Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Overview of organohalide-respiring bacteria and a proposal for a classification system for reductive dehalogenases
    Hug, L.A. ; Maphosa, F. ; Leys, D. ; Loffler, F.E. ; Smidt, H. ; Edwards, E.A. ; Adrian, L. - \ 2013
    Philosophical Transactions of the Royal Society B. Biological sciences 368 (2013)1616. - ISSN 0962-8436
    dehalococcoides sp strain - vinyl-chloride reductase - desulfitobacterium-frappieri pcp-1 - strictly anaerobic bacterium - multiple sequence alignment - complete genome sequence - best-fit models - dehalospirillum-multivorans - enrichment culture - dehalobacter-re
    Organohalide respiration is an anaerobic bacterial respiratory process that uses halogenated hydrocarbons as terminal electron acceptors during electron transport-based energy conservation. This dechlorination process has triggered considerable interest for detoxification of anthropogenic groundwater contaminants. Organohalide-respiring bacteria have been identified from multiple bacterial phyla, and can be categorized as obligate and non-obligate organohalide respirers. The majority of the currently known organohalide-respiring bacteria carry multiple reductive dehalogenase genes. Analysis of a curated set of reductive dehalogenases reveals that sequence similarity and substrate specificity are generally not correlated, making functional prediction from sequence information difficult. In this article, an orthologue-based classification system for the reductive dehalogenases is proposed to aid integration of new sequencing data and to unify terminology.
    Metagenome analysis reveals yet unexplored reductive dechlorinating potential of Dehalobacter sp. E1 growing in coculture with Sedimentibacter sp.
    Maphosa, F. ; Passel, M.W.J. van; Vos, W.M. de; Smidt, H. - \ 2012
    Environmental Microbiology Reports 4 (2012)6. - ISSN 1758-2229 - p. 604 - 616.
    desulfitobacterium-frappieri pcp-1 - complete genome sequence - dehalococcoides spp. - online tool - hafniense - tetrachloroethene - dehalogenation - vitamin-b-12 - restrictus - bacterium
    The importance of Dehalobacter species in bioremediation as dedicated degraders of chlorinated organics has been well recognized. However, still little is known about Dehalobacter's full genomic repertoires, including the genes involved in dehalogenation. Here we report the first insights into the genome sequence of Dehalobacter sp. E1 that grows in strict co-culture with Sedimentibacter sp. B4. Based on the co-culture metagenome and the genome of strain B4 (4.2¿Mbp) we estimate the genome sequence of strain E1 to be 2.6¿Mbp. Ten putative reductive dehalogenase homologue (Rdh)-encoding gene clusters were identified. One cluster has a putative tetrachloroethene Rdh-encoding gene cluster, similar to the pceABCT operon previously identified in Dehalobacter restrictus. Metagenome analysis indicated that the inability of strain E1 to synthesize cobalamin, an essential cofactor of reductive dehalogenases, is complemented by Sedimentibacter. The metagenomic exploration described here maps the extensive dechlorinating potential of Dehalobacter, and paves way for elucidation of the interactions with its co-cultured Sedimentibacter
    High-Rate Sulfate Reduction at High Salinity (up to 90 mS.cm-1) in Mesophilic UASB Reactors
    Vallero, M.V.G. ; Sipma, J. ; Lettinga, G. ; Lens, P.N.L. - \ 2004
    Biotechnology and Bioengineering 86 (2004)2. - ISSN 0006-3592 - p. 226 - 235.
    sulfaat - reductie - chemische reacties - zoutgehalte - geactiveerd slib - biodegradatie - acetaten - propionaten - ethanol - waterzuivering - sulfate - reduction - chemical reactions - salinity - activated sludge - biodegradation - acetates - propionates - ethanol - water treatment - desulfitobacterium-frappieri pcp-1 - anaerobic granular sludge - long-term competition - waste-water - methanogenic bacteria - biological treatment - reducing reactors - bed reactor - wastewaters - ammonia
    Sulfate reduction in salt-rich wastewaters using unadapted granular sludge was investigated in 0.9 L UASB reactors (pH 7.0 ± 0.2; hydraulic retention time from 8-14 h) fed with acetate, propionate, or ethanol at organic loading rates up to 10 gCOD.L-1.day-1 and in excess sulfate (COD/SO of 0.5). High-rate sulfate reduction rates (up to 3.7 gSO42-.L-1.day-1) were achieved at salinities exceeding 50 gNaCl.L-1 and 1 gMgCl2.L-1. Sulfate reduction proceeded at a salinity of up to 70 gNaCl.L-1 and 1 gMgCl2.L-1 (corresponding to a conductivity of about 85-90 mS.cm-1), although at lower rates compared to a conductivity of 60-70 mS.cm-1. Ethanol as well as propionate were suitable substrates for sulfate reduction, with acetate and sulfide as the end products. The successful high-rate treatment was due to the proliferation of a halotolerant incomplete oxidizing SRB population present in the unadapted inoculum sludge. Bioaugmentation of this sludge with the acetate oxidizing halotolerant SRB Desulfobacter halotolerans was unsuccessful, as the strain washed out from the UASB reactor without colonizing the UASB granules. © 2004 Wiley Periodicals, Inc.
    Anaerobic microbial dehalogenation
    Smidt, H. ; Vos, W.M. de - \ 2004
    Annual Review of Microbiology 58 (2004). - ISSN 0066-4227 - p. 43 - 73.
    desulfitobacterium-frappieri pcp-1 - polymerase-chain-reaction - reductively dechlorinates tetrachloroethene - bacterium rhodopseudomonas-palustris - chloroethene-contaminated sites - chlorinated aliphatic-compounds - sp strain cbdb1 - vinyl-chloride - sp-nov - de
    The natural production and anthropogenic release of halogenated hydrocarbons into the environment has been the likely driving force for the evolution of an unexpectedly high microbial capacity to dehalogenate different classes of xenobiotic haloorganics. This contribution provides an update on the current knowledge on metabolic and phylogenetic diversity of anaerobic microorganisms that are capable of dehalogenating-or completely mineralizing-halogenated hydrocarbons by fermentative, oxidative, or reductive pathways. In particular, research of the past decade has focused on halorespiring anaerobes, which couple the dehalogenation by dedicated enzyme systems to the generation of energy by electron transport-driven phosphorylation. Significant advances in the biochemistry and molecular genetics of degradation pathways have revealed mechanistic and structural similarities between dehalogenating enzymes from phylogenetically distinct anaerobes. The availability of two almost complete genome sequences of halorespiring isolates recently enabled comparative and functional genomics approaches, setting the stage for the further exploitation of halorespiring and other anaerobic dehalogenating microbes as dedicated degraders in biological remediation processes.
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