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 and proteome analysis of Pseudomonas chloritidismutans AW-1T that grows on n-decane with chlorate or oxygen as electron acceptor
Mehboob, F. ; Oosterkamp, M.J. ; Koehorst, J.J. ; Farrakh, S. ; Veuskens, T. ; Plugge, C.M. ; Boeren, S. ; Vos, W.M. de; Schraa, G. ; Stams, A.J.M. ; Schaap, P.J. - \ 2016
Environmental Microbiology 18 (2016)10. - ISSN 1462-2912 - p. 3247 - 3257.
Growth of Pseudomonas chloritidismutans AW-1T on C7 to C12 n-alkanes with oxygen or chlorate as electron acceptor was studied by genome and proteome analysis. Whole genome shotgun sequencing resulted in a 5 Mbp assembled sequence with a G+C content of 62.5% The automatic annotation identified 4767 protein-encoding genes and a putative function could be assigned to almost 80% of the predicted proteins. The distinct phylogenetic position of P. chloritidismutans AW-1T within the Pseudomonas stutzeri cluster became clear by comparison of average nucleotide identity values of sequenced genomes. Analysis of the proteome of P. chloritidismutans AW-1T showed the versatility of this bacterium to adapt to aerobic and anaerobic growth conditions with acetate or n-decane as substrates. All enzymes involved in the alkane oxidation pathway were identified. An alkane monooxygenase was detected in n-decane-grown cells, but not in acetate-grown cells. The enzyme was found when grown in the presence of oxygen or chlorate, indicating that under both conditions an oxygenase-mediated pathway is employed for alkane degradation. Proteomic and biochemical data also showed that both chlorate reductase and chlorite dismutase are constitutively present, but most abundant under chlorate-reducing conditions
Metallic nanoparticles: microbial synthesis and unique properties for biotechnological applications, bioavailability and biotransformation
Pereira, L. ; Mehboob, F. ; Stams, A.J.M. ; Mota, M.M. ; Rijnaarts, H.H.M. ; Alves, M.M. - \ 2015
Critical Reviews in Biotechnology 35 (2015)1. - ISSN 0738-8551 - p. 114 - 128.
fungus fusarium-oxysporum - sulfate-reducing bacteria - zero-valent iron - immobilized rhodobacter-sphaeroides - reductase-mediated synthesis - silver nanoparticles - gold nanoparticles - magnetotactic bacteria - magnetic nanoparticles - extracellular biosynthesis
The impact of nanotechnology in all areas of science and technology is evident. The expanding availability of a variety of nanostructures with properties in the nanometer size range has sparked widespread interest in their use in biotechnological systems, including the field of environmental remediation. Nanomaterials can be used as catalysts, adsorbents, membranes, water disinfectants and additives to increase catalytic activity and capability due to their high specific surface areas and nanosize effects. Thus, nanomaterials appear promising for new effective environmental technologies. Definitely, nanotechnology applications for site remediation and wastewater treatment are currently in research and development stages, and new innovations are underway. The synthesis of metallic nanoparticles has been intensively developed not only due to its fundamental scientific interest but also for many technological applications. The use of microorganisms in the synthesis of nanoparticles is a relatively new eco-friendly and promising area of research with considerable potential for expansion. On the other hand, chemical synthesis occurs generally under extreme conditions (e.g. pH, temperature) and also chemicals used may have associated environmental and human health impacts. This review is an overview of current research worldwide on the use of microorganisms during the biosynthesis of metallic nanoparticles and their unique properties that make them good candidates for many applications, including in biotechnology.
Anaerobic Degradation of Lindane and Other HCH Isomers
Mehboob, F. ; Langenhoff, A.A.M. ; Schraa, G. ; Stams, A.J.M. - \ 2013
In: Management of Microbial Resources in the Environment / Malik, A., Grohmann, E., Alves, M., - p. 495 - 521.
Lindane (¿-HCH) is a pesticide that has mainly been used in agriculture. Lindane and the other HCH isomers are highly chlorinated hydrocarbons. The presence of a large number of electron withdrawing chlorine groups makes some of the HCH isomers rather recalcitrant in oxic environments. Especially ß-HCH is poorly degraded by aerobic bacteria. The chlorine groups make HCH isomers more accessible for an initial reductive attack, a common mechanism in anoxic environments. Among the HCH isomers, ¿-HCH is degraded most easily while ß-HCH is most persistent. Little is known about the diversity of the microorganisms involved in anaerobic HCH degradation. Thus far, species within the genera Clostridium and Bacillus, two Desulfovibrio species, and one species each of Desulfococcus, Desulfobacter, Citrobacter and Dehalobacter have been found to metabolize lindane and other HCH isomers. Benzene and monochlorobenzene are the end products of anaerobic degradation, while in some studies pentachlorocyclohexane, tetrachlorocyclohexene, chlorobenzenes and chlorophenols have been detected as intermediates. Enzymes and coding genes involved in the reductive dechlorination of HCH isomers are largely unknown. Recently, a metagenomic analysis has indicated the presence of numerous putative reductive dehalogenase genes in the genome of ß-HCH degrading Dehalobacter sp. High-throughput omics techniques can help to explore the key players and enzymes involved in the reductive dehalogenation of lindane and other HCH isomers.
Environmental biotechnology and microbiology of (per)chlorate reducing bacteria
Mehboob, F. ; Schraa, G. ; Stams, A.J.M. - \ 2011
In: Perchlorates: Production, uses and health effects / Matthews, L.E., Nova Science Publishers (Chemical Engineering Methods and Technology ) - ISBN 9781611221435 - p. 211 - 235.
Perchlorates are the salts derived from perchloric acid (HClO4). They occur both naturally and through manufacturing. They have been used as a medicine for more than 50 years to treat thyroid gland disorders and are used extensively within the pyrotechnics industry, and ammonium perchlorate is also a component of solid rocket fuel. This book presents current research data from across the globe in the study of perchlorates, their production, uses, and health effects. Some topics discussed, herein, are: trends in the study of the electrochemical stability of perchlorate ions; the structural and vibrational properties of chromyl perchlorate; perchlorate formation in electrochemical water disinfection; metal perchlorates as Lewis acids; alkaline earth metal perchlorates; and removal of perchlorate from water. (Imprint: Nova)
Nitrate and (per)chlorate reduction pathways in (per)chlorate-reducing bacteria
Oosterkamp, M.J. ; Mehboob, F. ; Schraa, G. ; Plugge, C.M. ; Stams, A.J.M. - \ 2011
Biochemical Society Transactions 39 (2011)1. - ISSN 0300-5127 - p. 230 - 235.
chlorite dismutase - pseudomonas-chloritidismutans - ideonella-dechloratans - chlorate reductase - strain gr-1 - perchlorate reductase - molybdenum cofactor - electron-acceptor - escherichia-coli - 1st step
The reduction of (per)chlorate and nitrate in (per)chlorate-reducing bacteria shows similarities and differences. (Per)chlorate reductase and nitrate reductase both belong to the type II DMSO family of enzymes and have a common bis(molybdopterin guanine dinucleotide)molybdenum cofactor. There are two types of dissimilatory nitrate reductases. With respect to their localization, (per)chlorate reductase is more similar to the dissimilatory periplasmic nitrate reductase. However, the periplasmic, unlike the membrane-bound, respiratory nitrate reductase, is not able to use chlorate. Structurally, (per)chlorate reductase is more similar to respiratory nitrate reductase, since these reductases have analogous subunits encoded by analogous genes. Both periplasmic (per)chlorate reductase and membrane-bound nitrate reductase activities are induced under anoxic conditions in the presence of (per)chlorate and nitrate respectively. During microbial (per)chlorate reduction, molecular oxygen is generated. This is not the case for nitrate reduction, although an atypical reaction in nitrite reduction linked to oxygen formation has been described recently. Microbial oxygen production during reduction of oxyanions may enhance biodegradation of pollutants under anoxic conditions
(Per)chlorate reduction by an acetogenic bacterium, Sporomusa sp., isolated from an underground gas storage
Balk, M. ; Mehboob, F. ; Gelder, A.H. van; Rijpstra, I. ; Sinninghe-Damsté, J.S. ; Stams, A.J.M. - \ 2010
Applied Microbiology and Biotechnology 88 (2010)2. - ISSN 0175-7598 - p. 595 - 603.
sp-nov - homoacetogenic bacterium - strain gr-1 - perchlorate - chlorate - metabolism - water - milk - soil - identification
A mesophilic bacterium, strain An4, was isolated from an underground gas storage reservoir with methanol as substrate and perchlorate as electron acceptor. Cells were Gram-negative, spore-forming, straight to curved rods, 0.5-0.8 microm in diameter, and 2-8 microm in length, growing as single cells or in pairs. The cells grew optimally at 37 degrees C, and the pH optimum was around 7. Strain An4 converted various alcohols, organic acids, fructose, acetoin, and H(2)/CO(2) to acetate, usually as the only product. Succinate was decarboxylated to propionate. The isolate was able to respire with (per)chlorate, nitrate, and CO(2). The G+C content of the DNA was 42.6 mol%. Based on the 16S rRNA gene sequence analysis, strain An4 was most closely related to Sporomusa ovata (98% similarity). The bacterium reduced perchlorate and chlorate completely to chloride. Key enzymes, perchlorate reductase and chlorite dismutase, were detected in cell-free extracts
Anaerobic microbial degradation of organic pollutants with chlorate as electron acceptor
Mehboob, F. - \ 2010
Wageningen University. Promotor(en): Fons Stams, co-promotor(en): Gosse Schraa. - [S.l. : S.n. - ISBN 9789085855453 - 138
microbiële afbraak - anaërobe omstandigheden - anaërobe afbraak - elektronenoverdracht - chloraten - organische verontreinigende stoffen - microbial degradation - anaerobic conditions - anaerobic digestion - electron transfer - chlorates - organic pollutants
Aliphatic and aromatic hydrocarbons are two groups of compounds that are widespread pollutants. The aerobic microbial degradation of aliphatic and aromatic hydrocarbons proceeds in general fast and has been widely studied, while the biodegradation in anoxic environments is often incomplete, proceeds at lower rates and is less characterized. Chlorate reduction is a unique process, which yields molecular oxygen upon microbial reduction in anoxic environments. This can be of practical importance, since the oxygen released can be incorporated into the anaerobically recalcitrant compounds by oxygenases to form hydroxylated derivatives, which can be further degraded easily either aerobically or anaerobically. We have found that Pseudomonas chloritidismutans AW-1T, which is a known chlorate-reducing bacterium, can combine the oxidation of n-alkanes and the reduction of chlorate. Similarly this bacterium can combine the degradation of benzoate and catechol with chlorate reduction. We studied the physiological and biochemical properties of this bacterium. With the help of proteogenomics we annotated the key proteins involved in alkane and benzoate oxidation with chlorate. Our findings suggest that oxygen released during chlorate reduction can be used to degrade the anaerobically recalcitrant compounds and chlorate reduction has a very high potential for bioremediation of anoxic soils.

Microbial degradation of aliphatic and aromatic hydrocarbons with (per)chlorate as electron acceptor
Mehboob, F. ; Weelink, S.A.B. ; Talarico Saia, F. ; Junca, H. ; Stams, A.J.M. ; Schraa, G. - \ 2009
In: Handbook of hydrocarbon and lipid microbiology / Timmis, K, McGenity, T, van der Meer, JR, de Lorenzo, V, New York, Berlin : Springer - ISBN 9783540775881
"Water is life!" All active cellular systems require water as the medium and solvent of their metabolic activities. Hydrophobic compounds and structures, which tend to exclude water, though providing inter alia excellent sources of energy and a means of biological compartmentalization, present problems of cellular handling, poor bioavailability and, in some cases, toxicity. Microbes both synthesize and exploit a vast range of hydrophobic organics, especially petroleum oil hydrocarbons and industrial pollutants, and the underlying interactions not only have major consequences for the lifestyles of the microbes involved, but also for biogeochemistry, climate change, environmental pollution, human health and a range of biotechnological applications. The aim of this handbook is to be the definitive resource of current knowledge on the diverse and multifaceted aspects of these interactions, the microbial players, and the physiological mechanisms and adaptive strategies characteristic of the microbial lifestyle that plays out at hydrophobic material: aqueous liquid interfaces
Growth of Pseudomonas chloritidismutans AW-1(T) on n-alkanes with chlorate as electron acceptor
Mehboob, F. ; Junca, H. ; Schraa, G. ; Stams, A.J.M. - \ 2009
Applied Microbiology and Biotechnology 83 (2009)4. - ISSN 0175-7598 - p. 739 - 747.
sp strain m-1 - sulfate-reducing bacterium - functional-analysis - omega-hydroxylase - anoxic conditions - escherichia-coli - fatty-acids - genes - monooxygenase - oleovorans
Microbial (per)chlorate reduction is a unique process in which molecular oxygen is formed during the dismutation of chlorite. The oxygen thus formed may be used to degrade hydrocarbons by means of oxygenases under seemingly anoxic conditions. Up to now, no bacterium has been described that grows on aliphatic hydrocarbons with chlorate. Here, we report that Pseudomonas chloritidismutans AW-1(T) grows on n-alkanes (ranging from C7 until C12) with chlorate as electron acceptor. Strain AW-1(T) also grows on the intermediates of the presumed n-alkane degradation pathway. The specific growth rates on n-decane and chlorate and n-decane and oxygen were 0.5 +/- 0.1 and 0.4 +/- 0.02 day(-1), respectively. The key enzymes chlorate reductase and chlorite dismutase were assayed and found to be present. The oxygen-dependent alkane oxidation was demonstrated in whole-cell suspensions. The strain degrades n-alkanes with oxygen and chlorate but not with nitrate, thus suggesting that the strain employs oxygenase-dependent pathways for the breakdown of n-alkanes
Purification and characterization of a chlorite dismutase from Pseudomonas chloritidismutans
Mehboob, F. ; Wolterink, A.F.W.M. ; Vermeulen, A.J. ; Jiang, B. ; Hagedoorn, P.L. ; Stams, A.J.M. ; Kengen, S.W.M. - \ 2009
FEMS Microbiology Letters 293 (2009)1. - ISSN 0378-1097 - p. 115 - 121.
desulfovibrio-vulgaris hildenborough - (per)chlorate-reducing bacteria - strain gr-1 - reductase - catalase
The chlorite dismutase (Cld) of Pseudomonas chloritidismutans was purified from the periplasmic fraction in one step by hydroxyapatite chromatography. The enzyme has a molecular mass of 110 kDa and consists of four 31-kDa subunits. Enzyme catalysis followed Michaelis-Menten kinetics, with Vmax and K(m) values of 443 U mg(-1) and 84 microM, respectively. A pyridine-NaOH-dithionite-reduced Cld revealed a Soret peak at 418 nm, indicative for protoheme IX. The spectral data indicate the presence of 1.5 mol protoheme IX mol(-1) tetrameric enzyme while metal analysis revealed 2.2 mol iron mol(-1) tetrameric enzyme. High concentrations of chlorite resulted in the disappearance of the Soret peak, which coincided with loss in activity. Electron paramagnetic resonance analyses showed an axial high-spin ferric iron signal. Cld was inhibited by cyanide, azide, but not by hydroxylamine or 3-amino-1,2,3-triazole. Remarkably, the activity was drastically enhanced by kosmotropic salts, and chaotropic salts decreased the activity, in accordance with the Hofmeister series. Chlorite conversion in the presence of 18O-labeled water did not result in the formation of oxygen with a mass of 34 (16O-18O) or a mass of 36 ((18)O-(18)O), indicating that water is not a substrate in the reaction and that both oxygen atoms originate from chlorite
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