Large eddy simulation of turbulence and solute transport in a forested headwater stream

The large eddy simulation (LES) module of the Virtual StreamLab (VSL3D) model is applied to simulate the flow and transport of a conservative tracer in a headwater stream in Minnesota, located in the south Twin Cities metropolitan area. The detailed geometry of the stream reach, which is _135 m long, _2.5 m wide, and _0.15 m deep, was surveyed and used as input to the computational model. The detailed geometry and location of large woody debris and bed roughness elements up to _0.1 m in size were also surveyed and incorporated in the numerical simulation using the Curvilinear Immersed Boundary approach employed in VSL3D. The resolution of the simulation, which employs up to a total of 25 million grid nodes to discretize the flow domain, is sufficiently fine to directly account for the effect of large woody debris and small cobbles (on the streambed) on the flow patterns and transport processes of conservative solutes. Two tracer injection conditions, a pulse and a plateau release, and two cross sections of measured velocity were used to validate the LES results. The computed results are shown to be in good agreement with the field measurements and tracer concentration time series. To our knowledge, the present study is the first attempt to simulate via high-resolution LES solute transport in a natural stream environment taking into account a range of roughness length scales spanning an order of magnitude: From small cobbles on the streambed (_0.1 m in diameter) to large woody debris up to _3 m long. © 2016. American Geophysical Union. All Rights Reserved

Effect of near‐bed turbulence on chronic detachment of epilithic biofilm: Experimental and modeling approaches.

The biomass dynamics of epilithic biofilm, a collective term for a complex microorganism community that grows on gravel bed rivers, was investigated by coupling experimental and numerical approaches focusing on epilithic biofilm‐flow interactions. The experiment was conducted during 65 days in an artificial rough open‐channel flow, where filtered river water circulated at a constant discharge. To characterize the effect of near‐bed turbulence on the chronic detachment process in the dynamics of epilithic biofilm, local hydrodynamic conditions were measured by laser Doppler anemometry and turbulent boundary layer parameters inferred from double‐averaged quantities. Numerical simulations of the EB biomass dynamics were performed using three different models of chronic detachment based upon three different descriptors for the flow conditions: Discharge Q, friction velocity u*, and roughness Reynolds number k+. Comparisons of numerical simulation results with experimental data revealed chronic detachment to be better simulated by taking the roughness Reynolds number as the external physical variable forcing chronic detachment. Indeed, the loss of epilithic matter through the chronic detachment process is related not only to hydrodynamic conditions, but also to change in bottom roughness. This suggests that changes in the behavior and dimensions of river bed roughness must be considered when checking the dynamics of epilithic biofilm in running waters

Microscale measurements reveal contrasting effects of photosynthesis and epiphytes on frictional drag on the surfaces of filamentous algae

SUMMARY 1. Filamentous algae are widespread in freshwater ecosystems worldwide with a significant presence in streams, rivers and lakes with sufficient light and nutrients. Although typically not a preferred food source for grazers, dense filamentous mats provide surfaces for epiphytic microorganisms that are more palatable, thus adding to stream productivity. 2. We tested the hypothesis that epiphytes change velocity gradients, and consequently shear stress and skin friction drag, near the surface of algal filaments. Using both digital holography and particle image velocimetry to measure micrometre-scale velocity fields, we found that the surface shear stress on filamentous algae was much greater when the algae were actively photosynthesising. The presence of attached diatoms significantly reduced surface shear stress, while those filaments were photosynthesising, compared with bare filaments. 3. A nutrient flux model, based on boundary layer thickness and surface shear stress, predicts that nutrient flux to the surface of a photosynthesising filament under measured flow conditions will be 1.5 times greater than for a preserved (i.e. dead) filament. Modelled nutrient flux to filaments with epiphytic assemblages dominated by diatoms is 75% of the flux to bare filaments under similar flow conditions. 4. The proposed positive feedback between photosynthesis, surface shear stress and nutrient flux could be an important biophysical mechanism that overcomes diffusion limited nutrient supply within dense algal mats, enhancing algal survival through increased nutrient flux to actively photosynthesising filaments and decreased sloughing risk for filaments with lower rates of photosynthesis (due to epiphyte coverage or other light-limiting factors)

Daphnia Inhibits the Emergence of Spatial Pattern in a Simple Consumer-Resource System

Spatial self-organization can occur in many ecosystems with important effects on food web dynamics and the maintenance of biodiversity. The consumer-resource interaction is known to generate spatial patterning, but only a few empirical studies have investigated the effect of the consumer on resource distribution. Here we report results from a large aquatic mesocosm experiment used to investigate the effect of the consumer Daphnia magna on the distribution of its resource, the green algae Chlorella vulgaris. We maintained large tanks with capacity for 26 ,000 L with either algae or both algae and Daphnia in different temperature conditions. We found that the presence of D. magna inhibited spatial structure in algal distribution that arose as a consequence of increasing temperature. We conjecture that this homogenization effect might be caused by a combination of high mobility combined with high rates of algal consumption by Daphnia. Our study emphasizes the importance of both local constraints on growth and behavioral responses in either promoting or suppressing spatial self-organization in natural populations

Delving deeper: metabolic processes in the metalimnion of stratified lakes

Many lakes exhibit seasonal stratification, during which they develop strong thermal and chemical gradients. An expansion of depth-integrated monitoring programs has provided insight into the importance of organic carbon processing that occurs below the upper mixed layer. However, the chemical and physical drivers of metabolism and metabolic coupling remain unresolved, especially in the metalimnion. In this depth zone, sharp gradients in key resources such as light and temperature co-occur with dynamic physical conditions that influence metabolic processes directly and simultaneously hamper the accurate tracing of biological activity. We evaluated the drivers of metalimnetic metabolism and its associated uncertainty across 10 stratified lakes in Europe and North America. We hypothesized that the metalimnion would contribute highly to whole-lake functioning in clear oligotrophic lakes, and that metabolic rates would be highly variable in unstable polymictic lakes. Depth-integrated rates of gross primary production (GPP) and ecosystem respiration (ER) were modelled from diel dissolved oxygen curves using a Bayesian approach. Metabolic estimates were more uncertain below the epilimnion, but uncertainty was not consistently related to lake morphology or mixing regime. Metalimnetic rates exhibited high day-to-day variability in all trophic states, with the metalimnetic contribution to daily whole-lake GPP and ER ranging from 0% to 87% and<1% to 92%, respectively. Nonetheless, the metalimnion of low-nutrient lakes contributed strongly to whole-lake metabolism on average, driven by a col- linear combination of highlight, low surface-water phosphorous concentration and high metalimnetic volume. Consequently, a single-sensor approach does not necessarily reflect whole-ecosystem carbon dynamics in stratified lakes