Bioengineered microbes for soil health restoration: present status and future

References

• OECD, 2014. Environmental quality of life.
   Google Scholar
• Jian J, Du X, Stewart RD. A database for global soil health assessment. Sci Data. 2020;7(1):16.
   PubMed Web of Science ®Google Scholar
• Samaddar S, Karp DS, Schmidt R, et al. Role of soil in the regulation of human and plant pathogens: soils’ contributions to people. Philos Trans Royal Soc B. 2021;376(1834):20200179.
   PubMed Web of Science ®Google Scholar
• Cardoso EJBN, Vasconcellos RLF, Bini D, et al. Soil health: looking for suitable indicators. What should be considered to assess the effects of use and management on soil health? Scientia Agricola. 2013;70(4):274–289.
   Web of Science ®Google Scholar
• Fernandez IJ, Rustad LE, Norton SA, et al. Experimental acidification causes soil base‐cation depletion at the bear brook watershed in maine. Soil Sci Soc Am J. 2003;67(6):1909–1919.
   Web of Science ®Google Scholar
• Hashim G, Coughlan K, Syers J, et al. On-site nutrient depletion: an effect and a cause of soil erosion. In Penning de Vries, F W T, Agus, F, and Kerr, J M(eds)., Soil erosion at multiple scales: principles and methods for assessing causes and impacts, (New York). 1998. p. 207–221.
   Google Scholar
• Maximillian J, Brusseau, ML, Glenn, EP, et al. Chapter 25 - pollution and environmental perturbations in the global system. In: Brusseau ML, Pepper IL, and Gerba CP, editors. Environmental and pollution science. Third. Amsterdam: Academic Press, 457–476, 2019.
   Google Scholar
• Parikh SJ, James BR. Soil: the foundation of agriculture. Nat Educ Knowledge. 2012;3(10):2.
   Google Scholar
• Maroun W, Atkins J. A practical application of accounting for biodiversity: the case of soil health. Social and Environmental Accountability Journal. 2021;41(1–2):37–65
   Google Scholar
• Rejesus RM, Aglasan S, Knight LG, et al. Economic dimensions of soil health practices that sequester carbon: promising research directions. J Soil Water Conserv. 2021;76(3):55A–60A.
   Web of Science ®Google Scholar
• Brevik EC, Slaughter L, Singh BR, et al. Soil and human health: current status and future needs. Air Soil Water Res. 2020;13:1178622120934441.
   Web of Science ®Google Scholar
• Girija Veni V, Srinivasarao, C, Sammi Reddy, K, et al. Chapter 26 - Soil health and climate change. In: Prasad MNV, and Pietrzykowski M, editors. climate change and soil interactions. San Diego, California: Elsevier; 2020. p. 751–767.
   Google Scholar
• Bunea A, Pacurar, I, Dulf, V et al, Study concerning the soil resources used in agriculture and forestry worldwide . ProEnvironment. 2020: 13; 39–43.
   Google Scholar
• Macdonald C, Singh B. Harnessing plant-microbe interactions for enhancing farm productivity. Bioengineered. 2014;5(1):5–9.
   PubMed Web of Science ®Google Scholar
• Hernandez‐Raquet G, Durand E, Braun F, et al. Impact of microbial diversity depletion on xenobiotic degradation by sewage‐activated sludge. Environ Microbiol Rep. 2013;5(4):588–594.
   PubMed Web of Science ®Google Scholar
• Bharadwaj A Bioremediation of xenobiotics: an eco-friendly cleanup approach. In Parmar, V S, Malhotra, P, and Mathur, D(eds).,: Green chemistry in environmental sustainability and chemical education. Singapore: Springer; 2018. p. 1–13.
   Google Scholar
• Rebello S, Sivaprasad MS, Anoopkumar AN, et al. Cleaner technologies to combat heavy metal toxicity. J Environ Manage. 2021;296:113231 doi:10.1016/j.jenvman.2021.113231.
   PubMed Web of Science ®Google Scholar
• Rashid MI, Mujawar LH, Shahzad T, et al. Bacteria and fungi can contribute to nutrients bioavailability and aggregate formation in degraded soils. Microbiol Res. 2016;183:26–41.
   PubMed Web of Science ®Google Scholar
• Rishad KS, Rebello S, Shabanamol PS, et al. Biocontrol potential of Halotolerant bacterial chitinase from high yielding novel Bacillus Pumilus MCB-7 autochthonous to mangrove ecosystem. Pestic Biochem Physiol. 2017;137:36–41.
   PubMed Web of Science ®Google Scholar
• Nair AM, Rebello S, Rishad KS, et al. Biosurfactant facilitated biodegradation of quinalphos at high concentrations by Pseudomonas aeruginosa Q10. Soil Sediment Contaminat. 2015;24(5):542–553.
   Web of Science ®Google Scholar
• Gunjal AB Role of plant growth–promoting rhizobacteria in degradation of xenobiotic compounds. In Verma, J P, Macdonald, C A, and Podile, A R. (eds)., New and future developments in microbial biotechnology and bioengineering. Amsterdam: Elsevier; 2021. p. 25–33.
   Google Scholar
• Cf SF, Rebello S, Mathachan Aneesh E, et al. Bioprospecting of gut microflora for plastic biodegradation. Bioengineered. 2021;12(1):1040–1053.
   PubMed Web of Science ®Google Scholar
• Mishra S, Lin, Z, Pang, S, et al. Recent advanced technologies for the characterization of xenobiotic-degrading microorganisms and microbial communities. Front Bioeng Biotechnol. 2021;9(31);1–26.
   Google Scholar
• Docherty KM, Gutknecht JLM. Soil microbial restoration strategies for promoting climate-ready prairie ecosystems. Ecol Appl. 2019;29(3):e01858.
   PubMed Web of Science ®Google Scholar
• Tejada M, Benítez C, Parrado J. Application of biostimulants in benzo (a) pyrene polluted soils: short-time effects on soil biochemical properties. Appl Soil Ecol. 2011;50:21–26.
   Web of Science ®Google Scholar
• Finkel OM, Castrillo G, Herrera Paredes S, et al. Understanding and exploiting plant beneficial microbes. Curr Opin Plant Biol. 2017;38:155–163.
   PubMed Web of Science ®Google Scholar
• Lakshmanan V, Selvaraj G, Bais HP. Functional soil microbiome: belowground solutions to an aboveground problem. Plant Physiol. 2014;166(2):689–700.
   PubMed Web of Science ®Google Scholar
• Kumar A, Dubey A. Rhizosphere microbiome: engineering bacterial competitiveness for enhancing crop production. J Adv Res. 2020;24:337–352.
   PubMed Web of Science ®Google Scholar
• Lyu D, Msimbira LA, Nazari M, et al. The coevolution of plants and microbes underpins sustainable agriculture. Microorganisms. 2021;9(5):1036.
   PubMed Web of Science ®Google Scholar
• Ke W, Zhang X, Zhu F, et al. Appropriate human intervention stimulates the development of microbial communities and soil formation at a long-term weathered bauxite residue disposal area. J Hazard Mater. 2021;405:124689.
   PubMed Web of Science ®Google Scholar
• Basu S, Kumar , G, Chhabra, S et al, et al. Role of soil microbes in biogeochemical cycle for enhancing soil fertility. In Verma, J P, Macdonald, C A, and Podille, A R(eds)., New and future developments in microbial biotechnology and bioengineering. Amsterdam: Elsevier, 2021. 149–157.
   Google Scholar
• Nehal N, Rathore US, Sharma N Microbes and soil health for sustainable crop production. In Nath, Manoj, Bhatt, Deepesh, Bhargava, Prachi, and D.K., Choudhary(eds)., Microbial metatranscriptomics belowground, 1 . Switzerland: Springer. 2021. p. 581–613.
   Google Scholar
• Rogers C, Oldroyd GE. Synthetic biology approaches to engineering the nitrogen symbiosis in cereals. J Exp Bot. 2014;65(8):1939–1946.
   PubMed Web of Science ®Google Scholar
• Ryu M-H, Zhang J, Toth T, et al. Control of nitrogen fixation in bacteria that associate with cereals. Nat Microbiol. 2020;5(2):314–330.
   PubMed Web of Science ®Google Scholar
• Wu Q, Jiao S, Ma M, et al. Microbial fuel cell system: a promising technology for pollutant removal and environmental remediation. Environ Sci Pollut Res. 2020;27(7):6749–6764.
   PubMed Web of Science ®Google Scholar
• Bhalerao TS, Puranik PR. Biodegradation of organochlorine pesticide, endosulfan, by a fungal soil isolate, Aspergillus Niger. Int Biodeterior Biodegrad. 2007;59(4):315–321.
   Web of Science ®Google Scholar
• Malghani S, Chatterjee N, Yu HX, et al. Isolation and identification of profenofos degrading bacteria. Braz J Microbiol. 2009;40(4):893–900.
   PubMed Web of Science ®Google Scholar
• Zhang X, Hao X, Huo S, et al. Isolation and identification of the Raoultella ornithinolytica-ZK4 degrading pyrethroid pesticides within soil sediment from an abandoned pesticide plant. Arch Microbiol. 2019;201(9):1207–1217.
   PubMed Web of Science ®Google Scholar
• Kumari S, Mangwani N, Das S. Synergistic effect of quorum sensing genes in biofilm development and PAHs degradation by a marine bacterium. Bioengineered. 2016;7(3):205–211.
   PubMed Web of Science ®Google Scholar
• Rebello S, Asok AK, Mundayoor S, et al. Surfactants: toxicity, remediation and green surfactants. Environ Chem Lett. 2014;12(2):275–287.
   Web of Science ®Google Scholar
• Liu X, Germaine KJ, Ryan D, et al. Genetically modified Pseudomonas biosensing biodegraders to detect PCB and chlorobenzoate bioavailability and biodegradation in contaminated soils. Bioengineered Bugs. 2010;1(3):198–206.
   PubMedGoogle Scholar
• Vandana UK, Gulzar, A, Laskar, IH, et al. Role of microbes in bioremediation of radioactive waste. In Panpatte, D G, and Jhala, Y K(eds)., Microbial rejuvenation of polluted environment. Singapore: Springer, 2021. 329–352.
   Google Scholar
• Rebello S, Anoopkumar AN, Aneesh EM, et al. Hazardous minerals mining: challenges and solutions. J Hazard Mater. 2021;402:123474.
   PubMed Web of Science ®Google Scholar
• Furukawa K. ‘Super bugs’ for bioremediation. Trends Biotechnol. 2003;21(5):187–190.
   PubMed Web of Science ®Google Scholar
• Ortiz-hernández M, Sánchez-Salinas E. Biodegradation of the organophosphate pesticide tetrachlorvinphos by bacteria isolated from agricultural soils in México. Revista internacional de contaminación ambiental. 2010;26(1):27–38.
   Web of Science ®Google Scholar
• Li J, Wu C, Chen S, et al. Enriching indigenous microbial consortia as a promising strategy for xenobiotics’ cleanup. J Clean Prod. 2020;261:121234.
   Web of Science ®Google Scholar
• Qin Y, Druzhinina IS, Pan X, et al. Microbially mediated plant salt tolerance and microbiome-based solutions for saline agriculture. Biotechnol Adv. 2016;34(7):1245–1259.
   PubMed Web of Science ®Google Scholar
• Estrada B, Aroca R, Azcón-Aguilar C, et al. Importance of native arbuscular mycorrhizal inoculation in the halophyte Asteriscus maritimus for successful establishment and growth under saline conditions. Plant Soil. 2013;370(1):175–185.
   Web of Science ®Google Scholar
• Armada E, Portela G, Roldán A, et al. Combined use of beneficial soil microorganism and agrowaste residue to cope with plant water limitation under semiarid conditions. Geoderma. 2014;232:640–648.
   Web of Science ®Google Scholar
• Rani R, Kumar V, Usmani Z, et al. Influence of plant growth promoting rhizobacterial strains Paenibacillus sp. IITISM08, Bacillus sp. PRB77 and Bacillus sp. PRB101 using Helianthus annuus on degradation of endosulfan from contaminated soil. Chemosphere. 2019;225:479–489.
   PubMed Web of Science ®Google Scholar
• Sundari SK, Prakash, A, Yadav, P, et al. Plant growth-promoting microbes as front-runners for on-site remediation of organophosphate pesticide residues in agriculture soils. In Arora, N K, and Kumar, N, Phyto and rhizo remediation. Singapore: Springer, 2019. 249–285.
   Google Scholar
• DalCorso G, Fasani E, Manara A, et al. Heavy metal pollutions: state of the art and innovation in phytoremediation. Int J Mol Sci. 2019;20(14):3412.
   PubMed Web of Science ®Google Scholar
• Nathiya S, Janani R, Kannan VR. Potential of plant growth promoting Rhizobacteria to overcome the exposure of pesticide in Trigonella foenum-graecum (fenugreek leaves). Biocatal Agric Biotechnol. 2020;23:101493.
   Web of Science ®Google Scholar
• Verbruggen E, Van Der HEIJDEN MARCELGA, Weedon JT, et al. Community assembly, species richness and nestedness of arbuscular mycorrhizal fungi in agricultural soils. Mol Ecol. 2012;21(10):2341–2353.
   PubMed Web of Science ®Google Scholar
• Nemergut DR, Schmidt SK, Fukami T, et al. Patterns and processes of microbial community assembly. Microbiol Mol Biol Rev. 2013;77(3):342–356.
   PubMed Web of Science ®Google Scholar
• Cordero OX, Polz MF. Explaining microbial genomic diversity in light of evolutionary ecology. Nature Rev Microbiol. 2014;12(4):263–273.
   PubMed Web of Science ®Google Scholar
• Bello-Akinosho M, Makofane R, Adeleke R, et al. Potential of polycyclic aromatic hydrocarbon-degrading bacterial isolates to contribute to soil fertility. Biomed Res Int. 2016;2016:1–10.
   Web of Science ®Google Scholar
• Rebello S, Joseph BV, Joseph SV, et al. Bioconversion of sodium dodecyl sulphate to rhamnolipids by transformed Escherichia coli DH5 α cells-a novel strategy for rhamnolipid synthesis. J Appl Microbiol. 2016;120(3):638–646.
   PubMed Web of Science ®Google Scholar
• Begum N, Qin C, Ahanger MA, et al. Role of arbuscular mycorrhizal fungi in plant growth regulation: implications in abiotic stress tolerance. Front Plant Sci. 2019;10(1068). DOI:10.3389/fpls.2019.01068.
   PubMedGoogle Scholar
• Jan S, Singh R, Bhardwaj R, et al. Plant growth regulators: a sustainable approach to combat pesticide toxicity. 3 Biotech. 2020;10(11):466.
   PubMedGoogle Scholar
• Verma P, Rawat S Rhizoremediation of heavy metal-and xenobiotic-contaminated soil: an eco-friendly approach. In Shah, M P, Removal of emerging contaminants through microbial processes. Singapore: Springer; 2021. p. 95–113.
   Google Scholar
• Parewa HP, Meena, VS, Jain, LK, et al. Sustainable crop production and soil health management through plant growth-promoting rhizobacteria. In Meena, V J., Role of rhizospheric microbes in soil. Singapore: Springer, 2018. 299–329.
   Google Scholar
• Kumar G, Patel, JS, Maharshi, A, et al. 25 PGPR-mediated defence responses in plants under biotic and abiotic stresses. Advances in PGPR research. 2017; 427
   Google Scholar
• Hou J, Liu W, Wang B, et al. PGPR enhanced phytoremediation of petroleum contaminated soil and rhizosphere microbial community response. Chemosphere. 2015;138:592–598.
   PubMed Web of Science ®Google Scholar
• Robas M, Jiménez PA, González D et al. Bio-mercury remediation suitability index: a novel proposal that compiles the PGPR features of bacterial strains and its potential use in phytoremediation. Int J Environ Res Public Health. 2021;18(8):4213.
   PubMed Web of Science ®Google Scholar
• Asad SA Soil–PCB–PGPR interactions in changing climate scenarios. In Hashmi, M Z, Kumar, V, and Varma, A (eds)., Xenobiotics in the Soil Environment. Switzerland: Springer; 2017. p. 281–298.
   Google Scholar
• Turan M, Hashmi, M Z, Kumar, V, and Varma, A . Plant Growth Promoting Rhizobacteria’s (PGPRS) enzyme dynamics in soil remediation. In Larramendy, M L, and Soloneski, S (eds)., Soil contamination-current consequences and further solutions. Croatia: IntechOpen; 2016:209–231.
   Google Scholar
• Kaur J Kumar, Vivek, Prasad, Ram, and Kumar, Manoj. PGPR in management of soil toxicity. Rhizobiont in bioremediation of hazardous waste. Singapore: Springer; 2021. p. 317–344.
   Google Scholar
• Ajeng AA, Abdullah R, Malek MA, et al. The effects of biofertilizers on growth, soil fertility, and nutrients uptake of oil palm (Elaeis guineensis) under greenhouse conditions. Processes. 2020;8(12):1681.
   Web of Science ®Google Scholar
• Chia WY, Chew KW, Le CF, et al. Sustainable utilization of biowaste compost for renewable energy and soil amendments. Environ Pollut. 2020;267:115662.
   PubMed Web of Science ®Google Scholar
• Yuanfan H, Jin Z, Qing H, et al. Characterization of a fenpropathrin-degrading strain and construction of a genetically engineered microorganism for simultaneous degradation of methyl parathion and fenpropathrin. J Environ Manage. 2010;91(11):2295–2300.
   PubMed Web of Science ®Google Scholar
• Kumar NM, Muthukumaran C, Sharmila G, et al. Genetically modified organisms and its impact on the enhancement of bioremediation. In Varjani, S J, Agarwal, A K, Gnansounou, E, and Gurunathan, B (eds)., Bioremediation, in bioremediation: applications for environmental protection and management. Singapore: Springer; 2018:53–76.
   Google Scholar
• Pant G, Garlapati D, Agrawal U, et al. Biological approaches practised using genetically engineered microbes for a sustainable environment: a review. J Hazard Mater. 2021;405:124631.
   PubMed Web of Science ®Google Scholar
• Diep P, Mahadevan R, Yakunin AF. Heavy metal removal by bioaccumulation using genetically engineered microorganisms. Front Bioeng Biotechnol. 2018;6:157.
   PubMed Web of Science ®Google Scholar
• Li C, Li Z, Li Y, et al. A Ferritin from Dendrorhynchus zhejiangensis with heavy metals detoxification activity. PLOS ONE. 2012;7(12):e51428.
   PubMed Web of Science ®Google Scholar
• Misra CS, Sounderajan S, Apte SK. Metal removal by metallothionein and an acid phosphatase PhoN, surface-displayed on the cells of the extremophile, Deinococcus radiodurans. J Hazard Mater. 2021;419:126477.
   PubMed Web of Science ®Google Scholar
• Ma L, Xu J, Chen N, et al. Microbial reduction fate of chromium (Cr) in aqueous solution by mixed bacterial consortium. Ecotoxicol Environ Saf. 2019;170:763–770.
   PubMed Web of Science ®Google Scholar
• Mahbub KR, Krishnan K, Megharaj M, et al. Bioremediation potential of a highly mercury resistant bacterial strain Sphingobium SA2 isolated from contaminated soil. Chemosphere. 2016;144:330–337.
   PubMed Web of Science ®Google Scholar
• Wang P, Sun G, Jia Y, et al. A review on completing arsenic biogeochemical cycle: microbial volatilization of arsines in environment. J Environ Sci. 2014;26(2):371–381.
   Web of Science ®Google Scholar
• Neumann G, Teras R, Monson L, et al. Simultaneous degradation of atrazine and phenol by Pseudomonas sp. strain adp: effects of toxicity and adaptation. Appl Environ Microbiol. 2004;70(4):1907–1912.
   PubMed Web of Science ®Google Scholar
• Strong LC, McTavish H, Sadowsky MJ, et al. Field‐scale remediation of atrazine‐contaminated soil using recombinant Escherichia coli expressing atrazine chlorohydrolase. Environ Microbiol. 2000;2(1):91–98.
   PubMed Web of Science ®Google Scholar
• Zhang R, Cui Z, Zhang X, et al. Cloning of the organophosphorus pesticide hydrolase gene clusters of seven degradative bacteria isolated from a methyl parathion contaminated site and evidence of their horizontal gene transfer. Biodegradation. 2006;17(5):465–472.
   PubMed Web of Science ®Google Scholar
• Zhongli C, Shunpeng L, Guoping F. Isolation of methyl parathion-degrading strain M6 and cloning of the methyl parathion hydrolase gene. Appl Environ Microbiol. 2001;67(10):4922–4925.
   PubMed Web of Science ®Google Scholar
• Lu J, Guo C, Li J, et al. A fusant of Sphingomonas sp. GY2B and Pseudomonas sp. GP3A with high capacity of degrading phenanthrene. World J Microbiol Biotechnol. 2013;29(9):1685–1694.
   PubMed Web of Science ®Google Scholar
• Yang J, Liu R, Song W, et al. Construction of a genetically engineered microorganism that simultaneously degrades organochlorine and organophosphate pesticides. Appl Biochem Biotechnol. 2012;166(3):590–598.
   PubMed Web of Science ®Google Scholar
• Dillon AJP, Camassola M, Henriques JAP, et al. Generation of recombinants strains to cellulases production by protoplast fusion between Penicillium echinulatum and Trichoderma harzianum. Enzyme Microb Technol. 2008;43(6):403–409.
   Web of Science ®Google Scholar
• Kang DG, Choi SS, Cha HJ. Enhanced biodegradation of toxic organophosphate compounds using recombinant Escherichia coli with sec pathway‐driven periplasmic secretion of organophosphorus hydrolase. Biotechnol Prog. 2006;22(2):406–410.
   PubMed Web of Science ®Google Scholar
• Carpenter A. Oil pollution in the North Sea: the impact of governance measures on oil pollution over several decades. Hydrobiologia. 2019;845(1):109–127.
   Web of Science ®Google Scholar
• Ndimele PE. The political ecology of oil and gas activities in the Nigerian aquatic ecosystem. London, UK: Academic Press; 2017.
   Google Scholar
• Zheng C, Yu L, Huang L, et al. Investigation of a hydrocarbon-degrading strain, Rhodococcus ruber Z25, for the potential of microbial enhanced oil recovery. J Pet Sci Eng. 2012;81:49–56.
   Web of Science ®Google Scholar
• Ismail S, Dadrasnia A. Biotechnological potential of Bacillus salmalaya 139SI: a novel strain for remediating water polluted with crude oil waste. PLoS One. 2015;10(4):e0120931.
   PubMed Web of Science ®Google Scholar
• Mishra S, Sarma PM, Lal B. Crude oil degradation efficiency of a recombinant Acinetobacter baumannii strain and its survival in crude oil-contaminated soil microcosm. FEMS Microbiol Lett. 2004;235(2):323–331.
   PubMed Web of Science ®Google Scholar
• Gallo G, Lo Piccolo L, Renzone G, et al. Differential proteomic analysis of an engineered Streptomyces coelicolor strain reveals metabolic pathways supporting growth on n-hexadecane. Appl Microbiol Biotechnol. 2012;94(5):1289–1301.
   PubMed Web of Science ®Google Scholar
• Xie Y, Yu F, Wang Q, et al. Cloning of catechol 2, 3-dioxygenase gene and construction of a stable genetically engineered strain for degrading crude oil. Indian J Microbiol. 2014;54(1):59–64.
   PubMed Web of Science ®Google Scholar
• Parrilli E, Papa R, Tutino ML, et al. Engineering of a psychrophilic bacterium for the bioremediation of aromatic compounds. Bioengineered Bugs. 2010;1(3):213–216.
   PubMedGoogle Scholar
• Zhao Q, Yue S, Bilal M, et al. Comparative genomic analysis of 26 Sphingomonas and Sphingobium strains: dissemination of bioremediation capabilities, biodegradation potential and horizontal gene transfer. SciTotal Environ. 2017;609:1238–1247.
   Google Scholar
• Hu N-J, Huang P, Liu J-H, et al. Characterization and source apportionment of polycyclic aromatic hydrocarbons (PAHs) in sediments in the Yellow River Estuary, China. Environ Earth Sci. 2014;71(2):873–883.
   Web of Science ®Google Scholar
• Nguyen TC, Loganathan P, Nguyen TV, et al. Polycyclic aromatic hydrocarbons in road-deposited sediments, water sediments, and soils in Sydney, Australia: comparisons of concentration distribution, sources and potential toxicity. Ecotoxicol Environ Saf. 2014;104:339–348.
   PubMed Web of Science ®Google Scholar
• Aylward FO, McDonald BR, Adams SM, et al. Comparison of 26 sphingomonad genomes reveals diverse environmental adaptations and biodegradative capabilities. Appl Environ Microbiol. 2013;79(12):3724–3733.
   PubMed Web of Science ®Google Scholar
• Sandoval Á, Arias-Barrau E, Bermejo F, et al. Production of 3-hydroxy-n-phenylalkanoic acids by a genetically engineered strain of Pseudomonas putida. Appl Microbiol Biotechnol. 2005;67(1):97–105.
   PubMed Web of Science ®Google Scholar
• Hart MM, Antunes PM, Abbott LK. Unknown risks to soil biodiversity from commercial fungal inoculants. Nat Ecol Evol. 2017;1(4):1.
   PubMed Web of Science ®Google Scholar
• Hart MM, Antunes PM, Chaudhary VB, et al. Fungal inoculants in the field: is the reward greater than the risk? Funct Ecol. 2018;32(1):126–135.
   Web of Science ®Google Scholar
• Dechesne A, Pallud C, Bertolla F, et al. Impact of the microscale distribution of a Pseudomonas strain introduced into soil on potential contacts with indigenous bacteria. Appl Environ Microbiol. 2005;71(12):8123–8131.
   PubMed Web of Science ®Google Scholar
• Hernández-Sánchez V, Wittich R-M. Possible reasons for past failures of genetic engineering techniques for creating novel, xenobiotics-degrading bacteria. Bioengineered. 2012;3(5):260–261.
   PubMed Web of Science ®Google Scholar
• Gibson DG, Glass JI, Lartigue C, et al. Creation of a bacterial cell controlled by a chemically synthesized genome. science. 2010;329(5987):52–56.
   PubMed Web of Science ®Google Scholar
• Sanchez-Romero JM, Diaz-Orejas R, De Lorenzo V. Resistance to tellurite as a selection marker for genetic manipulations of Pseudomonas strains. Appl Environ Microbiol. 1998;64(10):4040–4046.
   PubMed Web of Science ®Google Scholar
• Herrero M, De Lorenzo V, Timmis KN. Transposon vectors containing non-antibiotic resistance selection markers for cloning and stable chromosomal insertion of foreign genes in gram-negative bacteria. J Bacteriol. 1990;172(11):6557–6567.
   PubMed Web of Science ®Google Scholar
• French KE, Zhou Z, Terry N. Horizontal ‘gene drives’ harness indigenous bacteria for bioremediation. Sci Rep. 2020;10(1):15091.
   PubMed Web of Science ®Google Scholar
• Dejonghe W, Goris J, El Fantroussi S, et al. Effect of dissemination of 2, 4-dichlorophenoxyacetic acid (2, 4-D) degradation plasmids on 2, 4-D degradation and on bacterial community structure in two different soil horizons. Appl Environ Microbiol. 2000;66(8):3297–3304.
   PubMed Web of Science ®Google Scholar
• Min MG, Kawabata Z, Ishii N, et al. Fate of a PCBS degrading recombinant pseudomonas putida AC30(PMFB2) and its effect on the densities of microbes in marine microcosms contaminated with PCBS. Int J Environ Stud. 1998;55(4):271–285.
   Google Scholar
• Pandey G, Paul D, Jain RK. Conceptualizing “suicidal genetically engineered microorganisms” for bioremediation applications. Biochem Biophys Res Commun. 2005;327(3):637–639.
   PubMed Web of Science ®Google Scholar
• Paul D, Pandey G, Jain RK. Suicidal genetically engineered microorganisms for bioremediation: need and perspectives. Bioessays. 2005;27(5):563–573.
   PubMed Web of Science ®Google Scholar
• Singh A, Billingsley K, Ward O. Composting: a potentially safe process for disposal of genetically modified organisms. Crit Rev Biotechnol. 2006;26(1):1–16.
   PubMed Web of Science ®Google Scholar
• Amarger N. Genetically modified bacteria in agriculture. Biochimie. 2002;84(11):1061–1072.
   PubMed Web of Science ®Google Scholar
• Viebahn M, Glandorf DCM, Ouwens TWM, et al. Repeated introduction of genetically modified pseudomonas putida WCS358r without intensified effects on the indigenous microflora of field-grown wheat. Appl Environ Microbiol. 2003;69(6):3110–3118.
   PubMed Web of Science ®Google Scholar
• Johansen A, Olsson S. Using phospholipid fatty acid technique to study short-term effects of the biological control agent Pseudomonas fluorescens DR54 on the microbial microbiota in barley rhizosphere. Microb Ecol. 2005;49(2):272–281.
   PubMed Web of Science ®Google Scholar
• De Cárcer DA, Martín M, Mackova M, et al. The introduction of genetically modified microorganisms designed for rhizoremediation induces changes on native bacteria in the rhizosphere but not in the surrounding soil. ISME J. 2007;1(3):215–223.
   PubMed Web of Science ®Google Scholar
• Schweitzer JA, Bailey JK, Fischer DG, et al. Plant–soil–microorganism interactions: heritable relationship between plant genotype and associated soil microorganisms. Ecology. 2008;89(3):773–781.
   PubMed Web of Science ®Google Scholar
• Panke-Buisse K, Poole AC, Goodrich JK, et al. Selection on soil microbiomes reveals reproducible impacts on plant function. ISME J. 2015;9(4):980–989.
   PubMed Web of Science ®Google Scholar
• Mueller UG, Sachs JL. Engineering microbiomes to improve plant and animal health. Trends Microbiol. 2015;23(10):606–617.
   PubMed Web of Science ®Google Scholar
• Sergaki C, Lagunas B, Lidbury I, et al. Challenges and approaches in microbiome research: from fundamental to applied. Front Plant Sci. 2018;9:1205.
   PubMed Web of Science ®Google Scholar
• Banerjee S, Schlaeppi K, van der Heijden MG. Keystone taxa as drivers of microbiome structure and functioning. Nature Rev Microbiol. 2018;16(9):567–576.
   PubMed Web of Science ®Google Scholar
• Ray P, Lakshmanan V, Labbé JL, et al. Microbe to microbiome: a paradigm shift in the application of microorganisms for sustainable agriculture. Front Microbiol. 2020;11:3323.
   Web of Science ®Google Scholar
• Saxena P, Singh, NK, Harish,et al. 5 - Recent advances in phytoremediation using genome engineering CRISPR–Cas9 technology. In: Pandey VC, and Singh V, editors. Bioremediation of pollutants. Amsterdam: Elsevier; 2020. p. 125–141.
   Google Scholar
• Stein HP, Navajas-Pérez R, Aranda E, et al. Potential for CRISPR genetic engineering to increase xenobiotic degradation capacities in model fungi. In Prasad, Ram: Approaches in bioremediation. Switzerland: Springer; 2018. p. 61–78.
   Google Scholar
• Jaiswal S, Singh DK, Shukla P. Gene editing and systems biology tools for pesticide bioremediation: a review. Front Microbiol. 2019;10:87.
   PubMed Web of Science ®Google Scholar
• Allouzi MMA, Tang DYY, Chew KW, et al. Micro (nano) plastic pollution: the ecological influence on soil-plant system and human health. SciTotal Environ. 2021;788:147815.
   Google Scholar
• Liu C, Lin H, Dong Y, et al. Identification and characterization of plant growth–promoting endophyte RE02 from Trifolium repens L. in mining smelter. Environ Sci Pollut Res. 2019;26(17):17236–17247.
   PubMed Web of Science ®Google Scholar
• Ke T, Zhang J, Tao Y, et al. Individual and combined application of Cu-tolerant Bacillus spp. enhance the Cu phytoextraction efficiency of perennial ryegrass. Chemosphere. 2021;263:127952.
   PubMed Web of Science ®Google Scholar
• He X, Xu M, Wei Q, et al. Promotion of growth and phytoextraction of cadmium and lead in Solanum nigrum L. mediated by plant-growth-promoting rhizobacteria. Ecotoxicol Environ Saf. 2020;205:111333.
   PubMed Web of Science ®Google Scholar
• Abdelkrim S, Jebara SH, Saadani O, et al. In situ effects of Lathyrus sativus-PGPR to remediate and restore quality and fertility of Pb and Cd polluted soils. Ecotoxicol Environ Saf. 2020;192:110260.
   PubMed Web of Science ®Google Scholar
• Tirry N, Kouchou A, El Omari B, et al. Improved chromium tolerance of Medicago sativa by plant growth-promoting rhizobacteria (PGPR). J Genet Eng Biotechnol. 2021;19(1):1–14.
   PubMed Web of Science ®Google Scholar
• Jeyasundar PGSA, Ali A, Azeem M, et al. Green remediation of toxic metals contaminated mining soil using bacterial consortium and Brassica juncea. Environ Pollut. 2021;277:116789.
   PubMed Web of Science ®Google Scholar
• Xu Z, Lei Y, Patel J. Bioremediation of soluble heavy metals with recombinant Caulobacter crescentus. Bioengineered Bugs. 2010;1(3):207–212.
   PubMedGoogle Scholar
• Kou S, Yang Z, Luo J, et al. Entirely recombinant protein-based hydrogels for selective heavy metal sequestration. Polym Chem. 2017;8(39):6158–6164.
   Web of Science ®Google Scholar
• Si K, Ming T, Li Y, et al. Heavy metal detoxification by recombinant ferritin from Apostichopus japonicus. RSC Adv. 2017;7(66):41909–41918.
   Web of Science ®Google Scholar
• Pazirandeh M, Chrisey LA, Mauro JM, et al. Expression of the Neurospora crassa metallothionein gene in Escherichia coli and its effect on heavy-metal uptake. Appl Microbiol Biotechnol. 1995;43(6):1112–1117.
   PubMed Web of Science ®Google Scholar
• Sauge-Merle S, Lecomte-Pradines C, Carrier P, et al. Heavy metal accumulation by recombinant mammalian metallothionein within Escherichia coli protects against elevated metal exposure. Chemosphere. 2012;88(8):918–924.
   PubMed Web of Science ®Google Scholar
• Bai F, Tian H. Recombinant Rhodococcus erythropolis expressing HAO and AMO genes promotes nitrogen and organic matter removal efficiency in the treatment of landfill leachate. Water and Environment Journal. 2021. doi:10.1111/wej.12743.
   PubMed Web of Science ®Google Scholar