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.

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    North Sea reefs : benthic biodiversity of artificial and rocky reefs in the southern North Sea
    Coolen, Joop Waltherus Petrus - \ 2017
    Wageningen University. Promotor(en): S. Degraer. - Wageningen : Wageningen University - ISBN 9789463430876 - 199
    coral reefs - benthos - biodiversity - north sea - marine ecology - marine organisms - ecosystems - koraalriffen - benthos - biodiversiteit - noordzee - mariene ecologie - zee-organismen - ecosystemen

    The objective of the research presented in this thesis was to understand the patterns of benthic biodiversity on reefs in the North Sea. To gain this understanding, I studied which species are present on natural and artificial reefs, what environmental and biotic variables influence the presence and absence of a selection of these species and one of the possible pathways by which these species may colonise the reefs studied; the stepping stone effect. The first goal was to increase the available knowledge on which species are present at reefs. The second goal was to understand the patterns observed in the variation of species at these reefs. The third goal was to evaluate whether Mytilus edulis utilises offshore artificial structures as stepping stone to colonise very far offshore locations. The final goal was to assess the impact artificial reefs have on the benthic biodiversity of the North Sea. To attain these goals, natural and artificial reefs were sampled using diver operated airlift samplers and box corers. To evaluate the effects generalised linear and additive models were created. When available, additional data from other sources were also used.

    The following conclusions are drawn: Lanice conchilega is an ecosystem engineer creating intermediate sand-reef systems. When rocky reefs are present on a sandy bottom, local biodiversity is doubled. Distributions of the native Caprella linearis and the invasive Caprella mutica showed a significant difference, demonstrating that C. linearis’ habitat preference does not fully overlap with that of C. mutica. Thus, the native and alien Caprellids are likely to be able to co-exist in the North Sea. M. edulis presence increases habitat heterogeneity, which increases species richness. Mytilus edulis uses offshore structures as stepping stones to colonise locations in the North Sea that cannot be reached in a single generation.

    Depth, location effect and habitat type influence the species composition on North Sea reefs most strongly. The relation between depth and species richness on artificial reefs is non-linear, with a maximum at intermediate depths. Although substrates with mixed surface orientation (i.a. rocks) hold the most species rich communities, biodiversity is also strongly influenced by M. edulis and Psammechinus miliaris. When artificial reefs are to be colonised by communities that are similar to natural reefs, their structures should resemble natural reefs as much as possible.

    Data from: Evidence for water-mediated mechanisms in coral–algal interactions
    Jorissen, Hendrikje ; Skinner, Christina ; Osinga, R. ; Beer, Dirk De; Nugues, Maggy M. - \ 2016
    Wageningen University & Research
    coral reefs - coral-algal interactions - turf algae - water flow - oxygen concentrations
    Although many coral reefs have shifted from coral-to-algal dominance, the consequence of such a transition for coral–algal interactions and their underlying mechanisms remain poorly understood. At the microscale, it is unclear how diffusive boundary layers (DBLs) and surface oxygen concentrations at the coral–algal interface vary with algal competitors and competitiveness. Using field observations and microsensor measurements in a flow chamber, we show that coral (massive Porites) interfaces with thick turf algae, macroalgae, and cyanobacteria, which are successful competitors against coral in the field, are characterized by a thick DBL and hypoxia at night. In contrast, coral interfaces with crustose coralline algae, conspecifics, and thin turf algae, which are poorer competitors, have a thin DBL and low hypoxia at night. Furthermore, DBL thickness and hypoxia at the interface with turf decreased with increasing flow speed, but not when thick turf was upstream. Our results support the importance of water-mediated transport mechanisms in coral–algal interactions. Shifts towards algal dominance, particularly dense assemblages, may lead to thicker DBLs, higher hypoxia, and higher concentrations of harmful metabolites and pathogens along coral borders, which in turn may facilitate algal overgrowth of live corals. These effects may be mediated by flow speed and orientation.
    Simplifying complexity : reflections on ecosystems, psychiatric disorders and biogeochemical pathways
    Leemput, I.A. van de - \ 2016
    Wageningen University. Promotor(en): Marten Scheffer; Egbert van Nes. - Wageningen : Wageningen University - ISBN 9789462577930 - 211
    ecosystems - models - biogeochemistry - nitrogen - coral reefs - climate - aquatic ecology - ecosystemen - modellen - biogeochemie - stikstof - koraalriffen - klimaat - aquatische ecologie
    Status and trends of St. Eustatius Coral reef ecosystem and fisheries: 2015 report card
    Graaf, M. de; Piontek, S. ; Miller, D.C.M. ; Brunel, T.P.A. ; Nagelkerke, L.A.J. - \ 2015
    IJmuiden : IMARES (Report / IMARES C167/15) - 41
    coral reefs - ecosystems - fisheries - algae - fishery management - pollution - habitat degradation - nature conservation - sint eustatius - koraalriffen - ecosystemen - visserij - algen - visserijbeheer - verontreiniging - habitatdegradatie - natuurbescherming - sint eustatius
    An integrated ecosystem model for coral reef management where oceanography, ecology and socio-economics meet
    Weijerman, M. - \ 2015
    Wageningen University. Promotor(en): Rik Leemans; Wolf Mooij, co-promotor(en): E.A. Fulton; R.E. Brainard. - Wageningen : Wageningen University - ISBN 9789462574304 - 285
    koraalriffen - milieubeheer - aquatische ecosystemen - aquatische ecologie - oceanografie - modellen - ecosystemen - sociale economie - coral reefs - environmental management - aquatic ecosystems - aquatic ecology - oceanography - models - ecosystems - socioeconomics


    Widespread coral reef decline, including decline in reef fish populations upon which many coastal human populations depend, have led to phase-shifts from the coral-dominated systems, found desirable by humans, to algal-dominated systems that provide less ecosystem services, and the loss of functionally important species. Marine resource managers are challenged with providing strategies that can mitigate or prevent such phase shifts and losses and promote the sustainable use of marine resources. Additionally, managers need to take into account the impacts of these strategies on the socioeconomic conditions of the many resource users. To respond to these challenges scientists, managers and policy makers have advocated for an ecosystem-based approach instead of the traditional focus on individual (economically important) species. Ecosystem-based management includes the various dynamic processes that influence an ecosystem, such as hydrology, ecology, biogeochemistry, and human activities.

    The management strategy evaluation (MSE) tool commonly used in single species stock assessments for evaluating socioeconomic and ecological tradeoffs of alternative management strategies, has now become more widely applied in multi-species or ecosystem assessments. Ecosystem modelling can include more of the key dynamic processes that drive ecosystems and by using that in an MSE framework provides a better understanding of the socio-ecological consequences of management options and quantifies these tradeoffs.

    In this thesis, I review the use of minimal, intermediate and complex coral reef ecosystem models for their suitability of MSE applications. I conclude that complex models can integrate the myriad dynamic processes that govern coral reef ecosystems and are most suitable for MSE, but that minimal and intermediate models are needed to provide the relationships relevant to these dynamics. The main objective of this thesis was to develop a complex model and quantify the effects of watershed management and fishery regulations on coral reef ecosystem services against a backdrop of climate change impacts. For this model development, I selected the Atlantis ecosystem model framework and applied it to a case study of the coral reef ecosystems around Guam to evaluate the performance of alternative management strategies against identified ecosystem metrics.

    Following the step-wise approach recommended for Integrated Ecosystem Assessments, I started with a workshop involving local stakeholders (including resource managers and other coral reef users) to identify the (1) overarching goal of coral reef management, (2) ecological indicators of reef status, and (3) socioeconomic indicators of reef users. Using an Ecopath model I identified additional ecosystem indicators of fishing impacts that could also be used as performance metrics in the ecosystem modelling of alternative strategies. Published relationships for key coral reef dynamics were used to apply the Atlantis framework to coral reef ecosystems. I then developed and parameterized the Guam Atlantis model including 42 functional species groups and the system impacts of eutrophication, sedimentation, fishing and ocean warming and acidification. I validated the model simulations of no local or global stressors, a ‘control run’, following common guidelines for Atlantis development and I validated the added dynamics with published and empirical data or with expert judgement. Due to the absence of time series, model skill assessment was difficult but I could compare biomass of included fish groups after a 1985–2015 simulation with observational data in 2011. These results showed that the model is biased and overestimates various fish groups. However, because the origin of the bias is unknown, rectifying the bias at this point was not possible. Despite this, based on the model validations I concluded that the model was ‘scenario ready’ and suitable for use as a basis of relative comparisons of management strategies, allowing for evaluations to be conducted in an internally consistent context.

    I applied the model to evaluate the relative performance of management strategies against a set of criteria based on the overall goals identified by local resource managers. These included: (1) improved water quality, (2) increased reef resilience, (3) enhanced fish biomass, and (4) similar or improved fishery landings. Comparing tradeoffs across the selected scenarios showed that each scenario performed ‘best’ for at least one of the performance indicators. The integrated ‘full regulation’ scenario (size and bag limits, marine preserves and no land-based sources of pollution) outperformed other scenarios with two thirds of the performance metrics approaching the criteria at the cost of reef-fish landings. When the effects of climate change were taken into account, the selected scenarios performed fairly equally, but none could prevent a collapse in coral biomass by mid-century under a business-as-usual greenhouse gas emission scenario. To get a better understanding of how these same management scenarios influence the economically important tourism sector and the socially important reef-fishing sector, I coupled the Guam Atlantis model to two human behavior models, one representing divers and the other fishers.

    Ecosystem modelling also allows for the comparison of cumulative impacts. Assessments of individual and cumulative impacts of three stressors to reef ecosystems: land-based sources of pollution, fishing and climate change, showed that, to-date, fishing has had the most negative influence on ecosystem metrics that represent reef status, resilience and functioning, and climate change will have the most negative effect in the future most noticeably on the benthic community structure. Cumulative simulations generally showed that the actual effect was slightly less than could be expected based on the sum of their individual effects, keeping in mind that the actual effect size was negative.

    With this model now developed, it provides a tool for assessing and quantifying a range of questions in support for EBM for coral reef ecosystems.

    Baseline assessment of the coral reef fish assemblages of St. Eustatius
    Kuijk, T. van; Graaf, M. de; Nagelkerke, L.A.J. ; Boman, E. ; Debrot, A.O. - \ 2015
    IJmuiden : IMARES (Report / IMARES Wageningen UR C058/15) - 49
    vissen - koraalriffen - aquatische gemeenschappen - aquatische ecologie - mariene parken - sint eustatius - fishes - coral reefs - aquatic communities - aquatic ecology - marine parks - sint eustatius
    In this study we present a fishery independent survey of the finfish populations at depths ranging from 5-30 m in the shallow reef habitats around the island of St. Eustatius.
    A review of coral reef restoration techniques
    Meesters, H.W.G. ; Smith, S.R. ; Becking, L.E. - \ 2015
    Den Burg : IMARES (Report / IMARES Wageningen UR C028/14) - 37
    koraalriffen - herstel - mariene gebieden - caribische eilanden - coral reefs - rehabilitation - marine areas - caribbean islands
    In this review the following three reef restoration techniques are discussed: 1. Coral gardening, 2. Larval seeding, and 3. Reef balls. In this report we provide a description of each method and review the pro/cons using the following criteria: 1. Survival of fragments and larvae before transplantation to the reef; 2. Survival of transplants at the restoration site; 3. Introduction of exonogous material; 4. Indirect effects of coral restoration on the reef; 5. Genetic diversity; 6. Feasibility and effectiveness. We also suggest further research to answer current gaps in our knowledge in the Dutch Caribbean.
    Duurzaamheid - Koraalkweek
    Imares, - \ 2014
    coral - corals - aquaculture - sustainability - coral reefs
    The potential Outstanding Universal Value and natural heritage values of Bonaire National Marine Park: an ecological perspective
    Beek, I.J.M. van; Cremer, J.S.M. ; Meesters, H.W.G. ; Becking, L.E. ; Langley, J.M. - \ 2014
    Den Helder : IMARES (Report / IMARES Wageningen UR C145/14) - 51
    mariene gebieden - nationale parken - koraalriffen - caribisch gebied - bonaire - marine areas - national parks - coral reefs - caribbean - bonaire
    The Bonaire National Marine Park is an outstanding example of a fringing coral reef that has evolved to one of the most diverse reef in the Caribbean. The Bonaire Marine Park, protected since 1979 and declared a National Park in 1999, includes one of the healthiest coral reef in the Caribbean and two Ramsar sites which include mangrove forests and seagrass meadows, globally important for 4 species of endangered species of marine turtles and at least 29 species of migratory waterbirds and a nursery habitat for many reef fish species.
    Classifying benthic habitats and deriving bathymetry at the Caribbean Netherlands using multispectral Imagery. Case study of St. Eustatius
    Nieto, P. ; Mücher, C.A. ; Meesters, H.W.G. ; Clevers, J.G.P.W. - \ 2013
    Wageningen : IMARES (Alterra report 2467) - 96
    benthos - habitats - coral reefs - remote sensing - sint eustatius - caribbean islands - benthos - habitats - koraalriffen - remote sensing - sint eustatius - caribische eilanden
    Towards a predictive model supporting coral reef management of Bonaire's coral reef. Progress report 2012
    Meesters, H.W.G. ; Brinkman, A.G. ; Duyl, F.C. van; Gerla, D.J. ; Groot, A.V. de; Meer, J. van der; Ruardij, P. ; Vries, P. de - \ 2013
    Den Burg : IMARES (Report / IMARES Wageningen UR C070/13) - 10
    coral reefs - models - environmental management - aquatic environment - bonaire - koraalriffen - modellen - milieubeheer - aquatisch milieu - bonaire
    De prijs van het onbetaalbare : wetenschap
    Groot, Dolf de - \ 2012
    coral reefs - nature conservation - ecosystem services - calculation - caribbean
    Functional Valuation of Ecosystem Services on Bonaire: an ecological analysis of ecosystem functions provided by coral reefs
    Beek, I.J.M. van - \ 2011
    Wageningen : Wageningen Universiteit (MSc-report Aquatic Ecology and Water Quality Management 009/2011) - 115
    koraalriffen - ecosysteemdiensten - mariene ecologie - taxatie - bonaire - coral reefs - ecosystem services - marine ecology - valuation - bonaire
    This research is a semi-quantitative analysis of the functional value of coral reef habitats on Bonaire to support ecosystem services. It is part of an economic valuation study of marine and terrestrial ecosystem services on Bonaire.
    Eutrophication status of Lac, Bonaire, Dutch Caribbean Including propolsals for measures
    Slijkerman, D.M.E. ; Peachey, R.B.J. ; Hausmann, P.S. ; Meesters, H.W.G. - \ 2011
    Den Helder : IMARES (Report / IMARES Wageningen UR C093/11) - 40
    eutrofiëring - koraalriffen - aquatische ecologie - mariene ecologie - bonaire - eutrophication - coral reefs - aquatic ecology - marine ecology - bonaire
    Lac is a semi-enclosed lagoon located on the south-eastern side of Bonaire, and contains a diversity of shallow water coral reef associated habitats in close proximity such as mangroves, seagrass beds, Halimeda algal beds, the back reef and sand flats. These habitats support a diversity of fish and invertebrates. Nutrient poor waters are a requirement for healthy coral reefs. When these become enriched with nutrients, it results e.g. in increased algae and affected reef condition. One area of interest for management is the eutrophication status of Lac. Eutrophication is a pressure that might explain some of observed changes in the bay. However, no baseline on the eutrophication status of Lac exists. IMARES and Environics NV conducted a snapshot assessment of the eutrophication status for current understanding and as a basis for future management. Environics conducted the field measurements at Lac, and most of the data analysis. IMARES analysed geographical data and together with Environics cowrited the report. The purpose of this baseline study was to assess the trophic status of Lac by analyzing 4 potential indicators of eutrophication simultaneously: • Nutrient levels; • Levels of fecal indicator bacteria (enterococci); • Epiphyte loads of seagrasses; • Benthic community composition of the back reef. The monitoring was performed at 32 sites within the bay and 1 control site outside the bay in December 2010.
    Optimalisatie van de aquacultuur van koralen
    Wijgerde, T.H.M. ; Osinga, R. - \ 2007
    Aquacultuur 22 (2007)5. - ISSN 1382-2764 - p. 12 - 13.
    aquacultuur - koraal - koralen - biodiversiteit - onderzoeksprojecten - samenwerking - dierentuinen - universiteiten - europese unie - koraalriffen - aquatische ecosystemen - kweken - aquaculture - coral - corals - biodiversity - research projects - cooperation - zoological gardens - universities - european union - coral reefs - aquatic ecosystems - rearing
    Koraalriffen over de gehele wereld vormen wondere ecosystemen met een zeer hoge biodiversiteit. Zij herbergen ongeveer 25% van alle vissoorten, ondanks het feit dat zij slechts een kleine fractie van het zeeoppervlak innemen. Barrière- en franjeriffen over de gehele wereld beschermen de kustlijnen van 109 landen. Verder is het Great Barrier Reef in Australië alleen al goed voor een jaarlijkse omzet van meer dan 10 miljard dollar
    Monitoring fisheries in data-limited situations : a case study of the artisanal reef fisheries of Eritrea
    Tsehaye, I.W. - \ 2007
    Wageningen University. Promotor(en): Johan Verreth, co-promotor(en): Leo Nagelkerke. - [S.l.] : S.n. - ISBN 9789085047735 - 183
    visserij - vis vangen - kleine bedrijven - monitoring - gegevens verzamelen - simulatie - gevalsanalyse - eritrea - koraalriffen - visstand - visvangsten - aquatische ecosystemen - fisheries - fishing - small businesses - monitoring - data collection - simulation - case studies - eritrea - coral reefs - fish stocks - fish catches - aquatic ecosystems
    Elucidating trends in catch rate and composition is important to evaluate the impact of fishing on fish stocks, and thereby guide fisheries management action. Since major changes in fish community structure can take place even at the initial stages in the development of fisheries, the onset of reef fisheries in the Eritrean Red Sea provides a good opportunity to assess the effects of fishing on fish community structure in the early stages of fisheries. The artisanal reef fisheries of Eritrea were launched into a renewed development in 1991 after the end of a decades-long standstill, which was caused by the war for Eritrea’s independence. The main objective of this thesis was to evaluate the sustainability of existing fishing practices in the newly developing artisanal reef fisheries of Eritrea, while simultaneously exploring more effective ways of monitoring of fisheries and fish stocks. Analysis of official statistics from the artisanal fisheries showed that annual effort and annual catch increased upon the expansion of the fisheries, while the total catch rate remained unchanged over the years. However, disaggregation of catch rates into different taxonomic and ecological categories showed varying trends in catch rates of the different groups of fishes, resulting in a clear shift in catch composition over the years. These results are not unlikely given the supposedly large amounts of unreported catches, which are mostly taken illegally to Yemen. This is more so given the highly selective nature of species targeting strategies in the artisanal fisheries. These findings are also consistent with other studies suggesting that stocks of reef-associated demersal species are highly vulnerable to fishing and can decline even at the early stages of fisheries. Furthermore, the results from this study show that the impacts of fishing in the artisanal fisheries could even become more severe if market conditions improve leading to the activation of latent fishing capacity. That having been said, even though the changes in catch rate could be interpreted as reflecting changes in the underlying fish community structure, they could also be partly due to shifts in fish targeting strategies driven by socio-economic circumstances. The relationship between catch rate and effort in the artisanal fisheries could be elucidated more accurately by standardizing catch rates for systematic variations among fishing vessels, which would otherwise cause non-random variations in catch rate unrelated to abundance. The effectiveness of the monitoring program in these fisheries could also be improved through aggregation of catch data. The catch data from the artisanal fisheries could be aggregated into three distinct ecological categories, without considerable loss of information on trends in the catch rate of individual species. These categories included reef-associated demersals, open-water pelagics and near-reef pelagics. Aggregation of catch data into these ecological categories was found to improve the statistical power to detect trends. Moreover, besides improving statistical power, aggregate catch rates could provide better insight into community-level responses to exploitation. An Ecopath with Ecosim model was used to verify if the fishery-induced changes in yield and abundance of fish implied by official statistics are likely, given the existing levels of fishing intensity. This model was also used to explore optimal harvesting strategies for the artisanal fisheries by examining the ecosystem effects of fishing. A retrospective simulation of trends in catch rate (yield) using Ecosim showed that, given the existing fishing intensity as suggested by official statistics, a decline in yield or abundance of reef-associated demersals of the magnitude suggested by trends in catch rate are unlikely. The decline in yield observed in these fisheries could however be reproduced in an Ecosim simulation when the existing fishing level was assumed to be fivefold the official estimate, as suggested by anecdotal evidence on unreported catches. The simulation results also suggest that an optimal fishing strategy could be achieved in the artisanal fisheries through a slight reduction in the annual catch of reef-associated fishes and an increase in the capture of near-reef pelagics and large pelagics from the putative levels of fishing.
    Critical review of the proposed irrigation and effluent standards for Bonaire
    Kekem, A.J. van; Roest, C.W.J. ; Salm, C. van der - \ 2006
    Wageningen : Alterra (Alterra-rapport 1289) - 129
    afvalwater - afvoerwater - normen - irrigatie - hergebruik van water - bonaire - nederlandse antillen - voedingsstoffen - koraalriffen - waste water - effluents - standards - irrigation - water reuse - bonaire - netherlands antilles - nutrients - coral reefs
    The quality of Bonaire’s coral reef is declining which is caused by the high loads of nutrients that reach the sea. A waste water treatment plant is planned to treat the waste water of all hotels and other premises of Kralendijk’s coastal zone. The effluent is to be used for irrigation. The soils in this zone have been studied and erosion and run-off modelled. Nutrient budgets for N and P were calculated and the irrigation requirements of different types of hotel gardens estimated. The proposed effluent norms comply with international standards and reduce the N load to the sea. P is not a problem as this is fixed by the calcareous rock. Despite the high nutrient losses from hotel gardens when using the treated water in hotel gardens, the nutrient loads from the sensitive zone to the sea will be reduced to the 1970 levels when the coral reef was still in good quality. To avoid unnecessary losses, however, it is recommended either to add a denitrification step to the wastewater treatment plant, or use the treated water in horticulture
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