Abstract
Bioremediation uses microbes or plants, or their enzymes to neutralize pollutants from environments. It is a new technology that can be used in combination with other physical and chemical treatment approaches to handle the complex community of contaminants. It seems to be a sustainable approach to the management of environmental pollution and hence more work is needed in this field. In silico approaches have tremendous potential to accelerate bioremediation research and its advancements. Several computer programs and database resources are available for carrying out research to assist the bioremediation process using analysis and integration of omics datasets, i.e. genomics, transcriptomics, proteomics, metabolomics, and other molecular data. This chapter addresses the injurious effect of heavy metal emissions and processes employed for bioremediation by microorganisms and plants. Besides, it also highlights the significance of in silico techniques in enhancing the ability of microbial and plant enzymes to rapidly, degrade pollutants, emphasizes advancements made in bioremediation, and outlines future prospects and limitations.
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References
Aldridge BB, Rhee KY (2014) Microbial metabolomics: innovation, application, insight. Curr Opin Microbiol 19:90–96. https://doi.org/10.1016/j.mib.2014.06.009
Alexander M (1994) Biodegradation and bioremediation. Academic, San Diego, CA
Andrews S (2010) FastQC: a quality control tool for high throughput sequence data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc
Awasthi MK, Ravindran B, Sarsaiya S, Chen H, Wainaina S, Singh E (2020) Metagenomics for taxonomy profiling: tools and approaches. Bioengineered 11:356–374. https://doi.org/10.1080/21655979.2020.1736238
Banta G, Kahlon RS (2007) Dehalogenation of 4-chlorobenzoic acid by Pseudomonas isolates. Ind J Micorbiol 47:139–143. https://doi.org/10.1007/s12088-007-0027-5
Beale DJ, Karpe AV, Ahmed W, Cook S, Morrison PD, Staley C (2017) A community multi-omics approach towards the assessment of surface water quality in an urban river system. Int J Environ Res Public Health 14:E303. https://doi.org/10.3390/ijerph14030303
Bhatt P, Rene ER, Kumar AJ, Kumar AJ, Zhang W, Chen S (2020) Binding interaction of allethrin with esterase: bioremediation potential and mechanism. Bioresour Technol 315:13845
Bhatt P, Bhatt K, Sharma A, Zhang W, Mishra S, Chen S (2021a) Biotechnological basis of microbial consortia for the removal of pesticides from the environment. Crit Rev Biotechnol 41(3):317–338
Bhatt P, Joshi T, Bhatt K, Zhang W, Huang Y, Chen S (2021b) Binding interaction of glyphosate oxidoreductase and C-P lyase: molecular docking and molecular dynamics simulation studies. J Hazard Mater 5:409:124927
Bihari Z (2013) Current trends in bioremediation and biodegradation: next-generation sequencing. J Bioremed Biodegr 4(08):e138. https://doi.org/10.4172/2155-6199.1000e138
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30(15):2114–2120
Buermans H, Den Dunnen J (2014) Next generation sequencing technology: advances and applications. Biochem Biophys Acta 1842:1932–1941
Callaghan AV (2013) Metabolomic investigations of anaerobic hydrocarbon-impacted environments. Curr Opin Biotechnol 24:506–515. https://doi.org/10.1016/j.copbio.2012.08.012
Carbajosa G, Trigo A, Valencia A, Cases I (2009) Bionemo: molecular information on biodegradation metabolism. Nucleic Acids Res 37(Suppl 1):D598–D602
Caspi R, Billington R, Keseler IM, Kothari A, Krummenacker M, Midford PE, Ong WK, Paley S, Subhraveti P, Karp PD (2020) The MetaCyc database of metabolic pathways and enzymes-a 2019 update. Nucleic Acids Res 48(D1):D445–D453
Chandran H, Meena M, Sharma K (2020) Microbial biodiversity and bioremediation assessment through omics approaches. Front Environ Chem 1:570326. https://doi.org/10.3389/fenvc.2020.570326
Chauhan A, Jain RK (2010) Biodegradation: gaining insight through proteomics. Biodegradation 21(6):861–879
Combourieu B, Besse P, Sancelme M, Godin JP et al (2000) Common degradative pathways of morpholine, thiomorpholine and piperidine by Mycobacterium aurum MO1: evidence from 1H-nuclear magnetic resonance and ionspray mass spectrometry performed directly on the incubation medium. Appl Environ Microbiol 66:3187–3193
Combourieu B, Haroune N, Besse P, Sancelme M, Delort AM (2003) In: Mohan RM (ed) Research advances in microbiology, vol 3. Global research network, pp 1–22
Conesa A, Götz S, GarcÃa-Gómez JM, Terol J, Talón M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21(18):3674–3676
Conklin D, Haldeman B, Gao Z (2005) Gene finding for the helical cytokines. Bioinformatics 21(9):1776–1781
Dash B, Sahu N, Singh AK, Gupta SB, Soni R (2021) Arsenic efflux in Enterobacter cloacae RSN3 isolated from arsenic-rich soil. Folia Microbiol 66:189–196
Debbarma P, Raghuwanshi S, Singh J, Suyal DC, Zaidi MGH, Goel R (2017) Comparative in situ biodegradation studies of polyhydroxybutyrate film composites. 3Biotech 7(178):1–9. https://doi.org/10.1007/s13205-017-0789-3
Divya B, Kumar MD (2011) Plant-microbe interaction with enhanced bioremediation. Res J Biotechnol 6:72–79
Dixit R, Malaviya D, Pandiyan K, Singh UB, Sahu A, Shukla R, Singh BP, Rai JP, Sharma PK, Lade H (2015) Bioremediation of heavy metals from soil and aquatic environment: an overview of principles and criteria of fundamental processes. Sustainability 7:2189–2212
Eiler A, Heinric F, Bertilsson S (2012) Coherent dynamics and association networks among lake bacterioplankton taxa. ISME J 6:330–342. https://doi.org/10.1038/ismej.2011.113
Espinosa MJC, Blanco AC, Schmidgall T, Atanasoff-Kardjalieff AK, Kappelmeyer U, Tischler D et al (2020) Toward biorecycling: isolation of a soil bacterium that grows on a polyurethane oligomer and monomer. Front Microbiol 11:404. https://doi.org/10.3389/fmicb.2020.00404
Fulekar MH (2005) Bioremediation technologies for environment. Indian J Environ Prot 25:358–364
Funahashi A, Morohashi M, Kitano H, Tanimura N (2003) CellDesigner: a process diagram editor for gene-regulatory and biochemical networks. Biosilico 1(5):159–162
Ghosal D, Ghosh S, Dutta TK, Ahn Y (2016) Current state of knowledge in microbial degradation of polycyclic aromatic hydrocarbons (PAHS): a review. Front Microbiol 7:1369
Gilbert JA, Dupont CL (2011) Microbial metagenomics: beyond the genome. Annu Rev Mar Sci 3:347–371. https://doi.org/10.1146/annurev-marine-120709-142811
Giri K, Rai JPN, Pandey S, Mishra G, Kumar R, Suyal DC (2017a) Performance evaluation of isoproturon-degrading indigenous bacterial isolates in soil microcosm. Chem Ecol 33(9):817–825. https://doi.org/10.1080/02757540.2017.1393535
Giri K, Suyal DC, Mishra G, Pandey S, Kumar R, Meena DK, Rai JPN (2017b) Biodegradation of isoproturon by Bacillus pumilus K1 isolated from foothill agroecosystem of north west Himalaya. Proc Natl Acad Sci India Sect B-Biol Sci 87(3):839–848. https://doi.org/10.1007/s40011-015-0667-x
Goel R, Zaidi MGH, Soni R, Kusumlata SYS (2008) Implication of Arthrobacter and Enterobacter species for polycarbonate degradation. Int Biodeterior Biodegrad 61(2):167–172
Griffin JL (2004) Metabolic profiles to define the genome: can we hear the phenotypes? Philos Trans R Soc Lond B Biol Sci 359:857–871
Gupta K, Biswas R, Sarkar A (2020) Advancement of omics: prospects for bioremediation of contaminated soils. In: Shah M (ed) Microbial bioremediation & biodegradation. Springer, Singapore, pp 113–142
Gutleben J, Chaib De Mares M, van Elsas JD, Smidt H, Overmann J, Sipkema D (2018) The multi-omics promise in context: from sequence to microbial isolate. Crit Rev Microbiol 44:212–229. https://doi.org/10.1080/1040841X.2017.1332003
Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, MacManes MD (2013) De novo transcript sequence reconstruction from RNA-seq using the trinity platform for reference generation and analysis. Nat Protoc 8(8):1494–1512
Han D, Gao P, Li R, Tan P, Xie J, Zhang R et al (2020) Multicenter assessment of microbial community profiling using 16S rRNA gene sequencing and shotgun metagenomic sequencing. J Adv Res. https://doi.org/10.1016/j.jare.2020.07.010
Hart EH, Creevey CJ, Hitch T, Kingston-Smith AH (2018) Metaproteomics of rumen microbiota indicates niche compartmentalisation and functional dominance in a limited number of metabolic pathways between abundant bacteria. Sci Rep 8:10504. https://doi.org/10.1038/s41598-018-28827-
Hill CB, Czauderna T, Klapperstück M, Roessner U, Schreiber F (2015) Metabolomics, standards, and metabolic modeling for synthetic biology in plants. Front Bioeng Biotechnol 3:167. https://doi.org/10.3389/fbioe.2015.00167
Hivrale AU, Pawar PK, Rane NR, Govindwar SP Application of genomics and proteomics in bioremediation. In: Toxicity and waste management using bioremediation 2016. IGI Global, pp 97–112
Kamaludeen SPB, Arunkumar KR, Avudainayagam S, Ramasamy K (2003) Bioremediation of chromium contaminated environments. Ind J Exp Bio 41:972985
Kapley A, Purohit HJ (2009) Diagnosis of treatment efficiency in industrial wastewater treatment plants: a case study at a refinery ETP. Environ Sci Technol 43:3789–3795. https://doi.org/10.1021/es803296r
Kim HJ, Ishidou E, Kitagawa E, Momose Y, Iwahashi H (2004) A yeast DNA microarray for the evaluation of toxicity in environmental water containing burned ash. Environ Monit Assess 92:253–272. https://doi.org/10.1023/B:EMAS.0000014504.03500.41
Kou S, Vincent G, Gonzalez E, Pitre FE, Labrecque M, Brereton NJB (2018) The response of a 16S ribosomal RNA gene fragment amplified community to lead, zinc, and copper pollution in a Shanghai field trial. Front Microbiol 9:366. https://doi.org/10.3389/fmicb.2018.00366
Kour D, Kaur T, Devi R, Yadav A, Singh M et al (2021) Beneficial microbiomes for bioremediation of diverse contaminated environments for environmental sustainability: present status and future challenges. Environ Sci Pollut Res 28:24917–24939
Krumsiek J, Mittelstrass K, Do KT, Stückler F, Ried J, Adamski J et al (2015) Gender-specific pathway differences in the human serum metabolome. Metabolomics 11:1815–1833. https://doi.org/10.1007/s11306-015-0829-0
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. https://doi.org/10.1111/j.1365-2672.2009.04523.x
Kumar A, Bisht BS, Joshi VD, Dhewa T (2011) Review on bioremediation of polluted environment: a management tool. Int J Environ Sci 1:1079–1093
Kumar A, Pathak RK, Gupta SM, Gaur VS, Pandey D (2015) Systems biology for smart crops and agricultural innovation: filling the gaps between genotype and phenotype for complex traits linked with robust agricultural productivity and sustainability. Omics 19(10):581–601
Kumar P, Dash B, Suyal D C, Gupta SB, Singh AK, Chowdhury T, Soni R (2021) Characterization of arsenic-resistant Klebsiella pneumoniae RnASA11 from contaminated soil and water samples and its bioremediation potential. Curr Microbiol. https://doi.org/10.1007/s00284-021-02602-w
Lovley DR (2003) Cleaning up with genomics: applying molecular biology to bioremediation. Nat Rev Microbiol 1:35–44. https://doi.org/10.1038/nrmicro731
Ma J, Zhai G (2012) Microbial bioremediation in omics era: opportunities and challenges. J Bioremed Biodegr 3:e120. https://doi.org/10.4172/2155-6199.1000e120
Malla MA, Dubey A, Yadav S, Kumar A, Hashem A, Abd Allah EF (2018) Understanding and designing the strategies for the microbe-mediated remediation of environmental contaminants using omics approaches. Front Microbiol 9:1132. https://doi.org/10.3389/fmicb.2018.01132
Mallick H, Franzosa EA, Mclver LJ, Banerjee S, Sirota-Madi A, Kostic AD et al (2019) Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences. Nat Commun 10:3136. https://doi.org/10.1038/s41467-019-10927-1
Mani D, Kumar C (2014) Biotechnological advances in bioremediation of heavy metals contaminated ecosystems: an overview with special reference to phytoremediation. Int J Environ Sci Technol 11:843–872
McMahon MA, Prakash TP, Cleveland DW, Bennett CF, Rahdar M (2018) Chemically modified Cpf1-CRISPR RNAs mediate efficient genome editing in mammalian cells. Mol Ther 26:1228–1240. https://doi.org/10.1016/j.ymthe.2018.02.031
Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ (2009) AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem 30(16):2785–2791
Nierman WC, Nelson KE (2002) Genomics for applied microbiology. Adv Appl Microbiol 51:201–248. https://doi.org/10.1016/S0065-2164(02)51007-8
Oliveira JS, Araújo W, Lopes Sales AI, Brito Guerra AD, Silva Araújo SCD, de Vasconcelos ATR, Agnez-Lima LF, Freitas AT (2015) BioSurfDB: knowledge and algorithms to support biosurfactants and biodegradation studies. Database 2015
Pandey A, Tripathi PH, Tripathi AH, Pandey SC, Gangola S (2019) Omics technology to study bioremediation and respective enzymes. In: Bhatt P (ed) Smart bioremediation technologies: microbial enzymes. Academic, New Delhi, pp 23–43. https://doi.org/10.1016/B978-0-12-818307-6.00002-0
Pathak RK, Singh DB (2020) Systems biology approaches for food and health. In: Advances in agri-food biotechnology. Springer, Singapore, pp 409–426
Pathak RK, Baunthiyal M, Pandey N, Pandey D, Kumar A (2017a) Modeling of the jasmonate signaling pathway in Arabidopsis thaliana with respect to pathophysiology of Alternaria blight in brassica. Sci Rep 7(1):1–12
Pathak RK, Baunthiyal M, Shukla R, Pandey D, Taj G, Kumar A (2017b) In silico identification of mimicking molecules as defense inducers triggering jasmonic acid mediated immunity against alternaria blight disease in brassica species. Front Plant Sci 8:609
Pathak RK, Gupta A, Shukla R, Baunthiyal M (2018) Identification of new drug-like compounds from millets as xanthine oxidoreductase inhibitors for treatment of hyperuricemia: a molecular docking and simulation study. Comput Biol Chem 76:32–41
Pathak RK, Singh DB, Sagar M, Baunthiyal M, Kumar A (2020) Computational approaches in drug discovery and design. In: Computer-aided drug design. Springer, Singapore, pp 1–21
Paul D, Singh R, Jain RK (2006) Chemotaxis of Ralstonia sp. SJ98 towards p-nitrophenol i soil. Environ Microbiol 8:1797–1804. https://doi.org/10.1111/j.1462-2920.2006.01064.x
Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A (2020) Using SPAdes de novo assembler. Curr Protocols Bioinform 70(1):e102
Reena R, Majhi MC, Arya AK, Kumar R, Kumar A (2012) BioRadBase: a database for bioremediation of radioactive waste. Afr J Biotechnol 11(35):8718–8721
Resource Coordinators NCBI (2012) Database resources of the national center for biotechnology information. Nucleic Acids Res 41(D1):D8–D20
RodrÃguez A, Castrejón-GodÃnez ML, Salazar-Bustamante E, Gama-MartÃnez Y, Sánchez-Salinas E, Mussali-Galante P et al (2020) Omics approaches to pesticide biodegradation. Curr Microbiol 77:545–563. https://doi.org/10.1007/s00284-020-01916-5
Rogers SL, McClure N (2003) The role of microbiological studies in bioremediation process optimization. In: Head IM, Singleton I, Milner M (eds) Bioremediation: a critical review. Horizon Scientific Press, Norfolk, pp 27–59
Roume H, Heintz-Buschart A, Muller EEL, May P, Satagopam VP, Laczny CC et al (2015) Comparative integrated omics: identification of key functionalities in microbial community-wide metabolic networks. NPJ Biofilms Microb 1:15007. https://doi.org/10.1038/npjbiofilms.2015.7
Sakshi Haritash AK (2020) A comprehensive review of metabolic and genomic aspects of PAH-degradation. Arch Microbiol 202:2033–2058. https://doi.org/10.1007/s00203-020-01929-5
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13(11):2498–2504
Shrivastava R, Upreti RK, Chaturvedi UC (2003) Various cells of the immune system and intestine differ in their capacity to reduce hexavalent chromium. FEMS Immunol Med Microbio 38:65–70. https://doi.org/10.1016/S0928-8244(03)00107-X
Singh M, Singh D, Rai P, Suyal DC, Saurabh S, Soni R, Giri K, Yadav AN (2021) Fungi in remediation of hazardous wastes: current status and future. In: Yadav AN (ed) Recent trends in mycological research, fungal biology. Springer Nature, Cham
Suyal DC, Soni R, Singh DK, Goel R (2021) Microbiome change of agricultural soil under organic farming practices. Biologia 76:1315–1325
Viant MR, Sommer U (2013) Mass spectrometry based environmental metabolomics: a primer and review. Metabolomics 9:144–158. https://doi.org/10.1007/s11306-012-0412-x
Vidali M (2001) Bioremediation. An overview. Pure Appl Chem 73:1163–1172. https://doi.org/10.1351/pac200173071163
Wang JH, Byun J, Pennathur S (2010) Analytical approaches to metabolomics and applications to systems biology. Semin Nephrol 30:500–511. https://doi.org/10.1016/j.semnephrol.2010.07.007
Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18(5):821–829
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Verma, S., Kour, S., Pathak, R.K. (2022). In Silico Approaches in Bioremediation Research and Advancements. In: Suyal, D.C., Soni, R. (eds) Bioremediation of Environmental Pollutants. Springer, Cham. https://doi.org/10.1007/978-3-030-86169-8_9
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