Different activity levels of Dehalococcoides mccartyi revealed by FISH and CARD-FISH under non-steady and pseudo-steady state conditions

A mixed culture capable of dechlorinating perchloroethylene (PCE) to ethene was analyzed under non steady and pseudo-steady state conditions. Dehalococcoides mccartyi, considered to be the primary dechlorinating bacterium able to completely degrade chlorinated hydrocarbons to non toxic ethene, could be detected by CAtalyzed Reporter Deposition Fluorescence In Situ Hybridization (CARD-FISH) since the beginning of culture operation but highlighted by conventional FISH only during active PCE dechlorination to ethene and vinyl chloride (VC). Data generated from FISH and CARD-FISH analyses were compared to those generated from applying PCR-based techniques directed at defining cell abundances (Real Time PCR, qPCR) and assessing cell activities (Reverse Transcription qPCR, RT-qPCR) of Dehalococcoides strains involved in the PCE reductive dechlorination (RD) process. qPCR targeting reductive dehalogenase genes coding for enzymes involved in the individual steps of the RD process, showed that Dehalococcoides strains carrying the tceA gene dominated the community. This observation was consistent with PCE conversion products detected under pseudo-steady state (ethene and VC production), since this tceA gene is known to be associated to strains capable of reducing chlorinated solvents beyond 1,2-cis-dichloroethene (cis-DCE). In line with the FISH data, Dehalococcoides 16S rRNA and tceA genes were expressed only during pseudo-steady state conditions when PCE was converted completely to the final metabolic product ethene. Furthermore, Dehalococcoides cell abundances estimated by CARD-FISH correlated positively with their 16SrRNA gene copy numbers quantified by qPCR. This is consistent with the ability of both these methods to estimate total Dehalococcoides cell numbers including those with low metabolic activities. Thus, this study shows that application potential of FISH analysis to quantify rapidly and efficiently only active dechlorinators in complex communities.