The Dehalococcoides (DHC) are known for their ability to gain energy by dechlorinating organochlorine compounds.  Bioremediation utilizing DHC is growing in use, particularly at sites contaminated with the chlorinated solvents tetrachloroethene (PCE) and trichloroethene (TCE).  Each DHC strain, however, has a uniquely wide substrate range (in addition to PCE/TCE, strains can dechlorinate PCBs, chlorobenzenes, chlorophenols, dioxins, and chloroethanes).  While all DHC genomes sequenced thus far contain a core set of about 1000 genes, substantial differences are seen in the suite of reductive dehalogenase (RDase) genes contained in the different genomes. 

To explore expression patterns for both the conserved genes and the strain-specific RDases we have employed shotgun proteomics on DHC-containing cultures. Analyses with and without isobaric tags (iTRAQ) detected dozens of DHC proteins simultaneously in different culture samples.  The results have been analyzed to elucidate candidate bioindicator proteins/enzymes that might be monitored at contaminated sites to assess in situ bioremediation.  In follow up work, peptide-specific quantification assays were developed to monitor selected bioindicators (including specific RDases) and report them in fmole/mL or proteins/cell. Results will be discussed for two dechlorinating microbial communities: the commercially viable KB1 culture and a mixed culture containing D. ethenogenes Strain 195.

Despite their importance and promise for bioremediation, our understanding of the biology of DHC is quite limited.  Ultimately, the proteome results from growth under a range of conditions will be analyzed with probabilistic network inference algorithms to elucidate possible gene networks in the DHC– particularly those associated with desirable substrate conversion capabilities.