Phylogenetic analysis of aerobic freshwater and marine enrichment cultures efficient in hydrocarbon degradation: effect of profiling method

TY - JOUR

T1 - Phylogenetic analysis of aerobic freshwater and marine enrichment cultures efficient in hydrocarbon degradation: effect of profiling method

AU - Chang, Y.J.

AU - Stephen, J.R.

AU - Richter, A.P.

AU - Venosa, A.D.

AU - Bruggemann, J.

AU - MacNaughton, S.J.

AU - Kowalchuk, G.A.

AU - Haines, J.R.

AU - Kline, E.

AU - White, D.C.

N1 - Reporting year: 2000 Metis note: 2966; CTE; TME ; ME file:///L:/Endnotedatabases/NIOOPUB/pdfs/Pdfs2000/Chang_ea_2966.pdf

PY - 2000

Y1 - 2000

N2 - Aerobically grown enrichment cultures derived from hydrocarbon- contaminated seawater and freshwater sediments were generated by growth on crude oil as sole carbon source. Both cultures displayed a high rate of degradation for a wide range of hydrocarbon compounds. The bacterial species composition of these cultures was investigated by PCR of the 16S rDNA gene using multiple primer combinations. Near full-length 16S rDNA clone libraries were generated and screened by restriction analysis prior to sequence analysis. Polymerase chain reaction- denaturing gradient gel electrophoresis (PCR-DGGE) was carried out using two other PCR primer sets targeting either the V3 or V6-V8 regions, and sequences derived from prominent DGGE bands were compared to sequences obtained via cloning. All data sets suggested that the seawater culture was dominated by alpha- subgroup proteobacteria, whereas the freshwater culture was dominated by members of the beta- and gamma-proteobacteria. However, the V6-V8 primer pair was deficient in the recovery of Sphingomonas-like 16S rDNA due to a 3' terminal mismatch with the reverse primer. Most 16S rDNA sequences recovered from the marine enrichment were not closely related to genera containing known oil-degrading organisms, although some were detected. All methods suggested that the freshwater enrichment was dominated by genera containing known hydrocarbon-degrading species. [KEYWORDS: enrichment cultures; DGGE; hydrocarbon degradation; polymerase chain reaction; phylogenetic analysis; 16S rDNA 16s ribosomal-rna; gradient gel-electrophoresis; degrading bacteria; microbial-populations; genus sphingomonas; activated-sludge; ecology; diversity; database; probes]

AB - Aerobically grown enrichment cultures derived from hydrocarbon- contaminated seawater and freshwater sediments were generated by growth on crude oil as sole carbon source. Both cultures displayed a high rate of degradation for a wide range of hydrocarbon compounds. The bacterial species composition of these cultures was investigated by PCR of the 16S rDNA gene using multiple primer combinations. Near full-length 16S rDNA clone libraries were generated and screened by restriction analysis prior to sequence analysis. Polymerase chain reaction- denaturing gradient gel electrophoresis (PCR-DGGE) was carried out using two other PCR primer sets targeting either the V3 or V6-V8 regions, and sequences derived from prominent DGGE bands were compared to sequences obtained via cloning. All data sets suggested that the seawater culture was dominated by alpha- subgroup proteobacteria, whereas the freshwater culture was dominated by members of the beta- and gamma-proteobacteria. However, the V6-V8 primer pair was deficient in the recovery of Sphingomonas-like 16S rDNA due to a 3' terminal mismatch with the reverse primer. Most 16S rDNA sequences recovered from the marine enrichment were not closely related to genera containing known oil-degrading organisms, although some were detected. All methods suggested that the freshwater enrichment was dominated by genera containing known hydrocarbon-degrading species. [KEYWORDS: enrichment cultures; DGGE; hydrocarbon degradation; polymerase chain reaction; phylogenetic analysis; 16S rDNA 16s ribosomal-rna; gradient gel-electrophoresis; degrading bacteria; microbial-populations; genus sphingomonas; activated-sludge; ecology; diversity; database; probes]

U2 - 10.1016/S0167-7012(99)00134-7

DO - 10.1016/S0167-7012(99)00134-7

M3 - Article

SN - 0167-7012

VL - 40

SP - 19

EP - 31

JO - Journal of Microbiological Methods

JF - Journal of Microbiological Methods

IS - 1

ER -