Jonathan Malarkey

The pervasive role of biological cohesion in bedform development

Sediment fluxes in aquatic environments are crucially dependent on bedform dynamics. However, sediment-flux predictions rely almost completely on clean-sand studies, despite most environments being composed of mixtures of non-cohesive sands, physically cohesive muds and biologically cohesive extracellular polymeric substances (EPS) generated by microorganisms. EPS associated with surficial biofilms are known to stabilize sediment and increase erosion thresholds. Here we present experimental data showing that the pervasive distribution of low levels of EPS throughout the sediment, rather than the high surficial levels of EPS in biofilms, is the key control on bedform dynamics. The development time for bedforms increases by up to two orders of magnitude for extremely small quantities of pervasively distributed EPS. This effect is far stronger than for physical cohesion, because EPS inhibit sand grains from moving independently. The results highlight that present bedform predictors are overly simplistic, and the associated sediment transport processes require re-assessment for the influence of EPS.

Sticky stuff: Redefining bedform prediction in modern and ancient environments

The dimensions and dynamics of subaqueous bedforms are well known for cohesionless sediments. However, the effect of physical cohesion imparted by cohesive clay within mixed sand-mud substrates has not been examined, despite its recognized influence on sediment stability. Here we present a series of controlled laboratory experiments to establish the influence of substrate clay content on subaqueous bedform dynamics within mixtures of sand and clay exposed to unidirectional flow. The results show that bedform dimensions and steepness decrease linearly with clay content, and comparison with existing predictors of bedform dimensions, established within cohesionless sediments, reveals significant over-prediction of bedform size for all but the lowermost clay contents examined. The profound effect substrate clay content has on bedform dimensions has a number of important implications for interpretation in a range of modern and ancient environments, including reduced roughness and bedform heights in estuarine systems and the often cited lack of large dune cross-sets in turbidites. The results therefore offer a step change in our understanding of bedform formation and dynamics in these, and many other, sedimentary environments.

Discrete vortex modelling of oscillatory flow over ripples

Two discrete vortex models of oscillating flow above two-dimensional vortex ripples are presented. These are a simple inviscid model, which contains no diffusion of vorticity, and a cloud-in-cell (CIC) model with diffusion represented by random walk. For values of D0=l corresponding to the vortex ripple regime (D0 is the wave orbital diameter and l is the ripple wavelength), both models are shown to be capable of producing the time-varying vortex strengths, positions and bed stresses observed in oscillating-flow laboratory experiments. For relatively large values of D0=l ð* 3Þ; the CIC model has the advantage of being able to represent the first stages of breakdown of vortices into more homogenous turbulence. For relatively low values of D0=l ð& 1Þ; the inviscid model is shown to produce the expected tendency towards non-separating flow behaviour which is markedly different from that of classical flat-bed models particularly in respect of the bed friction. q 2002 Elsevier Science Ltd. All rights reserved.

The role of biophysical cohesion on subaqueous bed form size

Abstract Biologically active, fine‐grained sediment forms abundant sedimentary deposits on Earths surface, and mixed mud‐sand dominates many coasts, deltas, and estuaries. Our predictions of sediment transport and bed roughness in these environments presently rely on empirically based bed form predictors that are based exclusively on biologically inactive cohesionless silt, sand, and gravel. This approach underpins many paleoenvironmental reconstructions of sedimentary successions, which rely on analysis of cross‐stratification and bounding surfaces produced by migrating bed forms. Here we present controlled laboratory experiments that identify and quantify the influence of physical and biological cohesion on equilibrium bed form morphology. The results show the profound influence of biological cohesion on bed form size and identify how cohesive bonding mechanisms in different sediment mixtures govern the relationships. The findings highlight that existing bed form predictors require reformulation for combined biophysical cohesive effects in order to improve morphodynamic model predictions and to enhance the interpretations of these environments in the geological record.

A simple model of unsteady sheet-flow sediment transport

A simple, quasi-steady, one-dimensional, vertical (1DV) model of unsteady sheet flow is presented. The central aim is to provide greater realism in the near-bed, high-concentration layer, than is possible using models based on the classical referenceconcentration approach. This is achieved by tracking erosion and deposition at the bottom of the mobile sediment layer in relation to the amount of sediment present in the sheet-flow and suspension layers. The model relies on empirical assumptions for the time-varying sheet-flow layer thickness (d) and time-varying equivalent bed roughness (ks). The formulations adopted yield realistic instantaneous vertical profiles of velocity and sediment concentration from the stationary bed, through the highconcentration sheet-flow layer up into the outer suspension layer. The suspension layer itself is modelled using a standard k–e turbulence-closure scheme, together with the sediment continuity equation. Matching conditions are applied at the interface between the sheet-flow and suspension layers. Preliminary results presented here include initial validation comparisons with the data set of Horikawa et al. [Horikawa, K., Watanabe, A., Katori, S., 1982. Sediment transport under sheet flow conditions. Proceedings of the 18th International Conference on Coastal Engineering, Cape Town. ASCE, Reston VA, USA, 1335–1352.]. Further comparisons with the experiments of Dohmen-Janssen et al. [J. Geophys. Res. 106 (2001) 27103] cover a wide range of wave–current conditions and sand grain sizes. The results are satisfactory with respect to the measured velocity and concentration profiles, apart from cases involving fine sand for which the effects of flow unsteadiness are not accounted for in the formulation. In addition, the new model provides satisfactory predictions of sand transport rates. D 2003 Elsevier Science B.V. All rights reserved.

Modelling wave–current interactions in rough turbulent bottom boundary layers

Abstract The aim of the present paper is to explain some of the differences between previously published analytical and numerical models of combined wave and current bottom boundary layer flow. To this end, the Grant and Madsen (1979) model for wave–current, rough turbulent flow is modified to include both first and second harmonic time variations in the eddy viscosity (K). The functional form of the coefficients controlling the amount of time variation is established by analysing the numerical model results of Davies (1990) . The addition of time variation in K reduces the strong non-linearity exhibited by the mean stress in the original Grant and Madsen model for current dominated cases, and reproduces the veering of the current predicted by numerical turbulence closure models.

Soil stabilization linked to plant diversity and environmental context in coastal wetlands

Abstract Background Plants play a pivotal role in soil stabilization, with above‐ground vegetation and roots combining to physically protect soil against erosion. It is possible that diverse plant communities boost root biomass, with knock‐on positive effects for soil stability, but these relationships are yet to be disentangled. Question We hypothesize that soil erosion rates fall with increased plant species richness, and test explicitly how closely root biomass is associated with plant diversity. Methods We tested this hypothesis in salt marsh grasslands, dynamic ecosystems with a key role in flood protection. Using step‐wise regression, the influences of biotic (e.g. plant diversity) and abiotic variables on root biomass and soil stability were determined for salt marshes with two contrasting soil types: erosion‐resistant clay (Essex, southeast UK) and erosion‐prone sand (Morecambe Bay, northwest UK). A total of 132 (30‐cm depth) cores of natural marsh were extracted and exposed to lateral erosion by water in a re‐circulating flume. Results Soil erosion rates fell with increased plant species richness (R 2 = 0.55), when richness was modelled as a single explanatory variable, but was more important in erosion‐prone (R 2 = 0.44) than erosion‐resistant (R 2 = 0.18) regions. As plant species richness increased from two to nine species·m−2, the coefficient of variation in soil erosion rate decreased significantly (R 2 = 0.92). Plant species richness was a significant predictor of root biomass (R 2 = 0.22). Step‐wise regression showed that five key variables accounted for 80% of variation in soil erosion rate across regions. Clay‐silt fraction and soil carbon stock were linked to lower rates, contributing 24% and 31%, respectively, to variation in erosion rate. In regional analysis, abiotic factors declined in importance, with root biomass explaining 25% of variation. Plant diversity explained 12% of variation in the erosion‐prone sandy region. Conclusion Our study indicates that soil stabilization and root biomass are positively associated with plant diversity. Diversity effects are more pronounced in biogeographical contexts where soils are erosion‐prone (sandy, low organic content), suggesting that the pervasive influence of biodiversity on environmental processes also applies to the ecosystem service of erosion protection.

A simple procedure for calculating the mean and maximum bed stress under wave and current conditions for rough turbulent flow based on Soulsby and Clarke's (2005) method

In the marine environment, particularly on continental shelves, the processes of wave dissipation and sediment transport depend crucially on the bed shear stress. When waves and currents are superimposed the bed shear stress exhibits non-linear behaviour such that it is insufficient to simply sum vectorially the wave-alone and current-alone stress components. Soulsby and Clarke (2005) [Bed shear-stresses under combined waves and currents on smooth and rough beds. Report TR 137. HR Wallingford, Wallingford, UK, 22 pp.] developed a simple analytical, non-iterative method for calculating the mean and maximum bed shear stress in combined wave and current flows. For rough turbulent flow their method produces non-linearities in the mean and maximum bed stress that are consistent with those measured, while it under-predicts the non-linearities in the bed stresses in comparison with model predictions. Here their method is generalised such that it may be used to predict non-linearities in the bed stresses that are consistent with either the measurements or the models, for the case of rough turbulent flow. Also the Soulsby and Clarke method relies on the fact that the depth-averaged current is already known. However, in the field it is often the case that the current at a particular height above the bed is measured, so here their method is reposed in terms of a current measured at a particular height. A MATLAB script is provided for this modified Soulsby and Clarke method, such that either strong or weak non-linearity can be included in the wave-current interaction and the current can be input at a particular height or as a depth average.

Line vortices and the vacillation of Langmuir circulation

AbstractThree types of breakdown of Langmuir circulation (Lc) are observed, two of which are represented in large-eddy simulation (LES) models, but the third, vacillation, is not. The stability of Lc can be examined by representing the downwind-aligned vortices by line vortices that are subjected to perturbations. Earlier conclusions relating to stability in homogeneous water of infinite depth are found to be in error because no stationary unperturbed state exists. The motion of vortices is examined and shown to be consistent with an explanation of Lc devised by Csanady. Motion of line vortices in water of limited depth or bounded below by a thermocline is examined. The motion replicates some of the features of vacillation observed by Smith in deep water bounded by a thermocline, including its periodicity and fluctuations in the formation of bubble bands. Vortices describe closed orbits within the Langmuir cells. Particle motions in the vacillating Lc pattern exhibit trapping close to the line vortices or...

A transport model of graded sands in the oscillatory sheet-flow regime

The 1DV two-layer model of oscillatory sheet flow of Malarkey et al. (2003) which was developed for a single grain size has been modified to include grain fractions. The model includes a suspension layer above a sheet-flow layer consisting of prescribed profiles of concentration and velocity. Since this model keeps track of the total sediment in the water column through the wave cycle it is ideally suited for representing graded sediments. The modified model has been compared with the graded sediment data of Hassan et al. (1999). The results show that the model can reproduce the statistical characteristics of the sediment in suspension and produces fractional transport rates that are consistent with the experiments. However, it also demonstrates that a sediment weighting function limited by the amount of sediment in suspension is not sufficient to give rise to the apparent effects of hiding and exposure seen in the data.