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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    Host-specific microbial communities in three sympatric North Sea sponges
    Naim, M.A. ; Morillo, J.A. ; Sørensen, S.J. ; Waleed, A.A. ; Smidt, H. ; Sipkema, D. - \ 2014
    FEMS microbiology ecology 90 (2014)2. - ISSN 0168-6496 - p. 390 - 403.
    ribosomal-rna genes - marine sponges - halichondria-panicea - bacterial communities - abundance sponges - genomic insights - sequence data - diversity - symbionts - chlamydiae
    The establishment of next-generation technology sequencing has deepened our knowledge of marine sponge-associated microbiota with the identification of at least 32 phyla of Bacteria and Archaea from a large number of sponge species. In this study, we assessed the diversity of the microbial communities hosted by three sympatric sponges living in a semi-enclosed North Sea environment using pyrosequencing of bacterial and archaeal 16S ribosomal RNA gene fragments. The three sponges harbor species-specific communities each dominated by a different class of Proteobacteria. An a-proteobacterial Rhodobacter-like phylotype was confirmed as the predominant symbiont of Halichondria panicea. The microbial communities of Haliclona xena and H. oculata are described for the first time in this study and are dominated by Gammaproteobacteria and Betaproteobacteria, respectively. Several common phylotypes belonging to Chlamydiae, TM6, Actinobacteria, and Betaproteobacteria were detected in all sponge samples. A number of phylotypes of the phylum Chlamydiae were present at an unprecedentedly high relative abundance of up to 14.4 ± 1.4% of the total reads, which suggests an important ecological role in North Sea sponges. These Chlamydiae-affiliated operational taxonomic units may represent novel lineages at least at the genus level as they are only 86–92% similar to known sequences.
    Fungal Planet description sheets: 214–280
    Crous, P.W. ; Shivas, R.G. ; Quaedvlieg, W. ; Bank, M. van der; Zhang, Y. ; Summerell, B.A. ; Guarro, J. ; Wingfield, M.J. ; Wood, A.R. ; Alfenas, A.C. ; Braun, U. ; Cano-Lira, J.F. ; Garcia, D. ; Marin-Felix, Y. ; Alvarado, P. ; Andrade, J.P. ; Armengol, J. ; Assefa, A. ; Breeÿen, A. den; Camele, I. ; Cheewangkoon, R. ; Souza, J.T. De; Duong, T.A. ; Esteve-Raventós, F. ; Fournier, J. ; Frisullo, S. ; García-Jiménez, J. ; Gardiennet, A. ; Gené, J. ; Hernández-Restrepo, M. ; Hirooka, Y. ; Hospenthal, D.R. ; King, A. ; Lechat, C. ; Lombard, L. ; Mang, S.M. ; Marbach, P.A.S. ; Marincowitz, S. ; Montaño-Mata, N.J. ; Moreno, G. ; Perez, C.A. ; Pérez Sierra, A.M. ; Robertson, J.L. ; Roux, J. ; Rubio, E. ; Schumacher, R.K. ; Stchigel, A.M. ; Sutton, D.A. ; Tan, Y.P. ; Thompson, E.H. ; Vanderlinde, E. ; Walker, A.K. ; Walker, D.M. ; Wickes, B.L. ; Wong, P.T.W. ; Groenewald, J.Z. - \ 2014
    Persoonia 32 (2014). - ISSN 0031-5850 - p. 184 - 306.
    sp-nov - phylogeny reveals - eucalyptus-microfungi - host-associations - gene phylogeny - sequence data - diaporthales - morphology - gnomoniaceae - conioscypha
    Novel species of microfungi described in the present study include the following from South Africa: Cercosporella dolichandrae from Dolichandra unguiscati, Seiridium podocarpi from Podocarpus latifolius, Pseudocercospora parapseudarthriae from Pseudarthria hookeri, Neodevriesia coryneliae from Corynelia uberata on leaves of Afrocarpus falcatus, Ramichloridium eucleae from Euclea undulata and Stachybotrys aloeticola from Aloe sp. (South Africa), as novel member of the Stachybotriaceae fam. nov. Several species were also described from Zambia, and these include Chaetomella zambiensis on unknown Fabaceae, Schizoparme pseudogranati from Terminalia stuhlmannii, Diaporthe isoberliniae from Isoberlinia angolensis, Peyronellaea combreti from Combretum mossambiciensis, Zasmidium rothmanniae and Phaeococcomyces rothmanniae from Rothmannia engleriana, Diaporthe vangueriae from Vangueria infausta and Diaporthe parapterocarpi from Pterocarpus brenanii. Novel species from the Netherlands include: Stagonospora trichophoricola, Keissleriella trichophoricola and Dinemasporium trichophoricola from Trichophorum cespitosum, Phaeosphaeria poae, Keissleriella poagena, Phaeosphaeria poagena, Parastagonospora poagena and Pyrenochaetopsis poae from Poa sp., Septoriella oudemansii from Phragmites australis and Dendryphion europaeum from Hedera helix (Germany) and Heracleum sphondylium (the Netherlands). Novel species from Australia include: Anungitea eucalyptorum from Eucalyptus leaf litter, Beltraniopsis neolitseae and Acrodontium neolitseae from Neolitsea australiensis, Beltraniella endiandrae from Endiandra introrsa, Phaeophleospora parsoniae from Parsonia straminea, Penicillifer martinii from Cynodon dactylon, Ochroconis macrozamiae from Macrozamia leaf litter, Triposporium cycadicola, Circinotrichum cycadis, Cladosporium cycadicola and Acrocalymma cycadis from Cycas spp. Furthermore, Vermiculariopsiella dichapetali is described from Dichapetalum rhodesicum (Botswana), Marasmius vladimirii from leaf litter (India), Ophiognomonia acadiensis from Picea rubens (Canada), Setophoma vernoniae from Vernonia polyanthes and Penicillium restingae from soil (Brazil), Pseudolachnella guaviyunis from Myrcianthes pungens (Uruguay) and Pseudocercospora neriicola from Nerium oleander (Italy). Novelties from Spain include: Dendryphiella eucalyptorum from Eucalyptus globulus, Conioscypha minutispora from dead wood, Diplogelasinospora moalensis and Pseudoneurospora canariensis from soil and Inocybe lanatopurpurea from reforested woodland of Pinus spp. Novelties from France include: Kellermania triseptata from Agave angustifolia, Zetiasplozna acaciae from Acacia melanoxylon, Pyrenochaeta pinicola from Pinus sp. and Pseudonectria rusci from Ruscus aculeatus. New species from China include: Dematiocladium celtidicola from Celtis bungeana, Beltrania pseudorhombica, Chaetopsina beijingensis and Toxicocladosporium pini from Pinus spp. and Setophaeosphaeria badalingensis from Hemerocallis fulva. Novel genera of Ascomycetes include Alfaria from Cyperus esculentus (Spain), Rinaldiella from a contaminated human lesion (Georgia), Hyalocladosporiella from Tectona grandis (Brazil), Pseudoacremonium from Saccharum spontaneum and Melnikomyces from leaf litter (Vietnam), Annellosympodiella from Juniperus procera (Ethiopia), Neoceratosperma from Eucalyptus leaves (Thailand), Ramopenidiella from Cycas calcicola (Australia), Cephalotrichiella from air in the Netherlands, Neocamarosporium from Mesembryanthemum sp. and Acervuloseptoria from Ziziphus mucronata (South Africa) and Setophaeosphaeria from Hemerocallis fulva (China). Several novel combinations are also introduced, namely for Phaeosphaeria setosa as Setophaeosphaeria setosa, Phoma heteroderae as Peyronellaea heteroderae and Phyllosticta maydis as Peyronellaea maydis. Morphological and culture characteristics along with ITS DNA barcodes are provided for all taxa.
    Influence of setup and carbon source on the bacterial community of biocathodes in microbial electrolysis cells
    Croesea, E. ; Jeremiasse, A.W. ; Marshall, I.P.G. ; Spormann, A.M. ; Euverink, G.J.W. ; Geelhoed, J.S. ; Stams, A.J.M. ; Plugge, C.M. - \ 2014
    Enzyme and Microbial Technology 61-62 (2014). - ISSN 0141-0229 - p. 67 - 75.
    hydrogen-production - fuel-cells - desulfovibrio-vulgaris - sp-nov. - sequence data - gen. nov. - diversity - system - classification - acetate
    The microbial electrolysis cell (MEC) biocathode has shown great potential as alternative for expensive metals as catalyst for H2 synthesis. Here, the bacterial communities at the biocathode of five hydrogen producing MECs using molecular techniques were characterized. The setups differed in design (large versus small) including electrode material and flow path and in carbon source provided at the cathode (bicarbonate or acetate). A hydrogenase gene-based DNA microarray (Hydrogenase Chip) was used to analyze hydrogenase genes present in the three large setups. The small setups showed dominant groups of Firmicutes and two of the large setups showed dominant groups of Proteobacteria and Bacteroidetes. The third large setup received acetate but no sulfate (no sulfur source). In this setup an almost pure culture of a Promicromonospora sp. developed. Most of the hydrogenase genes detected were coding for bidirectional Hox-type hydrogenases, which have shown to be involved in cytoplasmatic H2 production.
    Anaerobic benzene degradation under denitrifying conditions: Peptococcaceae was identified as dominant benzene degrader by Stable Isotope Probing (SIP)
    Zaan, B.M. van der; Talarico Saia, F. ; Plugge, C.M. ; Vos, W.M. de; Smidt, H. ; Stams, A.J.M. ; Langenhoff, A.A.M. ; Gerritse, J. - \ 2012
    Environmental Microbiology 14 (2012)5. - ISSN 1462-2912 - p. 1171 - 1181.
    reducing enrichment culture - molecular characterization - microbial communities - contaminated aquifer - nitrate reduction - sequence data - bacteria - identification - oxidation - biodegradation
    An anaerobic microbial community was enriched in a chemostat that was operated for more than 8 years with benzene and nitrate as electron acceptor. The coexistence of multiple species in the chemostat and the presence of a biofilm, led to the hypothesis that benzene-degrading species coexist in a syntrophic interaction, and that benzene can be degraded in syntrophy by consortia with various electron acceptors in the same culture. The benzene-degrading microorganisms were identified by DNA-stable isotope probing with [U-(13) C]-labelled benzene, and the effect of different electron donors and acceptors on benzene degradation was investigated. The degradation rate constant of benzene with nitrate (0.7 day(-1) ) was higher than reported previously. In the absence of nitrate, the microbial community was able to use sulfate, chlorate or ferric iron as electron acceptor. Bacteria belonging to the Peptococcaceae were identified as dominant benzene consumers, but also those related to Rhodocyclaceae and Burkholderiaceae were found to be associated with the anaerobic benzene degradation process. The benzene degradation activity in the chemostat was associated with microbial growth in biofilms. This, together with the inhibiting effect of hydrogen and the ability to degrade benzene with different electron acceptors, suggests that benzene was degraded via a syntrophic process
    A new subfamilial and tribal classification of the pantropical flowering plant family Annonaceae informed by molecular phylogenetics
    Chatrou, L.W. ; Pirie, M.D. ; Erkens, R.H.J. ; Couvreur, T.L.P. ; Neubig, K.M. ; Abbott, J.R. ; Mols, J.B. - \ 2012
    Botanical Journal of the Linnean Society 169 (2012)1. - ISSN 0024-4074 - p. 5 - 40.
    historical biogeography - anaxagorea annonaceae - maximum-likelihood - uvaria annonaceae - character evolution - taxonomic revision - neotropical genera - sequence data - mixed models - missing data
    The pantropical flowering plant family Annonaceae is the most species-rich family of Magnoliales. Despite long-standing interest in the systematics of Annonaceae, no authoritative classification has yet been published in the light of recent molecular phylogenetic analyses. Here, using the largest, most representative, molecular dataset compiled on Annonaceae to date, we present, for the first time, a robust family-wide phylogenetic tree and subsequent classification. We used a supermatrix of up to eight plastid markers sequenced from 193 ingroup and seven outgroup species. Some of the relationships at lower taxonomic levels are poorly resolved, but deeper nodes generally receive high support. Annonaceae comprises four major clades, which are here given the taxonomic rank of subfamily. The description of Annonoideae is amended, and three new subfamilies are described: Anaxagoreoideae, Ambavioideae and Malmeoideae. In Annonoideae, seven tribes are recognized, one of which, Duguetieae, is described as new. In Malmeoideae, seven tribes are recognized, six of which are newly described: Dendrokingstonieae, Fenerivieae, Maasieae, Malmeeae, Monocarpieae and Piptostigmateae. This new subfamilial and tribal classification is discussed against the background of previous classifications and characters to recognize subfamilies are reviewed
    The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates
    Zoetendal, E.G. ; Raes, J. ; Bogert, B. van den; Arumugam, M. ; Booijink, C.C.G.M. ; Troost, F.J. ; Borkent, P. ; Wels, M.W.W. ; Vos, W.M. de; Kleerebezem, M. - \ 2012
    ISME Journal 6 (2012)7. - ISSN 1751-7362 - p. 1415 - 1426.
    human gastrointestinal-tract - fragment-length-polymorphism - gut microbiome - bacterial diversity - microarray analysis - sequence data - human ileal - samples - twins - mucosa
    The human gastrointestinal tract (GI tract) harbors a complex community of microbes. The microbiota composition varies between different locations in the GI tract, but most studies focus on the fecal microbiota, and that inhabiting the colonic mucosa. Consequently, little is known about the microbiota at other parts of the GI tract, which is especially true for the small intestine because of its limited accessibility. Here we deduce an ecological model of the microbiota composition and function in the small intestine, using complementing culture-independent approaches. Phylogenetic microarray analyses demonstrated that microbiota compositions that are typically found in effluent samples from ileostomists (subjects without a colon) can also be encountered in the small intestine of healthy individuals. Phylogenetic mapping of small intestinal metagenome of three different ileostomy effluent samples from a single individual indicated that Streptococcus sp., Escherichia coli, Clostridium sp. and high G+C organisms are most abundant in the small intestine. The compositions of these populations fluctuated in time and correlated to the short-chain fatty acids profiles that were determined in parallel. Comparative functional analysis with fecal metagenomes identified functions that are overrepresented in the small intestine, including simple carbohydrate transport phosphotransferase systems (PTS), central metabolism and biotin production. Moreover, metatranscriptome analysis supported high level in-situ expression of PTS and carbohydrate metabolic genes, especially those belonging to Streptococcus sp. Overall, our findings suggest that rapid uptake and fermentation of available carbohydrates contribute to maintaining the microbiota in the human small intestine
    DNA Barcoding of Recently Diverged Species: Relative Performance of Matching Methods
    Velzen, R. van; Weitschek, E. ; Felici, G. ; Bakker, F.T. - \ 2012
    PLoS ONE 7 (2012)1. - ISSN 1932-6203 - 12 p.
    mitochondrial-dna - phylogenetic trees - molecular markers - sequence data - identification - diptera - fish - diversity - selection - taxonomy
    Recently diverged species are challenging for identification, yet they are frequently of special interest scientifically as well as from a regulatory perspective. DNA barcoding has proven instrumental in species identification, especially in insects and vertebrates, but for the identification of recently diverged species it has been reported to be problematic in some cases. Problems are mostly due to incomplete lineage sorting or simply lack of a ‘barcode gap’ and probably related to large effective population size and/or low mutation rate. Our objective was to compare six methods in their ability to correctly identify recently diverged species with DNA barcodes: neighbor joining and parsimony (both tree-based), nearest neighbor and BLAST (similarity-based), and the diagnostic methods DNA-BAR, and BLOG. We analyzed simulated data assuming three different effective population sizes as well as three selected empirical data sets from published studies. Results show, as expected, that success rates are significantly lower for recently diverged species (~75%) than for older species (~97%) (P
    Analysis of the microbial community of the biocathode of a hydrogen-producing microbial electrolysis cell
    Croese, E. ; Pereira, M.A. ; Euverink, G.J.W. ; Stams, A.J.M. ; Geelhoed, J.S. - \ 2011
    Applied Microbiology and Biotechnology 92 (2011)5. - ISSN 0175-7598 - p. 1083 - 1093.
    desulfovibrio-vulgaris hildenborough - geobacter-sulfurreducens - fuel-cells - exchange membranes - oxide reduction - gene-expression - organic-matter - sequence data - electrodes - electricity
    The microbial electrolysis cell (MEC) is a promising system for hydrogen production. Still, expensive catalysts such as platinum are needed for efficient hydrogen evolution at the cathode. Recently, the possibility to use a biocathode as an alternative for platinum was shown. The microorganisms involved in hydrogen evolution in such systems are not yet identified. We analyzed the microbial community of a mixed culture biocathode that was enriched in an MEC bioanode. This biocathode produced 1.1 A m(-2) and 0.63 m3 H2 m(-3) cathode liquid volume per day. The bacterial population consisted of 46% Proteobacteria, 25% Firmicutes, 17% Bacteroidetes, and 12% related to other phyla. The dominant ribotype belonged to the species Desulfovibrio vulgaris. The second major ribotype cluster constituted a novel taxonomic group at the genus level, clustering within uncultured Firmicutes. The third cluster belonged to uncultured Bacteroidetes and grouped in a taxonomic group from which only clones were described before; most of these clones originated from soil samples. The identified novel taxonomic groups developed under environmentally unusual conditions, and this may point to properties that have not been considered before. A pure culture of Desulfovibrio strain G11 inoculated in a cathode of an MEC led to a current development from 0.17 to 0.76 A m(-2) in 9 days, and hydrogen gas formation was observed. On the basis of the known characteristics of Desulfovibrio spp., including its ability to produce hydrogen, we propose a mechanism for hydrogen evolution through Desulfovibrio spp. in a biocathode system
    Correlation between protection against sepsis by probiotic therapy and stimulation of a novel bacterial phylotype
    Gerritsen, J. ; Timmerman, H.M. ; Fuentes, S. ; Minnen, L.P. van; Panneman, H. ; Konstantinov, S.R. ; Rombouts, F.M. ; Gooszen, H.G. ; Akkermans, L.M.A. ; Smidt, H. ; Rijkers, G.T. - \ 2011
    Applied and Environmental Microbiology 77 (2011)21. - ISSN 0099-2240 - p. 7749 - 7756.
    severe acute-pancreatitis - ribosomal-rna - necrotizing pancreatitis - clinical-course - sequence data - overgrowth - gut - translocation - microbiota - cirrhosis
    Prophylactic probiotic therapy has shown beneficial effects in an experimental rat model for acute pancreatitis on the health status of the animals. Mechanisms by which probiotic therapy interferes with severity of acute pancreatitis and associated sepsis, however, are poorly understood. The aims of this study were to identify the probiotic-induced changes in the gut microbiota and to correlate these changes to disease outcome. Duodenum and ileum samples were obtained from healthy and diseased rats subjected to pancreatitis for 7 days and prophylactically treated with either a multispecies probiotic mixture or a placebo. Intestinal microbiota was characterized by terminal-restriction fragment length polymorphism (T-RFLP) analyses of PCR-amplified 16S rRNA gene fragments. These analyses showed that during acute pancreatitis the host-specific ileal microbiota was replaced by an “acute pancreatitis-associated microbiota.” This replacement was not reversed by administration of the probiotic mixture. An increase, however, was observed in the relative abundance of a novel bacterial phylotype most closely related to Clostridium lituseburense and referred to as commensal rat ileum bacterium (CRIB). Specific primers targeting the CRIB 16S rRNA gene sequence were developed to detect this phylotype by quantitative PCR. An ileal abundance of CRIB 16S rRNA genes of more than 7.5% of the total bacterial 16S rRNA gene pool was correlated with reduced duodenal bacterial overgrowth, reduced bacterial translocation to remote organs, improved pancreas pathology, and reduced proinflammatory cytokine levels in plasma. Our current findings and future studies involving this uncharacterized bacterial phylotype will contribute to unraveling one of the potential mechanisms of probiotic therapy.
    Consistent phenological shifts in the making of biodiversity hotspots: the Cape flora.
    Warren, B. ; Bakker, F.T. ; Bellstedt, D.U. ; Bytebier, B. ; Claszen-Bockhoff, R. ; Dreyer, L.L. ; Edwards, A. ; Forest, F. ; Galley, C. ; Hardy, C.R. ; Linder, H.P. ; Muasya, A.M. ; Mummenhoff, K. ; Oberlander, K.C. ; Quint, M. ; Richardson, J.E. ; Savolainen, V. ; Schrire, B.D. ; Niet, T. van der; Verboom, G.A. ; Yesson, C. ; Hawkins, J.A. - \ 2011
    BMC Evolutionary Biology 11 (2011). - ISSN 1471-2148 - 11 p.
    climate-change - southern africa - ecological niches - flowering time - heterogeneous environments - evolutionary responses - adaptive radiation - rapid evolution - fossil record - sequence data
    Background The best documented survival responses of organisms to past climate change on short (glacial-interglacial) timescales are distributional shifts. Despite ample evidence on such timescales for local adaptations of populations at specific sites, the long-term impacts of such changes on evolutionary significant units in response to past climatic change have been little documented. Here we use phylogenies to reconstruct changes in distribution and flowering ecology of the Cape flora - South Africa's biodiversity hotspot - through a period of past (Neogene and Quaternary) changes in the seasonality of rainfall over a timescale of several million years. Results Forty-three distributional and phenological shifts consistent with past climatic change occur across the flora, and a comparable number of clades underwent adaptive changes in their flowering phenology (9 clades; half of the clades investigated) as underwent distributional shifts (12 clades; two thirds of the clades investigated). Of extant Cape angiosperm species, 14-41% have been contributed by lineages that show distributional shifts consistent with past climate change, yet a similar proportion (14-55%) arose from lineages that shifted flowering phenology. Conclusions Adaptive changes in ecology at the scale we uncover in the Cape and consistent with past climatic change have not been documented for other floras. Shifts in climate tolerance appear to have been more important in this flora than is currently appreciated, and lineages that underwent such shifts went on to contribute a high proportion of the flora's extant species diversity. That shifts in phenology, on an evolutionary timescale and on such a scale, have not yet been detected for other floras is likely a result of the method used; shifts in flowering phenology cannot be detected in the fossil record.
    Microarray analysis and barcoded pyrosequencing provide consistent microbial profiles depending on the source of human intestinal samples
    Bogert, B. van den; Vos, W.M. de; Zoetendal, E.G. ; Kleerebezem, M. - \ 2011
    Applied and Environmental Microbiology 77 (2011)6. - ISSN 0099-2240 - p. 2071 - 2080.
    gastrointestinal-tract microbiota - ribosomal-rna genes - real-time pcr - phylogenetic microarray - quantitative-analysis - bacterial community - gut microbiome - fecal samples - extensive set - sequence data
    Large-scale and in-depth characterization of the intestinal microbiota necessitates application of high-throughput 16S rRNA gene-based technologies, such as barcoded pyrosequencing and phylogenetic microarray analysis. In this study, the two techniques were compared and contrasted for analysis of the bacterial composition in three fecal and three small intestinal samples from human individuals. As PCR remains a crucial step in sample preparation for both techniques, different forward primers were used for amplification to assess their impact on microbial profiling results. An average of 7,944 pyrosequences, spanning the V1 and V2 region of 16S rRNA genes, was obtained per sample. Although primer choice in barcoded pyrosequencing did not affect species richness and diversity estimates, detection of Actinobacteria strongly depended on the selected primer. Microbial profiles obtained by pyrosequencing and phylogenetic microarray analysis (HITChip) correlated strongly for fecal and ileal lumen samples but were less concordant for ileostomy effluent. Quantitative PCR was employed to investigate the deviations in profiling between pyrosequencing and HITChip analysis. Since cloning and sequencing of random 16S rRNA genes from ileostomy effluent confirmed the presence of novel intestinal phylotypes detected by pyrosequencing, especially those belonging to the Veillonella group, the divergence between pyrosequencing and the HITChip is likely due to the relatively low number of available 16S rRNA gene sequences of small intestinal origin in the DNA databases that were used for HITChip probe design. Overall, this study demonstrated that equivalent biological conclusions are obtained by high-throughput profiling of microbial communities, independent of technology or primer choice
    Real-time PCR detection of Holophagae (Acidobacteria) and Verrucomicrobia subdivision 1 groups in bulk and leek (Allium porrum) rhizosphere soils
    Nunes da Rocha, U. ; Elsas, J.D. van; Overbeek, L.S. van - \ 2010
    Journal of Microbiological Methods 83 (2010)2. - ISSN 0167-7012 - p. 141 - 148.
    hitherto-uncultured bacteria - ribosomal-rna - molecular characterization - sequence data - diversity - communities - members - phylum - environment - software
    In the light of the poor culturability of Acidobacteria and Verrucomicrobia species, group-specific real-time (qPCR) systems were developed based on the 165 rRNA gene sequences from culturable representatives of both groups. The number of DNA targets from three different groups, i.e. Holophagae (Acidobacteria group 8) and Luteolibacter/Prosthecobacter and unclassified Verrucomicrobiaceae subdivision 1, was determined in DNA extracts from different leek (Allium porrum) rhizosphere soil compartments and from bulk soil with the aim to determine the distribution of the three bacterial groups in the plant-soil ecosystem. The specificity of the designed primers was evaluated in three steps. First, in silico tests were performed which demonstrated that all designed primers 100% matched with database sequences of their respective groups, whereas lower matches with other non-target bacterial groups were found. Second, PCR amplification with the different primer sets was performed on genomic DNA extracts from target and from non-target bacteria. This test demonstrated specificity of the designed primers for the target groups, as single amplicons of expected sizes were found only for the target bacteria. Third, the qPCR systems were tested for specific amplifications from soil DNA extracts and 48 amplicons from each primer system were sequenced. All sequences were >97% similar to database sequences of the respective target groups. Estimated cell numbers based on Holophagae-, Luteabacter/Prosthecobacter- and unclassified Verrucomicrobiaceae subdivision 1-specific qPCRs from leek rhizosphere compartments and bulk soils demonstrated higher preference for one or both rhizosphere compartments above bulk soil for all three bacterial groups.
    Cultivation of hitherto-uncultured bacteria belonging to the Verrucomicrobia subdivision 1 from the potato (Solanum tuberosum L.) rhizosphere
    Rocha, U.N. da; Andreote, F.D. ; Azevedo, J.L. ; Elsas, J.D. van; Overbeek, L.S. van - \ 2010
    Journal of Soils and Sediments 10 (2010)2. - ISSN 1439-0108 - p. 326 - 339.
    16s ribosomal-rna - soil bacteria - community structure - sequence data - pure culture - diversity - culturability - growth - genes - electrophoresis
    The role of dominant bacterial groups in the plant rhizosphere, e.g., those belonging to the phyla Acidobacteria and Verrucomicrobia, has, so far, not been elucidated, and this is mainly due to the lack of culturable representatives. This study aimed to isolate hitherto-uncultured bacteria from the potato rhizosphere by a combination of cultivation approaches. An agar medium low in carbon availability (oligotrophic agar medium) and either amended with potato root exudates or catalase or left unamended was used with the aim to improve the culturability of bacteria from the potato rhizosphere. The colony forming unit numbers based on colonies and microcolonies were compared with microscopically determined fluorescence-stained cell numbers. Taxonomical diversity of the colonies was compared with that of library clones made from rhizosphere DNA, on the basis of 16S rRNA gene comparisons. The oligotrophic media amended or not with catalase or rhizosphere extract recovered up to 33.6% of the total bacterial numbers, at least seven times more than the recovery observed on R2A. Four hitherto-uncultured Verrucomicrobia subdivision 1 representatives were recovered on agar, but representatives of this group were not found in the clone library. The use of oligotrophic medium and its modifications enabled the growth of colony numbers, exceeding those on classical agar media. Also, it led to the isolation of hitherto-uncultured bacteria from the potato rhizosphere. Further improvement in cultivation will certainly result in the recovery of other as-yet-unexplored bacteria from the rhizosphere, making these groups accessible for further investigation, e.g., with respect to their possible interactions with plants.
    Biological characterisation of Haliclona (?gellius) sp.: sponge and associated microorganisms.
    Sipkema, D. ; Holmes, B. ; Nichols, S.A. ; Blanch, H.W. - \ 2009
    Microbial Ecology 58 (2009)4. - ISSN 0095-3628 - p. 903 - 920.
    chondrilla-nucula demospongiae - marine sponge - phylogenetic analysis - bacterial diversity - ribosomal-rna - vertical transmission - microbial communities - halichondria-panicea - spatial-distribution - sequence data
    We have characterised the northern Pacific undescribed sponge Haliclona (?gellius) sp. based on rDNA of the sponge and its associated microorganisms. The sponge is closely related to Amphimedon queenslandica from the Great Barrier Reef as the near-complete 18S rDNA sequences of both sponges were identical. The microbial fingerprint of three specimens harvested at different times and of a transplanted specimen was compared to identify stably associated microorganisms. Most bacterial phyla were detected in each sample, but only a few bacterial species were determined to be stably associated with the sponge. A sponge-specific beta- and gamma-Proteobacterium were abundant clones and both of them were present in three of the four specimens analysed. In addition, a Planctomycete and a Crenarchaea were detected in all sponge individuals. Both were closely related to operational taxonomic units that have been found in other sponges, but not exclusively in sponges. Interestingly, also a number of clones that are closely related to intracellular symbionts from insects and amoeba were detected.
    Endophytic Colonization of Potato (Solanum tuberosum L.) by a Novel Competent Bacterial Endophyte, Pseudomonas putida Strain P9, and Its Effect on Associated Bacterial Communities
    Andreote, F.D. ; Araujo, W.L. ; Azevedo, J.L. ; Elsas, J.D. van; Rocha, U.N. da; Overbeek, L.S. van - \ 2009
    Applied and Environmental Microbiology 75 (2009)11. - ISSN 0099-2240 - p. 3396 - 3406.
    gradient gel-electrophoresis - 16s ribosomal-rna - soil microbial community - ralstonia-solanacearum - rhizosphere bacteria - systemic resistance - fluorescens strain - sequence data - plant-growth - tomato
    Pseudomonas putida strain P9 is a novel competent endophyte from potato. P9 causes cultivar-dependent suppression of Phytophthora infestans. Colonization of the rhizoplane and endosphere of potato plants by P9 and its rifampin-resistant derivative P9R was studied. The purposes of this work were to follow the fate of P9 inside growing potato plants and to establish its effect on associated microbial communities. The effects of P9 and P9R inoculation were studied in two separate experiments. The roots of transplants of three different cultivars of potato were dipped in suspensions of P9 or P9R cells, and the plants were planted in soil. The fate of both strains was followed by examining colony growth and by performing PCR-denaturing gradient gel electrophoresis (PCR-DGGE). Colonies of both strains were recovered from rhizoplane and endosphere samples of all three cultivars at two growth stages. A conspicuous band, representing P9 and P9R, was found in all Pseudomonas PCR-DGGE fingerprints for treated plants. The numbers of P9R CFU and the P9R-specific band intensities for the different replicate samples were positively correlated, as determined by linear regression analysis. The effects of plant growth stage, genotype, and the presence of P9R on associated microbial communities were examined by multivariate and unweighted-pair group method with arithmetic mean cluster analyses of PCR-DGGE fingerprints. The presence of strain P9R had an effect on bacterial groups identified as Pseudomonas azotoformans, Pseudomonas veronii, and Pseudomonas syringae. In conclusion, strain P9 is an avid colonizer of potato plants, competing with microbial populations indigenous to the potato phytosphere. Bacterization with a biocontrol agent has an important and previously unexplored effect on plant-associated communities.
    Microbial diversity and community structure of a highly active anaerobic methane-oxidizing sulfate-reducing enrichment
    Jagersma, C.G. ; Meulepas, R.J.W. ; Heikamp-de Jong, G.A.M. ; Gieteling, J. ; Klimiuk, A. ; Schouten, S. ; Sinninghe Damsté, J.S. ; Lens, P.N.L. ; Stams, A.J.M. - \ 2009
    Environmental Microbiology 11 (2009)12. - ISSN 1462-2912 - p. 3223 - 3232.
    16s ribosomal-rna - marine-sediments - cold-seep - in-vitro - sequence data - mud volcano - black-sea - oxidation - bacteria - archaea
    Summary Anaerobic oxidation of methane (AOM) is an important methane sink in the ocean but the microbes responsible for AOM are as yet resilient to cultivation. Here we describe the microbial analysis of an enrichment obtained in a novel submerged-membrane bioreactor system and capable of high-rate AOM (286 mumol g(dry weight) (-1) day(-1)) coupled to sulfate reduction. By constructing a clone library with subsequent sequencing and fluorescent in situ hybridization, we showed that the responsible methanotrophs belong to the ANME-2a subgroup of anaerobic methanotrophic archaea, and that sulfate reduction is most likely performed by sulfate-reducing bacteria commonly found in association with other ANME-related archaea in marine sediments. Another relevant portion of the bacterial sequences can be clustered within the order of Flavobacteriales but their role remains to be elucidated. Fluorescent in situ hybridization analyses showed that the ANME-2a cells occur as single cells without close contact to the bacterial syntrophic partner. Incubation with (13)C-labelled methane showed substantial incorporation of (13)C label in the bacterial C(16) fatty acids (bacterial; 20%, 44% and 49%) and in archaeal lipids, archaeol and hydroxyl-archaeol (21% and 20% respectively). The obtained data confirm that both archaea and bacteria are responsible for the anaerobic methane oxidation in a bioreactor enrichment inoculated with Eckernförde bay sediment
    Long-term performance and microbial community analysis of a full-scale synthesis gas fed reactor treating sulfate- and zinc-rich wastewater
    Houten, B.H.G.W. van; Doesburg, W.C.J. van; Dijkman, H. ; Copini, C.F.M. ; Smidt, H. ; Stams, A.J.M. - \ 2009
    Applied Microbiology and Biotechnology 84 (2009)3. - ISSN 0175-7598 - p. 555 - 563.
    sequence data - hybridization - methanogens - diversity - bacteria - reducers - arb
    The performance of a full-scale (500 m3) sulfidogenic synthesis gas fed gas-lift reactor treating metal- and sulfate-rich wastewater was investigated over a period of 128 weeks. After startup, the reactor had a high methanogenic activity of 46 Nm3·h-1. Lowering the carbon dioxide feed rate during the first 6 weeks gradually lowered the methane production rate. Between weeks 8 and 93, less than 1% of the hydrogen supplied was used for methanogenesis. Denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified 16S rRNA gene fragments showed that the archaeal community decreased in diversity but did not disappear completely. After the carbon dioxide feed rate increased in week 88, the methane production rate also increased, confirming that methane production was carbon dioxide limited. Even though lowering the carbon dioxide feed appeared to affect part of the sulfate-reducing community, it did not prevent achieving the desired rates of sulfate reduction. The average sulfate conversion rate was 181 kg·h-1 for the first 92 weeks. After 92 weeks, the sulfate input rate was increased and from week 94 to 128, the average weekly sulfate conversion rate was 295 kg.h-1 (SD-±-87). Even higher sulfate conversion rates of up to 400 kg·h-1 could be sustained for weeks 120-128. The long-term performance and stability together with the ability to control methanogenesis demonstrates that synthesis gas fed reactor can be used successfully at full scale to treat metal and sulfate-rich wastewater
    Degradation of 1,2-dichloroethane by microbial communities from river sediment at various redox conditions
    Zaan, B.M. van der; Weert, J.P.A. de; Rijnaarts, H. ; Vos, W.M. de; Smidt, H. ; Gerritse, J. - \ 2009
    Water Research 43 (2009)13. - ISSN 0043-1354 - p. 3207 - 3216.
    rivieren - sediment - biodegradatie - redoxreacties - oxidatie - micro-organismen - anaërobe omstandigheden - elbe - rivers - sediment - biodegradation - redox reactions - oxidation - microorganisms - anaerobic conditions - river elbe - halogenated aliphatic-compounds - dichloroeliminans strain dca1 - reductive dechlorination - methanogenic bacteria - contaminated aquifer - chlorinated ethenes - pure cultures - sequence data - dehalogenation - groundwater
    Insight into the pathways of biodegradation and external factors controlling their activity is essential in adequate environmental risk assessment of chlorinated aliphatic hydrocarbon pollution. This study focuses on biodegradation of 1,2-dichloroethane (1,2-DCA) in microcosms containing sediment sourced from the European rivers Ebro, Elbe and Danube. Biodegradation was studied under different redox conditions. Reductive dechlorination of 1,2-DCA was observed with Ebro and Danube sediment with chloroethane, or ethene, respectively, as the major dechlorination products. Different reductively dehalogenating micro-organisms (Dehalococcoides spp., Dehalobacter spp., Desulfitobacterium spp. and Sulfurospirillum spp.) were detected by 16S ribosomal RNA gene-targeted PCR and sequence analyses of 16S rRNA gene clone libraries showed that only 2-5 bacterial orders were represented in the microcosms. With Ebro and Danube sediment, indications for anaerobic oxidation of 1,2-DCA were obtained under denitrifying or iron-reducing conditions. No biodegradation of 1,2-DCA was observed in microcosms with Ebro sediment under the different tested redox conditions. This research shows that 1,2-DCA biodegradation capacity was present in different river sediments, but not in the water phase of the river systems and that biodegradation potential with associated microbial communities in river sediments varies with the geochemical properties of the sediments
    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
    Diversification of myco-heterotrophic angiosperms: evidence from Burmanniaceae.
    Merckx, V. ; Chatrou, L.W. ; Lemaire, B. ; Sainge, M.N. ; Huysmans, S. ; Smets, E.F. - \ 2008
    BMC Evolutionary Biology 8 (2008). - ISSN 1471-2148 - 16 p.
    long-distance dispersal - arbuscular mycorrhizal fungi - historical biogeography - molecular phylogenies - divergence times - chloroplast genome - flowering plants - absolute rates - sequence data - rain-forest
    Background - Myco-heterotrophy evolved independently several times during angiosperm evolution. Although many species of myco-heterotrophic plants are highly endemic and long-distance dispersal seems unlikely, some genera are widely dispersed and have pantropical distributions, often with large disjunctions. Traditionally this has been interpreted as evidence for an old age of these taxa. However, due to their scarcity and highly reduced plastid genomes our understanding about the evolutionary histories of the angiosperm myco-heterotrophic groups is poor. Results - We provide a hypothesis for the diversification of the myco-heterotrophic family Burmanniaceae. Phylogenetic inference, combined with biogeographical analyses, molecular divergence time estimates, and diversification analyses suggest that Burmanniaceae originated in West Gondwana and started to diversify during the Late Cretaceous. Diversification and migration of the species-rich pantropical genera Burmannia and Gymnosiphon display congruent patterns. Diversification began during the Eocene, when global temperatures peaked and tropical forests occurred at low latitudes. Simultaneous migration from the New to the Old World in Burmannia and Gymnosiphon occurred via boreotropical migration routes. Subsequent Oligocene cooling and breakup of boreotropical flora ended New-Old World migration and caused a gradual decrease in diversification rate in Burmanniaceae. Conclusion - Our results indicate that extant diversity and pantropical distribution of myco-heterotrophic Burmanniaceae is the result of diversification and boreotropical migration during the Eocene when tropical rain forest expanded dramatically
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