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2018 | 67 | 3 |
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The emergence of different functionally equivalent PAH degrading microbial communities from a single soil in liquid PAH enrichment cultures and soil microcosms receiving PAHs with and without bioaugmentation

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Polycyclic aromatic hydrocarbon (PAHs) are common soil contaminants of concern due to their toxicity toward plants, animals and microorganisms. The use of indigenous or added microbes (bioaugmentation) is commonly used for bioremediation of PAHs. In this work, the biodegradation rates and changes in the bacterial community structure were evaluated. The enrichment culture was useful for unambiguously identifying members of the soil bacterial community associated with PAH degradation and yielded a low diversity community. No significant difference in the rate of PAH degradation was observed between the microcosm receiving only PAHs or PAHs and bioaugmentation. Moreover, identical matches to the bioaugmentation inoculum were only observed at the initial stages of PAH degradation on day 8. After 22 days of incubation, the substantial degradation of all PAHs had occurred in both microcosms and the PAH contaminated soil had statistically significant increases in Alphaproteobacteria. There were also increases in Betaproteobacteria. In contrast, the PAH contaminated and bioaugmented soil was not enriched in PAH degrading Proteobacteria genera and, instead, an increase from 1.6% to 8% of the population occurred in the phylum Bacteroidetes class Flavobacteria, with Flavobacterium being the only identified genus. In addition, the newly discovered genus Ohtaekwangia increased from 0% to 3.2% of the total clones. These results indicate that the same soil microbial community can give rise to different PAH degrading consortia that are equally effective in PAH degradation efficiency. Moreover, these results suggest that the lack of efficacy of bioaugmentation in soils can be attributed to a lack of persistence of the introduced microbes, yet nonetheless may alter the microbial community that arises in response to PAH contamination in unexpected ways.
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  • Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
  • Department of Food Science - FEA, University of Campinas (UNICAMP), Campinas, Sao Paulo, Brazil
  • Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
  • Laboratory of Molecular Biology, DGE-Federal University of Sao Carlos (DGE/UFSCar), Sao Carlos, SP, Brazil
  • Department of Food Science - FEA, University of Campinas (UNICAMP), Campinas, Sao Paulo, Brazil
  • Department of Food Science - FEA, University of Campinas (UNICAMP), Campinas, Sao Paulo, Brazil
  • Abbasian F, Lockington R, Megharaj M, Naidu R. 2016a. The bio-diversity changes in the microbial population of soils contaminated with crude oil. Curr Microbiol. 72:663–670.
  • Abbasian F, Palanisami T, Megharaj M, Naidu R, Lockington R, Ramadass R. 2016b. Microbial diversity and hydrocarbon degrading gene capacity of a crude oil field soil as determined by meta-genomics analysis. Biotechnol. Prog. 32:638–648.
  • Aleer S, Adetutu EM, Weber J, Ball AS, Juhasz AL. 2014. Potential impact of soil microbial heterogeneity on the persistence of hydrocarbons in contaminated subsurface soils J Environ Manag. 136:27–36.
  • Bento FM, Camargo FA, Okeke BC, Frankenberger WT. 2005. Comparative bioremediation of soils contaminated with diesel oil by natural attenuation, biostimulation and bioaugmentation. Bioresour Technol. 96:1049–1055.
  • Brown SD, Utturkar SM, Klingeman DM, Johnson CM, Martin SL, Land ML, Lu TY, Schadt CW, Doktycz MJ, Pelletier DA. 2012. Twenty-one genome sequences from Pseudomonas species and 19 genome sequences from diverse bacteria isolated from the rhizosphere and endosphere of Populus deltoides. J Bacteriol. 194:5991–5993.
  • Cao BY, Ma T, Ren Y, Li GQ, Li P, Guo X, Ding P, Feng L. 2011. Complete genome sequence of Pusillimonas sp. T7-7, a cold-tolerant diesel oil-degrading bacterium isolated from the Bohai Sea in China. J Bacteriol. 193:4021–4022.
  • Chaudhary DK, Kim J. 2018. Flavobacterium naphthae sp. nov., isolated from oil-contaminated soil. Int J Syst Evol Microbiol. 68:305–309.
  • Cole JR, Chai B, Farris RJ, Wang Q, Kulam SA, McGarrell DM, Garrity GM, Tiedje JM. 2005. The Ribosomal Database Project (RDP-II), sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res. 33:D294–D296.
  • Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, Tiedje JM. 2009. The Ribosomal Database Project, improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 37:D141–145.
  • Curry JC, Jurelevicius DA, Villena HDM, Jesus HE, Peixoto RS, Schaefer CEGR, Bícego MC, Seldin L, Rosado AS. 2015. Microbial diversity and hydrocarbon depletion in low and high diesel-polluted soil samples from Keller Peninsula, South Shetland Islands. Antarct Sci. 27:263–273.
  • Eisler R. 1987. Polycyclic aromatic hydrocarbon hazards to fish, wildlife and invertebrates, a synoptic review. Contaminant Hazard Reviews. Report 11: Biological Report 85(1.11). Laurel, MD (USA): U.S. Department of the Interior, Fish and Wildlife Service.
  • Eriksson M, Sodersten E, Yu Z, Dalhammar G, Mohn WW. 2003. Degradation of polycyclic aromatic hydrocarbons at low temperature under aerobic and nitrate-reducing conditions in enrichment cultures from northern soils. Appl Environ Microbiol. 69:275–284.
  • Ferrari B, Winsley T, Ji M, Neilan B. 2014. Insights into the distribution and abundance of the ubiquitous candidatus Saccharibacteria phylum following tag pyrosequencing. Sci Rep. 4:3957.
  • Guazzaroni ME, Herbst FA, Lores I, Tamames J, Peláez AI, López-Cortés N, Alcaide M, Del Pozo MV, Vieites JM, von Bergen M, et al. 2013. Metaproteogenomic insights beyond bacterial response to naphthalene exposure and bio-stimulation. ISME J. 7:122–136.
  • Gutierrez T, Rhodes G, Mishamandani S, Berry D, Whitman WB, Nichols PD, Semple KT, Aitken MD. 2014. Polycyclic aromatic hydrocarbon degradation of phytoplankton-associated Arenibacter spp. and description of Arenibacter algicola sp. nov., an aromatic hydrocarbon-degrading bacterium. Appl Environ Microbiol. 80(2): 618–628.
  • Haritash AK, Kaushik CP. 2009. Biodegradation aspects of polycyclic aromatic hydrocarbons (PAHs): A review. J Hazard Mater. 169:1–15.
  • Hilyard EJ, Jones-Meehan JM, Spargo BJ, Hill RT. 2008. Enrichment, isolation and phylogenetic identification of polycyclic aromatic hydrocarbon-degrading bacteria from Elizabeth River sediments. Appl Environ Microbiol. 74:1176–1182.
  • Ho Y, Jackson MM, Yang Y, Mueller JG, Pritchard PH. 2000. Characterization of fluoranthene- and pyrene-degrading bacteria isolated from PAH-contaminated soils and sediments and comparison of several Sphingomonas spp. J Ind Microbiol Biotech. 24:100–112.
  • Janssen PH. 2006. Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl Environ Microbiol. 72:1719–1728.
  • Juhasz AL, Naidu R. 2000. Bioremediation of high molecular weight polycyclic aromatic hydrocarbons, a review of the microbial degradation of benzo[a]pyrene. Int Biodeterior Biodegradation. 45:57–88.
  • Kadali KK, Simons KL, Skuza PP, Moore RB, Ball AS. 2012. A complementary approach to identifying and assessing the remediation potential of hydrocarbonoclastic bacteria. J Microbiol Methods. 88:348–355.
  • Kertesz MA, Kawasaki A. 2010. Hydrocarbon-degrading Sphingomonads, Sphingomonas, Sphingobium, Novosphingobium, and Sphingopyxis. In: Timmis KN, McGenity T, Meer JR, Lorenzo V, editors. Handbook of hydrocarbon and lipid microbiology. Berlin Heidelberg (Germany): Springer. p. 1693–1705.
  • Khan MAI, Biswas B, Smith E, Mahmud SA, Hasan NA, Khan MAW, Naidu R, Megharaj M. 2018. Microbial diversity changes with rhizosphere and hydrocarbons in contrasting soils. Ecotoxicol Environ Saf. 156:434–442.
  • Kostka JE, Prakash O, Overholt WA, Green SJ. Freyer G, Canion A, Delgardio J, Norton N, Hazen TC, Huettel M. 2011. Hydrocarbon-degrading bacteria and the bacterial community response in Gulf of Mexico beach sands impacted by the deepwater horizon oil spill. Appl Environ Microbiol. 77:7962–7974.
  • Kuske CR, Barns SM, Busch JD. 1997. Diverse uncultivated bacterial groups from soils of the arid southwestern United States those are present in many geographic regions. Appl Environ Microbiol. 63:3614–3621.
  • Lane DJ. 1991. 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M, editors. Nucleic acid techniques in bacterial systematics. New York (USA): John Wiley and Sons. p. 115–175.
  • Lauber CL, Strickland MS, Bradford MA, Fierer N. 2008. The influence of soil properties on the structure of bacterial and fungal communities across land-use types. Soil Biol Biochem. 40:2407–2415.
  • Liang Y, Zhao H, Zhang X, Zhou J, Li G. 2014. Contrasting microbial functional genes in two distinct saline-alkali and slightly acidic oil-contaminated sites. Sci Total Environ. 487:272–278.
  • Lindstrom JE, Prince RC, Clark JC, Grossman MJ, Yeager TR, Braddock JF, Brown, EJ. 1991. Microbial populations and hydrocarbon biodegradation potentials in fertilized shoreline sediments affected by the T/V Exxon Valdez oil spill. Appl Environ Microbiol. 57:2514–2522.
  • Margesin R, Hämmerle M, Tscherko D. 2007. Microbial activity and community composition during bioremediation of diesel-oil-contaminated soil: effects of hydrocarbon concentration, fertilizers, and incubation time. Microbiol Ecol. 53:259–269.
  • Megharaj M, Ramakrishnan B, Venkateswarlu K, Sethunathan N, Naidu R. 2011. Bioremediation approaches for organic pollutants: a critical perspective. Environ Int. 37:1362–1375.
  • Militon C, Boucher D, Vachelard C, Perchet G, Barra V, Troquet J, Peyretaillade E, Peyret P. 2010. Bacterial community changes during bioremediation of aliphatic hydrocarbon-contaminated soil. FEMS Microbiol Ecol. 74:669–681.
  • Mrozik A, Piotrowska-Seget Z. 2010. Bioaugmentation as a strategy for cleaning up of soils contaminated with aromatic compounds. Microbiol Res. 165:363–375.
  • Naether A, Foesel BU, Naegele V, Wüst PK, Weinert J, Bonkowski M, Alt F, Oelmann Y, Polle A, Lohaus G, et al. 2012. Environmental factors affect Acidobacterial communities below the subgroup level in grassland and forest soils. Appl Environ Microbiol. 78:7398–7406.
  • Patel V, Cheturvedula S, Madamwar D. 2012. Phenanthrene degradation by Pseudoxanthomonas sp. DMVP2 isolated from hydrocarbon contaminated sediment of Amlakhadi canal, Gujarat, India. J Hazard Mater. 201–202:43–51.
  • Petry T, Schmid P, Schlatter C. 1996. The use of toxic equivalency factors in assessing occupational and environmental health risk associated with exposure to airborne mixtures of polycyclic aromatic hydrocarbons (PAHs). Chemosphere. 32:639–648.
  • Philp JC, Atlas RM. 2005. Bioremediation of contaminated soil and aquifers. In: Atlas R M, Jim CP, editors. Bioremediation: Applied Microbial Solution for Real – World Environmental Clean Up. Washington DC (USA): ASM Press. p. 139.
  • Phillips LA, Germida JJ, Farrell RE, Greer CW. 2008. Hydrocarbon degradation potential and activity of endophytic bacteria associated with prairie plants. Soil Biol Biochem. 40:3054–3064.
  • Prince R, Gramain A, McGenity T. 2010. Prokaryotic hydrocarbon degraders. In: Timmis KN, McGenity TJ, van der Meer JR, de Lorenzo V, editors. Handbook of hydrocarbon and lipid microbiology. Berlin (Germany): Springer. p. 1669–1692.
  • Rambeloarisoa E, Rontani JF, Giusti G, Duvvnjak Z, Bertrand JC. 1984. Degradation of crude oil by a mixed population of bacteria isolated from sea surface foams. Mar Biol. 83:69–81.
  • Samanta SK, Singh OV, Jain RK. 2002. Polycyclic aromatic hydrocarbons, environmental pollution and bioremediation. Trends Biotechnol. 20:243–248.
  • Sayara T, Borras E, Caminal G, Sarra M, Sanchez A. 2011. Bioremediation of PAHs-contaminated soil through composting: Influence of bioaugmentation and biostimulation on contaminant biodegradation. Int Biodeterior Biodegrad. 65:859–865.
  • Seo JS, Keum YS, Harada RM, Li,p QX. 2007. Isolation and characterization of bacteria capable of degrading polycyclic aromatic hydrocarbons (PAHs) and organophosphorus pesticides from PAH-contaminated soil in Hilo, Hawaii. J Sci Food Agric. 55:5383–5389.
  • Seo JS, Keum YS, Li QX. 2009. Bacterial degradation of aromatic compounds. Int J Environ Res Public Health. 6:278–309.
  • Shokrollahzadeh S, Golmohammad F, Shokouhi H. 2012. Study of Sphingopyxis isolates in degradation of polycyclic aromatic hydrocarbons. Chem Eng Trans. 27:55–60.
  • Silva IS, Costa SE, Ragagnin MC, Fonseca FA, Franciscon GDE, Grossman MJ, Durrant LR. 2009. Bioremediation of a polyaromatic hydrocarbon contaminated soil by native soil microbiota and bioaugmentation with microbial isolates and consortia. Bioresour Technol. 100:4669–4675.
  • Singleton DR, Richardson SD, Aitken MD. 2011. Pyrosequence analysis of bacterial communities in aerobic bioreactors treating polycyclic aromatic hydrocarbon-contaminated soil. Biodegradation 22:1061–1073.
  • Sutton NB, Maphosa F, Morillo JA, Al-Soud WA, Langenhoff AAM, Grotenhuis T, Smidt H. 2013. Impact of long-term diesel contamination on soil microbial community structure. Appl Environ Microbiol. 79:619–630.
  • Szczepaniak Z, Cyplik P, Juzwa W, Czarny J, Staninska J, Piotrowska-Cyplik A. 2015. Antibacterial effect of the Trichoderma viride fungi on soil microbiome during PAH’s biodegradation. Int Biodeter Biodegr. 104:170–177.
  • Szulc A, Ambrożewicz D, Sydow M, Ławniczak Ł, Piotrowska-Cyplik A, Marecik R, Chrzanowski Ł. 2014. The influence of bioaugmentation and biosurfactant addition on bioremediation efficiency of diesel-oil contaminated soil: Feasibility during field studies. J Environ Manage. 132:121–128.
  • Thompson IP, Van Der Gast CJ, Ciric L, Singer AC. 2005. Bioaugmentation for bioremediation: the challenge of strain selection. Environ Microbiol. 7(7):909–915.
  • Tyagi M, da Fonseca MM, de Carvalho CC. 2011. Bioaugmentation and biostimulation strategies to improve the effectiveness of bioremediation processes. Biodegradation. 22:231–241.
  • Van Hamme JD, Singh A, Ward OP. 2003. Recent advances in petroleum microbiology. Microbiol Mol Biol Rev. 67:503–549.
  • Vinas M, Sabate J, Espuny MJ, Solanas AM. 2005. Bacterial community dynamics and polycyclic aromatic hydrocarbon degradation during bioremediation of heavily creosotecontaminated soil. Appl Environ Microbiol. 71:7008–7018.
  • Wang Q, Garrity GM, Tiedje JM, Cole JR. 2007. Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy. Appl Environ Microbiol. 73:5261–5267.
  • Widada J, Nojiri H, Kasuga K, Yoshida T, Habe H, Omori T. 2002. Molecular detection and diversity of polycyclic aromatic hydrocarbon-degrading bacteria isolated from geographically diverse sites. Appl Microbiol Biotechnol. 58:202–209.
  • Wilson SC, Jones KC. 1993. Bioremediation of soil contaminated with polynuclear aromatic hydrocarbons (PAHs): a review. Environ Pollut. 81:229–249.
  • Wolin EA, Wolin MJ, Wolfe RS. 1963. Formation of methane by bacterial extracts. J Biol Chem. 238:2882–2886.
  • Wyrwas B, Dymaczewski Z, Zgoła-Grześkowiak A, Szymański A, Frańska M, Kruszelnicka I, Ginter-Kramarczyk D, Cyplik P, Ławniczak Ł, Chrzanowski Ł. 2013. Biodegradation of Triton X-100 and its primary metabolites by a bacterial community isolated from activated sludge. J Environ Manage. 128:292–299.
  • Yoon JH, Kang SJ, Lee SY, Lee JS, Park S. 2011. Ohtaekwangia koreensis gen. nov., sp. nov. and Ohtaekwangia kribbensis sp. nov., isolated from marine sand, deep-branching members of the phylum Bacteroidetes. Int J Syst Evol Microbiol. 61:1066–1072.
  • Xie S, Sun W, Luo C, Cupples AM. 2011. Novel aerobic benzene degrading microorganisms identified in three soils by stable isotope probing. Biodegradation. 22:71–81.
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