Skip to main content

Bioremediation Assessment in Industrial Wastewater Treatment: The Omics Approach

  • Chapter
  • First Online:
Omics Insights in Environmental Bioremediation

Abstract

As the number of industries is increasing day by day, the amount of toxic and non-biodegradable pollutants released by them into the environment is also increasing, thus adversely affecting ecosystems. Generally, industries consume various chemicals for the production of different types of materials, and, at the end of the process, different types of noxious wastes are released. Microbial bioremediation has already proven itself to be an economically feasible technology that can help in the removal of contaminants from the environment in an effective manner. In this context, isolation and identification of microbial consortia from pollutant soils may be used as bioremediation agents. A current advancement in the bioremediation of industrial effluents is the omics approach, which helps in exploring the microbial diversity present in contaminated sites. In addition to this, omics helps understand the microbial physiology and regulatory mechanisms. Recent advancements in omics technology have explored proteomics, transcriptomics, metagenomics, and metabolomics through in-depth analyses. Moreover, whole-genome sequence data have revealed microbial diversity at polluted sites. The present chapter investigates the functional role of microbes using the omics approach and its limitations in industrial applications. Omics also deciphers the potential connection between the genetic and functional similarity among numerous microbes, which helps in hastening in situ bioremediation and in minimizing the pollution load.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Aardema MJ, MacGregor JT (2003) Toxicology and genetic toxicology in the new era of “toxicogenomics”: impact of “-omics” technologies. In: Toxicogenomics, pp 171–193

    Chapter  Google Scholar 

  • 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

  • Aparicio JD, Saez JM, Raimondo EE, Benimeli CS, Polti MA (2018) Comparative study of single and mixed cultures of actinobacteria for the bioremediation of co-contaminated matrices. J Environ Chem Eng 6(2):2310–2318. https://doi.org/10.1016/j.jece.2018.03.030

    Article  CAS  Google Scholar 

  • Balakrishnan SL, Rao PP (2019) Monocrotophos degradation potential of bacterial isolates isolated from agricultural soils of Visakhapatnam Dist. J Pure Appl Microbiol 13(1):393–402. https://doi.org/10.22207/JPAM.13.1.43

    Article  CAS  Google Scholar 

  • Bharagava RN, Purchase D, Saxena G, Mulla SI (2019) Applications of metagenomics in microbial bioremediation of pollutants: from genomics to environmental cleanup. In: Microbial diversity in the genomic era. Academic Press, pp 459–477. https://doi.org/10.1016/B978-0-12-814849-5.00026-5

    Chapter  Google Scholar 

  • Bhatt P, Gangola S, Chaudhary P, Khati P, Kumar G, Sharma A, Srivastava A (2019) Pesticide induced up-regulation of esterase and aldehyde dehydrogenase in indigenous Bacillus spp. Bioremediat J 23(1):42–52. https://doi.org/10.1080/10889868.2019.1569586

    Article  CAS  Google Scholar 

  • Bhatt P, Rene ER, Kumar AJ, Zhang W, Chen S (2020) Binding interaction of allethrin with esterase: bioremediation potential and mechanism. Bioresour Technol 315:123845. https://doi.org/10.1016/j.biortech.2020.123845

    Article  CAS  PubMed  Google Scholar 

  • Cappelletti M, Fedi S, Zampolli J, Di Canito A, D’Ursi P, Orro A, Viti C, Milanesi L, Zannoni D, Di Gennaro P (2016) Phenotype microarray analysis may unravel genetic determinants of the stress response by Rhodococcus aetherivorans BCP1 and Rhodococcus opacus R7. Res Microbiol 167(9–10):766–773. https://doi.org/10.1016/j.resmic.2016.06.008

    Article  CAS  PubMed  Google Scholar 

  • Castrejón-Godínez ML, Ortiz-Hernández ML, Salazar E, Encarnación S, Mussali-Galante P, Tovar-Sánchez E, Sánchez-Salinas E, Rodríguez A (2019) Transcriptional analysis reveals the metabolic state of Burkholderia zhejiangensis CEIB S4-3 during methyl parathion degradation. PeerJ 7:e6822. https://doi.org/10.7717/peerj.6822

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chandra R, Kumar V (2015) Biotransformation and biodegradation of organophosphates and organohalides. In: Chandra R (ed) Environmental waste management. CRC Press, Boca Raton. https://doi.org/10.1201/b19243-17

    Chapter  Google Scholar 

  • Chandra R, Kumar V (2017a) Detection of Bacillus and Stenotrophomonas species growing in an organic acid and endocrine-disrupting chemicals rich environment of distillery spent wash and its phytotoxicity. Environ Monit Assess 189:26. https://doi.org/10.1007/s10661-016-5746-9

    Article  CAS  PubMed  Google Scholar 

  • Chandra R, Kumar V (2017b) Detection of androgenic-mutagenic compounds and potential autochthonous bacterial communities during in-situ bioremediation of post methanated distillery sludge. Front Microbiol 8:87. https://doi.org/10.3389/fmicb.2017.00887

    Article  Google Scholar 

  • Chandran H, Meena M, Sharma K (2020) Microbial biodiversity and bioremediation assessment through omics approaches. Front Environ Chem 1:9. https://doi.org/10.3389/fenvc.2020.570326

    Article  Google Scholar 

  • Clements T, Rautenbach M, Ndlovu T, Khan S, Khan W (2021) A metabolomics and molecular networking approach to elucidate the structures of secondary metabolites produced by Serratia marcescens strains. Front Chem 9. https://doi.org/10.3389/fchem.2021.633870

  • da Silva Araújo SC, Silva-Portela RC, de Lima DC, da Fonsêca MMB, Araújo WJ, da Silva UB, Napp AP, Pereira E, Vainstein MH, Agnez-Lima LF (2020) MBSP1: a biosurfactant protein derived from a metagenomic library with activity in oil degradation. Sci Rep 10(1):1–13. https://doi.org/10.1038/s41598-020-58330-x

    Article  CAS  Google Scholar 

  • Daims H, Taylor MW, Wagner M (2006) Wastewater treatment: a model system for microbial ecology. Trends Biotechnol 24(11):483–489. https://doi.org/10.1016/j.tibtech.2006.09.002

    Article  CAS  PubMed  Google Scholar 

  • Dangi AK, Sharma B, Hill RT, Shukla P (2019) Bioremediation through microbes: systems biology and metabolic engineering approach. Crit Rev Biotechnol 39(1):79–98. https://doi.org/10.1080/07388551.2018.1500997

    Article  CAS  PubMed  Google Scholar 

  • Das AJ, Ambust S, Singh T, Kumar R (2021) Biosurfactant assisted design treatments for remediation of petroleum contaminated soil and metabolomics based interactive study with Brassica nigra L. Environ Chall 4:100080. https://doi.org/10.1016/j.envc.2021.100080

    Article  CAS  Google Scholar 

  • Datta S, Rajnish KN, Samuel MS, Pugazlendhi A, Selvarajan E (2020) Metagenomic applications in microbial diversity, bioremediation, pollution monitoring, enzyme and drug discovery. A review. Environ Chem Lett 18(4):1229–1241. https://doi.org/10.1007/s10311-020-01010-z

    Article  CAS  Google Scholar 

  • Dennis P, Edwards EA, Liss SN, Fulthorpe R (2003) Monitoring gene expression in mixed microbial communities by using DNA microarrays. Appl Environ Microbiol 69(2):769–778. https://doi.org/10.1128/AEM.69.2.769-778.2003

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dhanjal DS, Sharma D (2018) Microbial metagenomics for industrial and environmental bioprospecting: the unknown envoy. In: Microbial bioprospecting for sustainable development. Springer, Singapore, pp 327–352

    Chapter  Google Scholar 

  • Diggle SP, Griffin AS, Campbell GS, West SA (2007) Cooperation and conflict in quorum-sensing bacterial populations. Nature 450(7168):411–414

    Article  CAS  PubMed  Google Scholar 

  • Dubinsky EA, Conrad ME, Chakraborty R, Bill M, Borglin SE, Hollibaugh JT, Mason OU, Piceno M, Reid FC, Stringfellow WT, Tom LM (2013) Succession of hydrocarbon-degrading bacteria in the aftermath of the Deepwater Horizon oil spill in the Gulf of Mexico. Environ Sci Technol 47(19):10860–10867. https://doi.org/10.1021/es401676y

    Article  CAS  PubMed  Google Scholar 

  • Floros DJ, Jensen PR, Dorrestein PC, Koyama N (2016) A metabolomics guided exploration of marine natural product chemical space. Metabolomics 12(9):1–11

    Article  CAS  Google Scholar 

  • Garg M (2019) Treatment and recycling of wastewater from beverages/the soft drink bottling industry. In: Advances in biological treatment of industrial waste water and their recycling for a sustainable future. Springer, Singapore, pp 333–361

    Chapter  Google Scholar 

  • Gaur VK, Manickam N (2021) Microbial biosurfactants: production and applications in circular bioeconomy. In: Biomass, biofuels, biochemicals. Elsevier, pp 353–378

    Chapter  Google Scholar 

  • Gregson BH, Metodieva G, Metodiev MV, Golyshin PN, McKew BA (2020) Protein expression in the obligate hydrocarbon-degrading psychrophile Oleispira antarctica RB-8 during alkane degradation and cold tolerance. Environ Microbiol 22(5):1870–1883. https://doi.org/10.1111/1462-2920.14956

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gupta R, Sati B, Gupta A (2019) Treatment and recycling of wastewater from pharmaceutical industry. In: Advances in biological treatment of industrial waste water and their recycling for a sustainable future. Springer, Singapore, pp 267–302

    Chapter  Google Scholar 

  • Hillmann B, Al-Ghalith GA, Shields-Cutler RR, Zhu Q, Gohl DM, Beckman KB, Knight R, Knights D (2018) Evaluating the information content of shallow shotgun metagenomics. Msystems 3(6):e00069-18. https://doi.org/10.1128/mSystems.00069-18

    Article  PubMed  PubMed Central  Google Scholar 

  • Holmes DE, O’Neil RA, Chavan MA, N’Guessan LA, Vrionis HA, Perpetua LA, Larrahondo MJ, Didonato R, Liu A, Lovley DR (2009) Transcriptome of Geobacter uraniireducens growing in uranium-contaminated subsurface sediments. ISME J 3:216–230

    Article  CAS  PubMed  Google Scholar 

  • Huettel M, Overholt WA, Kostka JE, Hagan C, Kaba J, Wells WB, Dudley S (2018) Degradation of Deepwater Horizon oil buried in a Florida beach influenced by tidal pumping. Mar Pollut Bull 126:488–500. https://doi.org/10.1016/j.marpolbul.2017.10.061

    Article  CAS  PubMed  Google Scholar 

  • Jehmlich N, Kleinsteuber S, Vogt C, Benndorf D, Harms H, Schmidt F, Von Bergen M, Seifert J (2010) Phylogenetic and proteomic analysis of an anaerobic toluene-degrading community. J Appl Microbiol 109(6):1937–1945. https://doi.org/10.1111/j.1365-2672.2010.04823.x

    Article  CAS  PubMed  Google Scholar 

  • John EM, Sreekumar J, Jisha MS (2016) Optimization of chlorpyrifos degradation by assembled bacterial consortium using response surface methodology. Soil Sediment Contam 25(6):668–682. https://doi.org/10.1080/15320383.2016.1190684

    Article  CAS  Google Scholar 

  • Joye S, Kostka J (2020) Microbial genomics of the global ocean system. American Society for Microbiology, Washington

    Book  Google Scholar 

  • Karthikeyan S, Rodriguez-R LM, HeritierRobbins P, Kim M, Overholt WA, Gaby JC, Hatt JK, Spain JC, Rosselló-Móra R, Huettel M, Kostka JE, Konstantinidis KT (2019) “Candidatus Macondimonas diazotrophica”, a novel gammaproteobacterial genus dominating crude-oil-contaminated coastal sediments. ISME J 13:2129–2134

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Katsuyama C, Nakaoka S, Takeuchi Y, Tago K, Hayatsu M, Kato K (2009) Complementary cooperation between two syntrophic bacteria in pesticide degradation. J Theoretical Biol 256(4):644–654. https://doi.org/10.1016/j.jtbi.2008.10.024

    Article  CAS  Google Scholar 

  • Keum YS, Seo JS, Li QX, Kim JH (2008) Comparative metabolomic analysis of Sinorhizobium sp. C4 during the degradation of phenanthrene. Appl Microbiol Biotechnol 80(5):863–872

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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(1):253–272

    Article  CAS  PubMed  Google Scholar 

  • Krivobok S, Kuony S, Meyer C, Louwagie M, Willison JC, Jouanneau Y (2003) Identification of pyrene-induced proteins in Mycobacterium sp. strain 6PY1: evidence for two ring-hydroxylating dioxygenases. J Bacteriol 185(13):3828–3841. https://doi.org/10.1128/JB.185.13.3828-3841.2003

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kumar V, Chandra R (2020a) Bioremediation of melanoidins containing distillery waste for environmental safety. In: Bharagava R, Saxena G (eds) Bioremediation of industrial waste for environmental safety. Springer, Singapore. https://doi.org/10.1007/978-981-13-3426-9_20

    Chapter  Google Scholar 

  • Kumar V, Chandra R (2020b) Metagenomics analysis of rhizospheric bacterial communities of Saccharum arundinaceum growing on organometallic sludge of sugarcane molasses-based distillery. 3 Biotech 10(7):316. https://doi.org/10.1007/s13205-020-02310-5

    Article  PubMed  PubMed Central  Google Scholar 

  • Kumar V, Shahi SK, Singh S (2018) Bioremediation: an eco-sustainable approach for restoration of contaminated sites. In: Singh J, Sharma D, Kumar G, Sharma N (eds) Microbial bioprospecting for sustainable development. Springer, Singapore. https://doi.org/10.1007/978-981-13-0053-0_6

    Chapter  Google Scholar 

  • Kumar SS, Ayyadurai GK, Ramamurthy V, Raveendran S (2019) Comparative studies on various physico-chemical parameters of different industrial waste water. Int J Res Anal Rev 6(1):664–666

    Google Scholar 

  • 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

    Chapter  Google Scholar 

  • 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. https://doi.org/10.1016/B978-0-12-821925-6.00013-7

    Chapter  Google Scholar 

  • Li H, Qiu Y, Yao T, Ma Y, Zhang H, Yang X, Li C (2020) Evaluation of seven chemical pesticides by mixed microbial culture (PCS-1): degradation ability, microbial community, and Medicago sativa phytotoxicity. J Hazard Mater 389:121834

    Article  CAS  PubMed  Google Scholar 

  • Liu XY, Luo XJ, Li CX, Lai QL, Xu JH (2014) Draft genome sequence of Burkholderia sp. Strain MP-1, a Methyl Parathion (MP)-degrading bacterium from MP-contaminated soil. Genome Announc 2(3):e00344–e00314. https://doi.org/10.1128/genomeA.00344-14

    Article  PubMed  PubMed Central  Google Scholar 

  • Liu J, Wang S, Qin T, Li N, Niu Y, Li D, Yuan Y, Geng H, Xiong L, Liu D (2015) Whole transcriptome analysis of Penicillium digitatum strains treatmented with prochloraz reveals their drug-resistant mechanisms. BMC Genomics 16(1):1–13. https://doi.org/10.1186/s12864-015-2043-x

    Article  CAS  Google Scholar 

  • Lu H, Zhang T, Zhou Y, Zhou J, Wang J, Wang X (2019) Enhanced dechlorination and biodegradation of 2-chloroaniline by a 2-aminoanthraquinone-graphene oxide composite under anaerobic conditions. Sci Rep 9(1):1–11

    Google Scholar 

  • Malik G, Arora R, Chaturvedi R, Paul MS (2021) Implementation of genetic engineering and novel omics approaches to enhance bioremediation: a focused review. In: Bulletin of environmental contamination and toxicology, pp 1–8. https://doi.org/10.1007/s00128-021-03218-3

    Chapter  Google Scholar 

  • Martínez-Ocampo F, Fernández López MG, Lozano-Aguirre Beltrán LF, Popoca-Ursino EC, Ortiz-Hernández ML, Sánchez-Salinas E, Ramos Quintana F, Villalobos-López MA, Dantán-González E (2016) Draft genome sequence of Burkholderia cenocepacia strain CEIB S5-2, a methyl parathion-and p-Nitrophenol-degrading bacterium, isolated from agricultural soils in Morelos, Mexico. Genome Announc 4(2):e00220–e00216. https://doi.org/10.1128/genomeA.00220-16

    Article  PubMed  PubMed Central  Google Scholar 

  • Medić A, Stojanović K, Izrael-Živković L, Beškoski V, Lončarević B, Kazazić S, Karadžić I (2019) A comprehensive study of conditions of the biodegradation of a plastic additive 2, 6-di-tert-butylphenol and proteomic changes in the degrader Pseudomonas aeruginosa san ai. RSC Adv 9(41):23696–23710

    Article  PubMed  PubMed Central  Google Scholar 

  • Meng D, Zhang L, Meng J, Tian Q, Zhai L, Hao Z, Guan Z, Cai Y, Liao X (2019) Evaluation of the Strain Bacillus amyloliquefaciens YP6 in Phoxim degradation via transcriptomic data and product analysis. Molecules 24(21):3997

    Article  CAS  PubMed Central  Google Scholar 

  • Mesnage R, Oestreicher N, Poirier F, Nicolas V, Boursier C, Vélot C (2020) Transcriptome profiling of the fungus Aspergillus nidulans exposed to a commercial glyphosate-based herbicide under conditions of apparent herbicide tolerance. Environ Res 182:109116. https://doi.org/10.1016/j.envres.2020.109116

    Article  CAS  PubMed  Google Scholar 

  • Mishra M, Singh SK, Kumar A (2021) Role of omics approaches in microbial bioremediation. In: Microbe mediated remediation of environmental contaminants. Woodhead Publishing, pp 435–445

    Chapter  Google Scholar 

  • Misra R, Satyanarayan S, Potle N (2013) Treatment of agrochemical/pesticide wastewater by coagulation/flocculation process. Int J Chem Phys Sci 2:38

    Google Scholar 

  • Mohanty SS, Koul Y, Varjani S, Pandey A, Ngo HH, Chang JS, Wong JW, Bui XT (2021) A critical review on various feedstocks as sustainable substrates for biosurfactants production: a way towards cleaner production. Microb Cell Fact 20(1):1–13. https://doi.org/10.1186/s12934-021-01613-3

    Article  Google Scholar 

  • Moutinho LF, Moura FR, Silvestre RC, Romão-Dumaresq AS (2021) Microbial biosurfactants: a broad analysis of properties, applications, biosynthesis, and techno-economical assessment of rhamnolipid production. Biotechnol Progr 37(2):e3093

    Article  CAS  Google Scholar 

  • Muller EE, Pinel N, Gillece JD, Schupp JM, Price LB, Engelthaler DM, Levantesi C, Tandoi V, Luong K, Baliga NS, Korlach J (2012) Genome sequence of “Candidatus Microthrix parvicella” Bio17-1, a long-chain-fatty-acid-accumulating filamentous actinobacterium from a biological wastewater treatment plant. J Bacteriol 194(23). https://doi.org/10.1128/JB.01765-12

  • Nagata Y, Ohtsubo Y, Endo R, Ichikawa N, Ankai A, Oguchi A, Fukui S, Fujita N, Tsuda M (2010) Complete genome sequence of the representative γ-hexachlorocyclohexane-degrading bacterium Sphingobium japonicum UT26. J Bacteriol 192:5852–5853. https://doi.org/10.1128/JB.00961-10

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ngara TR, Zhang H (2018) Recent advances in function-based metagenomic screening. Genomics Proteomics Bioinform 16(6):405–415. https://doi.org/10.1016/j.gpb.2018.01.002

    Article  Google Scholar 

  • Nguyen DD, Melnik AV, Koyama N, Lu X, Schorn M, Fang J, Aguinaldo K, Lincecum TL, Ghequire MG, Carrion VJ, Cheng TL (2016) Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides. Nat Microbiol 2(1):1–10. https://doi.org/10.1038/nmicrobiol.2016.197

    Article  CAS  Google Scholar 

  • Pan X, Lin D, Zheng Y, Zhang Q, Yin Y, Cai L, Fang H, Yu Y (2016) Biodegradation of DDT by Stenotrophomonas sp. DDT-1: characterization and genome functional analysis. Sci Rep 6(1):1–10. https://doi.org/10.1038/srep21332

    Article  CAS  Google Scholar 

  • Parakhia MV, Tomar RS, Dalal H, Kothari VV, Rathod VM, Golakiya BA (2019) Genome sequence analysis and identification of genes associated to pesticide degradation from enterobacter cloacae strain MR2. Int J Curr Microbiol App Sci 8:2289–2304. https://doi.org/10.20546/ijcmas.2019.801.240

    Article  CAS  Google Scholar 

  • Perruchon C, Chatzinotas A, Omirou M, Vasileiadis S, Menkissoglou-Spiroudi U, Karpouzas DG (2017) Isolation of a bacterial consortium able to degrade the fungicide thiabendazole: the key role of a Sphingomonas phylotype. Appl Microbiol Biotechnol 101(9):3881–3893

    Article  CAS  PubMed  Google Scholar 

  • Pitocchi R, Cicatiello P, Birolo L, Piscitelli A, Bovio E, Varese GC, Giardina P (2020) Cerato-platanins from marine fungi as effective protein biosurfactants and bioemulsifiers. Int J Mol Sci 21(8):2913. https://doi.org/10.3390/ijms21082913

    Article  CAS  PubMed Central  Google Scholar 

  • Raju SM, Bidlan R (2017) 16S metagenomic analysis and taxonomic distribution of enriched microbial consortia capable of simultaneous biodegradation of organochlorines by illumina platform. Biotechnol Commun 10:697–703

    Google Scholar 

  • Ramirez CAO, Kwan A, Li QX (2020) Rhamnolipids induced by glycerol enhance dibenzothiophene biodegradation in Burkholderia sp. C3. Engineering 6(5):533–540. https://doi.org/10.1016/j.eng.2020.01.006

    Article  CAS  Google Scholar 

  • Ranjan R, Rani A, Kumar R (2015) Exploration of microbial cells: the storehouse of bio-wealth through metagenomics and metatranscriptomics. In: Microbial factories, pp 7–27

    Chapter  Google Scholar 

  • Rodríguez E, García-Encina PA, Stams AJ, Maphosa F, Sousa DZ (2015) Meta-omics approaches to understand and improve wastewater treatment systems. Rev Environ Sci Biotechnol 14(3):385–406. https://doi.org/10.1007/s11157-015-9370-x

    Article  CAS  Google Scholar 

  • Rodríguez A, Castrejón-Godínez ML, Salazar-Bustamante E, Gama-Martínez Y, Sánchez-Salinas E, Mussali-Galante P, Tovar-Sánchez E, Ortiz-Hernández ML (2020) Omics approaches to pesticide biodegradation. Curr Microbiol 77(4):545–563. https://doi.org/10.1007/s00284-020-01916-5

    Article  CAS  PubMed  Google Scholar 

  • Rodríguez-Castillo G, Molina-Rodríguez M, Cambronero-Heinrichs JC, Quirós-Fournier JP, Lizano-Fallas V, Jiménez-Rojas C, Masís-Mora M, Castro-Gutiérrez V, Mata-Araya I, Rodríguez-Rodríguez CE (2019) Simultaneous removal of neonicotinoid insecticides by a microbial degrading consortium: Detoxification at reactor scale. Chemosphere 235:1097–1106

    Article  PubMed  Google Scholar 

  • Sasikala C, Jiwal S, Rout P, Ramya M (2012) Biodegradation of chlorpyrifos by bacterial consortium isolated from agriculture soil. World J Microbiol Biotechnol 28(3):1301–1308

    Article  CAS  PubMed  Google Scholar 

  • Sato Y, Hori T, Koike H, Navarro RR, Ogata A, Habe H (2019) Transcriptome analysis of activated sludge microbiomes reveals an unexpected role of minority nitrifiers in carbon metabolism. Commun Biol 2(1):1–8. https://doi.org/10.1038/s42003-019-0418-2

    Article  Google Scholar 

  • Schiffmann CL, Jehmlich N, Otto W, Hansen R, Nielsen PH, Adrian L, Seifert J, von Bergen M (2014) Proteome profile and proteogenomics of the organohalide-respiring bacterium Dehalococcoides mccartyi strain CBDB1 grown on hexachlorobenzene as electron acceptor. J Proteome 98:59–64. https://doi.org/10.1016/j.jprot.2013.12.009

    Article  CAS  Google Scholar 

  • Shabir G, Afzal M, Tahseen R, Iqbal S, Khan QM, Khalid ZM (2013) Treatment of oil refinery wastewater using pilot scale fed batch reactor followed by coagulation and sand filtration. Am J Environ Protect 1(1):10–13

    Article  Google Scholar 

  • Sharma I (2020) Bioremediation techniques for polluted environment: concept, advantages, limitations, and prospects. In: Trace metals in the environment-new approaches and recent advances. IntechOpen

    Google Scholar 

  • Sharma P, Pandey AK, Kim SH, Singh SP, Chaturvedi P, Varjani S (2021) Critical review on microbial community during in-situ bioremediation of heavy metals from industrial wastewater. Environ Technol Innov 24:101826. https://doi.org/10.1016/j.eti.2021.101826

    Article  CAS  Google Scholar 

  • Siggins A, Gunnigle E, Abram F (2012) Exploring mixed microbial community functioning: recent advances in metaproteomics. FEMS Microbiol Ecol 80(2):265–280. https://doi.org/10.1111/j.1574-6941.2011.01284.x

    Article  CAS  PubMed  Google Scholar 

  • Singanan M (2017) Silica interfaced biocarbon technology for decolourization and removal of pollutants from distillery wastewater and its safe use in farming practice–a green concept. Int J Water Resour Arid Environ 6(1):96–102

    Google Scholar 

  • Singh OV, Nagaraj NS (2006) Transcriptomics, proteomics and interactomics: unique approaches to track the insights of bioremediation. Brief Funct Genomics 4(4):355–362. https://doi.org/10.1093/bfgp/eli006

    Article  CAS  Google Scholar 

  • Tiso T, Ihling N, Kubicki S, Biselli A, Schonhoff A, Bator I, Thies S, Karmainski T, Kruth S, Willenbrink AL, Loeschcke A (2020) Integration of genetic and process engineering for optimized rhamnolipid production using Pseudomonas putida. Front Bioeng Biotechnol 8:976. https://doi.org/10.3389/fbioe.2020.00976

    Article  PubMed  PubMed Central  Google Scholar 

  • Tiwari B, Verma E, Chakraborty S, Srivastava AK, Mishra AK (2018) Tolerance strategies in cyanobacterium Fischerella sp. under pesticide stress and possible role of a carbohydrate-binding protein in the metabolism of methyl parathion (MP). Int Biodeterior Biodegradation 127:217–226. https://doi.org/10.1016/j.ibiod.2017.11.025

    Article  CAS  Google Scholar 

  • Vandera E, Samiotaki M, Parapouli M, Panayotou G, Koukkou AI (2015) Comparative proteomic analysis of Arthrobacter phenanthrenivorans Sphe3 on phenanthrene, phthalate and glucose. J Proteome 113:73–89

    Article  CAS  Google Scholar 

  • Varjani S, Upasani VN (2021) Bioaugmentation of Pseudomonas aeruginosa NCIM 5514—a novel oily waste degrader for treatment of petroleum hydrocarbons. Bioresour Technol 319:124240

    Article  CAS  PubMed  Google Scholar 

  • Varjani S, Pandey A, Upasani VN (2021) Petroleum sludge polluted soil remediation: Integrated approach involving novel bacterial consortium and nutrient application. Sci Total Environ 763:142934

    Article  CAS  PubMed  Google Scholar 

  • Villaverde J, Rubio-Bellido M, Merchán F, Morillo E (2017) Bioremediation of diuron contaminated soils by a novel degrading microbial consortium. J Environm Manag 188:379–386. https://doi.org/10.1016/j.jenvman.2016.12.020

    Article  CAS  Google Scholar 

  • Villaverde J, Rubio-Bellido M, Lara-Moreno A, Merchan F, Morillo E (2018) Combined use of microbial consortia isolated from different agricultural soils and cyclodextrin as a bioremediation technique for herbicide contaminated soils. Chemosphere 193:118–125

    Article  CAS  PubMed  Google Scholar 

  • Wang Y, Tian H, Huang F, Long W, Zhang Q, Wang J, Zhu Y, Wu X, Chen G, Zhao L, Bakken LR (2017) Time-resolved analysis of a denitrifying bacterial community revealed a core microbiome responsible for the anaerobic degradation of quinoline. Sci Rep 7(1):1–11

    PubMed  PubMed Central  Google Scholar 

  • Wang X, Xue L, Chang S, He X, Fan T, Wu J, Niu J, Emaneghemi B (2019) Bioremediation and metabolism of clothianidin by mixed bacterial consortia enriched from contaminated soils in Chinese greenhouse. Process Biochem 78:114–122

    Article  CAS  Google Scholar 

  • WHO (2002) Water pollutants: biological agents, dissolved chemicals, non-dissolved chemicals, sediments, heat. WHO CEHA, Amman

    Google Scholar 

  • Williams W, Trindade M (2017) Metagenomics for the discovery of novel biosurfactants. In: Functional metagenomics: tools and applications. Springer, Cham, pp 95–117

    Chapter  Google Scholar 

  • Williams W, Kunorozva L, Klaiber I, Henkel M, Pfannstiel J, Van Zyl LJ, Hausmann R, Burger A, Trindade M (2019) Novel metagenome-derived ornithine lipids identified by functional screening for biosurfactants. Appl Microbiol Biotechnol 103(11):4429–4441. https://doi.org/10.1007/s00253-019-09768-1

    Article  CAS  PubMed  Google Scholar 

  • Xu B, Xue R, Zhou J, Wen X, Shi Z, Chen M, Xin F, Zhang W, Dong W, Jiang M (2020) Characterization of acetamiprid biodegradation by the microbial consortium ACE-3 enriched from contaminated soil. Front Microbiol 11:1429

    Article  PubMed  PubMed Central  Google Scholar 

  • Yoneda A, Henson WR, Goldner NK, Park KJ, Forsberg KJ, Kim SJ, Pesesky MW, Foston M, Dantas G, Moon TS (2016) Comparative transcriptomics elucidates adaptive phenol tolerance and utilization in lipid-accumulating Rhodococcus opacus PD630. Nucleic Acids Res 44(5):2240–2254. https://doi.org/10.1093/nar/gkw055

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yunusa YR, Umar ZD (2021) Effective microbial bioremediation via the multi-omics approach: an overview of trends, problems and prospects. UMYU J Microbiol Res 6(1):127–145. https://doi.org/10.47430/ujmr.2161.022

    Article  Google Scholar 

  • Zampolli J, Di Canito A, Manconi A, Milanesi L, Di Gennaro P, Orro A (2020) Transcriptomic analysis of Rhodococcus opacus R7 grown on o-xylene by RNA-Seq. Front Microbiol 11:1808

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhang L, Hang P, Hu Q, Chen XL, Zhou XY, Chen K, Jiang JD (2018) Degradation of phenylurea herbicides by a novel bacterial consortium containing synergistically catabolic species and functionally complementary hydrolases. J Agric Food Chem 66(47):12479–12489. https://doi.org/10.1021/acs.jafc.8b03703

    Article  CAS  PubMed  Google Scholar 

  • Zhang C, Hao Q, Zhang S, Zhang Z, Zhang X, Sun P, Pan H, Zhang H, Sun F (2019) Transcriptomic analysis of Chlorimuronethyl degrading bacterial strain Klebsiella jilinsis 2N3. Ecotoxicol Environ Saf 183:109581. https://doi.org/10.1016/j.ecoenv.2019.109581

    Article  CAS  PubMed  Google Scholar 

  • Zhang W, Lin Z, Pang S, Bhatt P, Chen S (2020a) Insights into the biodegradation of lindane (γ-hexachlorocyclohexane) using a microbial system. Front Microbiol 11:522

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang F, Huo K, Song X, Quan Y, Gao W, Wang S, Yang C (2020b) Engineering modification of genome-reduced strain Bacillus amyloliquefaciens for enhancing surfactin production. Microb Cell Factories 19(1):22. https://doi.org/10.21203/rs.3.rs-41198/v3

    Article  Google Scholar 

  • Zhi Y, Wu Q, Xu Y (2017) Genome and transcriptome analysis of surfactin biosynthesis in Bacillus amyloliquefaciens MT45. Sci Rep 7(1):1–13

    Article  Google Scholar 

  • Zhou D, Hu F, Lin J, Wang W, Li S (2019) Genome and transcriptome analysis of Bacillus velezensis BS-37, an efficient surfactin producer from glycerol, in response to d-/l-leucine. MicrobiologyOpen 8(8):e00794. https://doi.org/10.1002/mbo3.794

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Sanjeev Kumar .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2022 The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Chaurasia, P., Jasuja, N.D., Kumar, S. (2022). Bioremediation Assessment in Industrial Wastewater Treatment: The Omics Approach. In: Kumar, V., Thakur, I.S. (eds) Omics Insights in Environmental Bioremediation. Springer, Singapore. https://doi.org/10.1007/978-981-19-4320-1_20

Download citation

Publish with us

Policies and ethics