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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Genome sequencing of one-carbon degrading acetogenic bacteria Moorella glycerini Strain NMP
Liebensteiner, M. ; Pinkse, M.W.H. ; Nijsse, B. ; Verhaert, P.D.E.M. ; Tsesmetzis, N. ; Stams, A.J.M. ; Lomans, B.P. - \ 2015
PRJEB8377 - ERP009454 - Moorella glycerini
The genus Moorella contains, up to now, only one sequenced genome, that of M. thermoacetica. Sequencing more strains is essential in understanding their common and specific physiology. Moreover, Moorella species typically grow with one-carbon substrates, but there are differences in their ability to grow with for example carbon monoxide. By comparing the already sequenced genomes of the type strains M. thermoacetica with close related strains we can assess which genes are responsible for the physiological differences.
Perchlorate and chlorate reduction by the Crenarchaeon Aeropyrum pernix and two thermophilic Firmicutes
Liebensteiner, M.G. ; Pinkse, M.W.H. ; Nijsse, B. ; Verhaert, P.D.E.M. ; Tsesmetzis, N. ; Stams, A.J.M. ; Lomans, B.P. - \ 2015
Environmental Microbiology Reports 7 (2015)6. - ISSN 1758-2229 - p. 936 - 945.
This study reports the ability of one hyperthermophilic and two thermophilic microorganisms to grow anaerobically by the reduction of chlorate and perchlorate. Physiological, genomic and proteome analyses suggest that the Crenarchaeon Aeropyrum pernix reduces perchlorate with a periplasmic enzyme related to nitrate reductases, but that it lacks a functional chlorite-disproportionating enzyme (Cld) to complete the pathway. Aeropyrum pernix, previously described as a strictly aerobic microorganism, seems to rely on the chemical reactivity of reduced sulfur compounds with chlorite, a mechanism previously reported for perchlorate-reducing Archaeoglobus fulgidus. The chemical oxidation of thiosulfate (in excessive amounts present in the medium) and the reduction of chlorite result in the release of sulfate and chloride, which are the products of a biotic-abiotic perchlorate reduction pathway in Ae.¿pernix. The apparent absence of Cld in two other perchlorate-reducing microorganisms, Carboxydothermus hydrogenoformans and Moorella glycerini strain NMP, and their dependence on sulfide for perchlorate reduction is consistent with the observations made on Ar.¿fulgidus. Our findings suggest that microbial perchlorate reduction at high temperature differs notably from the physiology of perchlorate- and chlorate-reducing mesophiles and that it is characterized by the lack of a chlorite dismutase and is enabled by a combination of biotic and abiotic reactions
Archaeal (Per)Chlorate Reduction at High Temperature: An Interplay of Biotic and Abiotic Reactions
Liebensteiner, M. ; Pinkse, M.W.H. ; Schaap, P.J. ; Stams, A.J.M. ; Lomans, B.P. - \ 2013
Science 340 (2013)85. - ISSN 0036-8075 - p. 85 - 87.
archaeoglobus-fulgidus - perchlorate
Perchlorate and chlorate anions [(per)chlorate] exist in the environment from natural and anthropogenic sources, where they can serve as electron acceptors for bacteria. We performed growth experiments combined with genomic and proteomic analyses of the hyperthermophile Archaeoglobus fulgidus that show (per)chlorate reduction also extends into the archaeal domain of life. The (per)chlorate reduction pathway in A. fulgidus relies on molybdo-enzymes that have similarity with bacterial enzymes; however, chlorite is not enzymatically split into chloride and oxygen. Evidence suggests that it is eliminated by an interplay of abiotic and biotic redox reactions involving sulfur compounds. Biological (per)chlorate reduction by ancient archaea at high temperature may have prevented accumulation of perchlorate in early terrestrial environments and consequently given rise to oxidizing conditions on Earth before the rise of oxygenic photosynthesis
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
Diversity, activity, and abundance of sulfate-reducing bacteria in saline nad hypersaline soda lakes
Foti, M. ; Sorokin, D.Y. ; Lomans, B.P. ; Mussman, M. ; Zacharova, E.E. ; Pimenov, N.V. ; Kuenen, J.G. ; Muyzer, G. - \ 2007
Applied and Environmental Microbiology 73 (2007)7. - ISSN 0099-2240 - p. 2093 - 2100.
sulfur-oxidizing bacteria - fresh-water sediment - 16s ribosomal-rna - sp-nov. - mono lake - gen. nov. - environment - reduction - community - microorganisms
Soda lakes are naturally occurring highly alkaline and saline environments. Although the sulfur cycle is one of the most active element cycles in these lakes, little is known about the sulfate-reducing bacteria (SRB). In this study we investigated the diversity, activity, and abundance of SRB in sediment samples and enrichment cultures from a range of (hyper)saline soda lakes of the Kulunda Steppe in southeastern Siberia in Russia. For this purpose, a polyphasic approach was used, including denaturing gradient gel electrophoresis of dsr gene fragments, sulfate reduction rate measurements, serial dilutions, and quantitative real-time PCR (qPCR). Comparative sequence analysis revealed the presence of several novel clusters of SRB, mostly affiliated with members of the order Desulfovibrionales and family Desulfobacteraceae. We detected sulfate reducers and observed substantial sulfate reducing rates (between 12 and 423 µmol/dm3 day¿1) for most lakes, even at a salinity of 475 g/liter. Enrichments were obtained at salt saturating conditions (4 M Na+), using H2 or volatile fatty acids as electron donors, and an extremely halophilic SRB, strain ASO3-1, was isolated. Furthermore, a high dsr gene copy number of 108 cells per ml was detected in a hypersaline lake by qPCR. Our results indicate the presence of diverse and active SRB communities in these extreme ecosystems.
Degradation of Methanethiol by Methylotrophic Methanogenic Archaea in a Lab-Scale Upflow Anaerobic Sludge Blanket Reactor
Bok, F.A.M. de; Leerdam, R.C. van; Lomans, B.P. ; Smidt, H. ; Lens, P.N.L. ; Janssen, A.J.H. ; Stams, A.J.M. - \ 2006
Applied and Environmental Microbiology 72 (2006)12. - ISSN 0099-2240 - p. 7540 - 7547.
dimethyl sulfide - sulfur-compounds - waste-water - sediments - communities - bioreactor - conversion - digestion - bacteria - sulfate
In a lab-scale upflow anaerobic sludge blanket reactor inoculated with granular sludge from a full-scale wastewater treatment plant treating paper mill wastewater, methanethiol (MT) was degraded at 30°C to H2S, CO2, and CH4. At a hydraulic retention time of 9 h, a maximum influent concentration of 6 mM MT was applied, corresponding to a volumetric loading rate of 16.5 mmol liter-1 day-1. The archaeal community within the reactor was characterized by anaerobic culturing and denaturing gradient gel electrophoresis analysis, cloning, and sequencing of 16S rRNA genes and quantitative PCR. Initially, MT-fermenting methanogenic archaea related to members of the genus Methanolobus were enriched in the reactor. Later, they were outcompeted by Methanomethylovorans hollandica, which was detected in aggregates but not inside the granules that originated from the inoculum, the microbial composition of which remained fairly unchanged. Possibly other species within the Methanosarcinacaea also contributed to the fermentation of MT, but they were not enriched by serial dilution in liquid media. The archaeal community within the granules, which was dominated by Methanobacterium beijingense, did not change substantially during the reactor operation. Some of the species related to Methanomethylovorans hollandica were enriched by serial dilutions, but their growth rates were very low. Interestingly, the enrichments could be sustained only in the presence of MT and did not utilize any of the other typical substrates for methylotrophic methanogens, such as methanol, methyl amine, or dimethylsulfide
Volatile organic sulfur compounds in anaerobic sludge and sediments: biodegradation and toxicity
Leerdam, R.C. van; Bok, F.A.M. de; Lomans, B.P. ; Stams, A.J.M. ; Lens, P.N.L. ; Janssen, A.J.H. - \ 2006
Environmental Toxicology and Chemistry 25 (2006)12. - ISSN 0730-7268 - p. 3101 - 3109.
microbiële afbraak - slib - sediment - anaërobe behandeling - afvalwaterbehandeling - sulfaten - thiolen - reductie - sulfaat - methanol - biodegradatie - microbial degradation - sludges - anaerobic treatment - waste water treatment - sulfates - thiols - reduction - sulfate - biodegradation - fresh-water sediments - dimethyl sulfide - membrane bioreactor - waste air - methanethiol - degradation - inhibition - removal - ph - methanogens
A variety of environmental samples was screened for anaerobic degradation of methanethiol, ethanethiol, propanethiol, dimethylsulfide, and dimethyldisulfide. All sludge and sediment samples degraded methanethiol, dimethylsulfide, and dimethyldisulfide anaerobically. In contrast, ethanethiol and propanethiol were not degraded by the samples investigated under any of the conditions tested. Methanethiol, dimethylsulfide, and dimethyldisulfide were mainly degraded by methanogenic archaea. In the presence of sulfate and the methanogenic inhibitor bromoethane sulfonate, degradation of these compounds coupled to sulfate reduction occurred as well, but at much lower rates. Besides their biodegradability, also the toxicity of methanethiol, ethanethiol, and propanethiol to methanogenesis with methanol, acetate, and H2/CO2 as the substrates was assessed. The 50% inhibition concentration of methanethiol on the methane production from these substrates ranged between 7 and 10 mM. The 50% inhibition concentration values of ethanethiol and propanethiol for the degradation of methanol and acetate were between 6 and 8 mM, whereas hydrogen consumers were less affected by ethanethiol and propanethiol, as indicated by their higher 50% inhibition concentration (14 mM). Sulfide inhibited methanethiol degradation already at relatively low concentrations: methanethiol degradation was almost completely inhibited at an initial sulfide concentration of 8 mM. These results define the operational limits of anaerobic technologies for the treatment of volatile organic sulfur compounds in sulfide-containing wastewater streams
Methanomethylovorans thermophila sp. nov., a thermophilic, methylotrophic methanogen form an anaerobic reactor fed with methanol
Jiang, B. ; Parshina, S.N. ; Doesburg, W.C.J. van; Lomans, B.P. ; Stams, A.J.M. - \ 2005
International Journal of Systematic and Evolutionary Microbiology 55 (2005). - ISSN 1466-5026 - p. 2465 - 2470.
dimethyl sulfide - gen. nov. - bacteria - methanosarcina - populations - strain - dna - methanethiol - diversity - sediments
A novel thermophilic, obligately methylotrophic, methanogenic archaeon, strain L2FAWT, was isolated from a thermophilic laboratory-scale upflow anaerobic sludge blanket reactor fed with methanol as the carbon and energy source. Cells of strain L2FAWT were non-motile, irregular cocci, 0·7¿1·5 µm in diameter and usually occurred singly (sometimes forming clusters of two or four cells). The cells stained Gram-negative and lysed immediately in 0·1 % (w/v) SDS. Growth was inhibited by chloramphenicol and tetracycline, but not by penicillin, bacitracin, spectinomycin, vancomycin or kanamycin. Methanol and mono-, di- and trimethylamine were used as substrates, but H2/CO2, formate, acetate, propanol, dimethyl sulfide and methanethiol were not. The temperature range for growth was 42¿58 °C, with an optimum at 50 °C. The fastest growth was observed at a salinity below 100 mM NaCl; no growth occurred above 300 mM NaCl. The optimal pH for growth was 6·5; growth was observed from pH 5 to pH 7·5. The G+C content of the genomic DNA was 37·6 mol%. Analysis of the 16S rRNA gene sequence and the partial methyl-CoM reductase gene sequence revealed that the organism was phylogenetically closely related to Methanomethylovorans hollandica DMS1T (98 % similarity for the 16S rRNA gene sequence and 91 % similarity for the methyl-CoM reductase gene sequence). The DNA¿DNA relatedness between L2FAWT and Methanomethylovorans hollandica DMS1T was 46 %. On the basis of these results, strain L2FAWT (=DSM 17232T=ATCC BAA-1173T) represents the type strain of a novel species, for which the name Methanomethylovorans thermophila sp. nov. is proposed.
Anaerobic degradation of volatile organic sulfur compounds
Bok, F.A.M. de; Leerdam, R.C. van; Lomans, B.P. ; Janssen, A.J.H. ; Stams, A.J.M. - \ 2004
In: Book of Abstracts, Conference, Cancun, Mexico 2004. - Cancun, Mexico : ISME 10 - p. 20 - 20.
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