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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    Evaluation of solid polymeric organic materials for use in bioreactive sediment capping to stimulate the degradation of chlorinated aliphatic hydrocarbons
    Atashgahi, S. ; Maphosa, F. ; Vrieze, J. de; Haest, P.J. ; Boon, N. ; Smidt, H. ; Springael, D. ; Dejonghe, W. - \ 2014
    Applied Microbiology and Biotechnology 98 (2014)5. - ISSN 0175-7598 - p. 2255 - 2266.
    reductive dechlorination - trichloroethylene tce - natural attenuation - groundwater plume - vinyl-chloride - hydrogen - tetrachloroethene - river - contaminants - communities
    In situ bioreactive capping is a promising technology for mitigation of surface water contamination by discharging polluted groundwater. Organohalide respiration (OHR) of chlorinated ethenes in bioreactive caps can be stimulated through incorporation of solid polymeric organic materials (SPOMs) that provide a sustainable electron source for organohalide respiring bacteria. In this study, wood chips, hay, straw, tree bark and shrimp waste, were assessed for their long term applicability as an electron donor for OHR of cis-dichloroethene (cDCE) and vinyl chloride (VC) in sediment microcosms. The initial release of fermentation products, such as acetate, propionate and butyrate led to the onset of extensive methane production especially in microcosms amended with shrimp waste, straw and hay, while no considerable stimulation of VC dechlorination was obtained in any of the SPOM amended microcosms. However, in the longer term, short chain fatty acids accumulation decreased as well as methanogenesis, whereas high dechlorination rates of VC and cDCE were established with concomitant increase of Dehalococcoides mccartyi and vcrA and bvcA gene numbers both in the sediment and on the SPOMs. A numeric simulation indicated that a capping layer of 40 cm with hay, straw, tree bark or shrimp waste is suffice to reduce the groundwater VC concentration below the threshold level of 5 µg/l before discharging into the Zenne River, Belgium. Of all SPOMs, the persistent colonization of tree bark by D. mccartyi combined with the lowest stimulation of methanogenesis singled out tree bark as a long-term electron donor for OHR of cDCE/VC in bioreactive caps
    Tracking Functional Guilds: Dehalococcoides spp. in European River Basins Contaminated with Hexachlorobenzene
    Tas, N. ; Eekert, M.H.A. van; Schraa, G. ; Zhou, J. ; Vos, W.M. de; Smidt, H. - \ 2009
    Applied and Environmental Microbiology 75 (2009)14. - ISSN 0099-2240 - p. 4696 - 4704.
    16s ribosomal-rna - lower ebro river - enrichment culture - environmental processes - microbial-communities - chlorinated benzenes - ethenogenes 195 - vinyl-chloride - sequence data - ne spain
    Hexachlorobenzene (HCB) has been widely used in chemical manufacturing processes and as pesticide. Due to its resistance to biological degradation, HCB mainly accumulated in fresh water bodies and agricultural soils. Dehalococcoides spp., anaerobic dechlorinating bacteria that are capable of degrading HCB, were previously isolated from river sediments. Yet there is limited knowledge about the abundance, diversity and activity of this genus in the environment. This study focused on the molecular analysis of the composition and abundance of active Dehalococcoides spp. in HCB-contaminated European river basins. 16S ribosomal RNA-based real-time quantitative PCR and denaturing gradient gel electrophoresis in combination with multivariate statistics were applied. Moreover, a functional gene array was used to determine reductive dehalogenase (rdh) gene diversity. Spatial and temporal fluctuations were observed not only in the abundance of Dehalococcoides spp. but also in the composition of the populations and rdh gene diversity. Multivariate statistics revealed that Dehalococcoides spp. abundance is primarily affected by spatial differences, whereas species composition is under the influence of several environmental parameters, such as seasonal changes, total organic carbon and/or nitrogen content and HCB contamination. This study provides new insight in the natural occurrence and dynamics of active Dehalococcoides spp. in HCB contaminated river basins
    Degradation pathway of 2-chloroethanol in Pseudomonas stutzeri strain JJ under denitrifying conditions
    Dijk, J.A. ; Gerritse, J. ; Schraa, G. ; Stams, A.J.M. - \ 2004
    Archives of Microbiology 182 (2004)6. - ISSN 0302-8933 - p. 514 - 519.
    vinyl-chloride - pyrroloquinoline quinone - dehydrogenase - metabolism - pqq - mineralization - chloroethanol - intermediate - oxidation - aquifer
    The pathway of 2-chloroethanol degradation in the denitrifying Pseudomonas stutzeri strain JJ was investigated. In cell-free extracts, activities of a phenazine methosulfate (PMS)-dependent chloroethanol dehydrogenase, an NAD-dependent chloroacetaldehyde dehydrogenase, and a chloroacetate dehalogenase were detected. This suggested that the 2-chloroethanol degradation pathway in this denitrifying strain is the same as found in aerobic bacteria that degrade chloroethanol. Activity towards primary alcohols, secondary alcohols, diols, and other chlorinated alcohols could be measured in cell-free extracts with chloroethanol dehydrogenase (CE-DH) activity. PMS and phenazine ethosulfate (PES) were used as primary electron acceptors, but not NAD, NADP or ferricyanide. Cells of strain JJ cultured in a continuous culture under nitrate limitation exhibited chloroethanol dehydrogenase activity that was a 12 times higher than in cells grown in batch culture. However, under chloroethanol-limiting conditions, CE-DH activity was in the same range as in batch culture. Cells grown on ethanol did not exhibit CE-DH activity. Instead, NAD-dependent ethanol dehydrogenase (E-DH) activity and PMS-dependent E-DH activity were detected
    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.
    Hydrogen treshold concentrations in pure cultures of halorespiring bacteria and at a site polluted with chlorinated ethenes
    Luijten, M.L.G.C. ; Roelofsen, W. ; Langenhoff, A.A.M. ; Schraa, G. ; Stams, A.J.M. - \ 2004
    Environmental Microbiology 6 (2004)6. - ISSN 1462-2912 - p. 646 - 650.
    anaerobic mixed culture - reductive dechlorination - enrichment culture - electron-acceptor - redox processes - vinyl-chloride - tetrachloroethene - dehalogenation - sediments - sulfate
    Halorespiring microorganisms are not only able to oxidize organic electron donors such as formate, acetate, pyruvate and lactate, but also H-2. Because these microorganisms have a high affinity for H-2, this may be the most important electron donor for halorespiration in the environment. We have studied the role of H-2-threshold concentrations in pure halorespiring cultures and compared them with mixed cultures and field data. We have found H-2-threshold values between 0.05 and 0.08 nM for Sulfurospirillum halorespirans, S. multivorans and Dehalobacter restrictus under PCE-reducing and nitrate-reducing conditions. The reduction of PCE and TCE can proceed at H-2 concentrations of below 1 nM at a polluted site. However, for the reduction of lower chlorinated ethenes a higher H-2 concentration is required. This indicates that the measured H-2 concentration in situ can be an indicator of the extent of anaerobic reductive dechlorination.
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