scholarly journals Genome-Guided Identification of Organohalide-RespiringDeltaproteobacteriafrom the Marine Environment

mBio ◽  
2018 ◽  
Vol 9 (6) ◽  
Author(s):  
Jie Liu ◽  
Max M. Häggblom
Keyword(s):  
Marine Environment ◽  
Gene Diversity ◽  
Anthropogenic Activities ◽  
Reductive Dehalogenation ◽  
Important Process ◽  
Organohalide Respiration ◽  
Content Type ◽  
Reductive Dehalogenase ◽  
Comprehensive Survey ◽  
Reductive Dehalogenase Genes

ABSTRACTOrganohalide compounds are widespread in the environment as a result of both anthropogenic activities and natural production. The marine environment, in particular, is a major reservoir of organohalides, and reductive dehalogenation is thought to be an important process in the overall cycling of these compounds.Deltaproteobacteriaare important members of the marine microbiota with diverse metabolic capacities, and reductive dehalogenation has been observed in someDeltaproteobacteria. In this study, a comprehensive survey ofDeltaproteobacteriagenomes revealed that approximately 10% contain reductive dehalogenase (RDase) genes, which are found within a common gene neighborhood. The dehalogenating potential of select RDase A-containingDeltaproteobacteriaand their gene expression were experimentally verified. ThreeDeltaproteobacteriastrains isolated from marine environments representing diverse species,Halodesulfovibrio marinisediminis,Desulfuromusa kysingii, andDesulfovibrio bizertensis, were shown to reductively dehalogenate bromophenols and utilize them as terminal electron acceptors in organohalide respiration. Their debrominating activity was not inhibited by sulfate or elemental sulfur, and these species are either sulfate- or sulfur-reducing bacteria. The analysis of RDase A gene transcripts indicated significant upregulation induced by 2,6-dibromophenol. This study extends our knowledge of the phylogenetic diversity of organohalide-respiring bacteria and their functional RDase A gene diversity. The identification of reductive dehalogenase genes in diverseDeltaproteobacteriaand confirmation of their organohalide-respiring capability suggest thatDeltaproteobacteriaplay an important role in natural organohalide cycling.IMPORTANCEThe marine environment is a major reservoir for both anthropogenic and natural organohalides, and reductive dehalogenation is thought to be an important process in the overall cycling of these compounds. Here we demonstrate that the capacity of organohalide respiration appears to be widely distributed in members of marineDeltaproteobacteria. The identification of reductive dehalogenase genes in diverseDeltaproteobacteriaand the confirmation of their dehalogenating activity through functional assays and transcript analysis in select isolates extend our knowledge of organohalide-respiringDeltaproteobacteriadiversity. The presence of functional reductive dehalogenase genes in diverseDeltaproteobacteriaimplies that they may play an important role in organohalide respiration in the environment.

scholarly journals Transcriptomic and Proteomic Responses of the Organohalide-Respiring Bacterium Desulfoluna spongiiphila to Growth with 2,6-Dibromophenol as the Electron Acceptor

2019 ◽  
Vol 86 (5) ◽  
Author(s):  
Jie Liu ◽  
Lorenz Adrian ◽  
Max M. Häggblom
Keyword(s):  
Gene Expression ◽  
Secondary Metabolites ◽  
Electron Acceptor ◽  
Marine Sponge ◽  
Reductive Dehalogenation ◽  
Important Process ◽  
Organohalide Respiration ◽  
Content Type ◽  
Reductive Dehalogenase ◽  
Significant Difference

ABSTRACT Organohalide respiration is an important process in the global halogen cycle and for bioremediation. In this study, we compared the global transcriptomic and proteomic analyses of Desulfoluna spongiiphila strain AA1, an organohalide-respiring member of the Desulfobacterota isolated from a marine sponge, with 2,6-dibromophenol or with sulfate as an electron acceptor. The most significant difference of the transcriptomic analysis was the expression of one reductive dehalogenase gene cluster (rdh16), which was significantly upregulated with the addition of 2,6-dibromophenol. The corresponding protein, reductive dehalogenase RdhA16032, was detected in the proteome under treatment with 2,6-dibromophenol but not with sulfate only. There was no significant difference in corrinoid biosynthesis gene expression levels between the two treatments, indicating that the production of corrinoid in D. spongiiphila is constitutive or not specific for organohalide versus sulfate respiration. Electron-transporting proteins or mediators unique for reductive dehalogenation were not revealed in our analysis, and we hypothesize that reductive dehalogenation may share an electron-transporting system with sulfate reduction. The metabolism of D. spongiiphila, predicted from transcriptomic and proteomic results, demonstrates high metabolic versatility and provides insights into the survival strategies of a marine sponge symbiont in an environment rich in organohalide compounds and other secondary metabolites. IMPORTANCE Respiratory reductive dehalogenation is an important process in the overall cycling of both anthropogenic and natural organohalide compounds. Marine sponges produce a vast array of bioactive compounds as secondary metabolites, including diverse halogenated compounds that may enrich for dehalogenating bacteria. Desulfoluna spongiiphila strain AA1 was originally enriched and isolated from the marine sponge Aplysina aerophoba and can grow with both brominated compounds and sulfate as electron acceptors for respiration. An understanding of the overall gene expression and the protein production profile in response to organohalides is needed to identify the full complement of genes or enzymes involved in organohalide respiration. Elucidating the metabolic capacity of this sponge-associated bacterium lays the foundation for understanding how dehalogenating bacteria may control the fate of organohalide compounds in sponges and their role in a symbiotic organobromine cycle.

scholarly journals Dehalococcoides mccartyi Strain DCMB5 Respires a Broad Spectrum of Chlorinated Aromatic Compounds

2014 ◽  
Vol 81 (2) ◽  
pp. 587-596 ◽  
Author(s):  
Marlén Pöritz ◽  
Christian L. Schiffmann ◽  
Gerd Hause ◽  
Ulrike Heinemann ◽  
Jana Seifert ◽  
...  
Keyword(s):  
Electron Acceptor ◽  
Aromatic Compounds ◽  
Lag Phase ◽  
Organohalide Respiration ◽  
Content Type ◽  
Reductive Dehalogenase ◽  
Dehalococcoides Mccartyi ◽  
Type Iv ◽  
Transmission Electron ◽  
Almost All

ABSTRACTPolyhalogenated aromatic compounds are harmful environmental contaminants and tend to persist in anoxic soils and sediments.Dehalococcoides mccartyistrain DCMB5, a strain originating from dioxin-polluted river sediment, was examined for its capacity to dehalogenate diverse chloroaromatic compounds. Strain DCMB5 used hexachlorobenzenes, pentachlorobenzenes, all three tetrachlorobenzenes, and 1,2,3-trichlorobenzene as well as 1,2,3,4-tetra- and 1,2,4-trichlorodibenzo-p-dioxin as electron acceptors for organohalide respiration. In addition, 1,2,3-trichlorodibenzo-p-dioxin and 1,3-, 1,2-, and 1,4-dichlorodibenzo-p-dioxin were dechlorinated, the latter to the nonchlorinated congener with a remarkably short lag phase of 1 to 4 days following transfer. Strain DCMB5 also dechlorinated pentachlorophenol and almost all tetra- and trichlorophenols. Tetrachloroethene was dechlorinated to trichloroethene and served as an electron acceptor for growth. To relate selected dechlorination activities to the expression of specific reductive dehalogenase genes, the proteomes of 1,2,3-trichlorobenzene-, pentachlorobenzene-, and tetrachloroethene-dechlorinating cultures were analyzed. Dcmb_86, an ortholog of the chlorobenzene reductive dehalogenase CbrA, was the most abundant reductive dehalogenase during growth with each electron acceptor, suggesting its pivotal role in organohalide respiration of strain DCMB5. Dcmb_1041 was specifically induced, however, by both chlorobenzenes, whereas 3 putative reductive dehalogenases, Dcmb_1434, Dcmb_1339, and Dcmb_1383, were detected only in tetrachloroethene-grown cells. The proteomes also harbored a type IV pilus protein and the components for its assembly, disassembly, and secretion. In addition, transmission electron microscopy of DCMB5 revealed an irregular mode of cell division as well as the presence of pili, indicating that pilus formation is a feature ofD. mccartyiduring organohalide respiration.

scholarly journals Complete Genome Sequence of Dehalococcoides mccartyi Strain FL2, a Trichloroethene-Respiring Anaerobe Isolated from Pristine Freshwater Sediment

2019 ◽  
Vol 8 (33) ◽  
Author(s):  
Jun Yan ◽  
Yi Yang ◽  
Xiuying Li ◽  
Frank E. Löffler
Keyword(s):  
Complete Genome Sequence ◽  
Reductive Dechlorination ◽  
Complete Genome ◽  
Hydrogen Oxidation ◽  
Protein Coding ◽  
Coding Sequences ◽  
Content Type ◽  
Reductive Dehalogenase ◽  
Dehalococcoides Mccartyi ◽  
Reductive Dehalogenase Genes

Dehalococcoides mccartyi strain FL2 couples growth to hydrogen oxidation and reductive dechlorination of trichloroethene and cis- and trans-1,2-dichloroethenes. Strain FL2 has a 1.42-Mb genome with a G+C content of 47.0% and carries 1,465 protein-coding sequences, including 24 reductive dehalogenase genes.

scholarly journals Quantitative Analysis of the Relative Transcript Levels of Four Chlorophenol Reductive Dehalogenase Genes in Desulfitobacterium hafniense PCP-1 Exposed to Chlorophenols

2011 ◽  
Vol 77 (17) ◽  
pp. 6261-6264 ◽  
Author(s):  
Ariane Bisaillon ◽  
Réjean Beaudet ◽  
François Lépine ◽  
Richard Villemur
Keyword(s):  
Quantitative Analysis ◽  
Transcript Levels ◽  
Content Type ◽  
Reductive Dehalogenase ◽  
Reductive Dehalogenase Genes ◽  
Desulfitobacterium Hafniense

ABSTRACTRelative to those of unexposed cultures, the transcript levels of the four CprA-type reductive dehalogenase genes (cprA2,cprA3,cprA4, andcprA5) inDesulfitobacterium hafniensePCP-1 were measured in cultures exposed to chlorophenols. In 2,4,6-trichlorophenol-amended cultures,cprA2andcprA3were upregulated, as wascprA5, but concomitantly with the appearance of 2,4-dichlorophenol (DCP). In 3,5-DCP-amended cultures, onlycprA5was upregulated. In pentachlorophenol-amended cultures grown for 12 h,cprA2andcprA3were upregulated but notcprA5. cprA4was not upregulated significantly in cultures containing any tested chlorophenols.

scholarly journals The MarR-Type Regulator Rdh2R RegulatesrdhGene Transcription in Dehalococcoides mccartyi Strain CBDB1

2016 ◽  
Vol 198 (23) ◽  
pp. 3130-3141 ◽  
Author(s):  
Lydia Krasper ◽  
Hauke Lilie ◽  
Anja Kublik ◽  
Lorenz Adrian ◽  
Ralph Golbik ◽  
...  
Keyword(s):  
Heterologous Expression ◽  
Direct Repeat ◽  
Negative Regulator ◽  
Control Of Gene Expression ◽  
Organohalide Respiration ◽  
Content Type ◽  
Reductive Dehalogenase ◽  
Dehalococcoides Mccartyi ◽  
Transcriptional Start Sites

ABSTRACTReductive dehalogenases are essential enzymes in organohalide respiration and consist of a catalytic subunit A and a membrane protein B, encoded byrdhABgenes. Thirty-twordhABgenes exist in the genome ofDehalococcoides mccartyistrain CBDB1. To gain a first insight into the regulation ofrdhoperons, the control of gene expression of twordhABgenes (cbdbA1453/cbdbA1452 and cbdbA1455/cbdbA1454) by the MarR-type regulator Rdh2R (cbdbA1456) encoded directly upstream was studied using heterologous expression andin vitrostudies. Promoter-lacZreporter fusions were generated and integrated into the genome of theEscherichia colihost. ThelacZreporter activities of bothrdhApromoters decreased upon transformation of the cells with a plasmid carrying therdh2Rgene, suggesting that Rdh2R acts as repressor, whereas thelacZreporter activity of therdh2Rpromoter was not affected. The transcriptional start sites of bothrdhAgenes in strain CBDB1 and/or the heterologous host mapped to a conserved direct repeat with 11- to 13-bp half-sites. DNase I footprinting revealed binding of Rdh2R to a ∼30-bp sequence covering the complete direct repeat in both promoters, including the transcriptional start sites. Equilibrium sedimentation ultracentrifugation revealed that Rdh2R binds as tetramer to the direct-repeat motif of therdhA(cbdbA1455) promoter. Using electrophoretic mobility shift assays, a similar binding affinity was found for bothrdhApromoters. In the presence of only one half-site of the direct repeat, the interaction was strongly reduced, suggesting a positive cooperativity of binding, for which unusual short palindromes within the direct-repeat half-sites might play an important role.IMPORTANCEDehalococcoides mccartyistrains are obligate anaerobes that grow by organohalide respiration. They have an important bioremediation potential because they are capable of reducing a multitude of halogenated compounds to less toxic products. We are now beginning to understand how these organisms make use of this large catabolic potential, wherebyD. mccartyiexpresses dehalogenases in a compound-specific fashion. MarR-type regulators are often encoded in the vicinity of reductive dehalogenase genes. In this study, we made use of heterologous expression andin vitrostudies to demonstrate that the MarR-type transcription factor Rdh2R acts as a negative regulator. We identify its binding site on the DNA, which suggests a mechanism by which it controls the expression of two adjacent reductive dehalogenase operons.

scholarly journals Impact of Ammonium on Syntrophic Organohalide-Respiring and Fermenting Microbial Communities

mSphere ◽  
2016 ◽  
Vol 1 (2) ◽  
Author(s):  
Anca G. Delgado ◽  
Devyn Fajardo-Williams ◽  
Kylie L. Kegerreis ◽  
Prathap Parameswaran ◽  
Rosa Krajmalnik-Brown
Keyword(s):  
Chlorinated Solvents ◽  
Reductive Dehalogenation ◽  
Ammonium Concentration ◽  
Organohalide Respiration ◽  
Content Type ◽  
Dehalococcoides Mccartyi ◽  
Metabolic Capability ◽  
Subsurface Environments ◽  
Fermentative Bacteria ◽  
High Concentrations

ABSTRACT Contamination with ammonium and chlorinated solvents has been reported in numerous subsurface environments, and these chemicals bring significant challenges for in situ bioremediation. Dehalococcoides mccartyi is able to reduce the chlorinated solvent trichloroethene to the nontoxic end product ethene. Fermentative bacteria are of central importance for organohalide respiration and bioremediation to provide D. mccartyi with H2, their electron donor, acetate, their carbon source, and other micronutrients. In this study, we found that high concentrations of ammonium negatively correlated with rates of trichloroethene reductive dehalogenation and fermentation. However, detoxification of trichloroethene to nontoxic ethene occurred even at ammonium concentrations typical of those found in animal waste (up to 2 g liter−1 NH4 +-N). To date, hundreds of subsurface environments have been bioremediated through the unique metabolic capability of D. mccartyi. These findings extend our knowledge of D. mccartyi and provide insight for bioremediation of sites contaminated with chlorinated solvents and ammonium. Syntrophic interactions between organohalide-respiring and fermentative microorganisms are critical for effective bioremediation of halogenated compounds. This work investigated the effect of ammonium concentration (up to 4 g liter−1 NH4 +-N) on trichloroethene-reducing Dehalococcoides mccartyi and Geobacteraceae in microbial communities fed lactate and methanol. We found that production of ethene by D. mccartyi occurred in mineral medium containing ≤2 g liter−1 NH4 +-N and in landfill leachate. For the partial reduction of trichloroethene (TCE) to cis-dichloroethene (cis-DCE) at ≥1 g liter−1 NH4 +-N, organohalide-respiring dynamics shifted from D. mccartyi and Geobacteraceae to mainly D. mccartyi. An increasing concentration of ammonium was coupled to lower metabolic rates, longer lag times, and lower gene abundances for all microbial processes studied. The methanol fermentation pathway to acetate and H2 was conserved, regardless of the ammonium concentration provided. However, lactate fermentation shifted from propionic to acetogenic at concentrations of ≥2 g liter−1 NH4 +-N. Our study findings strongly support a tolerance of D. mccartyi to high ammonium concentrations, highlighting the feasibility of organohalide respiration in ammonium-contaminated subsurface environments. IMPORTANCE Contamination with ammonium and chlorinated solvents has been reported in numerous subsurface environments, and these chemicals bring significant challenges for in situ bioremediation. Dehalococcoides mccartyi is able to reduce the chlorinated solvent trichloroethene to the nontoxic end product ethene. Fermentative bacteria are of central importance for organohalide respiration and bioremediation to provide D. mccartyi with H2, their electron donor, acetate, their carbon source, and other micronutrients. In this study, we found that high concentrations of ammonium negatively correlated with rates of trichloroethene reductive dehalogenation and fermentation. However, detoxification of trichloroethene to nontoxic ethene occurred even at ammonium concentrations typical of those found in animal waste (up to 2 g liter−1 NH4 +-N). To date, hundreds of subsurface environments have been bioremediated through the unique metabolic capability of D. mccartyi. These findings extend our knowledge of D. mccartyi and provide insight for bioremediation of sites contaminated with chlorinated solvents and ammonium.

scholarly journals Comparative Single-Cell Genomics of Chloroflexi from the Okinawa Trough Deep-Subsurface Biosphere

2016 ◽  
Vol 82 (10) ◽  
pp. 3000-3008 ◽  
Author(s):  
Heather Fullerton ◽  
Craig L. Moyer
Keyword(s):  
Single Cell ◽  
Okinawa Trough ◽  
Reductive Dehalogenation ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Metabolic Potential ◽  
Deep Subsurface ◽  
Content Type ◽  
Reductive Dehalogenase ◽  
The Okinawa Trough

ABSTRACTChloroflexismall-subunit (SSU) rRNA gene sequences are frequently recovered from subseafloor environments, but the metabolic potential of the phylum is poorly understood. The phylumChloroflexiis represented by isolates with diverse metabolic strategies, including anoxic phototrophy, fermentation, and reductive dehalogenation; therefore, function cannot be attributed to these organisms based solely on phylogeny. Single-cell genomics can provide metabolic insights into uncultured organisms, like the deep-subsurfaceChloroflexi. Nine SSU rRNA gene sequences were identified from single-cell sorts of whole-round core material collected from the Okinawa Trough at Iheya North hydrothermal field as part of Integrated Ocean Drilling Program (IODP) expedition 331 (Deep Hot Biosphere). Previous studies of subsurfaceChloroflexisingle amplified genomes (SAGs) suggested heterotrophic or lithotrophic metabolisms and provided no evidence for growth by reductive dehalogenation. Our nineChloroflexiSAGs (seven of which are from the orderAnaerolineales) indicate that, in addition to genes for the Wood-Ljungdahl pathway, exogenous carbon sources can be actively transported into cells. At least one subunit for pyruvate ferredoxin oxidoreductase was found in four of theChloroflexiSAGs. This protein can provide a link between the Wood-Ljungdahl pathway and other carbon anabolic pathways. Finally, one of the sevenAnaerolinealesSAGs contains a distinct reductive dehalogenase homologous (rdhA) gene.IMPORTANCEThrough the use of single amplified genomes (SAGs), we have extended the metabolic potential of an understudied group of subsurface microbes, theChloroflexi. These microbes are frequently detected in the subsurface biosphere, though their metabolic capabilities have remained elusive. In contrast to previously examinedChloroflexiSAGs, our genomes (several are from the orderAnaerolineales) were recovered from a hydrothermally driven system and therefore provide a unique window into the metabolic potential of this type of habitat. In addition, a reductive dehalogenase gene (rdhA) has been directly linked to marine subsurfaceChloroflexi, suggesting that reductive dehalogenation is not limited to the classDehalococcoidia. This discovery expands the nutrient-cycling and metabolic potential present within the deep subsurface and provides functional gene information relating to this enigmatic group.

scholarly journals Functional Genotyping of Sulfurospirillum spp. in Mixed Cultures Allowed the Identification of a New Tetrachloroethene Reductive Dehalogenase

2013 ◽  
Vol 79 (22) ◽  
pp. 6941-6947 ◽  
Author(s):  
Géraldine F. Buttet ◽  
Christof Holliger ◽  
Julien Maillard
Keyword(s):  
Anaerobic Respiration ◽  
Bacterial Genomes ◽  
Content Type ◽  
Reductive Dehalogenase ◽  
Bacterial Consortia ◽  
Sequence Identity ◽  
Reductive Dehalogenase Genes ◽  
High Level ◽  
Substrate Prediction ◽  
Groundwater Pollutant

ABSTRACTReductive dehalogenases are the key enzymes involved in the anaerobic respiration of organohalides such as the widespread groundwater pollutant tetrachloroethene. The increasing number of available bacterial genomes and metagenomes gives access to hundreds of new putative reductive dehalogenase genes that display a high level of sequence diversity and for which substrate prediction remains very challenging. In this study, we present the development of a functional genotyping method targeting the diverse reductive dehalogenases present inSulfurospirillumspp., which allowed us to unambiguously identify a new reductive dehalogenase from our tetrachloroethene-dechlorinating SL2 bacterial consortia. The new enzyme, named PceATCE, shows 92% sequence identity with the well-characterized PceA enzyme ofSulfurospirillum multivorans, but in contrast to the latter, it is restricted to tetrachloroethene as a substrate. Its apparent higher dechlorinating activity with tetrachloroethene likely allowed its selection and maintenance in the bacterial consortia among other enzymes showing broader substrate ranges. The sequence-substrate relationships within tetrachloroethene reductive dehalogenases are also discussed.

Determinants of housing demand in the Erzurum province, Turkey

2014 ◽  
Vol 7 (4) ◽  
pp. 586-602 ◽  
Author(s):  
Erkan Oktay ◽  
Abdulkerim Karaaslan ◽  
Ömer Alkan ◽  
Ali Kemal Çelik
Keyword(s):  
Housing Prices ◽  
Binary Logistic Regression ◽  
Housing Demand ◽  
Outcome Variable ◽  
Binary Logistic Regression Analysis ◽  
Cross Sectional Survey ◽  
Cross Sectional ◽  
Content Type ◽  
Comprehensive Survey ◽  
Income Expectations

Purpose – The main aim of this study is to determine the factors that influence the housing demand of households in Erzurum, northeastern Turkey. Housing demand is generally affected by several factors including housing prices, individuals’ income, expectations and choices and so on, as a means of its demographic and socio-psychological contexts. Design/methodology/approach – A questionnaire-based cross-sectional survey was carried out, in which the outcome variable had binary responses such as whether to invest in housing or not. A binary logistic regression analysis was performed to estimate the underlying data. Findings – The questionnaire was conducted in 2,927 households living in Erzurum city center, and 47 per cent of the respondents claimed that they would consider investing in housing in the future. The estimation results reveal that demographic or socio-economic factors that may possibly influence housing demand of the respondents are as follows: household head’s and spouse’s occupation, monthly income, the number of individuals in the family and car ownership. Originality/value – This paper involves the most comprehensive survey addressing the housing demand in the East Anatolian Region, Turkey. Additionally, this paper aims to contribute to the existing housing literature through establishing the statistical analysis of housing demand in an unstudied territory of the world.

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