The microbiota of an unpolluted calcareous soil faces up chlorophenols: Evidences of resistant strains with potential for bioremediation

Chemosphere

Volumn 83, Issue 2, 2011, Pages 104-116

  Caliz, Joan ^a   Vila, Xavier ^a   Martí, Esther ^b   Sierra, Jordi ^b   Nordgren, Johan ^c   Lindgren, Per Eric ^c   Bañeras, Lluís ^a   Montserrat, Genoveva ^a  

^a UNIVERSITY OF GIRONA   (Spain)

^b UNIVERSITY OF BARCELONA   (Spain)

^c LINKÖPING UNIVERSITY   (Sweden)

Author keywords

Bacillus; Biodegradation; Chlorophenols; Microbial resistance; PCR DGGE; Respirometry

Indexed keywords

BACILLI; BACTERIA; BACTERIOLOGY; BIODEGRADATION; BIOREMEDIATION; BIOTECHNOLOGY; PHENOLS; POLYMERASE CHAIN REACTION; RNA; SOILS; TRANSMISSION CONTROL PROTOCOL;

2 ,4 ,6-TRICHLOROPHENOL; BACTERIAL COMMUNITY COMPOSITION; CHLOROPHENOLS; CONTROLLED LABORATORIES; MICROBIAL RESISTANCE; PCR-DGGE; POLLUTANT CONCENTRATION; RESPIROMETRY;

SOIL POLLUTION;

2 MONOCHLOROPHENOL; 2,4,6 TRICHLOROPHENOL; BACTERIAL DNA; BACTERIAL RNA; CHLOROPHENOL; PENTACHLOROPHENOL; RIBOSOME RNA; UNCLASSIFIED DRUG;

BACTERIUM; BIOCHEMICAL COMPOSITION; BIODEGRADATION; BIOREMEDIATION; CALCAREOUS SOIL; CHLOROPHENOL; ELECTROKINESIS; MEDITERRANEAN SOIL; MICROBIAL COMMUNITY; MICROCOSM; POLYMERASE CHAIN REACTION; SOIL MICROORGANISM; SOIL POLLUTION;

ADAPTATION; AGRICULTURAL LAND; ARTICLE; BACILLUS; BACTERIAL STRAIN; BACTERIAL SURVIVAL; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATION; BIOREMEDIATION; CONCENTRATION (PARAMETERS); KOCURIA PALUSTRIS; LYSOBACTER; LYSOBACTER GUMMOSUS; MICROBIAL COMMUNITY; MICROBIAL DEGRADATION; MICROBIAL POPULATION DYNAMICS; MICROCOSM; NONHUMAN; NUCLEOTIDE SEQUENCE; OXYGEN CONSUMPTION; PHYLOGENY; PSEUDOMONAS PUTIDA; SEQUENCE HOMOLOGY; SOIL MICROFLORA; SOIL POLLUTANT; SOIL POLLUTION; SOUTHERN EUROPE; UNINDEXED SEQUENCE;

BACILLUS (BACTERIUM); BACILLUS SP.; BACTERIA (MICROORGANISMS); KOCURIA PALUSTRIS; LYSOBACTER GUMMOSUS; PSEUDOMONAS PUTIDA;

EID: 79952103116     PISSN: 00456535     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.chemosphere.2011.01.016     Document Type: Article

References (73)

1. Andreoni V., Baggi G., Colombo M., Cavalca L., Zangrossi M., Bernasconi S. Degradation of 2,4,6-trichlorophenol by a specialized organism and by indigenous soil microflora: bioaugmentation and self-remediability for soil restoration. Lett. Appl. Microbiol. 1998, 27:86-92.
2. Baker G.C., Smith J.J., Cowan D.A. Review and re-analysis of domain-specific 16S primers. J. Microbiol. Meth. 2003, 55:541-555.
3. Barbeau C., Deschênes L., Karamanev D., Comeau Y., Samson R. Bioremediation of pentachlorophenol-contaminated soil by bioaugmentation using activated soil. Appl. Microbiol. Biotechnol. 1997, 48:745-752.
4. Beaulieu M., Bécaert V., Deschênes L., Villemur R. Evolution of bacterial diversity during enrichment of PCP-degrading activated soils. Microb. Ecol. 2000, 40:345-355.
5. Briggs A. The resistances of spores of the genus Bacillus to phenol, heat and radiation. J. Appl. Microbiol. 1966, 29:490-504.
6. Campbell J., Clark J., Zak J. PCR-DGGE comparison of bacterial community structure in fresh and archived soils sampled along a Chihuahuan Desert elevational gradient. Microb. Ecol. 2009, 57:261-266.
7. Cavalca L., Zanchi R., Corsini A., Colombo M., Romagnoli C., Canzi E., Andreoni V. Arsenic-resistant bacteria associated with roots of the wild Cirsium arvense (L.) plant from an arsenic polluted soil, and screening of potential plant growth-promoting characteristics. Syst. Appl. Microbiol. 2010, 33:154-164.
8. Chaudri A.M., Lawlor K., McGrath S.P. Pentachlorophenol utilization by indigenous soil microorganisms. Soil Biol. Biochem. 2000, 32:429-432.
9. Chen D., Chen J., Zhong W., Cheng Z. Degradation of methyl tert-butyl ether by gel immobilized Methylibium petroleiphilum PM1. Bioresour. Technol. 2008, 99:4702-4708.
10. Cho Y.G., Rhee1 S.K., Lee S.T. Effect of soil moisture on bioremediation of chlorophenol-contaminated soil. Biotechnol. Lett. 2000, 22:915-919.
11. Coello M.D., Barragán J., Aragón C., Quiroga J.M. A new approach to toxicity determination by respirometry. Environ. Technol. 2009, 30:1601-1605.
12. D'Angelo E., Reddy K.R. Aerobic and anaerobic transformations of pentachlorophenol in wetland soils. Soil Sci. Soc. Am. J. 2000, 64:933-943.
13. Dechesne A., Owsianiak M., Bazire A., Grundmann G., Binning P.J., Smets B.F. Biodegradation in a partially saturated sand matrix: compounding effects of water content, bacterial spatial distribution, and motility. Environ. Sci. Technol. 2010, 44:2386-2392.
14. Edenborn S.L., Sexstone A.J. DGGE fingerprinting of culturable soil bacterial communities complements culture-independent analyses. Soil Biol. Biochem. 2007, 39:1570-1579.
15. Elbanna K., Lütke-Eversloh T., Jendrossek D., Luftmann H., Steinbüchel A. Studies on the biodegradability of polythioester copolymers and homopolymers by polyhydroxyalkanoate (PHA)-degrading bacteria and PHA depolymerases. Arch. Microbiol. 2004, 182:212-225.
16. Evans F.F., Seldin L., Sebastian G.V., Kjelleberg S., Holmström C., Rosado A.S. Influence of petroleum contamination and biostimulation treatment on the diversity of Pseudomonas spp. in soil microcosms as evaluated by 16S rRNA based-PCR and DGGE. Lett. Appl. Microbiol. 2004, 38:93-98.
17. FAO-UNESCO (Ed.), 1998. FAO-UNESCO. World Reference Base for Soil Resources. FAO-UNESCO, Rome.
18. Felske A., Akkermans A.D.L. Spatial homogeneity of abundant bacterial 16S rRNA molecules in grassland soils. Microb. Ecol. 1998, 36:31-36.
19. Field J., Sierra-Alvarez R. Microbial degradation of chlorinated phenols. Rev. Environ. Sci. Biot. 2008, 7:211-241.
20. Francisco, R., Moreno, A., Morais, P., 2010. Different Physiological Responses to Chromate and Dichromate in the Chromium Resistant and Reducing Strain Ochrobactrum tritici 5bvl1. BioMetals.
21. Gautam S.K., Sharma R., Ahmad A.H., Thakur I.S. Evaluation of pentachlorophenol-degrading potentiality of Pseudomonas sp. in a soil microcosm. World J. Microb. Biot. 2003, 19:73-78.
22. Girvan M.S., Bullimore J., Pretty J.N., Osborn A.M., Ball A.S. Soil type is the primary determinant of the composition of the total and active bacterial communities in arable soils. Appl. Environ. Microbiol. 2003, 69:1800-1809.
23. Gribble G.W. The natural production of chlorinated compounds. Environ. Sci. Technol. 1994, 28:310A-319A.
24. Haggblom M.M., Nohynek L.J., Salkinoja-Salonen M.S. Degradation and O-methylation of chlorinated phenolic compounds by Rhodococcus and Mycobacterium strains. Appl. Environ. Microbiol. 1988, 54:3043-3052.
25. Hanson J.R., Ackerman C.E., Scow K.M. Biodegradation of methyl tert-butyl ether by a bacterial pure culture. Appl. Environ. Microbiol. 1999, 65:4788-4792.
26. Hilyard E.J., Jones-Meehan J.M., Spargo B.J., Hill R.T. Enrichment, isolation, and phylogenetic identification of polycyclic aromatic hydrocarbon-degrading bacteria from Elizabeth River sediments. Appl. Environ. Microbiol. 2008, 74:1176-1182.
27. Huber T., Faulkner G., Hugenholtz P. Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 2004, 20:2317-2319.
28. Karn S., Chakrabarti S., Reddy M. Degradation of pentachlorophenol by Kocuria sp. CL2 isolated from secondary sludge of pulp and paper mill. Biodegradation 2010, 1-7.
29. Kerkhof L., Kemp P. Small ribosomal RNA content in marine Proteobacteria during non-steady-state growth. FEMS Microbiol. Ecol. 1999, 30:253-260.
30. Kharoune L., Kharoune M., Lebeault J.M. Aerobic degradation of 2,4,6-trichlorophenol by a microbial consortium - selection and characterization of microbial consortium. Appl. Microbiol. Biotechnol. 2002, 59:112-117.
31. Kiyohara H., Hatta T., Ogawa Y., Kakuda T., Yokoyama H., Takizawa N. Isolation of Pseudomonas pickettii strains that degrade 2,4,6-trichlorophenol and their dechlorination of chlorophenols. Appl. Environ. Microbiol. 1992, 58:1276-1283.
32. Lane D.J. 16S/23S r RNA sequencing. Nucleic Acid Techniques in Bacterial Systematics 1991, John Wiley, Chichester, England. E. Stackebrant, M. Goodfellow (Eds.).
33. Ludwig W., Strunk O., Westram R., Richter L., Meier H., Yadhukumar, Buchner A., Lai T., Steppi S., Jobb G., Forster W., Brettske I., Gerber S., Ginhart A.W., Gross O., Grumann S., Hermann S., Jost R., Konig A., Liss T., Lussmann R., May M., Nonhoff B., Reichel B., Strehlow R., Stamatakis A., Stuckmann N., Vilbig A., Lenke M., Ludwig T., Bode A., Schleifer K.H. ARB: a software environment for sequence data. Nucl. Acids Res. 2004, 32:1363-1371.
34. Mahmood S., Paton G., Prosser J. Cultivation-independent in situ molecular analysis of bacteria involved in degradation of pentachlorophenol in soil. Environ. Microbiol. 2005, 7:1349-1360.
35. Männistö M.K., Tiirola M.A., Salkinoja-Salonen M.S., Kulomaa M.S., Puhakka J.A. Diversity of chlorophenol-degrading bacteria isolated from contaminated boreal groundwater. Arch. Microbiol. 1999, 171:189-197.
36. Martí E., Sierra J., Sánchez M., Cruañas R., Garau M.A. Ecotoxicological tests assessment of soils polluted by chromium (VI) or pentachlorophenol. Sci. Total Environ. 2007, 378:53-57.
37. McAllister K.A., Lee H., Trevors J.T. Microbial degradation of pentachlorophenol. Biodegradation 1996, 7:1-40.
38. McCaig A.E., Glover L.A., Prosser J.I. Numerical analysis of grassland bacterial community structure under different land management regimens by using 16S Ribosomal DNA sequence data and denaturing gradient gel electrophoresis banding patterns. Appl. Environ. Microbiol. 2001, 67:4554-4559.
39. McGrath R., Singleton I. Pentachlorophenol transformation in soil: a toxicological assessment. Soil Biol. Biochem. 2000, 32:1311-1314.
40. Mitsevich E.V., Mitsevich I.P., Perelygin V.V. Microbial destructors of certain chlorinated organics. Appl. Biochem. Microbiol. 2000, 36:555-558.
41. Montserrat G., Martí E., Sierra J., Garau M.A., Cruañas R. Discriminating inhibitory from enhancing effects in respirometry assays from metal polluted-sewage sludge amended soils. Appl. Soil Ecol. 2006, 34:52-61.
42. Muyzer G., Smalla K. Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie van Leeuwenhoek Int. J. G 1998, 73:127-141.
43. 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.
44. Muyzer G., Teske A., Wirsen C., Jannasch H. Phylogenetic relationships of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments. Arch. Microbiol. 1995, 164:165-172.
45. Nakatsu C.H., Hristova K., Hanada S., Meng X.Y., Hanson J.R., Scow K.M., Kamagata Y. Methylibium petroleiphilum gen. nov., sp. nov., a novel methyl tert-butyl ether-degrading methylotroph of the Betaproteobacteria. Int. J. Syst. Evol. Microbiol. 2006, 56:983-989.
46. Nicol G.W., Webster G., Glover L.A., Prosser J.I. Differential response of archaeal and bacterial communities to nitrogen inputs and pH changes in upland pasture rhizosphere soil. Environ. Microbiol. 2004, 6:861-867.
47. 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 biphenyl-polluted moorland soil. Environ. Microbiol. 1999, 1:199-212.
48. Nogales B., Moore E.R.B., Llobet-Brossa E., Rossello-Mora R., Amann R., Timmis K.N. Combined use of 16S ribosomal DNA and 16S rRNA to study the bacterial community of polychlorinated biphenyl-polluted soil. Appl. Microbiol. Biotechnol. 2001, 67:1874-1884.
49. Nordin K., Unell M., Jansson J.K. Novel 4-chlorophenol degradation gene cluster and degradationroute via hydroxyquinol in Arthrobacter chlorophenolicus A6. Appl. Environ. Microbiol. 2005, 71:6538-6544.
50. OECD, 2000. OECD Guidelines for the Testing of Chemicals. Soil Microorganisms: Carbon Transformation Test, p. 217.
51. Otte M.P., Gagnon J., Comeau Y., Matte N., Greer C.W., Smason R. Activation of an indigenous microbial consortium for bioaugmentation of pentachlorophenol/creosate contaminated soils. Appl. Microbiol. Biotechnol. 1994, 40:926-932.
52. Plaza G., Ulfig K., Worsztynowicz A., Malina G., Krzeminska B., Brigmon R.L. Respirometry for assessing the biodegradation of petroleum hydrocarbons. Environ. Technol. 2005, 26:161-170.
53. Prat C., Ruiz-Rueda O., Trias R., Antico E., Capone D., Sefton M., Baneras L. Molecular fingerprinting by PCR-denaturing gradient gel electrophoresis reveals differences in the levels of microbial diversity for musty-earthy tainted corks. Appl. Environ. Microbiol. 2009, 75:1922-1931.
54. Pruesse E., Quast C., Knittel K., Fuchs B.M., Ludwig W., Peplies J., Glockner F.O. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucl. Acids Res. 2007, 35:7188-7196.
55. Pu X., Cutright T. Degradation of pentachlorophenol by pure and mixed cultures in two different soils. Environ. Sci. Pollut. R 2007, 14:244-250.
56. Radehaus P.M., Schmidt S.K. Characterization of a novel Pseudomonas sp. that mineralizes high concentrations of pentachlorophenol. Appl. Microbiol. Biotechnol. 1992, 58:2879-2885.
57. Resnick S.M., Chapman P.J. Physiological properties and substrate specificity of a pentachlorophenol-degrading Pseudomonas species. Biodegradation 1994, 5:47-54.
58. Ruckdeschel G., Renner G., Schwarz K. Effects of pentachlorophenol and some of its known and possible metabolites on different species of bacteria. Appl. Microbiol. Biotechnol. 1987, 53:2689-2692.
59. Russell A.D. Bacterial spores and chemical sporicidal agents. Clin. Microbiol. Rev. 1990, 3:99-119.
60. Saber D.L., Crawford R.L. Isolation and characterization of Flavobacterium strains that degrade pentachlorophenol. Appl. Microbiol. Biotechnol. 1985, 50:1512-1518.
61. Sagripanti J., Bonifacino A. Comparative sporicidal effects of liquid chemical agents. Appl. Environ. Microbiol. 1996, 62:545-551.
62. Sanchez M.A., Vasquez M., Gonzalez B. A previously unexposed forest soil microbial community degrades high levels of the pollutant 2,4,6-trichlorophenol. Appl. Microbiol. Biotechnol. 2004, 70:7567-7570.
63. Shah S., Thakur I.S. Enrichment and characterization of a microbial community from tannery effluent for degradation of pentachlorophenol. World J. Microbiol. Biotechnol. 2002, 18:693-698.
64. Stanlake G.J., Finn R.K. Isolation and characterization of a pentachlorophenol-degrading bacterium. Appl. Environ. Microbiol. 1982, 44:1421-1427.
65. Steiert J.G., Pignatello J.J., Crawford R.L. Degradation of chlorinated phenols by a pentachlorophenol-degrading bacterium. Appl. Microbiol. Biotechnol. 1987, 53:907-910.
66. 2 evolution test and a multicomponent biodegradation test system. Appl. Environ. Microbiol. 2004, 70:4621-4628.
67. Utkin I., Dalton D., Wiegel J. Specificity of reductive dehalogenation of substituted ortho- chlorophenols by Desulfitobacterium dehalogenans JW/IU-DC1 [published erratum appears in Appl Environ Microbiol 1995 Apr;61(4):1677]. Appl Environ Microbiol 1995, 61:346-351.
68. Van Agteren M.H., Keuning S., Janssen D.B. Handbook on Biodegradation and Biological Treatment of Hazardous Organic Compounds 1998, Kluwer Academic Publishers, London.
69. Vrdoljak G., Feil W.S., Feil H., Detter J.C., Fields P. Characterization of a diesel sludge microbial consortia for bioremediation. Scanning 2005, 27:8-14.
70. Wagner R. The regulation of ribosomal RNA synthesis and bacterial cell growth. Arch. Microbiol. 1994, 161:100-109.
71. Wang, G.L., Wang, L., Chen, H.H., Shen, B., Li, S.P., Jiang, J.D., 2010. Lysobacter ruishenii sp. nov., a chlorothalonil-degrading bacterium isolated from a long-term chlorothalonil-contaminated soil in China. Int J Syst Evol Microbiol ijs.0.020990-020990.
72. Wu S., Zhang L., Wang J., Chen J. Bacillus circulans WZ-12-a newly discovered aerobic dichloromethane-degrading methylotrophic bacterium. Appl. Microbiol. Biotechnol. 2007, 76:1289-1296.
73. Yang C.F., Lee C.M., Wang C.C. Isolation and physiological characterization of the pentachlorophenol degrading bacterium Sphingomonas chlorophenolica. Chemosphere 2006, 62:709-714.