Advertisement

Marine Microbes in Bioremediation: Current Status and Future Trends

  • Neetu Sharma
  • Abhinashi Singh
  • Sonu Bhatia
  • Navneet Batra
Chapter
Part of the Microorganisms for Sustainability book series (MICRO, volume 16)

Abstract

As per evolutionary studies, life was believed to be originated in the marine environment. About 70% of earth’s surface is covered with water which hosts a wide variety of life forms under extreme conditions. Vast research has been carried out to explore the terrestrial habitats for a variety of products, but the marine environment still remains little explored. The marine microorganisms have undergone great evolutionary changes due to variable and extreme marine conditions. Hence enzymes from marine microflora bear novel properties with wide applications in multidisciplinary areas. Due to highly challenging environmental conditions, the aquatic ecosystem inhabits microorganisms that produce enzymes having unique/novel characteristics such as thermostability, cold adaptability, high pressure, pH, and extreme salt tolerance. Desulfurococcus sp., Pyrococcus sp., Thermococcus sp., and Geobacillus sp. are aquatic producers of thermostable amylases, peptidases, and lipases. Cold-active enzymes such as beta-glycosidases and peptidases have been isolated from psychrophiles inhabiting in cold marine areas such as deep-sea muds. Other polysaccharide-degrading enzymes are also well studied in aquatic systems including chitinase, alginate lyases, agarases, carrageenans, and cellulose hydrolases. Halophilic microbes from waters of the Pacific Ocean, Black Sea, and Mediterranean Sea have been explored for enzymes like beta-D-galactosidase, alpha-D-galactosidase, etc. These enzymes have a wide range of applicability in pulp and paper, biofuel, food, and textile industry, replacing the conventional processes and making the process eco-friendly and cost-effective. Further fungal enzymes lignin peroxidase, manganese peroxidase, and laccase can be used in the treatment and bioremediation of industrial effluents and wastewater contaminants which escapes traditional treatment processes. This chapter deals with the review of the research work associated with the present scenario of marine microbes in bioremediation and their future trends.

Keywords

Bioremediation Oxygenases Degradation Pollutants Marine enzymes 

Notes

Acknowledgments

The authors are thankful to the Goswami Ganesh Dutta Sanatan Dharma College, Chandigarh for providing the facilities.

References

  1. Aakvik T, Degnes KF, Dahlsrud R, Schmidt F, Dam R, Yu L, Völker U, Ellingsen TE, Valla S (2009) A plasmid RK2-based broad-host-range cloning vector useful for transfer of metagenomic libraries to a variety of bacterial species. FEMS Microbiol Lett 296(2):149–158PubMedCrossRefGoogle Scholar
  2. Abdelatey LM, Khalil WK, Ali TH, Mahrous KF (2011) Heavy metal resistance and gene expression analysis of metal resistance genes in gram-positive and gram-negative bacteria present in Egyptian soils. J Appl Sci Environ Sanitat 6(2)Google Scholar
  3. Aguilar-Barajas E, Paluscio E, Cervantes C, Rensing C (2008) Expression of chromate resistance genes from Shewanella sp. strain ANA-3 in Escherichia coli. FEMS Microbiol Lett 285(1):97–100PubMedCrossRefGoogle Scholar
  4. Alexander DE (1999) Encyclopedia of environmental science. Springer, New York, 0-412-74050-8Google Scholar
  5. Arora PK, Kumar M, Chauhan A, Raghava GP, Jain RK (2009) OxDBase: a database of oxygenases involved in biodegradation. BMC Res Not 2(1):67PubMedPubMedCentralCrossRefGoogle Scholar
  6. Arun A, Raja PP, Arthi R, Ananthi M, Kumar KS, Eyini M (2008) Polycyclic aromatic hydrocarbons (PAHs) biodegradation by basidiomycetes fungi, Pseudomonas isolate, and their cocultures: comparative in vivo and in silico approach. Appl Biochem Biotechnol 151(2–3):132–142PubMedCrossRefGoogle Scholar
  7. Barnes NM, Khodse VB, Lotlikar NP, Meena RM, Damare SR (2018) Bioremediation potential of hydrocarbon-utilizing fungi from select marine niches of India. 3 Biotech 8(1):21PubMedCrossRefGoogle Scholar
  8. Birolli WG, Santos DDA, Alvarenga N, Garcia AC, Romão LP, Porto AL (2018) Biodegradation of anthracene and several PAHs by the marine-derived fungus Cladosporium sp. CBMAI 1237. Mar Pollut Bull 129(2):525–533PubMedCrossRefGoogle Scholar
  9. Bonugli-Santos RC, dos Santos Vasconcelos MR, Passarini MR, Vieira GA, Lopes VC, Mainardi PH, Dos Santos JA, de Azevedo Duarte L, Otero IV, da Silva Yoshida AM, Feitosa VA (2015) Marine-derived fungi: diversity of enzymes and biotechnological applications. Front Microbiol 6:269PubMedPubMedCentralCrossRefGoogle Scholar
  10. Bowers KJ, Mesbah NM, Wiegel J (2009) Biodiversity of poly-extremophilic Bacteria: does combining the extremes of high salt, alkaline pH and elevated temperature approach a physicochemical boundary for life? Saline Syst 5(1):9PubMedPubMedCentralCrossRefGoogle Scholar
  11. Chellaiah, E.R., 2018. Cadmium (heavy metals) bioremediation by Pseudomonas aeruginosa: a minireview. Applied water science, 8(6), p.154Google Scholar
  12. Ciullini I, Tilli S, Scozzafava A, Briganti F (2008) Fungal laccase, cellobiose dehydrogenase, and chemical mediators: combined actions for the decolorization of different classes of textile dyes. Bioresour Technol 99(15):7003–7010PubMedCrossRefGoogle Scholar
  13. Copley SD (1997) Diverse mechanistic approaches to difficult chemical transformations: microbial dehalogenation of chlorinated aromatic compounds. Chem Biol 4(3):169–174PubMedCrossRefGoogle Scholar
  14. Couto SR, Sanromán MA, Gübitz GM (2005) Influence of redox mediators and metal ions on synthetic acid dye decolourization by crude laccase from Trametes hirsuta. Chemosphere 58(4):417–422CrossRefGoogle Scholar
  15. Cripps C, Bumpus JA, Aust SD (1990) Biodegradation of azo and heterocyclic dyes by Phanerochaete chrysosporium. Appl Environ Microbiol 56(4):1114–1118PubMedPubMedCentralGoogle Scholar
  16. D’Souza-Ticlo D, Sharma D, Raghukumar C (2009) A thermostable metal-tolerant laccase with bioremediation potential from a marine-derived fungus. Mar Biotechnol 11(6):725–737PubMedCrossRefGoogle Scholar
  17. Dash HR, Das S (2012) Bioremediation of mercury and the importance of bacterial mer genes. Intl Biodeterior Biodegrad 75:207–213CrossRefGoogle Scholar
  18. Dash HR, Mangwani N, Chakraborty J, Kumari S, Das S (2013) Marine bacteria: potential candidates for enhanced bioremediation. Appl Microbiol Biotechnol 97(2):561–571PubMedCrossRefGoogle Scholar
  19. Delong EF, Yayanos AA (1987) Properties of the glucose-transport system in some deep-sea bacteria. Appl Environ Microbiol 53:527–532PubMedPubMedCentralGoogle Scholar
  20. Deshmukh R, Khardenavis AA, Purohit HJ (2016) Diverse metabolic capacities of fungi for bioremediation. Indian J Microbiol 56(3):247–264PubMedPubMedCentralCrossRefGoogle Scholar
  21. Dewapriya P, Kim SK (2014) Marine microorganisms: an emerging avenue in modern nutraceuticals and functional foods. Food Res Int 56:115–125CrossRefGoogle Scholar
  22. Diwaniyan S, Kharb D, Raghukumar C, Kuhad RC (2010) Decolorization of synthetic dyes and textile effluents by basidiomycetous fungi. Water Air Soil Pollut 210(1–4):409–419CrossRefGoogle Scholar
  23. Felczykowska A, Krajewska A, Zielińska S, Łoś JM, Bloch SK, Nejman-Faleńczyk B (2015) The most widespread problems in the function-based microbial metagenomics. Acta Biochim Pol 62(1):161PubMedCrossRefGoogle Scholar
  24. Ferrer M, Martínez-Martínez M, Bargiela R, Streit WR, Golyshina OV, Golyshin PN (2016) Estimating the success of enzyme bioprospecting through metagenomics: current status and future trends. Microb Biotechnol 9(1):22–34PubMedCrossRefGoogle Scholar
  25. Fritsche W, Hofrichter M (2000) Aerobic degradation by microorganisms. Biotechnology 11:146–164Google Scholar
  26. Gadd GM, White C (1993) Microbial treatment of metal pollution: working biotechnology? Trends Biotechnol 11:353–359PubMedCrossRefGoogle Scholar
  27. Gallego JLR, Loredo J, Lamas JF, Azquez FV, Anchez JS (2001) Bioremediation of diesel-contaminated soils: evaluation of potential in situ techniques by the study of bacterial degradation. Biodegradation 12:325–335PubMedCrossRefGoogle Scholar
  28. Ghosal D, Ghosh S, Dutta TK, Ahn Y (2016) The current state of knowledge in microbial degradation of polycyclic aromatic hydrocarbons (PAHs): a review. Front Microbiol 7:1369PubMedPubMedCentralGoogle Scholar
  29. Goodfellow M, Haynes JA (1984) Actinomycetes in marine sediments. In: Oritz-Oritz L et al (eds) Biological, biochemical and biomedical aspects of actinomycetes. Academic, New York/London, pp 453–472CrossRefGoogle Scholar
  30. Guzik U, Greń I, Hupert-Kocurek K, Wojcieszyńska D (2011) Catechol 1, 2-dioxygenase from the new aromatic compounds–degrading Pseudomonas putida strain N6. Int Biodeterior Biodegradation 65(3):504–512CrossRefGoogle Scholar
  31. Harms H, Schlosser D, Wick LY (2011) Untapped potential: exploiting fungi in bioremediation of hazardous chemicals. Nat Rev Microbiol 9(3):177PubMedCrossRefGoogle Scholar
  32. Hase CC, Fedorova ND, Galperin MY, Dibrov PA (2001) Sodium ion cycle in bacterial pathogens: evidence from cross-genome comparisons. Microbiol Mol Biol Rev 65(3):353–370PubMedPubMedCentralCrossRefGoogle Scholar
  33. Hiner AN, Ruiz JH, López JNR, Cánovas FG, Brisset NC, Smith AT, Arnao MB, Acosta M (2002) Reactions of the class II peroxidases, lignin peroxidase andArthromyces ramosus peroxidase, with hydrogen peroxide catalase-like activity, compound III formation, and enzyme inactivation. J Biol Chem 277(30):26879–26885PubMedCrossRefGoogle Scholar
  34. Hong YH, Deng MC, Xu XM, Wu CF, Xiao X, Zhu Q, Sun XX, Zhou QZ, Peng J, Yuan JP, Wang JH (2016) Characterization of the transcriptome of Achromobacter sp. HZ01 with the outstanding hydrocarbon-degrading ability. Gene 584(2):185–194PubMedCrossRefGoogle Scholar
  35. Inagaki F, Nunoura T, Nakagawa S, Teske A, Lever M, Lauer A, Suzuki M, Takai K, Delwiche M, Colwell FS, Nealson KH (2006) Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin. Proc Natl Acad Sci 103(8):2815–2820PubMedCrossRefGoogle Scholar
  36. Kadri T, Rouissi T, Brar SK, Cledon M, Sarma S, Verma M (2017) Biodegradation of polycyclic aromatic hydrocarbons (PAHs) by fungal enzymes: a review. J Environ Sci 51:52–74CrossRefGoogle Scholar
  37. Karigar CS, Rao SS (2011) Role of microbial enzymes in the bioremediation of pollutants: a review. Enzyme Res 2011:1.  https://doi.org/10.4061/2011/805187CrossRefGoogle Scholar
  38. Lal R, Saxena DM (1982) Accumulation, metabolism, and effects of organochlorine insecticides on microorganisms. Microbiol Rev 46(1):95PubMedPubMedCentralGoogle Scholar
  39. Latus M, Seitz H, Eberspacher J, Lingens F (1995) Purification and characterization of Hydroxyquinol 1, 2-dioxygenase from Azotobacter sp. strain GP1. Appl Environ Microbiol 61(7):2453–2460PubMedPubMedCentralGoogle Scholar
  40. Lecavalier MP, Lechevalier H (1970) Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Evol Microbiol 20(4):435–443Google Scholar
  41. Lee DW, Lee H, Lee AH, Kwon BO, Khim JS, Yim UH, Kim BS, Kim JJ (2018) Microbial community composition and PAHs removal potential of indigenous bacteria in oil contaminated sediment of Taean coast, Korea. Environ Pollut 234:503–512PubMedCrossRefGoogle Scholar
  42. Li MZ, Squires CH, Monticello DJ, Childs JD (1996) Genetic analysis of the dsz promoter and associated regulatory regions of Rhodococcus erythropolis IGTS8. J Bacteriol 178(22):6409–6418PubMedPubMedCentralCrossRefGoogle Scholar
  43. Maneerat S, Phetrong K (2007) Isolation of biosurfactant-producing marine bacteria and characteristics of selected biosurfactant. Songklanakarin J Sci Technol 29:781–791Google Scholar
  44. Margesin R, Schinner F (2001) Biodegradation and bioremediation of hydrocarbons in extreme environments. Appl Microbiol Biotechnol 56:650–663PubMedCrossRefGoogle Scholar
  45. Moghimi H, Tabar RH, Hamedi J (2017) Assessing the biodegradation of polycyclic aromatic hydrocarbons and laccase production by new fungus Trematophoma sp. UTMC 5003. World J Microbiol Biotechnol 33(7):136PubMedCrossRefGoogle Scholar
  46. Mohiuddin M, Fakhruddin ANM (2012) Degradation of phenol via meta-cleavage pathway by Pseudomonas fluorescens PU1. ISRN Microbiol 2012:1–6CrossRefGoogle Scholar
  47. Nies DH, Silver S (1995) Ion efflux systems involved in bacterial metal resistances. J Ind Microbiol 14(2):186–199PubMedCrossRefGoogle Scholar
  48. Niku-Paavola ML, Viikari L (2000) Enzymatic oxidation of alkenes. J Mol Catal B Enzym 10(4):435–444CrossRefGoogle Scholar
  49. Parales RE, Resnick SM (2006) Aromatic ring-hydroxylating dioxygenases. In Pseudomonas. Springer, Boston, pp 287–340Google Scholar
  50. Passarini MR, Rodrigues MV, da Silva M, Sette LD (2011) Marine-derived filamentous fungi and their potential application for polycyclic aromatic hydrocarbon bioremediation. Mar Pollut Bull 62(2):364–370PubMedCrossRefGoogle Scholar
  51. Piskorska M, Smith G, Weil E (2007) Bacteria associated with the coral Echinopora lamellosa (Esper 1795) in the Indian Ocean-Zanzibar region. Afr J Environ Sci Technol 1(5):93–98Google Scholar
  52. Prasad MP, Manjunath K (2011) Comparative study on biodegradation of lipid-rich wastewater using lipase producing bacterial species. Indian J Biotechnol 10:121–124Google Scholar
  53. Pulicherla KK, Rao KS (2013) Marine biocatalysts and their stability: a molecular approach. In: Marine enzymes for biocatalysis. Woodhead Publishing, Cambridge, pp 71–87CrossRefGoogle Scholar
  54. Purushothaman A (1998) Microbial diversity. In: Proceedings of the technical workshop on biodiversity of Gulf of Mannar Marine Biosphere Reserve, M. S. Swaminathan Research Foundation, Chennai, pp 86–91Google Scholar
  55. Que L Jr, Ho RY (1996) Dioxygen activation by enzymes with mononuclear non-heme iron active sites. Chem Rev 96(7):2607–2624PubMedCrossRefGoogle Scholar
  56. Rainbow PS (1995) Bio monitoring of heavy metal availability in the marine environment. Mar Poll Bull 31:183–192CrossRefGoogle Scholar
  57. Reid PC, Edwards M (2001) Plankton and climate. In Steele JH et al (eds) Encyclopedia of ocean sciences, vol. 4. Academic, New York, pp 2194–2200CrossRefGoogle Scholar
  58. Riffaldi R, Levi-Minzi R, Cardelli R, Palumbo S, Saviozzi A (2006) Soil biological activities in monitoring the bioremediation of diesel oil-contaminated soil. Water Air Soil Pollut 170(1–4):3–15CrossRefGoogle Scholar
  59. Rubilar O, Diez MC, Gianfreda L (2008) Transformation of chlorinated phenolic compounds by white rot fungi. Crit Rev Environ Sci Technol 38(4):227–268CrossRefGoogle Scholar
  60. Samin G, Pavlova M, Arif MI, Postema CP, Damborsky J, Janssen DB (2014) A Pseudomonas putida strain genetically engineered for 1, 2, 3-trichloropropane bioremediation. Appl Environ Microbiol 80(17):5467–5476PubMedPubMedCentralCrossRefGoogle Scholar
  61. Sarma VV (2018) Obligate marine fungi and bioremediation. In: Mycoremediation and environmental sustainability. Springer, Cham, pp 307–323Google Scholar
  62. Sayler GS, Ripp S (2000) Field applications of genetically engineered microorganisms for bioremediation processes. Curr Opin Biotechnol 11(3):286–289PubMedCrossRefGoogle Scholar
  63. Slater SC, Voige WH, Dennis DE (1988) Cloning and expression in Escherichia coli of the Alcaligenes eutrophus H16 poly-beta-hydroxybutyrate biosynthetic pathway. J Bacteriol 170(10):4431–4436PubMedPubMedCentralCrossRefGoogle Scholar
  64. Soares GM, Costa-Ferreira M, de Amorim MP (2001) Decolorization of an anthraquinone-type dye using a laccase formulation. Bioresour Technol 79(2):171–177PubMedCrossRefGoogle Scholar
  65. Sousa S, Duffy C, Weitz H, Glover LA, Bär E, Henkler R, Killham K (1998) Use of a lux-modified bacterial biosensor to identify constraints to bioremediation of btexcontaminated sites. Environ Toxicol Chem 17(6):1039–1045CrossRefGoogle Scholar
  66. Stramski D, Kiefer DA (1998) Can heterotrophic bacteria be important to marine light absorption? J Plankton Res 20:1489–1500CrossRefGoogle Scholar
  67. Sutiknowati LI (2010) Hydrocarbon-degrading bacteria: isolation and identification. Makara J Sci 11(2007):98–103Google Scholar
  68. Torres JMO, Cardenas CV, Moron LS, Guzman APA, dela Cruz TEE (2011) Dye decolorization activities of marine-derived fungi isolated from Manila Bay and Calatagan Bay, Philippines. Philippine J Sci 140(2):133–143Google Scholar
  69. Uchiyama T, Miyazaki K (2010) Product-induced gene expression, a product-responsive reporter assay used to screen metagenomic libraries for enzyme-encoding genes. Appl Environ Microbiol 76(21):7029–7035PubMedPubMedCentralCrossRefGoogle Scholar
  70. UchiyamaT, Watanabe K (2008) Substrate-induced gene expression (SIGEX) screening of metagenome libraries. Nature Protocols 3(7):1202PubMedCrossRefGoogle Scholar
  71. Urlacher VB, Lutz-Wahl S, Schmid RD (2004) Microbial P450 enzymes in biotechnology. Appl Microbiol Biotechnol 64(3):317–325PubMedCrossRefGoogle Scholar
  72. Van Berkel WJH, Kamerbeek NM, Fraaije MW (2006) Flavoprotein monooxygenases, a diverse class of oxidative biocatalysts. J Biotechnol 124(4):670–689PubMedCrossRefGoogle Scholar
  73. Van Dyke MI, Lee H, Trevors JT (1996) Survival of luxAB-marked Alcaligenes eutrophus H850 in PCB-contaminated soil and sediment. J Chem Technol Biotechnol Intl Res Process Environ Clean Technol 65(2):115–122Google Scholar
  74. Vasileva-Tonkova E, Galabova D (2003) Hydrolytic enzymes and surfactants of bacterial isolates from lubricant-contaminated wastewater. Zeitschrift für Naturforschung C 58(1–2):87–92CrossRefGoogle Scholar
  75. Velmurugan N, Lee YS (2012) Enzymes from marine fungi: current research and future prospects. Marine Fungi and Fungal-like Organisms (Marine and Freshwater Botany), pp 441–474Google Scholar
  76. Wai SN, Mizunoe Y, Yoshida S (1999) How Vibrio cholerae survive during starvation. FEMS Microbiol Lett 180:123–131PubMedCrossRefGoogle Scholar
  77. Zhang C, Kim SK (2012) Application of marine microbial enzymes in the food and pharmaceutical industries. Advances in food and nutrition research, vol 65. Academic, New York, pp 423–435Google Scholar
  78. Zhang JJ, Liu H, Xiao Y, Zhang XE, Zhou Zhang JJ, Liu H, Xiao Y, Zhang XE, Zhou NY (2009) Identification and characterization of catabolic para-nitrophenol 4-monooxygenase and para-benzoquinone reductase from Pseudomonas sp. strain WBC-3. J Bacteriol 191(8):2703–2710PubMedPubMedCentralCrossRefGoogle Scholar
  79. Zhang R, Xu X, Chen W, Huang Q (2016) Genetically engineered Pseudomonas putida X3 strain and its potential ability to bioremediate soil microcosms contaminated with methyl parathion and cadmium. Appl Microbiol Biotechnol 100(4):1987–1997PubMedCrossRefGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2019

Authors and Affiliations

  • Neetu Sharma
    • 1
  • Abhinashi Singh
    • 1
  • Sonu Bhatia
    • 1
  • Navneet Batra
    • 1
  1. 1.GGDSD CollegeChandigarhIndia

Personalised recommendations