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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    We will mail you new results for this query: keywords==Microcosm
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The effects of experimental oil-contaminated marine snow on meiofauna in a microcosm
Rohal, Melissa ; Barrera, Noe ; Eenennaam, Justine S. Van; Foekema, Edwin M. ; Montagna, Paul A. ; Murk, Albertinka J. ; Pryor, Marissa ; Romero, Isabel C. - \ 2020
Marine Pollution Bulletin 150 (2020). - ISSN 0025-326X - p. 110656 - 110656.
Benthic meiofauna - Microcosm - Marine snow - MOSSFA - Oil - Nematode:Copepod ratio
During an oil spill, a marine oil snow sedimentation and flocculent accumulation (MOSSFA) event can transport oil residue to the seafloor. Microcosm experiments were used to test the effects of oil residues on meiofaunal
abundance and the nematode:copepod ratio under different oil concentrations and in the presence and absence of marine snow. Total meiofaunal abundance was 1.7 times higher in the presence of snow regardless of oil concentration. The nematode:copepod ratio was 13.9 times lower in the snow treatment regardless of the oil concentration. Copepod abundance was 24.3 times higher in marine snow treatments and 4.3 times higher at the highest oil concentration. Nematode abundance was 1.7 times lower at the highest oil concentration. The result of the experiment was an enrichment effect. The lack of a toxic response in the experiments may be attributable to relatively low oil concentrations, weathering processes, and the absence of chemically dispersed oil.
Response of sediment bacterial community to triclosan in subtropical freshwater benthic microcosms
Peng, Feng Jiao ; Diepens, Noël J. ; Pan, Chang Gui ; Ying, Guang Guo ; Salvito, Daniel ; Selck, Henriette ; Brink, Paul J. Van den - \ 2019
Environmental Pollution 248 (2019). - ISSN 0269-7491 - p. 676 - 683.
Benthic macroinvertebrates - Microcosm - Sediment bacterial community - Toxicity - Triclosan

The response of sediment bacterial communities in subtropical freshwater benthic microcosms to sediment-associated triclosan (TCS; 28 d exposure) was analysed using Illumina high-throughput sequencing. This study highlights the interactive effects of TCS and the presence of benthic macroinvertebrates (Limnodrilus hoffmeisteri and Viviparidae bellamya) on sediment bacterial communities. Our results show that TCS alone significantly altered the taxonomic composition and decreased alpha diversity of sediment bacterial communities at concentrations ≥80 μg TCS/g dry weight (dw) sediment (sed). Regarding dominant phyla, TCS significantly reduced the relative abundance of Bacteroidetes and Firmicutes at these concentrations, whereas the relative abundance of Chloroflexi and Cyanobacteria increased. In the presence of benthic macroinvertebrates, the sediment bacterial community was affected by 8 μg TCS/g dw sed as well. However, the presence of benthic macroinvertebrates did not cause measurable changes to bacterial community in unspiked (i.e., control) sediment. These results indicate that TCS alone would not alter the sediment bacterial community at environmentally relevant concentrations (up till 8 μg/g dw sed), but may have an effect in combination with the presence of benthic macroinvertebrates. Therefore, we recommend to include benthic macroinvertebrates when assessing the response of sediment bacterial communities during exposure to environmental stress such as organic contaminants.

Insights into the sediment toxicity of personal care products to freshwater oligochaete worms using Fourier transform infrared spectroscopy
Peng, Feng Jiao ; Hu, Li Xin ; Pan, Chang Gui ; Ying, Guang Guo ; Brink, Paul J. van den - \ 2019
Ecotoxicology and Environmental Safety 172 (2019). - ISSN 0147-6513 - p. 296 - 302.
Biochemical fingerprint - Deposit-feeder - FTIR spectroscopy - Microcosm - Musk - Triclosan

Personal care products (PCPs) are ubiquitous in the environment due to their wide use in daily life. However, there are insufficient sediment toxicity data of PCPs under ecologically relevant conditions. Here we used Fourier transform infrared spectroscopy (FTIR) to investigate the sediment toxicity of triclosan (TCS) and galaxolide (HHCB) to two freshwater benthic macroinvertebrates, Limnodrilus hoffmeisteri and Branchiura sowerbyi, in microcosms containing a diverse biological community. Exposure to 8 µg TCS/g and 100 µg HHCB/g dry weight (dw) sediment induced significant biochemical alterations in the L. hoffmeisteri tissue. 8 µg TCS/g primarily affected proteins and nucleic acid while 100 µg HHCB/g mainly affected proteins and lipids of L. hoffmeisteri. However, 0.8 µg TCS/g and 30 µg HHCB/g did not cause significant subcellular toxicity to L. hoffmeisteri. In contrast, exposure of B. sowerbyi to 30 µg HHCB/g led to significant biochemical changes, including proteins, polysaccharides and lipids. Therefore, B. sowerbyi was more sensitive to sediment-associated HHCB than L. hoffmeisteri. Such effects were significantly enhanced when the HHCB concentration increased to 100 µg/g dw where death of B. sowerbyi occurred. These results demonstrate the application of FTIR spectroscopy to sediment toxicity testing of chemicals to benthic invertebrates with biochemical alterations as endpoints that are more sensitive than standard toxic endpoints (e.g., survival and growth).

Legacy effects on the recovery of soil bacterial communities from extreme temperature perturbation
Jurburg, Stephanie D. ; Nunes, Inês ; Brejnrod, Asker ; Jacquiod, Samuel ; Priemé, Anders ; Sørensen, Søren J. ; Elsas, J.D. van; Salles, Joana F. - \ 2017
Frontiers in Microbiology 8 (2017). - ISSN 1664-302X - 13 p.
Disturbance - Microcosm - Resilience - RNA - Secondary succession - Soil bacteria

The type and frequency of disturbances experienced by soil microbiomes is expected to increase given predicted global climate change scenarios and intensified anthropogenic pressures on ecosystems. While the direct effect of multiple disturbances to soil microbes has been explored in terms of function, their effect on the recovery of microbial community composition remains unclear. Here, we used soil microcosm experiments and multiple model disturbances to explore their short-term effect on the recovery of soil microbiota after identical or novel stresses. Soil microcosms were exposed to a heat shock to create an initial effect. Upon initial community recovery (25 days after stress), they were subjected to a second stress, either a heat or a cold shock, and they were monitored for additional 25 days. To carefully verify the bacterial response to the disturbances, we monitored changes in community composition throughout the experiment using 16S rRNA gene transcript amplicon sequencing. The application of a heat shock to soils with or without the initial heat shock resulted in similar successional dynamics, but these dynamics were faster in soils with a prior heat shock. The application of a cold shock had negligible effects on previously undisturbed soils but, in combination with an initial heat shock, caused the largest shift in the community composition. Our findings show that compounded perturbation affects bacterial community recovery by altering community structure and thus, the community's response during succession. By altering dominance patterns, disturbance legacy affects the microbiome's ability to recover from further perturbation within the 25 days studied. Our results highlight the need to consider the soil's disturbance history in the development of soil management practices in order to maintain the system's resilience.

Metagenomic analysis of the complex microbial consortium associated with cultures of the oil-rich alga Botryococcus braunii
Sambles, Christine ; Moore, Karen ; Lux, Thomas M. ; Jones, Katy ; Littlejohn, George R. ; Gouveia, João D. ; Aves, Stephen J. ; Studholme, David J. ; Lee, Rob ; Love, John - \ 2017
MicrobiologyOpen 6 (2017)4. - ISSN 2045-8827
Botryococcus braunii - Biofuel - Consortium - Metagenomics - Microcosm
Microalgae are widely viewed as a promising and sustainable source of renewable chemicals and biofuels. Botryococcus braunii synthesizes and secretes significant amounts of long-chain (C30-C40) hydrocarbons that can be subsequently converted into gasoline, diesel, and aviation fuel. B. braunii cultures are not axenic and the effects of co-cultured microorganisms on B. braunii growth and hydrocarbon yield are important, but sometimes contradictory. To understand the composition of the B. braunii microbial consortium, we used high throughput Illumina sequencing of metagenomic DNA to profile the microbiota within a well established, stable B. braunii culture and characterized the demographic changes in the microcosm following modification to the culture conditions. DNA sequences attributed to B. braunii were present in equal quantities in all treatments, whereas sequences assigned to the associated microbial community were dramatically altered. Bacterial species least affected by treatments, and more robustly associated with the algal cells, included members of Rhizobiales, comprising Bradyrhizobium and Methylobacterium, and representatives of Dyadobacter, Achromobacter and Asticcacaulis. The presence of bacterial species identified by metagenomics was confirmed by additional 16S rDNA analysis of bacterial isolates. Our study demonstrates the advantages of high throughput sequencing and robust metagenomic analyses to define microcosms and further our understanding of microbial ecology.
The effects of zinc on the structure and functioning of a freshwater community : A microcosm experiment
Perre, Dimitri Van de; Roessink, Ivo ; Janssen, Colin R. ; Smolders, Erik ; Regenmortel, Tina van; Wichelen, Jeroen Van; Vyverman, Wim ; Brink, Paul J. van den; Schamphelaere, Karel A.C. De - \ 2016
Environmental Toxicology and Chemistry 35 (2016)11. - ISSN 0730-7268 - p. 2698 - 2712.
Biotic ligand model - Community-level effect - Microcosm - Plankton - Zinc

A major problem with risk assessment of chemicals is the extrapolation of laboratory single-species toxicity tests, which oversimplify the actual field situation by ignoring species interactions, to natural communities. The authors tested if the bioavailability-normalized 5% hazardous concentration (HC5) estimated from chronic planktonic single-species toxicity data (HC5plankton) for zinc (Zn) is protective for a plankton community and investigated the direct and indirect effects of Zn (at HC5 and HC50) on a freshwater community's structure and function. Microcosms were exposed to 3 different Zn concentrations (background, HC5plankton=75μgZn/L and HC50plankton=300μgZn/L) for 5wk. The planktonic groups revealed a consistent no-observed-effect concentration for the community of 75μgZn/L, similar to or higher than the HC5plankton, thus suggesting its protectiveness in the present study. At 300μgZn/L a significant reduction in cladocerans resulted in increases of rotifer, ciliate, and phytoplankton abundance. In addition, the phytoplankton community shifted in dominance from grazing-resistant to edible species. Contrary to the species sensitivity distribution (SSD) prediction, which identified phytoplankton as the most sensitive group, only the total chlorophyll and the abundance of 2 phytoplankton species were adversely affected at 300μgZn/L. Thus, although the HC5 estimated from the bioavailability-normalized SSD was overall protective for the plankton community, the SSD was not able to correctly predict the species sensitivity ranking within their community context at the HC50.

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