Correlation of Dehalococcoides 16S rRNA and Chloroethene-Reductive Dehalogenase Genes with Geochemical Conditions in Chloroethene-Contaminated Groundwater

Abstract

Quantitative analysis of genes that code for Dehalococcoides 16S rRNA and chloroethene-reductive dehalogenases TceA, VcrA, and BvcA was done on groundwater sampled from 150 monitoring wells spread over 11 chlorinated ethene polluted European locations. Redundancy analysis was used to relate molecular data to geochemical conditions. Dehalococcoides 16S rRNA-and vinyl chloride (VC)-reductase genes were present at all tested locations in concentrations up to 10 6 gene copies per ml of groundwater. However, differences between and also within locations were observed. Variation in Dehalococcoides 16S rRNA gene copy numbers were most strongly correlated to dissolved organic carbon concentration in groundwater and to conditions appropriate for biodegradation of chlorinated ethenes (U.S. Environmental Protection Agency score). In contrast, vcrA gene copy numbers correlated most significantly to VC and chlorinated ethene concentrations. Interestingly, bvcA and especially tceA were more correlated with oxidizing conditions. In groundwater microcosms, dechlorination of 1 mM VC was correlated to an increase of vcrA and/or bvcA gene copies by 2 to 4 orders of magnitude. Interestingly, in 34% of the monitoring wells and in 40% of the active microcosms, the amount of individual VC-reductase gene copies exceeded that of Dehalococcoides 16S rRNA gene copies. It is concluded that the geographical distribution of the genes was not homogeneous, depending on the geochemical conditions, whereby tceA and bvcA correlated to more oxidized conditions than Dehalococcoides 16S rRNA and vcrA. Because the variation in VC-reductase gene numbers was not directly correlated to variation in Dehalococcoides spp., VC-reductase genes are better monitoring parameters for VC dechlorination capacity than Dehalococcoides spp.

Identification of chlorinated solvents degradation zones in clay till by high resolution chemical, microbial and compound specific isotope analysis

“…The activity of the vcrA gene is higher in borehole B compared to the screens in borehole C where the vcrA gene is also observed (Table 1). However, the number of Dhc present is similar (10 7 cells/L, specific numbers given in Table 1) illustrating that there is no correlation between the VC reductase gene numbers and the variation in Dhc which was also observed in a study by van der Zaan et al (2010). Similar, to observations made by Carreón-Diazconti et al (2009) the presence of bacteria and activity of the functional genes in the three boreholes at the site (see Table 1) are very heterogeneously distributed.…”

Quantitative PCR for Tracking the Megaplasmid-Borne Biodegradation Potential of a Model Sphingomonad

“…This observation suggests that biodegradative genes can be lost, so culture-based assays or methods targeting chromosomal genes, e.g., 16S rRNA genes, may overestimate biodegradative capability when the necessary genes are carried on plasmids, as is often the case with sphingomonads (2). Similar observations have been made in the anaerobic world concerning vinyl chloride reductase genes in Dehalococcoides (22), which are flanked by insertion sequences (9) and therefore also subject to loss in the absence of positive pressure (3).…”

“…A protein-based detection method for dioxin dioxygenase exists (4), and standard PCR primers have been published for the study of the dxnA1A2 cistron (1, 2) and for ring-hydroxylating dioxygenases in general (8). However, due to the amplicon length or lack of specificity, these primers are not appropriate for quantitation, which is important in linking microbial activity with chemical transformations to track bioremediation (22).…”

Assessment of Anaerobic Toluene Biodegradation Activity by bssA Transcript/Gene Ratios

“…Of particulate note is the use of quantitative PCR (qPCR) for the detection and quantification of functional genes associated with the degradation of contaminants. However, as has been repeatedly demonstrated in both column and field studies, functional gene abundance is not always predictive of contaminant degradation, nor does it consistently correlate with gene expression or contaminant concentration (1,2). Furthermore, high gene copy numbers are often sustained when there is little or no active degradation (3,4), making such measurements difficult to interpret.…”

“…Toluene in the sample was removed by sparging with helium gas, which was also used to keep the sample anoxic, and the sample was incubated at room temperature. Subsamples (100 ml) for RNA analysis were collected at the beginning of the experiment (t ϭ 0) and at 2,4,8,12,20, and 30 h. Samples for DNA analysis (25 ml) were also collected at the beginning and end of the experiment. Samples for both DNA and RNA analyses were filtered as described, frozen in liquid nitrogen, and stored at Ϫ80°C until extraction of nucleic acids.…”