Modeling gene networks in Dehalococcoides and development of bioindicator assays for bioremediation of chlorinated solvents
This project will study how cultures of Dehalococcoides (DHC), the genus of bacteria involved in dechlorinating and degrading chlorinated hydrocarbon contaminants like TCE (trichloroethene) respond to environmental conditions. Based on this work, the investigators will develop appropriate dehalorespiration bioindicator assays that can be applied at contaminated field sites. The work will combine laboratory studies with field biomass sampling. In the first phase of work, two well-studied DHC-containing mixed cultures will be grown under a wide range of conditions and a subset of studies will include chemical stressors (O2, pH, chloroform). Heterogeneous datasets (genomics, chemical levels, dehalorespiration rates, populations) will be collected and incorporated into systems biology algorithms to generate gene network models. In the second phase, field biomass will be collected at bioaugmented sites to compare gene expression profiles of field-deployed DHC with those predicted from lab-derived models. In the final phase, genes highly correlated with dehalorespiration types and rates will be selected as bioindicators. Two types of bioindicator assays will be developed for field application?quantitative reverse transcription PCR (qRTPCR) and dipstick-style RNA-biosensors. The assays will be tested for robustness against other DHC strains and, ultimately, against field-sampled biomass.
