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Trent A Key, Dray P Richmond, Kimberly S Bowman, Yong-Joon Cho, Jongsik Chun, Milton S da Costa, Fred A Rainey, William M Moe
Dehalogenimonas alkenigignens IP3-3(T) is a strictly anaerobic, mesophilic, Gram negative staining bacterium that grows by organohalide respiration, coupling the oxidation of H2 to the reductive dehalogenation of polychlorinated alkanes. Growth has not been observed with any non-polyhalogenated alkane electron acceptors. Here we describe the features of strain IP3-3(T) together with genome sequence information and its annotation. The 1,849,792 bp high-quality-draft genome contains 1936 predicted protein coding genes, 47 tRNA genes, a single large subunit rRNA (23S-5S) locus, and a single, orphan, small unit rRNA (16S) locus...
2016: Standards in Genomic Sciences
Chris M D Kocur, Line Lomheim, Olivia Molenda, Kela P Weber, Leanne M Austrins, Brent E Sleep, Hardiljeet K Boparai, Elizabeth A Edwards, Denis M O'Carroll
Nanoscale zerovalent iron (nZVI) is an emerging technology for the remediation of contaminated sites. However, there are concerns related to the impact of nZVI on in situ microbial communities. In this study, the microbial community composition at a contaminated site was monitored over two years following the injection of nZVI stabilized with carboxymethyl cellulose (nZVI-CMC). Enhanced dechlorination of chlorinated ethenes to nontoxic ethene was observed long after the expected nZVI oxidation. The abundance of Dehalococcoides (Dhc) and vinyl chloride reductase (vcrA) genes, monitored using qPCR, increased by over an order of magnitude in nZVI-CMC-impacted wells...
July 19, 2016: Environmental Science & Technology
Ivonne Nijenhuis, Kevin Kuntze
Contamination and remediation of groundwater with halogenated organics and understanding of involved microbial reactions still poses a challenge. Over the last years, research in anaerobic microbial dehalogenation has advanced in many aspects providing information about the reaction, physiology of microorganisms as well as approaches to investigate the activity of microorganisms in situ. Recently published crystal structures of reductive dehalogenases (Rdh), heterologous expression systems and advanced analytical, proteomic and stable isotope approaches allow addressing the overall reaction and specific enzymes as well as co-factors involved during anaerobic microbial dehalogenation...
April 2016: Current Opinion in Biotechnology
Chih-Ming Kao, Hung-Yu Liao, Chih-Ching Chien, Yi-Kuan Tseng, Petrus Tang, Chih-En Lin, Ssu-Ching Chen
The compositions of bacterial community in one site contaminated with PCE/TCE after the slow polycolloid-releasing substrate (SPRS) (contained vegetable oil, cane molasses, and surfactants) addition were analyzed. Results show that SPRS caused a rapid enhancement of reductive dechlorination of TCE. The transformation of PCE/TCE into ethene was observed after 20 days of operation. To compare the change of bacterial communities before and after SPRS addition, 16S rRNA amplicon sequencing using the metagenome analysis was performed...
January 25, 2016: Journal of Hazardous Materials
Olivia Molenda, Andrew T Quaile, Elizabeth A Edwards
The Dehalogenimonas population in a dechlorinating enrichment culture referred to as WBC-2 was previously shown to be responsible for trans-dichloroethene (tDCE) hydrogenolysis to vinyl chloride (VC). In this study, blue native polyacrylamide gel electrophoresis (BN-PAGE) followed by enzymatic assays and protein identification using liquid chromatography coupled with mass spectrometry (LC-MS/MS) led to the functional characterization of a novel dehalogenase, TdrA. This new reductive dehalogenase (RDase) catalyzes the dechlorination of tDCE to VC...
January 2016: Applied and Environmental Microbiology
L Martín-González, S Hatijah Mortan, M Rosell, E Parladé, M Martínez-Alonso, N Gaju, G Caminal, L Adrian, E Marco-Urrea
A stable enrichment culture derived from Besòs river estuary sediments stoichiometrically dechlorinated 1,2-dichloropropane (1,2-DCP) to propene. Sequential transfers in defined anaerobic medium with the inhibitor bromoethanesulfonate produced a sediment-free culture dechlorinating 1,2-DCP in the absence of methanogenesis. Application of previously published genus-specific primers targeting 16S rRNA gene sequences revealed the presence of a Dehalogenimonas strain, and no amplification was obtained with Dehalococcoides-specific primers...
July 21, 2015: Environmental Science & Technology
Jie Chen, Kimberly S Bowman, Fred A Rainey, William M Moe
Representatives from the genus Dehalogenimonas have the metabolic capacity to anaerobically transform a variety of environmentally important polychlorinated aliphatic compounds. In light of the recent isolation of additional strains, description of a new species, and an expanded number of uncultured DNA sequences, PCR primers and protocols intended to uniquely target members of this organohalide-respiring genus were reevaluated. Nine of fourteen primer combinations reported previously as genus-specific failed to amplify 16S rRNA genes of recently isolated Dehalogenimonas strains...
September 2014: Biodegradation
Dasha A Ravinesan, Radhey S Gupta
The bacteria belonging to the class Dehalococcoidia, due to their ability to dehalogenate chlorinated compounds, are of much interest for bioremediation of contaminated sites. We report here comparative analyses on different genes/proteins from the genomes of members of the class Dehalococcoidia. These studies have identified numerous novel molecular markers in the forms of conserved signature indels (CSIs) in broadly distributed proteins and conserved signature genes/proteins (CSPs), which are uniquely found in members of the class Dehalococcoidia, but except for an isolated exception, they are not found in other sequenced bacterial genomes...
June 2014: International Journal of Systematic and Evolutionary Microbiology
Kalpataru Mukherjee, Kimberly S Bowman, Fred A Rainey, Shivakumara Siddaramappa, Jean F Challacombe, William M Moe
The genome sequence of the organohalide-respiring bacterium Dehalogenimonas lykanthroporepellensBL-DC-9(T) contains numerous loci annotated as reductive dehalogenase homologous (rdh) genes based on inferred protein sequence identity with functional dehalogenases of other bacterial species. Many of these genes are truncated, lack adjacent regulatory elements, or lack cognate genes coding for membrane-anchoring proteins typical of the functionally characterized active reductive dehalogenases of organohalide-respiring bacteria...
May 2014: FEMS Microbiology Letters
Jacob L Dillehay, Kimberly S Bowman, Jun Yan, Fred A Rainey, William M Moe
When chlorinated alkanes are present as soil or groundwater pollutants, they often occur in mixtures. This study evaluated substrate interactions during the anaerobic reductive dehalogenation of chlorinated alkanes by the type strains of two Dehalogenimonas species, D. lykanthroporepellens and D. alkenigignens. Four contaminant mixtures comprised of combinations of the chlorinated solvents 1,2-dichloroethane (1,2-DCA), 1,2-dichloropropane (1,2-DCP), and 1,1,2-trichloroethane (1,1,2-TCA) were assessed for each species...
April 2014: Biodegradation
Shanquan Wang, Jianzhong He
Microbial reductive dechlorination of the persistent polychlorinated biphenyls (PCBs) is attracting much attention in cleanup of the contaminated environment. Nevertheless, most PCB dechlorinating cultures require presence of sediment or sediment substitutes to maintain their dechlorination activities which hinders subsequent bacterial enrichment and isolation processes. The information on enriching sediment-free PCB dechlorinating cultures is still limited. In this study, 18 microcosms established with soils and sediments were screened for their dechlorination activities on a PCB mixture - Aroclor 1260...
2013: PloS One
Ruth Ellen Richardson
In the last few years there has been a burst of genomes released for organohalide respiring bacteria (referred to as OHRB herein though the process is otherwise known as dehalorespiration, reductive dechlorination, or halorespiration). The microorganisms are employed in bioremediation of sites contaminated with chlorinated ethene, ethane, and methanes, as well as chlorinated aromatics. Of particular note are the releases of the first Dehalogenimonas genome (a Dehalococcoides-related Chloroflexi) and not one but seven Dehalobacter (meta)genomes...
June 2013: Current Opinion in Biotechnology
Andrew D Maness, Kimberly S Bowman, Jun Yan, Fred A Rainey, William M Moe
The contaminant concentrations over which type strains of the species Dehalogenimonas alkenigignens and Dehalogenimonas lykanthroporepellens were able to reductively dechlorinate 1,2-dichloroethane (1,2-DCA), 1,2-dichloropropane (1,2-DCP), and 1,1,2-trichloroethane (1,1,2-TCA) were evaluated. Although initially isolated from an environment with much lower halogenated solvent concentrations, D. alkenigignens IP3-3T was found to reductively dehalogenate chlorinated alkanes at concentrations comparable to D. lykanthroporepellens BL-DC-9T...
2012: AMB Express
Kimberly S Bowman, M Fernanda Nobre, Milton S da Costa, Fred A Rainey, William M Moe
Two strictly anaerobic bacterial strains, designated IP3-3(T) and SBP-1, were isolated from groundwater contaminated by chlorinated alkanes and alkenes at a Superfund Site located near Baton Rouge, Louisiana (USA). Both strains reductively dehalogenate a variety of polychlorinated aliphatic alkanes, including 1,2-dichloroethane, 1,2-dichloropropane, 1,1,2,2-tetrachloroethane, 1,1,2-trichloroethane and 1,2,3-trichloropropane, when provided with hydrogen as the electron donor. To clarify their taxonomic position, strains IP3-3(T) and SBP-1 were characterized using a polyphasic approach...
April 2013: International Journal of Systematic and Evolutionary Microbiology
Shivakumara Siddaramappa, Jean F Challacombe, Susana F Delano, Lance D Green, Hajnalka Daligault, David Bruce, Chris Detter, Roxanne Tapia, Shunsheng Han, Lynne Goodwin, James Han, Tanja Woyke, Sam Pitluck, Len Pennacchio, Matt Nolan, Miriam Land, Yun-Juan Chang, Nikos C Kyrpides, Galina Ovchinnikova, Loren Hauser, Alla Lapidus, Jun Yan, Kimberly S Bowman, Milton S da Costa, Fred A Rainey, William M Moe
Dehalogenimonas lykanthroporepellens is the type species of the genus Dehalogenimonas, which belongs to a deeply branching lineage within the phylum Chloroflexi. This strictly anaerobic, mesophilic, non spore-forming, Gram-negative staining bacterium was first isolated from chlorinated solvent contaminated groundwater at a Superfund site located near Baton Rouge, Louisiana, USA. D. lykanthroporepellens was of interest for genome sequencing for two reasons: (a) an unusual ability to couple growth with reductive dechlorination of environmentally important polychlorinated aliphatic alkanes and (b) a phylogenetic position that is distant from previously sequenced bacteria...
May 25, 2012: Standards in Genomic Sciences
Marie J Manchester, Laura A Hug, Matt Zarek, Anna Zila, Elizabeth A Edwards
The WBC-2 consortium is an organohalide-respiring anaerobic microbial enrichment culture capable of dechlorinating 1,1,2,2-tetrachloroethane (TeCA) to ethene. In the WBC-2 culture, TeCA is first transformed to trans-dichloroethene (tDCE) by dichloroelimination; tDCE is subsequently transformed to vinyl chloride (VC) and then to ethene by hydrogenolysis. Analysis of 16S rRNA gene clone libraries from culture DNA revealed sequences from three putative dechlorinating organisms belonging to Dehalococcoides, Dehalobacter, and Dehalogenimonas genera...
August 2012: Applied and Environmental Microbiology
Jun Yan, Brian A Rash, Fred A Rainey, William M Moe
Members of the haloalkane dechlorinating genus Dehalogenimonas are distantly related to "Dehalococcoides" but share high homology in some variable regions of their 16S rRNA gene sequences. In this study, primers and PCR protocols intended to uniquely target Dehalococcoides were reevaluated, and primers and PCR protocols intended to uniquely target Dehalogenimonas were developed and tested. Use of the genus-specific primers revealed the presence of both bacterial groups in groundwater at a Louisiana Superfund site...
December 2009: Applied and Environmental Microbiology
William M Moe, Jun Yan, M Fernanda Nobre, Milton S da Costa, Fred A Rainey
Two recently reported bacterial strains that are able to reductively dehalogenate polychlorinated aliphatic alkanes, including 1,2,3-trichloropropane, 1,2-dichloropropane, 1,1,2,2-tetrachloroethane, 1,1,2-trichloroethane and 1,2-dichloroethane, were further characterized to clarify their taxonomic position. The two strains, designated BL-DC-8 and BL-DC-9(T), were mesophilic, non-spore-forming, non-motile, Gram-negative staining and strictly anaerobic. Cells were irregular cocci, 0.3-0.6 mum in diameter. The two strains were resistant to ampicillin and vancomycin...
November 2009: International Journal of Systematic and Evolutionary Microbiology
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