Abstract
Environmental pollution and its remediation are one of the major problems around the globe. Broad varieties of pollutants viz. pesticides, hydrocarbons, heavy metals, and dyes, etc. are the key players, which are mainly responsible for environmental pollution. Residual contaminants are also difficult to eliminate. Bioremediation is one of the most efficient technologies for the reduction of environmental pollutants that recovers the contaminated site back to its actual form. So far only a small number of microbes (culturable microbes) have been exploited and a huge microbial diversity is still unexplored. To enhance the metabolic potential of the microbes, ecological restoration and degradation of recalcitrant pollutants, various bioremediation approaches like chemotaxis, biostimulation, bioaugmentation, biofilm formation, application of genetically engineered microorganisms, advanced omics, have been widely used. In the last few years, the metabolic potential of microbes has tremendously improved the realization of degradation and remediation of environmental pollution. Microorganisms help in the restoration of contaminated habitats by cleaning up waste in a environmentally safe manner along with the production of safe end products. This review discusses the important processes involved in enhancing bioremediation and recent advances in microbes and plants associated bioremediation.
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Adamson DT, McDade JM, Hughes JB (2003) Inoculation of a DNAPL source zone to initiate reductive dechlorination of PCE. Environ Sci Technol 37:2525–2533
Akilandeswari K, Sona V (2013) Efficiency of Staphylococcus aureusin the degradation an organo phosphorous pesticide Malathion. J Pharm Sci Innov 2:15
Alexander M (1994) Biodegradation and bioremediation. Academic Press, New York
Alkorta I, Hernández-Allica J, Becerril JM, Amezaga I, Albizu I, Garbisu C (2004) Recent findings on the phytoremediation of soils contaminated with environmentally toxic heavy metals and metalloids such as zinc, cadmium, lead, and arsenic. Rev Environ Sci Biotechnol 3:71–90
Arora NK (2018) Bioremediation: a green approach for restoration of polluted ecosystems. Env Sustain 1:305–307
Arora NK, Panosyan H (2019) Extremophiles: applications and roles in environmental sustainability. Env Sustain 2:217–218
Arora PK, Sasikala C, Ramana CV (2012) Degradation of chlorinated nitroaromatic compounds. Appl Microbiol Biotechnol 93:2265–2277
Ayotamuno JM, Kogbara RB, Agele EA, Agoro OS (2010) Composting and phytoremediation treatment of petroleum sludge. Soil Sediment Contam 19:686–695
Bargiela R, Herbst FA, Martínez-Martínez M, Seifert J, Rojo D, Cappello S (2015) Metaproteomics and metabolomics analyses of chronically petroleum-polluted sites reveal the importance of general anaerobic processes uncoupled with degradation. Proteomics 15:3508–3520
Basumatary B, Bordoloi S, Sarma HP (2012) Crude oil-contaminated soil phytoremediation by using Cyperus brevifolius (Rottb.) Hassk Water. Air Soil Pollut 223:3373–3383
Basumatary B, Saikia R, Chandra Das H, Bordoloi S (2013) Field note: phytoremediation of petroleum sludge contaminated field using sedge species, Cyperus rotundus (Linn.) and Cyperus brevifolius (Rottb.) Hassk. Int J Phytoremediation 15:877–888
Brune KD, Bayer TS (2012) Engineering microbial consortia to enhance biomining and bioremediation. Front Microbiol 2:203
Bursle E, Robson J (2016) Non-culture methods for detecting infection. Aust Prescr 39:171
Chakraborty R, Wu CH, Hazen TC (2012) Systems biology approach to bioremediation. Curr Opin Biotechnol 23:483–490
Chiuchiolo AL (2004) Persistent organic pollutants at the base of the Antarctic marine food web. Environ Sci Technol 38:3551–3557
Cybulski Z, Dzuirla E, Kaczorek E, Olszanowski A (2003) The influence of emulsifiers on hydrocarbon biodegradation by Pseudomonadacea and Bacillacea strains. Spill Sci Technol Bull 8:503–507
Da Silva ML, Alvarez PJ (2004) Enhanced anaerobic biodegradation of benzene-toluene-ethylbenzene-xylene-ethanol mixtures in bioaugmented aquifer columns. Appl Environ Microbiol 70:4720–4726
Daane L, Häggblom M (1999) Earthworm egg capsules as vectors for the environmental introduction of biodegradative bacteria. Appl Environ Microbiol 65:2376–2381
Daniel R (2004) The soil metagenome—a rich resource for the discovery of novel natural products. Curr Opin Biotechnol 15:199–204
Dean-Ross D, Moody J, Cerniglia CE (2002) Utilization of mixtures of polycyclic aromatic hydrocarbons by bacteria isolated from contaminated sediment. FEMS Microbiol Ecol 41:1–7
Dickson RP, Erb-Downward JR, Prescott HC, Martinez FJ, Curtis JL, Lama VN, Huffnagle GB (2014) Analysis of culture-dependent versus culture-independent techniques for identification of bacteria in clinically obtained bronchoalveolar lavage fluid. J Clin Microbiol 52:3605–3613
Dong X et al (2019) Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments. Nat Commun 10:1816
Duarte M, Nielsen A, Camarinha-Silva A, Vilchez-Vargas R, Bruls T, Wos-Oxley ML (2017) Functional soil metagenomics: elucidation of polycyclic aromatic hydrocarbon degradation potential following 12 years of in situ bioremediation. Environ Microbiol 19:2992–3011
Dybas MJ et al (2002) Development, operation, and long-term performance of a full-scale biocurtain utilizing bioaugmentation. Environ Sci Technol 36:3635–3644
El-Bestawy E, Sabir J, Mansy A, Zabermawi N (2014) Comparison among the efficiency of different bioremediation technologies of Atrazine-contaminated soils. J Bioremed Biodeg 5:237
Fuentes MS, Benimeli CS, Cuozzo SA, Saez JM, Amoroso MJ (2010) Microorganisms capable to degrade organochlorine pesticides. Curr Res Technol Educ Top Appl Microbiol Microb Biotechnol 2(2):1255–1264
Gangola S, Joshi S, Kumar S, Pandey SC (2019) Comparative analysis of fungal and bacterial enzymes in biodegradation of xenobiotic compounds. Smart bioremediation technologies: microbial enzymes. Academic Press, Cambridge, MA, pp 169–189
Garcia-Junco M, Gomez-Lahoz C, Niqui-Arroyo J-L, Ortega-Calvo J-J (2003) Biosurfactant-and biodegradation-enhanced partitioning of polycyclic aromatic hydrocarbons from nonaqueous-phase liquids. Environ Sci Technol 37:2988–2996
Gordillo F, Chavez FP, Jerez CA (2007) Motility and chemotaxis of Pseudomonas sp. B4 towards polychlorobiphenyls and chlorobenzoates. FEMS Microbiol Ecol 60:322–328
Goux S, Shapir N, El Fantroussi S, Lelong S, Agathos SN, Pussemier L (2003) Long-term maintenance of rapid atrazine degradation in soils inoculated with atrazine degraders. Water Air Soil Pollut Focus 3:131–142
Guang-Guo Y (2018) Remediation and mitigation strategies. Integrated analytical approaches for pesticide management. Elsevier, Amsterdam
Gupta G, Chandra A, Varjani SJ, Banerjee C, Kumar V (2018) Role of biosurfactants in enhancing the microbial degradation of pyrene. In: Bioremediation: applications for environmental protection and management. Springer, Singapore
Gupta G, Kumar V, Pal AK (2019) Microbial degradation of high molecular weight polycyclic aromatic hydrocarbons with emphasis on pyrene. Polycycl Aromat Compd 39:124–138
Hall J, Soole K, Bentham R (2011) Hydrocarbon phytoremediation in the family Fabacea—a review. Int J Phytoremediation 13:317–332
Harwood CS, Gibson J (1997) Shedding light on anaerobic benzene ring degradation: a process unique to prokaryotes? J Bacteriol 179:301–309
Holmes DE, O’Neil RA, Chavan MA, N’Guessan LA, Vrionis HA, Perpetua LA (2009) Transcriptome of Geobacter uraniireducens growing in uranium-contaminated subsurface sediments. ISME J 3:216–230
https://www.mdeq.ms.gov/wp-content/uploads/2017/06/Bioremediation
Jaiswal S, Singh DK, Shukla P (2019) Gene editing and systems biology tools for pesticide bioremediation: a review. Front Microbiol 10:87
Jennings LK, Chartrand MMG, Lacrampe-Couloume G, Lollar BS, Spain JC, Gossett JM (2009) Proteomic and transcriptomic analyses reveal genes upregulated by cis-dichloroethene in Polaromonas sp. strain JS666. Appl Environ Microbiol 75:3733–3744
Jitnuyanont P, Sayavedra-Soto LA, Semprini L (2001) Bioaugmentation of butane-utilizing microorganisms to promote cometabolism of 1,1,1-trichloroethane in groundwater microcosms. Biodegradation 12:11–22
Karami A, Shamsuddin ZH (2010) Phytoremediation of heavy metals with several efficiency enhancer methods. Afr J Biotechnol 9:3689–3698
Kariyama R, Kumon H (2003) Biofilm infections. Nihon rinsho Jpn J Clin Med 61:266
Keum YS, Seo JS, Li QX, Kim JH (2008) Comparative metabolomic analysis of Sinorhizobium sp. C4 during the degradation of phenanthrene. Appl Microbiol Biotechnol 80:863–872
Kim S-J, Kweon O, Jones RC, Freeman JP, Edmondson RD, Cerniglia CE (2007) Complete and integrated pyrene degradation pathway in Mycobacterium vanbaalenii PYR-1 based on systems biology. J Bacteriol 189:464–472
Kumar A, Bisht B, Joshi V, Dhewa T (2011) Review on bioremediation of polluted environment: a management tool. Int J Environ Sci 1:1079
Lacerda CM, Reardon KF (2009) Environmental proteomics: applications of proteome profiling in environmental microbiology and biotechnology. Brief Funct Genom Proteom 8:75–87
Lambert JM, Yang T, Thomson NR, Barker JF (2009) Pulsed biosparging of a residual fuel source emplaced at CFB borden. Int J Soil Sediment Water 2:6
Lange C et al (2007) Genome-wide analysis of growth phase-dependent translational and transcriptional regulation in halophilic archaea. BMC Genom 8:415
Law AM, Aitken MD (2003) Bacterial chemotaxis to naphthalene desorbing from a nonaqueous liquid. Appl Environ Microbiol 69:5968–5973
Lima D et al (2009) Evaluating a bioremediation tool for atrazine contaminated soils in open soil microcosms: the effectiveness of bioaugmentation and biostimulation approaches. Chemosphere 74:187–192
Luo Q, Zhang X, Wang H, Qian Y (2005) The use of non-uniform electrokinetics to enhance in situ bioremediation of phenol-contaminated soil. J Hazard Mater 121:187–194
MacNaughton SJ, Stephen JR, Venosa AD, Davis GA, Chang YJ, White DC (1999) Microbial population changes during bioremediation of an experimental oil spill. Appl Environ Microbiol 65:3566–3574
Major DW et al (2002) Field demonstration of successful bioaugmentation to achieve dechlorination of tetrachloroethene to ethene. Environ Sci Technol 36:5106–5116
Malik A (2006) Bioremediation. In: Environmental Microbiology. national science digital library, (xth five year plan network project of NISCAIR (CSIR), UGC, MHRD, New Delhi)
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
Martinez A, Kolvek SJ, Yip CL, Hopke J, Brown KA, MacNeil IA, Osburne MS (2004) Genetically modified bacterial strains and novel bacterial artificial chromosome shuttle vectors for constructing environmental libraries and detecting heterologous natural products in multiple expression hosts. Appl Environ Microbiol 70:2452–2463
Meckenstock RU, Morasch B, Warthmann R, Schink B, Annweiler E, Michaelis W, Richnow HH (1999) 13C/12C isotope fractionation of aromatic hydrocarbons during microbial degradation. Environ Microbiol 1:409–414
Mesjasz-Przybylowicz J et al (2004) Uptake of cadmium, lead, nickel and zinc from soil and water solutions by the nickel hyperaccumulator Berkheya coddii. Acta Biol Cracov Bot 46:75–85
Molin S, Klemm P, Poulsen L, Biehl H, Gerdes K, Andersson P (1987) Conditional suicide system for containment of bacteria and plasmids. Nat Biotechnol 5:1315
Naik M, Duraphe M (2012) Review paper on–parameters affecting bioremediation. Int J Life Sci Pharma Res 2:L77–L80
Niu H, Wang J, Zhuang W, Liu D, Chen Y, Zhu C (2018) Comparative transcriptomic and proteomic analysis of Arthrobacter sp. CGMCC 3584 responding to dissolved oxygen for cAMP production. Sci Rep 8:1–13
Odukkathil G, Vasudevan N (2013) Enhanced biodegradation of endosulfan and its major metabolite endosulfate by a biosurfactant producing bacterium. J Environ Sci Health Part B 48:462–469
Olawale A, Akintobi O (2011) Biodegradation of glyphosate pesticide by bacteria isolated from agricultural soil Report and Opinion 3:124–128
Olson MS, Ford RM, Smith JA, Fernandez EJ (2004) Quantification of bacterial chemotaxis in porous media using magnetic resonance imaging. Environ Sci Technol 38:3864–3870
Pande V, Pandey SC, Joshi T, Sati D, Gangola S, Kumar S, Samant M (2019) Biodegradation of toxic dyes: a comparative study of enzyme action in a microbial system. In: Smart bioremediation technologies: microbial enzymes. pp 255
Pandey SC, Pande V, Sati D, Gangola S, Kumar S, Pandey A, Samant M (2019) Microbial keratinase: a tool for bioremediation of feather waste. In: Smart bioremediation technologies: microbial enzyme. pp 217
Pandey SC, Pandey A, Joshi T, Pande V, Sati D, Samant M (2019) Microbiological monitoring in the biodegradation of food waste. in: global initiatives for waste reduction and cutting food loss. In: IGI Global. pp 116–140
Petersen J (2011) Phylogeny and compatibility: plasmid classification in the genomics era. Arch Microbiol 193:313–321
Prescott LM, Harley JP, Klein DA (2002) Microbiology, 5th edn. McGrawHill, New York
Roane TM, Josephson KL, Pepper IL (2001) Dual-bioaugmentation strategy to enhance remediation of cocontaminated soil. Appl Environ Microbiol 67:3208–3215
Rondon MR et al (2000) Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl Environ Microbiol 66:2541–2547
Roy M, Giri AK, Dutta S, Mukherjee P (2015) Integrated phytobial remediation for sustainable management of arsenic in soil and water. Environ Int 75:180–198
Samant M, Pandey SC, Pandey A (2018) Impact of hazardous waste material on environment and their management strategies. In: Microbial biotechnology in environmental monitoring and cleanup. pp 175–192
Sardrood BP, Goltapeh EM, Varma A (2013) An introduction to bioremediation. Fungi as bioremediators. Springer, Berlin, Heidelberg, pp 3–27
Schloss PD, Handelsman J (2003) Biotechnological prospects from metagenomics. Curr Opin Biotechnol 14:303–310
Shinde S (2013) Bioremediation. Overview Recent Res Sci Technol 5:67–72
Singer A, Gilbert E, Luepromchai E, Crowley D (2000) Bioremediation of polychlorinated biphenyl-contaminated soil using carvone and surfactant-grown bacteria. Appl Microbiol Biotechnol 54:838–843
Garima T, Singh, SP (2016) Application of bioremediation on solid waste management: a review. Solid Waste Manag Policy Plan Sustain Soc 143
Singh D, Fulekar MH (2010) Biodegradation of petroleum hydrocarbons by Pseudomonas putida strain MHF 7109 CLEAN–soil. Air Water 38:781–786
Singh BK, Walker A, Morgan JA, Wright DJ (2004a) Biodegradation of chlorpyrifos by enterobacter strain B-14 and its use in bioremediation of contaminated soils. Appl Environ Microbiol 70:4855–4863
Singh P, Suri CR, Cameotra SS (2004b) Isolation of a member of Acinetobacter species involved in atrazine degradation. Biochem Biophys Res Commun 317:697–702
Smith AE, Hristova K, Wood I, Mackay DM, Lory E, Lorenzana D, Scow KM (2005) Comparison of biostimulation versus bioaugmentation with bacterial strain PM1 for treatment of groundwater contaminated with methyl tertiary butyl ether (MTBE). Environ Health Perspect 113:317–322
Streger SH, Vainberg S, Dong H, Hatzinger PB (2002) Enhancing transport of hydrogenophaga flava ENV735 for bioaugmentation of aquifers contaminated with methyl tert-butyl ether. Appl Environ Microbiol 68:5571–5579
Tang YJ, Martin HG, Dehal PS, Deutschbauer A, Llora X, Meadows A (2009) Metabolic flux analysis of Shewanella spp. reveals evolutionary robustness in central carbon metabolism. Biotechnol Bioeng 102:1161–1169
Tang J, Wang R, Niu X, Zhou Q (2010) Enhancement of soil petroleum remediation by using a combination of ryegrass (Lolium perenne) and different microorganisms. Soil Tillage Res 110:87–93
Techtmann SM, Hazen TC (2016) Metagenomic applications in environmental monitoring and bioremediation. J Ind Microbiol Biotechnol 43:1345–1354
Torres B, Jaenecke S, Timmis KN, García JL, Díaz E (2003) A dual lethal system to enhance containment of recombinant micro-organisms. Microbiology 149:3595–3601
Torsvik V, Ovreas L (2002) Microbial diversity and function in soil: from genes to ecosystems. Curr Opin Microbiol 5:240–245
Tripathi M, Singh D, Vikram S, Singh V, Kumar S (2018) Metagenomic approach towards bioprospection of novel biomolecule(s) and environmental bioremediation. Annu Res Rev Biol 22:1–12
Urgun-Demirtas M, Stark B, Pagilla K (2006) Use of genetically engineered microorganisms (GEMs) for the bioremediation of contaminants. Crit Rev Biotechnol 26:145–164
Van Deuren J, Lloyd T, Chhetry S, Raycharn L, Peck J (2002) Remediation technologies screening matrix and reference guide, vol 4. Federal Remediation Technologies Roundtable
Venter JC et al (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66–74
Verberkmoes NC, Russell AL, Shah M, Godzik A, Rosenquist M, Halfvarson J, Lefsrud MG, Apajalahti J, Tysk C, Hettich RL, Jansson JK (2009) Shotgun metaproteomics of the human distal gut microbiota. ISME J 3:179
Voget S, Leggewie C, Uesbeck A, Raasch C, Jaeger KE, Streit WR (2003) Prospecting for novel biocatalysts in a soil metagenome. Appl Environ Microbiol 69:6235–6242
Wenderoth D, Rosenbrock P, Abraham W-R, Pieper D, Höfle M (2003) Bacterial community dynamics during biostimulation and bioaugmentation experiments aiming at chlorobenzene degradation in groundwater. Microb Ecol 46:161–176
Yousaf S, Ripka K, Reichenauer T, Andria V, Afzal M, Sessitsch A (2010) Hydrocarbon degradation and plant colonization by selected bacterial strains isolated from Italian ryegrass and birdsfoot trefoil. J Appl Microbiol 109:1389–1401
Zhao B, Yeo CC, Poh CL (2005) Proteome investigation of the global regulatory role of s54 in response to gentisate induction in Pseudomonas alcaligenes NCIMB 9867. Proteomic 5:1868–1876
Zhao X, Hardin IR, Hwang HM (2006) Biodegradation of a model azo disperse dye by the white rot fungus Pleurotus ostreatus. Int Biodeterior Biodegrad 57:1–6
Zhou J et al (2003) Bacterial phylogenetic diversity and a novel candidate division of two humid region, sandy surface soils. Soil Biol Biochem 35:915–924
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Authors are thankful to the Department of Zoology, Kumaun University, SSJ Campus, Almora (Uttarakhand), India and for providing facility and space for this research work.
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Pande, V., Pandey, S.C., Sati, D. et al. Bioremediation: an emerging effective approach towards environment restoration. Environmental Sustainability 3, 91–103 (2020). https://doi.org/10.1007/s42398-020-00099-w
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DOI: https://doi.org/10.1007/s42398-020-00099-w