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

Toward a Unified Science of the Earth\u27s Surface: Opportunities for Synthesis Among Hydrology, Geomorphology, Geochemistry, and Ecology

The Earth\u27s surface is shaped by the interaction of tectonics, water, sediment, solutes, and biota over a wide range of spatial and temporal scales and across diverse environments. Development of a predictive science of Earth surface dynamics integrates many disciplines and approaches, including hydrology, geomorphology, ocean and atmospheric science, sedimentary and structural geology, geochemistry, and ecology. This paper discusses challenges, opportunities, and a few example problems that can serve as pathways toward this integration

StreamLab Collaboratory: Experiments, Data Sets, and Research Synthesis

A series of community-led, large-scale laboratory experiments, termed “StreamLab”, were performed by the National Center for Earth-surface Dynamics (NCED) with the purpose of advancing multidisciplinary research, education, and knowledge transfer at the interface of physical/chemical/biological processes in streams, science-based stream restoration practice, and environmental sensing technologies. Two series of experiments, StreamLab06 and StreamLab08, were conducted in the Main Channel of the St. Anthony Falls Laboratory at the University of Minnesota, a flume 84 m long and 2.75 m wide with water fed by the Mississippi River at a rate of up to 8.5 m3/s. The purpose of this paper is to share with the broader community the data collected with the hope of stimulating further analysis and future experimental campaigns toward advancing our predictive understanding of the physical, chemical, and biological processes in streams. Toward this end, a brief summary of the results to date is included and some ideas for further research are provided

Temperature, recreational fishing and diapause egg connections : dispersal of spiny water fleas (Bythotrephes longimanus)

© The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution Noncommercial License. The definitive version was published in Biological Invasions 13 (2011): 2513-2531, doi:10.1007/s10530-011-0078-8.The spiny water flea (Bythotrephes longimanus) is spreading from Great Lakes coastal waters into northern inland lakes within a northern temperature-defined latitudinal band. Colonization of Great Lakes coastal embayments is assisted by winds and seiche surges, yet rapid inland expansion across the northern states comes through an overland process. The lack of invasions at Isle Royale National Park contrasts with rapid expansion on the nearby Keweenaw Peninsula. Both regions have comparable geology, lake density, and fauna, but differ in recreational fishing boat access, visitation, and containment measures. Tail spines protect Bythotrephes against young of the year, but not larger fish, yet the unusual thick-shelled diapausing eggs can pass through fish guts in viable condition. Sediment traps illustrate how fish spread diapausing eggs across lakes in fecal pellets. Trillions of diapausing eggs are produced per year in Lake Michigan and billions per year in Lake Michigamme, a large inland lake. Dispersal by recreational fishing is linked to use of baitfish, diapausing eggs defecated into live wells and bait buckets, and Bythothephes snagged on fishing line, anchor ropes, and minnow seines. Relatively simple measures, such as on-site rinsing of live wells, restricting transfer of certain baitfish species, or holding baitfish for 24 h (defecation period), should greatly reduce dispersal.Study of Lakes Superior and Michigan was funded from NSF OCE-9726680 and OCE-9712872 to W.C.K., OCE-9712889 to J. Churchill. Geographic survey sampling and Park studies in the national parks during 2008-2010 were funded by a grant from the National Park Service Natural Resource Preservation Program GLNF CESU Task Agreement No. J6067080012

Voronoi Tessellation Captures Very Early Clustering of Single Primary Cells as Induced by Interactions in Nascent Biofilms

Biofilms dominate microbial life in numerous aquatic ecosystems, and in engineered and medical systems, as well. The formation of biofilms is initiated by single primary cells colonizing surfaces from the bulk liquid. The next steps from primary cells towards the first cell clusters as the initial step of biofilm formation remain relatively poorly studied. Clonal growth and random migration of primary cells are traditionally considered as the dominant processes leading to organized microcolonies in laboratory grown monocultures. Using Voronoi tessellation, we show that the spatial distribution of primary cells colonizing initially sterile surfaces from natural streamwater community deviates from uniform randomness already during the very early colonisation. The deviation from uniform randomness increased with colonisation — despite the absence of cell reproduction — and was even more pronounced when the flow of water above biofilms was multidirectional and shear stress elevated. We propose a simple mechanistic model that captures interactions, such as cell-to-cell signalling or chemical surface conditioning, to simulate the observed distribution patterns. Model predictions match empirical observations reasonably well, highlighting the role of biotic interactions even already during very early biofilm formation despite few and distant cells. The transition from single primary cells to clustering accelerated by biotic interactions rather than by reproduction may be particularly advantageous in harsh environments — the rule rather than the exception outside the laboratory

Hydrologic Variability Affects Invertebrate Grazing on Phototrophic Biofilms in Stream Microcosms

The temporal variability of streamflow is known to be a key feature structuring and controlling fluvial ecological communities and ecosystem processes. Although alterations of streamflow regime due to habitat fragmentation or other anthropogenic factors are ubiquitous, a quantitative understanding of their implications on ecosystem structure and function is far from complete. Here, by experimenting with two contrasting flow regimes in stream microcosms, we provide a novel mechanistic explanation for how fluctuating flow regimes may affect grazing of phototrophic biofilms (i.e., periphyton) by an invertebrate species (Ecdyonurus sp.). In both flow regimes light availability was manipulated as a control on autotroph biofilm productivity and grazer activity, thereby allowing the test of flow regime effects across various ratios of biofilm biomass to grazing activity. Average grazing rates were significantly enhanced under variable flow conditions and this effect was highest at intermediate light availability. Our results suggest that stochastic flow regimes, characterised by suitable fluctuations and temporal persistence, may offer increased windows of opportunity for grazing under favourable shear stress conditions. This bears important implications for the development of comprehensive schemes for water resources management and for the understanding of trophic carbon transfer in stream food webs

Advective velocity and energy dissipation rate in an oscillatory flow

Characterizing the transport processes at the sediment-water interface along sloping boundaries in lakes and reservoirs is of fundamental interest in lake and reservoir water quality management. The turbulent bottom boundary layer (TBBL) along a slope, induced by the breaking of internal waves in a linearly stratified fluid, was investigated through laboratory measurements. Fast response micro-scale conductivity and temperature probes in conjunction with laser-Doppler velocimetry were used to measure the time series of salinity, temperature, and velocity along a sloping boundary. Turbulent energy spectra were computed from the velocity data using a time-dependent advective velocity and Taylor's hypothesis. The energy spectra were used to estimate the energy dissipation rate at different positions in the TBBL. The advective velocity in this near-zero mean shear flow is based on an integral time scale (Tint). The integral time scale is related to the average frequency of the spectral energy density of the flow velocity. The energy dissipation rate estimated from the variable advective velocity with an averaging time window equal to the integral time scale (T = T-int) was 43% higher than the energy dissipation rate estimated from a constant advective velocity. The estimated dissipation rates with T = T-int were comparable to values obtained by curve-fitting a theoretical Batchelor spectrum for the temperature gradient spectra. This study proposes the integral time scale to be used for the oscillatory flows as (a) a time-averaging window to estimate the advective velocity and associated energy dissipation level, and (b) a normalizing parameter in the energy spectrum