Plant Soil Environ., 2020, 66(5):191-199 | DOI: 10.17221/673/2019-PSE

Laboratory tests for aerobic bioremediation of the contaminated sites in the Czech RepublicReview

Jana Chumchalová ORCID...*, Martin Kubal
Department of Environmental Chemistry, Faculty of Environmental Technology, University of Chemistry and Technology Prague, Prague, Czech Republic

Laboratory-scale testing methods applicable to evaluation of contaminated subsurface microbial communities are discussed in relation to their potential in supporting effective site bioremediation. Both culture-dependent and culture-independent techniques are considered here with special emphasis on their capacity to contribute to bioremediation system design, in optimal cases by providing information on contaminant degradation rates. In this regard, microbial soil respiration tests seem to be the most useful tool since microbial soil respiration is a sensitive and easily measurable parameter for determination of metabolic activity within the sample and is closely related to other microbial parameters such as microbial biomass.

Keywords: culture-dependent and culture-independent techniques; contamination; microorganism; dehydrogenase; molecular method

Published: May 31, 2020  Show citation

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Chumchalová J, Kubal M. Laboratory tests for aerobic bioremediation of the contaminated sites in the Czech Republic. Plant Soil Environ.. 2020;66(5):191-199. doi: 10.17221/673/2019-PSE.
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    References

    1. Bachoon D.S., Hodson R.E., Araujo R. (2001): Microbial community assessment in oil-impacted salt marsh sediment microcosms by traditional and nucleic acid-based indices. Journal of Microbiological Methods, 46: 37-49. Go to original source... Go to PubMed...
    2. Baek K.H., Yoon B.D., Cho D.H., Kim B.H., Oh H.M., Kim H.S. (2009): Monitoring bacteria population dynamics using realtime PCR during the bioremediation of crude-oil-contaminated soil. Journal of Microbiology and Biotechnology, 19: 339-345. Go to original source... Go to PubMed...
    3. Baldrian P. (2009): Microbial enzyme-catalyzed processes in soils and their analysis. Plant, Soil and Environment, 55: 370-378. Go to original source...
    4. Bargiela R., Herbst F.A., Martínez-Martínez M., Seifert J., Rojo D., Cappello S., Genovese M., Crisafi F., Denaro R., Chernikova T.N., Barbas C., von Bergen M., Yakimov M.M., Ferrer M., Golyshin P.N. (2015): Metaproteomics and metabolomics analyses of chronically petroleum-polluted sites reveal the importance of general anaerobic processes uncoupled with degradation. Proteomics, 15: 3508-3520. Go to original source... Go to PubMed...
    5. Cikánková J., Koblí¾ková E., Mertl J., Pokorný J., Ponocná T., Rollerová M., Vlèková V. (2015): Report on the Environment of the Czech Republic. Prague, Ministry of the Environment of the Czech Republic. Available at https://www.cenia.cz/wp-content/uploads/2019/03/Report-on-the-Environment-of-the-Czech-Republic_2015.pdf
    6. Chikere C.B., Okpokwasili G.C., Chikere B.O. (2011): Monitoring of microbial hydrocarbon remediation in the soil. 3 Biotech, 1: 117-138. Go to original source... Go to PubMed...
    7. Coccia A.M., Gucci P.M.B., Lacchetti I., Beccaloni E., Paradiso R., Beccaloni M., Musmeci L. (2009): Hydrocarbon contaminated soil treated by bioremediation technology: microbiological and toxicological preliminary findings. Environmental Biotechnology, 5: 61-72.
    8. Dangi A.K., Sharma B., Hill R.T., Shukla P. (2019): Bioremediation through microbes: systems biology and metabolic engineering approach. Critical Reviews in Biotechnology, 39: 79-98. Go to original source... Go to PubMed...
    9. Dawson J.J.C., Godsiffe E.J., Thompson I.P., Ralebitso-Senior T.K., Killham K.S., Paton G.I. (2007): Application of biological indicators to assess recovery of hydrocarbon impacted soils. Soil Biology and Biochemistry, 39: 164-177. Go to original source...
    10. Desai C., Pathak H., Madamwar D. (2010): Advances in molecular and "-omics" technologies to gauge microbial communities and bioremediation at xenobiotic/anthropogen contaminated sites. Bioresource Technology, 101: 1558-1569. Go to original source... Go to PubMed...
    11. Diplock E., Mardlin D.P., Killham K.S., Paton G.I. (2009): Predicting bioremediation of hydrocarbons: laboratory to field scale. Environmental Pollution, 157: 1831-1840. Go to original source... Go to PubMed...
    12. Eisentraeger A., Hund-Rinke K., Roembke J. (2005): Assessment of ecotoxicity of contaminated soil using bioassays. In: Margesin R., Schinner F. (eds.): Manual of Soil Analysis. Heidelberg, SpringerVerlag, 321-359. ISBN 978-3-540-28904-3 Go to original source...
    13. Foght J., Aislabie J. (2005): Enumeration of soil microorganisms. In: Margesin R., Schinner F. (eds.): Manual of Soil Analysis. Heidelberg, Springer-Verlag, 261-280. ISBN 978-3-540-28904-3 Go to original source...
    14. Frankenberg W.T.Jr., Dick W.A. (1983): Relationships between enzyme activities and microbial growth and activity indices in soil. Soil Science Society of America Journal, 47: 945-951. Go to original source...
    15. Ga³±zka A., Grz±dziel J., Ga³±zka R., Ukalska-Jaruga A., Strzelecka J., Smreczak B. (2018): Genetic and functional diversity of bacterial microbiome in soils with long term impacts of petroleum hydrocarbons. Frontiers in Microbiology, 9: 1923. Go to original source... Go to PubMed...
    16. Galiulin R.V., Bashkin V.N., Galiulina R.A. (2012): Degradation of petroleum hydrocarbons in soil under the action of peat compost. Solid Fuel Chemistry, 46: 328-329. Go to original source...
    17. Guo H., Yao J., Cai M.M., Qian Y.G., Guo Y., Richnow H.H., Blake R.E., Doni S., Ceccanti B. (2012): Effects of petroleum contamination on soil microbial numbers, metabolic activity and urease activity. Chemosphere, 87: 1273-1280. Go to original source... Go to PubMed...
    18. Hollender J., Althoff K., Mundt M., Dott W. (2003): Assessing the microbial activity of soil samples, its nutrient limitation and toxic effects of contaminants using a simple respiration test. Chemosphere, 53: 269-275. Go to original source... Go to PubMed...
    19. Insam H. (2001): Developments in soil microbiology since the mid 1960s. Geoderma, 100: 389-402. Go to original source...
    20. Jørgensen K.S. (2007): In situ bioremediation. In: Laskin A.I., Sariaslani S., Gadd G.M. (eds.): Advances in Applied Microbiology. California, Academic Press, 61: 285-305. ISBN: 9780123870445 Go to original source...
    21. Kaczyñska G., Borowik A., Wyszkowska J. (2015): Soil dehydrogenases as an indicator of contamination of the environment with petroleum products. Water, Air, and Soil Pollution, 226: 372. Go to original source... Go to PubMed...
    22. Kao C.M., Chen C.S., Tsa F.Y., Yang K.H., Chien C.C., Liang S.H., Yang C.A., Chen S.C. (2010): Application of real-time PCR, DGGE fingerprinting, and culture-based method to evaluate the effectiveness of intrinsic bioremediation on the control of petroleum-hydrocarbon plume. Journal of Hazardous Materials, 178: 409-416. Go to original source... Go to PubMed...
    23. Li C.Y., Xia F.J., Zhang Y.H., Chang C.C., Wei D., Wei L. (2017): Molecular biological methods in environmental engineering. Water Environment Research, 89: 942-959. Go to original source... Go to PubMed...
    24. Littlefield-Wyer J.G., Brooks P., Katouli M. (2008): Application of biochemical fingerprinting and fatty acid methyl ester profiling to assess the effect of the pesticide Atradex on aquatic microbial communities. Environmental Pollution, 153: 393-400. Go to original source... Go to PubMed...
    25. Liu Q., Tang J., Bai Z., Hecker M., Giesy J.P. (2015): Distribution of petroleum degrading genes and factor analysis of petroleum contaminated soil from the Dagang Oilfield, China. Scientific Reports, 5: 11068. Go to original source... Go to PubMed...
    26. Loick N., Weisener C. (2014): Novel molecular tools to assess microbial activity in contaminated environments. In: Parmar N., Singh A. (eds): Geomicrobiology and Biogeochemistry. Berlin, Heidelberg, Springer, 17-35. ISBN 978-3-642-41837-2 Go to original source...
    27. Malik S., Beer M., Megharaj M., Naidu R. (2008): The use of molecular techniques to characterize the microbial communities in contaminated soil and water. Environment International, 34: 265-276. Go to original source... Go to PubMed...
    28. Malla M.A., Dubey A., Yadav S., Kumar A., Hashem A., Abd-Allah E.F. (2018): Understanding and designing the strategies for the microbemediated remediation of environmental contaminants using omics approaches. Frontiers in Microbiology, 9: 1132. Go to original source... Go to PubMed...
    29. Margesin R., Zimmerbauer A., Schinner F. (2000): Monitoring of bioremediation by soil biological activities. Chemosphere, 40: 339-346. Go to original source... Go to PubMed...
    30. Margesin R., Hämmerle M., Tscherko D. (2007): Microbial activity and community composition during bioremediation of diesel-oilcontaminated soil: effects of hydrocarbon concentration, fertilizers, and incubation time. Microbial Ecology, 53: 259-269. Go to original source... Go to PubMed...
    31. Modrzyñski J.J., Christensen J.H., Mayer P., Brandt K.K. (2016): Limited recovery of soil microbial activity after transient exposure to gasoline vapors. Environmental Pollution, 216: 826-835. Go to original source... Go to PubMed...
    32. Moeskops B., Sukristiyonubowo, Buchan D., Sleutel S., Herawaty L., Husen E., Saraswati R., Setyorini D., De Neve S. (2010): Soil microbial communities and activities under intensive organic and conventional vegetable farming in West Java, Indonesia. Applied Soil Ecology, 45: 112-120. Go to original source...
    33. M®P ÈR (2011): Methodological Guidance for Contaminated Sites Risk Assessment. Prague, Ministry of the Environment of the Czech Republic.
    34. National Research Council (1993): In Situ Bioremediation: When Does it Work? Washington, The National Academies Press. ISBN: 978-0-309-04896-5
    35. Ngom B., Liu X.D. (2014): Techniques for tracking microbial community structure and function in natural environment and engineered systems. International Journal of Science and Research, 3: 800-807.
    36. Nybroe O., Brandt K.K., Nicolaisen M.H., Sørensen J. (2006): Methods to detect and quantify bacteria in soil. In: van Elsas J.D., Jansson J.K., Trevors J.T. (eds.): Modern Soil Microbiology. Boca Raton, CRC Press, 283-316. ISBN: 9780429196300
    37. Pacwa-P³ociniczak M., P³aza G.A., Piotrowska-Seget Z. (2016): Monitoring the changes in a bacterial community in petroleumpolluted soil bioaugmented with hydrocarbon-degrading strains. Applied Soil Ecology, 105: 76-85. Go to original source...
    38. Panagos P., Van Liedekerke M., Yigini Y., Montanarella L. (2013): Contaminated sites in Europe: review of the current situation based on data collected through a European network. Journal of Environmental and Public Health, 2013: 158764. Go to original source... Go to PubMed...
    39. Paton G.I., Iroegbu C.O., Dawson J.J.C. (2003): Microbiological characterisation of a diesel contaminated beach site. Marine Pollution Bulletin, 46: 903-906. Go to original source... Go to PubMed...
    40. Paton G.I., Viventsova E., Kumpene J., Wilson M.J., Weitz H.J., Dawson J.J.C. (2006): An ecotoxicity assessment of contaminated forest soils from Kola Peninsula. Science of The Total Environment, 355: 106-117. Go to original source... Go to PubMed...
    41. Polyak Y.M., Bakina L.G., Chugunova M.V., Mayachkina N.V., Gerasimov A.O., Bure V.M. (2018): Effect of remediation strategies on biological activity of oil-contaminated soil - A field study. International Biodeterioration and Biodegradation, 126: 57-68. Go to original source...
    42. 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, and Soil Pollution, 170: 3-15. Go to original source...
    43. Rosselló-Mora R., Amann R. (2001): The species concept of prokaryotes. FEMS Microbiology Reviews, 25: 39-67. Go to original source... Go to PubMed...
    44. Sandrin T.R., Herman D.C., Maier R.M. (2009): Physiological methods. In: Maier R.M., Pepper I.L., Gerba Ch.P. (eds.): Environmental Microbiology. 2nd Edition. Burlington, Academic Press, 191-223. ISBN: 9780080919409 Go to original source...
    45. Sanscartier D., Reimer K., Koch I., Laing T., Zeeb B. (2009): An investigation of the ability of a 14C-labeled hydrocarbon mineralization test to predict bioremediation of soils contaminated with petroleum hydrocarbons. Bioremediation Journal, 13: 92-101. Go to original source...
    46. Schinner F., Ohlinger R., Kandeler E., Margesin R. (1996): Methods in Soil Biology. Berlin, Heidelberg, Springer-Verlag. ISBN 978-3-642-60966-4 Go to original source...
    47. SEKM (2009): Information System of the Czech Contaminated Sites. Prague, Ministry of the Environment of the Czech Republic. Available at http://info.sekm.cz/statistiky
    48. Siles J.A., Margesin R. (2018): Insights into microbial communities mediating the bioremediation of hydrocarbon-contaminated soil from an Alpine former military site. Applied Microbiology and Biotechnology, 102: 4409-4421. Go to original source... Go to PubMed...
    49. Rastogi G., Sani R.K. (2011): Molecular techniques to assess microbial community structure, function, and dynamics in the environment. In: Ahmad I., Ahmad F., Pichtel J. (eds.): Microbes and Microbial Technology: Agricultural and Environmental Applications. New York, Springer Science+Business Media, 29-57. ISBN 978-1-4419-7931-5 Go to original source...
    50. US EPA (1991): Site Characterization for Subsurface Remediation. EPA/625/4-91/026. Washington, United States Environmental Protection Agency, 193-201.
    51. Utobo E.B., Tewari L. (2015): Soil enzymes as bioindicators of soil ecosystem status. Applied Ecology and Environmental Research, 13: 147-169. Go to original source...
    52. Wang S.Y., Kuo Y.C., Hong A., Chang Y.M., Kao C.M. (2016): Bioremediation of diesel and lubricant oil-contaminated soils using enhanced landfarming system. Chemosphere, 164: 558-567. Go to original source... Go to PubMed...
    53. Whiteley A.S., Bailey M.J. (2000): Bacterial community structure and physiological state within an industrial phenol bioremediation system. Applied and Environmental Microbiology, 66: 2400-2407. Go to original source... Go to PubMed...
    54. Woliñska A., Ku¼niar A., Szafranek-Nakonieczna A., Jastrzêbska N., Roguska E., Stêpniewska Z. (2016): Biological activity of autochthonic bacterial community in oil-contaminated soil. Water, Air, and Soil Pollution, 227: 130-141. Go to original source... Go to PubMed...
    55. Wu M., Li W., Dick W.A., Ye X., Chen K., Kost D., Chen L. (2017): Bioremediation of hydrocarbon degradation in a petroleum-contaminated soil and microbial population and activity determination. Chemosphere, 169: 124-130. Go to original source... Go to PubMed...
    56. Yao H.Y., Chapman S., Thornton B., Paterson E. (2015): 13C PLFAs: a key to open the soil microbial black box? Plant and Soil, 392: 3-15. Go to original source...
    57. Yergeau E., Arbour M., Brousseau R., Juck D., Lawrence J.R., Masson L., Whyte L.G., Greer C.W. (2009): Microarray and real-time PCR analyses of the responses of high-arctic soil bacteria to hydrocarbon pollution and bioremediation treatments. Applied and Environmental Microbiology, 75: 6258-6267. Go to original source... Go to PubMed...

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