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Cited by 195Microbial bioremediation and biosurfactantsMicrobial Metabolic Engineering and BioproductionMicrobial Fuel Cells and Bioremediation

Alternative Strategies for Microbial Remediation of Pollutants via Synthetic Biology

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Jaiswal, Shweta, Shukla, Pratyoosh·2020·Frontiers in Microbiology
DOI 10.3389/fmicb.2020.00808PMC PMC7249858
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Abstract

Continuous contamination of the environment with xenobiotics and related recalcitrant compounds has emerged as a serious pollution threat. Bioremediation is the key to eliminating persistent contaminants from the environment. Traditional bioremediation processes show limitations, therefore it is necessary to discover new bioremediation technologies for better results. In this review we provide an outlook of alternative strategies for bioremediation via synthetic biology, including exploring the prerequisites for analysis of research data for developing synthetic biological models of microbial bioremediation. Moreover, cell coordination in synthetic microbial community, cell signaling, and quorum sensing as engineered for enhanced bioremediation strategies are described, along with promising gene editing tools for obtaining the host with target gene sequences responsible for the degradation of recalcitrant compounds. The synthetic genetic circuit and two-component regulatory system (TCRS)-based microbial biosensors for detection and bioremediation are also briefly explained. These developments are expected to increase the efficiency of bioremediation strategies for best results.

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  1. Adams B. L. (2016). The next generation of synthetic biology chassis: moving synthetic biology from the laboratory to the field. ACS Synth Biol. 5 1328– 1330. 10.1021/acssynbio.6b00256 27665861 · DOI
  2. Adhikari B. R. (2019). “ Advances in the oligonucleotide-based sensor technology for detection of pharmaceutical contaminants in the environment,” in Tools, Techniques and Protocols for Monitoring Environmental Contaminants, eds Brar S. K. Hegde K. Pachapur V. L. (Amsterdam: Elsevier), 125– 146.
  3. Agapakis C. M. Boyle P. M. Silver P. A. (2012). Natural strategies for the spatial optimization of metabolism in synthetic biology. Nat. Chem. Biol. 8 527– 535. 10.1038/nchembio.975 22596204 · DOI
  4. Ahankoub M. Mardani G. Ghasemi-Dehkordi P. Mehri-Ghahfarrokhi A. Doosti A. Jami M. S. (2020). Biodecomposition of phenanthrene and pyrene by a genetically engineered Escherichia coli. Recent Patents Biotechnol. 10.2174/1872208314666200128103513 [Online ahead of print]. 31994474 · DOI
  5. Alves L. D. F. Westmann C. A. Lovate G. L. de Siqueira G. M. V. Borelli T. C. Guazzaroni M. E. (2018). Metagenomic approaches for understanding new concepts in microbial science. Int. J. Genom. 2018: 2312987. 10.1155/2018/2312987 30211213 PMC6126073 · DOI
  6. Andres J. Bertin P. N. (2016). The microbial genomics of arsenic. FEMS Microbiol. Rev. 40 299– 322. 10.1093/femsre/fuv050 26790947 · DOI
  7. Antonacci A. Scognamiglio V. (2019). Biotechnological advances in the design of algae-based biosensors. Trends Biotechnol. 38 334– 347. 10.1016/j.tibtech.2019.10.005 31706693 · DOI · Paper page
  8. Arora P. K. Bae H. (2014). Integration of bioinformatics to biodegradation. Biol. Procedures Online 16: 8. 10.1186/1480-9222-16-8 24808763 PMC4012781 · DOI
  9. Atashgahi S. Hornung B. Waals M. J. Rocha U. N. Hugenholtz F. Nijsse B. (2018). A benzene-degrading nitrate-reducing microbial consortium displays aerobic and anaerobic benzene degradation pathways. Sci. Rep. 8: 4490. 10.1038/s41598-018-22617-x 29540736 PMC5852087 · DOI
  10. Azubuike C. C. Chikere C. B. Okpokwasili G. C. (2016). Bioremediation techniques–classification based on site of application: principles, advantages, limitations and prospects. World J. Microbiol. Biotechnol. 32: 180. 10.1007/s11274-016-2137-x 27638318 PMC5026719 · DOI
  11. Banerjee C. Singh P. K. Shukla P. (2016). Microalgal bioengineering for sustainable energy development: recent transgenesis and metabolic engineering strategies. Biotechnol. J. 11 303– 314. 10.1002/biot.201500284 26844808 · DOI
  12. Bao Y. J. Xu Z. Li Y. Yao Z. Sun J. Song H. (2017). High-throughput metagenomic analysis of petroleum-contaminated soil microbiome reveals the versatility in xenobiotic aromatics metabolism. J. Environ. Sci. 56 25– 35. 10.1016/j.jes.2016.08.022 28571861 · DOI
  13. Berger B. Peng J. Singh M. (2013). Computational solutions for omics data. Nat. Rev. Genet. 14: 333. 10.1038/nrg3433 23594911 PMC3966295 · DOI
  14. Bertin P. N. Heinrich-Salmeron A. Pelletier E. Goulhen-Chollet F. Arsène-Ploetze F. Gallien S. (2011). Metabolic diversity among main microorganisms inside an arsenic-rich ecosystem revealed by meta-and proteo-genomics. ISME J. 5: 1735. 10.1038/ismej.2011.51 21562598 PMC3197163 · DOI
  15. Bharagava R. N. Purchase D. Saxena G. Mulla S. I. (2019). “ Applications of metagenomics in microbial bioremediation of pollutants: from genomics to environmental cleanup,” in Microbial Diversity in the Genomic Era, eds Das S. Dash H. R. (Cambridge, MA: Academic Press), 459– 477.
  16. Biggs M. B. Medlock G. L. Kolling G. L. Papin J. A. (2015). Metabolic network modeling of microbial communities. Wiley Interdiscipl. Rev. 7 317– 334. 10.1002/wsbm.1308 26109480 PMC4575871 · DOI · Paper page
  17. Bordbar A. Monk J. M. King Z. A. Palsson B. O. (2014). Constraint-based models predict metabolic and associated cellular functions. Nat. Rev. Genet. 15: 107. 10.1038/nrg3643 24430943 · DOI
  18. Bordel S. (2014). “ Genome-scale metabolic models of yeast, methods for their reconstruction, and other applications,” in Yeast Metabolic Engineering, ed. Mapelli V. (New York, NY: Humana Press), 269– 279. 10.1007/978-1-4939-0563-8_16 24744039 · DOI
  19. Boudh S. Singh J. S. Chaturvedi P. (2019). “ Microbial resources mediated bioremediation of persistent organic pollutants,” in New and Future Developments in Microbial Biotechnology and Bioengineering, eds Singh J. S. Singh D. P. (Amsterdam: Elsevier), 283– 294.
  20. Bruggeman F. J. Westerhoff H. V. (2007). The nature of systems biology. TRENDS Microbiol. 15 45– 50. 17113776
  21. Bruneel O. Volant A. Gallien S. Chaumande B. Casiot C. Carapito C. (2011). Characterization of the active bacterial community involved in natural attenuation processes in arsenic-rich creek sediments. Microb. Ecol. 61 793– 810. 10.1007/s00248-011-9808-9 21318282 · DOI
  22. Butler J. E. Young N. D. Lovley D. R. (2010). Evolution of electron transfer out of the cell: comparative genomics of six Geobacter genomes. BMC Genomics 11: 40. 10.1186/1471-2164-11-40 20078895 PMC2825233 · DOI
  23. Carbajosa G. Cases I. (2010). “ Transcriptional networks that regulate hydrocarbon biodegradation,” in Handbook of Hydrocarbon and Lipid Microbiology, eds Timmis K. N. McGenity T. van der Meer J. R. de Lorenzo V. (Berlin: Springer), 1399– 1410.
  24. Casino P. Rubio V. Marina A. (2010). The mechanism of signal transduction by two-component systems. Curr. Opin. Struct. Biol 20 763– 771. 10.1016/j.sbi.2010.09.010 20951027 · DOI
  25. Cavalca L. Corsini A. Zaccheo P. Andreoni V. Muyzer G. (2013). Microbial transformations of arsenic: perspectives for biological removal of arsenic from water. Future Microbiol. 8 753– 768. 10.2217/fmb.13.38 23586329 · DOI
  26. Cervelli E. Pindozzi S. Capolupo A. Okello C. Rigillo M. Boccia L. (2016). Ecosystem services and bioremediation of polluted areas. Ecol. Eng. 87 139– 149. 10.1016/j.copbio.2013.10.010 24863896 · DOI
  27. Chakraborty J. Jana T. Saha S. Dutta T. K. (2014). R ing-H ydroxylating O xygenase database: a database of bacterial aromatic ring-hydroxylating oxygenases in the management of bioremediation and biocatalysis of aromatic compounds. Environ. Microbiol. Rep. 6 519– 523. 10.1111/1758-2229.12182 25646545 · DOI
  28. Chandra D. General T. Chandra S. (2019). “ Microorganisms: an asset for decontamination of soil,” in Smart Bioremediation Technologies, Ed. Bhatt P. (Cambridge, MA: Academic Press), 319– 345.
  29. Checa S. K. Zurbriggen M. D. Soncini F. C. (2012). Bacterial signaling systems as platforms for rational design of new generations of biosensors. Curr. Opin. Biotechnol 23 766– 772. 10.1016/j.copbio.2012.05.003 22658939 · DOI
  30. Chen S. Chang C. Deng Y. An S. Dong Y. H. Zhou J. (2014). Fenpropathrin biodegradation pathway in Bacillus sp. DG-02 and its potential for bioremediation of pyrethroid-contaminated soils. J. Agricult. Food Chem. 62 2147– 2157. 10.1021/jf404908j 24576059 · DOI
  31. Chen W. Zhang Y. Zhang Y. Pi Y. Gu T. Song L. (2018). CRISPR/Cas9-based genome editing in Pseudomonas aeruginosa and cytidine deaminase-mediated base editing in Pseudomonas species. IScience 6 222– 231. 10.1016/j.isci.2018.07.024 30240613 PMC6137401 · DOI
  32. Choe S. I. Sheppard D. C. (2016). “ Bioremediation of arsenic using an aspergillus system,” in New and Future Developments in Microbial Biotechnology and Bioengineering, ed. Gupta V. K. (Amsterdam: Elsevier Science), 267– 274.
  33. Covert M. W. Schilling C. H. Famili I. Edwards J. S. Goryanin I. I. Selkov E. (2001). Metabolic modeling of microbial strains in silico. Trends Biochem. Sci. 26 179– 186. 10.1016/s0968-0004(00)01754-0 11246024 · DOI
  34. Coyte K. Z. Schluter J. Foster K. R. (2015). The ecology of the microbiome: networks, competition, and stability. Science 350 663– 666. 10.1126/science.aad2602 26542567 · DOI
  35. Dangi A. K. Sharma B. Hill R. T. Shukla P. (2019). Bioremediation through microbes: systems biology and metabolic engineering approach. Crit. Rev. Biotechnol. 39 79– 98. 10.1080/07388551.2018.1500997 30198342 · DOI
  36. Das S. Dash H. R. Chakraborty J. (2016). Genetic basis and importance of metal resistant genes in bacteria for bioremediation of contaminated environments with toxic metal pollutants. Appl. Microbiol. Biotechnol. 100 2967– 2984. 10.1007/s00253-016-7364-4 26860944 · DOI
  37. Davison J. (2002). Towards safer vectors for the field release of recombinant bacteria. Environ. Biosaf. Res. 1 9– 18. 10.1051/ebr:2002001 15612252 · DOI
  38. De Jong H. (2002). Modeling and simulation of genetic regulatory systems: a literature review. J. Comput. Biol. 9 67– 103. 10.1089/10665270252833208 11911796 · DOI
  39. de la Pena Mattozzi M. Tehara S. K. Hong T. Keasling J. D. (2006). Mineralization of paraoxon and its use as a sole C and P source by a rationally designed catabolic pathway in Pseudomonas putida. Appl. Environ. Microbiol. 72 6699– 6706. 10.1128/AEM.00907-06 17021221 PMC1610300 · DOI
  40. Dellagnezze B. M. de Sousa G. V. Martins L. L. Domingos D. F. Limache E. E. de Vasconcellos S. P. (2014). Bioremediation potential of microorganisms derived from petroleum reservoirs. Mar. Pollut. Bull. 89 191– 200. 10.1016/j.marpolbul.2014.10.003 25457810 · DOI
  41. Desai C. Pathak H. Madamwar D. (2010). Advances in molecular and “-omics” technologies to gauge microbial communities and bioremediation at xenobiotic/anthropogen contaminated sites. Bioresour. Technol. 101 1558– 1569. 10.1016/j.biortech.2009.10.080 19962886 · DOI
  42. Dhar D. Roy S. Nigam V. K. (2019). “ Advances in protein/enzyme-based biosensors for the detection of pharmaceutical contaminants in the environment,” in Tools, Techniques and Protocols for Monitoring Environmental Contaminants, eds Brar S. K. Hegde K. Pachapur V. L. (Amsterdam: Elsevier), 207– 229.
  43. Duarte M. Nielsen A. Camarinha-Silva A. Vilchez-Vargas R. Bruls T. Wos-Oxley M. L. (2017). Functional soil metagenomics: elucidation of polycyclic aromatic hydrocarbon degradation potential following 12 years of in situ bioremediation. Environ. Microbiol. 19 2992– 3011. 10.1111/1462-2920.13756 28401633 · DOI
  44. Dvorak P. Bidmanova S. Damborsky J. Prokop Z. (2014). Immobilized synthetic pathway for biodegradation of toxic recalcitrant pollutant 1, 2, 3-trichloropropane. Environ. Sci. Technol. 48 6859– 6866. 10.1021/es500396r 24787668 · DOI
  45. Dvořák P. Nikel P. I. Damborský J. de Lorenzo V. (2017). Bioremediation 3.0: engineering pollutant-removing bacteria in the times of systemic biology. Biotechnol. Adv. 35 845– 866. 10.1016/j.biotechadv.2017.08.001 28789939 · DOI
  46. El Amrani A. Dumas A. S. Wick L. Y. Yergeau E. Berthome R. (2015). Omics” insights into PAH degradation toward improved green remediation biotechnologies. Environ. Sci. Technol. 49 11281– 11291. 10.1021/acs.est.5b01740 26352597 · DOI
  47. Fernandez M. Paisio C. E. Perotti R. Pereira P. P. Agostini E. González P. S. (2019). Laboratory and field microcosms as useful experimental systems to study the bioaugmentation treatment of tannery effluents. J. Environ. Manag. 234 503– 511. 10.1016/j.jenvman.2019.01.019 30648649 · DOI
  48. Foster K. R. Bell T. (2012). Competition, not cooperation, dominates interactions among culturable microbial species. Curr. Biol. 22 1845– 1850. 10.1016/j.cub.2012.08.005 22959348 · DOI
  49. French K. E. Zhou Z. Terry N. (2019). Horizontal” gene drives” harness indigenous bacteria for bioremediation. bioRxiv [Preprint] 10.1101/735886v2 PMC7492276 32934307 · DOI
  50. Futagami T. Goto M. Furukawa K. (2014). “ Genetic system of organohalide-respiring bacteria,” in Biodegradative Bacteria, eds Kamagata Y. Tsuda M. Nojiri H. (Tokyo: Springer), 59– 81.
  51. Gangar T. Bhardwaj K. K. Gupta R. (2019). “ Microbes and processes in bioremediation of soil,” in Microbes and Enzymes in Soil Health and Bioremediation, eds Kumar A. Sharma S. (Singapore: Springer), 11– 37.
  52. Gardner C. M. Gunsch C. K. (2020). “ Environmental microbiome analysis and manipulation,” in Women in Water Quality, Ed. O’Bannon D. J. (Cham: Springer), 113– 133.
  53. Gillan D. C. Roosa S. Kunath B. Billon G. Wattiez R. (2015). The long-term adaptation of bacterial communities in metal-contaminated sediments: a metaproteogenomic study. Environ. Microbiol. 17 1991– 2005. 10.1111/1462-2920.12627 25244307 · DOI
  54. Gómez-Tatay L. Hernández-Andreu J. M. (2019). Biosafety and biosecurity in synthetic biology: a review. Crit. Rev. Environ. Sci. Technol. 49 1587– 1621.
  55. Gong J. Liu X. Cao X. Diao Y. Gao D. Li H. (2012). PTID: an integrated web resource and computational tool for agrochemical discovery. Bioinformatics 29 292– 294. 10.1093/bioinformatics/bts651 23162083 · DOI
  56. Gong T. Liu R. Zuo Z. Che Y. Yu H. Song C. (2016). Metabolic engineering of Pseudomonas putida KT2440 for complete mineralization of methyl parathion and γ-hexachlorocyclohexane. ACS Synthetic Biol. 5 434– 442. 10.1021/acssynbio.6b00025 26854500 · DOI
  57. Großkopf T. Soyer O. S. (2014). Synthetic microbial communities. Curr. Opin. Microbiol. 18 72– 77. 10.1016/j.mib.2014.02.002 24632350 PMC4005913 · DOI
  58. Gupta S. Pathak B. (2020). “ Mycoremediation of polycyclic aromatic hydrocarbons,” in Abatement of Environmental Pollutants, eds Singh P. Kumar A. Borthakur A. (Amsterdam: Elsevier), 127– 149.
  59. Gupte A. Tripathi A. Patel H. Rudakiya D. Gupte S. (2016). Bioremediation of polycyclic aromatic hydrocarbon (PAHs): a perspective. Open Biotechnol. J. 10 363– 378. 10.1016/j.chemosphere.2013.03.025 23582404 · DOI
  60. Hamilton T. A. Pellegrino G. M. Therrien J. A. Ham D. T. Bartlett P. C. Karas B. J. (2019). Efficient inter-species conjugative transfer of a CRISPR nuclease for targeted bacterial killing. Nat. Commun. 10 1– 9. 10.1038/s41467-019-12448-3 31586051 PMC6778077 · DOI
  61. Hawley E. R. Piao H. Scott N. M. Malfatti S. Pagani I. Huntemann M. (2014). Metagenomic analysis of microbial consortium from natural crude oil that seeps into the marine ecosystem offshore Southern California. Standards Genom. Sci. 9: 1259. 10.4056/sigs.5029016 25197496 PMC4149020 · DOI
  62. Hellweger F. L. Clegg R. J. Clark J. R. Plugge C. M. Kreft J. U. (2016). Advancing microbial sciences by individual-based modelling. Nat. Rev. Microbiol. 14: 461. 10.1038/nrmicro.2016.62 27265769 · DOI · Paper page
  63. Hemmat-Jou M. H. Safari-Sinegani A. A. Mirzaie-Asl A. Tahmourespour A. (2018). Analysis of microbial communities in heavy metals-contaminated soils using the metagenomic approach. Ecotoxicology 27 1281– 1291. 10.1007/s10646-018-1981-x 30242595 · DOI
  64. Heng L. Y. Ooi L. Mori I. C. Futra D. (2018). “ Environmental toxicity and evaluation,” in Environmental Risk Analysis for Asian-Oriented, Risk-Based Watershed Management, eds Yoneda M. Mokhtar M. (Singapore: Springer), 71– 94.
  65. Hong Y. H. Ye C. C. Zhou Q. Z. Wu X. Y. Yuan J. P. Peng J. (2017). Genome sequencing reveals the potential of Achromobacter sp. HZ01 for bioremediation. Front. Microbiol. 8: 1507. 10.3389/fmicb.2017.01507 28848520 PMC5552670 · DOI
  66. Jacquiod S. Demanèche S. Franqueville L. Ausec L. Xu Z. Delmont T. O. (2014). Characterization of new bacterial catabolic genes and mobile genetic elements by high throughput genetic screening of a soil metagenomic library. J. Biotechnol. 190 18– 29. 10.1016/j.jbiotec.2014.03.036 24721211 · DOI
  67. Jadeja N. B More R. P Purohit H. J Kapley A. (2014). Metagenomic analysis of oxygenases from activated sludge. Bioresour. Technol. 165 250– 256. 10.1016/j.biortech.2014.02.045 24631150 · DOI
  68. Jaiswal S. Singh D. K. Shukla P. (2019b). Gene editing and systems biology tools for pesticide bioremediation: a review. Front. Microbiol. 10: 87. 10.3389/fmicb.2019.00087 30853940 PMC6396717 · DOI
  69. Janssen D. B. Stucki G. (2020). Perspectives of genetically engineered microbes for groundwater bioremediation. Environ. Sci. Process. Impacts 22 487– 499. 10.1039/c9em00601j 32095798 · DOI
  70. Johns N. I. Blazejewski T. Gomes A. L. Wang H. H. (2016). Principles for designing synthetic microbial communities. Curr. Opin. Microbiol. 31 146– 153. 10.1016/j.mib.2016.03.010 27084981 PMC4899134 · DOI
  71. Joshi G. Schmidt R. Scow K. M. Denison M. S. Hristova K. R. (2016). Effect of benzene and ethylbenzene on the transcription of methyl-tert-butyl ether degradation genes of Methylibium petroleiphilum PM1. Microbiology 162 1563– 1571. 10.1099/mic.0.000338 27450417 PMC5903209 · DOI
  72. Junghare M. Spiteller D. Schink B. (2019). Anaerobic degradation of xenobiotic isophthalate by the fermenting bacterium Syntrophorhabdus aromaticivorans. ISME J. 13 1252– 1268. 10.1038/s41396-019-0348-5 30647456 PMC6474229 · DOI
  73. Jusiak B. Cleto S. Perez-Pińera P. Lu T. K. (2016). Engineering synthetic gene circuits in living cells with CRISPR technology. Trends Biotechnol. 34 535– 547. 10.1016/j.tibtech.2015.12.014 26809780 · DOI
  74. Kachienga L. Jitendra K. Momba M. (2018). Metagenomic profiling for assessing microbial diversity and microbial adaptation to degradation of hydrocarbons in two South African petroleum-contaminated water aquifers. Sci. Rep. 8: 7564. 10.1038/s41598-018-25961-0 29765091 PMC5954097 · DOI
  75. Kanchiswamy C. N. Maffei M. Malnoy M. Velasco R. Kim J. S. (2016). Fine-tuning next-generation genome editing tools. Trends Biotechnol. 34 562– 574. 10.1016/j.tibtech.2016.03.007 27167723 · DOI
  76. Kapetanovic I. M. (2008). Computer-aided drug discovery and development (CADDD): in silico-chemico-biological approach. Chem. Biol. Interact 171 165– 176. 10.1016/j.cbi.2006.12.006 17229415 PMC2253724 · DOI · Paper page
  77. Karimi B. Habibi M. Esvand M. (2015). Biodegradation of naphthalene using Pseudomonas aeruginosa by up flow anoxic–aerobic continuous flow combined bioreactor. J. Environ. Health Sci. Eng. 13 26. 10.1186/s40201-015-0175-1 25859393 PMC4391106 · DOI
  78. Khan F. I. Husain T. Hejazi R. (2004). An overview and analysis of site remediation technologies. J. Environ. Manag. 71 95– 122. 10.1016/j.jenvman.2004.02.003 15135946 · DOI
  79. Khan S. Nawab J. Waqas M. (2020). “ Constructed wetlands: a clean-green technology for degradation and detoxification of industrial wastewaters,” in Bioremediation of Industrial Waste for Environmental Safety, eds Bharagava R. N. Saxena G. (Singapore: Springer), 127– 163.
  80. Khan S. Ullah M. W. Siddique R. Nabi G. Manan S. Yousaf M. (2016). Role of recombinant DNA technology to improve life. Int. J. Genom. 2016: 2405954. 10.1155/2016/2405954 28053975 PMC5178364 · DOI
  81. Khan S. H. (2019). Genome-editing technologies: concept, pros, and cons of various genome-editing techniques and bioethical concerns for clinical application. Mol. Ther. Nucleic Acids 16: 326. 10.1016/j.omtn.2019.02.027 30965277 PMC6454098 · DOI
  82. Khandelwal R. A. Olivier B. G. Röling W. F. Teusink B. Bruggeman F. J. (2013). Community flux balance analysis for microbial consortia at balanced growth. PLoS One 8: e64567. 10.1371/journal.pone.0064567 23741341 PMC3669319 · DOI
  83. Khudur L. S. Shahsavari E. Webster G. T. Nugegoda D. Ball A. S. (2019). The impact of lead co-contamination on ecotoxicity and the bacterial community during the bioremediation of total petroleum hydrocarbon-contaminated soils. Environ. Pollut. 253 939– 948. 10.1016/j.envpol.2019.07.107 31351302 · DOI
  84. Kim B. Kim W. J. Kim D. I. Lee S. Y. (2015). Applications of genome-scale metabolic network model in metabolic engineering. J. Indus. Microbiol. Biotechnol. 42 339– 348. 10.1007/s10295-014-1554-9 25465049 · DOI
  85. Kim S. J. Park S. J. Cha I. T. Min D. Kim J. S. Chung W. H. (2014). Metabolic versatility of toluene-degrading, iron-reducing bacteria in tidal flat sediment, characterized by stable isotope probing-based metagenomic analysis. Environ. Microbiol. 16 189– 204. 10.1111/1462-2920.12277 24118987 · DOI
  86. Kondo R. (2017). “ Microbial degradation of endsulfan and endsulfan sulfate,” in Microbe-Induced Degradation of Pesticides, Ed. Singh S. N. (Cham: Springer), 151– 166.
  87. Košnár Z. Èástková T. Wiesnerová L. Praus L. Jablonský I. Koudela M. (2019). Comparing the removal of polycyclic aromatic hydrocarbons in soil after different bioremediation approaches in relationto the extracellular enzyme activities. J. Environ. Sci. 76 249– 258. 10.1016/j.jes.2018.05.007 30528015 · DOI
  88. Kües U. (2015). Fungal enzymes for environmental management. Curr. Opin. Biotechnol 33 268– 278. 10.1016/j.copbio.2015.03.006 25867110 · DOI
  89. Kumar A. Bisht B. S. Joshi V. D. Dhewa T. (2011). Review on bioremediation of polluted environment: a management tool. Int. J. Environ. Sci. 1: 1079.
  90. Kumar M. Jaiswal S. Sodhi K. K. Shree P. Singh D. K. Agrawal P. K. (2019). Antibiotics bioremediation: perspectives on its ecotoxicity and resistance. Environ. Int. 124 448– 461. 10.1016/j.envint.2018.12.065 30684803 · DOI
  91. Kumar N. M. Muthukumaran C. Sharmila G. Gurunathan B. (2018). “ Genetically modified organisms and its impact on the enhancement of bioremediation,” in Bioremediation: Applications for Environmental Protection and Management, eds Varjani S. J. Agarwal A. K. Gnansounou E. Gurunathan B. (Singapore: Springer), 53– 76.
  92. Kumar V. Dangi A. K. Shukla P. (2018). Engineering thermostable microbial xylanases toward its industrial applications. Mol. Biotechnol. 60 226– 235. 10.1007/s12033-018-0059-6 29380253 · DOI
  93. Lebrazi S. Fikri-Benbrahim K. (2018). “ Rhizobium-Legume Symbioses: heavy metal effects and principal approaches for bioremediation of contaminated soil,” in Legumes for Soil Health and Sustainable Management, eds Meena R. S. Das A. Yadav G. S. Lal R. (Singapore: Springer), 205– 233.
  94. Leong Y. K. Chang J. S. (2020). Bioremediation of heavy metals using microalgae: recent advances and mechanisms. Bioresour. Technol. 303: 122886. 10.1016/j.biortech.2020.122886 32046940 · DOI · Paper page
  95. Liang Y. Jiao S. Wang M. Yu H. Shen Z. (2020). A CRISPR/Cas9-based genome editing system for Rhodococcus ruber TH. Metab. Eng. 57 13– 22. 10.1016/j.ymben.2019.10.003 31610242 · DOI
  96. Libis V. Delepine B. Faulon J. L. (2016a). Expanding biosensing abilities through computer-aided design of metabolic pathways. ACS Synthet. Biol. 5 1076– 1085. 10.1021/acssynbio.5b00225 27028723 · DOI
  97. Libis V. Delépine B. Faulon J. L. (2016b). Sensing new chemicals with bacterial transcription factors. Curr. Opin. Microbiol. 33 105– 112. 10.1016/j.mib.2016.07.006 27472026 · DOI
  98. Liu H. Zhang J. J. Wang S. J. Zhang X. E. Zhou N. Y. (2005). Plasmid-borne catabolism of methyl parathion and p-nitrophenol in Pseudomonas sp. strain WBC-3. Biochem. Biophys. Res. Commun. 334 1107– 1114. 10.1016/j.bbrc.2005.07.006 16039612 · DOI
  99. Luo J. Bai Y. Liang J. Qu J. (2014). Metagenomic approach reveals variation of microbes with arsenic and antimony metabolism genes from highly contaminated soil. PLoS One 9: e108185. 10.1371/journal.pone.0108185 25299175 PMC4191978 · DOI
  100. Malla M. A. Dubey A. Yadav S. Kumar A. Hashem A. Abd_Allah E. F. (2018). Understanding and designing the strategies for the microbe-mediated remediation of environmental contaminants using omics approaches. Front. Microbiol. 9: 1132. 10.3389/fmicb.2018.01132 29915565 PMC5994547 · DOI
  101. Marco D. E. Abram F. (2019). Using genomics, metagenomics and other” omics” to assess valuable microbial ecosystem services and novel biotechnological applications. Front. Microbiol. 10: 151. 10.3389/fmicb.2019.00151 30809205 PMC6379446 · DOI
  102. Marshall R. Maxwell C. S. Collins S. P. Jacobsen T. Luo M. L. Begemann M. B. (2018). Rapid and scalable characterization of CRISPR technologies using an E. coli cell-free transcription-translation system. Mol. Cell 69 146– 157. 10.1016/j.molcel.2017.12.007 29304331 PMC5976856 · DOI
  103. McPartland J. M. McKernan K. J. (2017). “ Contaminants of concern in cannabis: microbes, heavy metals and pesticides,” in Cannabis sativa L.-Botany and Biotechnology, eds Chandra S. Lata H. ElSohly M. A. (Cham: Springer), 457– 474.
  104. Michel C. Jean M. Coulon S. Dictor M. C. Delorme F. Morin D. (2007). Biofilms of As (III)-oxidising bacteria: formation and activity studies for bioremediation process development. Appl. Microbiol. Biotechnol. 77 457– 467. 10.1007/s00253-007-1169-4 17846760 · DOI
  105. Mills M. G. Ramsden R. Ma E. Y. Corrales J. Kristofco L. A. Steele W. B. (2019). CRISPR-generated Nrf2a loss-and gain-of-function mutants facilitate mechanistic analysis of chemical oxidative stress-mediated toxicity in zebrafish. Chem. Res. Toxicol. 33 426– 435. 10.1021/acs.chemrestox.9b00346 31858786 PMC7749997 · DOI
  106. Miyazaki R. Sato Y. Ito M. Ohtsubo Y. Nagata Y. Tsuda M. (2006). Complete nucleotide sequence of an exogenously isolated plasmid, pLB1, involved in γ-hexachlorocyclohexane degradation. Appl. Environ. Microbiol. 72 6923– 6933. 10.1128/AEM.01531-06 16963556 PMC1636184 · DOI
  107. Mohapatra B. Kazy S. K. Sar P. (2019). Comparative genome analysis of arsenic reducing, hydrocarbon metabolizing groundwater bacterium Achromobacter sp. KAs 3-5T explains its competitive edge for survival in aquifer environment. Genomics 111 1604– 1619. 10.1016/j.ygeno.2018.11.004 30445215 · DOI
  108. Mónica M. G. A. Jaime M. Q. (2019). “ Phenoloxidases of Fungi and Bioremediation,” Fungal Bioremediation: Fundamentals and Applications, eds Campocosio A. T. Santiesteban H. H. L. (Boca Raton, FL: CRC Press), 62– 90.
  109. Mougiakos I. Bosma E. F. de Vos W. M. van Kranenburg R. van der Oost J. (2016). Next generation prokaryotic engineering: the CRISPR-Cas toolkit. Trends Biotechnol. 34 575– 587. 10.1016/j.tibtech.2016.02.004 26944793 · DOI
  110. Mujawar S. Y. Shamim K. Vaigankar D. C. Dubey S. K. (2019). Arsenite biotransformation and bioaccumulation by Klebsiella pneumoniae strain SSSW7 possessing arsenite oxidase (aioA) gene. Biometals 32 65– 76. 10.1007/s10534-018-0158-7 30471007 · DOI
  111. Nogales J. Mueller J. Gudmundsson S. Canalejo F. J. Duque E. Monk J. (2020). High-quality genome-scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities. Environ. Microbiol. 255– 269. 31657101 PMC7078882
  112. Nora L. C. Westmann C. A. Martins-Santana L. Alves L. D. F. Monteiro L. M. O. Guazzaroni M. E. (2019). The art of vector engineering: towards the construction of next-generation genetic tools. Microb. Biotechnol. 12 125– 147. 10.1111/1751-7915.13318 30259693 PMC6302727 · DOI
  113. O’Brien E. J. Monk J. M. Palsson B. O. (2015). Using genome-scale models to predict biological capabilities. Cell 161 971– 987. 10.1016/j.cell.2015.05.019 26000478 PMC4451052 · DOI
  114. Obst U. (2007). Quorum sensing: bacterial chatting. Anal. Bioanal. Chem. 387 369– 370. 17139482
  115. Ofaim S. Zarecki R. Porob S. Gat D. Lahav T. Xu X. (2019). Genome-Scale reconstruction of Paenarthrobacter aurescens TC1 metabolic model towards the study of atrazine bioremediation. bioRxiv [Preprint] 10.1101/536011 PMC7398907 32747737 · DOI
  116. Okino-Delgado C. H. Zanutto-Elgui M. R. do Prado D. Z. Pereira M. S. Fleuri L. F. (2019). “ Enzymatic bioremediation: current status, challenges of obtaining process, and applications,” in Microbial Metabolism of Xenobiotic Compounds, eds Arora P. K. (Singapore: Springer), 79– 101.
  117. Pabo C. O. Nekludova L. (2000). Geometric analysis and comparison of protein-DNA interfaces: why is there no simple code for recognition? 1. J. Mol. Biol. 301 597– 624. 10.1006/jmbi.2000.3918 10966773 · DOI
  118. Paniagua-Michel J. Fathepure B. Z. (2018). “ Microbial consortia and biodegradation of petroleum hydrocarbons in marine environments,” in Microbial Action on Hydrocarbons, eds Kumar V. Kumar M. Prasad R. (Singapore: Springer), 1– 20.
  119. Panigrahi S. Velraj P. Rao T. S. (2019). “ Functional microbial diversity in contaminated environment and application in bioremediation,” in Microbial Diversity in the Genomic Era, eds Das S. Dash H. R. (Amsterdam: Academic Press), 359– 385.
  120. Patel R. Zaveri P. Mukherjee A. Agarwal P. K. More P. Munshi N. S. (2019). Development of fluorescent protein-based biosensing strains: a new tool for the detection of aromatic hydrocarbon pollutants in the environment. Ecotoxicol. Environ. Saf. 182: 109450. 10.1016/j.ecoenv.2019.109450 31349104 · DOI
  121. Pavan M. Worth A. P. (2006). Review of QSAR Models for Ready Biodegradation. Brussels: European Commission Directorate General Joint Research Centre.
  122. Peijnenburg W. J. Damborský J. (eds) (2012). Biodegradability Prediction, Vol. 23 Berlin: Springer Science & Business Media.
  123. Petsas A. S. Vagi M. C. (2019). Trends in the bioremediation of pharmaceuticals and other organic contaminants using native or genetically modified microbial strains: a review. Curr. Pharm. Biotechnol 20 787– 824. 10.2174/1389201020666190527113903 31131748 · DOI
  124. Pietro-Souza W. de Campos Pereira F. Mello I. S. Stachack F. F. F. Terezo A. J. da Cunha C. N. (2020). Mercury resistance and bioremediation mediated by endophytic fungi. Chemosphere 240: 124874. 10.1016/j.chemosphere.2019.124874 31546184 · DOI
  125. Pineda M. Lear A. Collins J. P. Kiani S. (2019). Safe CRISPR: challenges and possible solutions. Trends Biotechnol. 37 389– 401. 10.1016/j.tibtech.2018.09.010 30352704 · DOI
  126. Plewniak F. Crognale S. Rossetti S. Bertin P. N. (2018). A genomic outlook on bioremediation: the case of arsenic removal. Front. Microbiol. 9: 820. 10.3389/fmicb.2018.00820 29755441 PMC5932151 · DOI
  127. Pontrelli S. Chiu T. Y. Lan E. I. Chen F. Y. H. Chang P. Liao J. C. (2018). Escherichia coli as a host for metabolic engineering. Metab. Eng. 50 16– 46. 10.1016/j.ymben.2018.04.008 29689382 · DOI
  128. Ravikumar S. Baylon M. G. Park S. J. Choi J. I. (2017). Engineered microbial biosensors based on bacterial two-component systems as synthetic biotechnology platforms in bioremediation and biorefinery. Microb. Cell Fact. 16: 62. 10.1186/s12934-017-0675-z 28410609 PMC5391612 · DOI
  129. Rawls K. D. Dougherty B. V. Blais E. M. Stancliffe E. Kolling G. L. Vinnakota K. (2019). A simplified metabolic network reconstruction to promote understanding and development of flux balance analysis tools. Comput. Biol. Med. 105 64– 71. 10.1016/j.compbiomed.2018.12.010 30584952 · DOI
  130. Ray S. Panjikar S. Anand R. (2018). Design of protein-based biosensors for selective detection of benzene groups of pollutants. ACS Sens. 3 1632– 1638. 10.1021/acssensors.8b00190 30084640 · DOI
  131. Rayu S. Karpouzas D. G. Singh B. K. (2012). Emerging technologies in bioremediation: constraints and opportunities. Biodegradation 23 917– 926. 10.1007/s10532-012-9576-3 22836784 · DOI
  132. Rochfort S. (2005). Metabolomics reviewed: a new “omics” platform technology for systems biology and implications for natural products research. J. Nat. Prod. 68 1813– 1820. 10.1021/np050255w 16378385 · DOI
  133. Rucká L. Nešvera J. Pátek M. (2017). Biodegradation of phenol and its derivatives by engineered bacteria: current knowledge and perspectives. World J. Microbiol. Biotechnol. 33: 174. 10.1007/s11274-017-2339-x 28879631 · DOI
  134. Russo F. Ceci A. Pinzari F. Siciliano A. Guida M. Malusà E. (2019). Bioremediation of DDT-contaminated agricultural soils: the potential of two autochthonous saprotrophic fungal strains. Appl. Environ. Microbiol. 85 e01720– 19. 10.1128/AEM.01720-19 31444208 PMC6803318 · DOI
  135. Rycroft T. Hamilton K. Haas C. N. Linkov I. (2019). A quantitative risk assessment method for synthetic biology products in the environment. Sci. Total Environ. 696: 133940. 10.1016/j.scitotenv.2019.133940 31446290 · DOI
  136. Sadańoski M. A. Velázquez J. E. Fonseca M. I. Zapata P. D. Levin L. N. Villalba L. L. (2018). Assessing the ability of white-rot fungi to tolerate polychlorinated biphenyls using predictive mycology. Mycology 9 239– 249. 10.1080/21501203.2018.1481152 30533250 PMC6282474 · DOI
  137. Salam L. B. Ishaq A. (2019). Biostimulation potentials of corn steep liquor in enhanced hydrocarbon degradation in chronically polluted soil. 3 Biotech 9: 46. 10.1007/s13205-019-1580-4 30729070 PMC6346607 · DOI
  138. Saxena G. Purchase D. Bharagava R. N. (2020). “ Environmental hazards and toxicity profile of organic and inorganic pollutants of tannery wastewater and bioremediation approaches,” in Bioremediation of Industrial Waste for Environmental Safety, eds Bharagava R. N. Saxena G. (Singapore: Springer), 381– 398. 10.1007/398_2015_5009 · DOI
  139. Sayler G. S. Cox C. D. Burlage R. Ripp S. Nivens D. E. Werner C. (1999). “ Field application of a genetically engineered microorganism for polycyclic aromatic hydrocarbon bioremediation process monitoring and control,” in Novel Approaches for Bioremediation of Organic Pollution, eds Reuveny S. Flashner Y. Fass R. (Boston, MA: Springer), 241– 254.
  140. Schloss P. D. Handelsman J. (2008). A statistical toolbox for metagenomics: assessing functional diversity in microbial communities. BMC Bioinformatics 9: 34. 10.1186/1471-2105-9-34 18215273 PMC2238731 · DOI
  141. Shah S. B. Ali F. Huang L. Wang W. Xu P. Tang H. (2018). Complete genome sequence of Bacillus sp. HBCD-sjtu, an efficient HBCD-degrading bacterium. 3 Biotech 8: 291. 10.1007/s13205-018-1326-8 29963351 PMC6020098 · DOI
  142. Shah V. Jain K. Desai C. Madamwar D. (2012). “ Molecular analyses of microbial activities involved in bioremediation,” in Microorganisms in Environmental Management, eds Prakash A. Satyanarayana T. (Dordrecht: Springer), 221– 247.
  143. Shanmugam K. Ramalingam S. Venkataraman G. Hariharan G. N. (2019). The CRISPR/Cas9 system for targeted genome engineering in free-living fungi: advances and opportunities for lichenized fungi. Front. Microbiol. 10: 62. 10.3389/fmicb.2019.00062 30792699 PMC6375251 · DOI
  144. Sharma A. Gupta G. Ahmad T. Krishan K. Kaur B. (2020). “ Next generation agents (synthetic agents): emerging threats and challenges in detection, protection, and decontamination,” in Handbook on Biological Warfare Preparedness, eds Flora S. J. S. Pachauri V. (Cambridge, MA: Academic Press), 217– 256.
  145. Sharma B. Dangi A. K. Shukla P. (2018). Contemporary enzyme based technologies for bioremediation: a review. J. Environ. Manag. 210 10– 22. 10.1016/j.jenvman.2017.12.075 29329004 · DOI
  146. Sharma J. K. Gautam R. K. Nanekar S. V. Weber R. Singh B. K. Singh S. K. (2018). Advances and perspective in bioremediation of polychlorinated biphenyl-contaminated soils. Environ. Sci. Pollut. Res. 25 16355– 16375. 10.1007/s11356-017-8995-4 28488147 PMC6360087 · DOI
  147. Shukla N. (2017). Bioinformatics in environmental bioremediation-a review. Int. J. Sci. Res. Sci. Eng. Technol. 3 195– 205.
  148. Singh A. Gothalwal R. (2018). A reappraisal on biodegradation of fluoride compounds: role of microbes. Water Environ. J. 32 481– 487. 10.1111/wej.12322 · DOI
  149. Singh N. Kumar A. Sharma B. (2019). “ Role of fungal enzymes for bioremediation of hazardous chemicals,” in Recent Advancement in White Biotechnology Through Fungi, eds Yadav A. N. Mishra S. Singh S. Gupta A. (Cham: Springer), 237– 256.
  150. Singh N. Srivastava S. Rathaur S. Singh N. (2016). Assessing the bioremediation potential of arsenic tolerant bacterial strains in rice rhizosphere interface. J. Environ. Sci. 48 112– 119. 10.1016/j.jes.2015.12.034 27745656 · DOI
  151. Singh S. B. (2018). “ Enzyme Catalysis and Its Role in Food Processing Industries,” in Enzymes in Food Technology, Ed. Law B. A. (Singapore: Springer), 143– 165.
  152. Sinha R. Sharma B. Dangi A. K. Shukla P. (2019). Recent metabolomics and gene editing approaches for synthesis of microbial secondary metabolites for drug discovery and development. World J. Microbiol. Biotechnol. 35: 166. 10.1007/s11274-019-2746-2 31641867 · DOI
  153. Skinder B. M. Uqab B. Ganai B. A. (2020). “ Bioremediation: a sustainable and emerging tool for restoration of polluted aquatic ecosystem,” in Fresh Water Pollution Dynamics and Remediation, eds Qadri H. Bhat R. A. Mehmood M. A. Dar G. H. (Singapore: Springer), 143– 165.
  154. Stein H. P. Navajas-Pérez R. Aranda E. (2018). “ Potential for CRISPR genetic engineering to increase xenobiotic degradation capacities in model fungi,” in Approaches in Bioremediation, eds Prasad R. Aranda E. (Cham: Springer), 61– 78.
  155. Tang Q. Lu T. Liu S. J. (2018). Developing a synthetic biology toolkit for comamonas testosteroni, an emerging cellular chassis for bioremediation. ACS Synthetic Biol. 7 1753– 1762. 10.1021/acssynbio.7b00430 29860823 · DOI
  156. Tanveer T. Shaheen K. Parveen S. Misbah Z. T. Babar M. M. Gul A. (2018). “ Omics-based bioengineering in environmental biotechnology,” in Omics Technologies and Bio-Engineering, eds Barh D. Azevedo V. (Cambridge, MA: Academic Press), 353– 364.
  157. Tay P. K. R. Nguyen P. Q. Joshi N. S. (2017). A synthetic circuit for mercury bioremediation using self-assembling functional amyloids. ACS Synthetic Biol. 6 1841– 1850. 10.1021/acssynbio.7b00137 28737385 · DOI
  158. Techtmann S. M. Hazen T. C. (2016). Metagenomic applications in environmental monitoring and bioremediation. J. Indus. Microbiol. Biotechnol. 43 1345– 1354. 10.1007/s10295-016-1809-8 27558781 · DOI
  159. Thakur M. Medintz I. L. Walper S. A. (2019). Enzymatic bioremediation of organophosphate compounds-progress and remaining challenges. Front. Bioeng. Biotechnol. 7: 289. 10.3389/fbioe.2019.00289 31781549 PMC6856225 · DOI
  160. Thelusmond J. R. Strathmann T. J. Cupples A. M. (2019). Carbamazepine, triclocarban and triclosan biodegradation and the phylotypes and functional genes associated with xenobiotic degradation in four agricultural soils. Sci. Total Environ. 657 1138– 1149. 10.1016/j.scitotenv.2018.12.145 30677881 · DOI
  161. Trigo A. Valencia A. Cases I. (2008). Systemic approaches to biodegradation. FEMS Microbiol. Rev. 33 98– 108. 19054119
  162. Tropel D. Van Der Meer J. R. (2004). Bacterial transcriptional regulators for degradation pathways of aromatic compounds. Microbiol. Mol. Biol. Rev. 68 474– 500. 15353566 PMC515250
  163. Uluşeker C. Torres J. García J. L. Hanczyc M. M. Nogales J. Kahramanoğullarý O. (2017). “ September. a dynamic model of the phosphate response system with synthetic promoters in Escherichia coli,” in Proceedings of the Artificial Life Conference, Vol. 14 (Cambridge, MA: MIT Press), 412– 419.
  164. Utturkar S. M. Bollmann A. Brzoska R. M. Klingeman D. M. Epstein S. E. Palumbo A. V. (2013). Draft genome sequence for Ralstonia sp. strain OR214, a bacterium with potential for bioremediation. Genome Announc. 1: e00321-13. 10.1128/genomeA.00321-13 23792748 PMC3675513 · DOI
  165. van Dorst J. Wilkins D. King C. K. Spedding T. Hince G. Zhang E. (2020). Applying microbial indicators of hydrocarbon toxicity to contaminated sites undergoing bioremediation on subantarctic Macquarie Island. Environ. Pollut. 259: 113780. 10.1016/j.envpol.2019.113780 31887587 · DOI
  166. Wei K. Yin H. Peng H. Lu G. Dang Z. (2019). Bioremediation of triphenyl phosphate in river water microcosms: proteome alteration of Brevibacillus brevis and cytotoxicity assessments. Sci. Total Environ. 649 563– 570. 10.1016/j.scitotenv.2018.08.342 30176467 · DOI
  167. Wintermute E. H. Silver P. A. (2010). Dynamics in the mixed microbial concourse. Genes Dev. 24 2603– 2614. 10.1101/gad.1985210 21123647 PMC2994034 · DOI
  168. Wu Y. Chen Y. Wei N. (2020). Biocatalytic properties of cell surface display laccase for degradation of emerging contaminant acetaminophen in water reclamation. Biotechnol. Bioeng. 117 342– 353. 10.1002/bit.27214 31654417 · DOI
  169. Wynn D. Deo S. Daunert S. (2017). “ Engineering rugged field assays to detect hazardous chemicals using spore-based bacterial biosensors,” in Methods in Enzymology, Vol. 589 eds Abelson J. Simon M. Verdine G. Pyle A. (Cambridge, MA: Academic Press), 51– 85. 28336074
  170. Xu P. Lai C. Zeng G. Huang D. Chen M. Song B. (2018). Enhanced bioremediation of 4-nonylphenol and cadmium co-contaminated sediment by composting with Phanerochaete chrysosporium inocula. Bioresour. Technol. 250 625– 634. 10.1016/j.biortech.2017.11.069 29220806 · DOI
  171. Yadav T. C. Pal R. R. Shastri S. Jadeja N. B. Kapley A. (2015). Comparative metagenomics demonstrating different degradative capacity of activated biomass treating hydrocarbon contaminated wastewater. Bioresour. Technol. 188 24– 32. 10.1016/j.biortech.2015.01.141 25727998 · DOI
  172. Yergeau E. Sanschagrin S. Beaumier D. Greer C. W. (2012). Metagenomic analysis of the bioremediation of diesel-contaminated Canadian high arctic soils. PLoS One 7: e30058. 10.1371/journal.pone.0030058 22253877 PMC3256217 · DOI
  173. Zampolli J. Di Canito A. Cappelletti M. Collina E. Lasagni M. Di Gennaro P. (2020). Biodegradation of naphthenic acids: identification of Rhodococcus opacus R7 genes as molecular markers for environmental monitoring and their application in slurry microcosms. Appl. Microbiol. Biotechnol. 104 2675– 2689. 10.1007/s00253-020-10378-5 31993702 · DOI
  174. Zhang D. Liu Q. (2016). Biosensors and bioelectronics on smartphone for portable biochemical detection. Biosens. Bioelectron. 75 273– 284. 10.1016/j.bios.2015.08.037 26319170 · DOI
  175. Zhao B. Poh C. L. (2008). Insights into environmental bioremediation by microorganisms through functional genomics and proteomics. Proteomics 8 874– 881. 10.1002/pmic.200701005 18210372 · DOI
  176. Zhu Y. G. Xue X. M. Kappler A. Rosen B. P. Meharg A. A. (2017). Linking genes to microbial biogeochemical cycling: lessons from arsenic. Environ. Sci. Technol. 51 7326– 7339. 10.1021/acs.est.7b00689 28602082 PMC5871744 · DOI
  177. Zuo Z. Gong T. Che Y. Liu R. Xu P. Jiang H. (2015). Engineering Pseudomonas putida KT2440 for simultaneous degradation of organophosphates and pyrethroids and its application in bioremediation of soil. Biodegradation 26 223– 233. 10.1007/s10532-015-9729-2 25917649 · DOI
  178. Zuroff T. R. Xiques S. B. Curtis W. R. (2013). Consortia-mediated bioprocessing of cellulose to ethanol with a symbiotic Clostridium phytofermentans/yeast co-culture. Biotechnol. Biofuels 6: 59. 10.1186/1754-6834-6-59 23628342 PMC3653780 · DOI

Cited by

Sorted by citations

Authors
Jaiswal, S., & Shukla, P.
Affiliations
Maharshi Dayanand University (IN)
Corresponding author
Shukla, Pratyoosh
ORCID
Venue
Frontiers in Microbiology
Publisher
Frontiers Media SA
Published
2020-05-19
Volume
11
Pages
808-808
ISSN
1664-302X (ISSN-L)
DOI
10.3389/fmicb.2020.00808
PMC
PMC7249858
OpenAlex
W3026599105
Cited by
195
References
3
Citations by year
2026: 33 · 2025: 31 · 2024: 36 · 2023: 30 · 2022: 42 · 2021: 20 · 2020: 3
FWCI
1.06
Type
journal article
Language
en
Open access
Licence
Locations
  • Frontiers in Microbiology (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • eCommons - AKU (Aga Khan University) (submittedVersion, cc-by)
  • eCommons - AKU (Aga Khan University) (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Topics
  • Physical Sciences › Environmental Science › Pollution › Microbial bioremediation and biosurfactants
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
  • Physical Sciences › Environmental Science › Environmental Engineering › Microbial Fuel Cells and Bioremediation
Keywords
microbial bioremediation, synthetic biology, xenobiotics, recalcitrant pollutants, synthetic microbial communities, quorum sensing, signal transduction, genome editing, synthetic gene circuits, two-component systems, whole-cell biosensors, pollutant degradation

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