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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    The Influence of Long-Term Copper Contaminated Agricultural Soil at Different pH Levels on Microbial Communities and Springtail Transcriptional Regulation
    Boer, T.E. de; Tas, N. ; Braster, M. ; Temminghoff, E.J.M. ; Roling, W.F.M. ; Roelofs, D. - \ 2012
    Environmental Science and Technology 46 (2012)1. - ISSN 0013-936X - p. 60 - 68.
    heavy-metal contamination - bacterial community - organic status - fungal communities - arable soil - sandy soil - diversity - toxicity - microorganisms - microarray
    Copper has long been applied for agricultural practises. Like other metals, copper is highly persistent in the environment and biologically active long after its use has ceased. Here we present a unique study on the long-term effects (27 years) of copper and pH on soil microbial communities and on the springtail Folsomia candida an important representative of the soil macrofauna, in an experiment with a full factorial, random block. design. Bacterial communities were mostly affected by pH. These effects were prominent in Acidobacteria, while Actinobacteria and Gammaroteobacteria communities were affected by original and bioavailable copper. Reproduction and survival of the collembolan F. candida was not affected by the studied copper concentrations. However, the transcriptomic responses to copper reflected a mechanism of copper transport and detoxification, while pH exerted effects on nucleotide and protein metabolism and (acute) inflammatory response. We conclude that microbial community structure reflected the history of copper contamination, while gene expression analysis of F. candida is associated with the current level of bioavailable copper. The study is a first step in the development of a molecular strategy aiming at a more comprehensive assessment of various aspects of soil quality and ecotoxicology.
    Functional stability of microbial communities from long-term stressed soils to additional disturbance
    Tobor-Kaplon, M.A. ; Bloem, J. ; Ruiter, P.C. de - \ 2006
    Environmental Toxicology and Chemistry 25 (2006)8. - ISSN 0730-7268 - p. 1993 - 1999.
    heavy-metal tolerance - ecosystem function relationship - leucine incorporation - thymidine incorporation - bacterial communities - arable soil - diversity - biodiversity - transformations - adaptation
    Functional stability, measured in terms of resistance and resilience of soil respiration rate and bacterial growth rate, was studied in soils from field plots that have been exposed to copper contamination and low pH for more than two decades. We tested whether functional stability follows patterns predicted by either the "low stress-high stability" or the "high stress-high stability" theory. Treatments consisting of soils with no or high copper load (0 or 750 kg/ha) and with low or neutral pH (4.0 or 6.1) were used. Stability was examined by applying an additional disturbance by heat (50 degrees C for 18 h) or drying-rewetting cycles. After heating, the respiration rate indicated that the soils without copper were less stable (more affected) than the soils with 750 kg/ha. Bacterial growth rate was more stable (resistant) to heat in the pH 6.1 than in the pH 4.0 soils. Growth rate was stimulated rather than inhibited by heating and was highly resilient in all soils. The respiration rate was less affected by drying-rewetting cycles in the pH 4.0 soils than in the pH 6.1 soils. Bacterial growth rate after drying-rewetting disturbance showed no distinct pattern of stability. We found that the stability of a particular process could vary significantly, depending on the kind of disturbance; therefore, neither of the two theories could adequately predict the response of the microbial community to disturbance.
    Soil organic matter distribution and microaggregate characteristics as affected by agricultural management and earthworm activity
    Pulleman, M.M. ; Six, J. ; Breemen, N. van; Jongmans, A.G. - \ 2005
    European Journal of Soil Science 56 (2005)4. - ISSN 1351-0754 - p. 453 - 467.
    no-tillage agroecosystems - arable soil - carbon - casts - aggregation - dynamics - pasture - sequestration - oligochaeta - grassland
    Stable microaggregates can physically protect occluded soil organic matter (SOM) against decomposition. We studied the effects of agricultural management on the amount and characteristics of microaggregates and on SOM distribution in a marine loam soil in the Netherlands. Three long-term farming systems were compared: a permanent pasture, a conventional-arable system and an organic-arable system. Whole soil samples were separated into microaggregates (53–250 µm), 20–53 µm and <20 µm organo-mineral fractions, sand and particulate organic matter, after complete disruption of macroaggregates. Equal amounts of microaggregates were isolated, irrespective of management. However, microaggregates from the pasture contained a larger fraction of total soil organic C and were more stable than microaggregates from the two arable fields, suggesting greater SOM stabilization in microaggregates under pasture. Moreover, differences in the relative contribution of coarse silt (> 20 µm) versus fine mineral particles in the microaggregates of the different management systems demonstrate that different types of microaggregates were isolated. These results, in combination with micromorphological study of thin sections, indicate that the great earthworm activity under permanent pasture is an important factor explaining the presence of very stable microaggregates that are relatively enriched in organic C and fine mineral particles. Despite a distinctly greater total SOM content and earthworm activity in the organic- versus the conventional-arable system, differences in microaggregate characteristics between both arable systems were small. The formation of stable and strongly organic C-enriched microaggregates seems much less effective under arable conditions than under pasture. This might be related to differences in earthworm species' composition, SOM characteristics and/or mechanical disturbance between pasture and arable land.
    Functional stability of microbial communities in contaminated soils
    Tobor-Kaplon, M.A. ; Bloem, J. ; Römkens, P.F.A.M. ; Ruiter, P.C. de - \ 2005
    Oikos 111 (2005)1. - ISSN 0030-1299 - p. 119 - 129.
    heavy-metal tolerance - ecosystem function relationship - fatty-acid-composition - leucine incorporation - thymidine incorporation - bacterial communities - arable soil - biodiversity - diversity - pollution
    Functional stability, measured in terms of resistance and resilience of respiration and growth rate of bacteria and fungi, was studied in soils that have been exposed to copper and low pH for more than twenty years. We used treatments, consisting of soil with no or high copper load (0 or 750 kg ha(-1)) and low or neutral pH (4.0 or 6.1). Stability was examined by applying an additional stress in the form of lead or salt. After addition of lead, respiration (decomposition of freshly added lucerne meal) showed lower resistance at low than at neutral pH and at high copper than at low copper. The most acid and contaminated soil was the least resistant. Respiration showed no resilience after addition of lead. Bacterial growth rate (thymidine incorporation) also showed resistance at low pH but only in soils that were not contaminated with copper. After addition of salt, respiration showed no differences in resistance but the soils without copper contamination showed higher resilience. Bacterial growth rate showed lower resistance at low pH than at neutral pH, the latter in which the growth rate increased by on average 123%. This increase at high pH was faster in soil without copper than in soil with copper contamination in which the growth rate initially decreased and then increased. The effects of secondary stress depended on the nature of the stress (lead or salt) and on the parameter measured (respiration or bacterial growth rate). In general the highest resistance and/or resilience were found in the least contaminated soils with neutral pH and/or no copper contamination. Thus, the microbial communities in the cleaner soils showed the highest functional stability. The results seem to confirm the notion that environmental stress alters ecosystems such that supplementary stress will have stronger impacts than in an unstressed system. The results may also confirm the insurance-hypothesis that reduced biodiversity due to the first stress negatively affected community stability. As an alternative, we discuss the observed effects in terms of altered energy budget.
    Daily changes in bacterial-feeding nematode populations oscillate with similar periods as bacterial populations after a nutrient impulse in soil
    Zelenev, V.V. ; Berkelmans, R.A. ; Bruggen, A.H.C. van; Bongers, A.M.T. ; Semenov, A.M. - \ 2004
    Applied Soil Ecology 26 (2004). - ISSN 0929-1393 - p. 93 - 106.
    decomposing barley roots - microbial activity - nitrogen transformations - biological indicators - disease suppression - arable soil - carbon - protozoa - dynamics - wheat
    Previously, we showed that bacterial populations oscillated in a regular manner in response to a nutrient impulse in soil. For this paper we investigated if the wave-like fluctuations in bacterial populations could be explained by their interactions with populations of bacterial-feeding nematodes (BFN). In two microcosm experiments, soil bacterial populations-colony forming units (CFUs) 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. In another microcosm experiment, dynamics of bacteria and nematode populations were monitored in response to gamma-irradiated plant material added to gamma-irradiated soil mixed with filtered bacterial suspensions and in non-irradiated soil. In the first experiment, soil bacterial populations fluctuated significantly after incorporation of the plant material with two peaks within the first week and three or four smaller peaks thereafter. Populations of total nematodes and BFN started to increase in the second week after CG incorporation, but the proportion of BFN increased within 1 week. Inactive juvenile BFN (dauerlarvae) seemed to be activated after 2 days (as the percentage of Rhabditidae increased and dauerlarvae decreased), followed by stepwise increases in dauerlarvae every 4 days, indicating that there was a new generation every 4 days. There were significant wave-like fluctuations in daily population changes of BFN, but not for those of 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 relative to the bacterial fluctuations. Gamma-irradiation of soil significantly increased the periods and amplitudes of bacterial oscillations. Nematode populations were eliminated in gamma-irradiated soils, but small numbers 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. (C) 2003 Elsevier B.V. All rights reserved.
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