Molecular Analysis of Dehalococcoides 16S Ribosomal DNA from Chloroethene-Contaminated Sites throughout North America and Europe

Abstract

The environmental distribution of Dehalococcoides group organisms and their association with chloroethenecontaminated sites were examined. Samples from 24 chloroethene-dechlorinating sites scattered throughout North America and Europe were tested for the presence of members of the Dehalococcoides group by using a PCR assay developed to detect Dehalococcoides 16S rRNA gene (rDNA) sequences. Sequences identified by sequence analysis as sequences of members of the Dehalococcoides group were detected at 21 sites. Full dechlorination of chloroethenes to ethene occurred at these sites. Dehalococcoides sequences were not detected in samples from three sites at which partial dechlorination of chloroethenes occurred, where dechlorination appeared to stop at 1,2-cis-dichloroethene. Phylogenetic analysis of the 16S rDNA amplicons confirmed that Dehalococcoides sequences formed a unique 16S rDNA group. These 16S rDNA sequences were divided into three subgroups based on specific base substitution patterns in variable regions 2 and 6 of the Dehalococcoides 16S rDNA sequence. Analyses also demonstrated that specific base substitution patterns were signature patterns. The specific base substitutions distinguished the three sequence subgroups phylogenetically. These results demonstrated that members of the Dehalococcoides group are widely distributed in nature and can be found in a variety of geological formations and in different climatic zones. Furthermore, the association of these organisms with full dechlorination of chloroethenes suggests that they are promising candidates for engineered bioremediation and may be important contributors to natural attenuation of chloroethenes.The chloroethenes tetrachloroethene (PCE) and trichloroethene (TCE) are commonly used organic solvents and degreasing agents. As a result of past disposal practices and spills, chloroethenes are now widely distributed in the environment and are found in many sediments, soils, groundwater aquifers, and subsurface environments throughout the world (13,21,28). Traditional approaches to groundwater remediation practices, such as pump and treat methods, have been shown to be ineffective and costly when applied to chlorinated solvent plumes (2a, 2c, 23). Therefore, there is a need for microbebased remediation approaches that could provide an inexpensive way to clean up chlorinated solvent contamination.Chloroethene solvents were previously believed to be resistant to degradation by microorganisms. There now is rapidly accumulating laboratory and field evidence that microorganisms can transform chloroethenes to nontoxic products under a variety of environmental conditions (3, 8-10, 12, 15, 20, 22, 27, 28, 30, 31, 35). Maymó-Gatell et al. have isolated an organism from an anaerobic dechlorinating laboratory culture inoculated with municipal sewage sludge, which fully dechlorinates chlorinated ethenes (25,26). This organism, Dehalococcoides ethenogenes strain 195, was shown to meet its energy needs, which are essential for growth, by a process known as dehalore...

Dechlorination and organohalide-respiring bacteria dynamics in sediment samples of the Yangtze Three Gorges Reservoir

“…4b). These cultures showed complete dechlorination, thus confirming previous reports that bacteria of the Dehalococcoides group are the only known microorganism to completely dehalogenate PCE to ethene (Holliger et al 1999;Löffler et al 2000;Maymó-Gatell et al 2001;Hendrickson et al 2002;Smidt and de Vos 2004;Schmidt et al 2006). During 28 weeks and anaerobic transformation of approximately 60 mg/L PCE, the Dehalococcoides spp.…”

“…It has been shown recently that in the field, often several dechlorinating bacteria are present simultaneously (Rouzeau-Szynalski et al 2011). In the environment, the reductively dechlorinating bacteria have been detected in different compartments, mainly in contaminated soil (Löffler et al 2000;Hendrickson et al 2002) and polluted groundwater (Schmidt et al 2006;Schmidt and Tiehm 2008;Vancheeswaran et al 1999). For river sediments, their occurrence in the Dutch part of the Rhine River (Holliger et al 1993), the Red Cedar, Père Marquette (Löffler et al 2000), Tahquamenon and Pine Rivers in the USA, and the Perfume River in Vietnam (Griffin et al 2004) was reported.…”

Evaluating the fate of chlorinated ethenes in streambed sediments by combining stable isotope, geochemical and microbial methods

“…All DNA samples were PCR-amplifiable as positive results were obtained by PCR with these primers. The Dehalococcoides specific primers Fp DGC 774 and Rp DHC 1212 were used to substantiate anaerobic VC dechlorination (Hendrickson et al, 2002). The same PCR conditions as in the original works were used (Hendrickson et al, 2002;Coleman and Spain, 2003a).…”

“…The Dehalococcoides specific primers Fp DGC 774 and Rp DHC 1212 were used to substantiate anaerobic VC dechlorination (Hendrickson et al, 2002). The same PCR conditions as in the original works were used (Hendrickson et al, 2002;Coleman and Spain, 2003a). The DNA samples were also subjected to PCR with specific primers for the EaCoMT gene (CoM-F1L and CoM-R2E) which codes for the enzyme epoxyalkane:coenzyme M transferase that is involved in the aerobic degradation of VC and ethene (Coleman and Spain, 2003b;Danko et al, 2006).…”

“…Different methods have been proposed to evaluate the occurrence of complete reductive dechlorination of chlorinated ethenes including: 1) characterization of geochemical conditions (availability of electron donors such as H 2 , Luijten et al, 2004; assessment of redox conditions, Witt et al, 2002;Lu et al, 2006), 2) characterization of parent and daughter product patterns (Witt et al, 2002) and 3) assessment of the presence and activity of key organisms such as Dehalococcoides (Fennell et al, 2001;Hendrickson et al, 2002;Müller et al, 2004;Duhamel and Edwards, 2006;Rahm and Richardson, 2008;Imfeld et al, 2008;Lee et al, 2008). While geochemical conditions and the presence of certain organisms can indicate whether the conditions are favorable for reductive dechlor-ination, these parameters usually do not provide information about the degree of transformation.…”