Abstract
A degrading microbial consortium highly tolerant to three-, four- and five-ring polycyclic aromatic hydrocarbons (PAHs) was selected from 50 fungal and bacterial isolates obtained from crude oil-contaminated soils. Morphological and molecular studies indicated that isolated fungi belonged to genera Aspergillus, Penicillium, Fusarium, Trichoderma, Scedosporium, and Acremonium and bacteria to Pseudomonas, Klebsiella, Bacillus, Enterobacter, Streptomyces, Stenotrophomonas, Kocuria, and Delftia genera. Individual fungal and bacterial isolates were evaluated for their potential to tolerate high concentrations of different molecular weight PAHs, as phenantrene (Phe), pyrene (Pyr), and benzo[a]pyrene (BaP) by surface plate assays, showing significant differences in extension rates for fungi and inhibition ratios for bacteria when both were exposed to 0–6,000 mg of PAHs per liter. Trichoderma asperellum H15, Aspergillus nomius H7, Aspergillus flavus H6, Pseudomonas aeruginosa B7, Klebsiella sp. B10, and Stenotrophomonas maltophilia B14 grew using PAHs as sole carbon source and presented a remarkably high tolerance to PAHs, up to 6,000 mg l−1. The consortium composed of 12 fungal and bacterial PAH-tolerant isolates for the bioremediation of a PAH-contaminated soiled to a removal of 87.76 % Phe, 48.18 % Pyr, and 56.55 % BaP after 14 days. The degrading microbial consortium presented high potential for bioremediation and may be useful for the treatment of sites polluted with PAHs due to their elevated tolerance to high molecular weight (HMW) PAHs and their capacity to utilize them as energy source. This is the first study which evaluated the microbial tolerance to extreme concentrations of PAHs, resulting in a degrading consortium and highly tolerant consortium compared with those reported in other studies, where the concentrations tested are low.
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Acevedo, F., Pizzul, L., Castillo, M. D., Cuevas, R., & Diez, M. C. (2011). Degradation of polycyclic aromatic hydrocarbons by the Chilean white-rot fungus Anthracophyllum discolor. Journal of Hazardous Materials, 185(1), 212–219.
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215(3), 403–410.
Argumedo-Delira, R., Alarcon, A., Ferrera-Cerrato, R., Almaraz, J. J., & Pena-Cabriales, J. J. (2012). Tolerance and growth of 11 Trichoderma strains to crude oil, naphthalene, phenanthrene and benzo[a]pyrene. Journal of Environmental Management, 95(Suppl), S291–S299.
Atagana, H. I. (2009). Biodegradation of PAHs by fungi in contaminated-soil containing cadmium and nickel ions. African Journal of Biotechnology, 8(21), 5780–5789.
Avramova, T., Sotirova, A., Galabova, D., & Karpenko, E. (2008). Effect of Triton X-100 and rhamnolipid PS-17 on the mineralization of phenanthrene by Pseudomonas sp. cells. International Biodeterioration & Biodegradation, 62(4), 415–420.
Bautista, L. F., Sanz, R., Molina, M. C., Gonzalez, N., & Sanchez, D. (2009). Effect of different non-ionic surfactants on the biodegradation of PAHs by diverse aerobic bacteria. International Biodeterioration & Biodegradation, 63(7), 913–922.
Bhandari, A., Environmental and Water Resources Institute (U.S.), Environmental Council., & Environmental and Water Resources Institute (U.S.), & Remediation Technologies for Soils and Groundwater Task Committee. (2007). Remediation technologies for soils and groundwater. Reston: American Society of Civil Engineers.
Boonchan, S., Britz, M. L., & Stanley, G. A. (1998). Surfactant-enhanced biodegradation of high molecular weight polycyclic aromatic hydrocarbons by Stenotrophomonas maltophilia. Biotechnology and Bioengineering, 59(4), 482–494.
Boonchan, S., Britz, M. L., & Stanley, G. A. (2000). Degradation and mineralization of high-molecular-weight polycyclic aromatic hydrocarbons by defined fungal-bacterial cocultures. [Research Support, Non-U.S. Gov't]. Applied and Environmental Microbiology, 66(3), 1007–1019.
Bordenave, S., Goni-Urriza, M. S., Caumette, P., & Duran, R. (2007). Effects of heavy fuel oil on the bacterial community structure of a pristine microbial mat. [Research Support, Non-U.S. Gov't]. Applied and Environmental Microbiology, 73(19), 6089–6097.
Borras, E., Caminal, G., Sarra, M., & Novotny, C. (2010). Effect of soil bacteria on the ability of polycyclic aromatic hydrocarbons (PAHs) removal by Trametes versicolor and Irpex lacteus from contaminated soil. Soil Biology & Biochemistry, 42(12), 2087–2093.
Bouchez, M., Blanchet, D., & Vandecasteele, J. P. (1995). Substrate availability in phenanthrene biodegradation: transfer mechanism and influence on metabolism. Applied Microbiology and Biotechnology, 43(5), 952–960.
Byss, M., Elhottova, D., Triska, J., & Baldrian, P. (2008). Fungal bioremediation of the creosote-contaminated soil: influence of Pleurotus ostreatus and Irpex lacteus on polycyclic aromatic hydrocarbons removal and soil microbial community composition in the laboratory-scale study. [Research Support, Non-U.S. Gov't]. Chemosphere, 73(9), 1518–1523. doi:10.1016/j.chemosphere.2008.07.030.
Cazares-Garcia, S. V., Vazquez-Garciduenas, M. S., Vazquez-Marrufo, G. (2013). Structural and phylogenetic analysis of laccases from Trichoderma: a bioinformatic approach. PLoS One, 8(1): e55295. doi: 10.1371/journal.pone.0055295.
Cerniglia, C. E., & Sutherland, G. R. (2010). Degradation of polycyclic aromatic hydrocarbons by fungi. In K. N. Timmis (Ed.), Handbook of hydrocarbon and lipid microbiology. Berlin: Springer.
Chaudhary, P., Sharma, R., Singh, S. B., & Nain, L. (2011). Bioremediation of PAH by Streptomyces sp. Bulletin of Environmental Contamination and Toxicology, 86(3), 268–271.
Chavez-Gomez, B., Quintero, R., Esparza-Garcia, F., Mesta-Howard, A. M., Diaz, Z., de la Serna, F. J., et al. (2003). Removal of phenanthrene from soil by co-cultures of bacteria and fungi pregrown on sugarcane bagasse pith. Bioresource Technology, 89(2), 177–183.
Chen, S., & Hickey, W. J. (2011). Development of tools for genetic analysis of phenanthrene degradation and nanopod production by Delftia sp. Cs1-4. Frontiers in Microbiology, 2, 187.
Cheung, P. Y., & Kinkle, B. K. (2001). Mycobacterium diversity and pyrene mineralization in petroleum-contaminated soils. [Research Support, U.S. Gov't, P.H.S.]. Applied and Environmental Microbiology, 67(5), 2222–2229.
Conesa, A., Punt, P. J., & van den Hondel, C. A. M. J. J. (2002). Fungal peroxidases: molecular aspects and applications. Journal of Biotechnology, 93, 143–158.
Cortes-Espinosa, D. V., Fernandez-Perrino, F. J., Arana-Cuenca, A., Esparza-Garcia, F., Loera, O., & Rodriguez-Vazquez, R. (2006). Selection and identification of fungi isolated from sugarcane bagasse and their application for phenanthrene removal from soil. Journal of Environmental Science and Health. Part A, Toxic/Hazardous Substances & Environmental Engineering, 41(3), 475–486.
Cristica, M., Manoliu, A., T., B., Ciornea, E. (2010). Compared analysis of catalase and peroxidase activity in cellulolytic fungus Trichoderma reesei grown on medium with different concentrations ofgrinded wheat and barley straws. Annals of the ''Alexandru Ioan Cuza'' University Sect.II a., 12(3), 89–93.
Diaz-Ramirez, I. J., Ramirez-Saad, H., Gutierrez-Rojas, M., & Favela-Torres, E. (2003). Biodegradation of Maya crude oil fractions by bacterial strains and a defined mixed culture isolated from Cyperus laxus rhizosphere soil in a contaminated site. Canadian Journal of Microbiology, 49(12), 755–761.
Fernandez-Luqueno, F., Valenzuela-Encinas, C., Marsch, R., Martinez-Suarez, C., Vazquez-Nunez, E., & Dendooven, L. (2011). Microbial communities to mitigate contamination of PAHs in soil—possibilities and challenges: a review. [Review]. Environmental Science and Pollution Research International, 18(1), 12–30.
Field, J. A., Vledder, R. H., van Zelst, J. G., & Rulkens, W. H. (1996). The tolerance of lignin peroxidase and manganese-dependent peroxidase to miscible solvents and the in vitro oxidation of anthracene in solvent:water mixtures. Enzyme Microbiology and Technology, 18(4), 300–308.
Gochev, V. K., & Krastanov, A. I. (2007). Fungal laccases. Bulgarian Journal of Agricultural Science, 13, 75–83.
Grosser, R. J., Warshawsky, D., & Vestal, J. R. (1991). Indigenous and enhanced mineralization of pyrene, benzo[a]pyrene, and carbazole in soils. [Research Support, U.S. Gov't, P.H.S.]. Applied and Environmental Microbiology, 57(12), 3462–3469.
Hadibarata, T., Tachibana, S., & Itoh, K. (2007). Biodegradation of phenanthrene by fungi screened from nature. Pakistan Journalof Biological Sciences, 10(15), 2535–2543.
Haritash, A. K., & Kaushik, C. P. (2009). Biodegradation aspects of polycyclic aromatic hydrocarbons (PAHs): a review. [Review]. Journal of Hazardous Materials, 169(1–3), 1–15.
Hinga, K. R., & Batchellor, A. (2005). Waste processing and detoxification. In R. M. Hassan, R. Scholes, & N. Ash (Eds.), Ecosystems and human well-being: current state and trends volume 1 (pp. 917). Washington, DC: Island.
Hughes, K. A., & Bridge, P. (2009). Tolerance of antarctic soil fungi to hydrocarbons and their potential role in soil bioremediation. In Polar microbiology: the ecology, biodiversity and bioremediation potential of microorganisms in extremely cold environments. Boca Raton: Taylor & Francis.
Hughes, K. A., Bridge, P., & Clark, M. S. (2007). Tolerance of Antarctic soil fungi to hydrocarbons. Science of the Total Environment, 372(2–3), 539–548.
Jacques, R. J., Okeke, B. C., Bento, F. M., Teixeira, A. S., Peralba, M. C., & Camargo, F. A. (2008). Microbial consortium bioaugmentation of a polycyclic aromatic hydrocarbons contaminated soil. Bioresource Technology, 99, 2637–2643.
Johnsen, A. R., Schmidt, S., Hybholt, T. K., Henriksen, S., Jacobsen, C. S., & Andersen, O. (2007). Strong impact on the polycyclic aromatic hydrocarbon (PAH)-degrading community of a PAH-polluted soil but marginal effect on PAH degradation when priming with bioremediated soil dominated by mycobacteria. Applied and Environmental Microbiology, 73(5), 1474–1480.
Juhasz, A. L., & Naidu, R. (2000). Bioremediation of high molecular weight polycyclic aromatic hydrocarbons: a review of the microbial degradation of benzo[a]pyrene. International Biodeterioration & Biodegradation, 45, 57–88.
Juhasz, A., Britz, M. L., & Stanley, G. A. (1997). Degradation of fluoranthene, pyrene, benz[a]anthracene and dibenz[a, h]anthracene by Burkholderia cepacia. Water Science and Technology, 36(10), 45–51.
Kazunga, C., & Aitken, M. D. (2000). Products from the incomplete metabolism of pyrene by polycyclic aromatic hydrocarbon-degrading bacteria. [Research Support, U.S. Gov't, P.H.S.]. Applied and Environmental Microbiology, 66(5), 1917–1922.
Kim, J. D., & Lee, C. L. (2007). Microbial degradation of polycyclic aromatic hydrocarbons in soil by bacterium–fungus cocultures. Biotechnology and Bioprocess Engineering, 12, 410–416.
Kim, S. J., Kweon, O., Jones, R. C., Edmondson, R. D., & Cerniglia, C. E. (2008). Genomic analysis of polycyclic aromatic hydrocarbon degradation in Mycobacterium vanbaalenii PYR-1. Biodegradation, 19(6), 859–881.
Kim, Y. M., Ahn, C. K., Woo, S. H., Jung, G. Y., & Park, J. M. (2009). Synergic degradation of phenanthrene by consortia of newly isolated bacterial strains. [Research Support, Non-U.S. Gov't]. Journal of Biotechnology, 144(4), 293–298.
Kimura, M. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. [Comparative Study]. Journal of Molecular Evolution, 16(2), 111–120.
Lane, D. J. (1991). 16S/23S rRNA sequencing. In E. Stackebrandt & M. Goodfellow (Eds.), Nucleic acid techniques in bacterial systematics (pp. 115–175). Chichester: Wiley.
Lazaroaie, M. M. (2009). Mechanisms involved in organic solvent tesistance in gram-negative bacteria. World Academy of Science, Engineering and Technology, 30, 643–653.
Lazaroaie, M. M. (2010). Multiple responses of gram-positive and gram-negative bacteria to mixture of hydrocarbons. Brazilian Journal of Microbiology, 41(3), 649–667.
Li, X., Li, P., Lin, X., Zhang, C., Li, Q., & Gong, Z. (2008). Biodegradation of aged polycyclic aromatic hydrocarbons (PAHs) by microbial consortia in soil and slurry phases. Journal of Hazardous Materials, 150, 21–26.
Li, X., Li, P., Liu, W., Wang, L., Ma, F., & Chukwuka, K. S. (2009). Biodegradation of the low concentration of polycyclic aromatic hydrocarbons in soil by microbial consortium during incubation. Journal of Hazardous Materials, 172, 601–605.
Luthy, R. G. (2004). Organic contaminants in the environment: challenges for the water/environmental engineering community. In P. Norling, F. Wood-Black, & T. M. Masciangioli (Eds.), Water and sustainable development: opportunities for the chemical sciences: a workshop report to the chemical sciences roundtable (The National Academies Collection: reports funded by National Institutes of Health). Washington (DC): National Academies.
Margesin, R., & Schinner, F. (2001). Biodegradation and bioremediation of hydrocarbons in extreme environments. [review]. Applied Microbiology and Biotechnology, 56(5–6), 650–663.
Montgomery, M. T., Boyd, T. J., Osburn, C. L., & Smith, D. C. (2010). PAH mineralization and bacterial organotolerance in surface sediments of the Charleston Harbor estuary. [Research Support, Non-U.S. Gov't]. Biodegradation, 21(2), 257–266.
Mrozik, A., & Piotrowska-Seget, Z. (2010). Bioaugmentation as a strategy for cleaning up of soils contaminated with aromatic compounds. Microbiology Research, 165(5), 363–375.
Okoro, C. C., & Amund, O. O. (2010). Biodegradation of produced water hydrocarbons by Aspergillus fumigatus. Journal of American Science, 6(3), 143–149.
PEMEX (2002). Evaluación de Riesgo Ecológico e Impacto de las Operaciones Industriales (Análisis General). Resource document. Petroleos Mexicanos. http://pemex.com/files/content/Sonda-Master-_1_080302.pdf. Accesed 6 february 2013.
Premuzic, E. T., & Lin, M. S. (1999). Induced biochemical conversions of heavy crude oils. Journal of Petroleum Science and Engineering, 22(1–3), 171–180.
Ramos, J. L., Duque, E., Gallegos, M. T., Godoy, P., Ramos-Gonzalez, M. I., Rojas, A., et al. (2002). Mechanisms of solvent tolerance in gram-negative bacteria. [Research Support, Non-U.S. Gov't Review]. Annual Review of Microbiology, 56, 743–768.
Rentz, J. A., Alvarez, P. J., & Schnoor, J. L. (2008). Benzo[a]pyrene degradation by Sphingomonas yanoikuyae JAR02. [Research Support, U.S. Gov't, Non-P.H.S.]. Environmental Pollution, 151(3), 669–677.
Romero, M. C., Urrutia, M. I., Reinoso, H. E., & Kiernan, M. M. (2010). Benzo a pyrene degradation by soil filamentous fungi. Journal of Yeast and Fungal Research, 1(2), 25–29.
Sambrook, J., & Russell, D. W. (2001). Molecular cloning: a laboratory manual (3rd ed., Vol. 3). New York: Cold Spring Harbor Laboratory.
Saraswathy, A., & Hallberg, R. (2002). Degradation of pyrene by indigenous fungi from a former gasworks site. FEMS Microbiology Letters, 210(2), 227–232.
SEMARNAT. (2000). Norma Oficial Mexicana NOM-021-RECNAT-2000 que establece las especificaciones de fertilidad, salinidad y clasificación de suelos. Estudios, muestreo y análisis. Diario oficial Secretaría de Medio Ambiente y Recursos Naturales. http://dof.gob.mx/nota_detalle.php?codigo=717582&fecha=31/12/2002. Accesed 22 October 2012.
Seo, J. S., Keum, Y. S., & Li, Q. X. (2009). Bacterial degradation of aromatic compounds. [Research Support, U.S. Gov't, Non-P.H.S. Review]. International Journal of Environmental Research and Public Health, 6(1), 278–309.
Shen, X. H., Zhou, N. Y., & Liu, S. J. (2012). Degradation and assimilation of aromatic compounds by Corynebacterium glutamicum: another potential for applications for this bacterium? [Research Support, Non-U.S. Gov't Review]. Applied Microbiology and Biotechnology, 95(1), 77–89.
Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., & Kumar, S. (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. [Research Support, N.I.H., Extramural]. Molecular Biology and Evolution, 28(10), 2731–2739.
Torres, S., Pandey, A., & Castro, G. R. (2011). Organic solvent adaptation of gram positive bacteria: applications and biotechnological potentials. [Research Support, Non-U.S. Gov't Review]. Biotechnology Advances, 29(4), 442–452.
US-EPA (1996). Soil Screening Guidance: Users Guide. United States Environmental Protection Agency. Resource document. http://www.epa.gov/superfund/resources/soil/ssg496.pdf. Accesed 22 October 2012.
Verdin, A., Sahraoui, A. L.-H., & Durand, R. (2004). Degradation of benzo[a]pyrene by mitosporic fungi and extracellular oxidative enzymes. International Biodeterioration & Biodegradation, 53(2), 65–70.
White, T. J., Bruns, T. D., Lee, S. H., & Taylor, J. (1990). Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics (PCR protocols, a guide to methods and applications). San Diego: Academic.
Wong, J. W., Fang, M., Zhao, Z., & Xing, B. (2004). Effect of surfactants on solubilization and degradation of phenanthrene under thermophilic conditions. [Research Support, Non-U.S. Gov't]. Journal of Environmental Quality, 33(6), 2015–2025.
Wu, M., Chen, L., Tian, Y., Ding, Y., & Dick, W. A. (2013). Degradation of polycyclic aromatic hydrocarbons by microbial consortia enriched from three soils using two different culture media. Environmental Pollution, 178, 152–158.
Wunder, T., Kremer, S., Sterner, O., & Anke, H. (1994). Metabolism of the polycyclic aromatic hydrocarbon pyrene by Aspergillus niger SK 9317. [Research Support, Non-U.S. Gov't]. Applied Microbiology and Biotechnology, 42(4), 636–641.
Yu, K. S., Wong, A. H., Yau, K. W., Wong, Y. S., & Tam, N. F. (2005). Natural attenuation, biostimulation and bioaugmentation on biodegradation of polycyclic aromatic hydrocarbons (PAHs) in mangrove sediments. Marine Pollution Bulletin, 51(8–12), 1071–1077.
Yuan, S. Y., Chang, S. W., & Chang, B. V. (2003). Biodegradation of polycyclic aromatic hydrocarbons in sludge. Bulletin of Environmental Contamination and Toxicology, 71(3), 625–632.
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This work was supported by Consejo Nacional de Ciencia y Tecnología (CONACYT) project CB2008-105643, Instituto Politécnico Nacional project SIP20131157 and CONACYT grant 269828.
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Zafra, G., Absalón, Á.E., Cuevas, M.D.C. et al. Isolation and Selection of a Highly Tolerant Microbial Consortium with Potential for PAH Biodegradation from Heavy Crude Oil-Contaminated Soils. Water Air Soil Pollut 225, 1826 (2014). https://doi.org/10.1007/s11270-013-1826-4
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DOI: https://doi.org/10.1007/s11270-013-1826-4