Fate of fluid mixed at the boundaries of a lake

Three field studies were conducted in Ada Hayden Lake in Ames, Iowa to study generation of turbulence on the sloping boundary and to investigate boundary-interior communication in a lake with dye tracking experiments and measurements of meteorological conditions, internal wave response, and turbulence. The objectives of these studies were to (1) predict the occurrence and strength of turbulent mixing in terms of meteorological forcing and stratification by investigating the dependence of internal waves and turbulence on the slope on the Lake number, (2) investigate the fate of mixed fluid by tracking an intrusion generated at the boundary; and (3) evaluate offshore transport by basin scale seiches. To predict the Lake number conditions under which turbulence will be generated at the slopes (objective 1), the rate of dissipation of turbulent kinetic energy was determine from near-bottom velocity measurements using the structure function method, and histograms of ε/νN2 were analyzed for all the data and for five different Lake number regimes. Although a quantitative relationship between the Lake number and the turbulence intensity could not be determined, some relationships between the Lake number and ε/νN2 for different Lake number regimes could be observed. For example, for high Lake number, most of the values of ε/νN2 were low enough to suggest that transport was mainly caused by molecular diffusion, while for low Lake number, turbulence was energetic. For moderate Lake numbers, the value of ε/νN2 at the peak in the histogram increased as the Lake number decreased from 30 to 1. To investigate intrusion generation and propagation (objective 2), temperature microstructure measurements on the slope and horizontal and vertical dye mapping were used. Profiles of temperature microstructure measured soon after the injection both at the injection site and offshore showed large eddy diffusivity near the boundary. The propagation characteristics of the intrusion were predicted most closely by a formulation for an axisymmetric intrusion governed by a balance between buoyancy and inertia. To evaluate offshore transport by basin scale seiches (objective 3), the horizontal variation in internal wave shear and strain, which can increase the lateral dispersion between the boundary and the interior, was analyzed. The strain can spread the mixed fluid far enough from the boundary that vertical shear becomes an important dispersion process. These findings improve the understanding of the pathway from energy input from the wind to offshore transport

Artificially generated turbulence: A review of phycological nanocosm, microcosm, and mesocosm experiments

Building on a summary of how turbulence influences biological systems, we reviewed key phytoplankton-turbulence laboratory experiments (after Peters and Redondo in Scientia Marina: Lectures on plankton and turbulence, International Centre for Coastal Resources, Barcelona, 1997) and Peters and Marrase (Marine Ecology Progress Series 205:291-306, 2000) to provide a current overview of artificial turbulence generation methods and quantification techniques. This review found that most phytoplankton studies using artificial turbulence feature some form of quantification of turbulence; it is recommended to use turbulent dissipation rates (epsilon) for consistency with physical oceanographic and limnological observations. Grid-generated turbulence is the dominant method used to generate artificial turbulence with most experiments providing quantified epsilon values. Couette cylinders are also commonly used due to the ease of quantification, albeit as shear rates not epsilon. Dinoflagellates were the primary phytoplanktonic group studied due to their propensity for forming harmful algal blooms (HAB) as well as their apparent sensitivity to turbulence. This study found that a majority of experimental setups are made from acrylate plastics that could emit toxins as these materials degrade under UV light. Furthermore, most cosm systems studied were not sufficiently large to accommodate the full range of turbulent length scales, omitting larger vertical overturns. Recognising that phytoplankton-turbulence interactions are extremely complex, the continued promotion of more interdisciplinary studies is recommended

Dataset for "On biogenic turbulence production and mixing from 1 vertically migrating zooplankton in lakes"

The dataset provides information of data collected on 21 July, 28 July and 28 August 2016 in Vobster Quay, a 40-m quarry, located in Radstock (UK). Data were collected during the diel vertical migration (DVM) of zooplankton at dusk to understand whether small zooplankton can generated turbulence in the lake interior. The dataset contains: (1) backscatter strength data from a 500-kHz ADCP by Nortek, (2) profiles of zooplankton concentration and (3) profiles of dissipation rates of turbulent kinetic energy acquired with a microstructure profiler

Effect of temperature on zooplankton vertical migration velocity

Zooplankton diel vertical migration (DVM) is an ecologically important process, affecting nutrient transport and trophic interactions. Available measurements of zooplankton displacement velocity during the DVM in the field are rare; therefore, it is not known which factors are key in driving this velocity. We measured the velocity of the migrating layer at sunset (upward bulk velocity) and sunrise (downwards velocity) in summer 2015 and 2016 in a lake using the backscatter strength (VBS) from an acoustic Doppler current profiler. We collected time series of temperature, relative change in light intensity chlorophyll-a concentration and zooplankton concentration. Our data show that upward velocities increased during the summer and were not enhanced by food, light intensity or by VBS, which is a proxy for zooplankton concentration and size. Upward velocities were strongly correlated with the water temperature in the migrating layer, suggesting that temperature could be a key factor controlling swimming activity. Downward velocities were constant, likely because Daphnia passively sink at sunrise, as suggested by our model of Daphnia sinking rate. Zooplankton migrations mediate trophic interactions and web food structure in pelagic ecosystems. An understanding of the potential environmental determinants of this behaviour is therefore essential to our knowledge of ecosystem functioning

On biogenic turbulence production and mixing from vertically migrating zooplankton in lakes

Vertical mixing in lakes is a key driver of transport of ecologically important dissolved constituents, such as oxygen and nutrients. In this study we focus our attention on biomixing, which refers to the contribution of living organisms towards the turbulence and mixing of oceans and lakes. While several studies of biomixing in the ocean have been conducted, no in situ studies exist that assess the turbulence induced by freshwater zooplanktonic organisms under real environmental conditions. Here, turbulence is sampled during three different sampling days during the sunset diel vertical migration of Daphnia spp. in a small man-made lake. This common genus may create hydrodynamic disturbances in the lake interior where the thermal stratification usually suppresses the vertical diffusion. Concurrent biological sampling assessed the zooplankton vertical concentration profile. An acoustic-Doppler current profiler was also used to track zooplankton concentration and migration via the backscatter strength. Our datasets do not show biologically-enhanced dissipation rates of temperature variance and turbulent kinetic energy in the lake interior, despite Daphnia concentrations as high as 60 org. L−1. No large and significant turbulent patches were created within the migrating layer to generate irreversible mixing. This suggests that Daphnia do not affect the mixing in the lake at the organism concentrations observed here

A breaking internal wave in the surface ocean boundary layer

High-temporal resolution measurements in the Labrador Sea surface layer are presented using an upwardly profiling autonomous microstructure instrument, which captures an internal wave in the act of breaking at the base of the surface mixed layer, driving turbulence levels 2-3 orders of magnitude above the background. While lower-frequency (near-inertial) internal waves are known to be important sources of turbulence, we report here a higher-frequency internal wave breaking near the ocean surface. Due to observational limitations, the exact nature of the instability cannot be conclusively identified, but the interaction of wave-induced velocity with unresolved background shear appears to be the most likely candidate. These observations add a new process to the list of those currently being considered as potentially important for near-surface mixing. The geographical distribution and global significance of such features are unknown, and underscore the need for more extensive small-scale, rapid observations of the ocean surface layer

Pseudogene accumulation in the evolutionary histories of Salmonella enterica serovars Paratyphi A and Typhi

<p>Abstract</p> <p>Background</p> <p>Of the > 2000 serovars of <it>Salmonella enterica </it>subspecies I, most cause self-limiting gastrointestinal disease in a wide range of mammalian hosts. However, <it>S. enterica </it>serovars Typhi and Paratyphi A are restricted to the human host and cause the similar systemic diseases typhoid and paratyphoid fever. Genome sequence similarity between Paratyphi A and Typhi has been attributed to convergent evolution via relatively recent recombination of a quarter of their genomes. The accumulation of pseudogenes is a key feature of these and other host-adapted pathogens, and overlapping pseudogene complements are evident in Paratyphi A and Typhi.</p> <p>Results</p> <p>We report the 4.5 Mbp genome of a clinical isolate of Paratyphi A, strain AKU_12601, completely sequenced using capillary techniques and subsequently checked using Illumina/Solexa resequencing. Comparison with the published genome of Paratyphi A ATCC9150 revealed the two are collinear and highly similar, with 188 single nucleotide polymorphisms and 39 insertions/deletions. A comparative analysis of pseudogene complements of these and two finished Typhi genomes (CT18, Ty2) identified several pseudogenes that had been overlooked in prior genome annotations of one or both serovars, and identified 66 pseudogenes shared between serovars. By determining whether each shared and serovar-specific pseudogene had been recombined between Paratyphi A and Typhi, we found evidence that most pseudogenes have accumulated after the recombination between serovars. We also divided pseudogenes into relative-time groups: ancestral pseudogenes inherited from a common ancestor, pseudogenes recombined between serovars which likely arose between initial divergence and later recombination, serovar-specific pseudogenes arising after recombination but prior to the last evolutionary bottlenecks in each population, and more recent strain-specific pseudogenes.</p> <p>Conclusion</p> <p>Recombination and pseudogene-formation have been important mechanisms of genetic convergence between Paratyphi A and Typhi, with most pseudogenes arising independently after extensive recombination between the serovars. The recombination events, along with divergence of and within each serovar, provide a relative time scale for pseudogene-forming mutations, affording rare insights into the progression of functional gene loss associated with host adaptation in <it>Salmonella</it>.</p