Alteration of flow and sediment dynamics by coastal biogenic structures: case studies of crab burrows and mangrove roots

Abstract

In the coastal environment, a large number of structures may be observed. Apart from anthropogenic structures (e.g. dikes, piers), a great diversity of natural structures (e.g. seagrass meadows, oyster reefs) are found along the coast; these structures generated by living organisms are referred to as biogenic structures. This thesis was motivated to understand the interplay between natural biogenic structures, hydro- and sediment dynamics. In aquatic ecosystems, the flow controls the transport of particles in-cluding nutrients, organic matter and sediment; hydrodynamics are, consequently, of great relevance to the ecosystems. Flow alterations by the presence of biogenic structures have been extensively studied within arrays of aboveground structures. However, the modification of hydrodynamics by belowground structures such as cavities dug by animals is poorly known. Furthermore, the connection between flow change and sediment transport due to the presence of biogenic structures is still lacking knowledge since single biogenic structures exhibit many different geometries (e.g. shape, dimensions) and arrays of structures have various properties (e.g. density, arrangement). In this thesis, the role of structure dimensions and array properties was investigated by considering two case studies: crab burrows as a representative for belowground structures and mangrove roots as a representative for aboveground structures. The options to investigate these structures are various; however, in the present thesis, a twofold approach was chosen: on one hand numerical modelling and on the other hand field observations. A combined field-numerical study provided measurements on flow and sediment dynamics around crab burrows, whereas numerical modelling appeared as a suitable tool to investigate hydro- and sediment dynamics around mangrove roots. Numerical simulations were run by using an existing Computational Fluid Dynamics (CFD) code available in the C++ toolbox OpenFOAM that employs the Finite Volume Method (Chapter 2). In Chapter 3, a literature review was conducted to determine the state of the art in hydro- and sediment dynamics in mangrove ecosystems with a focus on the methods employed and the spatial scales of experiments. Results emphasized the missing knowledge of hydro- and sediment dynamics at rather small spatial scales (below 10 m) and the under-use of numerical modelling to investigate abiotic pro-cesses in mangrove ecosystems in comparison with field and flume experiments. In Chapter 4, to elucidate the impact of mangrove structures on flow and sediment transport at small spatial scales, a three-dimensional model was implemented and successfully validated. A first set of numerical simulations was carried out to determine how a simple mangrove structure (Rhizophora man-grove seedling) modifies the flow and the sediment transport in its close vicinity under five current ve-locities. A similar flow structure was reported for all tested velocities: (a) a downward flow, (b) a horse-shoe vortex, (c) a flow separation and (d) vortices that shed from the rear of the seedling, while flow conditions clearly controlled the magnitude of flow alteration and, consequently, sediment transport. This flow structure enhanced scouring around the foot of the seedling and sediment resuspension in its trail. In Chapter 5, a second set of numerical simulations was conducted to unravel the flow dynamics and sediment transport at a larger scale than a single mangrove seedling: around rows of pneumatophores (mangrove pencil-like roots) subject to a unidirectional current. Three flow directions were simulated in combination with two or four spacing values. Modelled results revealed that the properties of the pneu-matophore arrays (orientation and spacing) controlled the hydrodynamic mechanisms that were gener-ated around the pneumatophores as well as the magnitude of such effects. For a flow parallel to the row of pneumatophores, a “sheltering effect” reduced approaching velocity and enhanced turbulence that caused “global scour” around the array of pneumatophores regardless the spacing. For a flow perpen-dicular to the line of pneumatophores, a “blockage effect” led to flow constriction in-between pneumato-phores. The magnitude of this “blockage effect” was sufficiently high to bring about “global scour” around pneumatophores for small spacing values due to a high-flow blockage. In the case of oblique flow, no interaction between flow features stemming from adjacent pneumatophores was reported for large spac-ing value suggesting that pneumatophores acted as isolated obstructions that in turn caused “local scour”. A similar sedimentation pattern to the perpendicular case was observed for a small spacing due to a “blockage effect” and an increase in approaching velocity. In Chapter 6, a field study supported by a two-dimensional numerical model was carried out to inves-tigate the flow around crab burrows with different aspect ratios (depth/height) and, thus, to elucidate how these belowground biogenic structures affect the particle trapping. Field observations revealed that the material capture (sediment, organic matter) was larger in burrows with a large opening than in burrows with a small opening but same depth. This difference can be explained by the fact that the burrow aspect ratio control the flushing rate, as shown by the modelled results. In addition, an increase in sediment capture was observed, during the field campaign, in arrays that contained more burrows with a small opening, which likely resulted from a change in turbulence level. Numerical simulations revealed that turbulence was higher in burrows with a large opening; however, turbulence persisted for a longer dis-tance downstream of the burrows with a small opening. This turbulence pattern associated to burrows with a small opening may have increased sediment fluxes and, therefore, promoted the sediment cap-ture into neighbouring burrows. This thesis provides valuable insights into the abiotic processes (non-living factors) of flow alteration and sediment transport in response to coastal biogenic structures. The hydrodynamic mechanisms that control the sediment transport around biogenic structures with various geometries and spatial properties were identified and quantified through the large set of physical parameters mainly obtained via numerical simulations. While the study on crab burrows is one of the first applications of CFD to investigate bio-genic belowground structures, the model used in the studies on mangrove seedling and pneumatophores is, to my knowledge, one of the first attempts to simulate small-scale hydro- and sediment dy-namics within mangrove structures using CFD. Therefore, this innovative work lays the foundations for future CFD simulations of hydro- and sediment dynamics around biogenic structures and, this thesis emphasises the potential of the numerical approach for future research in the field of ecohydraulics.