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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    Influence of phenylacetic acid pulses on anaerobic digestion performance and archaeal community structure in WWTP sewage sludge digesters
    Cabrol, L. ; Urra, J. ; Rosenkranz, F. ; Kroff, P.A. ; Plugge, C.M. ; Lesty, Y. ; Chamy, R. - \ 2015
    Water Science and Technology 71 (2015)12. - ISSN 0273-1223 - p. 1790 - 1799.
    rioolslib - anaërobe behandeling - anaërobe afbraak - sewage sludge - anaerobic treatment - anaerobic digestion - waste-water treatment - olive mill wastewaters - volatile fatty-acids - 16s ribosomal-rna - biogas production - degradation efficiency - microbial-populations - aromatic-compounds - phenolic-compounds - inhibition
    The effect of phenylacetic acid (PAA) pulses on anaerobic digestion (AD) performance and archaeal community structure was evaluated in anaerobic digesters treating sewage sludge from a wastewater treatment plant (WWTP). Four pilot-scale continuous stirred tank reactors were set up at a full-scale municipal WWTP in Santiago de Chile, and fed with either primary or mixed sewage sludge. AD performance was evaluated by volatile fatty acid (VFA) and biogas production monitoring. Archaeal community structure was characterized by 16S rRNA denaturing gradient gel electrophoresis and band sequencing. In the primary sludge digester, a single PAA pulse at 200 mg L(-1) was sufficient to affect AD performance and archaeal community structure, resulting in long-term VFA accumulation, reduced biogas production and community shift from dominant acetoclastic (Methanosaeta concilii) to hydrogenotrophic (Methanospirillum hungatei) methanogens. By contrast, AD performance and archaeal community structure in the mixed sludge digester were stable and resistant to repeated PAA pulses at 200 and 600 mg L(-1). This work demonstrated that the effect of PAA pulses on methanogenic activity and archaeal community structure differed according to AD substrate, and suggests that better insights of the correlations between archaeal population dynamics and functional performance could help to better face toxic shocks in AD
    Genome Analysis and Physiological Comparison of Alicycliphilus denitrificans Strains BC and K601(T.)
    Oosterkamp, M.J. ; Veuskens, T. ; Talarico Saia, F. ; Weelink, S.A.B. ; Goodwin, L.A. ; Daligault, H.E. ; Bruce, D.C. ; Detter, J.C. ; Tapia, R. ; Han, C.S. ; Land, M. ; Hauser, L. ; Langenhoff, A.A.M. ; Gerritse, J. ; Berkel, W.J.H. van; Pieper, D.H. ; Junca, H. ; Smidt, H. ; Schraa, G. ; Davids, M. ; Schaap, P.J. ; Plugge, C.M. ; Stams, A.J.M. - \ 2013
    PLoS ONE 8 (2013)6. - ISSN 1932-6203
    periplasmic nitrate reductase - anaerobic benzene degradation - cytochrome-c-oxidase - aromatic-compounds - perchlorate reduction - chlorite dismutase - reducing bacteria - rna genes - 1st step - metabolism
    The genomes of the Betaproteobacteria Alicycliphilus denitrificans strains BC and K601(T) have been sequenced to get insight into the physiology of the two strains. Strain BC degrades benzene with chlorate as electron acceptor. The cyclohexanol-degrading denitrifying strain K601(T) is not able to use chlorate as electron acceptor, while strain BC cannot degrade cyclohexanol. The 16S rRNA sequences of strains BC and K601(T) are identical and the fatty acid methyl ester patterns of the strains are similar. Basic Local Alignment Search Tool (BLAST) analysis of predicted open reading frames of both strains showed most hits with Acidovorax sp. JS42, a bacterium that degrades nitro-aromatics. The genomes include strain-specific plasmids (pAlide201 in strain K601(T) and pAlide01 and pAlide02 in strain BC). Key genes of chlorate reduction in strain BC were located on a 120 kb megaplasmid (pAlide01), which was absent in strain K601(T). Genes involved in cyclohexanol degradation were only found in strain K601(T). Benzene and toluene are degraded via oxygenase-mediated pathways in both strains. Genes involved in the meta-cleavage pathway of catechol are present in the genomes of both strains. Strain BC also contains all genes of the ortho-cleavage pathway. The large number of mono- and dioxygenase genes in the genomes suggests that the two strains have a broader substrate range than known thus far
    The logicome of environmental bacteria: merging catabolic and regulatory events with Boolean formalisms
    Silva-Rocha, R. ; Tamames, J. ; Martins Dos Santos, V.A.P. ; Lorenzo, V. de - \ 2011
    Environmental Microbiology 13 (2011)9. - ISSN 1462-2912 - p. 2389 - 2402.
    pseudomonas-putida kt2440 - integration host factor - sigma(54)-dependent promoter pu - scale metabolic reconstruction - upper-pathway operon - tol plasmid pww0 - aromatic-compounds - transcriptional regulation - escherichia-coli - rna-polymerase
    The regulatory and metabolic networks that rule biodegradation of pollutants by environmental bacteria are wired to the rest of the cellular physiology through both transcriptional factors and intermediary signal molecules. In this review, we examine some formalisms for describing catalytic/regulatory circuits of this sort and advocate the adoption of Boolean logic for combining transcriptional and enzymatic occurrences in the same biological system. As an example, we show how known regulatory and metabolic actions that bring about biodegradation of m-xylene by Pseudomonas putida mt-2 can be represented as clusters of binary operations and then reconstructed as a digital network. Despite the many simplifications, Boolean tools still capture the gross behaviour of the system even in the absence of kinetic constants determined experimentally. On this basis, we argue that still with a limited volume of data binary formalisms allow us to penetrate the raison d'être of extant regulatory and metabolic architectures
    Degradation of BTEX by anaerobic bacteria: physiology and application
    Weelink, S.A.B. ; Eekert, M.H.A. van; Stams, A.J.M. - \ 2010
    Reviews in Environmental Science & Bio-technology 9 (2010)4. - ISSN 1569-1705 - p. 359 - 385.
    reducing enrichment culture - petroleum-contaminated aquifer - hydrogen isotope fractionation - dechloromonas strain rcb - denitrifying bacterium - benzene degradation - aromatic-compounds - benzylsuccinate synthase - thauera-aromatica - sp-nov.
    Pollution of the environment with aromatic hydrocarbons, such as benzene, toluene, ethylbenzene and xylene (so-called BTEX) is often observed. The cleanup of these toxic compounds has gained much attention in the last decades. In situ bioremediation of aromatic hydrocarbons contaminated soils and groundwater by naturally occurring microorganisms or microorganisms that are introduced is possible. Anaerobic bioremediation is an attractive technology as these compounds are often present in the anoxic zones of the environment. The bottleneck in the application of anaerobic techniques is the lack of knowledge about the anaerobic biodegradation of benzene and the bacteria involved in anaerobic benzene degradation. Here, we review the existing knowledge on the degradation of benzene and other aromatic hydrocarbons by anaerobic bacteria, in particular the physiology and application, including results on the (per)chlorate stimulated degradation of these compounds, which is an interesting new alternative option for bioremediation
    Polysaccharides and phenolic compounds as substrate for yeasts isolated from rotten wood and description of Cryptococcus fagi sp.nov.
    Middelhoven, W.J. - \ 2006
    Antonie van Leeuwenhoek: : Nederlandsch tijdschrift voor hygiëne, microbiologie en serologie 90 (2006)1. - ISSN 0003-6072 - p. 57 - 67.
    anamorphic basidiomycetous yeast - rainy valdivian forest - phylogenetic-relationships - ascomycetous yeasts - genus trichosporon - aromatic-compounds - candida-shehatae - southern chile - decayed wood - identification
    Pieces of rotten wood collected in the forest were screened for the presence of yeasts. In spring time 3 tree species were sampled, followed by 9 species in summer. Yeast strains were identified by traditional methods. Identifications were confirmed by sequencing of ribosomal DNA in case of doubt. In total 14 yeast species of ascomycetous affiliation and 6 anamorphic basidiomycetous yeasts were isolated and identified. Most species were represented by only one strain, but Candida bertae by two and Trichosporon porosum by six strains, all from different wood samples. Three strains represented novel species, one of which is described as Cryptococcus fagi Middelhoven et Scorzetti. The type strain is CBS 9964 (JCM 13614). All strains were tested for growth on several polysaccharides as sole carbon source. Only some of these polymers supported growth of ascomycetous yeasts. Basidiomycetous yeasts assimilated soluble starch, pullulan, dextran, xylan, polygalacturonate, galactomannan and tannic acid or at least some of these. Cryptococcus podzolicus and T. porosum were the most active in this respect. None of the isolated strains grew on carboxymethyl cellulose, colloidal chitin, arabinogalactan and gum xanthan. Phenolic compounds were assimilated by several strains, belonging to the Trichosporonales and the Microbotryum and Stephanoascus/Blastobotrys clades, but not by members of the Tremellales (Cryptococcus musci excepted) and the Debaryomyces/Lodderomyces clade. Most of the ascomycetes assimilated n-hexadecane.
    Enzymatic Baeyer-Villiger oxidation of benzaldehydes
    Moonen, M.J.H. ; Westphal, A.H. ; Rietjens, I.M.C.M. ; Berkel, W.J.H. van - \ 2005
    Advanced Synthesis and Catalysis 347 (2005)7-8. - ISSN 1615-4150 - p. 1027 - 1034.
    p-hydroxybenzoate hydroxylase - 4-hydroxyacetophenone monooxygenase - hydrogen-peroxide - cyclohexanone monooxygenases - pseudomonas-fluorescens - substrate-specificity - directed evolution - phenol hydroxylase - aromatic-compounds - crystal-structure
    The selectivity of the chemical Baeyer-Villiger oxidation of benzaldehydes depends on steric and electronic factors, the type of oxidizing agent and the reaction conditions. Here we report on the enzymatic Baeyer-Villiger oxidation of fluorobenzaldehydes as catalyzed by the flavoprotein 4-hydroxyacetophenone monooxygenase (HAPMO). HAPMO was most active with 4-amino- and 4-hydroxybenzaldehydes. With these compounds significant substrate inhibition occurred. Monofluoro- and difluorobenzaldehydes were readily oxidized by HAPMO without substrate inhibition. 19F NMR analysis revealed that 4-fluoro-, 2,6-difluoro-, 3,4-difluoro-, 2-fluoro-4-hydroxy- and 3-fluoro-4-hydroxybenzaldehyde were quantitatively converted by HAPMO to the corresponding fluorophenyl formates. These products spontaneously hydrolyzed to fluorophenols. The HAPMO-mediated conversion of 2-fluoro-, 3-fluoro-, 2,3-difluoro- and 2,4-difluorobenzaldehyde yielded, besides fluorophenols, also minor amounts of fluorobenzoic acids. The high preference of HAPMO for the production of fluorophenols is in disagreement with the rule derived from chemical studies that electron-poor benzaldehydes form mainly benzoic acids. This suggests that interactions of the benzaldehyde substrates with amino acids and/or the flavin cofactor in the enzyme active site influence the selection of the migratory group in favor of the phenyl ring
    Cryptococcus allantoinivorans sp.nov., an anamorphic basidiomycetous yeast (Tremellales) physiologicallt resembling other species of the Cryptococcus laurentii complex that degrade polysaccharides and C2 compounds
    Middelhoven, W.J. - \ 2005
    Antonie van Leeuwenhoek: : Nederlandsch tijdschrift voor hygiëne, microbiologie en serologie 87 (2005)2. - ISSN 0003-6072 - p. 101 - 108.
    sole source - uric-acid - sp-nov - normal-alkylamines - aromatic-compounds - energy - carbon - systematics - putrescine - nitrogen
    A novel Cryptococcus species is proposed to accommodate a yeast strain (CBS 9604) able to assimilate allantoin as sole carbon source, a characteristic very uncommon among yeasts. By traditional methods, the strain could not be distinguished from Cryptococcus laurentii, but nucleotide sequences of the D1D2 region of the large subunit (26S) and of the ITS region of ribosomal DNA showed relationship to the Bulleromyces clade of the genus Cryptococcus (order Tremellales) with some Tremella spp. as the closest relatives. A traditional morphological and physiological description of the strain is given. Data on the assimilation of some C2 compounds and polysaccharides are provided and compared with those of other type strains of novel species of the C. laurentii complex
    Systematics of the anamorphic basidiomycetous yeast genus Trichosporon Behrend with the description of the five novel species: Trichosporon vadense, T. smithiae, T. dehoogii, T. scarabaeorum and T. gamsii
    Middelhoven, W.J. ; Scorzetti, G. ; Fell, J.W. - \ 2004
    International Journal of Systematic and Evolutionary Microbiology 54 (2004)3. - ISSN 1466-5026 - p. 975 - 986.
    sp nov. - aromatic-compounds - benzene compounds - sole source - uric-acid - identification - energy - carbon
    Phylogenetic trees of the anamorphic basichomycetous yeast genus Trichosporon Behrend, based on molecular sequence analysis of the internal transcribed spacer region and the D1/D2 region of the large subunit of ribosomal (26S) DNA, are presented. This study includes three novel species from soils, Trichosporon vadense sp. nov. (type strain, CBS 8901(T)), Trichosporon smithiae sp. nov. (type strain, CBS 8370(T)) and Trichosporon gamsii sp. nov. (type strain, CBS 8245(T)), one novel species from an insect, Trichosporon scarabaeorum sp. nov. (type strain, CBS 5601(T)) and one species of unknown origin, Trichosporon dehoogii sp. nov. (type strain, CBS 8686(T)). The phylogenetic positions and physiological characteristics that distinguish the new taxa from related species, based partly on growth tests that are not traditionally used in yeast taxonomy (uric acid, ethylamine, L-4-hydroxyproline, tyramine and L-phenylalanine as sources of carbon and nitrogen, and polygalacturonate, quinate, 4-ethylphenol, phloroglucinol, 2,3-dihydroxybenzoate and orcinol as sole carbon sources), are discussed. Assimilation of L-rhamnose and erythritol and maximum growth temperature were also used to delineate species.
    Cryptococcus haglerorum, sp. nov., an anamorphic basidiomycetous yeast isolated from nests of the leaf-cutting ant Atta sexdens.
    Middelhoven, W.J. ; Fonseca, A. ; Carreiro, S.C. ; Pagnocca, F.C. ; Bueno, O.C. - \ 2003
    Antonie van Leeuwenhoek: : Nederlandsch tijdschrift voor hygiëne, microbiologie en serologie 83 (2003)2. - ISSN 0003-6072 - p. 167 - 174.
    aromatic-compounds - humicola complex - trichosporon
    A yeast strain (CBS 8902) was isolated from the nest of a leaf-cutting ant and was shown to be related to Cryptococcus humicola. Sequencing of the D1/D2 region of the 26S ribosomal DNA and physiological characterization revealed a separate taxonomic position. A novel species named Cryptococcus haglerorum is proposed to accommodate strain CBS 8902 that assimilates n-hexadecane and several benzene compounds. Physiological characteristics distinguishing the novel species from some other members of the C. humicola complex are presented. The phylogenetic relationship of these strains to species of the genus Trichosporon Behrend is discussed.
    Identification of clinically relevant Trichosporon species = Identifizierung von Triochosporon-Arten mit klinischer Bedeutung
    Middelhoven, W.J. - \ 2003
    Mycoses 46 (2003). - ISSN 0933-7407 - p. 7 - 11.
    anamorphic basidiomycetous yeast - aromatic-compounds - sp nov.
    A dichotomous identification key to pathogenic species of the basisiomycetous genus Trichosporon Behrend is provided. It is based on growth tests with carbon sources not traditionally used in yeast taxonomy, viz. uric acid, ethylamine, l-4-hydroxyproline, tyramine and L-phenylalanine as sources of carbon and nitrogen, and polygalacturonate, quinate, 4-ethylphenol, 2,3-dihydroxybenzoate and orcinol as sole carbon sources. Of the standard growth tests, assimilation of L-rhamnose and the maximum growth temperature proved to be useful. In addition to medically relevant species, other species able to grow at 37 degreesC were treated as well.
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