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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    Echte docententeams: cruciale schakel in professionele en organisatieontwikkeling
    Wesselink, R. ; Runhaar, P.R. ; Dolfing, R. ; Mulder, M. - \ 2013
    Nitrifier denitrification as a distinct and significant source of nitrous oxide from soil
    Kool, D.M. ; Dolfing, J. ; Wrage, N. ; Groenigen, J.W. van - \ 2011
    Soil Biology and Biochemistry 43 (2011)1. - ISSN 0038-0717 - p. 174 - 178.
    ammonia-oxidizing bacterium - complete genome sequence - nitrosomonas-europaea - nitrite reductase - nitrifying bacteria - oxygen-exchange - n2o - genes - nirk - h2o
    Soils are the major source of the greenhouse gas nitrous oxide (N2O) to our atmosphere. A thorough understanding of terrestrial N2O production is therefore essential. N2O can be produced by nitrifiers, denitrifiers, and by nitrifiers paradoxically denitrifying. The latter pathway, though well-known in pure culture, has only recently been demonstrated in soils. Moreover, nitrifier denitrification appeared to be much less important than classical nitrate-driven denitrification. Here we studied a poor sandy soil, and show that when moisture conditions are sub-optimal for denitrification, nitrifier denitrification can be a major contributor to N2O emission from this soil. We conclude that the relative importance of classical and nitrifier denitrification in N2O emitted from soil is a function of the soil moisture content, and likely of other environmental conditions as well. Accordingly, we suggest that nitrifier denitrification should be routinely considered as a major source of N2O from soil
    Evidence of Increasing Antibiotic Resistance Gene Abundances in Archived Soils since 1940
    Knapp, C.W. ; Dolfing, J. ; Ehlert, P.A.I. ; Graham, D.W. - \ 2010
    Environmental Science and Technology 44 (2010)2. - ISSN 0013-936X - p. 580 - 587.
    real-time pcr - spectrum beta-lactamases - staphylococcus-aureus - klebsiella-pneumoniae - rapid identification - fluorescence pcr - tetracycline - diversity - waste - environment
    Mass production and use of antibiotics and antimicrobials in medicine and agriculture have existed for over 60 years, and has substantially benefited public health and agricultural productivity throughout the world, However, there is growing evidence that resistance to antibiotics (AR) is increasing both in benign and pathogenic bacteria, posing an emerging threat to public and environmental health in the future. Although evidence has existed for years from clinical data of increasing AR, almost no quantitative environmental data exist that span increased industrial antibiotic production in the 1950s to the present, i.e., data that might delineate trends in AR potentially valuable for epidemiological studies. To address this critical knowledge gap, we speculated that AR levels might be apparent in historic soil archives as evidenced by antibiotic resistance gene (ARG) abundances over time. Accordingly, DNA was extracted from five long-term soil-series from different locations in The Netherlands that spanned 1940 to 2008, and 16S rRNA gene and 18 ARG abundances from different major antibiotic classes were quantified. Result; show that ARG from all classes of antibiotics tested have significantly increased since 1940, but especially within the tetracyclines, with some individual ARG being > 15 times more abundant now than in the 1970s. This is noteworthy because waste management procedures have broadly improved and stricter rules on nontherapeutic antibiotic use in agriculture are being promulgated. Although these data are local to The Netherlands, they suggest basal environmental levels of ARG still might be increasing, which has implications to similar locations around the world.
    Method and timing of grassland renovation affects herbage yield, nitrate leaching, and nitrous oxide emission in intensively managed grasslands
    Velthof, G.L. ; Hoving, I.E. ; Dolfing, J. ; Smit, A. ; Kuikman, P.J. ; Oenema, O. - \ 2010
    Nutrient Cycling in Agroecosystems 86 (2010)3. - ISSN 1385-1314 - p. 401 - 412.
    organic nitrogen - soil - mineralization - netherlands - clover - cultivation - fertilizer - pasture - swards
    Managed grasslands are occasionally ploughed up and reseeded in order to maintain or increase the sward productivity. It has been reported that this renovation of grassland is associated with a flush of soil organic nitrogen (N) mineralization and with a temporary increase in soil mineral N contents. Here, we report on the effects of method and time of grassland renovation on herbage yield, nitrate (NO3 -) leaching and nitrous oxide (N2O) emission. Field experiments were carried out at three sites (two sandy soils and a clay soil) in the Netherlands for three years. Renovation of grassland increased the percentage of Perennial ryegrass from 48–70% up to more than 90%. However, averaged over three years, dry matter yields were higher for the reference (not reseeded) swards (on average 13.6 Mg ha-1 for the highest N application rate) than for the renovated grasslands (12.2–13.1 Mg ha-1 dry matter). Grassland renovation in April did not increase N leaching in comparison to the reference. However, renovation in September increased the risk of leaching, because mineral N contents in the 0–90 cm were in November on average 46–77 kg N ha-1 higher than in the reference. Contents of dissolved organic N (DON) in the soil were not affected by renovation. Renovation increased N2O emissions by a factor of 1.8–3.0 relative to the reference grassland. Emissions of N2O were on average higher after renovation in April (8.2 kg N2O-N ha-1) than in September (5.8 kg N2O-N ha-1). Renovation without ploughing (i.e. only chemically destruction of the sward) resulted in a lower percentage of perennial ryegrass (60–84%) than with ploughing (>90%). Moreover, N2O emissions were higher after renovation without ploughing than with ploughing. Clearly, farmers need better recommendations and tools for determining when grassland renovation has beneficial agronomic effects. Losses of N via leaching and N2O emission after renovation can probably not be avoided, but renovation in spring in stead of autumn in combination with ploughing and proper timing of fertilizer application can minimize N losses.
    Effect of soil sample preservation, compared to the effect of other environmental variables, on bacterial and eukaryotic diversity
    Tzeneva, V.A. ; Salles, J.F. ; Naumova, N. ; Vos, W.M. de; Kuikman, P.J. ; Dolfing, J. ; Smidt, H. - \ 2009
    Research in Microbiology 160 (2009)2. - ISSN 0923-2508 - p. 89 - 98.
    gradient gel-electrophoresis - land-use history - microbial diversity - community structure - microorganisms - genes - dna - identification - crop
    Archived soil samples are a valuable source for retrospective ecological studies, and their recent analysis using molecular ecological approaches has drawn significant attention within the scientific community. However, the possibility of addressing ecological questions regarding detectable microbiota in dried and extensively stored soils has not yet been fully evaluated. To achieve this, soil samples collected from two long-term grassland experiments in the United Kingdom and The Netherlands were subjected to air-drying at 40-42 degrees C and stored at room temperature. Total bacterial, Bacillus benzoevorans-related and eukaryotic communities associated with these samples were analyzed by DGGE-fingerprinting of PCR-amplified ribosomal RNA gene fragments. Changes in microbial community structure due to drying and storage were evaluated by multivariate analysis in relation to changes caused by other environmental conditions, such as soil pH, type of fertilizer and vegetation. Soil drying and storage affected the detectable community structure, but did not materially impair our capacity to identify the effect of soil parameters studied in long-term grassland experiments. Although, in some cases, the amplitude of the influence of a given parameter changed due to sample preservation, analyses revealed that pH, fertilization and soil type significantly influenced microbial community structure in the analyzed samples
    Syntrophic growth on formate: a new microbial niche in anoxic environments
    Dolfing, J. ; Jiang, B. ; Henstra, A.M. ; Stams, A.J.M. ; Plugge, C.M. - \ 2008
    Applied and Environmental Microbiology 74 (2008)19. - ISSN 0099-2240 - p. 6126 - 6131.
    methane production - acetate oxidation - signal peptides - bacteria - methanogenesis - life - metabolism - archaea - association - prediction
    Anaerobic syntrophic associations of fermentative bacteria and methanogenic archaea operate at the thermodynamic limits of life. The interspecies transfer of electrons from formate or hydrogen as a substrate for the methanogens is key. Contrary requirements of syntrophs and methanogens for growth-sustaining product and substrate concentrations keep the formate and hydrogen concentrations low and within a narrow range. Since formate is a direct substrate for methanogens, a niche for microorganisms that grow by the conversion of formate to hydrogen plus bicarbonate--or vice versa--may seem unlikely. Here we report experimental evidence for growth on formate by syntrophic communities of (i) Moorella sp. strain AMP in coculture with a thermophilic hydrogen-consuming Methanothermobacter species and of (ii) Desulfovibrio sp. strain G11 in coculture with a mesophilic hydrogen consumer, Methanobrevibacter arboriphilus AZ. In pure culture, neither Moorella sp. strain AMP, nor Desulfovibrio sp. strain G11, nor the methanogens grow on formate alone. These results imply the existence of a previously unrecognized microbial niche in anoxic environments
    Denitrification and nitrate leaching in Dutch agricultural soils - in relation to the Water Framework Directive
    Velthof, G.L. ; Assinck, F.B.T. ; Beek, C.L. ; Dolfing, J. ; Groenigen, J.W. van; Heinen, M. ; Salm, C. van der; Smit, A. ; Vos, J.A. de; Zwart, K.B. - \ 2008
    In situ chemical reduction (ISCR) technologies: Significance of low eh reactions
    Dolfing, J. ; Eekert, M.H.A. van; Seech, A. ; Vogan, J. ; Mueller, J. - \ 2007
    Soil and Sediment Contamination 17 (2007)1. - ISSN 1532-0383 - p. 63 - 74.
    long-term performance - zero-valent zinc - carbon-tetrachloride - aliphatic-compounds - iron - dechlorination - groundwater - hydrogen - culture - enhancement
    Zero valent iron (ZVI; Fe(0)) has been successfully employed for the transformation and subsequent detoxification of a wide range of environmental contaminants, including chlorinated organics, heavy metals, nitroaromatics and, to some degree, perchlorate. The combined use of ZVI plus controlled release carbon has been shown to generate environmental conditions defined herein as in situ chemical reduction (ISCR) that facilitate the microbiological, chemical and/or physical destruction of various contaminants. In this context, the salient features of ISCR are: (i) its low redox potential; and (ii) its propensity to produce H-2. In this paper we discuss the thermodynamics of these characteristics (with special emphasis on ZVI reactions) and provide representative case studies documenting the safe and effective use of ISCR technology to rapidly remove halogenated organics from impacted subsurface environments.
    Oxygen exchange between (de)nitrifcation intermediates and H2O and its implications for source determination of NO3 and N2O: a review
    Kool, D.M. ; Wrage, N. ; Oenema, O. ; Dolfing, J. ; Groenigen, J.W. van - \ 2007
    Rapid Communications in Mass Spectrometry 21 (2007)22. - ISSN 0951-4198 - p. 3569 - 3578.
    ammonia-oxidizing bacteria - periplasmic nitrate reductase - nitrous-oxide - nitric-oxide - nitrobacter-agilis - nitrosomonas-europaea - dissimilatory nitrite - isotopic composition - microbial denitrification - denitrifying bacteria
    Stable isotope analysis of oxygen (O) is increasingly used to determine the origin of nitrate (NO) and nitrous oxide (N2O) in the environment. The assumption underlying these studies is that the 18O signature of NO and N2O provides information on the different O sources (O2 and H2O) during the production of these compounds by various biochemical pathways. However, exchange of O atoms between H2O and intermediates of the (de)nitrification pathways may change the isotopic signal and thereby bias its interpretation for source determination. Chemical exchange of O between H2O and various nitrogenous oxides has been reported, but the probability and extent of its occurrence in terrestrial ecosystems remain unclear. Biochemical O exchange between H2O and nitrogenous oxides, NO in particular, has been reported for monocultures of many nitrifiers and denitrifiers that are abundant in nature, with exchange rates of up to 100%. Therefore, biochemical O exchange is likely to be important in most soil ecosystems, and should be taken into account in source determination studies. Failing to do so might lead to (i) an overestimation of nitrification as NO source, and (ii) an overestimation of nitrifier denitrification and nitrification-coupled denitrification as N2O production pathways. A method to quantify the rate and controls of biochemical O exchange in ecosystems is needed, and we argue this can only be done reliably with artificially enriched 18O compounds. We conclude that in N source determination studies, the O isotopic signature of especially N2O should only be used with extreme caution
    Precise soil management as a tool to reduce CH4 and N2O emissions from agricultural soils
    Mosquera Losada, J. ; Hol, J.M.G. ; Rappoldt, C. ; Dolfing, J. - \ 2007
    Lelystad : Animal Sciences Group (Report / Animal Sciences Group 28) - 42
    distikstofmonoxide - emissie - broeikasgassen - bodemverdichting - rijspoorverdichtingen - mestgiften - akkergronden - landbouwgrond - akkerbouw - bemesting - nitrous oxide - emission - greenhouse gases - soil compaction - tractor pans - dressings - arable soils - agricultural land - arable farming - fertilizer application
    Soil compaction stimulates the emission of nitrous oxide (N2O) and methane (CH4) from agricultural soils. N2O and CH4 are potent greenhouse gases, with a global warming potential respectively 296 times and 23 times greater than CO2.. Agricultural soils are an important source of N2O. Hence there is much interest in a systematic evaluation of management options that are available to minimize agricultural greenhouse gas emissions, in particular N2O soil emissions. One such option would be to minimize soil compaction due to the use of heavy machinery. Soil compaction in arable land is relatively general. In this report it is discussed that emissions of N2O and CH4 from an arable field where soil compaction was minimized through application of the so-called ‘riding track’ (rijpaden) system was substantially lower than from plots where a traditional system was used. Laboratory experiments were used to underpin these observations. From these observations we developed a simple calculation model that relates N2O emission to gas filled pore space and soil respiration as input parameters. We suggest implementing the ‘riding track’ system on clay rather than sand as farmers benefit from lower compaction in terms of lower risk of compaction and better accessibility of fields for work. The potential reduction of the N2O emission from arable farming in the Netherlands is estimated at ~169 ton N2O-N per year
    Estimation of nitrogen losses via denitrification from a heavy clay soil under grass
    Salm, C. van der; Dolfing, J. ; Heinen, M. ; Velthof, G.L. - \ 2007
    Agriculture, Ecosystems and Environment 119 (2007)3-4. - ISSN 0167-8809 - p. 311 - 319.
    ammonia volatilization - field conditions - nitric-oxide - acetylene - rates - netherlands - cattle - level - model - top
    Denitrification is an important pathway for nitrogen (N) loss from agricultural soils, but measured field data on denitrification in clay soils are scarce. The objective of the present research was to obtain and compare three different approaches to estimate the annual N loss via denitrification from a heavy clay soil. Using the acetylene inhibition technique we measured denitrification monthly at 20 °C in intact soil cores of a clay soil under intensively managed grass over a period of 2 years. This approach resulted in estimates of N loss via denitrification of 127 kg N ha-1 year-1 in 2003 and 143 kg N ha-1 year-1 in 2004. We also measured potential denitrification. These data were used in combination with independently calibrated 'reduction functions' to correct for suboptimal soil nitrate contents, water filled pore space or soil temperature. This approach resulted in estimates of 143 and 325 kg N ha-1 year-1 for 2003 and 2004, respectively. These measurements furthermore indicated that 75% of the denitrification occurred in the upper 20 cm of the soil. Estimates of denitrification based on field balances, including measurements of leaching losses to ground and surface waters, were 152 kg N ha-1 year-1 for 2003 and 5 kg N ha-1 year-1 for 2004, when storage of nitrogen was assumed negligible. While all three different estimation methods have considerable uncertainty, they invariably lead to the conclusion that N losses via denitrification in this intensively managed clay soil are high (more than 79 kg N ha-1 year-1). Measurement of the actual denitrification gave the most consistent and least uncertain estimates and accordingly we concluded that direct measurement of the actual denitrification should be preferred despite it's theoretical shortcomings. This implies that about 25% of the N applied to the field as fertilizer and manure is lost to the environment. In this heavy clay soil 90% of this loss proceeds via denitrification, and 10% proceeds via leaching and drainage.
    Exocellular electron transfer in anaerobic microbial communities
    Stams, A.J.M. ; Bok, F.A.M. de; Plugge, C.M. ; Eekert, M.H.A. van; Dolfing, J. ; Schraa, G. - \ 2006
    Environmental Microbiology 8 (2006)3. - ISSN 1462-2912 - p. 371 - 382.
    degrading methanogenic coculture - syntrophic propionate oxidation - sulfate-reducing bacterium - shewanella-algae bry - nov gen-nov - geobacter-sulfurreducens - reductive dechlorination - electricity-generation - fuel-cell - syntrophobacter-fumaroxidans
    Exocellular electron transfer plays an important role in anaerobic microbial communities that degrade organic matter. Interspecies hydrogen transfer between microorganisms is the driving force for complete biodegradation in methanogenic environments. Many organic compounds are degraded by obligatory syntrophic consortia of proton-reducing acetogenic bacteria and hydrogen-consuming methanogenic archaea. Anaerobic microorganisms that use insoluble electron acceptors for growth, such as iron- and manganese-oxide as well as inert graphite electrodes in microbial fuel cells, also transfer electrons exocellularly. Soluble compounds, like humic substances, quinones, phenazines and riboflavin, can function as exocellular electron mediators enhancing this type of anaerobic respiration. However, direct electron transfer by cell-cell contact is important as well. This review addresses the mechanisms of exocellular electron transfer in anaerobic microbial communities. There are fundamental differences but also similarities between electron transfer to another microorganism or to an insoluble electron acceptor. The physical separation of the electron donor and electron acceptor metabolism allows energy conservation in compounds as methane and hydrogen or as electricity. Furthermore, this separation is essential in the donation or acceptance of electrons in some environmental technological processes, e.g. soil remediation, wastewater purification and corrosion.
    Diffuse belasting van het opervlaktewater met nutriënten vanuit grasland op een zware kleigrond; monitoring van nutriëntenemissies op een melkveehouderijbedrijf in Waardenburg
    Salm, C. van der; Dolfing, J. ; Groenigen, J.W. van; Heinen, M. ; Koopmans, G.F. ; Oenema, J. ; Pleijter, M. ; Toorn, A. van den - \ 2006
    Wageningen : Alterra (Alterra-rapport 1266) - 103
    zware kleigronden - drainage - graslanden - oppervlaktewater - fosfaten - nitraten - monitoring - betuwe - clay soils - drainage - grasslands - surface water - phosphates - nitrates - monitoring - betuwe
    Gedurende een periode van drie jaar is de nutriëntenemissie van een grasperceel op een zware kleigrond in de Betuwe gemeten. Het perceel werd gedraineerd met behulp van drains en greppels. De greppels zorgden voor 60% van de afvoer van het neerslagoverschot, 70% van de afvoer van stikstof en 75% van de afvoer van fosfaat naar de sloot. Denitrificatie vormde een belangrijke bron van stikstofverlies op deze kleigronden. Denitrificatiemetingen gaven aan dat denitrificatie leidde tot een gemiddeld stikstof verlies van 131 kg N ha-1 jr-1.
    Uit de mest- en mineralenprogramma's : Milieukundige effecten van graslandvernieuwing
    Velthof, G.L. ; Hoving, I.E. ; Dolfing, J. - \ 2005
    Wageningen : Alterra (Informatieblad / Alterra 398.98) - 2
    graslanden - mest - mineralen - mestverwerking - mineralenboekhouding - grasslands - manures - minerals - manure treatment - nutrient accounting system
    Het scheuren van grasland kan leiden tot stikstofverliezen. Bij graslandvernieuwing moet daarom de afweging worden gemaakt tussen de landbouwkundige en milieukundige gevolgen. In 2002-2004 is experimenteel onderzoek uitgevoerd naar de landbouwkundige en milieukundige effecten van tijdstip en methode van graslandvernieuwing. In dit informatieblad worden de belangrijkste resultaten met betrekking tot de milieukundige gevolgen van graslandvernieuwing besproken. Het informatieblad 398.83 gaat in op de landbouwkundige resultaten. De resultaten worden weergegeven in de rapporten van Dolfing et al. (2004) en Hoving & Velthof (2005)
    Trends in global nitrous oxide emissions from animal production systems
    Oenema, O. ; Wrage, N. ; Velthof, G.L. ; Groenigen, J.W. van; Dolfing, J. ; Kuikman, P.J. - \ 2005
    Nutrient Cycling in Agroecosystems 72 (2005)1. - ISSN 1385-1314 - p. 51 - 65.
    nitrifier denitrification - nitrosomonas-europaea - heterotrophic nitrification - soil - oxygen - n2o - grassland - ammonia - netherlands - challenges
    Wastes from animal production systems contribute as much as 30-50% to the global N2O emissions from agriculture, but relatively little attention has been given on improving the accuracy of the estimates and on developing mitigation options. This paper discusses trends and uncertainties in global N2O emission from animal waste and discusses possible mitigation strategies, on the basis of literature data and results of simple calculations. Total N2O emissions from animal production systems are estimated at 1.5 Tg. Dung and urine from grazing animals deposited in pastures (41%), indirect sources (27%), animal wastes in stables and storages (19%), application of animal wastes to land (10%) and burning of dung (3%) are the five sources distinguished. Most sensitive factors are N excretion per animal head, the emission factor for grazing animals and that for indirect emissions. Total N2O emissions are related to type and number of animals, N excretion per animal, and the management of animal wastes. Projections by FAO suggest that animal numbers will increase by 40% between 2000 and 2030. Mean N excretion per animal head will probably also increase. These trends combined suggest a strong increase in total N2O emission from animal production systems in the near future, which is opposite to the objectives of the Kyoto Protocol. Improving N use efficiency, combined with anaerobic digestion of animal wastes for bio fuel generation are the most feasible options for mitigation, but these options seem insufficient to reverse the trend of increasing N2O emission. In conclusion, animal production systems are a major and increasing source of N2O in agriculture. The uncertainties in the emission estimates are large, due to the many complexities involved and the lack of accurate data, especially about N excretion and the management of animal wastes in practice. Suggestions are made how to increase the accuracy of the emission estimates and to mitigate N2O emission from animal production systems.
    GIS-analyse van risico vuil oppervlaktewater voor vee in Friesland
    Querner, E.P. ; Harmsen, J. ; Dolfing, J. - \ 2004
    H2O : tijdschrift voor watervoorziening en afvalwaterbehandeling 37 (2004)18. - ISSN 0166-8439 - p. 39 - 42.
    waterkwaliteit - oppervlaktewater - waterverontreiniging - rundvee - diergezondheid - sloten - risicoschatting - geografische informatiesystemen - graslanden - nederland - friesland - water quality - surface water - water pollution - cattle - animal health - ditches - risk assessment - geographical information systems - grasslands - netherlands - friesland
    Vee dat in de wei loopt, drinkt water uit de sloot. Bij gezondheidsproblemen met vee wordt daarom ook gekeken in de richting van de kwaliteit van het slootwater, omdat dit water niet altijd even schoon is. De waterkwaliteit in sloten wordt beïnvloed door menselijke activiteiten, maar ook door natuurlijke processen. Om hiermee rekening te houden is via een GIS-analyse het risico in beeld gebracht als oppervlaktewater voor veedrenking wordt gebruikt. In een proefgebied van 20x20 km in Friesland is de methodiek getest. Op basis van beschikbare veldwaarnemingen was het mogelijk om de berekende risico's te toetsen. Hieruit blijkt dat met deze methodiek een goede inschatting van de risico voor veedrenking is te maken. Om een beeld te geven van het effect van maatregelen, zijn een drietal mogelijke scenario's geëvalueerd. De methodiek lijkt ook perspectiefvol om te gebruiken bij de analyses voor de Kaderrichtlijn Water
    Letter to the editor: Microbial diversity in archived soils
    Dolfing, J. ; Vos, A. ; Bloem, J. ; Ehlert, P.A.I. ; Naumova, N.B. ; Kuikman, P.J. - \ 2004
    Science 306 (2004)5697. - ISSN 0036-8075 - p. 813 - 813.
    A topic not covered in the recent special Section on Soils: The Final Frontier (11 June, pp. 1613-1637) is the possibility of using modern DNA-based molecular techniques to study microbial diversity in archived soil samples. Like other soil research institutes in countries such as the United Kingdom, the United States, and Switzerland, Alterra, as heir to the Research Institute for Soil Fertility in the Netherlands, has a soils archive with, in our case, 250,000 samples, many of them from field experiments that date as far back as 1879. Most of the samples are well documented. We selected a series of soil samples from the 1950s to 1970s from an experiment that was initiated in 1940 and analyzed time series from two field plots, one from a plot that had received animal manure and another one from a plot that had received chemical fertilizer. Genetic diversity in the archived soil samples was analyzed with 16S-based denaturing gradient gel electrophoresis (PCR-DGGE) of the DNA extracted from the soil. From densitometric profiling and multivariate analysis of the gels, it was clear that the community structure of manure-amended soils is distinct from the community structure of the soil that had received no manure and only mineral fertilizer (see figure). From this and other results (1), we conclude that it is possible to detect systematic differences in soil microbial community composition in samples that have been dried and stored for more than 50 years. This opens up the possibility of using historic material in existing soil archives to answer questions on the long-term effects of management and environmental change on soil microbial diversity
    Mogelijkheden tot vermindering van emissie van lachgas uit landbouwgronden bij toepassing van verschillende mestsoorten en nitrificatieremmers; laboratoriumproeven en aanbevelingen voor veldexperimenten
    Dolfing, J. ; Buchkina, N. ; Kuikman, P.J. - \ 2004
    Wageningen : Alterra (Alterra-rapport 890) - 39
    distikstofmonoxide - emissie - landbouwgrond - bodemchemie - reductie - mest - nitrificatieremmers - nitrous oxide - emission - agricultural land - soil chemistry - reduction - manures - nitrification inhibitors
    Landbouwgronden zijn een belangrijke bron van het broeikasgas lachgas (N2O). In het kader van het Reductieplan Overige Broeikasgassen (ROB) worden via onderzoek maatregelen verkend die kunnen leiden tot een vermindering van emissie van de overige broeikasgassen methaan en lachgas. Het gebruik van nieuwe (kunst)meststoffen is een van die maatregelen. Ze zijn ontwikkeld om de verliezen van stikstof via nitraatuitspoeling en denitrificatie ter beperken, en hun eventuele gebruik komt dus tegemoet aan het streven naar een meer duurzame landbouw. Bij het begrip nieuwe meststoffen moet gedacht worden aan meststoffen waaraan nitrificatieremmers zijn toegevoegd, of die gecoat zijn om de nutriëntenafgifte te vertragen. Het valt te verwachten dat deze eigenschappen ook de emissie van lachgas beïnvloeden. In het voorliggende onderzoek is door Alterra in een reeks laboratoriumexperimenten nagegaan wat de effecten zijn van het gebruik van aantal van dergelijke nieuwe mestsoorten op de emissie van lachgas uit een zand- en een kleigrond. De nieuwe mestsoorten zoals zijn niet beter dan de traditionele mestsoorten als ze worden beoordeeld op de het verminderen van de emissie van lachgas. De toevoeging van denitrificatieremmers resulteert in zand vaker in minder lachgas dan in klei. In klei leidt de toevoeging van denitrificatieremmers ook tot verhoging van de emissie van lachgas. Op grond van de resultaten van dit laboratorium-onderzoek worden aanbevelingen gedaan en keuzes gemaakt voor een nog uit te voeren veld-onderzoek.
    Phosphorus availability for plant uptake in a phosphorus-enriched noncalcareous sandy soil
    Koopmans, G.F. ; Chardon, W.J. ; Ehlert, P.A.I. ; Dolfing, J. ; Suurs, R.A.A. ; Oenema, O. ; Riemsdijk, W.H. van - \ 2004
    Journal of Environmental Quality 33 (2004)3. - ISSN 0047-2425 - p. 965 - 975.
    phosphate sorption - model - desorption - adsorption - iron - extraction - oxides - netherlands - saturation - simulation
    Mining soil phosphorus (i.e., harvesting P taken up from the soil by a crop grown without external P addition) has been proposed as a possible management strategy for P-enriched soils to decrease the risk of P leaching. We performed a pot experiment in a greenhouse where grass was cropped on a P-enriched noncalcareous sandy soil at zero P application over a period of 978 d. We determined the long-term availability of soil P and evaluated the effectiveness of mining soil P to decrease P in different pools. There were two treatments: soil layers in the pots of either 5 or 10 cm thickness. Soils were analyzed at various stages of the experiment. Phosphorus in soil solution and the total pool of sorbed P were estimated using 1:10 (w/v) 0.01 M CaCl2 extracts and acid ammonium oxalate (Pox), respectively. A desorption isotherm was constructed, which described the relationship between P in soil solution and the total pool of sorbed P for the soils of the 5- and 10-cm treatments. The Langmuir equation gave a very good description of the isotherm. In the long-term, 65% of Pox in the initial soil can be removed by plant uptake, as was calculated from the Langmuir equation and a critical P concentration in soil solution at which P uptake can just be maintained. Thus, Pox may be largely plant available. From the strong nonlinearity of the desorption isotherm, it can be understood why the relative decrease of the P concentration in the CaCl2 extracts was much larger than the relative decrease of Pox. Mining soil P decreased the P concentration in soil solution effectively and, therefore, risk of P leaching from our P-enriched soil.
    Microbial diversity in archived agricultural soils; the past as a guide to the future
    Dolfing, J. ; Vos, A. ; Bloem, J. ; Kuikman, P.J. - \ 2004
    Wageningen : Alterra (Alterra-rapport 916) - 55
    bodembiologie - bodembacteriën - organische verbeteraars - mest - bodembeheer - organisch bodemmateriaal - geschiedenis - landbouwgronden - microbiële diversiteit - soil biology - soil bacteria - organic amendments - manures - soil management - soil organic matter - history - agricultural soils - microbial diversity
    Bacterial diversity and bacterially mediated processes are considered key to soil ecosystem functioning through decomposition and mineralization. However, there is a lack of understanding as to how activity and diversity of prokaryotic communities respond to changes in the environment. At present this issue is mostly addressed by real-time monitoring of long term field experiments, which is costly and slow. Using modern molecular methods we re-analyzed soil samples of up to 50 years old that have been stored in the Alterra soil archive TAGA. We showed that it is indeed possible to detect bacterial fingerprints in those samples and that fingerprints from different samples can be distinctly different, for example between fields that have or have not received organic amendments. These results are a promising first step towards unlocking the microbial information present in archived soil samples. This will help to assess the (likelihood of) changes in soil microbial diversity in response to environmental change (climate change) and human interference (fertilization) and to establish a reference condition and situation. This may further enable coupling to more functional assessments of soil functioning in standardized decomposition essays with the stored samples with known differences in diversity.
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