Modifications of bacterial populations in anthracene contaminated soil

Applied Soil Ecology

Volumn 61, Issue , 2012, Pages 113-126

  Núñez, Edgar Vázquez ^a   Valenzuela Encinas, César ^a   Alcántara Hernández, Rocio J ^a   Navarro Noya, Yendi E ^a   Luna Guido, Marco ^a   Marsch, Rodolfo ^a   Dendooven, Luc ^a  

^a Laboratory of Soil Ecology   (Mexico)

Author keywords

Aerobic incubation; Bacterial groups; Phylogenetic analysis; Soil profiles

Indexed keywords

ACIDOBACTERIA; ACTINOBACTERIA; ALPHAPROTEOBACTERIA; BACTERIA (MICROORGANISMS); BURKHOLDERIALES; CHLOROFLEXI; CHLOROFLEXI (CLASS); GAMMAPROTEOBACTERIA; GEMMATIMONADETES; NITROSPIRAE; PROTEOBACTERIA; SPHINGOMONADALES; UNCLASSIFIED BACTERIA; XANTHOMONADALES;

EID: 84864037256     PISSN: 09291393     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.apsoil.2012.04.005     Document Type: Article

References (66)

1. Abed R.M.M., Safi N.M.D., Köster J., De Beer D., El-Nahhal Y., Rullkötter J., Garcia-Pichel F. Microbial diversity of a heavily polluted microbial mat and its community changes following degradation of petroleum compounds. Appl. Environ. Microbiol. 2002, 68:1674-1683.
2. Adkins A. Degradation of the phenoxy acid herbicide diclofop-methyl by Sphingomonas paucimobilis isolated from a Canadian prairie soil. J. Ind. Microbiol. Biotechnol. 1999, 4:332-335.
3. Alfano J.R., Collmer A. Bacterial pathogens in plants: life up against the wall. Plant Cell 1996, 8:1683-1698.
4. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25:3389-3402.
5. Ayyasamy P.M., Chun S., Sanghoon L. Desorption and dissolution of heavy metals from contaminated soil using Shewanella sp. (HN-41) amended with various carbon sources and synthetic soil organic matters. J. Hazard. Mater. 2009, 161:1095-1102.
6. Ballard R.W., Palleroni N.J., Doudoroff M., Stanier R.Y., Mandel M. Taxonomy of the aerobic pseudomonads: Pseudomonas cepacia, P. marginata, P. alliicola and P. caryophylli. J. Gen. Microbiol. 1970, 60:199-214.
7. Balser T., Kinzing A., Firestone M. The functional consequences of biodiversity. The Functional Consequences of Biodiversity 2002, 265-293. Princeton University Press, Princeton. A. Kinzing, S. Pacala, D. Tilman (Eds.).
8. Barns S.M., Cain E.C., Sommerville L., Kuske C.R. Acidobacteria phylum sequences in uranium-contaminated subsurface sediments greatly expand the known diversity within the phylum. Appl. Environ. Microbiol. 2007, 73:3113-3116.
9. Bashan Y. Field dispersal of Pseudomonas syringae pv. Tomato, Xanthomonas campestris pv. Vesicatoria, and Alternarioa macrospora by animals, people, birds, insects, mites, agricultural tools, aircraft, soil particles, and water sources. Can. J. Bot. 1986, 64:276-281.
10. Basta T., Buerger S., Stolz A. Structural and replicative diversity of large plasmids from sphingomonads that degrade polycyclic aromatic compounds and xenobiotics. Microbiology 2005, 151:2025-2037.
11. Betancur-Galvis L.A., Alvarez-Bernal D., Ramos-Valdivia A.C., Dendooven L. Bioremediation of polycyclic aromatic hydrocarbon-contaminates saline-alkaline soil of the former Lake Texcoco. Chemosphere 2006, 62:1749-1760.
12. Bowman J.P., McMeekin A.T. Alteromonadales ord. nov. The Proteobacteria. Part B: The Gammaproteobacteria 2007, vol. 2. second ed.
13. Bozal N., Montes M.J., Tudela E., Jimenez F., Guinea J. Shewanella frigidimarina and Shewanella livingstonensis sp. nov. isolated from Antarctic coastal areas. Int. J. Syst. Evol. Microbiol. 2002, 52:195-205.
14. Brodkorb T.S., Legge R.L. Enhanced biodegradation of phenanthrene in soil tar-contaminated soils supplemented with Phanerochate chrysosporium. Appl. Environ. Microbiol. 1992, 58:3117-3121.
15. Cai Q.-Y., Mo C.-H., Li Y.-H., Zeng Q.-Y., Katsoyiannis A., Wu Q.-T., Férard J.-F. Occurrence and assessment of polycyclic aromatic hydrocarbons in soils from vegetable fields of the Pearl River Delta, South China. Chemosphere 2007, 68:159-168.
16. Cassidy M.B., Lee H., Trevors J.T., Zablotowicz R.B. Chlorophenol and nitrophenol metabolism by Sphingomonas sp. UG30. J. Ind. Microbiol. Biotechnol. 1999, 23:232-241.
17. Contreras-Ramos S.M., álvarez-Bernal D., Dendooven L. Removal of polycyclic aromatic hydrocarbons from soil amended with biosolid or vermicompost in the presence of earthworms (Eisenia fetida). Soil Biol. Biochem. 2008, 40:1954-1959.
18. Crawford R.L., Ederer M.M. Phylogeny of Sphingomonas species that degrade pentachlorophenol. J. Ind. Microbiol. Biotechnol. 1999, 4:320-325.
19. Diezel E., Paquette G., Villemur R., Lepine F., Bisaillon J. Biosurfactant production by a soil Pseudomonas strain growing on polycyclic aromatic hydrocarbons. Appl. Environ. Microbiol. 1996, 62:1908-1912.
20. Edwards U., Rogall T., Blocker H., Emde M., Bottger E. Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Res. 1989, 17:7843-7853.
21. Ellis R.J., Morgan P., Weightman A.J., Fry J.C. Cultivation-dependent and -independent approaches for determining bacterial diversity in heavy-metal-contaminated soil. Appl. Environ. Microbiol. 2003, 69:3223-3230.
22. Eriksson M., Dalhammar G., Borg-Karlson A.-K. Biological degradation of selected hydrocarbons in an old PAH/creosote contaminated soil from a gas work site. Appl. Microbiol. Biotechnol. 2007, 53:619-626.
23. Felske A., de Vos W.M., Akkermans A.D.L. Spatial distribution of 16S rRNA levels from uncultured acidobacteria in soil. Lett. Appl. Microbiol. 2000, 31:18-122.
24. Fierer N., Schimel J.P., Holden P.A. Variations in microbial community composition through two soil depth profiles. Soil Biol. Biochem. 2003, 35:167-176.
25. Fontaine S., Mariotti A., Abbadie L. The priming effect of organic matter: a question of microbial competition?. Soil Biol. Biochem. 2003, 35:837-843.
26. Ganzert L., Lispki A., Hubberten H.W., Wagner D. The impact of different soil parameters on the community structure of dominant bacteria from nine different soils located on Livingston Island, South Shetland Archipelago, Antarctica. FEMS Microbiol. Ecol. 2011, 76:476-491.
27. Gentile G., Bonaseram V., Amico C., Giuliano L., Yakimov M.M. Shewanella sp. GA-22, a psychrophilic hydrocarbonoclastic antarctic bacterium producing polyunsaturated fatty acids. J. Appl. Microbiol. 2003, 95:1124-1133.
28. Gremion F., Chatzinotas A., Harms H. Comparative 16S rDNA and 16S rRNA sequence analysis indicates that Actinobacteria might be a dominant part of the metabolically active bacteria in heavy metal-contaminated bulk and rhizosphere soil. Environ. Microbiol. 2003, 5:896-907.
29. Griffiths B.S., Ritz K., Ebblewhite N., Dobson G. Soil microbial community structure. Soil Biol. Biochem. 1998, 31:145-153.
30. Guindon S., Gascuel O. PhyML - a simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 2003, 52:696-704.
31. Guo C., Sun W., Harsh J.B., Ogram A. Hybridization analysis of microbial DNA from fuel oil-contaminated and noncontaminated soil. Microb. Ecol. 1997, 34:178-187.
32. Hernandez-Raquet G., Buzinski H., Caumette P., Dabert P., Le Ménach K., Muyzer G., Duran R. Molecular diversity studies of bacterial communities of oil polluted mats from Etang de Berre (France). FEMS Microbiol. Ecol. 2006, 58:550-562.
33. Hugenholtz P., Goebel B.M., Pace N.R. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 1998, 180:4765-4774.
34. IARC (International Agency for Research on Cancer) Monographs on the evaluation of carcinogenic risk of clinical to humans. Polynuclear Aromatic Compounds. Part I Chemical, Environmental and Experimental Data 1983, vol. 3. International Agency for Research of Cancer, IARC Press, France.
35. Janssen P.H. Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl. Environ. Microbiol. 2006, 72:1719-1728.
36. 14C-labeled anthracene and hexadecane in compost-manured soil. Appl. Microbiol. Biotechnol. 1995, 43:1128-1135.
37. Kumar S., Tamura K., Jakobsen I., Nei M. MEGA 2: Molecular Evolutionary Genetics Analysis Software 2001, Arizona State University, Tempe.
38. Lande R., DeVries P.J., Walla T. When species accumulation curves intersect: implications for ranking diversity using small samples. Oikos 2000, 89:601-605.
39. Lafortune I., Juteau P., Déziel E., Lépine F., Beaudet R., Villemur R. Bacterial diversity of a consortium degrading high-molecular-weight polycyclic aromatic hydrocarbons in a two-liquid phase biosystem. Microb. Ecol. 2009, 57:455-468.
40. Li G., Huang W., Lerner D.N., Zhang X. Enrichment of degrading microbes and bioremediation of petrochemical contaminants in polluted soil. Water Res. 2000, 34:3845-3853.
41. Lin Y.T., Jangid K., Whitman W.B., Coleman D.C., Chiu C.Y. Soil bacterial communities in native and regenerated perhumid montane forests. Appl. Soil Ecol. 2011, 47:111-118.
42. Leys N.M.E.J., Ryngaert A., Bastiaens L., Verstraete W., Top E.M., Springael D. Occurrence and phylogenetic diversity of Sphingomonas strain in soil contaminated with polycyclic aromatic hydrocarbons. Appl. Environ. Microbiol. 2004, 70:1944-1955.
43. Magurran A.E. Measuring Biological Diversity 2004, Blackwell Publishing, 256 pp.
44. Mutnuri S., Vasudevan N., Kaestner M. Degradation of anthracene and pyrene supplied by microcrystals and non-aqueous-phase liquids. Appl. Environ. Microbiol. 2005, 67:569-576.
45. 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.
46. Nacke H., Thurmer A., Wollherr A., Will C., Hodac L., Herold N., Schoning I., Schrumpf M., Daniel R. Pyrosequencing-based assessment of bacterial community structure along different management types in German forest and grassland soils. PLoS One 2011, 6:e17000.
47. Nemergut D.R., Costello E.K., Hamady M., Lozupone C., Jiang L., Schmidt S.K., Fierer N., Townsend A.R., Cleveland C.C., Stanish L., Knight R. Global patterns in the biogeography of bacterial taxa. Environ. Microbiol. 2011, 13:135-144.
48. Nogales B., Moore E.R.B., Abraham W.R., Timmis K.N. Identification of the metabolically active members of a bacterial community in a polychlorinated byphenyl-polluted moorland soil. Environ. Microbiol. 1999, 1:199-212.
49. Paul E.A., Clark F.E. Soil Microbiology and Biochemistry 1989, Academic Press, San Diego.
50. Posada D. jModelTest: phylogenetic model averaging. Mol. Biol. Evol. 2008, 27:1253-1256.
51. Rohlf F.J. NTSYS-pc: numerical taxonomy and multivariate analysis system, version 2.01 2005, Applied Biostatistics, New York.
52. Rosello-Mora R., Amann R. The species concept for prokariotes. FEMS Microbiol. Rev. 2001, 25:39-67.
53. Russell N.J., Nichols D.S. Polyunsaturated fatty acids - a dogma rewritten. Microbiology 1999, 145:767-779.
54. SAS Institute SAS Institute, Statistic Guide for Personal Computers. Version 6.04 1989, SAS Institute, Cary.
55. Scelza R., Rao M.A., Gianfreda L. Effects of compost and bacterial cells on the decontamination and the chemical and biological properties of an agricultural soil artificially contaminated with phenantrene. Soil Biol. Biochem. 2007, 39:1303-1317.
56. Schloss P.D., Westcott S.L., Ryabin T., Hall J.R., Hartmann M., Hollister E.B., Lesniewski R.A., Oakley B.B., Parks D.H., Robinson C.J., Sahl J.W., Stres B., Thallinger G.G., Van Horn D.J., Weber C.F. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 2009, 75:7537-7541.
57. Stolz A. Molecular characteristics of xenobiotic-degrading sphingomonads. Appl. Microbiol. Biotechnol. 2009, 81:793-811.
58. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997, 25:4876-4882.
59. Ussiri A.N.D., Lal R. Long-term tillage effects n soil carbon storage and carbon dioxide emissions in continuous corn cropping system from an alfisol in Ohio. Soil Till. Res. 2009, 104:39-47.
60. Vandenbygaart A.J., Angers D.A. Towards accurate measurements of soil organic carbon stock change in agroecosystems. Can. J. Soil Sci. 2006, 86:465-471.
61. Valdez-Perez M.A., Fernández-Luqueño F., Franco-Hernandez O., Flores-Cotera L.B., Dendooven L. Cultivation of beans (Phaseolus vulgaris L.) in limed or unlimed wastewater sludge, vermicompost or inorganic amended soil. Sci. Hortic. Amsterdam 2011, 128:380-387.
62. Valenzuela-Encinas C., Neria-González I., Alcántara-Hernández R., Enríquez-Aragón J., Estrada-Alvarado I., Hernández-Rodríguez C., Dendooven L., Marsch R. Phylogenetic analysis of the archael community in an alkaline-saline soil of the former lake Texcoco (Mexico). Extremophiles 2008, 12:247-254.
63. Valenzuela-Encinas C., et al. Phylogenetic analysis of the archaeal community in an alkaline-saline soil of the former lake Texcoco (Mexico). Extremophiles 2009, 12:247-254.
64. Vázquez Núñez E., García-Gaytán A., Luna-Guido M., Marsch R., Dendooven L. Impact of moisture dynamic and sun light on anthracene removal from soil. Biodegradation 2009, 20:191-198.
65. Viñas M., Sabaté J., Espuny M.E., Solanas A.M. Bacterial community dynamics and polycyclic aromatic hydrocarbon degradation during bioremediation of heavily creosote-contaminated soil. Appl. Environ. Microbiol. 2005, 71:7008-7018.
66. Yu Z., Morrison M. Comparisons of different hypervariable regions of rrs genes for use in fingerprint of microbial communities by PCR-denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 2004, 70:4800-4806.