Polyphasic microbial community analysis of petroleum hydrocarbon-contaminated soils from two northern Canadian communities

Abstract

The cold-adapted bacterial communities in petroleum hydrocarbon-contaminated and non-impacted soils from two northern Canadian environments, Kuujjuaq, Que., and Alert, Nunavut, were analyzed using a polyphasic approach. Denaturing gradient gel electrophoresis (DGGE) separation of 16S rDNA PCR fragments from soil total community DNA revealed a high level of bacterial diversity, as estimated by the total number of bands visualized. Dendrogram analysis clustered the sample sites on the basis of geographical location. Comparison of the overall microbial molecular diversity suggested that in the Kuujjuaq sites, contamination negatively impacted diversity whereas in the Alert samples, diversity was maintained or increased as compared to uncontaminated controls. Extraction and sequencing analysis of selected 16S rDNA bands demonstrated a range of similarity of 86-100% to reference organisms, with 63.6% of the bands representing high G+C Gram-positive organisms in the order Actinomycetales and 36.4% in the class Proteobacteria. Community level physiological profiles generated using Biolog GN plates were analyzed by cluster analysis. Based on substrate oxidation rates, the samples clustered into groups similar to those of the DGGE dendrograms, i.e. separation based upon geographic origin. The coinciding results reached using culture-independent and -dependent analyses reinforces the conclusion that geographical origin of the samples, rather than petroleum contamination level, was more important in determining species diversity within these cold-adapted bacterial communities.

Microbial communities in different soil types do not converge after diesel contamination

“…They similarly concluded that this showed that oil contamination selected for a less diverse, but catabolically-versatile bacterial community. Juck et al (2000) found that, at two oil-contaminated Arctic sites investigated by DGGE and Biolog analysis, absolute diversity was decreased at one site and remained the same or increased at the other. Thus, it seems likely, on the basis of comparison with previous ®ndings, that the absolute diversity in each one of the different soil types tested in this study would have been decreased as a result of diesel contamination.…”

Phylogenetic analysis of bacterial communities in the shrimp and sea cucumber aquaculture environment in northern China by culturing and PCR–DGGE

“…It is possible that these bands were actually composed of two or more distinct sequences with similar migration ability in the DGGE gel (Beate et al 2005). Thus, the bacterial diversity in the samples would be underestimated if the total number of discernible bands were used to estimate the diversity (Juck et al 2000). To obtain complete list of sequences, cloning of these bands into a vector and resequencing of individual clone are needed.…”

Crude Oil Metagenomics for Better Bioremediation of Contaminated Environments

“…McKew et al (2007) reported that the indigenous microflora from an estuary in Brittany (France) adapted to crude oil degradation were dominated by Thalassolitucus Oleivorans and were composed of various other phylum such as Oceanospirillum, Roseobacter, and Arcobacter. In grounds contaminated by crude oil in the north of Canada, Juck et al (2000) showed that the bacterial population was composed mainly by Nocardioides, Arthrobater, and Xanthomonas. In Germany (the North Sea) Brakstad & Lødeng (2004) reported that the indigenous microflora of polluted environment was characterized by the presence of Sphingobacteria Flavobacteria, Pseudoalteromonas, Alteromonas, Vibrio, and Roseobacter.…”