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.

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    The genus Cladosporium
    Bench, K. ; Braun, U. ; Groenewald, J.Z. ; Crous, P.W. - \ 2012
    Studies in Mycology 72 (2012)1. - ISSN 0166-0616 - p. 1 - 401.
    leaf blotch pathogens - allii-cepae - sensu-lato - taxonomic revision - causal organism - lichenicolous fungi - sp-nov - sporotrichum-gougerotii - aromatic-hydrocarbons - molecular diagnostics
    A monographic revision of the hyphomycete genus Cladosporium s. lat. (Cladosporiaceae, Capnodiales) is presented. It includes a detailed historic overview of Cladosporium and allied genera, with notes on their phylogeny, systematics and ecology. True species of Cladosporium s. str. (anamorphs of Davidiella), are characterised by having coronate conidiogenous loci and conidial hila, i.e., with a convex central dome surrounded by a raised periclinal rim. Recognised species are treated and illustrated with line drawings and photomicrographs (light as well as scanning electron microscopy). Species known from culture are described in vivo as well as in vitro on standardised media and under controlled conditions. Details on host range/substrates and the geographic distribution are given based on published accounts, and a re-examination of numerous herbarium specimens. Various keys are provided to support the identification of Cladosporium species in vivo and in vitro. Morphological datasets are supplemented by DNA barcodes (nuclear ribosomal RNA gene operon, including the internal transcribed spacer regions ITS1 and ITS2, the 5.8S nrDNA, as well as partial actin and translation elongation factor 1-a gene sequences) diagnostic for individual species. In total 993 names assigned to Cladosporium s. lat., including Heterosporium (854 in Cladosporium and 139 in Heterosporium), are treated, of which 169 are recognized in Cladosporium s. str. The other taxa are doubtful, insufficiently known or have been excluded from Cladosporium in its current circumscription and re-allocated to other genera by the authors of this monograph or previous authors.
    Polyclonal Antibody-based ELISA in combination with specific PCR amplification of ITS 1 regions for the detection and quantitation of Lasiodiplodia theobromae, causal agent of 2 gummosis in cashew nut plants
    Muniz, C.R. ; Freire, F.C.O. ; Viana, F.M.P. ; Cardoso, J.E. ; Correia, D. ; Jalink, H. ; Kema, G.H.J. ; Silva, G.F. ; Guedes, M.I.F. - \ 2012
    Annals of Applied Biology 160 (2012)3. - ISSN 0003-4746 - p. 217 - 224.
    south-africa - sp-nov - botryosphaeriaceae - pathogens - endophytes - pinus - stem
    Members of Botryosphaeriaceae family are associated with serious diseases in different plants 18 across the world. In cashew nut plants (Anacardium occidentale L.), the fungus Lasiodiplodia 19 theobromae causes a severe group of symptoms related to gummosis that results in decreased nut 20 production. The aim of this work was to develop an indirect enzyme-linked immunosorbent 21 assay (ELISA) with sufficient sensitivity and specificity to detect the fungus both in vitro and in 22 planta (artificially and naturally infected) and to increase the detection specificity within the 23 fungi group using primers specific for the internal transcribed spacer (ITS) sequences. A 24 collection of L. theobromae isolates was obtained, and antisera against the fungus were raised in 25 rabbits. Cross-reactivity against Neofusicoccum sp., Colletotrichum gloeosporioides, Phomopsis 26 anacardii and Pestalotiopsis guepinii was examined. Naturally and artificially infected vegetal 27 material was employed in the ELISAs. The fungi ITS sequences were determined, and single 28 nucleotide polymorphisms were identified and used for primer design. For the naturally infected 29 2 plants, there was an approximately 4-fold variation in the absorbance values. Some positive 1 readings for asymptomatic samples were detected. For the artificially infected samples, an 2 ELISA-based weekly time-course analysis was conducted, and the values for samples from 0 and 3 7 days were lower than the threshold value. Beginning on day 14, the infection could be 4 detected, with rates varying from 40% on day 14 to 80% on day 21 and 100% by the end of the 5 experiment. The ITS sequencing revealed few polymorphisms among the L. theobromae isolates, 6 but for Colletotrichum gloeosporioides, Phomopsis anacardii, Pestalotiopsis guepinii and 7 Neofusicoccum sp., the sequences were sufficient to permit reliable discrimination. The 8 feasibility of ELISA as an early detection technique to assist in gummosis management was 9 demonstrated. PCR amplification based on ITS regions increases and complements serological 10 specificity
    Zhang, Y. ; Crous, P.W. ; Schoch, C.L. ; Hyde, K.D. - \ 2012
    Fungal Diversity 53 (2012)1. - ISSN 1560-2745 - p. 1 - 221.
    ribosomal dna-sequences - australian fresh-water - intertidal mangrove wood - sp-nov - north-america - marine fungi - molecular phylogeny - trematosphaeria-circinans - shiraia-bambusicola - multigene phylogeny
    One hundred and five generic types of Pleosporales are described and illustrated. A brief introduction and detailed history with short notes on morphology, molecular phylogeny as well as a general conclusion of each genus are provided. For those genera where the type or a representative specimen is unavailable, a brief note is given. Altogether 174 genera of Pleosporales are treated. Phaeotrichaceae as well as Kriegeriella, Zeuctomorpha and Muroia are excluded from Pleosporales. Based on the multigene phylogenetic analysis, the suborder Massarineae is emended to accommodate five families, viz. Lentitheciaceae, Massarinaceae, Montagnulaceae, Morosphaeriaceae and Trematosphaeriaceae.
    Degradation of 4-n-nonylphenol under nitrate reducing conditions
    Weert, J.P.A. de; Vinas, M. ; Grotenhuis, J.T.C. ; Rijnaarts, H.H.M. ; Langenhoff, A.A.M. - \ 2011
    Biodegradation 22 (2011)1. - ISSN 0923-9820 - p. 175 - 187.
    anaerobic degradation - desulfobacterium-phenolicum - polychlorinated-biphenyls - nonionic surfactants - sewage-sludge - n-hexadecane - sp-nov - nonylphenol - biodegradation - 4-nonylphenol
    Nonylphenol (NP) is an endocrine disruptor present as a pollutant in river sediment. Biodegradation of NP can reduce its toxicological risk. As sediments are mainly anaerobic, degradation of linear (4-n-NP) and branched nonylphenol (tNP) was studied under methanogenic, sulphate reducing and denitrifying conditions in NP polluted river sediment. Anaerobic bioconversion was observed only for linear NP under denitrifying conditions. The microbial population involved herein was further studied by enrichment and molecular characterization. The largest change in diversity was observed between the enrichments of the third and fourth generation, and further enrichment did not affect the diversity. This implies that different microorganisms are involved in the degradation of 4-n-NP in the sediment. The major degrading bacteria were most closely related to denitrifying hexadecane degraders and linear alkyl benzene sulphonate (LAS) degraders. The molecular structures of alkanes and LAS are similar to the linear chain of 4-n-NP, this might indicate that the biodegradation of linear NP under denitrifying conditions starts at the nonyl chain. Initiation of anaerobic NP degradation was further tested using phenol as a structure analogue. Phenol was chosen instead of an aliphatic analogue, because phenol is the common structure present in all NP isomers while the structure of the aliphatic chain differs per isomer. Phenol was degraded in all cases, but did not affect the linear NP degradation under denitrifying conditions and did not initiate the degradation of tNP and linear NP under the other tested conditions.
    A molecular, morphological and ecological re-appraisal of Venturiales¿a new order of Dothideomycetes
    Zhang, Y. ; Crous, P.W. ; Schoch, C.L. ; Bahkali, A.H. ; Guo, L.D. ; Hyde, K.D. - \ 2011
    Fungal Diversity 51 (2011)1. - ISSN 1560-2745 - p. 249 - 277.
    phylogenetic trees - bayesian-inference - sequence-data - apple scab - sp-nov - venturiaceae - genera - fungi - herpotrichiellaceae - classification
    The Venturiaceae was traditionally assigned to Pleosporales although its diagnostic characters readily distinguish it from other pleosporalean families. These include a parasitic or saprobic lifestyle, occurring on leaves or stems of dicotyledons; small to medium-sized ascomata, often with setae; deliquescing pseudoparaphyses; 8-spored, broadly cylindrical to obclavate asci; 1-septate, yellowish, greenish or pale brown to brown ascospores; and hyphomycetous anamorphs. Phylogenetically, core genera of Venturiaceae form a monophyletic clade within Dothideomycetes, and represent a separate sister lineage from current orders, thus a new order—Venturiales is introduced. A new family, Sympoventuriaceae, is introduced to accommodate taxa of a well-supported subclade within Venturiales, which contains Sympoventuria, Veronaeopsis simplex and Fusicladium-like species. Based on morphology and DNA sequence analysis, eight genera are included in Venturiaceae, viz. Acantharia, Apiosporina (including Dibotryon), Caproventuria, Coleroa, Pseudoparodiella, Metacoleroa, Tyrannosorus and Venturia. Molecular phylogenetic information is lacking for seven genera previously included in Venturiales, namely Arkoola, Atopospora, Botryostroma, Lasiobotrys, Trichodothella, Trichodothis and Rhizogenee and these are discussed, but their inclusion in Venturiaceae is doubtful. Crotone, Gibbera, Lineostroma, Phaeocryptopus, Phragmogibbera, Platychora, Polyrhizon, Rosenscheldiella, Uleodothis and Xenomeris are excluded from Venturiales, and their ordinal placement needs further investigation. Zeuctomorpha is treated as a synonym of Acantharia.
    Impact of subacute ruminal acidosis (SARA) adaptation and recovery on the density and diversity of bacteria in the rumen of dairy cows
    Hook, S.E. ; Steele, M.A. ; Northwood, K.S. ; Dijkstra, J. ; France, J. ; Wright, A.G. ; McBride, B.W. - \ 2011
    FEMS microbiology ecology 78 (2011)2. - ISSN 0168-6496 - p. 275 - 284.
    high-grain diet - real-time pcr - sp-nov - gen-nov - sequence - ph - dynamics - communities - population - cattle
    Subacute ruminal acidosis (SARA) is characterized by ruminal pH depression and microbial perturbation. The impact of SARA adaptation and recovery on rumen bacterial density and diversity was investigated following high-grain feeding. Four ruminally cannulated dairy cows were fed a hay diet, transitioned to a 65% grain diet for 3 weeks, and returned to the hay diet for 3 weeks. Rumen fluid, rumen solids, and feces were sampled during weeks 0 (hay), 1 and 3 (high grain), and 4 and 6 (hay). SARA was diagnosed during week 1, with a pH below 5.6 for 4.6±1.4 h. Bacterial density was significantly lower in the rumen solids with high grain (P=0.047). Rumen fluid clone libraries from weeks 0, 3, and 6 were assessed at the 98% level and 154 operational taxonomic units were resolved. Week 3 diversity significantly differed from week 0, and community structure differed from weeks 0 and 6 (P
    Biological treatment of refinery spent caustics under halo-alkaline conditions
    Graaff, M. de; Bijmans, M.F.M. ; Abbas, B. ; Euverink, G.J.W. ; Muyzer, G. ; Janssen, A.J.H. - \ 2011
    Bioresource Technology 102 (2011)15. - ISSN 0960-8524 - p. 7257 - 7264.
    sulfur-oxidizing bacteria - soda lake - sp-nov - oxidation processes - mono lake - gen. nov. - diversity - sulfide - water - bacteriochlorophyll
    The present research demonstrates the biological treatment of refinery sulfidic spent caustics in a continuously fed system under halo-alkaline conditions (i.e. pH 9.5; Na(+)= 0.8M). Experiments were performed in identical gas-lift bioreactors operated under aerobic conditions (80-90% saturation) at 35°C. Sulfide loading rates up to 27 mmol L(-1)day(-1) were successfully applied at a HRT of 3.5 days. Sulfide was completely converted into sulfate by the haloalkaliphilic sulfide-oxidizing bacteria belonging to the genus Thioalkalivibrio. Influent benzene concentrations ranged from 100 to 600 µM. At steady state, benzene was removed by 93% due to high stripping efficiencies and biodegradation. Microbial community analysis revealed the presence of haloalkaliphilic heterotrophic bacteria belonging to the genera Marinobacter, Halomonas and Idiomarina which might have been involved in the observed benzene removal. The work shows the potential of halo-alkaliphilic bacteria in mitigating environmental problems caused by alkaline waste.
    Exploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstruction
    Fang, K. ; Zhao, H. ; Changyue Sun, ; Lam, M.C. ; Chang, S. ; Zhang, K. ; Panda, G. ; Godinho, M. ; Martins Dos Santos, V.A.P. ; Wang, J. - \ 2011
    BMC Systems Biology 5 (2011). - ISSN 1752-0509 - 16 p.
    cystic-fibrosis sputum - coenzyme-a carboxylase - survival in-vivo - cepacia complex - pseudomonas-aeruginosa - escherichia-coli - drug targets - sp-nov - antimicrobial peptides - core-oligosaccharide
    BACKGROUND: Burkholderia cenocepacia is a threatening nosocomial epidemic pathogen in patients with cystic fibrosis (CF) or a compromised immune system. Its high level of antibiotic resistance is an increasing concern in treatments against its infection. Strain B. cenocepacia J2315 is the most infectious isolate from CF patients. There is a strong demand to reconstruct a genome-scale metabolic network of B. cenocepacia J2315 to systematically analyze its metabolic capabilities and its virulence traits, and to search for potential clinical therapy targets. RESULTS: We reconstructed the genome-scale metabolic network of B. cenocepacia J2315. An iterative reconstruction process led to the establishment of a robust model, iKF1028, which accounts for 1,028 genes, 859 internal reactions, and 834 metabolites. The model iKF1028 captures important metabolic capabilities of B. cenocepacia J2315 with a particular focus on the biosyntheses of key metabolic virulence factors to assist in understanding the mechanism of disease infection and identifying potential drug targets. The model was tested through BIOLOG assays. Based on the model, the genome annotation of B. cenocepacia J2315 was refined and 24 genes were properly re-annotated. Gene and enzyme essentiality were analyzed to provide further insights into the genome function and architecture. A total of 45 essential enzymes were identified as potential therapeutic targets. CONCLUSIONS: As the first genome-scale metabolic network of B. cenocepacia J2315, iKF1028 allows a systematic study of the metabolic properties of B. cenocepacia and its key metabolic virulence factors affecting the CF community. The model can be used as a discovery tool to design novel drugs against diseases caused by this notorious pathogen
    Microbiota of cocoa powder with particular reference to aerobic thermoresistant spore-formers
    Líma, L.J.R. ; Kamphuis, H.J. ; Nout, M.J.R. ; Zwietering, M.H. - \ 2011
    Food Microbiology 28 (2011)3. - ISSN 0740-0020 - p. 573 - 582.
    bacillus-subtilis - heat-resistance - sp-nov - aflp - heterogeneity - bacteria - sequence - strains - milk - rna
    The microbiological criteria of commercial cocoa powder are defined in guidelines instituted by the cocoa industry. Twenty-five commercial samples were collected with the aim of assessing the compliance with the microbiological quality guidelines and investigating the occurrence and properties of aerobic Thermoresistant Spores (ThrS). Seventeen samples complied with the guidelines, but one was positive for Salmonella, five for Enterobacteriaceae and two had mould levels just exceeding the maximum admissible level. The treatment of the cocoa powder suspensions from 100 °C to 170 °C for 10 min, revealed the presence of ThrS in 36% of the samples. In total 61 ThrS strains were isolated, of which the majority belonged to the Bacillus subtilis complex (65.6%). Strains resporulation and spore crops inactivation at 110 °C for 5 min showed a wide diversity of heat-resistance capacities. Amplified fragment length polymorphism analysis revealed not only a large intraspecies diversity, but also different clusters of heat-resistant spore-forming strains. The heat-resistance of spores of six B. subtilis complex strains was further examined by determination of their D and z-values. We concluded that B. subtilis complex spores, in particular those from strain M112, were the most heat-resistant and these may survive subsequent preservation treatments, being potentially problematic in food products, such as chocolate milk
    Hydrogenotrophic Sulfate Reduction in a Gas-Lift Bioreactor Operated at 9 degrees C
    Nevatalo, L.M. ; Bijmans, M.F.M. ; Lens, P.N.L. ; Kaksonen, A.H. ; Puhakka, J.A. - \ 2010
    Journal of Microbiology and Biotechnology 20 (2010)3. - ISSN 1017-7825 - p. 615 - 621.
    reducing bacteria - retention time - carbon-dioxide - growth-rate - sp-nov - reactor - temperature - methanogenesis - oxidation - sulfide
    The viability of low-temperature sulfate reduction with hydrogen as electron donor was studied with a bench-scale gas-lift bioreactor (GLB) operated at 9 degrees C. Prior to the GLB experiment, the temperature range of sulfate reduction of the inoculum was assayed. The results of the temperature gradient assay indicated that the inoculum was a psychrotolerant mesophilic enrichment culture that had an optimal temperature for sulfate reduction of 31 degrees C, and minimum and maximum temperatures of 7 degrees C and 41 degrees C, respectively. In the GLB experiment at 9 degrees C, a sulfate reduction rate of 500-600 mg l(-1) d(-1), corresponding to a specific activity of 173 mg SO42- g VSS-1 d(-1), was obtained. The electron flow from the consumed H-2-gas to sulfate reduction varied between 27% and 52%, whereas the electron flow to acetate production decreased steadily from 15% to 5%. No methane was produced. Acetate was produced from CO2 and H-2 by homoacetogenic bacteria. Acetate supported the growth of some heterotrophic sulfate-reducing bacteria. The sulfate reduction rate in the GLB was limited by the slow biomass growth rate at 9 degrees C and low biomass retention in the reactor. Nevertheless, this study demonstrated the potential sulfate reduction rate of psychrotolerant sulfate-reducing mesophiles at suboptimal temperature.
    Isolation and Partial Characterization of Bacterial Strains on Low Organic Carbon Medium from Soils Fertilized with Different Organic Amendments
    Senechkin, I.V. ; Speksnijder, A.G.C.L. ; Semenov, A.M. ; Bruggen, A.H.C. van; Overbeek, L.S. van - \ 2010
    Microbial Ecology 60 (2010)4. - ISSN 0095-3628 - p. 829 - 839.
    16s ribosomal-rna - oligotrophic bacteria - bradyrhizobium-japonicum - microbial-populations - sp-nov - diversity - community - nitrogen - dynamics - roots
    A total of 720 bacterial strains were isolated from soils with four different organic amendment regimes on a low organic carbon (low-C) agar medium (10 mu g C ml(-1)) traditionally used for isolation of oligotrophs. Organic amendments in combination with field history resulted in differences in dissolved organic carbon contents in these soils. There were negative correlations between total and dissolved organic carbon content and the number of isolates on low-C agar medium, whereas these correlations were absent for bacterial strains isolated from the same soil on high-C agar medium (1,000 mu g C ml(-1)). Repeated transfers (up to ten times) of the isolates from low-C agar medium to fresh low- and high-C agar media were done to test for exclusive growth under oligotrophic conditions. The number of isolates exclusively growing under oligotrophic conditions dropped after each subsequent transfer from 241 after the first to 98 after the third transfer step. Identification on the basis of partial 16S rRNA gene sequences revealed that most of the 241 isolates (as well as the subset of 98 isolates) belong to widespread genera such as Streptomyces, Rhizobium, Bradyrhizobium, and Mesorhizobium, and the taxonomic composition of dominant genera changed from the first transfer step to the third. A selected subset of 17 isolates were further identified and characterized for exclusive growth on low-C agar medium. Two isolates continued to grow only on low-C agar medium up to the tenth transfer step and matched most closely with Rhizobium sullae and an uncultured bacterium on the basis of the almost full-length 16S rRNA gene. It was concluded that the vast majority of strains which are isolated on low-C agar media belong to the trophic group of microorganisms adapted to a "broad range" of carbon concentrations, including well-known and widespread bacterial genera. Oligotrophy is a physiological, not a taxonomic property, and can only be identified by cultural means so far. We showed that true oligotrophs that are unable to grow on high carbon media are rare and belong to genera that also contain broad-range and copiotrophic strains.
    Sequence data reveals phylogenetic affinities of fungal anamorphs Bahusutrabeeja, Diplococcium, Natarajania, Paliphora, Polyschema, Rattania and Spadicoides
    Shenoy, B.D. ; Jeewon, R. ; Wang, H. ; Amandeep, K. ; Ho, W.H. ; Bhat, D.J. ; Crous, P.W. ; Hyde, K.D. - \ 2010
    Fungal Diversity 44 (2010)1. - ISSN 1560-2745 - p. 161 - 169.
    sp-nov - sensu-lato - molecular systematics - polyphasic approach - submerged wood - western-ghats - allied genera - hong-kong - gen. nov - chaetosphaeria
    Partial 28S rRNA gene sequence-data of the strains of the anamorphic genera Bahusutrabeeja, Diplococcium, Natarajania, Paliphora, Polyschema, Rattania and Spadicoides were analysed to predict their phylogenetic relationships and taxonomic placement within the Ascomycota. Results indicate that Diplococcium and morphologically similar genera, i.e. Spadicoides, Paliphora and Polyschema do not share a recent common ancestor. The type species of Diplococcium, D. spicatum is referred to Helotiales (Leotiomycetes). The placement of Spadicoides bina, the type of the genus, is unresolved but it is shown to be closely associated with Porosphaerella species, which are sister taxa to Coniochaetales (Sordariomycetes). Three Polyschema species analysed in this study represent a monophyletic lineage and are related to Lentithecium fluviatile and Leptosphaeria calvescens in Pleosporales (Dothideomycetes). DNA sequence analysis also suggests that Paliphora intermedia is a member of Chaetosphaeriaceae (Sordariomycetes). The type species of Bahusutrabeeja, B. dwaya, is phylogenetically related to Neodeightonia (=Botryosphaeria) subglobosa in Botryosphaeriales (Dothideomycetes). Monotypic genera Natarajania and Rattania are phylogenetically related to members of Diaporthales and Chaetosphaeriales, respectively. Future studies with extended gene datasets and type strains are required to resolve many novel but morphologically unexplainable phylogenetic scenarios revealed from this study. It is increasingly becoming evident that a fungal
    A case for re-inventory of Australia’s plant pathogens
    Hyde, K.D. ; Chomnunti, P. ; Crous, P.W. ; Groenewald, J.Z. ; Damm, U. ; Ko Ko, T.W. ; Shivas, R.G. ; Summerell, B.A. ; Tan, Y.P. - \ 2010
    Persoonia 25 (2010). - ISSN 0031-5850 - p. 50 - 60.
    phenotypic characters differentiate - multiple gene genealogies - sp-nov - western-australia - south-africa - colletotrichum-gloeosporioides - mycosphaerella-spp. - molecular phylogeny - polyphasic approach - cryptic speciation
    Australia has efficient and visible plant quarantine measures, which through various border controls and survey activities attempt to prevent the entry of unwanted pests and diseases. The ability to successfully perform this task relies heavily on determining what pathogens are present and established in Australia as well as those pathogens that are exotic and threatening. There are detailed checklists and databases of fungal plant pathogens in Australia, compiled, in part, from surveys over many years sponsored by Federal and State programmes. These checklists and databases are mostly specimen-based, which enables validation of records with reference herbarium specimens and sometimes associated cultures. Most of the identifications have been based on morphological examination. The use of molecular methods, particularly the analysis of DNA sequence data, has recently shown that several well-known and important plant pathogenic species are actually complexes of cryptic species. We provide examples of this in the important plant pathogenic genera Botryosphaeria and its anamorphs, Colletotrichum, Fusarium, Phomopsis / Diaporthe and Mycosphaerella and its anamorphs. The discovery of these cryptic species indicates that many of the fungal names in checklists need scrutiny. It is difficult, and often impossible, to extract DNA for sequence analysis from herbarium specimens in order to validate identifications that may now be considered suspect. This validation can only be done if specimens are recollected, re-isolated and subjected to DNA analysis. Where possible, herbarium specimens as well as living cultures are needed to support records. Accurate knowledge of the plant pathogens within Australia's borders is an essential prerequisite for the effective discharge of plant quarantine activities that will prevent or delay the arrival of unwanted plant pathogens.
    (Per)chlorate reduction by an acetogenic bacterium, Sporomusa sp., isolated from an underground gas storage
    Balk, M. ; Mehboob, F. ; Gelder, A.H. van; Rijpstra, I. ; Sinninghe-Damsté, J.S. ; Stams, A.J.M. - \ 2010
    Applied Microbiology and Biotechnology 88 (2010)2. - ISSN 0175-7598 - p. 595 - 603.
    sp-nov - homoacetogenic bacterium - strain gr-1 - perchlorate - chlorate - metabolism - water - milk - soil - identification
    A mesophilic bacterium, strain An4, was isolated from an underground gas storage reservoir with methanol as substrate and perchlorate as electron acceptor. Cells were Gram-negative, spore-forming, straight to curved rods, 0.5-0.8 microm in diameter, and 2-8 microm in length, growing as single cells or in pairs. The cells grew optimally at 37 degrees C, and the pH optimum was around 7. Strain An4 converted various alcohols, organic acids, fructose, acetoin, and H(2)/CO(2) to acetate, usually as the only product. Succinate was decarboxylated to propionate. The isolate was able to respire with (per)chlorate, nitrate, and CO(2). The G+C content of the DNA was 42.6 mol%. Based on the 16S rRNA gene sequence analysis, strain An4 was most closely related to Sporomusa ovata (98% similarity). The bacterium reduced perchlorate and chlorate completely to chloride. Key enzymes, perchlorate reductase and chlorite dismutase, were detected in cell-free extracts
    Novel fungal genera and species associated with the sooty blotch and flyspeck complex on apple in China and the USA
    Yang, H.L. ; Sun, G.Y. ; Batzer, J.C. ; Crous, P.W. ; Groenewald, J.Z. ; Gleason, M.L. - \ 2010
    Persoonia (2010)24. - ISSN 0031-5850 - p. 29 - 37.
    ribosomal dna - sp-nov - sporidesmium - sequences - disease
    Fungi in the sooty blotch and flyspeck (SBFS) complex cause blemishes on apple and pear fruit that result in economic losses for growers. The SBFS fungi colonise the epicuticular wax layer of pomaceous fruit but do not invade the cuticle. Fungi causing fuliginous and punctate mycelial types on apple are particularly difficult to identify based on morphological criteria because many species in the SBFS complex share the same mycelial phenotypes. We compared the morphology and nuclear ribosomal DNA phylogeny (ITS, LSU) of 11 fungal strains isolated from SBFS blemishes on apple obtained from two provinces in China and five states in the USA. Parsimony analysis, supported by cultural characteristics and morphology in vitro, provided support to delimit the isolates into three novel genera, representing five new species. Phaeothecoidiella, with two species, P. missouriensis and P. illinoisensis, is introduced as a new genus with pigmented endoconidia in the Dothideomycetes. Houjia (Capnodiales) is introduced for H. pomigena and H. yanglingensis. Although morphologically similar to Stanjehughesia (Chaetosphaeriaceae), Houjia is distinct in having solitary conidiogenous cells. Sporidesmajora (Capnodiales), based on S. pennsylvaniensis, is distinguished from Sporidesmium (Sordariomycetes) in having long, multiseptate conidiophores that frequently have a subconical, darkly pigmented apical cell, and very long, multi-euseptate conidia
    Phylogeny and systematics of the genus Calonectria
    Lombard, L. ; Crous, P.W. ; Wingfield, B.D. ; Wingfield, M.J. - \ 2010
    Studies in Mycology 66 (2010)1. - ISSN 0166-0616 - p. 31 - 69.
    internal transcribed spacers - sp-nov - cylindrocladium-floridanum - species concepts - dna-sequences - ribosomal dna - beta-tubulin - morphology - polymorphism - spathiphylli
    Species of Calonectria are important plant pathogens, several of which have a worldwide distribution. Contemporary taxonomic studies on these fungi have chiefly relied on DNA sequence comparisons of the ß-tubulin gene region. Despite many new species being described, there has been no phylogenetic synthesis for the group since the last monographic study almost a decade ago. In the present study, the identity of a large collection of Calonectria isolates from various geographic regions was determined using morphological and DNA sequence comparisons. This resulted in the discovery of seven new species; Ca. densa, Ca. eucalypti, Ca. humicola, Ca. orientalis, Ca. pini, Ca. pseudoscoparia and Ca. sulawesiensis, bringing the total number of currently accepted Calonectria species to 68. A multigene phylogeny was subsequently constructed for all available Calonectria spp., employing seven gene regions, namely actin, ß-tubulin, calmodulin, histone H3, the internal transcribed spacer regions 1 and 2 and the 5.8S gene of the ribosomal RNA, 28S large subunit RNA gene and translation elongation 1-alpha. Based on these data 13 phylogenetic groups could be distinguished within the genus Calonectria that correlated with morphological features. Dichotomous and synoptic keys to all Calonectria spp. currently recognised are also provided.
    Highlights of the Didymellaceae: A polyphasic approach to characterise Phoma and related pleosporalean genera
    Aveskamp, M.M. ; Gruyter, J. de; Woudenberg, J.H.C. ; Verkley, G.J.M. ; Crous, P.W. - \ 2010
    Studies in Mycology 65 (2010)1. - ISSN 0166-0616 - p. 1 - 60.
    ribosomal dna-sequences - powdery mildew fungi - transcribed spacer sequences - medicaginis var pinodella - maculans species complex - 7 mu-m - leptosphaeria-maculans - sp-nov - genetic diversity - ascochyta-rabiei
    Fungal taxonomists routinely encounter problems when dealing with asexual fungal species due to poly- and paraphyletic generic phylogenies, and unclear species boundaries. These problems are aptly illustrated in the genus Phoma. This phytopathologically significant fungal genus is currently subdivided into nine sections which are mainly based on a single or just a few morphological characters. However, this subdivision is ambiguous as several of the section-specific characters can occur within a single species. In addition, many teleomorph genera have been linked to Phoma, three of which are recognised here. In this study it is attempted to delineate generic boundaries, and to come to a generic circumscription which is more correct from an evolutionary point of view by means of multilocus sequence typing. Therefore, multiple analyses were conducted utilising sequences obtained from 28S nrDNA (Large Subunit - LSU), 18S nrDNA (Small Subunit - SSU), the Internal Transcribed Spacer regions 1 & 2 and 5.8S nrDNA (ITS), and part of the ß-tubulin (TUB) gene region. A total of 324 strains were included in the analyses of which most belonged to Phoma taxa, whilst 54 to related pleosporalean fungi. In total, 206 taxa were investigated, of which 159 are known to have affinities to Phoma. The phylogenetic analysis revealed that the current Boeremaean subdivision is incorrect from an evolutionary point of view, revealing the genus to be highly polyphyletic. Phoma species are retrieved in six distinct clades within the Pleosporales, and appear to reside in different families. The majority of the species, however, including the generic type, clustered in a recently established family, Didymellaceae. In the second part of this study, the phylogenetic variation of the species and varieties in this clade was further assessed. Next to the genus Didymella, which is considered to be the sole teleomorph of Phoma s. str., we also retrieved taxa belonging to the teleomorph genera Leptosphaerulina and Macroventuria in this clade. Based on the sequence data obtained, the Didymellaceae segregate into at least 18 distinct clusters, of which many can be associated with several specific taxonomic characters. Four of these clusters were defined well enough by means of phylogeny and morphology, so that the associated taxa could be transferred to separate genera. Aditionally, this study addresses the taxonomic description of eight species and two varieties that are novel to science, and the recombination of 61 additional taxa.
    Biohydrogen production from untreated and hydrolyzed potato steam peels by the extreme thermophiles Caldicellulosiruptor saccharolyticus and Thermotoga neapolitana
    Mars, A.E. ; Veuskens, T. ; Budde, M.A.W. ; Doeveren, P.F.N.M. van; Lips, S.J.J. ; Bakker, R.R. ; Vrije, G.J. de; Claassen, P.A.M. - \ 2010
    International Journal of Hydrogen Energy 35 (2010)15. - ISSN 0360-3199 - p. 7730 - 7737.
    fermentative hydrogen-production - sp-nov - starch - bacterium - waste - microflora - substrate
    Production of hydrogen by the extreme thermophiles Caldicellulosiruptor saccharolyticus and Thermotoga neapolitana was studied in serum flasks and in pH-controlled bioreactors with glucose, and hydrolyzed and untreated potato steam peels (PSP) as carbon sources. Two types of PSP hydrolysates were used: one in which the starch in the PSP was liquefied with alpha-amylase, and one in which the liquefied starch was further hydrolyzed to glucose by amyloglucosidase. When the PSP hydrolysates or untreated PSP were added at circa 10–14 g/L of glucose units, both strains grew well and produced hydrogen with reasonable to high molar yields (2.4–3.8 moles H2/mole glucose units), and no significant production of lactate. The hydrogen production rates and yields were similar with untreated PSP, hydrolyzed PSP, and pure glucose, showing that C. saccharolyticus and T. neapolitana are well equipped for the utilization of starch. When the concentrations of the substrates were increased, growth and hydrogen production of both strains were hampered. At substrate concentrations of circa 30–40 g/L of glucose units, the molar hydrogen yield of C. saccharolyticus was severely reduced due to the formation of high amounts of lactate, while T. neapolitana was unable to grow at all. The results showed that PSP and PSP hydrolysates are very suitable substrates for efficient fermentative hydrogen production at moderate substrate loadings.
    Population Dynamics of a Single-Stage Sulfidogenic Bioreactor Treating Synthetic Zinc-Containing Waste Streams
    Dar, S.A. ; Bijmans, M.F.M. ; Dinkla, I.J.T. ; Geurkink, B. ; Lens, P.N.L. ; Dopson, M. - \ 2009
    Microbial Ecology 58 (2009)3. - ISSN 0095-3628 - p. 529 - 537.
    sulfate-reducing bacteria - gradient gel-electrophoresis - polymerase-chain-reaction - scatologenes strain sl1 - acid-mine drainage - environmental-samples - microbial diversity - sulfide toxicity - ribosomal-rna - sp-nov
    Waste streams from industrial processes such as metal smelting or mining contain high concentrations of sulfate and metals with low pH. Dissimilatory sulfate reduction carried out by sulfate-reducing bacteria (SRB) at low pH can combine sulfate reduction with metal-sulfide precipitation and thus open possibilities for selective metal recovery. This study investigates the microbial diversity and population changes of a single-stage sulfidogenic gas-lift bioreactor treating synthetic zinc-rich waste water at pH 5.5 by denaturing gradient gel electrophoresis of 16S rRNA gene fragments and quantitative polymerase chain reaction. The results indicate the presence of a diverse range of phylogenetic groups with the predominant microbial populations belonging to the Desulfovibrionaceae from delta-Proteobacteria. Desulfovibrio desulfuricans-like populations were the most abundant among the SRB during the three stable phases of varying sulfide and zinc concentrations and increased from 13% to 54% of the total bacterial populations over time. The second largest group was Desulfovibrio marrakechensis-like SRB that increased from 1% to about 10% with decreasing sulfide concentrations. Desulfovibrio aminophilus-like populations were the only SRB to decrease in numbers with decreasing sulfide concentrations. However, their population was <1% of the total bacterial population in the reactor at all analyzed time points. The number of dissimilatory sulfate reductase (DsrA) gene copies per number of SRB cells decreased from 3.5 to 2 DsrA copies when the sulfide concentration was reduced, suggesting that the cells' sulfate-reducing capacity was also lowered. This study has identified the species present in a single-stage sulfidogenic bioreactor treating zinc-rich wastewater at low pH and provides insights into the microbial ecology of this biotechnological process.
    Multi-locus phylogeny of Pleosporales: a taxonomic, ecological and evolutionary re-evaluation
    Zhang, Y. ; Schoch, C.L. ; Fournier, J. ; Crous, P.W. ; Gruyter, J. de; Woudenberg, J.H.C. ; Hirayama, K. ; Tanaka, K. ; Pointing, S.B. ; Spatafora, J.W. ; Hyde, K.D. - \ 2009
    Studies in Mycology 64 (2009)1. - ISSN 0166-0616 - p. 85 - 102.
    ribosomal dna-sequences - stagonospora-nodorum - molecular phylogeny - leptosphaeria-maculans - phaeosphaeria-nodorum - multigene phylogeny - multiple alignment - endophytic fungi - sp-nov - ascomycota
    Five loci, nucSSU, nucLSU rDNA, TEF1, RPB1 and RPB2, are used for analysing 129 pleosporalean taxa representing 59 genera and 15 families in the current classification of Pleosporales. The suborder Pleosporineae is emended to include four families, viz. Didymellaceae, Leptosphaeriaceae, Phaeosphaeriaceae and Pleosporaceae. In addition, two new families are introduced, i.e. Amniculicolaceae and Lentitheciaceae. Pleomassariaceae is treated as a synonym of Melanommataceae, and new circumscriptions of Lophiostomataceae s. str, Massarinaceae and Lophiotrema are proposed. Familial positions of Entodesmium and Setomelanomma in Phaeosphaeriaceae, Neophaeosphaeria in Leptosphaeriaceae, Leptosphaerulina, Macroventuria and Platychora in Didymellaceae, Pleomassaria in Melanommataceae and Bimuria, Didymocrea, Karstenula and Paraphaeosphaeria in Montagnulaceae are clarified. Both ecological and morphological characters show varying degrees of phylogenetic significance. Pleosporales is most likely derived from a saprobic ancestor with fissitunicate asci containing conspicuous ocular chambers and apical rings. Nutritional shifts in Pleosporales likely occured from saprotrophic to hemibiotrophic or biotrophic.
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