Acinetobacter diversity in environmental samples assessed by 16S rRNA gene PCR-DGGE fingerprinting

FEMS Microbiology Ecology

Volumn 50, Issue 1, 2004, Pages 37-50

  Vanbroekhoven, Karolien ^a,b   Ryngaert, Annemie ^a   Wattiau, Pierre ^c   De Mot, René ^b   Springael, Dirk ^a,b  

^a Environmental and Process Technology   (Belgium)

^b UNIVERSITY OF LEUVEN   (Belgium)

^c UNIVERSITÉ CATHOLIQUE DE LOUVAIN   (Belgium)

Author keywords

Acinetobacter sp. diversity; DGGE fingerprinting; Genus specific PCR; Hydrocarbon contaminated soil

Indexed keywords

BACTERIAL DNA; BACTERIAL RNA; GENE PRODUCT; HYDROCARBON; KEROSENE; MINERAL OIL; RNA 16S;

BACTERIUM; MICROBIAL COMMUNITY; POLYMERASE CHAIN REACTION; SPECIES DIVERSITY;

ACINETOBACTER; ACINETOBACTER JOHNSONII; ACINETOBACTER LWOFFII; AMPLICON; ARTICLE; BACTERIAL FLORA; BACTERIUM; BACTERIUM DETECTION; CONTAMINATION; CONTROLLED STUDY; DENATURING GRADIENT GEL ELECTROPHORESIS; LABORATORY; MICROBIAL DIVERSITY; MOLECULAR CLONING; MONITORING; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RNA SEQUENCE; SENSITIVITY ANALYSIS; SOIL;

ACINETOBACTER; BIODIVERSITY; CLUSTER ANALYSIS; DNA FINGERPRINTING; DNA PRIMERS; DNA, BACTERIAL; DNA, RIBOSOMAL; ELECTROPHORESIS, POLYACRYLAMIDE GEL; ENVIRONMENTAL MICROBIOLOGY; GENES, RRNA; MOLECULAR SEQUENCE DATA; NUCLEIC ACID DENATURATION; PHYLOGENY; POLYMERASE CHAIN REACTION; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, DNA;

ACINETOBACTER; ACINETOBACTER JOHNSONII; ACINETOBACTER LWOFFII; ACINETOBACTER SP.; BACTERIA (MICROORGANISMS);

EID: 4644346316     PISSN: 01686496     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.femsec.2004.05.007     Document Type: Article

References (44)

1. Pantophlet R., Severin J.A., Nemec A., Brade L., Dijkshoorn L., Brade H. Identification of Acinetobacter isolates from species belonging to the Acinetobacter calcoaceticus Acinetobacter baumannii complex with monoclonal antibodies specific for O antigens of their lipopolysaccharides. Clin. Diagn. Lab. Immunol. 9:2002;60-65
2. Wagner M., Erhart R., Manz W., Amann R., Lemmer H., Wedi D., Schleifer K. Development of an rRNA-targeted oligonucleotide probe specific for the genus Acinetobacter and its application for in situ monitoring in activated sludge. Appl. Environ. Microbiol. 60:1994;792-800
3. Rosenberg E., Zuckerberg A., Rubinovitz C., Gutnick D.L. Emulsifier of Arthrobacter RAG-1: isolation and emulsifying properties. Appl. Environ. Microbiol. 37:1979;402-408
4. Tani A., Ishige T., Sakai Y., Kato N. Gene structures and regulation of the alkane hydroxylase complex in Acinetobacter sp. strain M-1. J. Bacteriol. 183:2001;1819-5827
5. Koma D., Hasumi F., Yamamoto E., Ohta T., Chung S.-Y., Kubo M. Biodegradation of long-chain n-paraffins from waste oil of car engine by Acinetobacter sp. J. Biosci. Bioeng. 91:2001;94-96
6. Di Cello F., Pepi M., Baldi F., Fani R. Molecular characterization of an n-alkane-degrading bacterial community and identification of a new species, Acinetobacter venetianus. Res. Microbiol. 148:1997;237-249
7. Caposio P., Pessione E., Giuffrida G., Conti A., Landolfo S., Giunta C., Gribaudo G. Cloning and characterization of two catechol 1,2-dioxygenase genes from Acinetobacter radioresistens S13. Res. Microbiol. 153:2002;69-74
8. Navon-Venezia S., Zosim Z., Gottlieb A., Legmann R., Carmeli S., Ron E., Rosenberg E. Alasan, a new bioemulsifier from Acinetobacter radioresistens. Appl. Environ. Microbiol. 61:1995;3240-3244
9. Toren A., Navon-Venezia S., Ron E.Z., Rosenberg E. Emulsifying activities of purified alasan proteins from Acinetobacter radioresistens KA53. Appl. Environ. Microbiol. 67:2001;1102-1106
10. Barkay T., Navon-Venezia S., Ron E.Z., Rosenberg E. Enhancement of solubilization and biodegradation of polyaromatic hydrocarbons by the bioemulsifier alasan. Appl. Environ. Microbiol. 65:1999;2697-2702
11. Maeng J., Sakai Y., Tani Y., Kato N. Isolation and characterization of a novel oxygenase that catalyzes the first step of n-alkane oxidation in Acinetobacter sp. strain M-1. J. Bacteriol. 178:1996;3695-3700
12. Mishra S., Jyot J., Kuhad R.C., Lal B. Evaluation of inoculum addition to stimulate in situ bioremediation of oily-sludge-contaminated soil. Appl. Environ. Microbiol. 67:2001;1675-1681
13. Gallego J.L.R., Loredo J., Llamas J.F., Vazquez F., Sanchez J. Bioremediation of diesel-contaminated soils: evaluation of potential in situ techniques by study of bacterial degradation. Biodegradation. 12:2001;325-335
14. Ishige T., Tani A., Sakai Y., Kato N. Long-chain aldehyde dehydrogenase that participates in n-alkane utilization and wax ester synthesis in Acinetobacter sp. strain M-1. Appl. Environ. Microbiol. 66:2000;3481-3486
15. Mergeay M. Heavy metal resistances in microbial ecosystems. Akkermans A.D.L., Van Elsas J.D., de Bruijn F.J. Molecular Microbial Ecology Manual. vol. 6.1.7:1995;1-17 Kluwer Academic Publishers
16. Bastiaens L., Springael D., Wattiau P., Harms H., De Wachter R., Verachtert H., Diels L. Isolation of adherent polycyclic aromatic hydrocarbon (PAH)-degrading bacteria using PAH-sorbing carriers. Appl. Environ. Microbiol. 66:2000;1834-1843
17. Krin E., Hommais F., Soutourina O., Ngo S., Danchin A., Bertin P. Description and application of a rapid method for genomic DNA direct sequencing. FEMS Microbiol. Lett. 199:2001;229-233
18. Boon N., Goris J., De P., Vos Verstraete W., Top E.M. Bioaugmentation of activated sludge by an indigenous 3-chloroaniline-degrading Comamonas testosteroni strain, I2gfp. Appl. Environ. Microbiol. 66:2000;2906-2913
19. Johnson J.L. Similarity analysis of rRNAs. Gerhardt R.G.E.M.P., Wood W.A., Krieg N.R. Methods for General and Molecular Bacteriology. 1994;683-700 ASM Press, Washington, DC
20. El Fantroussi S., Verschuere L., Verstraete W., Top E.M. Effect of phenylurea herbicides on soil microbial communities estimated by analysis of 16S rRNA gene fingerprints and community-level physiological profiles. Appl. Environ. Microbiol. 65:1999;982-988
21. Muyzer G., Dewaal 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 ribosomal RNA. Appl. Environ. Microbiol. 59:1993;695-700
22. Vaneechoutte M., Tjernberg I., Baldi F., Pepi M., Fani R., Sullivan E.R., Van Der Toorn J., Dijkshoorn L. Oil-degrading Acinetobacter strain RAG-1 and strains described as 'Acinetobacter venetianus sp. nov.' belong to the same genomic species. Res. Microbiol. 150:1999;69-73
23. Salles J.F., De Souza F.A., Van Elsas J.D. Molecular method to assess the diversity of Burkholderia species in environmental samples. Appl. Environ. Microbiol. 68:2002;1595-1603
24. Heilig H., Zoetendal E.G., Vaughan E.E., Marteau P., Akkermans A.D.L., de Vos W.M. Molecular diversity of Lactobacillus spp. and other lactic acid bacteria in the human intestine as determined by specific amplification of 16S ribosomal DNA. Appl. Environ. Microbiol. 68:2002;114-123
25. Rossi F., Torriani S., Dellaglio F. Genus- and species-specific PCR-based detection of dairy Propionibacteria in environmental samples by using primers targeted to the genes encoding 16S rRNA. Appl. Environ. Microbiol. 65:1999;4241-4244
26. Satokari R.M., Vaughan E.E., Akkermans A.D.L., Saarela M., de Vos W.M. Bifidobacterial diversity in human feces detected by genus-specific PCR and denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 67:2001;504-513
27. Calvo-Bado L.A., Morgan J.A.W., Sergeant M., Pettitt T.R., Whipps J.M. Molecular characterization of Legionella populations present within slow sand filters used for fungal plant pathogen suppression in horticultural crops. Appl. Environ. Microbiol. 69:2003;533-541
28. Nubel U., Engelen B., Felske A., Snaidr J., Wieshuber A., Amann R., Ludwig W., Backhaus H. Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis. J. Bacteriol. 178:1996;5636-5643
29. Stratz M., Mau M., Timmis K. System to study horizontal gene exchange among microorganisms without cultivation of recipients. Mol. Microbiol. 22:1996;207-215
30. Zavros Y., Rieder G., Ferguson A., Merchant J.L. Gastritis and hypergastrinemia due to Acinetobacter lwoffii in mice. Infect. Immun. 70:2002;2630-2639
31. Rathinavelu S., Zavros Y., Merchant J.L. Acinetobacter lwoffii infection and gastritis. Microbes Infect. 5:2003;651-657
32. Van Hamme J.D., Odumeru J.A., Ward O.P. Community dynamics of a mixed-bacterial culture growing on petroleum hydrocarbons in batch culture. Can. J. Microbiol. 46:2000;441-450
33. Lai B., Khanna S. Degradation of crude oil by Acinetobacter calcoaceticus and Alcaligenes odorans. J. Appl. Bacteriol. 81:1996;355-362
34. Marín M., Pedregosa A., Ríos S., Ortiz M.L., Laborda F. Biodegradation of diesel and heating oil by Acinetobacter calcoaceticus MM5: its possible applications on bioremediation. Int. Biodeterior. Biodegr. 35:1995;269-285
35. Chaineau C.H., Morel J., Dupont J., Bury E., Oudot J. Comparison of the fuel oil biodegradation potential of hydrocarbon-assimilating microorganisms isolated from a temperate agricultural soil. Sci. Total Environ. 227:1999;237-247
36. MacCormack W.P., Fraile E.R. Characterization of a hydrocarbon degrading psychrotrophic antarctic bacterium. Ant. Sci. 9:1997;150-155
37. Hanson K.G., Nigam A., Kapadia M., Desai A.J. Bioremediation of crude oil contamination with Acinetobacter sp. A3. Curr. Microbiol. 35:1997;191-193
38. Huy N.Q., et al. Characterization of petroleum-degrading bacteria from oil-contaminated sites in Vietnam. J. Biosci. Bioeng. 88:1999;100-102
39. Vaneechoutte M., Devriese L.A., Dijkshoorn L., Lamote B., Deprez P., Verschraegen G., Haesebrouck F. Acinetobacter baumannii-infected vascular catheters collected from horses in an equine clinic. J. Clin. Microbiol. 38:2000;4280-4281
40. Bastiaens, L., 1998. Isolation and characterization of PAH-degrading bacteria. Ph.D. thesis. Agricultural and Applied Biological Sciences, 1-290
41. Kremer L., Baulard A., Estaquier J., Poulain-Godefroy O., Locht C. Green fluorescent protein as a new expression marker in mycobacteria. Mol. Microbiol. 17:1995;913-922
42. Springael D., Ryngaert A., Merlin C., Toussaint A., Mergeay M. Occurrence of Tn4371-related mobile elements and sequences in (chloro)biphenyl-degrading bacteria. Appl. Environ. Microbiol. 67:2001;42-50
43. Mokross H., Schmidt E., Reineke W. Degradation of 3-chlorobiphenyl by in vivo constructed hybrid pseudomonads. FEMS Microbiol. Lett. 59:1990;179-185
44. Asturias J., Eltis L.D., Prucha M., Timmis K. Analysis of three 2,3-dihydroxybiphenyl 1,2-dioxygenases found in Rhodococcus globerulus P6. Identification of a new family of extradiol dioxygenases. J. Biol. Chem. 269:1994;7807-7815