Doctoral Programme on Marine Ecosystem Health and Conservation
 PhD Subject Catalogue Fifth Edition - 2014
Identifying the role of past and current benthos activities for estuarine ecosystem functioning
PhD Code: MARES_14_13:
  • Host institute 1: P1 - Ghent University
  • Host institute 2: P6 - Stichting Koninklijk Nederlands Instituut voor Zeeonderzoek (NIOZ)
  • Host institute 3: Plymouth University
Research fields:
  • T2 - Understanding biodiversity effects on the functioning of marine ecosystems
  • T6 - Habitat loss, urban development, coastal infrastructures and Marine Spatial Planning
  • Tom Moens
  • Martin Attrill
  • Carl Van Colen (UGent); Karline Soetaert (NIOZ)
Contact Person and email: Carl Van Colen -

Subject description
State of the art
Estuaries and shallow coastal habitats are among the most productive marine ecosystems [1]. In addition to nutrient supply from land run-off and the atmosphere, the recycling of nutrients within these systems through remineralization of organic matter in sediments and subsequent release of part of these nutrients to the water column (i.e. benthic-pelagic coupling) contributes to the nutrient load in the system [2]. These nutrients sustain primary production that determine eutrophication problems, and may lead to anoxia. In addition, (imported and) primary produced organic matter is at the base of the pelagic and benthic foodwebs [3, 4]. A prominent feature of many healthy estuaries is the high benthic biomass that forms an important food source for many birds, fish and mammals. Estuarine soft-sediment habitats worldwide are recovering from the severe eutrophication that they experienced about 50 years ago, e.g. [5, 6]. Reduced loads of nutrients have led to improved oxygen conditions, allowing recovery of benthic and pelagic communities [7, 8]. Sediments play a prominent role in recovery from eutrophication in shallow areas as they retard the restoration of the system with several years because the reservoir of nutrients accumulated in the sediment during eutrophic conditions is slowly released as the water-column conditions becomes less nutrient rich [9]. By affecting the sediment-water fluxes of organic matter and nutrients via bioturbation, bio-irrigation and biodeposition activities, benthic animals play an important part both in the storage of nutrients during the eutrophication phase (the ‘memory’) and the consequent release of nutrients during oligotrophication. While humans have abated eutrophication, several geomorphological changes of estuarine systems pose equally large threats, both directly and indirectly. Anthropogenic embankments and dredging destroy benthic habitat and thus induce changes that affect sediment biogeochemistry, biodiversity, ecosystem functioning and overall ecological value of the impacted sediments [10]. Indirectly, dredging alters estuarine hydro-morphology and hydrodynamics, causing an increase in tidal amplitude that pumps sediments upstream. The resulting increased amount of fine suspended matter (SPM) in the estuary reduces the hydraulic drag that in turn alters the currents. Under certain conditions, these effects may amplify and put the river in a hyper-turbid state, i.e. inducing a regime shift [11]. At moderate SPM concentrations, filter feeders may reduce SPM in the water-column by deposition in the sediment. The accumulation of fines in the sediments will prevent the accumulation of SPM in the water keeping the system in normal turbid conditions. However, as the intertidal area becomes smaller, or human induced SPM concentrations become critical, the potential of the fauna to keep SPM to manageable levels is reduced. Once the critical SPM concentration is surpassed, the transition to hyper-turbid conditions may be induced, and this will be aggravated by release of the fines that were stored in the sediments when benthic communities were healthy. This interaction between macrobenthos and SPM forms a feedback between macrobenthos and estuarine system dynamics and the second route where the macrobenthos impacts the memory of the system. 
Aim and methodology
The ultimate aim of this PhD project is to gain insight and predict the response of the estuarine ecosystem functioning to human-induced hydro-morphological and biogeochemical changes. We hypothesize that macrobenthos plays a key role, by their past and current activities. As the system deteriorates biogeochemically, i.e. the nutrient and organic load is high, macrobenthos will affect the storage of nutrients and reduced substances in the sediments. As water quality improves, macrobenthos will affect the rate at which (previously stored) nutrients are released. With respect to hydro-morphological changes, macrobenthos will affect storage of fines in the sediment and keep water column turbidity low, up to the extent where the increased load of SPM and/or habitat reduction will reach a point where this feedback stops to be effective, and the previously stored fines are released. We will use a combined field, mesocosm and modeling approach that focuses on the linkages between biogeochemical and SPM cycling, and macrobenthos functional role (suspension feeding, bio-irrigation and bioturbation). The study area is the Schelde estuary which is currently restoring from severe eutrophication and there is recent (unpublished) evidence that the estuary may currently be changing to a hyperturbid state by human-induced hydro-morphological changes. Newly acquired data, together with data from ongoing monitoring and research projects will be used to feed several types of models. Integration of these models will allow the prediction of organic matter cycling, SPM and nutrient dynamics under future scenarios of hydro-morphological change. The project is therefore divided in 4 work packages (WPs), each with specific objectives: 
WP 1 aims at the development of a species distribution model (SDM) predicting the occurrence of macrobenthos, and specific functional groups, as a function of environmental and specific hydro-morphological (e.g. flow velocities, critical shear stress) variables along the complete estuarine salinity and depth gradient, including the marine mouth region. We will use a multi-quantile regression approach since this method allows to model any quantile, meaning that the full distribution of data points is modeled, whereas more standard regression methods only model one property of this distribution [12].
The spatio-temporal variability in benthic-pelagic fluxes will be investigated in WP 2. A proper incorporation of biota-mediated benthic-pelagic fluxes in estuarine biogeochemical models requires establishing the link between the in situ community, their potential to rework the sediment, and the resulting benthic-pelagic exchanges. Thus, we will make direct rate measurements of sediment-water exchange of nutrients, bio-irrigation, biodeposition and bioturbation in mesocosms for the different communities in the Schelde, and in different periods of the year. 
In WP 3 a simple 1-D biogeochemical model describing the most relevant biogeochemical processes and SPM dynamics will be made, calibrated and validated against the historical database. A common model approach to account for the impact of macrobenthos on benthic-pelagic fluxes, is to assume a relation between bioturbation plus bio-irrigation and the mineralization rate [13, 14]. This is justified along the mineralization gradient from the coast to the deep sea [15-17], but these relations do not hold in shallow systems such as estuaries [15]. Based on the results of WP2 we will derive entirely novel parameterizations of bioturbation, bio-irrigation and biodeposition valid throughout the year along the estuarine gradients. 
In WP 4 we will use the novel developed models to make future projections of the impact of changing morphology and hydrodynamics on ecosystem functioning (benthic-pelagic coupling) through their impact on benthic processes. To this end, the SDM (WP 1) will be linked to the dynamic pelagic biogeochemical model (WP 3), to assess the current role of macrobenthos in biogeochemical cycling and SPM cycling. This model will allow the construction of ecosystem-wide budjets of O2, C, N and Si under different conditions.
1. Heip et al. 1995. Oceanography and Marine Biology 33: 1-149; 2. Boynton & Kemp 1985. Marine Ecology Progress Series 23: 45-55; 3. Van Oevelen et al. Journal of Marine Research 6: 453–482; 4. Nienhuis 1993. Hydrobiologia 265: 15-44, 5. Soetaert et al. 2006. Limnology and Oceanography 51: 45-55; 6. Cox et al. 2009. Biogeosciences 6: 2935-2948; 7. Rappé et al. 2011. Estuarine Coastal and Shelf Science 91: 187-197; 8. Cardoso et al. 2007. Estuarine, Coastal and Shelf Science 71: 301-308; 9. Jeppesen et al. 2005. Freshwater Biology 50: 1747-1771; 10. Thrush et al. 2004. Frontiers in Ecology and the Environment 2: 299-306; 11. Winterwerp J 2011. Ocean Dynamics 61: 203–215; 12. Guissan et al. 2006. Journal of Applied Ecology 43: 386-392; 13. Soetaert et al. 2000. Earth Science Reviews 51: 173-201; 14. Gypens et al. 2008. Progress in Oceanography 76: 89-110; 15. Soetaert et al. 1996. Geochimica Et Cosmochimica Acta 60: 1019-1040; 16. Middelburg et al. 1996. Global Biogeochemical Cycles 10: 661-673; 17. Middelburg et al. 1997. Deep-sea research Part I-Oceanographic research papers 44: 327-344

Expected outcomes
The results of the proposed PhD project will be published in high-standard international scientific journals. The PhD student will be part of a highly multidisciplinary team, including specialists in estuarine ecology, biogeochemical cycling and ecological modeling. The acquired knowledge on sediment inhabiting fauna and their effect on SPM, nutrient and oxygen dynamics will provide input to a set of models, making the new concepts more widely applicable. Due to the close connection of experimental results and the model parameterizations, these model simulations will effectively result in the upscaling to the ecosystem level through a system-wide integration of the experimental results. For example, the water quality model developed in WP4 will enable the assessment of the potential for change in ecological resilience in estuaries by making projections of the impact of future changing morphology and hydrodynamics on coupled biodiversity and ecosystem functioning.

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