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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    Mycorrhiza: duurzaam bodembeheer bij peer (met poster)
    Heijne, B. ; Maas, M.P. van der; Anbergen, R.H.N. - \ 2013
    fruitteelt - pyrus - plantenontwikkeling - mycorrhizae - wortels - bodemschimmels - biologische bodemactiviteit - plantenvoeding - fruit growing - pyrus - plant development - mycorrhizas - roots - soil fungi - biological activity in soil - plant nutrition
    Fruitkennisdag Wageningen 22 november 2013 voor 350 mensen
    Soil Ecology and Ecosystem Services
    Wall, D.H. ; Bardgett, R.D. ; Behan-Pelletier, V. ; Herrick, J.E. ; Jones, T.H. ; Ritz, K. ; Six, J. ; Strong, D.R. ; Putten, W.H. van der - \ 2012
    Oxford : Oxford University Press - ISBN 9780199575923 - 406
    bodemecologie - bodembiologie - ecosysteemdiensten - agro-ecosystemen - biologische bodemactiviteit - bodemflora - bodembiodiversiteit - plantengenetica - soil ecology - soil biology - ecosystem services - agroecosystems - biological activity in soil - soil flora - soil biodiversity - plant genetics
    This book synthesizes contributions from leading soil scientists and ecologists, describing cutting-edge research that provides a basis for the maintenance of soil health and sustainability. It covers these advances from a unique perspective of examining the ecosystem services produced by soil biota across different scales - from biotic interactions at microscales to communities functioning at regional and global scales. The book leads the user towards an understanding of how the sustainability of soils, biodiversity, and ecosystem services can be maintained and how humans, other animals, and ecosystems are dependent on living soils and ecosystem services.
    Zieke bodem zorgt voor lelijk bos
    Kemmers, R.H. - \ 2008
    Kennis Online 2008 (2008)nov. - p. 3 - 3.
    natuurbescherming - bodem - biologische bodemactiviteit - achteruitgang, bossen - bosecologie - bosgronden - natuur - nature conservation - soil - biological activity in soil - forest decline - forest ecology - forest soils - nature
    Op de bosgrond onder de bomen zouden allerhande mossen, bloemen en kruiden moeten kunnen groeien. In Nederland lijdt de kwaliteit van de ondergroei echter al enkele decennia onder verzuring, vermesting en verdroging. Natuurbeheerders doen hun best om de schade te herstellen, maar de genomen maatregelen hebben nog onvoldoende effect. De gewenste planten komen pas terug als de basis goed is: de bodem
    Analysis of the soil food web structure under grass and grass clover
    Eekeren, N.J.M. van; Smeding, F.W. ; Vries, F.T. de; Bloem, J. - \ 2006
    In: Proceedings of Cost action 852, Sward dynamics, N-flows and forage utilization in legume-based systems, Grado, Italy, November 10-12, 2005. - - p. 37 - 40.
    voedselwebben - biologische bodemactiviteit - graslandbeheer - bodemkunde - food webs - biological activity in soil - grassland management - soil science
    The below ground biodiversity of soil organisms plays an important role in the functioning of the the soil ecosystem, and consequently the above ground plant production. The objective of this study is to investigate the effect of grass or grass-clover in combination with fertilisation on the soil food web structure. In 2003 a fertilisation trial on grass and grassclover was sampled for soil organisms. Data were agglomerated in seven trophic groups, and classified by means of TWINSPAN. TWINSPAN clearly distinguished three main soil food web structures: Type 1: Grass plots with a high biomass of bacteria and fungi; Type 2: Grass-clover plots with a high biomass of earthworms; Type 3: Grass and grass-clover plots, that received relativily high fertilisation, with a high number of nematodes. Results suggest a microbial oriented soil food web for grass and an earthworm orientated soil food web for grass-clover.
    Bodemvoedselwebben op melkveebedrijven : Methode voor een kwalitatieve analyse van de voedselwebstructuur
    Smeding, F.W. ; Eekeren, N.J.M. van; Schouten, A.J. ; Livestock Research, - \ 2005
    Lelystad : Animal Sciences Group (Bioveem intern rapport 14) - 40
    biologische landbouw - dierhouderij - graslandbeheer - graslanden - biologische bodemactiviteit - bodembiologie - agrarische bedrijfsvoering - bodemvruchtbaarheid - melkveehouderij - organic farming - animal husbandry - grassland management - grasslands - biological activity in soil - soil biology - farm management - soil fertility - dairy farming
    Deze studie binnen het Bioveem project heeft als doel gehad een voor de veehouder visualiseerbare, meer natuurgetrouwe voorstelling van het bodemleven maken als aanvulling op het abstracte, gefragmenteerde beeld van microscopische en chemische bodemanalyses.Deze voorstelling van het bodemleven wordt vervolgens in verband gebracht met zijn dagelijkse beslissingen en handelen. Op die manier kan dan de kloof tussen praktijk en onderzoek overbrugd worden. Op basis van de studie lijkt inderdaad een typologie van voedselwebstructuren een geschikte methode om het fragmentarische beeld van het bodemleven vanuit microscopische metingen en chemische bepalingen te herleiden tot een voor de praktijk visualiseerbare voorstelling. Het herkennen van patronen sluit aanbijvaardigheden die practici ook gebruiken bij hun beslissingen ten aanzien van bijvoorbeeld graslandmanagement en veevoeding.
    Natuurlijke immobilisatie van zware metalen in de Roeventerpeel
    Harmsen, J. ; Toorn, A. van den; Zweers, A.J. - \ 2005
    Wageningen : Alterra (Alterra-rapport 1125) - 42
    bodemverontreiniging - zware metalen - immobilisatie - biologische bodemactiviteit - nederland - natuurverschijnselen - limburg - soil pollution - heavy metals - immobilization - biological activity in soil - netherlands - natural phenomena - limburg
    De waterbodem in Roeventerpeel is verontreinigd met cadmium en zink. Het is een voor de natuur potenteel belangrijk vengebied. Voor de ontwikkeling van dit gebied is verwijdering van de waterbodem van belang. De zware metalen in de waterbodem zijn via het grondwater aangevoerd en vastgelegd als sulfide. Naast de vastgelegde zware metalen is in de waterbodem een grote hoeveelheid ijzersulfide gevormd. Dit beperkt de mogelijkheden voor verwerking, omdat opsalg boven het grondwaterniveau zal leiden tot sterke verzuring Het principe van natuurlijke immobilisatie kan ook worden gebruikt voor de verwerking van de te verwijderen baggerspecie, zodat zowel de zware metalen als het ijzersulfide niet zullen zorgen voor schadelijke effecten. Het vengebied en de directe omgeving voldoen aan de te stellen randvoorwaarden.
    Spatial and temporal fluctuations in bacteria, microfauna and mineral nitrogen in response to a nutrient impulse in soil
    Zelenev, V.V. - \ 2004
    Wageningen University. Promotor(en): Ariena van Bruggen, co-promotor(en): A.M. Semenov. - Wageningen : s.n. - ISBN 9789058089885 - 190
    bodembiologie - bodemfauna - micro-organismen - bacteriën - biologische bodemactiviteit - rizosfeer - variatie - oscillatie - populatiedynamica - bevolkingsspreiding - organisch bodemmateriaal - organisch afval - voedingsstoffen - wiskundige modellen - simulatiemodellen - soil biology - soil fauna - microorganisms - bacteria - biological activity in soil - rhizosphere - variation - oscillation - population dynamics - population distribution - soil organic matter - organic wastes - nutrients - mathematical models - simulation models
    Fluctuations of bacterial populations can be observed when frequent and sufficiently long series of samples are obtained for direct microscopic or plate counts of bacteria. Such fluctuations in time and space have been observed for both bacteria and other soil inhabitants. These fluctuations of bacterial numbers are especially noticeable after some disturbance of soil such as tillage, drying and rewetting, and substrate addition, for example in the form of fresh plant material. However, very seldom were bacterial fluctuations subjected to proper statistical analysis to detect significant periodical components in the analyzed data (Chapter 1). The phenomenon of wave-like bacterial oscillations was investigated in short-term (1 month) controlled experiments for rhizosphere and bulk soil after substrate input from plant roots and fresh plant debris, respectively. Short-term oscillating dynamics of bacterial populations were simulated in a mechanistic model, which may contribute significantly to our understanding of the reasons and consequences of bacterial oscillations after addition of substrate to soil.



    To determine the spatial variation in density of different trophic bacterial groups (copiotrophic and oligotrophic) and carbon sources in the rhizosphere, colony-forming units (CFUs) and soluble total organic carbon (TOC) were quantified along the root from rhizosphere and corresponding bulk soil samples at 2 cm intervals along wheat roots two, three, and four weeks after planting (Chapter 2). There was a moderate rhizosphere effect in one experiment with soil rich in fresh plant debris (1% C in soil), and a very pronounced rhizosphere effect in the second experiment with soil low in organic matter (0.7% C). Wave-like patterns of both trophic groups of bacteria as well as TOC could be discerned along the whole root length (60 or 90 cm). Harmonical analysis revealed significant oscillations in bacterial populations and TOC. TOC concentrations were maximal at the root tip and base and minimal in the middle part of the roots. Populations of copiotrophic and oligotrophic bacteria had two maxima close to the root tip and at the root base, or three maxima close to the tip, in the middle section, and at the root base. Phases and periods of the two trophic groups differed slightly. The location and pattern of the waves in bacterial populations changed progressively from week to week, and was not consistently correlated with TOC concentrations or the location of lateral root formation. Thus, the traditional view that patterns in bacterial numbers along the root directly reflect patterns in exudation and rhizodeposition from several fixed sources along the root may not be true. We attributed the observed wave-like patterns in bacterial populations to bacterial growth and death cycles (due to autolysis or grazing by predators). Considering the root tip as a moving nutrient source, temporal oscillations in bacterial populations at any location where the root tip passed would result in moving waves along the root. This change in concept about bacterial populations in the rhizosphere could have significant implications for plant growth promotion and soil health.



    To check the hypothesis that the principal mechanism underlying the wave-like distribution of bacteria along the root is a cycle of growth, death, autolysis, and regrowth of copiotrophic bacteria in response to a moving substrate source (root tip) a simulation model was created (Chapter 3). After transformation of observed spatial data to presumed temporal data based on root growth rates, a simulation model was constructed with the Runge-Kutta integration method to simulate the dynamics of colony-forming bacterial biomass, with relative growth and death rates depending on substrate content so that the rate curves crossed over at a substrate concentration within the range of substrate availability. The original source of substrate was the root tip, supplemented with a background flux (BGF) of substrate from soil organic matter and dead root cells. Dead necromass from bacteria was partially recycled into substrate. This model was named "BACWAVE", standing for 'bacterial waves'. The model generated cyclic dynamics of bacteria, which were translated into traveling spatial waves along a moving nutrient source. Parameter values were estimated from calculated initial substrate concentrations and observed microbial distributions along wheat roots by an iterative optimization method. The kinetic parameter estimates fell in the range of values reported in the literature. The model was validated with an independent data set of bacteria along wheat roots in relatively C-rich soil. Calculated microbial biomass values produced spatial fluctuations similar to those obtained for experimental biomass data derived from colony forming units. Concentrations of readily utilizable substrate (RUS) calculated from biomass dynamics did not mimic measured concentrations of TOC, which consists not only of substrate but also various polymers and humic acids. Thus, a moving impulse of nutrients into soil resulting in cycles of growth and death of bacteria can explain the observed phenomenon of moving bacterial waves along roots. This was the first report of wave-like dynamics of micro-organisms in soil along a root resulting from the interaction of a single organism group with its substrate.



    The model "BACWAVE" for wave-like dynamics of copiotrophic bacteria (CB) was extended to include dynamics of oligotrophic bacteria (OB) (Chapter 4). CFUs ofOBand CB along wheat roots (24 samples) in a low C soil were transformed to temporal biomass taking root growth rate and cell sizes into account. Growth rates of both groups of bacteria increased with readily utilizable substrate (RUS) according to Monod equations, but each with their own characteristic parameter values. The death rate of CB decreased monotonically with substrate concentration, while the death rate ofOBfirst decreased and then increased with substrate concentration. Model parameters were estimated from literature and with an iterative optimization method. Initial biomass and kinetic parameters were lower forOBthan for CB, and fell in the range of values in the literature. The model was validated with an independent data set of bacteria along wheat roots in relatively C-rich soil, so that BGF and initial microbial populations were higher, but other model parameters were the same for both data sets. A satisfactory fit was obtained between experimental and modeled data. This is the first rhizosphere model in which oligotrophic bacteria are taken into account.



    Several microcosm experiments were carried out to investigate the hypothesis that an impulse of fresh substrate into soil would invoke oscillations in bacterial populations (Chapter 5). Soil bacterial populations, mineral nitrogen content, pH, and redox potential (ROP) were monitored daily for one month after incorporation of clover-grass (CG) plant material in soil. Colony-forming units (CFUs) and direct microscopic counts of FDA-stained and FITC-stained bacteria increased immediately after incorporation of the plant material, dropped within 2 days, and fluctuated thereafter. Harmonics analysis demonstrated that there were significant wave-like fluctuations with three or four significant peaks within one month after incorporation of clover-grass material. Ammonium (NH 4+ )concentrations increased from the start of the experiments until nitrification commenced. Nitrate (NO 3−) concentrations dropped immediately after plant incorporation, and then rose monotonically until the end of the experiments. There were no wave-like fluctuations in NH 4+and NO 3−concentrations, so that bacterial fluctuations could not be attributed to alternating mineral N shortage and sufficiency. pH levels rose and declined with NH 4+levels. ROP dropped shortly before NH 4+concentrations rose, and increased before NH 4+concentrations decreased; there were no regular fluctuations in ROP, so that temporary oxygen shortages may not have been responsible for the observed fluctuations in bacterial populations. Thus, for the first time, regular wave-like dynamics were demonstrated for bacterial populations after perturbation by addition of fresh organic matter to soil, and several potential reasons for the death phase of the fluctuations could be excluded from further consideration.



    To elucidate possible reasons for the oscillations in bacterial populations, potential interactions with populations of bacterial predators, in particular bacterial-feeding nematodes (BFN), were investigated (Chapter 6). In two microcosm experiments, soil bacteria (CFU's and microscopic counts of stained bacteria) and nematode populations in 22 families were monitored daily for 25 or 30 days after incorporation of clover+grass (CG) plant material into soil. Soil bacterial populations fluctuated significantly after incorporation of the plant material with 2 peaks within the first week and 3 or 4 smaller peaks thereafter. Total nematodes and BFN populations started to increase in the course of the second week after CG incorporation, but the proportion of BFN increased within one week. Inactive juvenile BFN (dauerlarvae) seemed to be activated after two days (as the percentage of Rhabditidae increased and dauerlarvae decreased), followed by step-wise increases in dauerlarvae every four days, indicating that there was a new generation every four days. There were significant wave-like fluctuations in daily population changes of BFN, but not in total nematode communities, over the duration of these experiments. These fluctuations had similar periods (5 days) as those of bacterial populations, but were shifted about 3 days relatively to the bacterial fluctuations.



    In another microcosm experiment, dynamics of bacterial populations were monitored in response to gamma-irradiated plant material added to gamma-irradiated soil mixed with filtered bacterial suspensions and to non-irradiated soil. Gamma-irradiation of soil significantly increased the periods and amplitudes of bacterial oscillations compared to untreated field soil. Nematode populations were decimated in gamma-irradiated soils, but a small number of protozoa were accidentally introduced in the irradiated soil, and may have been partially responsible for the delayed regulation of bacterial growth. We conclude that fluctuations in bacterial populations were not directly related to similar fluctuations in populations of BFN, as expected from classical Lotka-Volterra equations for predator-prey relationships, but were related to changes in growth rates of BFN. An alternation in active and inactive stages in a synchronized predator community after a disturbance could allow periods of bacterial growth alternated with periods of death. Fluctuations in bacterial populations were dampened after a much longer period when the soil fauna was largely eliminated.



    Findings of regular oscillations in bacterial populations and in the rate of change in numbers of bacterial predators after addition of fresh organic matter to soil stimulated the development of a simulation model to investigate potential mechanisms of those oscillations, and whether they were initiated by bacteria- substrate interactions or predatory regulation of bacteria (Chapter 7). The model could also be used to investigate mineral nitrogen release during short-term organic matter decomposition. A substrate-based food web model was constructed with 3 plant residue and 5 soil organic matter compartments, 3 trophic groups of bacteria (copiotrophic, oligotrophic and hydrolytic), and two predatory groups (BFN and protozoa). Both carbon and nitrogen flows were modeled. Fluctuations in microbial populations in soil after plant residue incorporation could be reproduced with and without participation of predators. The first two peaks in bacterial numbers were mainly related to bacteria-substrate interactions, while predators (particularly protozoa) influenced bacterial dynamics during later stages of bacterial community development. Oligotrophic bacteria had a stabilizing effect on fluctuations of other trophic groups, and were the main source of nutrients for predators. A peak in soil ammonium occurred within one week after residue incorporation. Nitrate increased sigmoidally after a short lag phase. The final nitrate concentration was primarily determined by bacterial dynamics and to a lesser extent by protozoa and nematodes. This model emphasized the importance of substrate-consumer relations for regulation of populations at different trophic levels and nutrient release from fresh organic matter added to soil.



    This research has given insight in potential mechanisms underlying oscillations in populations of soil bacteria and their predators after a disturbance. Despite the advances achieved in this thesis, there are still some problems to be solved. Precise regulation of substrate-consumer interactions and mechanisms that initiate growth and death cycles of soil bacteria have to be investigated in detail. Nevertheless, the "BACWAVE-WEB" model has good potential to predict responses of microbial communities to a disturbance, which could be used to characterize soil health. The model could be expanded to include denitrification and nitrate leaching, so that the extent of N losses after soil disturbance could be predicted.
    Microbial indicators
    Bloem, J. ; Breure, A.M. - \ 2003
    In: Bioindicators & biomonitors; principles, concepts and applications / Markert, B.A., Breure, A.M., Zechmeister, H.G., Amsterdam : Elsevier - p. 259 - 282.
    bodemverontreiniging - bodembiologie - biologische bodemactiviteit - microbiële activiteiten - bodemkwaliteit - biologische monitoring - soil pollution - soil biology - biological activity in soil - microbial activities - soil quality - biomonitoring
    On-farm impact of cattle slurry manure management on biological soil quality
    Goede, R.G.M. de; Brussaard, L. ; Akkermans, A.D.L. - \ 2003
    Netherlands Journal of Agricultural Science 51 (2003)1-2. - ISSN 0028-2928 - p. 103 - 133.
    rundveemest - rundveedrijfmest - behandeling - plantenvoeding - kunstmeststoffen - biologische bodemactiviteit - melkveehouderij - nederland - bodemfauna - mestverwerking - cattle manure - cattle slurry - treatment - plant nutrition - fertilizers - soil fauna - biological activity in soil - dairy farming - netherlands - manure treatment - gradient gel-electrophoresis - maturity index - nitrogen - nematodes - fragments - emissions - dynamics - carbon
    The effects of dairy cattle slurry management on soil biota, soil respiration and nitrogen (N) mineralization were evaluated in a farm trial across 12 farms and a field experiment on 2 farms located in a dairy farming area in the north of the Netherlands. The slurry management consisted of slit injection or surface application of slurry; the use or no use of additives [Euromestmix® (MX) and Effective Microbes® (EM)] and the type and level of inorganic N fertilization. Slit injection negatively affected epigeic earthworms whereas its effect on anecic and endogeic earthworms was absent or even positive. Enchytraeids were not affected in a consistent way, whereas numbers of nematodes indicative of nutrient- enriched conditions increased. Inorganic N fertilizer had similar effects. Bacterial diversity was not different among the treatments. Nitrifier diversity, however, was high at one of the farms in the field experiment, and was negatively affected by inorganic N fertilizer. The use of MX was usually associated with higher numbers of earthworms. EM affected numbers of earthworms and numbers of bacterial and plant-feeding nematodes, but only in specific combinations of field history, slurry type and slurry application method. We found no effects of EM on the composition of the microbial community. Soil respiration was increased when slurry was surface-applied. The calculated N mineralization by earthworms was in the order of 70–200 kg N ha -¹ year -¹. It was highest under farm-characteristic surface application of slurry with MX and lowest under farm-characteristic slit injection of slurry without additives. Compared with the N mineralization by earthworms, that by enchytraeids and nematodes was quantitatively insignificant. Negative treatment effects on earthworms led to corresponding reductions in calculated N mineralization.
    Ecologische kwaliteit van de bodem
    Breure, A.M. ; Rutgers, M. ; Bloem, J. ; Brussaard, L. ; Didden, W.A.M. ; Jagers op Akkerhuis, G.A.J.M. ; Mulder, C. ; Schouten, A.J. ; Wijnen, H.J. van - \ 2003
    Bilthoven : RIVM (RIVM rapport 607604005 / 2003) - 32
    bodembiologie - biologische bodemactiviteit - landgebruik - duurzaamheid (sustainability) - grondbewerking - bodemkwaliteit - soil biology - biological activity in soil - land use - sustainability - tillage - soil quality
    In dit rapport wordt beschreven wat ecologische kwaliteit van bodem is, en op welke wijze deze gekwantificeerd kan worden. In bodem vinden een groot aantal processen plaats, die van belang zijn voor de mens (nutsfuncties), omdat ze bijdragen aan bijvoorbeeld de voedselvoorziening, het type en de kwaliteit van de natuur en de levering van schoon grondwater (voor de productie van drinkwater). Bodemorganismen spelen een belangrijke rol in die processen. Bij een duurzaam gebruik van de bodem ishetvan belang, om de bodemorganismen zodanig te gebruiken en te beheren, dat deze processen ook voor de toekomst gewaarborgd zijn. Hierbij moet ook de mogelijkheid beschikbaar blijven om het bodemgebruik te veranderen. Ter onderbouwing van het duurzaamheidsbeleid van de bodem wordt gewerkt aan de ontwikkeling van een bodembiologische indicator (BoBI) voor gebruik op nationale schaal. Daarvoor worden ecologische gegevens over de soortdiversiteit, het aantal organismen per soort en deactiviteitvan de organismen verzameld
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