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Microbial-Mediated Management of Organic Xenobiotic Pollutants in Agricultural Lands

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Book cover Plant Responses to Xenobiotics

Abstract

Contamination of agricultural soil by organic xenobiotic compounds is becoming a serious problem in most of the developed and developing countries. Chemicals foreign to an organism or chemicals not natural to an ecosystem are considered as xenobiotic for an organism, and upon exposure they impose toxicity threats to the organism. The term is mainly used in the context of pollutants such as chemical fertilizers, pesticides, dyes, dioxins, polychlorinated biphenyls (PCBs), and polycyclic aromatic hydrocarbons (PAHs) and their side effect on the biota. High concentrations of these xenobiotics create a biological imbalance in soil leading to surface and groundwater pollution. Inside plants they block the functional groups of biologically important molecules like enzymes, transport system of nutrient ions, polynucleotides, etc. The degradation of these organic xenobiotic pollutants in nature is a serious challenge and microorganisms have been observed to play a vital role in their degradation. They transform hazardous organic xenobiotic compound into harmless or less hazardous form, generally carbon dioxide, water, methane, and nitrogen. The different groups of microbes produce different types of enzymes and organic acids that act on recalcitrant compounds and degrade them to simpler forms. As a consequence of biodegradation of xenobiotic compounds, microorganisms are helpful to overcome environmental pollution and considered as eco-friendly. This chapter tries to elaborate some of the mechanisms employed by the microorganisms to carry out the xenobiotic degradation and remediation process along with different genera of microbes involved in the process.

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References

  • Agrawal N, Shahi SK (2015) An environmental cleanup strategy-microbial transformation of xenobiotic compounds. Int J Curr Microbiol Appl Sci 4(4):429–461

    Google Scholar 

  • Agarwal T, Khillare P, Shridhar V, Ray S (2009) Pattern, sources and toxic potential of PAHs in the agricultural soils of Delhi, India. J Hazard Mater 163(2):1033–1039

    Article  CAS  PubMed  Google Scholar 

  • Alexander M (1977) Introduction to soil microbiology, vol Ed. 2. John Wiley & Sons, New York

    Google Scholar 

  • Alkorta I, Garbisu C (2001) Phytoremediation of organic contaminants in soils. Bioresour Technol 79(3):273–276

    Article  CAS  PubMed  Google Scholar 

  • Arora PK, Kumar M, Chauhan A, Raghava GP, Jain RK (2009) OxDBase: a database of oxygenases involved in biodegradation. BMC Res Notes 2(1):67

    Article  PubMed  PubMed Central  Google Scholar 

  • Åslund MLW, Rutter A, Reimer KJ, Zeeb BA (2008) The effects of repeated planting, planting density, and specific transfer pathways on PCB uptake by Cucurbita pepo grown in field conditions. Sci Total Environ 405(1):14–25

    Article  Google Scholar 

  • Azaizeh H, Castro PM, Kidd P (2011) Biodegradation of organic Xenobiotic pollutants in the Rhizosphere. In: Org Xenob plants. Springer, Dordrecht, pp 191–215

    Google Scholar 

  • Baloch UK, Haseeb M (1996) Xenobiotics in the third world agricultural environment. Environmental Xenobiotics. TJ Press, London, pp 64–81

    Google Scholar 

  • Bastos AER, Moon DH, Rossi A, Trevors JT, Tsai SM (2000) Salt-tolerant phenol-degrading microorganisms isolated from Amazonian soil samples. Arch Microbiol 174(5):346–352

    Article  CAS  PubMed  Google Scholar 

  • Bidlan R, Manonmani H (2002) Aerobic degradation of dichlorodiphenyltrichloroethane (DDT) by Serratia marcescens DT-1P. Process Biochem 38(1):49–56

    Article  CAS  Google Scholar 

  • Cao B, Nagarajan K, Loh K-C (2009) Biodegradation of aromatic compounds: current status and opportunities for biomolecular approaches. Appl Microbiol Biotechnol 85(2):207–228

    Article  CAS  PubMed  Google Scholar 

  • Castillo M, Felis N, Aragon P, Cuesta G, Sabater C (2006) Biodegradation of the herbicide diuron by streptomycetes isolated from soil. Int Biodeterior Biodegrad 58(3):196–202

    Article  CAS  Google Scholar 

  • Chandra S, Singh N (2015) Enhanced bioremediation techniques for agricultural soils. Int J Curr Res Acad Rev 3(7):166–173

    Google Scholar 

  • Chien CC, Kao CM, Chen DY, Chen SC, Chen CC (2014) Biotransformation of trinitrotoluene (TNT) by Pseudomonas spp. isolated from a TNT‐contaminated environment. Environ Toxicol Chem 33(5):1059–1063

    Article  CAS  PubMed  Google Scholar 

  • Chowdhury S, Mishra M, Adarsh V, Mukherjee A, Thakur AR, Chaudhuri SR (2008) Novel metal accumulator and protease secretor microbes from east Calcutta Wetland. Am J Biochem Biotechnol 4(3):255–264

    Article  CAS  Google Scholar 

  • Cookson JT Jr (1995) Bioremediation engineering: design and application. McGraw-Hill, Inc, New York

    Google Scholar 

  • Copley SD (2000) Evolution of a metabolic pathway for degradation of a toxic xenobiotic: the patchwork approach. Trends Biochem Sci 25(6):261–265

    Article  CAS  PubMed  Google Scholar 

  • Cuozzo SA, Rollán GG, Abate CM, Amoroso MJ (2009) Specific dechlorinase activity in lindane degradation by Streptomyces sp. M7. World J Microbiol Biotechnol 25(9):1539–1546

    Article  CAS  Google Scholar 

  • Curtis GP, Reinhard M (1994) Reductive dehalogenation of hexachloroethane, carbon tetrachloride, and bromoform by anthrahydroquinone disulfonate and humic acid. Environ Sci Technol 28(13):2393–2401

    Article  CAS  PubMed  Google Scholar 

  • Dıaz E, Prieto MA (2000) Bacterial promoters triggering biodegradation of aromatic pollutants. Curr Opin Biotechnol 11(5):467–475

    Article  PubMed  Google Scholar 

  • Dong X, Hong Q, He L, Jiang X, Li S (2008) Characterization of phenol-degrading bacterial strains isolated from natural soil. Int Biodeter Biodegr 62(3):257–262

    Article  CAS  Google Scholar 

  • Eapen S, Singh S, D’souza S (2007) Advances in development of transgenic plants for remediation of xenobiotic pollutants. Biotechnol Adv 25(5):442–451

    Article  CAS  PubMed  Google Scholar 

  • Fatta-Kassinos D, Kalavrouziotis I, Koukoulakis P, Vasquez M (2011) The risks associated with wastewater reuse and xenobiotics in the agroecological environment. Sci Total Environ 409(19):3555–3563

    Article  CAS  PubMed  Google Scholar 

  • Ferradji FZ, Mnif S, Badis A, Rebbani S, Fodil D, Eddouaouda K, Sayadi S (2014) Naphthalene and crude oil degradation by biosurfactant producing Streptomyces spp. isolated from Mitidja plain soil (North of Algeria). Int Biodeterior Biodegrad 86:300–308

    Article  CAS  Google Scholar 

  • Hernández-Castellanos B, Ortíz-Ceballos A, Martínez-Hernández S, Noa-Carrazana J, Luna-Guido M, Dendooven L, Contreras-Ramos S (2013) Removal of benzo (a) pyrene from soil using an endogeic earthworm Pontoscolex corethrurus. Appl Soil Ecol 70:62–69

    Article  Google Scholar 

  • Hong Q, Dong X, He L, Jiang X, Li S (2009) Isolation of a biphenyl-degrading bacterium, Achromobacter sp. BP3, and cloning of the bph gene cluster. Int Biodeter Biodegrad 63(4):365–370

    Article  CAS  Google Scholar 

  • Iovdijova A, Bencko V (2010) Potential risk of exposure to selected xenobiotic residues and their fate in the food chain – Part. I: Classification of xenobiotics. Ann Agric Environ Med 17(2):183–192

    CAS  PubMed  Google Scholar 

  • Jain RK, Kapur M, Labana S, Sarma P, Lal B, Bhattacharya D, Thakur IS (2005) Microbial diversity: application on micro-organisms for the biodegradation of xenobiotics. Curr Sci 89:101–112

    CAS  Google Scholar 

  • Jayasekara R, Harding I, Bowater I, Lonergan G (2005) Biodegradability of a selected range of polymers and polymer blends and standard methods for assessment of biodegradation. J Polym Environ 13(3):231–251

    Article  CAS  Google Scholar 

  • Jia L-Y, Zheng A-P, Xu L, Huang X-D, Zhang Q, Yang F-L (2008) Isolation and characterization of comprehensive polychlorinated biphenyl degrading bacterium, Enterobacter sp. LY402. J Microbiol Biotechnol 18(5):952–957

    CAS  PubMed  Google Scholar 

  • Kazumi J, Häggblom M, Young L (1995) Diversity of anaerobic microbial processes in chlorobenzoate degradation: nitrate, iron, sulfate and carbonate as electron acceptors. Appl Microbiol Biotechnol 43(5):929–936

    Article  CAS  PubMed  Google Scholar 

  • Kumar K, Devi SS, Krishnamurthi K, Kanade GS, Chakrabarti T (2007) Enrichment and isolation of endosulfan degrading and detoxifying bacteria. Chemosphere 68(2):317–322

    Article  CAS  PubMed  Google Scholar 

  • Kwon G-S, Sohn H-Y, Shin K-S, Kim E, Seo B-I (2005) Biodegradation of the organochlorine insecticide, endosulfan, and the toxic metabolite, endosulfan sulfate, by Klebsiella oxytoca KE-8. Appl Microbiol Biotechnol 67(6):845–850

    Article  CAS  PubMed  Google Scholar 

  • Langenbach T (2013) Persistence and bioaccumulation of persistent organic pollutants (POPs). Bioremediation-Active and passive approaches. InTech, pp 307–331

    Google Scholar 

  • Leung M (2004) Bioremediation: techniques for cleaning up a mess. Bio Tech J 2:18–22

    Google Scholar 

  • Lin W, Chang-Chien G, Kao C, Newman L, Wong T, Liu J (2014) Biodegradation of Polychlorinated Dibenzo–Dioxins by Strain NSYSU. J Environ Qual 43(1):349–357

    Article  CAS  PubMed  Google Scholar 

  • Liu H, Yao J, Yuan Z, Shang Y, Chen H, Wang F, Masakorala K, Yu C, Cai M, Blake RE (2014a) Isolation and characterization of crude-oil-degrading bacteria from oil-water mixture in Dagang oilfield, China. Int Biodeterior Biodegrad 87:52–59

    Article  Google Scholar 

  • Liu X-M, Chen K, Meng C, Zhang L, Zhu J-C, Huang X, Li S-P, Jiang J-D (2014b) Pseudoxanthobacter liyangensis sp. nov., isolated from dichlorodiphenyltrichloroethane-contaminated soil. Int J Syst Evol Microbiol 64(10):3390–3394

    Article  PubMed  Google Scholar 

  • Magnuson JK, Stern RV, Gossett JM, Zinder SH, Burris DR (1998) Reductive dechlorination of tetrachloroethene to ethene by a two-component enzyme pathway. Appl Environ Microbiol 64(4):1270–1275

    CAS  PubMed  PubMed Central  Google Scholar 

  • Mercimek HA, Dincer S, Guzeldag G, Ozsavli A, Matyar F (2013) Aerobic biodegradation of 2, 4, 6-trinitrotoluene (TNT) by Bacillus cereus isolated from contaminated soil. Microb Ecol 66(3):512–521

    Article  CAS  PubMed  Google Scholar 

  • Monica S, Karthik L, Mythili S, Sathiavelu A (2012) Formulation of effective microbial consortia and its application for sewage treatment. J Microb Biochem Technol 3(3):051–055

    Google Scholar 

  • Nawab A, Aleem A, Malik A (2003) Determination of organochlorine pesticides in agricultural soil with special reference to γ-HCH degradation by Pseudomonas strains. Bioresour Technol 88(1):41–46

    Article  CAS  PubMed  Google Scholar 

  • Park Y-C, Lee S, Cho M-H (2014) The simplest flowchart stating the mechanisms for organic xenobiotics-induced toxicity: can it possibly be accepted as a “central dogma” for toxic mechanisms? Toxicol Res 30(3):179

    Article  PubMed  PubMed Central  Google Scholar 

  • Patel V, Jain S, Madamwar D (2012) Naphthalene degradation by bacterial consortium (DV-AL) developed from Alang-Sosiya ship breaking yard, Gujarat, India. Bioresour Technol 107:122–130

    Article  CAS  PubMed  Google Scholar 

  • Piutti S, Semon E, Landry D, Hartmann A, Dousset S, Lichtfouse E, Topp E, Soulas G, Martin Laurent F (2003) Isolation and characterisation of Nocardioides sp. SP12, an atrazine-degrading bacterial strain possessing the gene trzN from bulk- and maize rhizosphere soil. FEMS Microbiol Lett 221(1):111–117

    Article  CAS  PubMed  Google Scholar 

  • Ross S (1994) Sources and forms of potentially toxic metals in soil-plant systems. Toxic metals in soil-plant systems. Wiley, Chichester, pp 3–26

    Google Scholar 

  • Sakai M, Ezaki S, Suzuki N, Kurane R (2005) Isolation and characterization of a novel polychlorinated biphenyl-degrading bacterium, Paenibacillus sp. KBC101. Appl Microbiol Biotechnol 68(1):111–116

    Article  CAS  PubMed  Google Scholar 

  • Schröter-Kermani C, Kreft D, Schilling B, Herrchen M, Wagner G (2006) Polycyclic aromatic hydrocarbons in pine and spruce shoots – temporal trends and spatial distribution. J Environ Monit 8(8):806–811

    Article  PubMed  Google Scholar 

  • Schwitzguébel J-P, Page V, Martins-Dias S, Davies LC, Vasilyeva G, Strijakova E (2011) Using plants to remove foreign compounds from contaminated water and soil. In: Schroder P, Collins CD (eds) Organic Xenobiotics and plants. Springer, Dordrecht, pp 149–189

    Chapter  Google Scholar 

  • Shimao M (2001) Biodegradation of plastics. Curr Opin Biotechnol 12(3):242–247

    Article  CAS  PubMed  Google Scholar 

  • Singh NS, Singh DK (2011) Biodegradation of endosulfan and endosulfan sulfate by Achromobacter xylosoxidans strain C8B in broth medium. Biodegradation 22(5):845–857

    Article  CAS  PubMed  Google Scholar 

  • Singh BK, Walker A (2006) Microbial degradation of organophosphorus compounds. FEMS Microbiol Rev 30(3):428–471

    Article  CAS  PubMed  Google Scholar 

  • Solouki T, Khalvati MA, Miladi M, Zekavat B (2011) State-of-the-art chemical analyses: Xenobiotics, plant proteomics, and residues in plant based products. In: Schroder P, Collins CD (eds) Organic Xenobiotics and plants. Springer, Dordrecht, pp 261–306

    Chapter  Google Scholar 

  • Su Y-H, Zhu Y-G (2007) Transport mechanisms for the uptake of organic compounds by rice (Oryza sativa) roots. Environ Pollut 148(1):94–100

    Article  CAS  PubMed  Google Scholar 

  • Suzuki S, Hiraishi A (2007) Novosphingobium naphthalenivorans sp. nov., a naphthalene-degrading bacterium isolated from polychlorinated-dioxin-contaminated environments. J Gen Appl Microbiol 53(4):221–228

    Article  CAS  PubMed  Google Scholar 

  • Theriot CM, Grunden AM (2011) Hydrolysis of organophosphorus compounds by microbial enzymes. Appl Microbiol Biotechnol 89(1):35–43

    Article  CAS  PubMed  Google Scholar 

  • Toussaint J-P, Pham TTM, Barriault D, Sylvestre M (2012) Plant exudates promote PCB degradation by a rhodococcal rhizobacteria. Appl Microbiol Biotechnol 95(6):1589–1603

    Article  CAS  PubMed  Google Scholar 

  • Tripathi BD (2012) A short term study on toxic effects of distillery sludge amendment on microbiological and enzymatic properties of agricultural soil in a tropical city. J Earth Sci Clim Change 2:1–8

    Google Scholar 

  • Tropel D, Van Der Meer JR (2004) Bacterial transcriptional regulators for degradation pathways of aromatic compounds. Microbiol Mol Biol Rev 68(3):474–500

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tuo B-H, Yan J-B, Fan B-A, Z-H Y, Liu J-Z (2012) Biodegradation characteristics and bioaugmentation potential of a novel quinoline-degrading strain of Bacillus sp. isolated from petroleum-contaminated soil. Bioresour Technol 107:55–60

    Article  CAS  PubMed  Google Scholar 

  • Umar AF, Tahir F, Larkin MJ, Oyawoye OM, Musa BL, Yerima MB, Agbo EB (2012) AtzABC catabolic gene probe from novel atrazine-degrading Rhodococcus strain isolated from a Nigerian agricultural soil. Adv Microbiol 2:593–597

    Article  Google Scholar 

  • Vangnai AS, Petchkroh W (2007) Biodegradation of 4-chloroaniline by bacteria enriched from soil. FEMS Microbiol Lett 268(2):209–216

    Article  CAS  PubMed  Google Scholar 

  • Vargas C, Song B, Camps M, Häggblom M (2000) Anaerobic degradation of fluorinated aromatic compounds. Appl Microbiol Biotechnol 53(3):342–347

    Article  CAS  PubMed  Google Scholar 

  • Varsha Y, Naga Deepthi CH, Chenna S (2012) An emphasis on xenobiotic degradation in environmental clean up. J Biorem Biodegrad 2(4):1–10

    Google Scholar 

  • Vidali M (2001) Bioremediation. an overview. Pure Appl Chem 73(7):1163–1172

    Article  CAS  Google Scholar 

  • Visioli F (2015) Xenobiotics and human health: a new view of their pharma-nutritional role. PharmaNutrition 3(2):60–64

    Article  CAS  Google Scholar 

  • Wang F, Grundmann S, Schmid M, Dörfler U, Roherer S, Munch JC, Hartmann A, Jiang X, Schroll R (2007) Isolation and characterization of 1, 2, 4-trichlorobenzene mineralizing Bordetella sp. and its bioremediation potential in soil. Chemosphere 67(5):896–902

    Article  CAS  PubMed  Google Scholar 

  • Wasi S, Tabrez S, Ahmad M (2013) Toxicological effects of major environmental pollutants: an overview. Environ Monit Assess 185(3):2585–2593

    Article  PubMed  Google Scholar 

  • Widehem P, Aıt-Aıssa S, Tixier C, Sancelme M, Veschambre H, Truffaut N (2002) Isolation, characterization and diuron transformation capacities of a bacterial strain Arthrobacter sp. N2. Chemosphere 46(4):527–534

    Article  CAS  PubMed  Google Scholar 

  • Yamaga F, Washio K, Morikawa M (2010) Sustainable biodegradation of phenol by Acinetobacter calcoaceticus P23 isolated from the rhizosphere of duckweed Lemna aoukikusa. Environ Sci & Technol 44(16):6470–6474

    Article  CAS  Google Scholar 

  • Zaidi S, Usmani S, Singh BR, Musarrat J (2006) Significance of Bacillus subtilis strain SJ-101 as a bioinoculant for concurrent plant growth promotion and nickel accumulation in Brassica juncea. Chemosphere 64(6):991–997

    Article  CAS  PubMed  Google Scholar 

  • Zeinali M, Vossoughi M, Ardestani SK, Babanezhad E, Masoumian M (2007) Hydrocarbon degradation by thermophilic Nocardia otitidiscaviarum strain TSH1: physiological aspects. J Basic Microbiol 47(6):534–539

    Article  CAS  PubMed  Google Scholar 

  • Zvyagintsev D (1990) Soil microorganisms and environment protection. Agrochem Soil Sci 39(3–4):283–285

    Google Scholar 

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Singh, A., Chaudhary, S., Dubey, B., Prasad, V. (2016). Microbial-Mediated Management of Organic Xenobiotic Pollutants in Agricultural Lands. In: Singh, A., Prasad, S., Singh, R. (eds) Plant Responses to Xenobiotics. Springer, Singapore. https://doi.org/10.1007/978-981-10-2860-1_9

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