Ophiostoma gemellus and Sporothrix variecibatus from mites infesting Protea infructescences in South Africa
Roets, F. ; Beer, Z.W. de; Wingfield, M.J. ; Crous, P.W. ; Dreyer, L.L. - \ 2008
Mycologia 100 (2008)3. - ISSN 0027-5514 - p. 496 - 510.
phoretic mites - bark beetles - sp-nov - phylogenetic inference - ceratocystis-minor - ips-typographus - fungi - scolytidae - coleoptera - complex
Ophiostoma (Ophiostomatales) represents a large genus of fungi mainly known from associations with bark beetles (Curculionidae: Scolytinae) infesting conifers in the northern hemisphere. Few southern hemisphere native species are known, and the five species that consistently occur in the infructescences of Protea spp. in South Africa are ecologically unusual. Little is known about the vectors of Ophiostoma spp. from Protea infructescences, however recent studies have considered the possible role of insects and mites in the distribution of these exceptional fungi. In this study we describe a new species of Ophiostoma and a new Sporothrix spp. with affinities to Ophiostoma, both initially isolated from mites associated with Protea spp. They are described as Ophiostoma gemellus sp. nov. and Sporothrix variecibatus sp. nov. based on their morphology and comparisons of DNA sequence data of the 28S ribosomal, ß-tubulin and internal transcribed spacer (ITS1, 5.8S, ITS2) regions. DNA sequences of S. variecibatus were identical to those of a Sporothrix isolate obtained from Eucalyptus leaf litter in the same area in which S. variecibatus occurs in Protea infructescences. Results of this study add evidence to the view that mites are the vectors of Ophiostoma spp. that colonize Protea infructescences. They also show that DNA sequence comparisons are likely to reveal additional cryptic species of Ophiostoma in this unusual niche.
Resolving the phylogenetic and taxonomic status of dark-spored teleomorph genera in the Botryosphaeriaceae
Phillips, A.J.L. ; Alves, A. ; Pennycook, S.R. ; Johnston, P.R. ; Ramaley, A. ; Akulov, A. ; Crous, P.W. - \ 2008
Persoonia 21 (2008). - ISSN 0031-5850 - p. 29 - 55.
sp-nov - primer sets - anamorph - characters - confidence - speciation - inference - prunus - trees - spp.
Species in the Botryosphaeriaceae are common plant pathogens and saprobes found on a variety of mainly woody hosts. Teleomorphs typically have hyaline, aseptate ascospores. However, some have been reported with brown ascospores and their taxonomic status is uncertain. A multi-gene approach (SSU, ITS, LSU, EF1-a and ß-tubulin) was used to resolve the correct phylogenetic position of the dark-spored 'Botryosphaeria' teleomorphs and related asexual species. Neodeightonia and Phaeobotryon are reinstated for species with brown ascospores that are either 1-septate (Neodeightonia) or 2-septate (Phaeobotryon). Phaeobotryosphaeria is reinstated for species with brown, aseptate ascospores that bear an apiculus at either end. The status of Sphaeropsis is clarified and shown to be the anamorph of Phaeobotryosphaeria. Two new genera, namely Barriopsis for species having brown, aseptate ascospores without apiculi and Spencermartinsia for species having brown, 1-septate ascospores with an apiculus at either end are introduced. Species of Dothiorella have brown, 1-septate ascospores and differ from Spencermartinsia in the absence of apiculi. These six genera can also be distinguished from one another based on morphological characters of their anamorphs. Although previously placed in the Botryosphaeriaceae, Dothidotthia, was shown to belong in the Pleosporales, and the new family Dothidotthiaceae is introduced to accommodate it
Anaerobic methanethiol degradation and methanogenic community analysis in an alkaline (pH 10) biological process for liquefied petroleum gas desulfurization
Leerdam, R.C. van; Bonilla-Salinas, M. ; Bok, F.A.M. de; Bruning, H. ; Lens, P.N.L. ; Stams, A.J.M. ; Janssen, A.J.H. - \ 2008
Biotechnology and Bioengineering 101 (2008)4. - ISSN 0006-3592 - p. 691 - 701.
organic sulfur-compounds - sludge-blanket reactor - methylotrophic methanogen - oxidizing bacteria - sulfide oxidation - soda lakes - sp-nov - sediments - dimethylsulfide - bioreactor
Anaerobic methanethiol (MT) degradation by mesophilic (30 degrees C) alkaliphilic (pH 10) communities was studied in a lab-scale Upflow Anaerobic Sludge Bed (UASB) reactor inoculated with a mixture of sediments from the Wadden Sea (The Netherlands), Soap Lake (Central Washington), and Russian soda lakes. MT degradation started after 32 days of incubation. During the first 252 days, complete degradation was achieved till a volumetric loading rate of 7.5 mmol MT/L/day, and sulfide, methane, and carbon dioxide were the main reaction products. Temporary inhibition of MT degradation occurred after MT peak loads and in the presence of dimethyl disulfide (DMDS), which is the autooxidation product of MT. From day 252 onwards, methanol was dosed to the reactor as co-substrate at a loading rate of 3-6 mmol/L/day to stimulate growth of methylotrophic methanogens. Methanol was completely degraded and also a complete MT degradation was achieved till a volumetric loading rate of 13 mmol MT/L/day (0.77 mmol MT/gVSS/day). However, from day 354 till the end of the experimental run (day 365), acetate was formed and MT was not completely degraded anymore, indicating that methanol-degrading homoacetogenic bacteria had partially outcompeted the methanogenic MT-degrading archea. The archeal community in the reactor sludge was analyzed by DGGE and sequencing of 16S rRNA genes. The methanogenic archea responsible for the degradation of MT in the reactor were related to Methanolobus oregonensis. A pure culture, named strain SODA, was obtained by serial dilutions in medium containing both trimethyl amine and dimethyl sulfide (DMS). Strain SODA degraded MT, DMS, trimethyl amine, and methanol. Flow sheet simulations revealed that for sufficient MT removal from liquefied petroleum gas, the extraction and biological degradation process should be operated above pH 9.
Methanethiol degradation in anaerobic bioreactors at elevated pH (>8): Reactor performance and microbial community analysis
Leerdam, R.C. van; Bok, F.A.M. de; Bonilla-Salinas, M. ; Doesburg, W. van; Lomans, B.P. ; Lens, P.N.L. ; Stams, A.J.M. ; Janssen, A.J.H. - \ 2008
Bioresource Technology 99 (2008)18. - ISSN 0960-8524 - p. 8967 - 8973.
organic sulfur-compounds - sludge-blanket reactor - methylotrophic methanogen - sp-nov - methanosarcina-mazei - dimethyl sulfide - estuarine methanogen - hydrogen transfer - sediments - bacteria
The degradation of methanethiol (MT) at 30 °C under saline¿alkaline (pH 8¿10, 0.5 M Na+) conditions was studied in a lab-scale Upflow Anaerobic Sludge Blanket (UASB) reactor inoculated with estuarine sediment from the Wadden Sea (The Netherlands). At a sodium concentration of 0.5 M and a pH between 8 and 9 complete MT degradation to sulfide, methane and carbon dioxide was possible at a maximum loading rate of 22 mmol MT L¿1 day¿1 and a hydraulic retention time of 6 h. The presence of yeast extract (100 mg/L) in the medium was essential for complete MT degradation. 16S rRNA based DGGE and sequence analysis revealed that species related to the genera Methanolobus and Methanosarcina dominated the archaeal community in the reactor sludge. Their relative abundance fluctuated in time, possibly as a result of the changing operational conditions in the reactor. The most dominant MT-degrading archaeon was enriched from the reactor and obtained in pure culture. This strain WR1, which was most closely related to Methanolobus taylorii, degraded MT, dimethyl sulfide (DMS), methanol and trimethylamine. Its optimal growth conditions were 0.2 M NaCl, 30 °C and pH 8.4. In batch and reactor experiments operated at pH 10, MT was not degraded
Pathways for the anaerobic microbial debromination ofpolybrominated diphenyl ethers
Robrock, K.R. ; Korytar, P. ; Alvarex-Cohen, L. - \ 2008
Environmental Science and Technology 42 (2008)8. - ISSN 0013-936X - p. 2845 - 2852.
sp-nov - reductive dechlorination - desulfitobacterium-dehalogenans - polychlorinated-biphenyls - dehalococcoides strains - enrichment cultures - gas-chromatography - flame-retardant - gen-nov - bacterium
The debromination pathways of seven polybrominated diphenyl ethers (PBDEs) by three different cultures of anaerobic dehalogenating bacteria were investigated using comprehensive two-dimensional gas chromatography (GC × GC). The congeners analyzed were the five major components of the industrially used octa-BDE mixture (octa-BDEs 196, 203, and 197, hepta-BDE 183, and hexa-BDE 153) as well as the two most commonly detected PBDEs in the environment, penta-BDE 99 and tetra-BDE 47. Among the dehalogenating cultures evaluated in this study were a trichloroethene-enriched consortium containing multiple Dehalococcoides species, and two pure cultures, Dehalobacter restrictus PER-K23 and Desulfitobacterium hafniense PCP-1. PBDE samples were analyzed by GC × GC coupled to an electron capture detector to maximize separation and identification of the product congeners. All studied congeners were debrominated to some extent by the three cultures and all exhibited similar debromination pathways with preferential removal of para and meta bromines. Debromination of the highly brominated congeners was extremely slow, with usually less than 10% of nM concentrations of PBDEs transformed after three months. In contrast, debromination of the lesser brominated congeners, such as penta 99 and tetra 47, was faster, with some cultures completely debrominating nM levels of tetra 47 within weeks.
Discovery of fungus-mite mutualism in a unique niche
Roets, F. ; Wingfield, M.J. ; Crous, P.W. ; Dreyer, L.L. - \ 2007
Environmental Entomology 36 (2007)5. - ISSN 0046-225X - p. 1226 - 1237.
protea infructescences - sp-nov - bark beetles - ophiostoma - gondwanamyces - symbiosis
The floral heads (infructescences) of South African Protea L. represent a most unusual niche for fungi of the economically important genus Ophiostoma Syd. and P. Syd. emend. Z.W. de Beer et al. Current consensus holds that most members of Ophiostoma are vectored by tree-infesting bark beetles. However, it has recently been suggested that mites, phoretic on these bark beetles, may play a central role in the dispersal of Ophiostoma. No bark beetles are known from Protea. Therefore, identifying the vectors of Ophiostoma in Protea infructescences would independently evaluate the role of various arthropods in the dispersal of Ophiostoma. Infructescence-colonizing arthropods were tested for the presence of Ophiostoma DNA using polymerase chain reaction (PCR) and for reproductive propagules by isolation on agar plates. PCR tests revealed that few insects carried Ophiostoma DNA. In contrast, various mites (Proctolaelaps vandenbergi Ryke, two species of Tarsonemus Canestrini and Fonzago, and one Trichouropoda Berlese species) frequently carried Ophiostoma propagules. DNA sequence comparisons for 28S ribosomal DNA confirmed the presence of O. splendens G. J. Marais and M. J. Wingf., O. palmiculminatum Roets et al., and O. phasma Roets et al. on these mites. Two apparently undescribed species of Ophiostoma were also identified. Light and scanning electron microscopy revealed specialized structures in Trichouropoda and one Tarsonemus sp. that frequently contained Ophiostoma spores. The Trichouropoda sp. was able to complete its life cycle on a diet consisting solely of its identified phoretic Ophiostoma spp. This study provides compelling evidence that mites are the primary vectors of infructescence-associated Ophiostoma spp. in South Africa.
Phylogenetic and morphotaxonomic revision of Ramichloridium and allied genera
Arzanlou, M. ; Groenewald, J.Z. ; Gams, W. ; Braun, U. ; Crous, P.W. - \ 2007
Studies in Mycology 58 (2007)1. - ISSN 0166-0616 - p. 57 - 93.
ribosomal dna - sp-nov - anamorphs - veronaea - taxonomy - fungi - herpotrichiellaceae - pheohyphomycosis - identification - phialophora
The phylogeny of the genera Periconiella, Ramichloridium, Rhinocladiella and Veronaea was explored by means of partial sequences of the 28S (LSU) rRNA gene and the ITS region (ITS1, 5.8S rDNA and ITS2). Based on the LSU sequence data, ramichloridium-like species segregate into eight distinct clusters. These include the Capnodiales (Mycosphaerellaceae and Teratosphaeriaceae), the Chaetothyriales (Herpotrichiellaceae), the Pleosporales, and five ascomycete clades with uncertain affinities. The type species of Ramichloridium, R. apiculatum, together with R. musae, R. biverticillatum, R. cerophilum, R. verrucosum, R. pini, and three new species isolated from Strelitzia, Musa and forest soil, respectively, reside in the Capnodiales clade. The human-pathogenic species R. mackenziei and R. basitonum, together with R. fasciculatum and R. anceps, cluster with Rhinocladiella (type species: Rh. atrovirens, Herpotrichiellaceae, Chaetothyriales), and are allocated to this genus. Veronaea botryosa, the type species of the genus Veronaea, also resides in the Chaetothyriales clade, whereas Veronaea simplex clusters as a sister taxon to the Venturiaceae (Pleosporales), and is placed in a new genus, Veronaeopsis. Ramichloridium obovoideum clusters with Carpoligna pleurothecii (anamorph: Pleurothecium sp., Chaetosphaeriales), and a new combination is proposed in Pleurothecium. Other ramichloridium-like clades include R. subulatum and R. epichloes (incertae sedis, Sordariomycetes), for which a new genus, Radulidium is erected. Ramichloridium schulzeri and its varieties are placed in a new genus, Myrmecridium (incertae sedis, Sordariomycetes). The genus Pseudovirgaria (incertae sedis) is introduced to accommodate ramichloridium-like isolates occurring on various species of rust fungi. A veronaea-like isolate from Bertia moriformis with phylogenetic affinity to the Annulatascaceae (Sordariomycetidae) is placed in a new genus, Rhodoveronaea. Besides Ramichloridium, Periconiella is also polyphyletic. Thysanorea is introduced to accommodate Peticoniella papuana (Herpotrichiellaceae), which is unrelated to the type species, P velutina (Mycosphaerellaceae).
Transcriptional activation by CprK1 is regulated by protein structural changes induced by effector binding and redox state
Mazon, H. ; Gabor, K. ; Leys, D. ; Heck, A.J.R. ; Oost, J. van der; Heuvel, R.H.H. van den - \ 2007
Journal of Biological Chemistry 282 (2007)15. - ISSN 0021-9258 - p. 11281 - 11290.
ionization mass-spectrometry - camp-receptor-protein - desulfitobacterium-dehalogenans - macromolecular complexes - reductive dehalogenase - conformational-changes - limited proteolysis - dna-binding - sp-nov - hafniense
The transcriptional activator CprK1 from Desulfitobacterium-hafniense, a member of the ubiquitous cAMP receptor protein/fumarate nitrate reduction regulatory protein family, activates transcription of genes encoding proteins involved in reductive dehalogenation of chlorinated aromatic compounds. 3-Chloro-4-hydroxyphenylacetate is a known effector for CprK1, which interacts tightly with the protein, and induces binding to a specific DNA sequence ("dehalobox," TTAAT¿-ATTAA) located in the promoter region of chlorophenol reductive dehalogenase genes. Despite the availability of recent x-ray structures of two CprK proteins in distinct states, the mechanism by which CprK1 activates transcription is poorly understood. In the present study, we have investigated the mechanism of CprK1 activation and its effector specificity. By using macromolecular native mass spectrometry and DNA binding assays, analogues of 3-chloro-4-hydroxyphenylacetate that have a halogenated group at the ortho position and a chloride or acetic acid group at the para position were found to be potent effectors for CprK1. By using limited proteolysis it was demonstrated that CprK1 requires a cascade of structural events to interact with dehalobox dsDNA. Upon reduction of the intermolecular disulfide bridge in oxidized CprK1, the protein becomes more dynamic, but this alone is not sufficient for DNA binding. Activation of CprK1 is a typical example of allosteric regulation; the binding of a potent effector molecule to reduced CprK1 induces local changes in the N-terminal effector binding domain, which subsequently may lead to changes in the hinge region and as such to structural changes in the DNA binding domain that are required for specific DNA binding.
Microbial communities involved in anaerobic degradation of unsaturated or saturated long chain fatty acids
Sousa, D.Z. ; Pereira, M.A. ; Stams, A.J.M. ; Alves, M.M. ; Smidt, H. - \ 2007
Applied and Environmental Microbiology 73 (2007)4. - ISSN 0099-2240 - p. 1054 - 1064.
sp-nov - methanogenic bacteria - oleic-acid - syntrophobacter-wolinii - syntrophic bacterium - enrichment culture - granular sludge - sp. nov. - gen-nov - coculture
Anaerobic long-chain fatty acid (LCFA)-degrading bacteria were identified by combining selective enrichment studies with molecular approaches. Two distinct enrichment cultures growing on unsaturated and saturated LCFAs were obtained by successive transfers in medium containing oleate and palmitate, respectively, as the sole carbon and energy sources. Changes in the microbial composition during enrichment were analyzed by denaturing gradient gel electrophoresis (DGGE) profiling of PCR-amplified 16S rRNA gene fragments. Prominent DGGE bands of the enrichment cultures were identified by 16S rRNA gene sequencing. A significant part of the retrieved 16S rRNA gene sequences was most similar to those of uncultured bacteria. Bacteria corresponding to predominant DGGE bands in oleate and palmitate enrichment cultures clustered with fatty acid-oxidizing bacteria within Syntrophomonadaceae and Syntrophobacteraceae families. A low methane yield, corresponding to 9 to 18% of the theoretical value, was observed in the oleate enrichment, and acetate, produced according to the expected stoichiometry, was not further converted to methane. In the palmitate enrichment culture, the acetate produced was completely mineralized and a methane yield of 48 to 70% was achieved from palmitate degradation. Furthermore, the oleate enrichment culture was able to use palmitate without detectable changes in the DGGE profile. However, the palmitate-specialized consortia degraded oleate only after a lag phase of 3 months, after which the DGGE profile had changed. Two predominant bands appeared, and sequence analysis showed affiliation with the Syntrophomonas genus. These bands were also present in the oleate enrichment culture, suggesting that these bacteria are directly involved in oleate degradation, emphasizing possible differences between the degradation of unsaturated and saturated LCFAs.
Diversity of the human gastrointestinal tract microbiota revisited
Rajilic-Stojanovic, M. ; Smidt, H. ; Vos, W.M. de - \ 2007
Environmental Microbiology 9 (2007)9. - ISSN 1462-2912 - p. 2125 - 2136.
16s ribosomal-rna - human fecal flora - gradient gel-electrophoresis - human clinical specimens - rdna sequence-analysis - human intestinal-tract - human oral-cavity - sp-nov - gen. nov. - human feces
Since the early days of microbiology, more than a century ago, representatives of over 400 different microbial species have been isolated and fully characterized from human gastrointestinal samples. However, during the past decade molecular ecological studies based on ribosomal RNA (rRNA) sequences have revealed that cultivation has been able only to access a small fraction of the microbial diversity within the gastrointestinal tract. The increasing number of deposited rRNA sequences calls for the setting up a curated database that allows handling of the excessive degree of redundancy that threatens the usability of public databases. The integration of data from cultivation-based studies and molecular inventories of small subunit (SSU) rRNA diversity, presented here for the first time, provides a systematic framework of the microbial diversity in the human gastrointestinal tract of more than 1000 different species-level phylogenetic types (phylotypes). Such knowledge is essential for the design of high-throughput approaches such as phylogenetic DNA microarrays for the comprehensive analysis of gastrointestinal tract microbiota at multiple levels of taxonomic resolution. Development of such approaches is likely to be pivotal to generating novel insights in microbiota functionality in health and disease.
Anaerobic methanethiol degradation in upflow anaerobic sludge bed reactors at high salinity (> 0.5 M Na+)
Leerdam, R.C. van; Bok, F.A.M. de; Lens, P.N.L. ; Stams, A.J.M. ; Janssen, A.J.H. - \ 2007
Biotechnology and Bioengineering 98 (2007)1. - ISSN 0006-3592 - p. 91 - 100.
mill waste-water - sulfur-compounds - methylotrophic methanogen - estuarine methanogen - blanket reactor - sp-nov - sediments - sulfide - sulfate - adaptation
The feasibility of anaerobic methanethiol (MT) degradation at elevated sodium concentrations was investigated in a mesophilic (30°C) lab-scale upflow anaerobic sludge bed (UASB) reactor, inoculated with estuarine sediment originating from the Wadden Sea (The Netherlands). MT was almost completely degraded (>95%) to sulfide, methane and carbon dioxide at volumetric loading rates up to 37 mmol MT·L-1·day-1, 0.5 M sodium (NaCl or NaHCO3) and between pH 7.3 and 8.4. Batch experiments revealed that inhibition of MT degradation started at sodium (both NaCl and NaHCO3) concentrations exceeding 0.8 M. Sulfide inhibited MT degradation already around 3 mM (pH 8.3).
Methanol utilizing Desulfotomaculum species utilizes hydrogen in a methanol-fed sulfate-reducing bioreactor
Balk, M. ; Weijma, J. ; Goorissen, H.P. ; Ronteltap, M. ; Hansen, T.A. ; Stams, A.J.M. - \ 2007
Applied Microbiology and Biotechnology 73 (2007)5. - ISSN 0175-7598 - p. 1203 - 1211.
sp-nov - anaerobic reactor - bacterium - acetate - propionate - degradation - metabolism - growth
A sulfate-reducing bacterium, strain WW1, was isolated from a thermophilic bioreactor operated at 65 degrees C with methanol as sole energy source in the presence of sulfate. Growth of strain WW1 on methanol or acetate was inhibited at a sulfide concentration of 200 mg l(-1), while on H-2/CO2, no apparent inhibition occurred up to a concentration of 500 mg l(-1). When strain WW1 was co-cultured under the same conditions with the methanol-utilizing, non-sulfate-reducing bacteria, Thermotoga lettingae and Moorella mulderi, both originating from the same bioreactor, growth and sulfide formation were observed up to 430 mg l(-1). These results indicated that in the co-cultures, a major part of the electron flow was directed from methanol via H-2/CO2 to the reduction of sulfate to sulfide. Besides methanol, acetate, and hydrogen, strain WW1 was also able to use formate, malate, fumarate, propionate, succinate, butyrate, ethanol, propanol, butanol, isobutanol, with concomitant reduction of sulfate to sulfide. In the absence of sulfate, strain WW1 grew only on pyruvate and lactate. On the basis of 16S rRNA analysis, strain WW1 was most closely related to Desulfotomaculum thermocisternum and Desulfotomaculum australicum. However, physiological properties of strain WW1 differed in some aspects from those of the two related bacteria.
Taxonomy, phylogeny and identification of Botryosphaeriaceae associated with pome and stone fruit trees in South Africa and other regions of the world
Slippers, B. ; Smit, W.A. ; Crous, P.W. ; Coutinho, T.A. ; Wingfield, B.D. ; Wingfield, M.J. - \ 2007
Plant Pathology 56 (2007)1. - ISSN 0032-0862 - p. 128 - 139.
sp-nov - apple fruit - western-australia - wetness duration - peach-trees - dothidea - obtusa - infection - fungi - rot
Species of Botryosphaeria are well-recognized pathogens of pome and stone fruit trees. The taxonomy of these fungi, however, has been confused in the past. Recent taxonomic changes to the Botryosphaeriaceae further influence the literature pertaining to these fungi. This study reviews the taxonomic status of Botryosphaeriaceae associated with fruit tree diseases, identifies them in South Africa and elsewhere, and develops a reliable identification technique for them. Comparisons were made using DNA sequence data from the nuclear ITS rRNA operon and anamorph morphology. These analyses distinguished six clades amongst isolates associated with fruit tree diseases, corresponding to Neofusicoccum ribis (= B. ribis), N. parvum (= B. parva), N. australe (= B. australis), B. dothidea, Diplodia mutila (= B. stevensii) and 'Botryosphaeria' obtusa (the genus Botryosphaeria is no longer available for the fungus known as B. obtusa, but a new name has not been proposed yet). Isolates from fruit trees in South Africa were grouped in the N. australe and 'Botryosphaeria' obtusa clades. This is the first report of N. australe from fruit trees. PCR-RFLP analysis using the restriction endonucleases CfoI and HaeIII distinguished the major clades. However, two groups of closely related species, N. ribis and N. parvum, and N. australe and N. luteum (= B. lutea), had identical RFLP profiles. Using RFLP, it was shown that 'Botryosphaeria' obtusa is the dominant species on fruit trees in the Western Cape Province of South Africa. These results and methods will be useful in future epidemiological studies and disease management of Botryosphaeriaceae from fruit trees
Identification of Bilophila wadsworthia by specific PCR which targets the taurine:pyruvate aminotransferase
Laue, H. ; Smits, T.H.M. ; Schumacher, U.K. ; Claros, M.C. ; Hartemink, R. ; Cook, A.M. - \ 2006
FEMS Microbiology Letters 261 (2006)1. - ISSN 0378-1097 - p. 74 - 79.
sp-nov - transcription - bacteria - quantification - dissimilation - purification - appendicitis - respiration - reduction - specimens
The bile-resistant, strictly anaerobic bacterium Bilophila wadsworthia is found in human faecal flora, in human infections and in environmental samples. A specific PCR primer set for the gene encoding the first metabolic enzyme in the degradative pathway for taurine in B. wadsworthia, taurine:pyruvate aminotransferase (tpa), was developed and tested. In addition, enrichment cultures were started from faecal samples of primates and felines and shown to contain B. wadsworthia. These were subcultured on agar media and then identified by PCR fingerprinting. PCR for tpa was successful in all positive enrichment cultures and showed no amplification signal in a variety of other bacterial species. Therefore, this PCR method could be a promising tool for rapid detection of B. wadsworthia in biological samples
Microbial CO conversions with applications in synthesis gas purification and bio-desulfurization.
Sipma, J. ; Henstra, A.M. ; Parshina, S.N. ; Lens, P.N.L. ; Lettinga, G. ; Stams, A.J.M. - \ 2006
Critical Reviews in Biotechnology 26 (2006)1. - ISSN 0738-8551 - p. 41 - 65.
carbon-monoxide dehydrogenase - acid-mine drainage - h-2-forming methylenetetrahydromethanopterin dehydrogenase - biological sulfate reduction - metal-free hydrogenase - sp-nov - carboxydothermus-hydrogenoformans - gen.-nov. - clostridium-thermoaceticum - rhodospi
Recent advances in the field of microbial physiology demonstrate that carbon monoxide is a readily used substrate by a wide variety of anaerobic micro-organisms, and may be employed in novel biotechnological. processes for production of bulk and fine chemicals or in biological treatment of waste streams. Synthesis gas produced from fossil fuels or biomass is rich in hydrogen and carbon monoxide. Conversion of carbon monoxide to hydrogen allows use of synthesis gas in existing hydrogen utilizing processes and is interesting in view of a transition from hydrogen production from fossil fuels to sustainable (CO2-neutral) biomass. The conversion of CO with H2O to CO2 and H-2 is catalyzed by a rapidly increasing group of micro-organisms. Hydrogen is a preferred electron donor in biotechnological desulfurization of wastewaters and flue gases. Additionally, CO is a good alternative electron donor considering the recent isolation of a CO oxidizing, sulfate reducing bacterium. Here we review CO utilization by various anaerobic micro-organisms and their possible role in biotechnological processes, with a focus on hydrogen production and bio-desulfurization.
Changes in agricultural management drive the diversity of Burkholderia species isolated from soil on PCAT medium
Salles, J.F. ; Samyn, E. ; Vandamme, P.A. ; Veen, J.A. van; Elsas, J.D. van - \ 2006
Soil Biology and Biochemistry 38 (2006)4. - ISSN 0038-0717 - p. 661 - 673.
gradient gel-electrophoresis - cepacia complex infection - land-use history - sp-nov - cystic-fibrosis - bacterial communities - microbial diversity - maize-rhizosphere - genetic diversity - genomovar-iii
In order to assess the diversity of culturable Burkholderia populations in rhizosphere and bulk soil and to evaluate how different agricultural management regimes and land use history affect this diversity, four treatments were evaluated: permanent grassland; grassland converted into maize monoculture; arable land and arable land converted into grassland. Burkholderia isolates obtained on PCAT medium were grouped in 47 clusters using 16S ribosomal RNA gene based PCR-DGGE combined with BOX genomic fingerprinting (DGGE-BOX). The distribution of the isolates in the DGGE-BOX clusters was used to calculate the Shannon diversity index per treatment. Interestingly, we observed that the Burkholderia diversity was affected by changes in the agricultural management, since the highest diversity was observed in permanent grassland and in continuous arable land. In addition, the diversity tended to be higher in the rhizosphere than in the corresponding bulk soil. The use of species abundance models indicated that rhizosphere communities had more even distributions than communities collected from the bulk soil. Identification of isolates revealed that only 2% of these belonged to the B. cepacia complex and that the majority was assigned to either (1) new Burkholderia species or (2) Burkholderia species that had originally been isolated from soil. Isolates classified as B. hospita, B. caledonica and Burkholderia sp. LMG 22934' and `LMG 22936' were found mainly in the arable land, while isolates belonging to Burkholderia sp. `LMG 22929 and B. phytofirmans were associated with the grassland area. Another potentially new Burkholderia species, `LMG 22932'', was found in both areas, in close association with the maize rhizosphere
Multi-gene phylogeny for Ophiostoma spp. reveals two new species from Protea infructescences
Roets, F. ; Beer, Z.W. de; Dreyer, L.L. ; Zipfel, R. ; Crous, P.W. ; Wingfield, M.J. - \ 2006
Studies in Mycology 55 (2006). - ISSN 0166-0616 - p. 199 - 212.
mycangial fungi - bark beetles - south-africa - sp-nov - complex - scolytidae - coleoptera - symbiosis - survival - genus
Ophiostoma represents a genus of fungi that are mostly arthropod-dispersed and have a wide global distribution. The best known of these fungi are carried by scolytine bark beetles that infest trees, but an interesting guild of Ophiostoma spp. occurs in the infructescences of Protea spp. native to South Africa. Phylogenetic relationships between Ophiostoma spp. from Protea infructescences were studied using DNA sequence data from the P-tubulin, 5.8S ITS (including the flanking internal transcribed spacers 1 and 2) and the large subunit DNA regions. Two new species, O. phasma sp. nov. and O. paimiculminatum sp. nov. are described and compared with other Ophiostoma spp. occurring in the same niche. Results of this study have raised the number of Ophiostoma species from the infructescences of serotinous Protea spp. in South Africa to five. Molecular data also suggest that adaptation to the Protea infructescence niche by Ophiostoma spp. has occurred independently more than once.
Phylogenetic lineages in the Botryosphaeriaceae
Crous, P.W. ; Slippers, B. ; Wingfield, M.J. ; Rheeder, J. ; Marasas, W.F.O. ; Philips, A.J.L. ; Alves, A. ; Burgess, T. ; Barber, P. ; Groenewald, J.Z. - \ 2006
Studies in Mycology 55 (2006). - ISSN 0166-0616 - p. 235 - 253.
ribosomal dna-sequences - sp-nov - fruit rot - anamorphic fungi - north-america - south-africa - morphology - eucalyptus - dothidea - characters
Botryosphaeria is a species-rich genus with a cosmopolitan distribution, commonly associated with dieback and cankers of woody plants. As many as 18 anamorph genera have been associated with Botryosphaeria, most of which have been reduced to synonymy under Diplodia (conidia mostly ovoid, pigmented, thick-walled), or Fusicoccum (conidia mostly fusoid, hyaline, thin-walled). However, there are numerous conidial anamorphs having morphological characteristics intermediate between Diplodia and Fusicoccum, and there are several records of species outside the Botryosphaeriaceae that have anamorphs apparently typical of Botryosphaeria s.str. Recent studies have also linked Botryosphaeria to species with pigmented, septate ascospores, and Dothiorella anamorphs, or Fusicoccum anamorphs with Dichomera synanamorphs. The aim of this study was to employ DNA sequence data of the 28S rDNA to resolve apparent lineages within the Botryosphaeriaceae. From these data, 12 clades are recognised. Two of these lineages clustered outside the Botryosphaeriaceae, namely Diplodia-like anamorphs occurring on maize, which are best accommodated in Stenocarpella (Diaporthales), as well as an unresolved clade including species of Camarosporium/Microdiplodia. We recognise 10 lineages within the Botryosphaeriaceae, including an unresolved clade (Diplodia/Lasiodiplodia/Tiarosporella), Botryosphaeria s.str. (Fusicoccum anamorphs), Macrophomina, Neoscytalidium gen. nov., Dothidotthia (Dothiorella anamorphs), Neofusicoccum gen. nov. (Botryosphaeria-like teleomorphs, Dichomera-like synanamorphs), Pseudofusicoccum gen. nov., Saccharata (Fusicoccum- and Diplodia-like synanamorphs), "Botryosphaeria" quercuum (Diplodia-like anamorph), and Guignardia (Phyllosticta anamorphs). Separate teleomorph and anamorph names are not provided for newly introduced genera, even where both morphs are known. The taxonomy of some clades and isolates (e.g. B. mamane) remains unresolved due to the absence of ex-type cultures.
How many species of fungi are there at the tip of Africa?
Crous, P.W. ; Rong, I.H. ; Wood, A. ; Lee, S. ; Glen, H. ; Botha, W. ; Slippers, B. ; Beer, W.Z. de; Wingfield, M.J. ; Hawksworth, D.L. - \ 2006
Studies in Mycology 55 (2006). - ISSN 0166-0616 - p. 13 - 33.
dna-sequence data - eucalyptus leaf fungi - south-africa - sp-nov - root-rot - interesting records - cercosporoid fungi - protea infructescences - lichen genus - rust fungi
Several recent studies have reviewed the extent of fungal biodiversity, and have used these data as basis for revised estimates of species numbers based on known numbers of plants and insects. None of these studies, however, have focused on fungal biodiversity in South Africa. Coinciding with the 100th anniversary of the National Collection of Fungi (PREM) in South Africa in 2005, it is thus timely to reflect on the taxonomic research that has been conducted in South Africa over the past Century. Information is presented on the extent of fungal collections preserved at PREM, and the associated research publications that have largely resulted from this resource. These data are placed in context of the known plant and insect biodiversity, and used as basis to estimate the potential number of fungi that could be expected in South Africa. The conservative estimate is of approximately 200 000 species without taking into account those associated with a substantial insect biodiversity.
Carbon monoxide conversion by thermophilic sulfate-reducing bacteria in pure culture and in co-culture with Carboxydothermus hydrogenoformans
Parshina, S.N. ; Kijlstra, S. ; Henstra, A.M. ; Sipma, J. ; Plugge, C.M. ; Stams, A.J.M. - \ 2005
Applied Microbiology and Biotechnology 68 (2005)3. - ISSN 0175-7598 - p. 390 - 396.
desulfovibrio-vulgaris hildenborough - anaerobic bioreactor sludges - sp-nov - gen.-nov. - methanogenic bacteria - growth - reduction - energy - gas - hydrogenases
Biological sulfate (SO4) reduction with carbon monoxide (CO) as electron donor was investigated. Four thermophilic SO4-reducing bacteria, Desulfotomaculum thermoacetoxidans (DSM 5813), Thermodesulfovibrio yellowstonii (ATCC 51303), Desulfotomaculum kuznetsovii (DSM 6115; VKM B-1805), and Desulfotomaculum thermobenzoicum subsp. thermosyntrophicum (DSM 14055), were studied in pure culture and in co-culture with the thermophilic carboxydotrophic bacterium Carboxydothermus hydrogenoformans (DSM 6008). D. thermoacetoxidans and T. yellowstonii were extremely sensitive to CO: their growth on pyruvate was completely inhibited at CO concentrations above 2% in the gas phase. D. kuznetsovii and D. thermobenzoicum subsp. thermosyntrophicum were less sensitive to CO. In pure culture, D. kuznetsovii and D. thermobenzoicum subsp. thermosyntrophicum were able to grow on CO as the only electron donor and, in particular in the presence of hydrogen/carbon dioxide, at CO concentrations as high as 50-70%. The latter SO4 reducers coupled CO oxidation to SO4 reduction, but a large part of the CO was converted to acetate. In co-culture with C. hydrogenoformans, D. kuznetsovii and D. thermobenzoicum subsp. thermosyntrophicum could even grow with 100% CO (P CO=120 kPa).
Preliminary studies on Botryosphaeria species from Southern Hemisphere conifers in Australasia and South Africa
Slippers, B. ; Summerbell, B.A. ; Crous, P.W. ; Coutinho, T.A. ; Wingfield, B.D. ; Wingfield, M.J. - \ 2005
Australasian Plant Pathology 34 (2005)2. - ISSN 0815-3191 - p. 213 - 220.
wollemia-nobilis - genetic-variation - sp-nov - eucalyptus - dothidea - characters - pathogens - sequences - cankers - ribis
Wollemia nobilis is an ancient coniferous tree species that was recently discovered in eastern Australia. This tree is highly threatened due to its limited distribution. No genetic variation has been detected within the wild populations of ~100 adult plants. A recent study has revealed that a species of Botryosphaeria is highly pathogenic to W. nobilis. The aim of the present study was to identify this fungus, as well as Botryosphaeria isolates of unknown identity from other Southern Hemisphere coniferous hosts, Araucaria from New Zealand and Widdringtonia from South Africa. To facilitate their identification, sequence data for the ITS rDNA, as well as the ß-tubulin and translation elongation factor 1-¿ genes were combined to determine the phylogenetic relationship of these isolates with those of known Botryosphaeria spp. Isolates from W. nobilis included two Botryosphaeria spp. The first is closely related to B. ribis, but also shares some unique sequence polymorphisms with B. parva. One isolate grouped with B. australis, but also varied slightly from this taxon in the gene regions analysed. Additional isolates will be needed to determine whether these sequence variations represent speciation events or merely variation within populations of B. ribis and B. australis. In addition to this, B. parva was identified from Araucaria in New Zealand, and B. australis was found on Widdringtonia trees in South Africa. All three reports of these fungi are new records for their various hosts and could represent important pathogens of these trees
Hosts, species and genotypes: opinions versus data
Crous, P.W. ; Groenewald, J.Z. - \ 2005
Australasian Plant Pathology 34 (2005)4. - ISSN 0815-3191 - p. 463 - 470.
south-africa - mycosphaerella-suberosa - botryosphaeria-dothidea - pyrenophora-teres - dna phylogeny - shoot blight - sp-nov - eucalyptus - phomopsis - phaeoacremonium
We are currently in the middle of a revolution in fungal taxonomy. Taxonomy is at the crossroads, where phenotypic data must be merged with DNA and other data to facilitate accurate identifications. These data, linked to open access journals and databases, will facilitate the stability of nomenclature in the future. To achieve this, however, plant pathologists must embrace new technologies, and implement these policies in their research programmes.
|Protea infructescences represent a unique fungal niche
Lee, S. ; Roets, F. ; Crous, P.W. - \ 2005
Fungal Diversity 19 (2005). - ISSN 1560-2745 - p. 69 - 78.
south-africa - species richness - cape fynbos - sp-nov - ophiostoma - genus - restionaceae - biodiversity - key
The biodiversity of the saprobic microfungi occurring in Protea infructescences (flowerheads) was investigated. A total of 28 fungal species including 14 ascomycetes and 14 anamorphic fungi were collected from 2000-2001. The mycoflora of the infructescences, especially the flowers, were found to differ totally from that of the bracts and other Protea tissues. This indicates their uniqueness as fungal micro-habitat. Furthermore, the majority of ascomycete species isolated from these flowers were characterised by having long ostiolar necks. This finding indicates that insects play a major role in the dispersal of the ascomycetes that occur on these infructescences, which is further corroborated by the unusually high number of insects that frequent these flowers. From these data it is clear that the saprobic fungal flora of Protea infructescences have a unique ecological role. However, the exact nature of this interaction will only become clear once further studies are conducted monitoring the individual components of this ecosystem.
High rate sulfate reduction in a submerged anaerobic membrane bioreactor (SAMBaR) at high salinity
Vallero, M.V.G. ; Lettinga, G. ; Lens, P.N.L. - \ 2005
Journal of Membrane Science 253 (2005)1-2. - ISSN 0376-7388 - p. 217 - 232.
methanogenic bacteria - thermophilic sulfate - waste-water - reducing bacterium - sulfite reduction - sp-nov - reactor - acetate - environments - degradation
Sulfate reduction in salt rich wastewaters (50 g NaCl L¿1 and 1 g MgCl2·6H2O L¿1; conductivity 60¿70 mS cm¿1) was investigated in a 6 L submerged anaerobic membrane bioreactor (SAMBaR) and inoculated solely with the halotolerant sulfate reducing bacterium Desulfobacter halotolerans. The SAMBaR was fed with acetate and ethanol at organic loading rates up to 14 g COD L¿1 day¿1 in excess of sulfate (COD/SO42¿ of 0.5) and operated at pH 7.2 ± 0.2 and a hydraulic retention time (HRT) from 8 to 36 h. A sulfate reduction rate up to 6.6 g SO42¿ L¿1 day¿1 was achieved in the SAMBaR operating at a flux of 17.1 L m¿2 h¿1, which resulted in a HRT of 9 h including the backflow of permeate used for backflushing. The fairly constant very high specific sulfate reduction rate of 5.5 g SO42¿ g VSS¿1 day¿1 showed that the performance of the SAMBaR was limited by the low amount of biomass (0.85 g VSS L¿1) present in the reactor at the end of the experiment. It was shown that sulfate reducing submerged anaerobic membrane bioreactors can be operated over extended periods of time without chemical cleaning of the membranes at a certain fixed flux if this flux is substantially below the nominal critical flux determined experimentally (18¿21 L m¿2 h¿1). Intermittent operation as well as backflush of the membranes were shown to slow the fouling in the membranes. Frequent backflush (e.g. 1 min each 10 min) is the suggested operational strategy to minimize fouling in anaerobic MBRs.
Bacterial mechanisms to overcome inhibitory effects of dietary tannins
Smith, A.H. ; Zoetendal, E.G. ; Mackie, R.I. - \ 2005
Microbial Ecology 50 (2005)2. - ISSN 0095-3628 - p. 197 - 205.
c-14-labeled condensed tannins - east-african ruminants - mulga acacia-aneura - sp-nov - streptococcus-gallolyticus - lotus-corniculatus - in-vitro - eubacterium-oxidoreducens - antimicrobial properties - gastrointestinal-tract
High concentrations of tannins in fodder plants inhibit gastrointestinal bacteria and reduce ruminant performance. Increasing the proportion of tannin-resistant bacteria in the rumen protects ruminants from antinutritional effects. The reason for the protective effect is unclear, but could be elucidated if the mechanism(s) by which tannins inhibit bacteria and the mechanisms of tannin resistance were understood. A review of the literature indicates that the ability of tannins to complex with polymers and minerals is the basis of the inhibitory effect on gastrointestinal bacteria. Mechanisms by which bacteria can overcome inhibition include tannin modification/degradation, dissociation of tannin¿substrate complexes, tannin inactivation by high-affinity binders, and membrane modification/repair and metal ion sequestration. Understanding the mechanism of action of tannins and the mechanism(s) bacteria use to overcome the inhibitory effects will allow better management of the rumen ecosystem to reduce the antinutritional effects of tannin-rich fodder plants and thereby improve ruminant production.
Structure and topology of microbial communities in the major gut compartments of Melolontha melolontha larvae (Coleoptera: Scarabaeidae)
Egert, M.G.G. ; Stingl, U. ; Dyhrberg Bruun, L. ; Pommerenke, B. ; Brune, A. ; Friedrich, M.W. - \ 2005
Applied and Environmental Microbiology 71 (2005)8. - ISSN 0099-2240 - p. 4556 - 4566.
sulfate-reducing bacteria - pachnoda-ephippiata coleoptera - termite mastotermes-darwiniensis - targeted oligonucleotide probes - humus-feeding larva - reticulitermes-flavipes - sp-nov - hindgut - oxygen - hybridization
Physicochemical gut conditions and the composition and topology of the intestinal microbiota in the major gut compartments of the root-feeding larva of the European cockchafer (Melolontha melolontha) were studied. Axial and radial profiles of pH, O2, H2, and redox potential were measured with microsensors. Terminal restriction fragment length polymorphism (T-RFLP) analysis of bacterial 16S rRNA genes in midgut samples of individual larvae revealed a simple but variable and probably nonspecific community structure. In contrast, the T-RFLP profiles of the hindgut samples were more diverse but highly similar, especially in the wall fraction, indicating the presence of a gut-specific community involved in digestion. While high acetate concentrations in the midgut and hindgut (34 and 15 mM) corroborated the presence of microbial fermentation in both compartments, methanogenesis was confined to the hindgut. Methanobrevibacter spp. were the only methanogens detected and were restricted to this compartment. Bacterial 16S rRNA gene clone libraries of the hindgut were dominated by clones related to the Clostridiales. Clones related to the Actinobacteria, Bacillales, Lactobacillales, and -Proteobacteria were restricted to the lumen, whereas clones related to the ß- and -Proteobacteria were found only on the hindgut wall. Results of PCR-based analyses and fluorescence in situ hybridization of whole cells with group-specific oligonucleotide probes documented that Desulfovibrio-related bacteria comprise 10 to 15% of the bacterial community at the hindgut wall. The restriction of the sulfate-reducer-specific adenosine-5'-phosphosulfate reductase gene apsA to DNA extracts of the hindgut wall in larvae from four other populations in Europe suggested that sulfate reducers generally colonize this habitat.
Characterisation and mode of action of an exopolygalacturonase from the hyperthermophilic bacterium Thermotoga maritime
Kluskens, L.D. ; Alebeek, G.J.W.M. van; Walther, J. ; Voragen, A.G.J. ; Vos, W.M. de; Oost, J. van der - \ 2005
FEBS Journal 272 (2005)21. - ISSN 1742-464X - p. 5464 - 5473.
site-directed mutagenesis - aspergillus-niger - crystal-structure - butyrivibrio-fibrisolvens - endopolygalacturonase ii - subsite affinities - genome sequence - bovine rumen - sp-nov - pectin
An intracellular pectinolytic enzyme, PelB (TM0437), from the hyperthermophilic bacterium Thermotoga maritima was functionally produced in Escherichia coli and purified to homogeneity. PelB belongs to family 28 of the glycoside hydrolases, consisting of pectin-hydrolysing enzymes. As one of the few bacterial exopolygalacturonases, it is able to remove monogalacturonate units from the nonreducing end of polygalacturonate. Detailed characterization of the enzyme showed that PelB is highly thermo-active and thermostable, with a melting temperature of 105 °C and a temperature optimum of 80 °C, the highest described to date for hydrolytic pectinases. PelB showed increasing activity on oligosaccharides with an increasing degree of polymerization. The highest activity was found on the pentamer (1000 U·mg1). In addition, the affinity increased in conjunction with the length of the oligoGalpA chain. PelB displayed specificity for saturated oligoGalpA and was unable to degrade unsaturated or methyl-esterified oligoGalpA. Analogous to the exopolygalacturonase from Aspergillus tubingensis, it showed low activity with xylogalacturonan. Calculations on the subsite affinity revealed the presence of four subsites and a high affinity for GalpA at subsite +1, which is typical of exo-active enzymes. The physiological role of PelB and the previously characterized exopectate lyase PelA is discussed.
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
Novel physiological features of Carboxydothermus hydrogenoformans and Thermoterrabacterium ferrireducens
Henstra, A.M. ; Stams, A.J.M. - \ 2004
Applied and Environmental Microbiology 70 (2004)12. - ISSN 0099-2240 - p. 7236 - 7240.
gradient gel-electrophoresis - sp-nov - thermophilic-bacterium - purification - reveals
Carboxydothermus hydrogenoformans is able to grow by conversion of CO to H2 and CO2. Besides CO, only pyruvate was described as serving as an energy source. Based on 16S rRNA gene sequence similarity, C. hydrogenoformans is closely related to Thermoterrabacterium ferrireducens. T. ferrireducens is like C. hydrogenoformans a gram-positive, thermophilic, strict anaerobic bacterium. However, it is capable of using various electron donors and acceptors for growth. Growth of C. hydrogenoformans with multiple electron donors and acceptors was tested. C. hydrogenoformans oxidized formate, lactate, glycerol, CO, and H2 with 9,10-anthraquinone-2,6-disulfonate as an electron acceptor. Sulfite, thiosulfate, sulfur, nitrate, and fumarate were reduced with lactate as an electron donor. T. ferrireducens oxidized CO with 9,10-anthraquinone-2,6-disulfonate as an electron acceptor but did not produce H2 from CO. In contrast to what was published before, T. ferrireducens was able to grow on lactate with sulfite, sulfur, and nitrate as electron acceptors
Speciation and distribution of Botryosphaeria spp. on native and introduced Eucalyptus trees in Australia and South Africa
Slippers, B. ; Fourie, G. ; Crous, P.W. ; Coutinho, T.A. ; Wingfield, B.D. ; Carnegie, A.J. ; Wingfield, M.J. - \ 2004
Studies in Mycology 50 (2004)2. - ISSN 0166-0616 - p. 343 - 358.
multiple gene genealogies - sphaeropsis-sapinea - primer sets - sp-nov - fungi - dothidea - sequences - cankers - ribis - characters
Botryosphaeria spp. are important canker and die-back pathogens that affect Eucalyptus spp. They also occur endophytically in Eucalyptus leaves and stems. For the purpose of this study, Botryosphaeria strains were isolated from diseased and symptomless Eucalyptus material from Australia and South Africa. These isolates were induced to sporulate in culture, and compared with known species of Botryosphaeria. Selected isolates were also compared with authentic isolates of known Botryosphaeria spp. based on nuclear DNA sequence data of the ITS rDNA, P-tubulin and elongation factor l-alpha regions. Five Botryosphaeria spp. were identified from Eucalyptus plants. The ITS rDNA sequence data were then used to develop a PCR RFLP technique that could distinguish these species. Botryosphaeria eucalyptorum and a new species, B. eucalypticola, were the most common species on Eucalyptus in eastern Australia. These species also occur on Eucalyptus in South Africa, where they have most likely been introduced. Botryosphaeria parva was common on Eucalyptus in exotic environments, but rare on this host in Australia. Although B. dothidea was previously thought to be common on eucalypts, only one isolate of each of B. dothidea and B. australis were found in all the areas surveyed. No isolates of B. ribis, which was also commonly reported from Eucalyptus, were identified during this survey from Eucalyptus. Data from the present study provide the first holistic overview of the species of Botryosphaeria associated with Eucalyptus in both native and exotic environments.
|Diversity of saprobic hyphomycetes on Proteaceae and Restionaceae from South Africa
Lee, S. ; Mel'nik, V. ; Taylor, J.E. ; Crous, P.W. - \ 2004
Fungal Diversity 17 (2004). - ISSN 1560-2745 - p. 91 - 114.
fungal succession - leaf-litter - interesting records - sp-nov - microfungi - fynbos - soils - decomposition - biodiversity - thailand
To assess the diversity of saprobic microfungi occurring on the Proteaceae and Restionaceae of the Western Cape province of South Africa, samples of leaf, stem, flowerhead and culm litter were collected from the year 2000 until the end of 2002. About 1 000 fungal collections were made, 117 of which were hyphomycetes, representing 66 species in 53 genera. Of these, 49 species were newly recorded from South Africa, and 64 occurred on previously unreported host substrates. The diversity of hyphomycetes on Proteaceae and Restionaceae is discussed, together with a list of the hyphomycetes.
Isolation and biodiversity of hitherto undescribed soil bacteria related to Bacillus niacini
Felske, A. ; Tzeneva, V.A. ; Heyrman, J. ; Langeveld, M.A. ; Akkermans, A.D.L. ; Vos, P. - \ 2004
Microbial Ecology 48 (2004)1. - ISSN 0095-3628 - p. 111 - 119.
16s ribosomal-rna - genus bacillus - culturable bacteria - agricultural soil - paddy soil - sp-nov - diversity - sequences - dna - identification
The hitherto largely not described phylogenetic neighborhood of Bacillus niacini has been explored by a comprehensive cultivation experiment and genomic variety studies. Previous culture-independent studies demonstrated that similar to15% of all Bacillus 16S rDNA directly extracted from soils worldwide was affiliated to B. niacini. Seven different media were inoculated with soil suspensions in serial dilutions and incubated at different temperatures. Then, bacterial colonies were picked and analyzed by sequencing. A mineral medium with acetate as carbon source yielded a B. niacini rate of >3% of all picked colonies. Other media were less efficient but also successful. Applying this culturing approach, we succeeded in obtaining 64 isolates from different Dutch soils. The isolates turned out to be diverse, although closely related to B. niacini as revealed by 16S rDNA sequencing. Close matches with environmental clones were also found, thus demonstrating much more diversity beyond previously known 16S rDNA sequences. The rep-PCR fingerprinting method revealed a high genomic variety, redundancy could not be observed among our isolates. Hence, the hitherto neglected B. niacini lineage, apparently among the most abundant soil Bacillus, was accessible to our cultivation approach.
Methanol utilization in defined mixed cultures of thermophilic anaerobes in the presence sulfate
Goorissen, H.P. ; Stams, A.J.M. ; Hansen, T.A. - \ 2004
FEMS microbiology ecology 49 (2004)3. - ISSN 0168-6496 - p. 489 - 494.
sp-nov - reducing bacterium - reactor - reduction - hydrogen - sulfide - strains
We studied thermophilic sulfate reduction with methanol as electron donor in continuous cultures. Mixed cultures of selected microorganisms were used, representing different methanol degrading pathways followed by various trophic groups of microorganisms. Our results show that direct competition for methanol between a homoacetogen, Moorella thermoautotrophica, and a sulfate reducer, Desulfotomaculum kuzrietsovii, is in favour of the sulfate reducer due to its affinity for methanol. Methanogenesis as a result of interspecies hydrogen transfer between D. kuznetsovii and a hydrogen-consuming methanogenic archaeon, Methanothermobacter thermoautotrophicus occurred only below 5 mM total sulfide. A similar result was obtained when M. thermoautotrophica was grown on methanol in the presence of Mb. thermoautotrophicus. Interestingly, D. kuznetsovii could coexist with a non-methanolutilizing sulfate reducer (Thermodesulfovibrio species). Our data show that it is possible to maintain a dominant sulfate-reducing process with methanol as electron donor at 60 degreesC in mixed continuous cultures. (C) 2004 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved.
Interspecies electron transfer in methanogenic propionate degrading consortia
Bok, F.A.M. de; Plugge, C.M. ; Stams, A.J.M. - \ 2004
Water Research 38 (2004)6. - ISSN 0043-1354 - p. 1368 - 1375.
sulfate-reducing bacterium - syntrophobacter-wolinii - oxidizing bacterium - granular sludge - sp-nov - methanospirillum-hungatei - formate dehydrogenases - anaerobic degradation - phylogenetic analysis - smithella-propionica
Propionate is a key intermediate in the conversion of complex organic matter under methanogenic conditions. Oxidation of this compound requires obligate syntrophic consortia of acetogenic proton- and bicarbonate reducing bacteria and methanogenic archaea. Although H-2 acts as an electron-carrier in these consortia, evidence accumulates that formate plays an even more important role. To make energy yield from propionate oxidation energetically feasible for the bacteria and archaea involved, the concentrations of H-2 and formate have to be extremely low. On the other hand, the diffusion distance of these carriers has to be small to allow high propionate conversion rates. Accordingly, the high conversion rates observed in methanogenic bioreactors are due to the fact that the propionate-oxidizing bacteria and their methanogenic partners form micro-colonies within the densely packed granules. (C) 2003 Elsevier Ltd. All rights reserved.
Anaerobic microbial dehalogenation
Smidt, H. ; Vos, W.M. de - \ 2004
Annual Review of Microbiology 58 (2004). - ISSN 0066-4227 - p. 43 - 73.
desulfitobacterium-frappieri pcp-1 - polymerase-chain-reaction - reductively dechlorinates tetrachloroethene - bacterium rhodopseudomonas-palustris - chloroethene-contaminated sites - chlorinated aliphatic-compounds - sp strain cbdb1 - vinyl-chloride - sp-nov - de
The natural production and anthropogenic release of halogenated hydrocarbons into the environment has been the likely driving force for the evolution of an unexpectedly high microbial capacity to dehalogenate different classes of xenobiotic haloorganics. This contribution provides an update on the current knowledge on metabolic and phylogenetic diversity of anaerobic microorganisms that are capable of dehalogenating-or completely mineralizing-halogenated hydrocarbons by fermentative, oxidative, or reductive pathways. In particular, research of the past decade has focused on halorespiring anaerobes, which couple the dehalogenation by dedicated enzyme systems to the generation of energy by electron transport-driven phosphorylation. Significant advances in the biochemistry and molecular genetics of degradation pathways have revealed mechanistic and structural similarities between dehalogenating enzymes from phylogenetically distinct anaerobes. The availability of two almost complete genome sequences of halorespiring isolates recently enabled comparative and functional genomics approaches, setting the stage for the further exploitation of halorespiring and other anaerobic dehalogenating microbes as dedicated degraders in biological remediation processes.
Anaerobic reduction and oxidation of quinine moieties and the reduction of oxidized metals by halorespiring and related organisms
Luijten, M.L.G.C. ; Weelink, S.A.B. ; Godschalk, B. ; Langenhoff, A.A.M. ; Eekert, M.H.A. van; Schraa, G. ; Stams, A.J.M. - \ 2004
FEMS microbiology ecology 49 (2004)1. - ISSN 0168-6496 - p. 145 - 150.
sp-nov - gen-nov - dehalospirillum-multivorans - electron-acceptors - humic substances - desulfitobacterium - bacterium - tetrachloroethene - sulfurospirillum - dechlorination
Halorespiring microorganisms have been detected in soils that were not polluted with chlorinated compounds. In this study, we describe alternative electron acceptor utilization by some halorespiring bacteria and phylogenetically related bacteria. It appears that oxidized metals like selenate, arsenate and manganese are rather common electron acceptors for halorespiring species of Desulfitobacterium and Sulfurospirillum and related bacteria. All tested microorganisms are able to reduce anthraquinone-2,6-disulfonate (AQDS) and four tested organisms (Desulfobacterium hafniense DP7, Sulfurospirillum barnesii, Sulfurospirillum deleyianum and Sulfurospirillum arsenophilum) are able to oxidize reduced anthrahydroquinone-2,6,-disulfonate (AH(2)QDS) as well. The characteristic to reduce oxidized metals, and to reduce and oxidize quinone moieties coupled to energy conservation is a likely explanation for the presence of halorespiring microorganisms in unpolluted soils. (C) 2004 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved.
Analysis of 16S rDNA reveals bacterial shift during in vitro fermentation of fermentable carbohydrate using piglet faeces as inoculum
Zhu Wei-Yun, ; Williams, B.A. ; Konstantinov, S.R. ; Tamminga, S. ; Vos, W.M. de; Akkermans, A.D.L. - \ 2003
Anaerobe 9 (2003)4. - ISSN 1075-9964 - p. 175 - 180.
gradient gel-electrophoresis - ribosomal-rna - grassland soils - gas-production - sp-nov - intestine - pigs - dna - communities - microbiota
In vitro fermentation of sugar beet pulp (SBP) was carried out to determine which bacterial species would be enriched by use of this carbohydrate source. Faeces from four weaning piglets as a source of inoculum was also compared. The microbial diversity of the prominent bacteria before and after this in vitro fermentation was analysed using denaturing gradient gel electrophoresis (DGGE) of PCR amplicons of 16S rDNA. Before fermentation, the DGGE profiles showed differences between cultures inoculated with faeces from different piglets, though some bands were common to all piglets. After fermentation of SBP, three dominant bands appeared, of which two bands appeared in all samples and one for both replicates of one piglet. Sequences of the corresponding 16S rDNA of two bands showed 92% similarity to Eubacterium eligens and 96% similarity to Lachnospira pectinoschiza, and that of the third band 95% to L. pectinoschiza. (C) 2003 Elsevier Ltd. All rights reserved.
Development of a novel Process for the Biological conversion of H2S and Methanethiol to Elemental Sulfur
Sipma, J. ; Janssen, A.J.H. ; Hulshoff Pol, L.W. ; Lettinga, G. - \ 2003
Biotechnology and Bioengineering 82 (2003)1. - ISSN 0006-3592 - p. 1 - 11.
afvalwaterbehandeling - anaërobe behandeling - zwavel - rioolafvalwater - slib - methanol - reductie - bioreactoren - waste water treatment - anaerobic treatment - sulfur - sewage effluent - sludges - methanol - reduction - bioreactors - granular sludge reactor - methylotrophic methanogen - sp-nov - waste-water - estuarine methanogen - sulfide - degradation - sediments - dimethylsulfide - bacterium
The feasibility of anaerobic treatment of wastewater containing methanethiol (MT), an extremely volatile and malodorous sulfur compound, was investigated in lab-scale bioreactors. Inoculum biomass originating from full-scale anaerobic wastewater treatment facilities was used. Several sludges were tested for their ability to degrade MT
The feasibility of anaerobic treatment of wastewater containing methanethiol (MT), an extremely volatile and malodorous sulfur compound, was investigated in lab-scale bioreactors. Inoculum biomass originating from full-scale anaerobic wastewater treatment facilities was used. Several sludges, tested for their ability to degrade MT, revealed the presence of organisms capable of metabolizing MT as their sole source of energy. Furthermore, batch tests were executed to gain a better understanding of the inhibition potential of MT. It was found that increasing MT concentrations affected acetotrophic organisms more dramatically than methylotrophic organisms. Continuous reactor experiments, using two lab-scale upflow anaerobic sludge bed (UASB) reactors (R1 and R2), aimed to determine the maximal MT load and the effect of elevated sulfide concentrations on MT conversion. Both reactors were operated at a hydraulic retention time (HRT) of about 7 hours, a temperature of 30degreesC, and a pH of between 7.3 and 7.6. At the highest influent MT concentration applied, 14 mM in R1, corresponding to a volumetric loading rate of about 50 mM MT per day, 87% of the organic sulfur was recovered as hydrogen sulfide (12.2 mM) and the remainder as volatile organic sulfur compounds (VOSCs). Upon decreasing the HRT to 3.5 to 4.0 h at a constant MT loading rate, the sulfide concentration in the reactor decreased to 8 mM and MT conversion efficiency increased to values near 100%. MT conversion was apparently inhibited by the high sulfide concentrations in the reactor. The specific MT degradation rate, as determined after 120 days of operation in R1, was 2.83 +/- 0.27 mmol MT g VSS-1 day(-1). During biological desulfurization of liquid hydrocarbon phases, such as with liquefied petroleum gas (LPG), the combined removal of hydrogen sulfide and MT is desired. In R2, the simultaneous addition of sodium sulfide and MT was therefore studied and the effect of elevated sulfide concentrations was investigated. The addition of sodium sulfide resulted in enhanced disintegration of sludge granules, causing significant washout of biomass. Additional acetate, added to stimulate growth of methanogenic bacteria to promote granulation, was hardly converted at the termination of the experimental period. (C) 2003 Wiley Periodicals, Inc.
Effect of NaCl on thermophilic (55°C) methanol degradation in sulfate reducing granular sludge reactors
Vallero, M.V.G. ; Hulshoff Pol, L.W. ; Lettinga, G. ; Lens, P.N.L. - \ 2003
Water Research 37 (2003)10. - ISSN 0043-1354 - p. 2269 - 2280.
anaërobe behandeling - afvalwaterbehandeling - methanol - reductie - natriumchloride - sulfaten - rioolafvalwater - slib - anaerobic treatment - waste water treatment - methanol - reduction - sodium chloride - sulfates - sewage effluent - sludges - sp-nov - processing wastewaters - sodium inhibition - bacteria - methanogenesis - temperature - antagonism - digestion
The effect of NaCl on thermophilic (55degreesC) methanol conversion in the presence of excess of sulfate (COD/SO42-=0.5) was investigated in two 6.5L lab-scale upflow anaerobic sludge bed reactors inoculated with granular sludge previously not adapted to NaCl
The effect of NaCl on thermophilic (55degreesC) methanol conversion in the presence of excess of sulfate (COD/SO42-=0.5) was investigated in two 6.5L lab-scale upflow anaerobic sludge bed reactors inoculated with granular sludge previously not adapted to NaCl. Methanol was almost completely used for sulfate reduction in the absence of NaCl when operating at an organic loading rate of 5 g COD L-1 day(-1) and a hydraulic retention time of 10 h. The almost fully sulfidogenic sludge consisted of both granules and flocs developed after approximately 100 days in both reactors. Sulfate reducing bacteria (SRB) outcompeted methane producing archaea (MPA) for methanol, but acetate represented a side-product, accounting for maximal 25% of the total COD converted. Either MPA or SRB did not use acetate as substrate in activity tests. High NaCl concentrations (25 g L-1) completely inhibited methanol degradation, whereas low salt concentrations (2.5 g NaCl L-1) provoked considerable changes in the metabolic fate of methanol. The MPA were most sensitive towards the NaCl shock (25 g L-1). In contrast, the addition of 2.5 g L-1 of NaCl stimulated MPA and homoacetogenic bacteria. (C) 2003 Elsevier Science Ltd. All rights reserved.
Crystal structure of Pyrococcus furiosus phosphoglucose isomerase: Implications for substrate binding and catalysis
Berrisford, J.M. ; Akerboom, A.P. ; Turnbull, A.P. ; Geus, D. de; Sedelnikova, S.E. ; Staton, I. ; McLeod, C.W. ; Verhees, C.H. ; Oost, J. van der; Rice, D.W. ; Baker, P.J. - \ 2003
Journal of Biological Chemistry 278 (2003). - ISSN 0021-9258 - p. 33290 - 33297.
cupin superfamily - thermococcus-litoralis - angstrom resolution - sugar fermentation - protein structures - sp-nov - pathway - enzyme - archaebacteria - evolution
Phosphoglucose isomerase (PGI) catalyzes the reversible isomerization between D-fructose 6-phosphate and D-glucose 6-phosphate as part of the glycolytic pathway. PGI from the Archaea Pyrococcus furiosus (Pfu) was crystallized, and its structure was determined by x-ray diffraction to a 2-Angstrom resolution. Structural comparison of this archaeal PGI with the previously solved structures of bacterial and eukaryotic PGIs reveals a completely different structure. Each subunit of the homodimeric Pfu PGI consists of a cupin domain, for which the overall structure is similar to other cupin domain-containing proteins, and includes a conserved transition metal-binding site. Biochemical data on the recombinant enzyme suggests that Fe2+ is bound to Pfu PGI. However, as catalytic activity is not strongly influenced either by the replacement of Fe2+ by a range of transition metals or by the presence or absence of the bound metal ion, we suggest that the metal may not be directly involved in catalysis but rather may be implicated in substrate recognition.
Molecular and biochemical characterisation of the thermoactive family 1 pectase lyase from the hyperthermophilic bacterium Thermotoga maritima
Kluskens, L.D. ; Alebeek, G.J.W.M. van; Voragen, A.G.J. ; Vos, W.M. de; Oost, J. van der - \ 2003
Biochemical Journal 370 (2003). - ISSN 0264-6021 - p. 651 - 659.
aspergillus-niger - sp-nov - sequence - enzymes - pectin - purification - oligogalacturonides - protopectinase - inhibitors - archaea
The ability of the hyperthermophilic bacterium Thermotoga maritima to grow on pectin as a sole carbon source coincides with the secretion of a pectate lyase A (PeplA) in the extracellular medium. The pe/A gene of T. maritima was functionally expressed in Escherichia coli as the first heterologously produced thermophilic pectinase, and purified to homogeneity. Gel filtration indicated that the native form of PelA is tetrameric. Highest activity (422 units/mg, with a K-m of 0.06 mM) was demonstrated on polygalacturonic acid (PGA), whereas pectins with an increasing degree of methylation were degraded at a decreasing rate. In the tradition of pectate lyases, PelA demonstrated full dependency on Ca2+ for stability and activity. The enzyme is highly thermoactive and thermostable, operating optimally at 90 degreesC and pH 9.0, with a half-life for thermal inactivation of almost 2 h at 95 degreesC and an apparent melting temperature of 102.5 degreesC. Detailed characterization of the product formation with PGA indicated that PelA has a unique eliminative exo-cleavage pattern liberating unsaturated trigalacturonate as the major product, in contrast with unsaturated digalacturonate for other exopectate lyases known. The unique exo-acting mode of action was supported by progression profiles of PelA on oligo-galacturonides (degree of polymerization, 3-8) and the examination of the bond cleavage frequencies.
Two W-containing formate dehydrogenase (CO2 reductases) involved in syntrophic propionate oxidation by Syntrophobacter fumaroxidans
Bok, F.A.M. de; Hagedoorn, P.L. ; Silva, P.J. ; Hagen, W.R. ; Schiltz, E. ; Fritsche, K. ; Stams, A.J.M. - \ 2003
European Journal of Biochemistry 270 (2003)11. - ISSN 0014-2956 - p. 2476 - 2485.
sulfate-reducing bacterium - desulfovibrio-gigas - oxidizing bacterium - spectroscopic characterization - clostridium-thermoaceticum - phylogenetic analysis - escherichia-coli - pure culture - sp-nov - purification
Two formate dehydrogenases (CO2-reductases) (FDH-1 and FDH-2) were isolated from the syntrophic propionate-oxidizing bacterium Syntrophobacter fumaroxidans. Both enzymes were produced in axenic fumarate-grown cells as well as in cells which were grown syntrophically on propionate with Methanospirillum hungatei as the H2 and formate scavenger. The purified enzymes exhibited extremely high formate-oxidation and CO2-reduction rates, and low Km values for formate. For the enzyme designated FDH-1, a specific formate oxidation rate of 700 U·mg-1 and a Km for formate of 0.04 mm were measured when benzyl viologen was used as an artificial electron acceptor. The enzyme designated FDH-2 oxidized formate with a specific activity of 2700 U·mg-1 and a Km of 0.01 mm for formate with benzyl viologen as electron acceptor. The specific CO2-reduction (to formate) rates measured for FDH-1 and FDH-2, using dithionite-reduced methyl viologen as the electron donor, were 900 U·mg-1 and 89 U·mg-1, respectively. From gel filtration and polyacrylamide gel electrophoresis it was concluded that FDH-1 is composed of three subunits (89 ± 3, 56 ± 2 and 19 ± 1 kDa) and has a native molecular mass of approximately 350 kDa. FDH-2 appeared to be a heterodimer composed of a 92 ± 3 kDa and a 33 ± 2 kDa subunit. Both enzymes contained tungsten and selenium, while molybdenum was not detected. EPR spectroscopy suggested that FDH-1 contains at least four [2Fe-2S] clusters per molecule and additionally paramagnetically coupled [4Fe-4S] clusters. FDH-2 contains at least two [4Fe-4S] clusters per molecule. As both enzymes are produced under all growth conditions tested, but with differences in levels, expression may depend on unknown parameters.
Carbon monoxide conversion by anaerobic bioreactor sludges
Sipma, J. ; Stams, A.J.M. ; Lens, P.N.L. ; Lettinga, G. - \ 2003
FEMS microbiology ecology 44 (2003)2. - ISSN 0168-6496 - p. 271 - 277.
slib - anaërobe behandeling - afvalwaterbehandeling - rioolafvalwater - reductie - koolmonoxide - bioreactoren - sludges - anaerobic treatment - waste water treatment - sewage effluent - reduction - carbon monoxide - bioreactors - carboxydothermus-hydrogenoformans - methanogenic bacteria - sulfate reduction - synthesis-gas - sp-nov - growth - metabolism - oxidation - reactor - energy
Seven different anaerobic sludges from wastewater treatment reactors were screened for their ability to convert carbon monoxide (CO) at 30 and 55degreesC
Seven different anaerobic sludges from wastewater treatment reactors were screened for their ability to convert carbon monoxide (CO) at 30 and 55degreesC. At 30degreesC, CO was converted to methane and/or acetate by all tested sludges. Inhibition experiments, using 2-bromoethanesulfonic acid and vancomycine, showed that CO conversion to methane at 30degreesC occurred via acetate, but not via H-2. At 55degreesC, four sludges originally cultivated at 30-35degreesC and one sludge cultivated at 55degreesC converted CO rapidly into hydrogen or into methane. In the latter case, inhibition experiments showed that methane was formed via hydrogen as the intermediate. (C) 2003 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.
Hydrogen production from paper sludge hydrolysate
Kádár, Z. ; Vrije, G.J. de; Budde, M.A.W. ; Szengyel, Z. ; Reczey, K. ; Claassen, P.A.M. - \ 2003
Applied Biochemistry and Biotechnology 107 (2003)1-3. - ISSN 0273-2289 - p. 557 - 566.
caldicellulosiruptor-saccharolyticus - thermotoga-elfii - sp-nov - bacterium
The main objective of this study was to develop a system for the production of 'renewable' hydrogen. Paper sludge is a solid industrial waste yielding mainly cellulose, which can be used, after hydrolysis, as a feedstock in anaerobic fermentation by (hyper)thermophilic organisms, such as Thermotoga elfii and Caldicellulosiruptor saccharolyticus. Tests on different medium compositions showed that both bacteria were able to produce hydrogen from paper sludge hydrolysate, but the amount of produced hydrogen and the requirement for other components differed. Hydrogen production by T. elfii strongly depended on the presence of yeast extract and salts. By contrast, C. saccharolyticus was less dependent on medium components but seemed to be inhibited by a component present in the sludge hydrolysate. Utilization of xylose was preferred over glucose by C. saccharolyticus.