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https://www.readbyqxmd.com/read/29724849/complete-genome-sequence-of-petrimonas-sp-strain-ibaraki-assembled-from-the-metagenome-data-of-a-culture-containing-dehalococcoides-spp
#1
Kentaro Ikegami, Yuto Aita, Akino Shiroma, Makiko Shimoji, Hinako Tamotsu, Noriko Ashimine, Misuzu Shinzato, Shun Ohki, Kazuma Nakano, Kuniko Teruya, Kazuhito Satou, Takashi Hirano, Masafumi Yohda
The complete genome sequence of Petrimonas sp. strain IBARAKI in a Dehalococcoides -containing culture was determined using the PacBio RS II platform. The genome is a single circular chromosome of 3,693,233 nucleotides (nt), with a GC content of 44%. This is the first genome sequence of a Petrimonas species.
May 3, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29718172/organohalide-respiratory-chains-composition-topology-and-key-enzymes
#2
Torsten Schubert, Lorenz Adrian, R Gary Sawers, Gabriele Diekert
The utilization of halogenated organic compounds as terminal electron acceptors separates the phylogenetically diverse organohalide-respiring bacteria from other respiratory anaerobes that predominantly use nitrate, fumarate, sulfate or oxidized metals. Organohalide respiration is unique in recruiting a cobamide-containing iron-sulfur protein, the extracellular membrane-bound reductive dehalogenase, as terminal reductase in the electron transfer chain. In recent years substantial contributions have been made to the understanding of how electron transfer paths couple mechanistically to chemiosmosis in the organohalide-respiring bacteria...
April 1, 2018: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29419787/biomarkers-responses-to-reductive-dechlorination-rates-and-oxygen-stress-in-bioaugmentation-culture-kb-1-tm
#3
Gretchen L W Heavner, Cresten B Mansfeldt, Garrett E Debs, Sage T Hellerstedt, Annette R Rowe, Ruth E Richardson
Using mRNA transcript levels for key functional enzymes as proxies for the organohalide respiration (OHR) rate, is a promising approach for monitoring bioremediation populations in situ at chlorinated solvent-contaminated field sites. However, to date, no correlations have been empirically derived for chlorinated solvent respiring, Dehalococcoides mccartyi (DMC) containing, bioaugmentation cultures. In the current study, genome-wide transcriptome and proteome data were first used to confirm the most highly expressed OHR-related enzymes in the bioaugmentation culture, KB-1TM , including several reductive dehalogenases (RDases) and a Ni-Fe hydrogenase, Hup...
February 8, 2018: Microorganisms
https://www.readbyqxmd.com/read/29413921/cathode-potential-regulation-in-a-coupled-bioelectrode-anaerobic-sludge-system-for-effective-dechlorination-of-2-4-dichloronitrobenzene
#4
Linlin Chen, Junjie Shao, Hui Chen, Caiqin Wang, Xinyi Gao, Xiangyang Xu, Liang Zhu
For enhanced dechlorination of 2,4-dichloronitrobenzene (2,4-DClNB), a coupled microbial electrosynthesis-upflow anaerobic sludge reactor (MES-UASB) was established, and the effect of cathode potential on the performance of combined process was investigated in this study. Results showed that a higher dechlorination efficiency of 78.5 ± 6.1% was achieved in the coupled MES-UASB at -660 mV, and the degradation rate of 4-chloroaniline (4-ClAn) reached 4.61 mg·L-1 ·d-1 within 120 h at -660 mV of cathode potential in batch experiments...
April 2018: Bioresource Technology
https://www.readbyqxmd.com/read/29390082/an-integrative-overview-of-genomic-transcriptomic-and-proteomic-analyses-in-organohalide-respiration-research
#5
Dominique Türkowsky, Nico Jehmlich, Gabriele Diekert, Lorenz Adrian, Martin von Bergen, Tobias Goris
Organohalide respiration (OHR) is a crucial process in the global halogen cycle and of interest for bioremediation. However, investigations on OHR are hampered by the restricted genetic accessibility and the poor growth yields of many organohalide-respiring bacteria (OHRB). Therefore, genomics, transcriptomics and proteomics are often used to investigate OHRB. In general, these gene expression studies are more useful when the data of the different 'omics' approaches are integrated and compared among a wide range of cultivation conditions and ideally involve several closely related OHRB...
March 1, 2018: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29385441/anaerobic-microbial-dehalogenation-and-its-key-players-in-the-contaminated-bitterfeld-wolfen-megasite
#6
Ivonne Nijenhuis, Reiner Stollberg, Ute Lechner
The megasite Bitterfeld-Wolfen is highly contaminated as a result of accidents and because of dumping of wastes from local chemical industries in the last century. A variety of contaminants including chlorinated ethenes and benzenes, hexachlorohexanes and chlorinated dioxins can still be found in the groundwater and (river) sediments. Investigations of the in situ microbial transformation of organohalides have been performed only over the last two decades at this megasite. In this review, we summarise the research on the activity of anaerobic dehalogenating bacteria at the field site in Bitterfeld-Wolfen, focusing on chlorinated ethenes, monochlorobenzene and chlorinated dioxins...
April 1, 2018: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29353790/remediation-of-chlorinated-ethenes-in-fractured-sandstone-by-natural-and-enhanced-biotic-and-abiotic-processes-a-crushed-rock-microcosm-study
#7
Rong Yu, Richard G Andrachek, Leo G Lehmicke, David L Freedman
Biostimulation was identified as a potential technology to treat a fractured sandstone aquifer contaminated with trichloroethene (TCE) and cis-1,2-dichloroethene (cis-DCE). Most of the mass of TCE and cis-DCE resides within the rock matrix and strategies to restore groundwater to pre-existing conditions are severely limited by back diffusion. A microcosm study using crushed rock and groundwater from the site was performed to assess biostimulation and natural attenuation. Lactate, hydrogen release compound® (HRC), and emulsified vegetable oil (EVO) significantly increased the rate of TCE reduction to cis-DCE...
June 1, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29283566/interaction-mode-and-regioselectivity-in-vitamin-b-12-dependent-dehalogenation-of-aryl-halides-by-dehalococcoides-mccartyi-strain-cbdb1
#8
Shangwei Zhang, Lorenz Adrian, Gerrit Schüürmann
The bacterium Dehalococcoides, strain CBDB1, transforms aromatic halides through reductive dehalogenation. So far, however, the structures of its vitamin B12 -containing dehalogenases are unknown, hampering clarification of the catalytic mechanism and substrate specificity as basis for targeted remediation strategies. This study employs a quantum chemical donor-acceptor approach for the Co(I)-substrate electron transfer. Computational characterization of the substrate electron affinity at carbon-halogen bonds enables discriminating aromatic halides ready for dehalogenation by strain CBDB1 (active substrates) from nondehalogenated (inactive) counterparts with 92% accuracy, covering 86 of 93 bromobenzenes, chlorobenzenes, chlorophenols, chloroanilines, polychlorinated biphenyls, and dibenzo-p-dioxins...
February 20, 2018: Environmental Science & Technology
https://www.readbyqxmd.com/read/29259088/homoacetogenesis-in-deep-sea-chloroflexi-as-inferred-by-single-cell-genomics-provides-a-link-to-reductive-dehalogenation-in-terrestrial-dehalococcoidetes
#9
Holly L Sewell, Anne-Kristin Kaster, Alfred M Spormann
The deep marine subsurface is one of the largest unexplored biospheres on Earth and is widely inhabited by members of the phylum Chloroflexi In this report, we investigated genomes of single cells obtained from deep-sea sediments of the Peruvian Margin, which are enriched in such Chloroflexi 16S rRNA gene sequence analysis placed two of these single-cell-derived genomes (DscP3 and Dsc4) in a clade of subphylum I Chloroflexi which were previously recovered from deep-sea sediment in the Okinawa Trough and a third (DscP2-2) as a member of the previously reported DscP2 population from Peruvian Margin site 1230...
December 19, 2017: MBio
https://www.readbyqxmd.com/read/29223901/thermally-enhanced-in-situ-bioremediation-of-groundwater-contaminated-with-chlorinated-solvents-a-field-test
#10
Jan Němeček, Jana Steinová, Roman Špánek, Tomáš Pluhař, Petr Pokorný, Petra Najmanová, Vladislav Knytl, Miroslav Černík
In situ bioremediation (ISB) using reductive dechlorination is a widely accepted but relatively slow approach compared to other technologies for the treatment of groundwater contaminated by chlorinated ethenes (CVOCs). Due to the known positive kinetic effect on microbial metabolism, thermal enhancement may be a viable means of accelerating ISB. We tested thermally enhanced ISB in aquifers situated in sandy saprolite and underlying fractured granite. The system comprised pumping, heating and subsequent injection of contaminated groundwater aiming at an aquifer temperature of 20-30°C...
May 1, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29195092/dechlorinating-performance-of-dehalococcoides-spp-mixed-culture-enhanced-by-tourmaline
#11
Wei Wang, Xingyu Liu, Kerui Li, Tielong Li
Dehalococcoides spp. were extensively studied and applied to in-situ trichloroethylene (TCE) remediation since it is the only genus that can reduce TCE to harmless ethene completely. However, this technology was hindered because of the requirement of electron donor (i.e. hydrogen or fermentable organic substrate). Considering the spontaneous electric field and in-situ hydrogen production capacity of tourmaline, this mineral was used as an environmental-friendly bio-promoter for dechlorinating mixed culture containing Dehalococcoides spp...
March 2018: Chemosphere
https://www.readbyqxmd.com/read/29178800/natural-attenuation-and-anaerobic-benzene-detoxification-processes-at-a-chlorobenzene-contaminated-industrial-site-inferred-from-field-investigations-and-microcosm-studies
#12
Wenjing Qiao, Fei Luo, Line Lomheim, Elizabeth Erin Mack, Shujun Ye, Jichun Wu, Elizabeth A Edwards
A five-year site investigation was conducted at a former chemical plant in Nanjing, China. The main contaminants were 1,2,4-trichlorobenzene (TCB) reaching concentrations up to 7300 μg/L, dichlorobenzene (DCB) isomers, monochlorobenzene (MCB), and benzene. Over time, these contaminants naturally attenuated to below regulatory levels under anaerobic conditions. To confirm the transformation processes and to explore the mechanisms, a corresponding laboratory microcosm study was completed demonstrating that 1,2,4-TCB was dechlorinated to 1,2-DCB, 1,3-DCB, and 1,4-DCB in approximately 2%/10%/88% molar proportions...
January 2, 2018: Environmental Science & Technology
https://www.readbyqxmd.com/read/29112726/reconstructed-genomes-of-novel-dehalococcoides-mccartyi-strains-from-1-2-3-4-tetrachlorodibenzo-p-dioxin-dechlorinating-enrichment-cultures-reveal-divergent-reductive-dehalogenase-gene-profiles
#13
Hang T Dam, John Vollmers, Anne-Kristin Kaster, Max M Häggblom
Polychlorinated dibenzo-p-dioxin (PCDD)-contaminated sites are widespread and associated with a variety of anthropogenic sources. PCDDs and other organohalide pollutants can serve as terminal electron acceptors for anaerobic respiration by specialized bacteria containing reductive dehalogenases (RdhA). These microorganisms, therefore, play an important role in the bioremediation of PCDD-contaminated sites. Two anaerobic enrichment cultures established using sediments collected from the PCDD-polluted Hackensack (USA) and Kymijoki (Finland) rivers showed robust reductive dechlorination of 1,2,3,4-tetrachlorodibenzo-p-dioxin (1,2,3,4-TeCDD)...
December 1, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29069488/triple-element-compound-specific-stable-isotope-analysis-of-1-2-dichloroethane-for-characterization-of-the-underlying-dehalogenation-reaction-in-two-dehalococcoides-mccartyi-strains
#14
Steffi Franke, Christina Lihl, Julian Renpenning, Martin Elsner, Ivonne Nijenhuis
Chlorinated ethanes belong to the most common groundwater and soil contaminants. Of these, 1,2-dichloroethane (1,2-DCA) is a man-made, persistent and toxic contaminant, released due to improper waste treatment at versatile production sites. This study investigated the anaerobic transformation of 1,2-DCA by Dehalococcoides mccartyi strain 195 and strain BTF08 using triple-element compound-specific stable isotope analysis of carbon, chlorine and hydrogen for the first time. Isotope fractionation patterns for carbon (εCBTF08 = -28...
December 1, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29040515/resilience-and-recovery-of-dehalococcoides-mccartyi-following-low-ph-exposure
#15
Yi Yang, Natalie L Cápiro, Jun Yan, Tyler F Marcet, Kurt D Pennell, Frank E Löffler
Bioremediation treatment (e.g. biostimulation) can decrease groundwater pH with consequences for Dehalococcoides mccartyi (Dhc) reductive dechlorination activity. To explore the pH resilience of Dhc, the Dhc-containing consortium BDI was exposed to pH 5.5 for up to 40 days. Following 8- and 16-day exposure periods to pH 5.5, dechlorination activity and growth recovered when returned to pH 7.2; however, the ability of the culture to dechlorinate vinyl chloride (VC) to ethene was impaired (i.e. decreased rate of VC transformation)...
December 1, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29040506/high-throughput-sequencing-revealed-novel-dehalococcoidia-in-dechlorinating-microbial-enrichments-from-pcb-contaminated-marine-sediments
#16
Bruna Matturro, Emanuela Frascadore, Simona Rossetti
In this study, six PCE-to-ethene dechlorinating cultures, fed with a fermentable substrate (lactate) or hydrogen as electron donor, were obtained from PCB and PCE dechlorinating microcosms constructed with PCB-contaminated marine sediments. A novel Chloroflexi member (OTU-DIS1) affiliated to Dehalococcoidales Incertae Sedis, only distantly related to known dechlorinating bacteria, dominated the enrichment cultures (up to 86% of total OTUs). Sulfate-, thiosulfate- and sulfur-reducing bacteria affiliated to genera Desulfobacter, Dethiosulfatibacter and Desulfuromusa were also found to lesser extent...
November 1, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29040474/co-occurrence-of-genes-for-aerobic-and-anaerobic-biodegradation-of-dichloroethane-in-organochlorine-contaminated-groundwater
#17
Jacob E Munro, Önder Kimyon, Deborah J Rich, Joanna Koenig, Sihui Tang, Adrian Low, Matthew Lee, Mike Manefield, Nicholas V Coleman
1,2-Dichloroethane (DCA) is a problematic groundwater pollutant. Factors influencing the distribution and activities of DCA-degrading bacteria are not well understood, which has hampered their application for bioremediation. Here, we used quantitative PCR to investigate the distribution of putative DCA-dehalogenating bacteria at a DCA-impacted site in Sydney (Australia). The dehalogenase genes dhlA, tceA and bvcA were detected in all groundwater samples (n = 15), while vcrA was found in 11/15 samples. The 16S rRNA gene sequences specific to the dehalogenating genera Dehalobacter, Desulfitobacterium and Dehalogenimonas were detected in 15/15, 13/15 and 13/15 samples, respectively, while Dehalococcoides sequences were found in 9/15 samples...
November 1, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29031631/most-probable-number-with-visual-based-lamp-for-the-quantification-of-reductive-dehalogenase-genes-in-groundwater-samples
#18
Yogendra H Kanitkar, Robert D Stedtfeld, Paul B Hatzinger, Syed A Hashsham, Alison M Cupples
The remediation of chlorinated solvent contaminated sites frequently involves bioaugmentation with mixed cultures containing Dehalococcoides mccartyi. Their activity is then examined by quantifying reductive dehalogenase (RDase) genes. Recently, we described a rapid, low cost approach, based on loop mediated isothermal amplification (LAMP), which allowed for the visual detection of RDase genes from groundwater. In that study, samples were concentrated (without DNA extraction), incubated in a water bath (avoiding the use of a thermal cycler) and amplification was visualized by the addition of SYBR green (post incubation)...
December 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28943350/spatial-distribution-and-diversity-of-organohalide-respiring-bacteria-and-their-relationships-with-polybrominated-diphenyl-ether-concentration-in-taihu-lake-sediments
#19
Juan Chen, Pei-Fang Wang, Chao Wang, Jia-Jia Liu, Han Gao, Xun Wang
It is acknowledged that organohalide-respiring bacteria (OHRB) can degrade polybrominated diphenyl ethers (PBDEs); however, very little is known about the distribution of OHRB or their response to PBDE contamination in natural sediments. We collected sediments from 28 sampling sites in Taihu Lake, China, and investigated the spatial distribution and diversity of OHRB, and the relationships between the PBDE contamination levels and the PBDE removal potential. The abundances of five typical OHRB genera, namely Dehalobacter, Dehalococcoides, Dehalogenimonas, Desulfitobacterium, and Geobacter, ranged from 0...
January 2018: Environmental Pollution
https://www.readbyqxmd.com/read/28919889/dehalococcoides-as-a-potential-biomarker-evidence-for-uncharacterized-organohalides-in-environmental-samples
#20
Qihong Lu, Ling Yu, Zhiwei Liang, Qingyun Yan, Zhili He, Tiangang Luan, Dawei Liang, Shanquan Wang
The massive production and improper disposal of organohalides resulted in worldwide contamination in soil and water. However, their environmental survey based on chromatographic methods was hindered by challenges in testing the extremely wide variety of organohalides. Dehalococcoides as obligate organohalide-respiring bacteria exclusively use organohalides as electron acceptors to support their growth, of which the presence could be coupled with organohalides and, therefore, could be employed as a biomarker of the organohalide pollution...
2017: Frontiers in Microbiology
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