their primary biodegradative processes at the molecular level. In this chapter, we are attempting to convey an overview that how functional one of the finest bioremediation adaptations that leads to the development of a clean non-toxic environment is metagenomics. We also went through the metagenomics analysis methods with respect to bioremediation. In addition to this, we provide an overview of examples of metagenomics in bioremediation which have recently been reported. Furthermore, our study clarifies the widespread use of metagenomes formed from metagenomics communities, which are capable of comprehending environmental pollutants and poisons.
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References
Agrawal N, Kumar V, Shahi SK (2021) Biodegradation and detoxification of phenanthrene in in-vitro and in-vivo conditions by a newly isolated ligninolytic fungus Coriolopsis byrsina strain APC5 and characterization of their metabolites for environmental safety. Environ Sci Pollut Res. https://doi.org/10.1007/s11356-021-15271-w
Atlas R, Bragg JR (2009) Bioremediation of marine oil spills: when and when not - the Exxon Valdez experience. Microb Biotechnol 2:213–221
Baker KH, Herson DS (1994) Bioremediation. McGraw-Hill, Inc., New York
Boll M, Löffler C, Morris BEL, Kung JW (2014) Anaerobic degradation of homocyclic aromatic compounds via arylcarboxyl-coenzyme A esters: organisms, strategies and key enzymes. Environ Microbiol 16:612–627
Boopathy R (2000) Factors limiting bioremediation technologies. Bioresour Technol 74:63–67
Chakraborty R, Wu CH, Hazen TC (2012) Systems biology approach to bioremediation. Curr Opin Biotechnol 23:483–490
Chandra R, Kumar V, Yadav S (2015) Microbial degradation of lignocellulosic waste and its metabolic products. In: Chandra R (ed) Environmental waste management. CRC Press, Boca Raton
Chauhan A, Singh J (2015) Biodegradation of DDT. J Textile Sci Eng 5:1–8
Chen Y, Murrell JC (2010) When metagenomics meets stable-isotope probing: progress and perspectives. Trends Microbiol 18:157–163
Dettmer K, Aronov PA, Hammock BD (2007) Mass spectrometry-based metabolomics. Mass Spectrom Rev 26:51–58
Fantroussi S, Agathos SN (2005) Is bioaugmentation a feasible strategy for pollutant removal and site remediation? Curr Opin Microbiol 8:268–275
Fomina M, Gadd GM (2014) Biosorption: current perspectives on concept, definition and application. Bioresour Technol 160:3–14
Franzosa EA, Hsu T, Sirota-Madi A, Shafquat A, Abu-Ali G, Morgan XC et al (2015) Sequencing and beyond: integrating molecular ‘omics’ for microbial community profiling. Nat Rev Microbiol 13:360–372
Garfield E, Merton RK (1979) Citation indexing: its theory and application in science, technology, and humanities, vol 8. Wiley, New York
Grath SP, Chaudri AM, Giller KE (1994) Summary 15th world congress of soil science. Acapulco, México
Handelsman J (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68(4):669–685
Handelsman J (2005) Sorting out metagenomes. Nat Biotechnol 23(1):38–39
Harekrushna S, Kumar DC (2012) A review on: bioremediation. Int J Res Chem Environ 2(1):13–21
Jain PK, Bajpai V (2012) Biotechnology of bioremediation- a review. Int J Environ Sci 3:535–549
Jan B, Beilen V, Neuenschwunder M (2003) Rubredoxins involved in alkane degradation. J Bacteriol 184(1722–1732):97
Jilani S, Altaf Khan M (2004) Isolation, characterization and growth response of pesticides degrading bacteria. J Biol Sci 4(15–20):96
Joshi MN et al (2014) Metagenomics of petroleum muck: revealing microbial diversity and depicting microbial syntrophy. Arch Microbiol 196(8):531–544
Kumar M, Khanna S (2010) Diversity of 16S rRNA and dioxygenase genes detected in coal-tar-contaminated site undergoing active bioremediation. J Appl Microbiol 108:1252–1262
Kumar V, Shahi SK, Singh S (2018) Bioremediation: an eco-sustainable approach for restoration of contaminated sites. In: Microbial bioprospecting for sustainable development. Springer, Singapore, pp 115–136
Kumar V, Thakur IS, Singh AK, Shah MP (2020) Application of metagenomics in remediation of contaminated sites and environmental restoration. In: Shah M, Rodriguez-Couto S, Sengor SS (eds) Emerging technologies in environmental bioremediation. Elsevier. https://doi.org/10.1016/B978-0-12-819860-5.00008-0
Kumar V, Singh K, Shah MP, Singh AK, Kumar A, Kumar Y (2021) Application of omics technologies for microbial community structure and function analysis in contaminated environment. In: Shah MP, Sarkar A, Mandal S (eds) Wastewater treatment: cutting edge molecular tools, techniques & applied aspects in waste water treatment. Elsevier, Cambridge, MA. https://doi.org/10.1016/B978-0-12-821925-6.00013-7
Kumar V, Agrawal S, Shahi SK, Motghare A, Singh S, Ramamurthy PC (2022) Bioremediation potential of newly isolated Bacillus albus strain VKDS9 for decolourization and detoxification of biomethanated distillery effluent and its metabolites characterization for environmental sustainability. Environ Technol Innov 26:102260. https://doi.org/10.1016/j.eti.2021.102260
Kumavath RN, Deverapalli P (2013) Scientific swift in bioremediation: an overview. Intech Publishers
Lee JH (2013) An overview of phytoremediation as a potentially promising technology for environmental pollution control. Biotechnol Bioprocess Eng 18(431):439
Leitão AL (2009) Potential of Penicillium species in the bioremediation field. Int J Environ Res Public Health 6(4):1393–1417
Liu L, Li YH, Li S, Hu N, He Y, Pong R et al (2012) Comparison of next-generation sequencing systems. J Biomed Biotechnol 2012:251364. https://doi.org/10.1155/2012/251364
Lovey DR (2003) Cleaning up with genomics: applying molecular biology to bioremediation. Nat Rev Microbiol 1:35–44
Metzker ML (2009) Sequencing technologies-the next generation. Nat Rev Genet 11(1):31–46
Meysami P, Baheri H (2003) Prescreening of fungi and bulking agents for contaminated soil bioremediation. Adv Environ Res 7(881–887):149
Paul D, Pandey G, Pandey J, Jain RK (2005) Accessing microbial diversity for bioremediation and environmental restoration. Trends Biotechnol 23:135–142
Perpetuo EA, Souza CB, Nascimento CAO (2011) Engineering bacteria for bioremediation. In: Carpi A (ed) Progress in molecular and environmental bioengineering—from analysis and modeling to technology applications. InTech, Rijeka, pp 605–632
Prasad R (2014) New approaches and insights into bioremediation of hazardous waste. Rev Environ Health 29(1–2):33–35
Röling WF (2015) Maths on microbes: adding microbial ecophysiology to metagenomics. Microb Biotechnol 8(1):21–22. https://doi.org/10.1111/1751-7915.12233
Shah V, Jain K, Desai C, Madamwar D (2011) Metagenomics and integrative – omics’ technologies in microbial bioremediation: current trends and potential applications. In: Metagenomics: current innovations and future trends. Caister Academic Press, Norfolk, pp 211–240
Sharma S (2012) Bioremediation: features, strategies and applications. Asian J Pharm Life Sci 2(2):202–213
Simon C, Daniel R (2009) Achievements and new knowledge unraveled by metagenomic approaches. Appl Microbiol Biotechnol 85(2):265–276
Singh R, Singh P, Sharma R (2014) Microorganism as a tool of bioremediation technology for cleaning environment: a review. Proc Int Acad Ecol Environ Sci 4(1):1–6
Taylor E, Reimer D (2008) Oil persistence on beaches in Prince William sound—a review of SCAT surveys conducted from 1989 to 2002. Mar Pollut Bull 43:458–474
Thapa B, Kumar A, Ghimire A (2012) A review on bioremediation of petroleum hydrocarbon contaminants in soil. Kathmandu Univ J Sci Eng Technol 8(1):164–170
Tijssen RJ (2002) Science dependence of technologies: evidence from inventions and their inventors. Res Policy 31(4):509–526
Tringe SG, Rubin EM (2005) Metagenomics: DNA sequencing of environmental samples. Nat Rev Genet 6(11):805–814
Valiente G, Pesole G (2012) Bioinformatics approaches and tools for metage nomic analysis. Editorial. Brief Bioinform 13(6):645
Varma R, Turner A, Brown MT (2011) Bioaccumulation of metals by Fucus ceranoides in estuaries of South West England. Mar Pollut Bull 62(11):2557–2562
Verma JP, Jaiswal DK (2016) Book review: advances in biodegradation and bioremediation of indust yerial waste. Front Microbiol 6:1–2
Watanabe K (2001) Microorganisms relevant to bioremediation. Curr Opin Biotechnol 12(3):237–241
Wood TK (2008) Molecular approaches in bioremediation. Curr Opin Biotechnol 19:572–578
Zhang C, Bennett GN (2005) Biodegradation of xenobiotics by anaerobic bacteria. Appl Microbiol Biotechnol 67(5):600–618
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Sokal, S., Palsania, P., Kaushik, G. (2022). Bioremediation and Functional Metagenomics: Advances, Challenges, and Opportunities. In: Kumar, V., Thakur, I.S. (eds) Omics Insights in Environmental Bioremediation. Springer, Singapore. https://doi.org/10.1007/978-981-19-4320-1_1
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