Comparative bioaugmentation with a consortium and a single strain in a phenanthrene-contaminated soil: Impact on the bacterial community and biodegradation

Applied Soil Ecology

Volumn 98, Issue , 2016, Pages 8-19

  Festa, S ^a   Coppotelli, B M ^a   Morelli, I S ^a,b  

^a Universidad Nacional de La Plata   (Argentina)

^b Centro Científico y Tecnológico Consejo Nacional de Investigaciones Científicas y Técnicas   (Argentina)

Author keywords

Bacterial consortium; Bioaugmentation; Community composition; Phenanthrene degradation; Pyrosequencing

Indexed keywords

EID: 84949460036     PISSN: 09291393     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.apsoil.2015.08.025     Document Type: Article

References (64)

1. Alexander M. Biodegradation and Bioremediation 1999, Academic Press, Inc., San Diego, Calif. 2nd ed.
2. Amann R.I., Ludwig W., Schleifer K.H. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 1995, 59:143-169.
3. Andreoni V., Cavalca L., Rao M.A., Nocerino G., Bernasconi S., Dell'Amico E., Colombo M., Gianfreda L. Bacterial communities and enzyme activities of PAHs polluted soils. Chemosphere 2004, 57:401-412.
4. ATSDR (Agency for Toxic Substances and Disease Registry), 2005. CERCLA Priority list of hazardous substances US Department of Health and Human Service. Atlanta, G., USA [WWW.document]. URL . http://www.asdr.cdc.gov/cercla/05list.html.
5. Bundy J.G., Paton G.I., Campbell C.D. Microbial communities in different soil types do not converge after diesel contamination. J. Appl. Microbiol. 2002, 92:276-288.
6. Cole J.R., Wang Q., Cardenas E., Fish J., Chai B., Farris R.J., Kulam-Syed-Mohideen A.S., McGarrell D.M., Marsh T., Garrity G.M., Tiedje J.M. The Ribosomal database project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 2009, 37:D141-D145.
7. Colwell, R.K., 2013. EstimateS: Statistical estimation of species richness and shared species from samples., Version 9. User's Guide and application published at: . http://viceroy.eeb.uconn.edu/estimates.
8. Coppotelli B.M., Ibarrolaza A., Del Panno M.T., Morelli I.S. Effects of the inoculant strain Sphingomonas paucimobilis 20006FA on soil bacterial community and biodegradation in phenanthrene-contaminated soil. Microb. Ecol. 2008, 55:173-183.
9. Coppotelli B.M., Ibarrolaza A., Dias R.L., Del Panno M.T., Berthe-Corti L., Morelli I.S. Study of the degradation activity and the strategies to promote the bioavailability of phenanthrene by Sphingomonas paucimobilis strain 20006FA. Microb. Ecol. 2010, 59:266-276.
10. Chao A. Species estimation and applications. Encyclopedia of Statistical Sciences 2005, vol. 12:7907-7916. Wiley, New York. 2nd ed.
11. Chao A., Chiu C.-H., Hsieh T.C. Proposing a esolution to debates on diversity partitioning. Ecology 2012, 93:2037-2051.
12. Chen H., Boutros P.C. VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R. BMC Bioinf. 2011, 12(1):35.
13. de Araujo J.C., Schneider R.P. DGGE with genomic DNA: suitable for detection of numerically important organisms but not for identification of the most abundant organisms. Water Res. 2008, 42:5002-5010.
14. Degens B.P., Schipper L.A., Sparling G.P., Duncan L.C. Is the microbial community in a soil with reduced catabolic diversity less resistant to stress or disturbance?. Soil Biol. Biochem. 2001, 33:1143-1153.
15. Dejonghe W., Boon N., Seghers D., Top E.M., Verstraete W. Bioaugmentation of soils by increasing microbial richness: missing links. Environ. Microbiol. 2001, 3:649-657.
16. Dowd S.E., Callaway T.R., Wolcott R.D., Sun Y., McKeehan T., Hagevoort R.G., EdringtonT S. Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP). BMC Microbiol. 2008, 125.
17. Dowd S.E., Sun Y., Wolcott R.D., Domingo A., Carroll J.A. Bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) for microbiome studies: bacterial diversity in the ileum of newly weaned Salmonella-infected pigs. Foodborne Pathog. Dis. 2008, 5:459-472.
18. Dowd S.E., Zaragoza J., Rodriguez J.R., Oliver M.J., Payton P.R. Windows .NET network distributed basic local alignment search toolkit (W.ND-BLAST). BMC Bioinform. 2005, 6:93.
19. Edgar R.C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 2010, 26:2460-2461.
20. Epelde L., Mijangos I., Becerril J.M., Garbisu C. Soil microbial community as bioindicator of the recovery of soil functioning derived from metal phytoextraction with sorghum. Soil Biol. Biochem. 2009, 41:1788-1794.
21. Festa S., Coppotelli B.M., Morelli I.S. Bacterial diversity and functional interactions between bacterial strains from a phenanthrene-degrading consortium obtained from a chronically contaminated-soil. Int. Biodeterior. Biodegrad. 2013, 85:42-51.
22. Fromin N., Hamelin J., Tarnawski S., Roesti D., Jourdain-Miserez K., Forestier N., Teyssier-Cuvelle S., Gillet F., Aragno M., Rossi P. Statistical analysis of denaturing gel electrophoresis (DGE) fingerprinting patterns. Environ. Microbiol. 2002, 4:634-643.
23. Ghazali F.M., Rahman R.N.Z.A., Salleh A.B., Basri M. Biodegradation of hydrocarbons in soil by microbial consortium. Int. Biodeterior. Biodegrad. 2004, 54:61-67.
24. Gojgic-Cvijovic G.D., Fau M.J., Solevic T.M., Beskoski V.P., Ilic M.V., Djokic L.S., Narancic T.M., Vrvic M.M. Biodegradation of petroleum sludge and petroleum polluted soil by a bacterial consortium: a laboratory study. Biodegradation 2012, 23:1-14.
25. Gomes N., Kosheleva I.A., Abraham W.R., Smalla K. Effects of the inoculant strain Pseudomonas putida KT2442 (pNF142) and of naphthalene contamination on the soil bacterial community. FEMS Microbiol. Ecol. 2005, 54:21-33.
26. González N., Simarro R., Molina M., Bautista L., Delgado L., Villa J. Effect of surfactants on PAH biodegradation by a bacterial consortium and on the dynamics of the bacterial community during the process. Bioresour. Technol. 2011, 102:9438-9446.
27. Goyal A.K., Zylstra G.J. Molecular cloning of novel genes for polycyclic aromatic hydrocarbon degradation from Comamonas testosteroni GZ39. Appl. Environ. Microbiol. 1996, 62:230-236.
28. Hennessee C., Li Q. Micrococcineae: arthrobacter and relatives. Handbook of Hydrocarbon and Lipid Microbiology 2010, 1853-1864. Springer.
29. Hervé V., Le Roux X., Uroz S., Gelhaye E., Frey-Klett P. Diversity and structure of bacterial communities associated with Phanerochaete chrysosporium during wood decay. Environ. Microbiol. 2014, 16:2238-2252.
30. Hill M.O. Diversity and evenness: a unifying notation and its consequences. Ecology 1973, 54(2):427-432.
31. Ibarrolaza A., Coppotelli B., Del Panno M., Donati E., Morelli I. Application of the knowledge based approach to strain selection for a bioaugmentation process of phenanthrene and Cr (VI) contaminated soil. J. Appl. Microbiol. 2011, 111:26-35.
32. Jacques R.J.S., Okeke B.C., Bento F.M., Teixeira A.S., Peralba M.C.R., Camargo F.A.O. Microbial consortium bioaugmentation of a polycyclic aromatic hydrocarbons contaminated soil. Bioresour. Technol. 2008, 99:2637-2643.
33. Jost L. Entropy and diversity. Oikos 2006, 113:363-375.
34. Kallimanis A., SF, Drainas C., Koukkou A.I. Taxonomic identification, phenanthrene uptake activity, and membrane lipid alterations of the PAH degrading Arthrobacter sp. strain Sphe3. Appl. Microbiol. Biotechnol. 2007, 76:709-717.
35. Kosaric N. Biosurfactants and their application for soil bioremediation. Food Technol. Biotechnol. 2001, 39:295-304.
36. Labud V., Garcia C., Hernandez T. Effect of hydrocarbon pollution on the microbial properties of a sandy and a clay soil. Chemosphere 2007, 66:1863-1871.
37. Madueño L., Alvarez H., Morelli I. Autochthonous bioaugmentation to enhance phenanthrene degradation in soil microcosms under arid conditions. Int. J. Environ. Sci. Technol. 2015, 12:2317-2326.
38. Madueño L., Coppotelli B., Alvarez H., Morelli I. Isolation and characterization of indigenous soil bacteria for bioaugmentation of PAH contaminated soil of semiarid Patagonia, Argentina. Int. Biodeterior. Biodegrad. 2011, 65:345-351.
39. Mrozik A., Piotrowska-Seget Z. Bioaugmentation as a strategy for cleaning up of soils contaminated with aromatic compounds. Microbiol. Res. 2010, 165:363-375.
40. Muckian L.M., Grant R.J., Clipson N.J., Doyle E.M. Bacterial community dynamics during bioremediation of phenanthrene-and fluoranthene-amended soil. Int. Biodeterior. Biodegrad. 2009, 63:52-56.
41. Mukherjee A.K., Bordoloi N.K. Bioremediation and reclamation of soil contaminated with petroleum oil hydrocarbons by exogenously seeded bacterial consortium: a pilot-scale study. Environ. Sci. Pollut. Res. 2011, 18:471-478.
42. Muratova A., Pozdnyakova N., Makarov O., Baboshin M., Baskunov B., Myasoedova N., Golovleva L., Turkovskaya O. Degradation of phenanthrene by the rhizobacterium Ensifer meliloti. Biodegradation 2014, 25:787-795.
43. Muyzer G., Brinkahoff T., Nübel U., Santegoedes C., Schäfer H., Wawer C. Denaturing gradient electrophoresis (DGGE) in microbial ecology. Molecular Microbial Ecology Manual 1998, 1-27. Kluwer Academic Press, Dordretch. A. Akkermanns, J. Van Elsas, F. deBrujin (Eds.).
44. Muyzer G., de Waal E.C., Uitterlinden A.G. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 1993, 59:695-700.
45. Neuwirth, E. 2014. RColorBrewer: ColorBrewer palettes. R package version 1.1-2. http://CRAN.R-project.org/package=RColorBrewer.
46. Patel V., Jain S., Madamwar D. Naphthalene degradation by bacterial consortium (DV-AL) developed from Alang-Sosiya ship breaking yard, Gujarat, India. Bioresour. Technol. 2012, 107:122-130.
47. Pearson, E., 1926. Review of Statistical Methods for Research Workers (R.A. Fisher), First edition, Sci. Prog., 20, 733-734.
48. Perez-Pantoja D., De la Iglesia R., Pieper D., Gonzalez B. Metabolic reconstruction of aromatic compounds degradation from the genome of the amazing pollutant-degrading bacterium Cupriavidus necator JMP134. FEMS Microbiol. Rev. 2008, 32:736-794.
49. Poder Ejecutivo Nacional, Ley Nacional 24051, 1992. Residuos Peligrosos, generación, manipulación, transporte y tratamiento., República Argentina. Decreto Reglamentario 831. Boletín Oficial 03/01/1993.
50. Puglisi E., Cappa F., Fragoulis G., Trevisan M., Del Re A.A. Bioavailability and degradation of phenanthrene in compost amended soils. Chemosphere 2007, 67:548-556.
51. Reasoner D., Geldreich E. A new medium for the enumeration and subculture of bacteria from potable water. Appl. Environ. Microbiol. 1985, 49:1-7.
52. Samanta S.K., Singh O., Jain R.K. Polycyclic aromatic hydrocarbons: environmental pollution and bioremediation. Trends Biotechnol. 2002, 20:243-248.
53. Seo J.-S., Keum Y.-S., Li Q.X. Bacterial degradation of aromatic compounds. Int. J. Res. Public Health 2009, 6:278-309.
54. Simarro R., Gonzalez N., Bautista L.F., Molina M.C. Assessment of the efficiency of in situ bioremediation techniques in a creosote polluted soil: change in bacterial community. J. Hazard Mater. 2013, 262:158-167.
55. Sun M.Y., Dafforn K.A., Johnston E.L., Brown M.V. Core sediment bacteria drive community response to anthropogenic contamination over multiple environmental gradients. Environ. Microbiol. 2013, 15:2517-2531.
56. Sutton N.B., Maphosa F., Morillo J.A., Al-Soud W.A., Langenhoff A.A., Grotenhuis T., Rijnaarts H.H., Smidt H. Impact of long-term diesel contamination on soil microbial community structure. Appl. Environ. Microbiol. 2013, 79:619-630.
57. Szulc A., Ambroz˙ewicz D., Sydow M., Ławniczak Ł., Piotrowska-Cyplik A., Marecik R., Chrzanowski Ł. The influence of bioaugmentation and biosurfactant addition on bioremediation efficiency of diesel-oil contaminated soil: feasibility during field studies. J. Environ. Manag. 2014, 132:121-128.
58. Tamaki H., Wright C., Li X., Lin Q., Hwang C., Wang S., Thimmapuram J., Kamagata Y., Liu W.-T. Analysis of 16S rRNA amplicon sequencing options on the roche/454 next-generation titanium sequencing platform. PLoS One 2011, 6.
59. Tamura K., Dudley J., Nei M., Kumar S. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 2007, 24:1596-1599.
60. Tyagi M., da Fonseca M.M.R., de Carvalho C.C. Bioaugmentation and biostimulation strategies to improve the effectiveness of bioremediation processes. Biodegradation 2011, 22:231-241.
61. Vecchioli G., Del Panno M., Painceira M. Use of selected autochthonous soil bacteria to enhanced degradation of hydrocarbons in soil. Environ. Pollut. 1990, 67:249-258.
62. Wang B., Lai Q., Cui Z., Tan T., Shao Z. A pyrene degrading consortium from deep sea sediment of the West Pacific and its key member Cycloclasticus sp. P1. Environ. Microbiol. 2008, 10:1948-1963.
63. Wrenn B.A., Venosa A.D. Selective enumeration of aromatic and aliphatic hydrocarbon degrading bacteria by a most-probable-number procedure. Can. J. Microbiol. 1996, 42:252-258.
64. Xie S., Sun W., Luo C., Cupples A.M. Novel aerobic benzene degrading microorganisms identifiedin three soils by stable isotope probing. Biodegradation 2011, 22-71.