KNAW Repository

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

Chang, Y.J. and Stephen, J.R. and Richter, A.P. and Venosa, A.D. and Bruggemann, J. and MacNaughton, S.J. and Kowalchuk, G.A. and Haines, J.R. and Kline, E. and White, D.C. (2000) Phylogenetic analysis of aerobic freshwater and marine enrichment cultures efficient in hydrocarbon degradation: effect of profiling method. Journal of Microbiological Methods, 40, 19-31. ISSN 0167-7012.

[img]PDF - Published Version
Restricted to KNAW only

608Kb

Official URL: http://dx.doi.org/10.1016/S0167-7012(99)00134-7

Abstract

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]

Item Type:Article
Institutes:Nederlands Instituut voor Ecologie (NIOO)
ID Code:10847
Deposited On:24 Nov 2011 01:00
Last Modified:31 Mar 2014 10:48

Repository Staff Only: item control page