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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    Assessing methane emission from dairy cows : modeling and experimental approaches on rumen microbial metabolism
    Lingen, Henk J. - \ 2017
    Wageningen University. Promotor(en): W.H. Hendriks, co-promotor(en): J. Dijkstra; A. Bannink; C.M. Plugge. - Wageningen : Wageningen University - ISBN 9789463431590 - 207
    dairy cows - methane - emission - microbial degradation - rumen metabolism - rumen fermentation - models - fatty acids - biochemical pathways - animal nutrition - nutrition physiology - melkkoeien - methaan - emissie - microbiële afbraak - pensmetabolisme - pensfermentatie - modellen - vetzuren - biochemische omzettingen - diervoeding - voedingsfysiologie

    Methane (CH4) is a greenhouse gas (GHG) with a global warming potential of 28 CO2 equivalents. The livestock sector was estimated to emit 7.1 gigatonnes of CO2 equivalents, which is approximately 14.5% of total global anthropogenic GHG emissions. Enteric CH4 production is the main source of GHG emissions from dairy cattle, representing 46% of the global GHG emissions in dairy supply chains. Dairy production has great value in view of the ability of ruminants to effectively turn human inedible biomass into human edible food and to produce food from non-arable land. Consequently, there is an urgent need to develop strategies to decrease dairy cattle enteric CH4 emission. Evaluation of these strategies requires meticulous quantification and increased understanding of anaerobic fermentation and methanogenesis in the rumen ecosystem. The overall aim of this PhD research was, therefore, to quantitatively evaluate enteric CH4 emission from dairy cows as affected by feeding and rumen microbial metabolism.

    A meta-analysis was performed to quantify relationships between enteric CH4 yield (per unit of feed and unit of milk) and milk FA profile in dairy cattle and to develop equations to predict CH4 yield based on milk FA profile of cows fed a wide variety of diets. Various milk FA concentrations were significantly or tended to be positively or negatively related to CH4 yield per unit of feed or milk. Mixed model multiple regression resulted in various milk FA included in optimal equations to predict CH4 yield per unit of feed and per unit of milk. These regression equations indicated a moderate potential for using milk FA profile to predict CH4 yield.

    For the development of a mechanistic model of CH4 production in the rumen, the thermodynamic control of pH2 on reaction rates of specific fermentation pathways, NADH oxidation and methanogenesis was theoretically explored. This control was determined using the thermodynamic potential factor (FT), which is a dimensionless factor that corrects a predicted kinetic reaction rate for the thermodynamic control exerted. The thermodynamic feasibility of these microbial conversions showed that the control of pH2 on individual VFA produced and associated yield of H2 and CH4 cannot be explained without considering NADH oxidation, with a considerable effect of pH.

    For obtaining experimental support of the conclusions drawn from the theoretical exploration, diurnal patterns of gaseous and dissolved metabolite concentrations in the bovine rumen, H2 and CH4 emitted, and the rumen microbiota were monitored. In addition, the effect of dietary inclusion of linseed oil on these patterns was assessed. An in vivo experiment with rumen cannulated dairy cows was performed to study the anaerobic metabolism and the microbiota composition in the rumen. A 100-fold increase in pH2 in the rumen headspace was observed at 0.5 h after feeding, followed by a decline. Qualitatively similar patterns after feeding were observed for H2 and CH4 emission, ethanol and lactate concentrations, and propionate molar proportion, whereas an opposite pattern was seen for acetate molar proportion. Associated with these patterns, a temporal biphasic change in the microbial composition was observed as based on 16S ribosomal RNA with certain taxa specifically associated with each phase. Bacterial concentrations were affected by time and increased by linseed oil supplementation. Archaeal concentrations tended to be affected by time and were not affected by diet, despite linseed oil supplementation tending to decrease the partial pressure and emission of CH4 and tending to increase propionate molar proportion. The various diurnal profiles that were monitored support the key role of the NAD+ to NADH ratio in rumen fermentation and the importance of diurnal dynamics when understanding VFA, H2 and CH4 production.

    A dynamic mechanistic model was developed, in which the thermodynamic control of pH2 on VFA fermentation pathways, and methanogenesis in the bovine rumen are incorporated. The model represents substrate degradation, microbial fermentation and methanogenesis in the rumen, with the type of VFA formed to be controlled by the NAD+ to NADH ratio, which in turn is controlled by pH2. Feed composition and feed intake rate representing a twice daily feeding regime were used as model input. The model predicted a marked peak in pH2 after feeding that rapidly declined in time. This peak in pH2 caused a decrease in NAD+ to NADH ratio followed by an increased propionate molar proportion at the expense of acetate molar proportion. In response to feeding, the model predicted a sudden increase and a steady decrease in CH4 production in time. The pattern of CH4 emission rate followed the patterns of pH2 and H2 emission rate, but its magnitude of increase in response to feeding was less pronounced. A global sensitivity analysis indicated the parameter that determines the NADH oxidation rate to explain the most substantial part of the variation of predicted daily CH4 emission. The modeling effort provides the integration of more detailed knowledge than accomplished in previous rumen fermentation models and enables assessment of diurnal dynamics of rumen metabolic pathways yielding VFA, H2 and CH4.

    For assessing the general value of the research reported in this thesis, the potential for predicting enteric CH4 emission from dairy cattle based on milk FA profile was discussed in the light of published studies and compared with empirical modeling of enteric CH4 based on feed input. Moreover, the concept of NAD-controlled fermentation was considered in a more general perspective by comparing the rumen ecosystem with bioreactor systems. Furthermore, the feasibility of the developed models as an alternative for IPCC tiered approaches was explored. In conclusion, the research reported in this thesis contributes to an increased understanding of rumen fermentation and microbial metabolism, and has provides a basis to further improve prediction models of enteric CH4 emissions from dairy cattle.

    Prof. Richard Kranenburg: Bacteriën als fabriekjes van de bio-economie
    Kranenburg, R. van - \ 2017
    Wageningen University & Research
    industriële microbiologie - bacteriën - biobased economy - microbiële afbraak - enzymen - genetische verandering - onderzoek - industrial microbiology - bacteria - biobased economy - microbial degradation - enzymes - genetic change - research
    Video over micro-organismen in de biobased economy
    Biological treatment of sulfidic spent caustics under haloalkaline conditions using soda lake bacteria
    Graaff, C.M. de - \ 2012
    Wageningen University. Promotor(en): Albert Janssen; G. Muyzer, co-promotor(en): M.F.M. Bijmans. - S.l. : s.n. - ISBN 9789461734457 - 132
    alkaliteit - thiobacillus denitrificans - thiobacillus - microbiële afbraak - biologische behandeling - afvalverwerking - zwavel - alkalinity - thiobacillus denitrificans - thiobacillus - microbial degradation - biological treatment - waste treatment - sulfur

    In this thesis, the development of a newbiotechnological process for the treatment of undiluted sulfidic spent caustics (SSC’s) using soda lake bacteria is described. SSC’s are waste solutions that are formed in the oil and gas industry due to the caustic (NaOH) scrubbing of hydrocarbon streams for the removal of sulfur compounds.Without treatment, SSC’s may impose serious environmental problems because of their alkalinity (pH>12), salinity (Na+ 5-12 wt%) and high sulfide (HS- and S2-) levels. Depending on the hydrocarbon stream that is treated, SSC’s may also contain organic sulfur compounds and monoaromatic hydrocarbons. Biological treatment of undiluted SSC’s would be a cheaper and safer alternative to the currently applied physico-chemical treatment methods (e.g., wet air oxidation or deep well disposal) since no additional chemicals are needed and the process works at ambient pressure and temperature conditions.

    In chapter 2 the biological treatment of refinery SSC’s is described in continuously fed systems under haloalkaline conditions (i.e. pH 9.5; Na+ 0.8 M). The experiments were performed in gas-lift bioreactors operated under aerobic conditions at 35 oC. Sulfide removal was complete up to 27 mmol L-1 day-1 by conversion to sulfate (SO42-). The sulfide conversion was accomplished by haloalkaliphilic sulfide-oxidizing bacteria (HA-SOB) belonging to the genus Thioalkalivibrio. Members of the this genus are extremophiles that are able to oxidize sulfide under a broad range of haloalkaline conditions (0.3 - 4.3 M Na+ and up to pH 10.6). In this chapter, it wasalso shown that benzene, at influent concentrations ranging from 100 to 600 µM, was removed by 93% due to air-stripping and biodegradation. Microbial community analysis revealed the presence of haloalkaliphilic heterotrophic bacteria belonging to the genera Marinobacter, Halomonas andIdiomarina which might have been involved in the observed benzene removal.

    Sour gases and SSC’s may also contain elevated amounts of methanethiol (MT; CH3SH). Hence, knowledge on the potential toxic effects of these type of compounds on the performance of this biotechnological process is required. Under sulfur (S0) forming conditions, MT reacts with biologically produced S0 particles resulting in a mixture of inorganic polysulfides (Sx2-), dimethyl disulfide (DMDS) and dimethyl trisulfide (DMTS). Respiration experiments with HA-SOB (Thioalkalivibrio mix) show in chapter 3 that biological oxidation of sulfide to S0 is inhibited by 50% (Ki value) at 0.05 mM MT. The measured Ki values for DMDS and DMTS were 1.5 and 1.0 mM, respectively.As DMDS and DMTS are products from the reaction between MT and S0, this reaction results in a partial detoxification of MT in a S0-producing bioreactor.The results from the respiration experiments as shown in chapter 3 indicate that the application of the biotechnological process for the treatment of H2S and MT containing gases and SSC’s is feasible as long as MT, DMDS and DMTS do not accumulate in the bioreactor.Accumulation of MT can be prevented by auto-oxidation of MT to DMDS, by the reaction between MT and biosulfur particles or biodegradation.

    Chapter 4 discusses the biological treatment of synthetically prepared SSC’s containing both sulfide and DMDS.Continuously fed gas-lift bioreactor experiments showed that biological sulfide oxidation (4-10 mmol L-1 day-1) is possible in the presence of low concentrations of DMDSunder haloalkaline conditions (i.e., pH 9.5; Na+ 0.8 M).Sulfide was completely oxidized to SO42- by members of the genus Thioalkalivibrio (closely related to Thioalkalivibriosp.K90-mix). It was also shown that severe inhibition of thebiological sulfide oxidation capacity and process deterioration occurs at DMDS effluent concentrations between 0.1 and 0.9 mM. The measured DMDS removal efficiency amounted up to 40-70% (0.05-0.37 DMDS-S L-1 day-1), of which 25% could be attributed to air stripping. It is yet unclear what other processes contributed to the total DMDS removal and it can only be speculated that the remainder was removed by biological conversion and/or adsorption. Results from respiration experiments presented in chapter 4 reveal that pure cultures of HA-SOB (Thioalkalivibrio sp.K90-mix and Thioalkalivibrio sulfidophilus) as well as biosludge taken from a full-scale installation for H2S removal (Thiopaq) are more severely inhibited by MT than DMDS. Furthermore, the Ki values for DMDS and MT were lower for Thioalkalivibrio sp. K90-mix and Thioalkalivibrio sulfidophilus compared to Thiopaq sludge. From bioreactor and respiration experiments it follows that, to ensure stable process conditions, MT and DMDS concentrations need to be below 0.02 and 0.1 mM, respectively. This clearly demonstrates that treating SSC’s with elevated MT and DMDS concentrations will easily inhibit the sulfide oxidation capacity of the process. Although auto-oxidation of MT will result in (partial) detoxification due to the formation of DMDS, the effluent levels still need to be kept very low. Successful biological treatment of MT and DMDS containing SSC’s will depend on the biological degradation of these compounds. When rapid biodegradation of organic VSC’s can be achieved, the concentrations in the reactor will remain below the critical levels.

    Chapter 5 shows that the application of a newly developed 2-step process for the biological treatments of SSC’s using HA-SOB allows significantly higher sulfide removal efficiencies compared to a 1-step process. The detoxification of sulfide by the abiotic oxidation to thiosulfate (S2O32-) in the first chemical oxidation step and the subsequent complete biological oxidation in the second step allowed total-S loading rates up to 33 mmol L-1 day-1. Experiments with synthetically prepared solutions were performed in a continuously fed system consisting of two gas-lift reactors in series. These reactors were operated at haloalkaline (pH 9.5; Na+ 0.8M) and aerobic conditions at 35oC.Mathematical modelling of the 2-step process shows that under the prevailing conditions an optimal reactor configuration consists of 40% ‘abiotic’ and 60% ‘biological’ volume, whilst the total reactor volume is 22% smaller than for the 1-step process. The major advantages of a 2-step process are the improved anticipation to shock loads of sulfideand lower investment and operational costs due to downsizing of the total reactor volume.

    Further research regarding the biological treatment of SSC’s may involve the potential of heterotrophic soda lake bacteria for the degradation of organic VSC’s as well as the mechanisms of toxicity of these compounds.

    Characterization of cell wall degrading enzymes from Chrysosporium lucknowense C1 and their use to degrade sugar beet pulp
    Kühnel, S. - \ 2011
    Wageningen University. Promotor(en): Harry Gruppen, co-promotor(en): Henk Schols. - [S.l.] : S.n. - ISBN 9789085859789 - 191
    celwandstoffen - microbiële afbraak - chrysosporium - enzymen - suikerbieten - bietenpulp - bioraffinage - cell wall components - microbial degradation - chrysosporium - enzymes - sugarbeet - beet pulp - biorefinery

    Key words: Pectin, arabinan, biorefinery, mode of action, branched arabinose oligomers, ferulic acid esterase, arabinohydrolase, pretreatment

    Sugar beet pulp is the cellulose and pectin-rich debris remaining after sugar extraction from sugar beets. In order to use sugar beet pulp for biorefinery purposes, these carbohydrates need to be degraded to fermentable monosaccharides.The influence of six mild sulfuric acid or water pretreatments at different temperatures on the enzymatic degradability of sugar beet pulp was examined. An optimal pretreatment of 15 min at 140 °C in water greatly facilitates the subsequent enzymatic cellulose degradation. Enzymatic degradation of pectin requires an array of different enzyme activities. To this end, cell wall degrading enzymes of the filamentous fungus Chrysosporium lucknowense C1 (C1) were purified and characterized. Four arabinohydrolases from C1 were characterized that released up to 80% of the arabinose present in sugar beet arabinan as monomers. A combination of three arabinohydrolases also released unknown branched arabinose oligomers, which were purified and identified using NMR analysis. With the help of these complex arabinose oligomers the mode of action of four C1 α-L-arabinohydrolases was determined to enable controlled and tailored degradation of arabinan. Complete degradation of sugar beet pulp also requires ferulic acid esterase activity. Three C1 ferulic acid esterases were purified and characterized, of which one could release up to 60% of ferulic acid from feruloylated sugar beet pectin oligomers, whereas the other two were more active toward feruloylated arabinoxylan.

    Monitoring biodegradation capacity of organic pollutants in the environment
    Zaan, B.M. van der - \ 2010
    Wageningen University. Promotor(en): Willem de Vos, co-promotor(en): J. Gerritse; Hauke Smidt. - [S.l. : S.n. - ISBN 9789085857778 - 158
    biodegradatie - microbiële afbraak - geochemie - bodemverontreiniging - waterverontreiniging - verontreinigingsbeheersing - organische verontreinigende stoffen - biodegradation - microbial degradation - geochemistry - soil pollution - water pollution - pollution control - organic pollutants
    Micro-organismen zijn in staat om organische verbindingen om te zetten in minder schadelijke stoffen en spelen daarom een belangrijke rol bij het opruimen van milieuvervuiling. Voor beleidsmakers, landgebruikers en landeigenaren is het belangrijk dat er bij milieuverontreiniging goed toezicht wordt gehouden op de biologische afbraakprocessen en dat deze goed worden beheerst. Aangezien microbiële activiteit in het milieu wordt beïnvloed door diverse fysische, geochemische en biologische factoren, is nauwkeurige kennis van het afbraakproces hierbij noodzakelijk. In dit promotieonderzoek wordt de relatie tussen geochemische condities en de biologische afbraakcapaciteit van micro-organismen in het milieu beschreven, inclusief methoden om de activiteit en metabole functies van deze micro-organismen in het milieu te meten
    Chasing organohalide respirers: ecogenomics approaches to assess the bioremediation capacity of soils
    Maphosa, F. - \ 2010
    Wageningen University. Promotor(en): Willem de Vos, co-promotor(en): Hauke Smidt. - [S.l. : S.n. - ISBN 9789085856566 - 172
    microbiële afbraak - biochemische omzettingen - gehalogeneerde koolwaterstoffen - organische halogeenverbindingen - bioremediëring - bodemverontreiniging - bodembiologie - microbial degradation - biochemical pathways - halogenated hydrocarbons - organic halogen compounds - bioremediation - soil pollution - soil biology
    Het opsporen van organohalogeen-reducerende bacteriën: ecogenomics benaderingen om de bioremediatie-capaciteit van de bodem te beoordelen. Organohalogeen-reducerende bacteriën (OHRB) zijn efficiënte afbrekers van organische chloorverbindingen, zoals gechloreerde ethenen, chloorfenolen en andere gehalogeneerde alifatische en aromatische koolwaterstoffen. Desondanks, lijken deze organische chloorverbindingen te volharden op verschillende locaties. De reden voor dit gebrek aan afbraak kan worden toegeschreven aan het ontbreken van OHRB in voldoende aantallen of aan verkeerde fysisch-chemische omstandigheden voor hun groei en activiteit. Derhalve is er een dringende behoefte aan snelle, robuuste en gevoelige methoden die het voorspellen van en het toezicht houden op het bioremediatie potentieel en de activiteit van OHRB mogelijk maken. Moleculaire monitoring en modelsimulaties werden toegepast om de in-situ afbraak prestaties van een on-site dechlorerende bioreactor te bepalen en zijn invloed op de vervuilingsspluim. De toepasbaarheid van dit systeem werd getest in verschillende verontreinigde bodems.
    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.

    Dehalococcoides spp. in river sediments: insights in functional diversity and dechlorination activity
    Tas, N. - \ 2009
    Wageningen University. Promotor(en): Willem de Vos, co-promotor(en): Hauke Smidt; Miriam van Eekert. - [S.l. : S.n. - ISBN 9789085853749 - 196
    waterverontreiniging - microbiële afbraak - coccoidea - ecotoxicologie - gechloreerde koolwaterstoffen - hexachloorbenzeen - uiterwaarden - water pollution - microbial degradation - coccoidea - ecotoxicology - chlorinated hydrocarbons - hexachlorobenzene - river forelands
    In dit proefschrift staan Dehaloccoides spp. centraal vanwege hun vermogen één van deze gechloreerde verbindingen, hexachloorbenzeen (HCB), af te breken tot een verbinding met minder chlooratomen. HCB werd tot voor kort voornamelijk toegepast als fungicide en pesticide en kan bijvoorbeeld vrijkomen bij de productie van synthetisch rubber. Daarnaast wordt het gevormd als bijproduct tijdens de productie van oplosmiddelen en pesticiden. HCB is kankerverwekkend, giftig en hoopt zich op in ecosystemen. Tegenwoordig is het gebruik ervan binnen de E.U. dan ook verboden, maar omdat de stof erg moeilijk afbreekbaar is zal deze nog gedurende lange tijd worden teruggevonden in het milieu. Grootschalig onderzoek is gedaan naar de aanwezigheid, activiteit en het dechlorinerende vermogen van Dehalococcoides spp. in riviersedimenten en de bodems in uiterwaarden van verschillende Europese rivieren (Elbe, Donau, Maas, Ebro, Brevilles).
    Degradation of benzene and other aromatic hydrocarbons by anaerobic bacteria
    Weelink, S.A.B. - \ 2008
    Wageningen University. Promotor(en): Fons Stams. - S.l. : S.n. - ISBN 9789085852391 - 128
    benzeen - aromatische koolwaterstoffen - microbiële afbraak - benzene - aromatic hydrocarbons - microbial degradation
    Accidental spills, industrial discharges and gasoline leakage from underground storage tanks have resulted in serious pollution of the environment with monoaromatic hydrocarbons, such as benzene, toluene, ethylbenzene and xylene (so-called BTEX). High concentrations of BTEX have been detected in soils, sediments and groundwater. The mobility and toxicity of the BTEX compounds are of major concern. In situ bioremediation of BTEX by using naturally occurring microorganisms or introduced microorganisms is a very attractive option. BTEX compounds are known to be transformed (or degraded) by microorganisms under aerobic and anaerobic conditions. As BTEX compounds are often present in the anaerobic zones of the environment, anaerobic bioremediation is an attractive remediation technique. The bottleneck in the application of anaerobic techniques is the lack of knowledge about the anaerobic biodegradation of benzene. In particular, little is known about the bacteria involved in anaerobic benzene degradation and the anaerobic benzene degradation pathway has still not been elucidated. The aim of the research presented in this thesis was to gain more insight in the degradation of benzene and other aromatic hydrocarbons by anaerobic bacteria. In particular, the physiology and phylogeny of the bacteria responsible for the degradation were studied and the results have been presented in this thesis.
    Anaerobic benzene and toluene degradation was studied with different electron acceptors in batch experiments inoculated with material from an aquifer polluted by BTEX-containing landfill leachate (Banisveld landfill near Boxtel, The Netherlands). Benzene was not degraded during one year of incubation. Toluene degradation, on the other hand, was observed with nitrate, MnO2 and Fe(III)NTA as electron acceptors. After further enrichment and several isolation attempts, a novel betaproteobacterial bacterium, strain G5G6, was obtained in pure culture. Strain G5G6 is able to grow with toluene as the sole electron donor and carbon source, and amorphous and soluble Fe(III)-species, nitrate and MnO2 as electron acceptors. Strain G5G6 has several other interesting physiological and phylogenetic characteristics, which will be subject of future research. Strain G5G6 represents a novel species in a novel genus for which we propose the name Georgfuchsia toluolica.
    In general, aerobic degradation of BTEX is a faster process than anaerobic BTEX degradation. However, for a number of reasons application of oxygen-dependent processes in the subsurface are technically and financially often not appealing. Therefore, an alternative bioremediation strategy would be to introduce oxygen in an alternative way, e.g. by in situ production. Chlorate reduction is a way to produce molecular oxygen in situ under anaerobic conditions. The formation of oxygen during chlorate reduction may result in rapid oxidation of compounds which are slowly degraded under anaerobic conditions; an example of such a compound is benzene. Therefore, benzene degradation coupled to the reduction of chlorate (ClO3-) was studied in this thesis. With mixed material from a wastewater treatment plant and soil samples obtained from a location contaminated with benzene, a benzene-degrading chlorate-reducing stable enrichment culture was obtained. This stable enrichment consisted of about five different bacterial species. Cross feeding involving interspecies oxygen transfer is a likely mechanism in this enrichment. One of these species, strain BC, was obtained in pure culture. Phylogenetic analysis showed that strain BC is a Alicycliphilus denitrificans strain. Strain BC is able to degrade benzene in conjunction with chlorate reduction. Oxygenase genes putatively encoding the enzymes performing the initial steps in aerobic degradation of benzene, were detected in strain BC. This demonstrates the existence of aerobic benzene bacterial biodegradation pathways under essentially anaerobic conditions. Thus, aerobic pathways can be employed under conditions where no external oxygen is supplied.
    The new insights into toluene degradation under anaerobic conditions and benzene degradation coupled to chlorate reduction, as described in this thesis, can be applied for the improvement or development of in situ bioremediation strategies for BTEX contamination.
    Biological sulfide oxidation by natron-alkaliphilic bacteria : application in gas desulfurization
    Bosch, P.L.F. van den - \ 2008
    Wageningen University. Promotor(en): Albert Janssen. - S.l. : S.n. - ISBN 9789085852087 - 191
    oxidatie - zwavelwaterstof - microbiële afbraak - oxidation - hydrogen sulfide - microbial degradation
    Biological selenium removal from wastewaters
    Lenz, M. - \ 2008
    Wageningen University. Promotor(en): Cees Buisman; Piet Lens. - S.l. : S.n. - ISBN 9789085048015 - 206
    selenium - microbiële afbraak - biologische behandeling - afvalwaterbehandeling - selenium - microbial degradation - biological treatment - waste water treatment
    In this thesis, microbial conversion of water-soluble, highly toxic forms of selenium (selenate, selenite) to less bioavailable elemental selenium was investigated. By the exploitation of different groups of microorganisms (selenium-respiring, nitrate-reducing and sulfate-reducing bacteria, methanogenic archaea) the operational window of conventional and new hybrid anaerobic bioreactors treating selenium containing anthropogenic waste streams has been determined. A special focus was given to selenium speciation in solid, liquid and gas phase. Selenium speciation in the solid phase was assessed by direct and non-destructive X-ray absorption fine structure spectroscopy. It was demonstrated that selenium solid phase speciation is more complex than initially expected, as different side products such as metal selenides and organic selenium compounds are (trans)formed. Regarding the liquid/gas phase speciation, selenium forms volatile alkylated species under interaction with reduced sulfur compounds depending on operational parameters applied. Selenium oxyanions are not only toxic to animal and human populations, but are here shown to largely influence anaerobic food webs, due to their effect on acetoclastic and hydrogenotrophic methanogens
    Microbial conversion of lignocellulose-derived carbohydrates into bioethanol and lactic acid
    Maas, R.H.W. - \ 2008
    Wageningen University. Promotor(en): Gerrit Eggink, co-promotor(en): Ruud Weusthuis. - [S.l.] : S.n. - ISBN 9789085048718 - 158
    tarwestro - lignocellulose - lignocellulosehoudend afval - microbiële afbraak - conversie - melkzuur - fermentatie - hydrolyse - bio-energie - bioethanol - wheat straw - lignocellulose - lignocellulosic wastes - microbial degradation - conversion - lactic acid - fermentation - hydrolysis - bioenergy - bioethanol
    Houtachtige biomassa (rest)stromen kan één van de duurzame alternatieven gaan worden voor aardolie omdat het kan dienen als grondstof voor de productie van biobrandstoffen en bulkchemicaliën. Belangrijk voordeel van deze technologie is dat er geen gebruik hoeft te worden gemaakt van plantaardige producten die geschikt zijn voor voedseldoeleinden. Binnen het huidige onderzoek zijn we erin geslaagd om op grote schaal houtachtige biomassa zoals stro via verschillende fysisch-chemische behandelingen en een enzymatische hydrolyse af te breken tot enkelvoudige suikers. Deze suikers werden door verschillende soorten micro-organismen omgezet naar gewenste producten zoals ethanol voor biobrandstoftoepassing of melkzuur als bouwsteen voor de productie van biologisch afbreekbaar plastic. De delen van het stro welke niet door de micro-organismen konden worden omgezet werden gebruikt voor biogasproductie of fungeerden als brandstof voor het verkrijgen van warmte en elektriciteit. Een productieproces waarbij, via een combinatie van verschillende voorbehandelingen, stro door bacteriën efficiënt werd omgezet naar melkzuur werd gepatenteerd.
    Mucin utilisation and host interactions of the novel intestinal microbe Akkermansia muciniphila
    Derrien, M.M.N. - \ 2007
    Wageningen University. Promotor(en): Willem de Vos, co-promotor(en): Erwin Zoetendal. - [S.l.] : S.n. - ISBN 9789085046448 - 174
    darmmicro-organismen - mucinen - microbiële afbraak - intestinal microorganisms - mucins - microbial degradation
    Keywords .Mucin, A. muciniphila , mucin degradation, molecular techniques, host response

    Mucins are the major organic components of the defence barrier, known as mucus, covering epithelial cells in many organs, including the entire gastrointestinal (GI) tract. Microbes that can associate with mucins benefit from this interaction since they can access nutrients. Mucin-degrading bacteria are therefore an important community that have not been extensively studied as the substrate itself, mucin, is a complex and high molecular weight glycoprotein.

    The work presented here is focused on the identification and isolation of mucin-degrading bacteria from the GI tract, their degradation of mucin and their interaction with the host.

    Mucin-degrading bacteria were analysed by combining molecular- and cultivation-based approaches. The faecal mucin-degrading bacterial community was found to be highly diverse and host-specific. A novel isolate, representing a novel genus, was cultured from the highest dilution of the enrichment of a single individual. This intestinal isolate, Akkermansia muciniphila, was found to grow to a limited extent on a very limited amount of substrates but grew efficiently on mucin. Phylogenetic analysis based on 16S rRNA sequences indicated that A. muciniphila belonged to the phylum Verrucomicrobia, which was not known to contain intestinal members. Moreover, 16S rRNA genes from A. muciniphila have been retrieved in several clone libraries derived from either faecal or biopsy samples from human and mice. In addition, A. muciniphila was found to be rather abundant in the GI tract. Based on fluorescent in situ hybridisation and quantitative PCR, A. muciniphila was found to represent an average of 10 9 cells / g faecal sample. A negative correlation between the concentration of faecal mucin and the number of A. muciniphila was observed, suggesting it to be involved in mucin degradation in vivo . Several specific enzymes, mostly glycosidases were found to be secreted during its growth on mucin that was degraded for a major part (85%). Hence, the specific impact of A. muciniphila on the host was investigated in germ-free mice and compared to that of the non mucin-degrading bacterium L. plantarum . Transcriptomic microarray analysis showed that both A. muciniphila and L. plantarum modulated a similar number of genes but that host response was found to be highly specific for each bacterium, depending on the anatomical location. Amongst the major responses, we could detect for A. muciniphila a regulation of the immune response, cell proliferation, cell adhesion and apoptosis, and for L. plantarum a regulation of the lipid metabolism.

    Overall, this work has brought new insights into the mucin-degrading community of bacteria, and in particular the role of A. muciniphila,an abundant human mucin-degrading bacterium.
    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 - sediment - anaerobic treatment - waste water treatment - sulfates - thiols - reduction - sulfate - methanol - 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
    Identification and characterization of some Aspergillus pectinolytic glycoside hydrolases
    Zandleven, J.S. - \ 2006
    Wageningen University. Promotor(en): Fons Voragen, co-promotor(en): Gerrit Beldman. - [S.l.] : S.n. - ISBN 9789085045519 - 160
    polygalacturonase - pectinen - celwandstoffen - aspergillus niger - microbiële afbraak - arabidopsis thaliana - polygalacturonase - pectins - cell wall components - aspergillus niger - microbial degradation - arabidopsis thaliana
    Keywords: Aspergillusniger , Arabidopsis thaliana , homogalacturonan, rhamnogalacturonan, xylogalacturonan, xylogalacturonan hydrolase, exo-polygalacturonase

    Pectinases are used for many food applications, in particular for the manufacture of fruit juices. However, the array of pectin modifying enzymes as available today is insufficient to completely degrade pectic polysaccharides from plants, which consequently can cause problems in food processing. As the genome sequence of Aspergillusniger indicated the presence of more pectin modifying enzymes than previously known, research was carried out to identify, produce, and characterize novel pectinases from this species.

    From the complete inventory of the pectinolytic glycoside hydrolase family 28 of A.niger a new gene group of seven exo-acting enzymes was found. Three of these enzymes (PGXA, PGXB, PGXC) were biochemically identified from which it was demonstrated that PGXB and PGXC act as an exo-polygalacturonase while PGXA rather acts like an exo-xylogalacturonan hydrolase.

    The xylogalacturonan hydrolase (XGH) was thoroughly investigated for its action towards a xylogalacturonan (XGA) derived from gum tragacanth by isolation and characterization of the produced oligosaccharides. Also XGH activity towards XGA in the saponified modified 'hairy' regions (MHR-s) of pectin from apples and potatoes was investigated. The enzyme predominantly released the di-saccharide GalAXyl from these substrates which illustrates the preference of XGH to act between two xylosylated GalA residues. However this enzyme was also able to release low substituted XGA oligosaccharides as well as linear GalA oligosaccharides, which shows its tolerance for unsubstituted GalA residues in its active site.

    By using XGH as analytical tool, the presence of XGA could also be demonstrated in the stem and the leaves of Arabidopsis thaliana , which shows that the presence of this polymer is not strictly confined to storage tissues or reproductive organs of plants as was previously thought to be the case.
    Molecular analysis of halorespiration in Desulfitobacterium spp. : catalysis and transcriptional regulation
    Gabor, K. - \ 2006
    Wageningen University. Promotor(en): Willem de Vos; John van der Oost, co-promotor(en): H. Schmidt. - [S.l.] : S.n. - ISBN 9789085045298 - 141
    ademhalingsketen - microbiële afbraak - katabolisme - organische halogeenverbindingen - transactivatie - respiratory chain - microbial degradation - catabolism - organic halogen compounds - transactivation
    Keywords: iron-sulphur proteins, protein-DNA interaction, allosteric regulation, redox regulation, gene redundancy, chlorophenols, bioremediation

    Soil and ground water contamination by halogenated organic compounds mainly used as biocides in agriculture or solvents and cleaning agents in industry has been a long-standing problem. The main barrier in the chemical degradation of organohalides is the presence of the halogen group in the molecule, which also contributes to the toxic nature of these compounds. However, a remarkable group of microorganisms, the halorespiring bacteria, are able to reductively dehalogenate organohalides under anaerobic conditions and use the energy generated via a proton gradient pump for bacterial growth (halorespiration). Due to their versatile dehalogenating capacity, halorespiring bacteria have a large potential in the clean-up of contaminated sites (bioremediation). The work described in this thesis aimed to gain knowledge on two aspects of the molecular basis of halorespiration: (i) the reaction mechanism of dehalogenation, catalyzed by the B 12 /iron-sulphur containing reductive dehalogenases, and (ii) the regulatory mechanism which enables transcriptional activation of genes involved in halorespiration. As model organisms, two Desulfitobacterium spp. were chosen, capable of ortho and/ormetadechlorination of chlorophenols and hydroxylated polychlorinated biphenyls.

    Unravelling of the novel reaction mechanism of reductive dehalogenases was so far hampered by difficulties in functional overproduction of these enzymes. We developed a protocol which involves co-expression of molecular chaperons to aid functional synthesis of the metalloenzymes in Escherichia coli . Next, multiple potential transcriptional activators were characterised from D. hafniense by promoter fusions and in vitro DNA-binding assays. We found that CprK1 and CprK2 activated transcription in the presence of an ortho -chlorophenol (CHPA) but not with its dechlorinated derivative (HPA), while meta -chlorophenols proved to be effectors for CprK4. All CprK paralogues recognized a conserved motif (dehalobox) in halorespiration-inducible promoters. Site-directed mutagenesis of CprK1 provided further insight on the role of conserved residues in the DNA-recognitiona-helix and on redox regulation of the protein.

    Crystalstructures of the CHPA-bound CprK1 and the effector-free form of the closely related CprK of D. dehalogenans revealed a possible mechanism by which the regulators distinguish between CHPA and the non-effector HPA ("pK a interrogation" theory). Native mass spectrometry of protein-DNA complexes confirmed these results and-together with limited proteolysis experiments-also contributed to the fundamental knowledge of ligand-induced changes in the conformation and dynamics of CprK-related transcriptional regulations.

    Efficiënt gebruik van snijmaïs. Deel 4: invloed rastype en oogststadium op afbraakkaraketeristieken van zetmeel en celwanden = Efficient use of silage maize. Part 4: effect of genotype and harvest stage on degradation characteristics of starch and cell walls
    Cone, J.W. ; Costa Ramos, I. da; Gelder, A.H. van - \ 2006
    Lelystad : Animal Sciences Group / Praktijkonderzoek (PraktijkRapport / Animal Sciences Group : Rundvee ) - 34
    maïs - zea mays - rassen (planten) - cultivars - maïskuilvoer - gewasopbrengst - zetmeelvertering - celwanden - microbiële afbraak - melkveehouderij - rundveevoeding - maize - zea mays - varieties - cultivars - maize silage - crop yield - starch digestion - cell walls - microbial degradation - dairy farming - cattle feeding
    In the period 2003-2005 effects of genotypes and maturity stage on yield, quality, conservation and nutrition were investigated. This research was focusing on degradability of starch and cell walls. Harvest stage had significant effects on degradability parameters. No clear systematic differences between the genotypes emerged from the research
    CO metabolism of carboxydothermus hydrogenoformans and archaeoglobus fulgidus
    Henstra, A.M. - \ 2006
    Wageningen University. Promotor(en): Fons Stams. - [S.l.] : S.n. - ISBN 9789085044086 - 117
    anaërobe afbraak - anaërobe micro-organismen - koolmonoxide - microbiële afbraak - oxidoreductasen - anaerobic digestion - anaerobes - carbon monoxide - microbial degradation - oxidoreductases
    Microbial CO metabolism was studied in detail with the ultimate aim to assess the feasibility of a biotechnological process that could replace the existing water gas shift technology in the production of a fuel cell grade hydrogen gas from synthesis gas. It is expected that a biotechnological process is less sensitive to impurities present in synthesis gas and can reach lower CO thresholds, and thus might be more cost effective than conventional catalysts. Low CO thresholds are especially required for polymer electrolyte membrane fuel cells. These fuel cells have a broad application potential in a future hydrogen economy. The bulk of hydrogen produced today is derived from natural gas in a steam reforming process that forms CO besides H 2 . CO is removed by its conversion to H 2 in the water gas shift reaction. However, due to thermodynamic limitations of the process operation temperature, the required CO thresholds are not obtained (<10 ppm). CO conversion at more ambient temperatures is in that respect advantageous for biological CO conversion to obtain a fuel cell grade H 2 .

    It was demonstrated in Chapter 2 that batch cultures of Carboxydothermus hydrogenoformans converted CO to levels below 2 ppm while accumulating H 2 . In these cultures it was necessary to remove CO 2 from the gas phase. Without removal of CO 2 , CO thresholds approached 100 ppm. CO limits that are generally communicated for PEM-FC, indicate 10 ppm as allowable threshold for CO in H 2 gas. The potential of a biotechnological process is thus supported, however, the time needed to reach these thresholds was considerable and needs attention. Biomass activity and gas/liquid mass transfer are possible rate limiting factors in the biological water gas shift reaction. As demonstrated in Chapter 3, higher conversion rates are possible in batch culture than achieved with the cultivation technique used in Chapter 2. In fact, it appears that only in the early stage of batch cultivation the biomass is limiting CO conversion rates. After some time biomass has grown to sufficient density and gas/mass transfer becomes limiting. Even in the most turbulent shaking regime allowed by the incubator, gas/liquid mass transfer remained rate limiting. Success of a tentative biotechnological process therefore likely depends on gas/liquid mass transfer rates of specific reactor types and associated restrictions dictated by process economics.

    Physiological Perspective

    In recent years it has become clear that CO is used as a substrate by a diverse group of strict anaerobic micro-organisms. While it previously was believed that CO predominantly inhibited the growth of many anaerobes, albeit at higher partial pressures than aerobes. Currently research has indicated that CO is a versatile substrate which is effectively used in many microbial metabolisms. The advances that were made especially show that many electron acceptors can be reduced by a wide variety of micro organisms with CO as electron donor. The advances could be made due to the fact that CO is generally neglected as a substrate in physiological studies of novel anaerobic isolates. Genome sequencing projects also demonstrate that the enzymes, CO dehydrogenases, involved in the CO metabolism are present in already well known organisms that have never been tested with CO. An example of this is Archaeoglobus fulgidus , which was tested for its ability to grow with CO in Chapter 5. While it was speculated that A. fulgidus could oxidise CO coupled to the reduction of protons to H 2 , it grew acetogenically with CO instead. In fact, A. fulgidus is the first true homo-acetogenic archaeon known. Remarkable of its metabolism was the intermediate accumulation of formate. It was proposed that A. fulgidus forms acetate via the acetyl-CoA pathway. In this pathway, CO 2 is reduced to form the methyl group of acetate. However, formate is not an intermediate in the expected pathway in which CO 2 is reduced to form formyl-methanofuran and subsequently formyl-tertahydromethanopterin. Besides the formation of acetate, A. fulgidus can reduce sulfate to sulfide with CO as electron donor. It distinguishes itself from bacterial sulfate reducers by its tolerance to CO. While most known sulfate-reducing bacteria are inhibited by elevated levels of CO, A. fulgidus was not noticeably inhibited in the presence of 136 kPa CO. Since A. fulgidus is not capable of growth with H 2 and CO 2 or sulfate as electron acceptors, this organism could be employed to selectively oxidise CO in gas mixtures containing H 2 and remove trace amounts of CO to levels below 10 ppm.

    Selective oxidation of CO is not possible with C. hydrogenoformans . Although C. hydrogenoformans can reduce various electron acceptors with CO, it also does so with H 2 (Chapter 4). C. hydrogenoformans is a true CO specialist. It is able to grow hydrogenogenically with CO, to reduce various other electron acceptors with CO, and to use CO as sole source of energy and carbon. C. hydrogenoformans contains five CO dehydrogenase genes. Besides the identified activities in H 2 formation, in NADPH generation and in autotrophic carbon fixation for three of these CO dehydrogenase, two CO dehydrogenases are still without function (Chapter 5). Conditions that may lead to expression of these CO dehydrogenases are proposed. In nitrate amended cultures a CO dehydrogenase was present, that was not present in cells grown with other substrates. Wu et al. (2005) already indicated that a CO dehydrogenase of C. hydrogenoformans might be involved in oxidative stress response and be expressed under micro aerophilic conditions. Clearly the microbial physiology regarding CO is still incomplete and is more diverse than thought up to now. Further studies are needed in this respect.

    Reductive decolourisation of azo dyes by mesophilic and thermophilic methanogenic consortia
    Cervantes, F.J. ; Santos, A.B. dos; Madrid, M.P. de; Stams, A.J.M. ; Lier, J.B. van - \ 2005
    Water Science and Technology 52 (2005)1-2. - ISSN 0273-1223 - p. 351 - 356.
    slib - ontkleuring - azoverbindingen - kleurstoffen (dyes) - anaërobe behandeling - redoxreacties - microbiële afbraak - afvalwaterbehandeling - sludges - decolorization - azo compounds - dyes - anaerobic treatment - redox reactions - microbial degradation - waste water treatment - anaerobic sludge - redox mediators - quinone-respiration - anthraquinone dyes - granular sludge - transformation - toxicity - bioreactors - inhibition - reactor
    The contribution of acidogenic bacteria and methanogenic archaea on the reductive decolourisation of azo dyes was assessed in anaerobic granular sludge. Acidogenic bacteria appeared to play an important role in the decolourising processes when glucose was provided as an electron donor; whereas methanogenic archaea showed a minor role when this substrate was supplemented in excess. In the presence of the methanogenic substrates acetate, methanol, hydrogen and formate, methane production became important only after colour was totally removed from the batch assays. This retardation in methane production may be due to either a toxic effect imposed by the azo dyes or to the competitive behaviour of azo dyes to the methanogenic consortia for the available reducing equivalents. Keywords Azo dyes; decolourisation; methanogenic consortium; redox mediator; inhibitors
    Organic matter decomposition in simulated aquaculture ponds
    Torres Beristain, B. - \ 2005
    Wageningen University. Promotor(en): Johan Verreth, co-promotor(en): Marc Verdegem. - [S.I.] : S.n. - ISBN 9789085041702 - 138
    visvijvers - visteelt - aquacultuur - organische verbindingen - decompositie - microbiële afbraak - microbiële ecologie - biomassa productie - recycling - fish ponds - fish culture - aquaculture - organic compounds - decomposition - microbial degradation - microbial ecology - biomass production - recycling

    Different kinds of organic and inorganic compounds (e.g. formulated food, manures, fertilizers) are added to aquaculture ponds to increase fish production. However, a large part of these inputs are not utilized by the fish and are decomposed inside the pond. The microbiological decomposition of the organic matter is a critical factor for water quality control and nutrient recycle. Usually, management practices are developed to control the survival and health of the cultured animals and to maintain good water quality. The microbiological processes are affected by these practices but usually unintentionally. A better control of culture conditions and sustainability of aquaculture ponds is possible with an improvement of the microbiological processes. The present thesis is divided in two parts, the first is a literature review of the microbial ecology of aquaculture ponds and the second is the description of a series of experiments in lab-sc ale aquaculture ponds.

    In the first part, the role of the microorganisms in aquaculture ponds is reviewed, focusing on the decomposition of organic matter and its influence on pond dynamics. It was theoretically estimated that the addition of I kg of formulated feed would yield approximately 125 g bacterial biomass. This bacterial biomass is potentially a valuable nutrients source for higher trophic levels. Sedimentation and resuspension processes are important factors affecting the decomposition pathways. Both processes are directly related with the feeding rate and the stocking density applied. The rate of organic matter loading, environmental factors and pond management practices influence the functioning of algae-bacteria interactions, which are extremely important in pond processes. Included is a literature that describes commercial probiotic products that claim to solve: nutritious, water quality and pathogens problems in pond aquaculture, were analyzed. Alternative management practices to steer the decomposition process were also presented (Chapter 2).

    The second part describes all the experiments that were conducted in lab scale microcosm systems, simulating the conditions of an intensive fish-less aquaculture pond with daily feeding rates. In Chapter 3 the influence of aerobic and anaerobic conditions and the organic C/N ratios on the decomposition process is described. Under aerobic decomposition less organic carbon remained in the systems. The results from this experiment suggest that a C/N ratio ranging between the tested values (6.3 and 12.8) does not have a significant influence on the carbon mineralization in the short term " 50 days). However, a C/N ratio decrease was observed in all the treatments during the experimental period; this reduction was especially fast and steep under aerobic conditions. This decrease in C/N ratio of the organic matter might explain why in all treatments the rate of decomposition slowed down at the end of the experiment. The C/N ratio also determined the concentration of inorganic nitrogen compounds in the water. Higher concentrations were found for the richest protein diet treatments. No nitrification was measured even though oxygen and ammonia were present.

    Bacterial biomass production was quantified testing two formulated fish feed with different protein content under aerobic and anaerobic conditions (Chapter 4). The oxic status significantly influences the bacterial abundance, bacterial biomass, bacterial respiration and bacterial efficiency. More bacterial biomass was produced under aerobic conditions. The two diets did not influence significantly the bacterial growth. The bacterial abundance at the end of the experiment was 3.4 x 109 cells ml-1 in aerobic treatments and 1.9 x 109 cells m1-1 in anaerobic treatments. The remaining amount of carbon, fixed in bacterial biomass and expressed on a per area basis, was 19 g m-2 day-t for aerobic system and 8 g m-2 day-1 for anaerobic systems.

    In Chapter 5 the effect of the oxic-anoxic range on fish feed decomposition was investigated. Different ranges, from completely aerobic to completely anaerobic, were tested. To establish intermediate oxic levels the following treatments were used: 1) alternated flows of 02 or N2 at different periods and 2) maintaining the coexistence of aerobic and anaerobic layers while applying short resuspension events. Similar amounts of carbon were converted to CO2 under completely aerobic conditions and under the different ranges of aerobic-anaerobic conditions. Under anaerobic conditions much less carbon was converted into CO2. This means that actually only limited periods of oxic conditions (or resuspension) are needed to stimulate complete organic matter decomposition. From our results it appears that only 6h per day of aerobic conditions or only once mixing of aerobic and anaerobic layers (i.e. resuspension) per four days are needed to reach the same carbon mineralization as in continuous aerobic conditions. Very limited nitrification was observed in the completely aerobic treatment. Nitrification and denitrification were registered for all the systems when aerobic and anaerobic conditions coexisted in time or space. The highest nitrogen removal (around 70%) was found in the resuspension treatments (and 12 h O2 flow treatment).

    The use of controlled lab scale microcosm simulating intensive aquaculture ponds allowed us to follow the fate of carbon and nitrogen during particular decomposition processes. The results found in the different chapters are discussed in Chapter 6. Both the quality and the quantity of the organic matter influenced the decomposition process and its products. The use of high protein diets increased the concentration of nitrogen species affecting the water quality. The aerobic and anaerobic conditions determined the nutrients pathway (mineralized, assimilated or partially decomposed). More bacterial biomass was produced under aerobic conditions than under anaerobic. The coexistence of aerobic and anaerobic conditions stimulated organic matter decomposition; it avoided the accumulation of ammonia while maintaining good water quality conditions.

    A better understanding and control of the organic matter decomposition in aquaculture ponds is crucial. The anaerobic decomposition only becomes a problem when it predominates in the sediment, causing the aerobic-anaerobic interface to move up into the water column, and thus remains disconnected from the aerobic decomposition. Management practices that link aerobic and anaerobic processes can stimulate fish production by recycling carbon and nitrogen compounds. The recycling of surplus organic matter through bacterial processes, however, has a limit. Increasing fish pond productivity should come along with practices to stimulate the autotrophic and heterotrophic food webs, without exceeding the capacity of this aquatic system.

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