Tetrachioroethene (PCE) is a human carcinogen, and together with trichloroethane (TCE), is widely used. Due to improper handling, they are among the most frequently found groundwater pollutants. A purified, PCE-dechlorinating enrichment culture was developed. This non-methanogenic, non-acetogenic culture could grow with H2 as the electron donor, indicating that H2/PCE serves as an electron donor/acceptor for energy conservation and growth. A novel anaerobic bacterium which dechlorinates PCE to the non-toxic product ethene (ETH), "Dehalococcoides ethenogenes' strain 195, was isolated from this enrichment. This is the first pure culture capable of complete PCE dechlorination. 'D. ethenogenes' strain 195 is an irregular coccus with an optimal growth temperature of 35 deg C and pH of 6.8-7.5. Phylogenetic analysis indicates that it is a eubacterium which shows no affiliation to known groups. Electron donors tested other than H2 were not utilized nor were electron donors other than TCE, cis-dichloroethene (cis-DCE), 1,1-DCE, and dichloroethane, which could be freely interchanged and were dechlorinated to ETH. This organism could not grow on vinyl chloride or trans-DCE when provided as sole electron acceptors, but both were dechlorinated cometabolically by cells previously grown on PCE. The reduction of VC to ETH was the rate-limiting reaction to the complete dechlorination of PCE. PCE, TCE, cis-DCE, and 1,1-DCE inhibited ETH formation from VC when present, but, at low concentrations, their dechlorination coexisted with ETH production. Cultures grown on cis-DCE as sole electron acceptor could not dechlorinate PCE unless PCE and cis-DCE were added together.

Vinyl chloride (VC) is a widespread groundwater pollutant and Group 1 carcinogen. Microbial respiration of VC is both critical for complete remediation of chloroethenes in situ, and a unique physiology only observed by certain strains of Dehalococcoides. Two different genes independently encoding VC respiration in Dehalococcoides, vcrA and bvcA, were identified previously, each a member of the diverse family of reductive dehalogenase homologous genes, or rdhA. In this thesis I report that vcrA and bvcA are among a subset of putative 'foreign' rdhA with a low GC3 codon usage that favors the nucleotide T, even though tRNAs recognizing T-ending codons are categorically absent in Dehalococcoides genomes. Comparative genomics of the first two complete genome sequences of microorganisms able to respire VC, Dehalococcoides strains VS and BAV1, reveals that vcrA and bvcA are both located within recently integrated, but different, genomic islands (GIs). These islands have different predicted integration sites and different relative positions in the genome, suggesting that bvcA and vcrA were acquired independently and through different mechanisms. In particular, the vcrA-containing GI appears to have integrated at the single-copy tmRNA encoding gene, ssrA, along with many other homologous elements that site-specifically integrate/excise at ssrA -- some of which contain other rdhA. A detailed analysis of these 'ssrA-GIs' in Dehalococcoides identifies the precise position of insertion as well as a conserved module of syntenic integration-associated genes that includes the likely ssrA-specific integrase. Further analysis of (meta)genomic data, as well as targeted sequencing from 4 additional VC-respiring cultures, provided a total of 8 syntenic vcr-GIs from independently derived cultures. Evolutionary estimates for the age of divergence of these 8 vcrA sequences is not confidently distinguishable from the first industrial synthesis of chlorinated ethenes approximately 100 years ago. By contrast, the estimated age of divergence of Dehalococcoides strains far precedes industrial civilization. Overall, ssrA-GIs appear to be a major contributor to the second of two high plasticity regions, genetically dynamic regions that interrupt an otherwise stable, syntenic, and streamlined Dehalococcoides genome -- among the smallest of any free living microorganism. The apparent compartmentalization of Dehalococcoides genome dynamics within specialized regions may enhance opportunistic adaptation to (new) organohalide respiratory niches while protecting a core genome that is highly adapted to life in the anoxic subsurface, exemplified here by the recent site-specific acquisition of VC reductase genes.

This book summarizes the current state of knowledge concerning bacteria that use halogenated organic compounds as respiratory electron acceptors. The discovery of organohalide-respiring bacteria has expanded the range of electron acceptors used for energy conservation, and serves as a prime example of how scientific discoveries are enabling innovative engineering solutions that have transformed remediation practice. Individual chapters provide in-depth background information on the discovery, isolation, phylogeny, biochemistry, genomic features, and ecology of individual organohalide-respiring genera, including Dehalococcoides, Dehalogenimonas, Dehalobacter, Desulfitobacterium and Sulfurospirillum, as well as organohalide-respiring members of the Deltaproteobacteria. The book introduces readers to the fascinating biology of organohalide-respiring bacteria, offering a valuable resource for students, engineers and practitioners alike.

This book contains a collection of different research activities that include the biodegradation compounds with contaminant characteristics and special products of different interests as an added value product or that allows following up various biological processes. The chapters consider the degradation of contaminant compounds generated by industrial activities, i.e., oil industry by-product compounds and halogen compounds or compound generated by natural phenomena such as tsunamis, which require interventions to recover damaged soils. In addition, the book contains chapters that involve special product degradation processes such as chlorophyll, which corresponds to a biological process indicator as photosynthesis.