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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    Genetic engineering at the heart of agroecology
    Lotz, Lambertus A.P. ; Wiel, Clemens C.M. van de; Smulders, Marinus J.M. - \ 2020
    Outlook on Agriculture 49 (2020)1. - ISSN 0030-7270 - p. 21 - 28.
    Agroecosystems - CRISPR/Cas - ecology - gene editing - genetic modification - IPM

    We discuss whether genetic engineering and agroecology are compatible. For this, we investigated three cases of genetically engineered crops and considered agroecology as scientific discipline as well as a social movement. One case was the use of cisgenic modifications to make potato durably resistant to late blight, the second was the use of CRISPR/Cas to make rice resistant to bacterial blight and as a third case, we evaluated experiences with cultivating transgenic Bt crops. These cases demonstrated that genetic engineering offers opportunities to grow crops in novel integrated pest management (IPM) systems with, as direct benefit, a decrease in the use of chemical crop protection agents, and as indirect effect that the role of predators and biological control agents can become more important than in present conventional systems based on pesticides. We used a framework based on four concerns (both cons and pros) that were gathered from an extensive societal interaction organized around the Dutch research project DuRPh, which produced a proof-of-concept of a cisgenic late blight-resistant potato. We concluded that genetic engineering and agroecology certainly have synergy in the context of agroecology as science, when applied to making crops less vulnerable to pests and diseases and when combined with cultivation using IPM. By contrast, within the movement context, genetically engineered varieties may be welcomed if they include traits that contribute to successful IPM schemes and are socially benign. Whether they would actually be deemed desirable or acceptable will, however, vary depending on the norms and values of the social movements. We propose that some concerns may be reconcilable in a dialogue. Deontological arguments such as naturalness are more difficult to reconcile, as they relate to deeply felt ethical or cultural values. A step forward would be when also for these arguments everyone can make an informed choice and when these choices can coexist in a respectful manner.

    Sediment Disposals in Estuarine Channels Alter the Eco-Morphology of Intertidal Flats
    Vet, P.L.M. de; Prooijen, B.C. van; Colosimo, I. ; Ysebaert, T. ; Herman, P.M.J. ; Wang, Z.B. - \ 2020
    Journal of Geophysical Research: Earth Surface 125 (2020)2. - ISSN 2169-9003
    ecology - estuaries - intertidal flats - morphology - sediment disposals - sediment management

    Dredging of navigation channels in estuaries affects estuarine morphology and ecosystems. In the Western Scheldt, a two-channel estuary in the Netherlands, the navigation channel is deepened and the sediment is relocated to other parts of the estuary. We analyzed the response of an intertidal flat to sediment disposals in its adjacent channel. Decades of high-frequency monitoring data from the intertidal flat show a shift from erosion toward accretion and reveal a sequence of cascading eco-morphological consequences. We document significant morphological changes not only at the disposal sites, but also at the nearby intertidal flats. Disposals influence channel bank migration, driving changes in the evolution of the intertidal flat hydrodynamics, morphology, and grain sizes. The analyzed disposals related to an expansion of the channel bank, an increase in bed level of the intertidal flat, a decrease in flow velocities on this higher elevated flat, and locally a decrease in grain sizes. These changes in turn affect intertidal flat benthic communities (increased in quantity in this case) and the evolution of the adjacent salt marsh (retreated less or even expanded in this case). The shifts in evolution may occur years after dredged disposal begins, especially in zones of the flats farther away from the disposal locations. The consequences of sediment disposals that we identify stress the urgency of managing such interventions with integrated strategies on a system scale.

    Entomophagy: Nutritional, ecological, safety and legislation aspects
    Raheem, Dele ; Raposo, António ; Oluwole, Oluwatoyin Bolanle ; Nieuwland, Maaike ; Saraiva, Ariana ; Carrascosa, Conrado - \ 2019
    Food Research International 126 (2019). - ISSN 0963-9969
    ecology - edible insects - food legislation - food safety - food security - nutrition - sustainability

    Globally, there is a need to seek alternative sources of protein in addition to meat. This has led to considerable interest in edible insects. Such insects form part of cultures and diets in many Asian and African countries, and are an excellent source of essential nutrients, minerals, vitamins and proteins. Furthermore, they have been reported to be sustainable. The ecological importance of insects is related to their short life cycles when reared and farmed. This makes them ideal in mitigating greenhouse gas emissions, cutting land uses and polluted water, and reducing environmental contamination. However, the use of edible insects as food in Europe is minimal. To ensure safety of insects when eaten as food, considerations should be made on: microbiological contamination; toxicological hazards, e.g. chemical hazards and antinutrients; allergenicity issues that are related to different exposures, including injection, ingestion, inhalation and skin contact. In this review, we summarize the nutritional and sustainable values of edible insects, look at safety and legislative measures and we finally discuss future issues.

    Hydrographic and Biological Survey of a Surface-Intensified Anticyclonic Eddy in the Caribbean Sea
    Boog, C.G. van der; Jong, M.F. de; Scheidat, M. ; Leopold, M.F. ; Geelhoed, S.C.V. ; Schulz, K. ; Dijkstra, H.A. ; Pietrzak, J.D. ; Katsman, C.A. - \ 2019
    Journal of Geophysical Research: Oceans 124 (2019)8. - ISSN 2169-9275 - p. 6235 - 6251.
    anticyclone - barrier layer - Caribbean Sea - ecology - hydrographic - thermohaline staircases

    In the Caribbean Sea, mesoscale anticyclonic ocean eddies impact the local ecosystem by mixing of low salinity river outflow with the nutrient-rich waters upwelling along the Venezuelan and Colombian coast. To gain insight into the physics and the ecological impact of these anticyclones, we performed a combined hydrographic and biological survey of one Caribbean anticyclone in February 2018. We found that the anticyclone had a radius of 90 km and was surface intensified with the strongest velocities (0.72 m/s) in the upper 150 m of the water column. Below, isopycnal displacements were found down to 700 dbar. The core of the anticyclone entrained waters from the Orinoco River plume and contained slightly elevated chlorophyll concentrations compared to the surroundings. At the edge of the anticyclone we observed higher densities of flying fish but not higher densities of predators like seabirds and cetaceans. Below the surface, a strong temperature inversion (0.98 °C) was present within a barrier layer. In addition, we found thermohaline staircases that originated from double diffusion processes within Tropical Atlantic Central Water.

    Dutch forest reserves database and network
    Bijlsma, R.J. ; Clerkx, A.P.P.M. - \ 2019
    forest reserve - monitoring - database - nin-intervention dynamics - ecology
    The Dutch forest reserves network encompasses about 60 forest reserves representing all major forest types in the Netherlands. The reserves were designated between 1983 and 2000. The present Access-database presents all measurements (mostly between 1982 and 2005) on trees and regeneration in circular sample plots throughout the reserves and in a one ha rectangular core area in each reserve. The data set also includes map data at the reserve level (such as reserve boundaries, samples plots and core areas) and of GIS files derived from tree measurements in the core area.
    Dataset: BioTIME: A database of biodiversity time series for the Anthropocene
    Dornelas, M. ; Antão, L.H. ; Moyes, F. ; Bates, A.E. ; Magurran, Anne E. ; Adam, D. ; Akhmetzhanova, A.A. ; Appeltans, W. ; Arcos, J.M. ; Arnold, H. ; Prins, Herbert - \ 2018
    University of St Andrews
    time series - ecology - biodiversity - Anthropocene - spatial and temporal analysis
    The BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. The database consists of 11 tables; one raw data table plus ten related meta data tables. For further information please see our associated data paper. This data consists of several elements: BioTIMESQL_02_04_2018.sql - an SQL file for the full public version of BioTIME which can be imported into any mySQL database. BioTIMEQuery_02_04_2018.csv - data file, although too large to view in Excel, this can be read into several software applications such as R or various database packages. BioTIMEMetadata_02_04_2018.csv - file containing the meta data for all studies. BioTIMECitations_02_04_2018.csv - file containing the citation list for all studies. BioTIMECitations_02_04_2018.xlsx - file containing the citation list for all studies (some special characters are not supported in the csv format). BioTIMEInteractions_02_04_2018.Rmd - an r markdown page providing a brief overview of how to interact with the database and associated .csv files (this will not work until field paths and database connections have been added/updated).
    TEEB & i-Tree models : Input for Aeres minor Growing Green Cities
    Hiemstra, J.A. ; Kuik, A.J. van - \ 2018
    Wageningen : Wageningen University & Research - 40 p.
    urban areas - trees - ecology - biodiversity - air quality - water storage - ecosystems - health - urban planning
    Soil or seed: which came first?
    Deyn, G.B. de - \ 2017
    Wageningen : WURcast
    ecology - plants
    Gerlinde De Deyn: Plants are amazingly diverse in the functions they provide. But how do plants get growing in the first place? In this talk, I will reveal the hidden half of plants and how the tiny organisms, that connect the world of the living and of the dead, rule the world.
    Counts of bovine monocyte subsets prior to calving are predictive for postpartum occurrence of mastitis and metritis
    Pomeroy, Brianna ; Sipka, Anja ; Hussen, Jamal ; Eger, Melanie ; Schukken, Ynte - \ 2017
    Cornell University
    medicine - cell biology - genetics - ecology - immunology - mathematical sciences - developmental biology - infectious diseases - computational biology
    The heightened susceptibility to infectious diseases in postpartum dairy cows is often attributed to immune dysfunction associated with the transition period. However, the cell populations involved in this immune dysfunction and the dynamics between those populations are not well defined. Monocytes play a crucial role in governing initial immune response in bacterial infections. Bovine monocytes are subdivided in classical (CD14+/CD16−), intermediate (CD14+/CD16+) and non-classical monocytes (CD14−/CD16+) with distinct phenotypic and functional differences. This study investigated the relationship of monocyte subsets counts in blood at 42 and 14 days prior to expected calving date to occurrence of metritis and mastitis within 2 weeks postpartum. In the enrolled prospective cohort of 27 German Holstein cows, housed at the Institute of Animal Nutrition of the Friedrich-Loeffler-Institute Braunschweig, Germany, n = 13 developed metritis and/or mastitis postpartum. A multivariable logistic regression was used to analyze the relationship between prepartum cell counts of monocyte subsets and neutrophils with postpartum disease. Our model revealed that higher counts of the two CD14+ monocyte subsets were predictive of disease. In contrast, higher numbers of the CD14− monocyte subset were negatively associated with disease. Interestingly, the neutrophil count, a common hallmark for inflammatory response, was not associated with the outcome variable at either time point. The results indicate that the number and composition of monocyte subsets before calving are related to the susceptibility to infectious disease within 2 weeks postpartum. Furthermore the oppositional effect of CD14+ and CD14− subsets strengthens the hypothesis that these subsets have different functional roles in the inflammatory response in dairy cows.
    Dunes, above and beyond : The interactions between ecological and geomorphological processes during early dune development
    Puijenbroek, Marinka E.B. - \ 2017
    Wageningen University. Promotor(en): F. Berendse, co-promotor(en): J. Limpens. - Wageningen : Wageningen University - ISBN 9789463432146 - 183
    dunes - geomorphology - ecology - vegetation - duneland plants - beaches - duinen - geomorfologie - ecologie - vegetatie - duinplanten - stranden

    Coastal dunes occur along the sandy shores of most continents where they serve as coastal defence against flooding, provide areas for recreation, store drinking water and harbour unique biodiversity. Coastal dunes and the services they provide are threatened by climate-induced sea-level rise. This threat may be mitigated by the spontaneous formation of new dunes, for example in combination with mega-nourishments aimed at increasing beach width. Coastal dunes form by the interaction between vegetation, wind and wave action. Persistent dune development begins with the establishment of vegetation on the beach: the vegetation traps the wind-blown sand, forming an embryo dune. Over time an embryo dune can develop into a bigger foredune, increasing coastal safety. The formation and development of embryo dunes into foredunes depend on the vegetation establishment on the beach, dune growth over summer and dune erosion during winter. Although vegetation succession and geomorphological processes are each well described, the interaction between ecological and geomorphological processes during embryo dune development are not well known. The thesis aimed at further exploring these interactions, using a combination of experiments and high-resolution dune monitoring to study the mechanisms underlying early dune development and their implications for mega-nourishment design.

    To explore whether soil salinity, salt spray or storms determine the vegetation limit of dune building plant species on the beach, we performed a field transplantation experiment and a glasshouse experiment with two dune building grasses Ammophila arenaria and Elytrigia juncea. In the field growth of grasses transplanted into four vegetation zones from sea to dune was monitored for over a year and the response of these species to salt spray and soil salinity was tested in a glasshouse experiment. In the field, the vegetation zones were associated with differences in summer soil salinity: zones with both species present were significantly less saline than zones with only E. juncea or the zones without any vegetation. However, in our experiments the transplanted A. arenaria performed equal or better than E. juncea in all vegetation zones, suggesting soil salinity did not limit species performance at the studied site. Both species showed severe winter mortality. In the glasshouse experiment, A. arenaria biomass decreased linearly with soil salinity, presumably as a result of osmotic stress. Elytrigia juncea showed a nonlinear response to soil salinity with an optimum at 0.75% soil salinity and a decrease in biomass at higher salt concentrations. Our findings suggest that soil salinity stress either takes place in winter during storm inundation, or that development of vegetated dunes is less sensitive to soil salinity than hitherto expected.

    To understand the boundary conditions for embryo dune development over a longer time period we explored the effects of beach morphology, meteorological conditions and sand nourishment on early dune development using a 30 year time series of aerial photographs and beach profile monitoring data. We concluded that 1) beach morphology is highly influential in determining the potential for new dune development, with wide beaches enabling development of larger embryo dune fields, 2) sand nourishments stimulate early dune development by increasing beach width, and 3) weather conditions and non-interrupted sequences of years without high-intensity storms determine whether progressive dune development will take place.

    Dune development is the result of the interaction between vegetation development and sedimentation and erosion processes. To disentangle the effects of vegetation characteristics and that of dune size we monitored a natural dune field of 8 hectares for one year using an Unmanned Aerial Vehicle (UAV) with a camera. By constructing a digital surface model and a geometrical corrected image (an orthomosaic) for each flight campaign we calculated changes in dune volume over summer and winter and related these changes to vegetation, dune size and degree of shelter. The dune growth over summer was mainly determined by dune size, whereas dune growth over winter was determined by vegetation characteristics. Degree of shelter determined whether dune growth was limited by storm erosion (exposed dunes) or sand supply (sheltered dunes). These results suggest that vegetation characteristic may be particularly important for resisting storm erosion and speeding up recovery after erosion.

    Embryo dunes have been hypothesised to facilitate development of species rich green beach vegetation in the sheltered location between the embryo dunes and the primary foredunes. To test this hypothesis we explored the relative impacts of abiotic soil conditions as affected by the geomorphological setting on the species richness and species turn-over of green beach vegetation. To this end we characterised the geomorphology and measured abiotic conditions and species composition of green beach vegetation along transects from beach to foredune. We found that the geomorphological setting influenced plant species composition indirectly by affecting soil salinity and rate of sand burial. We found that plant species richness declined less at sheltered conditions, where there was a build-up of organic matter and no sand burial. Our results further suggest a non-linear relationship between embryo dune volume and number of green beach species: embryo dunes can be a source of shelter, thus stimulating green beach development, but can also compete for space, reducing green beach development. The net effect of embryo dunes most likely depends on the sediment budget of the beach and storm intensity.

    Mega-nourishments are single large sand nourishments that are applied locally, and are expected to exist for about 20 years, providing opportunities for the development of embryo dunes and rare pioneer plant communities (green beach vegetation). We explored this potential by comparing growth and development of dune building species on natural beaches with the results of plant transplantation and monitoring data of two mega-nourishments: the low-elevated Hondsbossche Duinen and the high-elevated Sandmotor. Our results suggest that establishment of dune building species on high-elevated mega-nourishment proceed slower than on natural beaches due to dispersal limitation. Once vegetation has established however, embryo dune development on high-elevated mega-nourishments may proceed faster than natural beaches due to low salinity and protection against storm erosion. Development of dune-building vegetation on the low-elevated mega-nourishment Hondsbossche Duinen showed the same rate and pattern as that on a natural beach. The potential for embryo dune development on mega-nourishments is far bigger than the potential for green beach development, since green beach vegetation develops under a narrower range of abiotic conditions. Such abiotic conditions can develop behind the shelter of embryo dunes or foredunes at low beach elevations.

    In conclusion this thesis shows that, 1) the potential of embryo dune development depends on a large beach width and low storm erosion which determines the vegetation limit. 2) Embryo dune growth over summer is mainly determined by existing dune volume and sand supply. 3) Heavy storms limit embryo dune development during winter, although dune erosion can be mitigated by vegetation composition. 4) On accreting beaches which continuously provide area for the development of new embryo dunes green beach vegetation can develop. 5) The design of a mega-nourishment determines the potential for the development of embryo dunes and green beach vegetation. Our findings provide insights in the interaction between ecological and geomorphological processes that determine embryo dune development. This knowledge can help to obtain better predictions of embryo dune development under the threat of sea-level rise.

    A clash of plants : Vegetation succession and its interaction with permafrost dynamics in the Arctic lowland tundra
    Li, Bingxi - \ 2017
    Wageningen University. Promotor(en): F. Berendse, co-promotor(en): M.M.P.D. Heijmans. - Wageningen : Wageningen University - ISBN 9789463436168 - 100
    ecological succession - ecology - plant succession - vegetation - tundra - permafrost - lowland areas - arctic regions - siberia - ecologische successie - ecologie - plantensuccessie - vegetatie - toendra - permafrost - laaglandgebieden - arctische gebieden - siberië

    Arctic ecosystems have been affected by severe climate change during the last decades. The increase in temperature in the Arctic has been almost double of the global rate of warming since the beginning of the 20th century. Like other ecosystems in the high latitude region, Arctic tundra appears to be extremely sensitive to the continuous warming of the past decades, which has led to dramatic vegetation changes such as rapid shrub expansion. While researchers are keen to talk about the shrubification of the Arctic tundra, there has been rather little attention for alternative vegetation shifts, such as those related to local permafrost collapse in lowland tundra. The general vegetation succession route of the ice-rich lowland tundra ecosystem is yet largely unknown. Therefore, we choose a typical Arctic lowland site (Kytalyk natural reserve) in the Northeastern Siberia to explore how vegetation is changing in this ecosystem, and how changes in the abiotic environment and vegetation succession interact.

    On the basis of field observations I assumed that the plant species composition of each vegetation patch at the study site changes continuously following cycles over time. To test this assumption, two multiple-year field experiments (Chapter 2 and Chapter 3) were carried out. In addition, we applied dendrochronological techniques (Chapter 4 and Chapter 5) and molecular tools (Chapter 4). On the basis of the results of these studies, I depicted a complete vegetation succession loop in the Arctic lowland tundra, which is closely related to the dynamics of the permafrost. In this vegetation succession loop, four stages with distinctive vegetation types have been identified.

    The Betula nana L. shrubs mainly dominate the well-drained elevated areas. In a field experiment, removal of B. nana shrubs resulted in abrupt permafrost degradation, rapid soil moisture increase and invasion of the grass species Arctagrostis latifolia (R. Br.) Griseb. After a short time period, when small ponds or drainages had developed, this fast-responding grass species is replaced by Eriophorum sedges. In the subsequent stage the Sphagnum mosses invade the sedge vegetation. The new Sphagnum moss carpets not only suppress the growth of Eriophorum sedges, but also create moist but unsaturated substrates that appear to be appropriate for the germination of B. nana seeds. These conditions provide new opportunities for B. nana shrubs to establish.

    The reproduction mode of B. nana at the study site has been studied using molecular tools (micro- satellites), as it may explain how existing B. nana patches developed and how shrub vegetation may expand in the future (Chapter 4). The conventional point of view is that sexual reproduction of perennial plants in the Arctic tundra, like B. nana, is rare due to the pressure of the harsh environment. However, the results of our molecular study (Chapter 4) tell a different story. While vegetative reproduction of B. nana is common, sexual reproduction of B. nana is more prevalent. Seed dispersal of B. nana between different patches at the study site is not hampered by the short between-patch distances, but vegetative reproduction of B. nana appeared to be restricted to 1-2 m distances from the parent plants.

    The influences of the climate on B. nana shrubs were further investigated using the dendrochronological analyses (Chapter 4 and Chapter 5). The radial growth of B. nana is positively correlated with early summer temperature, while relatively high summer precipitation during the warm years also stimulates the growth of B. nana. Moreover, sufficient summer precipitation facilitates the establishment of B. nana seedlings. Since sexual reproduction is prevalent at the site, it is suggested that the present B. nana shrubs established simultaneously, during periods with suitable climate conditions.

    Along with the vegetation succession cycles, permafrost underlying the vegetation experiences clear degradation-recovery cycles. We detected a close interaction between vegetation shifts and permafrost dynamics. While abrupt permafrost degradation drove a quick vegetation shift from the B. nana dominated stage to the water-logged Eriophorum sedge dominate stage, the changes of vegetation cover affect the stability of the permafrost as well. The removal of B. nana shrub cover triggered rapid permafrost degradation (Chapter 2), while the development of Sphagnum moss carpets, which have a high isolation capacity, reduced permafrost temperature, facilitating permafrost recovery (Chapter 3).

    Vegetation composition in the Arctic tundra not only influences permafrost stability, but also affects the methane emission of the site. Eriophorum sedges are able to transport methane from deep soil to the air via their aerenchyma tissues, leading to high methane fluxes. In contrast, the Sphagnum mosses significantly suppress the methane emission, since endophytic CH4-oxidizing bacteria are widespread inside the aerobic unsaturated Sphagnum carpets (Chapter 3).

    To sum up, our findings provide crucial information to better understand changes in the Arctic tundra ecosystem, helping to obtain better predictions of future vegetation shifts and the associated consequences for greenhouse gas emissions, permafrost stability and the heat balance of the Earth surface.

    Feiten en cijfers vergroening GLB
    Doorn, Anne van; Smidt, Rob - \ 2017
    Wageningen : Wageningen Environmental Research (Wageningen Environmental Research rapport 2795) - 19
    landbouwbeleid - monitoring - ecologie - europa - agricultural policy - monitoring - ecology - europe
    The greening of the European common agricultural policy has started in 2015. This report
    present facts and figures about two years of greening.
    Seven Steps in Identifying Local Climate Change Responses for Agriculture in Vietnam
    Bosma, R.H. ; Ngo, An T. ; Huynh, Chuong V. ; Le, Huong T. ; Dang, Nhan K. ; Van, Tri P.D. ; Halsema, G.E. van - \ 2016
    Tropicultura 34 (2016)special. - ISSN 0771-3312 - p. 31 - 49.
    Climate change - autonomous - adaption - water management - ecology - Vietnam
    This study presents a seven-step approach to identify and support local climate change (CC) responses in agriculture. The following seven steps comprise this approach: 1. Analyse past trends on the climatic factors and model the future trends. 2. Simulate the possible impacts of CC on the selected system(s) or product(s). 3. Present and discuss the predicted impacts with the local stakeholders. 4. Identify and rank CC responses together with the local stakeholders. 5. Elaborate plans to develop and test the highest ranked response(s). 6. Evaluate the results of the tests and recommend implementation or changes. 7. Report the results to the involved authorities and suggest ways to implement the responses and/or advise new tests if the first ones were not able to sufficiently deal with the impacts. Six pilot studies in Vietnam were funded through two projects led by Wageningen University & Research. The first addressed several production systems in one southern province, and the second in three more northern districts, each with different problems. This paper reflects and communicates the seven-step approach in order to make local CC responses accessible to the larger rural development communities. Most of the identified solutions can spread autonomously, while others will require specific planned interventions.
    Voortgang realisatie nationaal natuurbeleid : technische achtergronden van een aantal indicatoren uit de digitale Balans van de Leefomgeving 2016
    Sanders, M.E. ; Wamelink, G.W.W. ; Wegman, R.M.A. ; Clement, J. - \ 2016
    Wageningen : Wettelijke Onderzoekstaken Natuur & Milieu (WOt-technical report 79) - 74
    ecologische hoofdstructuur - ecologie - ecosystemen - verdroging (milieu) - verzuring - depositie - natuurbeleid - ecological network - ecology - ecosystems - groundwater depletion - acidification - deposition - nature conservation policy
    The Dutch government is, together with its partners, taking measures to create a coherent network ofprotected nature areas and to improve environmental conditions. This in order to halt the decline in the areaof natural habitat and biodiversity and to improve their conservation status. The Government wants to stayinformed on the progress of this policy. The Netherlands Environmental Assessment Agency (PBL) has selectedindicators that should provide answers to the question: ‘What is the progress of the policy measures taken,especially for realising the nature network, improving the nature quality and the environmental conditions aswell?’ The selected indicators have been updated and analysed in order to assess this progress. This reportdescribes the results of the policy measures taken on the basis of the indicators, the technical setting of thedata and methods used to bring these indicators up to date and the reliability and acceptability of it
    The ecology of ditches : a modeling perspective
    Gerven, Luuk P.A. - \ 2016
    Wageningen University. Promotor(en): W.M. Mooij, co-promotor(en): Jeroen de Klein; J.H. Janse. - Wageningen : Wageningen University - ISBN 9789462579316 - 137
    ditches - aquatic ecology - ecology - modeling - aquatic plants - aquatic ecosystems - water flow - sloten - aquatische ecologie - ecologie - modelleren - waterplanten - aquatische ecosystemen - waterstroming

    The Netherlands is well-known for its extended networks of drainage ditches, with a total ditch length of about 300.000 km. Their main function is to enable agriculture by draining water. Nonetheless, ditches also have important ecological functions. They serve as ecological corridors and harbor a high biodiversity in which water plants play a crucial role. The last decades, the ecological quality of ditches is at stake. Enhanced nutrient inputs promoted the invasion by dense mats of free-floating plants like duckweed. Underneath these mats the water becomes dark and anoxic, which severely constrains aquatic life.

    In this thesis I developed new concepts to better understand, predict and combat the dominance by free-floating plants in ditches. The following questions are addressed. Are floating plants a self-stabilizing state - an alternative stable state - which would make it more difficult to combat floating-plant dominance (chapter 2)? Does it make sense to fight floating-plant dominance by reducing nitrogen (N) inputs to the ditches or will it lead to an invasion of floating plants that can fix N2 from the atmosphere (chapter 3)? What about spatial aspects, does the vulnerability of a ditch to floating plants depend on the position of a ditch in a polder, like its distance to the polder outlet (chapter 4)? To answer these questions, I used ecological models that predict the abundance of free-floating plants based on the competition for nutrients and light with other plants such as submerged plants, and where possible validated these models with field data. Starting from the ecosystem model PCDitch, I developed and combined models with different complexity to see how theoretical concepts, developed in minimal models, translate to the ecosystem level. Chapter 5 deals with a method that facilitates this up- and downscaling in model complexity.

    Are floating plants an alternative stable state? To answer this question I extended mechanistic resource competition theory with a framework (minimal model) describing the competition of floating and submerged plants for light and nutrients. The model predicts that the competitive advantage of floating plants - they have a primacy for light and shade submerged plants, giving rise to asymmetry in competition for light - makes that floating plants always dominate at high supply of light and nutrients. At intermediate nutrient supply, there can be alternative stable states: either the submerged plants or the floating plants dominate depending on who established first. However, based on the traits of common floating plants (duckweed; Lemna) and submerged plants (waterweed; Elodea) the model predicts, in line with field data, that floating plants are not an alternative stable state. Furthermore, from a theoretical point of view this study shows that the asymmetry in light competition ensures that common rules from standard competition theory do not apply anymore. Like the R* rule, which states that the species that can persist at the lowest resource levels always wins the competition.

    Can duckweed-dominance be combatted by reducing N inputs to the ditches? Or does this promote other floating plants like water fern (Azolla) that can fix N2 from the atmosphere? Important is the question whether such N2-fixers can provide enough N to prevent N-limitation and keep the system P-limited, which would make steering on N inputs ineffective. To investigate this, I considered the competition between Lemna and Azolla for N, P and light. Both a minimal model, an ecosystem model (PCDitch) and field data reveal that N2-fixation is unlikely to lead to P-limitation. This can be explained by N2-fixers typically requiring higher P concentrations to persist, implying that they cannot keep the P concentration low enough for non-N2-fixers to become P-limited. In combination with field data that hint at constraints on N2-fixation that prevent N2-fixers from becoming abundant at low N availability, this suggests that it certainly pays off to combat floating plant-dominance by reducing N inputs.

    Is every ditch in a polder equally vulnerable to floating plants? Each ditch in a polder receives water and nutrients from the adjacent land. This leads to a spatial gradient in water flow and associated nutrient loading, from low in the remote polder sites to high in the direction of the polder outlet where the water leaves the polder. I explored if this spatial gradient affects the vulnerability of a ditch to floating plants, by investigating with a simple nutrient model how this gradient affects the nutrient concentration of the ditches and by subsequently predicting the gradient's effect on the ditch ecology by applying the ecosystem model PCDitch spatially, through coupling PCDitch to the 1-D hydrodynamic model SOBEK. Surprisingly, we found that every ditch is equally vulnerable to floating plants, despite the spatial gradient in water flow and nutrient loading. It turned out that the ecological state of each ditch could already be predicted by regarding only the lateral supply of water and nutrients from the adjacent land, and not the supply from upstream ditches. However, these findings are violated when there is spatial heterogeneity in the water and nutrient supply from the adjacent land or in ditch characteristics like depth and sediment type. Then, the chance on floating-plant dominance differs throughout the network and a spatial modelling approach (PCDitch-SOBEK) is required to predict this chance.

    Developing and combining models of different complexity plays an important role in this thesis. To do so, I used a Database Approach To Modelling (DATM), a recently developed method in which a model is stored in tables in a clear and clean way, which facilitates model development. In addition, with DATM a model can be automatically implemented in a modelling environment of choice. This relieves technical implementation issues and leaves room to focus on ecology rather than technology. I illustrated the use of DATM by implementing and analyzing the ecosystem model PCDitch and its twin model for shallow lakes PCLake in different modelling environments by using DATM. This showed that DATM allows one to use the environment one is familiar with and eases the switch to other environments for complementary analyses, including analysis in a spatial 1-D to 3-D setting.

    The insights provided by this thesis can help us to improve the ecological quality of ditches. A challenging task, given the fast human-driven environmental changes at both local and global level. To predict and to anticipate the effect of these changes on the ecology, it is essential to understand how the ditch ecosystem functions. The developed and applied methods described in this thesis may be helpful in that. For example, using models of different complexity makes it possible to translate fundamental theory to the ecosystem scale, which is essential to better grasp the behavior of an ecosystem. Furthermore, the in this thesis established coupling between PCDitch and SOBEK breaks new grounds for spatial ecosystem modelling. In combination with the growing amount of remote sensing data from satellites and drones, which allow for the continuous and potentially real-time validation and calibration of spatial ecosystem models, such a spatial approach has the potential to greatly increase our ecological understanding of ditches. These advances facilitate the development of successful management strategies that make our ditch ecosystems future-proof.

    Making eco logic and models work : an integrative approach to lake ecosystem modelling
    Kuiper, Jan Jurjen - \ 2016
    Wageningen University. Promotor(en): W.M. Mooij, co-promotor(en): J.H. Janse; Jeroen de Klein. - Wageningen : Wageningen University - ISBN 9789462579446 - 192
    ecology - models - ecosystems - modeling - aquatic ecology - water management - water quality - databases - ecologie - modellen - ecosystemen - modelleren - aquatische ecologie - waterbeheer - waterkwaliteit - databanken

    Dynamical ecosystem models are important tools that can help ecologists understand complex systems, and turn understanding into predictions of how these systems respond to external changes. This thesis revolves around PCLake, an integrated ecosystem model of shallow lakes that is used by both scientists and water quality managers to understand and predict eutrophication effects in shallow lake ecosystems. Shallow lakes provide some of the clearest examples of alternative stable states in natural systems. PCLake can be used to calculate the critical nutrient loading, that is, the nutrient loading where an abrupt regime shift occurs from a clear aquatic plant dominated state to a turbid phytoplankton dominated state, or vice versa. Four different aspects of modelling with PCLake are addressed in this thesis: (1) making the model better accessible for the modelling community, (2) improving the model, (3) developing scientific theory, and (4) exploring new applications for water quality management.

    Following a general introduction to the thesis in chapter 1, the Database Approach To Modelling (DATM) is introduced in chapter 2. DATM is invented to make dynamic models more accessible. The idea of DATM is that the mathematical equations of a model are stored in a database independently of program language and software specific information. From the database, the information can be automatically translated, augmented and compiled into working model code of various different modelling frameworks (software programs).

    In chapter 3 the weak link between ecosystem models and real ecosystems is discussed in relation to model calibration and improvement. In a previous stage PCLake has been calibrated using data of more than 40 lakes to obtain a best overall fit, which has greatly increased the scope of the model by making it suitable for more generalized studies on temperate shallow lakes. However, because of this calibration, adding missing functional components to the model at a later stage does not automatically increase the validity of the model, as it may bring the model ‘out of balance’. This is exemplified by adding filter feeding zoobenthos to PCLake, which were previously ignored.

    In chapter 4, the relation between food-web theory and alternative stable states theory is scrutinized. Both theoretical paradigms are highly influential in modern ecology as they help scientists understand how stability emerges in complex natural ecosystems. Unfortunately, they developed independently and it is largely unclear how the resilience of a food web relates to the stability of the complete ecosystem. For this study PCLake was used as a virtual reality from which ‘empirical’ information is sampled to parameterize a food web model, following traditional food web methods. This allowed calculating the stability of the food web along a gradient of environmental change, knowing that the complete ecosystem shows a regime shift once the critical nutrient loading is exceeded.

    In chapter 5 the question is asked to what extent models of a different form can be used to describe the same natural phenomenon, and hence, how these models can be used for a better understanding of such natural phenomena. Using three classical extensions of the famous Lotka-Volterra equations, which unlike PCLake can be fully mathematically understood, we analyze the consequence of changing a system with a sophisticated functional response term (e.g. Holling type II or III) into a system with a simpler functional response term while maintaining equilibrium densities and material fluxes. These results give new insight into when empirical data can be linked to mathematical models to estimate the stability properties of real ecosystems.

    Although PCLake is predominantly applied in the context of ecosystem restoration of turbid phytoplankton dominated lakes, chapter 6 focusses on the clear water state after the reestablishment of aquatic plant dominance as occured. Dense stands of aquatic plants easily cause nuisance, and hence the removal of aquatic plants is an emerging management issue. Yet, because aquatic plants play an important role in stabilizing the clear water state, the removal of plant biomass can potentially trigger a critical transition back to the turbid water state. Currently there is only limited empirical and theoretical understanding of how harvesting of aquatic plants affects ecosystem functioning, which frustrates effective and efficient ecosystem management. With PCLake the impact of harvesting is evaluated, in terms of reducing nuisance and ecosystem stability, for a wide range of external nutrient loadings, mowing intensities and timings. Additionally, the model is used to estimate how much phosphorus is removed from the system during harvesting.

    In chapter 7 I discuss the added value of taking an integrative approach to modelling, and discuss the integrated nature of the studies presented in this thesis. It’s also important to note that these studies were part of a larger research project with the overall aim of increasing the usefulness and the validity of PCLake and its twin model PCDitch, and to enhance the confidence in the models among water quality managers. A synopsis of the overarching collaborative research project on PCLake and PCDitch is presented in chapter 8.

    Waar is het bosbeleid gebleven? : (en wie zit er eigenlijk op te wachten?)
    Arts, Bas ; Nabuurs, Gert-Jan - \ 2016
    forest policy - nature conservation policy - netherlands - felling - ecology - timber production
    Welk lid van de Tweede Kamer weet nog iets van bos? Hoeveel bosbouwers werken er nog bij het ministerie van Economische zaken? Waarom hebben we geen Boswet, bosvisie of Bosbeleidsplan meer? Allemaal vragen die bosbouwers onder elkaar zich regelmatig afvragen. Vindt de samenleving het bos niet meer de moeite waard? Of is er iets anders aan de hand?
    Improving communication and validation of ecological models : a case study on the dispersal of aquatic macroinvertebrates
    Augusiak, Jacqueline A. - \ 2016
    Wageningen University. Promotor(en): Paul van den Brink, co-promotor(en): V. Grimm. - Wageningen : Wageningen University - ISBN 9789462579378 - 192
    macroinvertebrates - aquatic invertebrates - ecological modeling - ecology - models - dispersal - environmental policy - macroinvertebraten - waterinvertebraten - ecologische modellering - ecologie - modellen - verspreiding - milieubeleid

    In recent years, ecological effect models have been put forward as tools for supporting environmental decision-making. Often they are the only way to take the relevant spatial and temporal scales and the multitude of processes characteristic to ecological systems into account. Particularly for environmental risk assessments of pesticides the potential benefits of including modelling studies were recognized and a dialogue between different stakeholder groups was opened. Representatives from academia, pesticide-producing industries, and regulators are nowadays discussing their needs, possibilities, and ways of implementation for improving the use and usefulness of such models. However, it quickly became evident that not all involved parties possess the same background knowledge in regards to modelling terminology and model quality understanding. Proper communication of a given model's structure, robustness, and soundness is crucial to render a model of real use to the decision-making. Doubts about a model's quality and mode of operation may lead to an immediate rejection of the conclusions drawn from its estimations.

    In this thesis, we addressed this point of concern, and performed a literature review focusing on aspects surrounding quality assessments, validation, and communication of models. "Validation" was identified as a catch-all term, which is thus useless for any practical purpose. Based on the review, we developed a framework that splits the seemingly blurry process into associated components and introduce the term ‘evaludation’, a fusion of ‘evaluation’ and ‘validation’, to describe the entire process of assessing a model's quality and reliability. Considering the iterative nature of model development, the modelling cycle, we identified six essential elements of evaludation: (i) ‘data evaluation’ for scrutinising the quality of numerical and qualitative data used for model development and testing; (ii) ‘conceptual model evaluation’ for examining the simplifying assumptions underlying a model's design; (iii) ‘implementation verification’ for testing the model's implementation in equations and as a computer programme; (iv) ‘model output verification’ for comparing model output to data and patterns that guided model design and were possibly used for calibration; (v) ‘model analysis’ for exploring the model's sensitivity to changes in parameters and process formulations to make sure that the mechanistic basis of main behaviours of the model has been well understood; and (vi) ‘model output corroboration’ for comparing model output to new data and patterns that were not used for model development and parameterisation.

    In a subsequent step, we used the evaludation framework to re-evaluate and adjust the documentation framework TRACE (TRAnsparent and Comprehensive Eco- logical modelling; Schmolke et al. 2010), a general framework for documenting a model's rationale, design, and testing. TRACE documents should provide convincing evidence that a model was thoughtfully designed, correctly implemented, thoroughly tested, well understood, and appropriately used for its intended purpose. TRACE documents link the science underlying a model to its application, thereby also linking modellers and model users, for example stakeholders, decision makers, and developers of policies. TRACE thus becomes a tool for planning, documenting, and assessing model evaludation, which includes understanding the rationale behind a model and its envisaged use.

    To provide an example of the measures that can be taken to increase general trust in a model's design and output, we chose MASTEP (Metapopulation model for Assessing Spatial and Temporal Effects of Pesticides) for a case study. MASTEP is an individual-based model used to describe the effects on and recovery of the water louse Asellus aquaticus after exposure to an insecticide in pond, ditch, and stream scenarios. The model includes processes of mortality of A. aquaticus, life history, random walk between cells and density dependence of population regulation. One of the submodels receiving particular criticism was the random walk procedure and the uncertainty attached to the parameters used. The parameters were estimated based on experimental studies performed under very limiting conditions.

    We designed and performed experiments to derive more precise parameters and to better understand the movement behaviour of this freshwater isopod. The experimental procedure that we developed employed video tracking of marked individuals that were introduced alone or as part of a group of unmarked individuals into arenas of approximately 1m2 in size. We recorded the paths of the marked individuals under a set of different conditions, i.e. presence or absence of food or shelter, population density, and after sublethal exposure to chlorpyrifos and imidacloprid. Based on the experimental findings, we refined the movement modelling procedure used in MASTEP to derive more realistic dispersal estimates, with which we revisited a modelling study performed previously by Galic et al. (2012). In this study, the effects of pesticide application timing on population dynamics and recovery times were tested and compared to outcomes from previous versions. It was furthermore possible to integrate an increased level of environmental complexity that could not be addressed before due to a lack of data. Compared to former versions of the population model, recovery times did not change significantly when the same movement parameters were applied to all simulated individuals. This indicates that the previous assumptions already yielded robust estimations. Accounting for life stage dependent movement restraints, though, delayed recovery when exposure occurred shortly before a reproduction cycle. Based on these findings, it was concluded that an increase of ever more realism and environmental complexity in modelling studies needs to be done carefully on a case-by-case basis. Increased realism in models can introduce an unwarranted increase in model complexity and uncertainty, which is not always supporting an improved credibility level of a model.

    Despite the need for basic ecological research for more comprehensive ecological models, we further argue that a modelling study in general can benefit greatly from an improved plan that considers communication needs from the start. Considering such needs early on can help develop a time- and cost-saving strategy for model testing and data collection, while providing a thorough understanding of a model's underlying mechanisms across several layers of stakeholder groups.

    Monitoring en Evaluatie Pilot Zandmotor Fase 2 - Ecotopenkaarten vooroever en getijdenstrand 2010 - 2015
    Wijsman, J.W.M. ; Tangelder, M. ; Visser, Pieter ; Hoekstra, R. - \ 2016
    IMARES (Rapport / IMARES C034/16) - 35
    getijden - stranden - zandsuppletie - natuurontwikkeling - ecologie - zuid-holland - tides - beaches - sand suppletion - nature development - ecology - zuid-holland
    Dit rapport presenteert een eerste aanzet voor de ontwikkeling van ecotopenkaarten voor de vooroever en het intergetijdenstrand van de Zandmotor over de jaren 2010 tot en met 2015. In de ecotopenclassificatie worden de abiotische parameters droogvalduur, bodemschuifspanning en getijdenstroming gecombineerd tot 11 ecotopen, waarvan 4 in de vooroever, 6 op het natte strand en 1 op het droge strand.
    Evaluatie van de ecologische effectiviteit van de houtconstructies in de Snelle loop
    Verdonschot, R.C.M. ; Brugmans, Bart ; Moeleker, Mieke ; Verdonschot, P.F.M. - \ 2016
    H2O online (2016)27 juli.
    ecologie - waterlopen - noord-brabant - hydrologie - macrofauna - monitoring - bemonsteren - hout - aquatische ecosystemen - dood hout - ecology - streams - noord-brabant - hydrology - macrofauna - monitoring - sampling - wood - aquatic ecosystems - dead wood
    In de Snelle Loop zijn in 2012 verschillende typen houtconstructies aangebracht. Waterschap Aa en Maas en studenten van de HAS Hogeschool in Den Bosch verrichten sindsdien jaarlijks fysisch-chemische, hydromorfologische en biologische metingen. In deze studie zijn de tot nu toe verzamelde gegevens over de effecten op de levensgemeenschap na drie jaar geëvalueerd. Het hout bleek effect te hebben op de levensgemeenschap, maar grote jaarlijkse verschillen lieten zien dat met name effecten op een groter schaalniveau een sturende rol spelen. Er worden aanbevelingen gedaan voor de opzet van monitoring om onderscheid te kunnen maken tussen effecten op verschillende schaalniveaus
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