Thermophilic Bacteria Investigation in Petroleum Contaminated Soils by Different Isolation Method

Thermophilic Bacteria Investigation in Petroleum Contaminated Soils by Different Isolation Method

There are many and various microorganisms earth flora, ranging from macroscopic tomicroscopic forms. When soil ecosystem is contaminated by complex compounds and heavymetals, which are difficult to separate from each other, in petroleum and petroleum derivedproducts, for that reason it would be unable to utilization of soil due to decomposition of itsphysical, chemical and biological characteristics. Biological decomposition of petroleum andpetroleum derived products by natural microorganism populations, is the primary mechanismfor eliminating the petroleum and other hydrocarbon pollution of environment. The purpose ofthis study is to research the best isolation method on the isolation of thermophilic bacteria fromthe soils which are contaminated by petroleum and petroleum derived products. Recent studiesrelated to thermophilic bacteria have been intensified since these bacteria are more resistant toextreme environmental conditions than other bacteria species. With this purpose, 4 differentisolation methods have been investigated in isolating the thermophilic bacteria from thepetroleum contaminated soil which is contaminated by petroleum and petroleum products. Atthe end of the research, in order to identify bacteria colonies which are considered to be pure,DNA isolation, Conventional PCR (polymerase chain reaction) Process, Gel Electrophoresisprocesses are applied. Different incubation times, carbon resources and enrichment solutionsare tried out to obtain a superior method and it is revealed that with the increase in the incubationperiod, more known/unknown species can be isolated without using additional carbon sourcefrom the soil.

___

  • Başkaya, Y., Kocabaş, A., “Topraktan izole edilen mikroorganizmaların anti-mikrobiyal madde üretim potansiyellerinin belirlenmesi”,KSU J. Nat. Sci.,19(4): 393-398, (2016).
  • Singh, J. S. , Pandey, V.C ., Singh D. P., “Efficient soil microorganisms: A new dimension for sustainable agriculture and environmental development”, Agriculture, Ecosystems & Environment, 140, 3(4): 339-353, (2011).
  • Torsvik, V., Ovreas, L., “Microbial diversity and function in soil: from genes to ecosystems”, Curr Opin Microbiol, 5: 240-245, (2002).
  • Karapire M., Özgönen H., “Doğada Yararlı Mikroorganizmalar Arasındaki Etkileşimler ve Tarımsal Üretimde Önemi”. Türk Bilimsel Derlemeler Dergisi, 6 (2): 149-157, (2013).
  • Nannipieri, P., Ascher, J., Ceccherini, M.T., Landi, L., Pietramellara, G., Renella, G.,“Microbial Diversity and Soil Functions, Eur J Soil Sci, 54: 655–670, (2003).
  • Roesch, L.F.W., Fulthorpe, R.R., Riva, A., Casella, G., Hadwin, A.K., Kent, A.D., Daroub, S.H., Camargo, F.A., Farmerie, W.G., Triplett, E.W., “Pyrosequencing enumerates and contrasts soil microbial diversity”,The ISME Journal, 1: 283–290, (2007).
  • Zhang Q., Wu J., Yang F., Lei Y., Zhang Q., Cheng X.,” Alterations in soil microbial community composition and biomass following agricultural land use change”. Scientific Reports, 6: 36587 , DOI: 10.1038/srep36587, (2016).
  • Rampelotto P. H., “Resistance of microorganisms to extreme environmental conditions and ıts contribution to astrobiology”, Sustainability, 2: 1602-1623, (2010).
  • Pikuta, E.V., Hoover, R.B., “Microbial extremophiles at the limits of life”, Crit. Rev. Microbiol., 33: 183-209, (2007).
  • Kristjansson, M.M., Asgeirsson, B., Properties of extremophilic enzymes and their ımportance in food science and technology. handbook of food enzymology (ed. J.R. Whitaker), NY, USA, p.77-99, (2002).
  • Seckbach J.,” Enigmatic Microorganisms and Life in Extreme Environments”, Springer Science & Business Media, (2013).
  • Demirjian, D.C., Moris-Vara, F., Sassidy, C.S., “Enzymes from extremophiles”,Curr Opin Chem Biol, 5: 144–51, (2001).
  • Güven R. G., “Termofilik bakteriler ve biyoteknolojik açıdan önemli bazı enzimleri”, Elektronik Mikrobiyoloji Dergisi TR , 9 (1): 1-10, (2011).
  • Marshall K.C., Advances in microbial ecology vol 12., Springer Science & Business Media, (2012).
  • Akkaya S. E., Kıvanç M., “Termofil bakteriler; sıcak su kaynaklarında yaşayan gram negatif basillerin izolasyon ve identifikasyon yöntemleri”, Elektronik Mikrobiyoloji Dergisi Tr, 7(1): 01-23, (2009).
  • Haki, G.D., Rakshit, S.K., “Developments in ındustrially ımportant thermostable enzymes: a review”, Bioresour Tecnol, 89: 17–34, (2003).
  • Bekler F.M., “Türkiye’deki dibekli sıcak su kaynağından termofilik geobacillus sp.DB2 suşunun fizyo-biyokimyasal karakterizasyonu ve 16S rRNA sekanslaması”, Iğdır Üni. Fen Bilimleri Enst. Der. / Iğdır Univ. J. Inst. Sci. & Tech., 7(1): 63-71, (2017).
  • Yılmaz M., “The energy potential of Turkey and its importance of renewable energy sources in terms of electricity production”, Ankara Üniversitesi Çevrebilimleri Dergisi, 4(2): 33-54, (2012).
  • Dindar E., Şağban F. O. T., Başkaya H. S., “Kirlenmiş topraklarda arıtma çamuru uygulamasının enzim aktivitelerine etkisi”, Uludağ Üniversitesi Mühendislik Fakültesi Dergisi, 22(1): 81-94, (2017).
  • Bollag J.M. Stotzky G., Soil Biochemistry volume 6, Marcell Dekker Inc, (2017).
  • Society Of American Bacteriologist Manual of Microbiological Methods. McGraw Hill Book Company. Inc: London, (1957).
  • Çetinkaya E. Aykan K., “Mikrobiyolojide kullanılan bazı moleküler teknikler”, Karaelmas Fen ve Mühendislik Dergisi /Karaelmas Science and Engineering Journal, 2 (1): 53-62, (2012).
  • Hall, T.A., “BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT”, Nucl. Acids. Symp. Ser, 41: 95-98, (1999).
  • Silva G.P., Mack M., Contiero J.G. “A promising and abundant carbon source for industrial microbiology”, Biotechnol. Adv, 27: 30–39, (2009).
  • Varjani, S.J., Thaker, M.B., Upasani, V.N., “Optimization of growth conditions of native hydrocarbon utilizing bacterial consortium ‘‘HUBC” obtained from petroleum pollutant contaminated sites”, Indian J. Appl. Res, 4(10): 474–476, (2014).
  • Leahy J. G., Colwell R. R. “Microbial degradation of hydrocarbons in the environment”, Microbiol. Rev, 54: 305–315, (1990).
  • Boopathy,R.,“Factors limiting bioremediation Technologies”, Bioresour.Technol,74: 63–67, (2000).
  • Ron,E.Z., Rosenberg, E., “Enhanced bioremediation of oil spills in the sea”, Curr.Opin. Biotechnol, 27: 191–194, (2014).
  • Bhattacharya, D., Sarma, P.M., Krishman, S., Mishra.S., Lal. B, “ Evaluation of genetic diversity among Pseudomanas citroneltolic strains isolated from oily sludge contaminated sites”, Appl. Environ. Microbiol., 69: 1435-1441, (2003).
  • Head, I.M., Jones, D.M,, Roling, W. F., “ Marine microorganisms make meal of oil”, Nature Review of Microbiolo, 4: 173-182, (2006).
  • Joshi P. A., Shekhawat D. B., “Effect of carbon and nitrogen source on biosurfactant production by biosurfactant producing bacteria isolated from petroleum contaminated site”, Appl. Sci. Res., 5(6): 159-164, (2014).
  • Varjani S.J. “Microbial degradation of petroleum hydrocarbons”, Bioresource Technology, 223: 277– 286, (2017).
  • Varjani, S.J., Upasani, V.N., “A new look on factors affecting microbial degradation of petroleum hydrocarbon pollutants”, Int. Biodeterior. Biodegradation, 120: 71-83, (2017).
  • Rahman, K.S.M., Rahman, T.J., Kourkoutas, Y., Petsas, I., Marchant, R., Banat, I.M., “Enhanced bioremediation of n-alkane in petroleum sludge using bacterial consortium amended with rhamnolipid and micronutrients”, Bioresour. Technol., 90(2): 159-168, (2003).
  • Kavitha, V., Mandal, A.B., Gnanamani, A., “Microbial biosurfactant mediated removal and/or solubilization of crude oil contamination from soil and aqueous phase: an approach with Bacillus licheniformis MTCC 5514”, Int. Biodeterior. Biodegrad, 94: 24-30, (2014).
  • Sajna, K.V., Sukumaran, R.K., Gottumukkala, L.D., Pandey, A., “Crude oil biodegradation aided by biosurfactants from Pseudozyma sp. NII 08165 or its culture broth”, Bioresour. Technol, 191: 133–139, (2015).
  • Varjani, S.J., Rana, D.P., Bateja, S., Sharma, M.C., Upasani, V.N., “Screening and identification of biosurfactant (bioemulsifier) producing bacteria from crude oil contaminated sites of Gujarat, India”, Int. J. Innovative Res. Sci. Eng. Technol, 3(2): 9205–9213, (2014).
  • Karlapudi A. P. , Venkateswarulu T.C. , Tammineedi J., Kanumuri L., Ravuru B. K., Dirisala V., Kodali V. P., “Role of biosurfactants in bioremediation of oil pollution-a review”, Petroleum , 4 (3): 241-249, (2018).
  • Elumalai, P., Parthipan, P., Karthikeyan, O.P., Rajasekar, “A Enzyme-mediated biodegradation of long-chain n-alkanes (C32 and C40) by thermophilic bacteria”, Biotech, 7: 116, (2017).
  • Zargari, S., Ramezani, A., Ostvar, S., Rezaei, R., Niazi, A., Ayatollahi, S., “Isolation and characterization of gram-positive biosurfactant-producing halothermophilic bacilli from Iranian petroleum reservoirs”, Jundishapur J Microbiol., 7(8), (2014).
  • Perfumo, A, Banat, IM, Marchant, R, Vezzulli, L., “Thermally enhanced approaches for bioremediation of hydrocarbon-contaminated soils”, Chemosphere, 66: 179–184, (2007).
  • Rahman, T.,J,Marchant R., Banat I.M., “Distribution and molecular investigation of highly thermophilic bacteria associated with cool soil environments”, Biochem Soc Trans, 32: 209–213, (2004).
  • Timmis, K.N.(ed.), Marchant, R., Banat, I.M., “21 The Genus Geobacillus and Hydrocarbon Utilization, Handbook of Hydrocarbon and Lipid Microbiology”, Springer-Verlag Berlin Heidelberg, (2010).
  • Logan, N.A., Vos, P. D. (eds.), “Endospore-forming Soil Bacteria”, Soil Biology 27, Springer-Verlag Berlin Heidelberg, (2011).
  • Al-Wahaibi, Y. M., Al-Bahry, S. N., Elshafie, A. E., Al-Bemani, A. S., Joshi, S. J., Al-Bahri, A. K., “Screening of minimal salt media for biosurfactant production by bacillus spp.”, World Academy of Science, Engineering and Technology International Journal of Environmental and Ecological Engineering, 8(2), (2014).
  • Marchant, R., Banat, I.M, The Genus Geobacillus and Hydrocarbon Utilization. In: Timmis K.N. (eds) Handbook of Hydrocarbon and Lipid Microbiology, Springer Berlin, Heidelberg, (2010).
  • Zhou, J.F., Gao, P.K., Dai, X.H., Cui, X.Y., Tian, H.M., Xie, J.J., Li, G.Q., Ma, T., “Heavy hydrocarbon degradation of crude oil by a novel thermophilic Geobacillus stearothermophilus strain A-2”, Int. Biodeterior. & Biodegradation, 126: 224-230, (2018).
  • Atlas, R.M., “Microbial degradation of petroleum hydrocarbons: an environmental perspective”, Microbiol. Rev, 45(1): 180-209, (1981).
  • Noordman, W.H., Janssen, D.B., “Rhamnolipid stimulates uptake of hydrophobic compounds by pseudomonas aeruginosa”, Appl. Environ. Microbiol, 68: 4502-4508, (2002).
  • Haghighat, S., Sepahy, A.A., Assadi, M.M., Pasdar, H., "Ability of indigenous Bacillus licheniformis and Bacillus subtilis in microbial enhanced oil recovery", Int. J. Environ. Sci. Tech., 5: 385-390, (2008).
  • Elazzazy, A.M., Abdelmoneim, T.S., Almaghrabia, O.A., “Isolation and characterization of biosurfactant production under extreme environmental conditions by alkali-halo-thermophilic bacteria from Saudi Arabia”, Saudi J Biol Sci., 22(4): 466–475, (2015).
  • Chen, C.C., Riadi, L., Suh, S.J., Ohman, D.E., Ju, L.K., “Degradation and synthesis kinetics of quorum-sensing autoinducer in Pseudomonas aeruginosa cultivation”, J. Biotechnol., 117: 1–10, (2005).
  • Tabatabaei, M., "Design and fabrication of ıntegrated plasmonic platforms for ultra-sensitive molecular and biomolecular detections", Electronic Thesis and Dissertation Repository, The University of Western Ontario, 3161, (2015).
  • Agnes, M.N. “Screening, isolation and characterization of hydrocarbonoclastic bacteria from oil contaminated soils”, Biochemistry of University of Nairob, MSc.Thesis,p 119, (2017).
  • Batista, S.B., Mounteer, A.H., Amorim, F.R., Totola, M.R., “Isolation and characterization of biosurfactant/bioemulsifier producing bacteria from petroleum contaminated sites”, Bioresour. Technol, 97: 868–875, (2006).
  • Ron, E.Z., Rosenberg, E., “Enhanced bioremediation of oil spills in the sea”, Curr. Opin. Biotechnol, 27: 191–194, (2014).
  • Varjani,S.J., Upasani, V.N., “Carbon spectrum utilization by an indigenous strain of Pseudomonas aeruginosa NCIM 5514: production, characterization and surface active properties of biosurfactant”, Bioresour. Technol, 221: 510–516, (2016).
  • Kaczorek, E., Pacholak, A., Zdarta, A., Smułek, W. “The ımpact of biosurfactants on microbial cell properties leading to hydrocarbon bioavailability increase”, Colloid. Interface., 2(3): 35, (2018).
  • Chen, Q., Li, J. , Liu, M., Sun, H., Bao, M., “Study on the biodegradation of crude oil by free and immobilized bacterial consortium in marine environment”, Plos One, 12(3), (2017).
  • Chandra, S., Sharma, R., Singh, K., Sharma, A., “Application of bioremediation technology in the environment contaminated with petroleum hydrocarbon”, Ann. Microbiol., 63: 417–431, (2013).
  • Varjani, S.J., Upasani, V.N., “Biodegradation of petroleum hydrocarbons by oleophilic strain of Pseudomonas aeruginosa NCIM 5514”, Bioresour. Technol., 222: 195–201,(2016).
  • Janssen, P. H., Yates, P.S., Grinton, B.E., Taylor, P.M., Sait, M., “ Improved cultivability of soil bacteria and isolation in pure culture of novel members of the divisions Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia ”, Appl. Environ. Microbiol, 68: 2391-2396, (2002).
  • Alexander, M. ,Advances in Microbial Ecology Vol 2, Springer Science and Business Media, 297, (2012).
  • Marshall, K. C., Advances in Microbial Ecology Vol 6, Springer Science and Business Media, 240, (2012).
  • Schoenborn, L., Yates, P. S., Grinton, B. E, Hugenholtz, P., Janssen, P. H., “Liquid serial dilution is inferior to solid media for isolation of cultures representing the phylum-level diversity of soil bacteria”, Appl. Environ. Microbiol, 70: 4363-4366, (2004).
  • Davis, K.E.R., Joseph, S.J., Janssen, P.H., “Effects of growth medium, inoculum size, and incubation time on culturability and isolation of soil bacteria”, Appl Environ Microbiol., 71(2): 826–834, (2005).