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The Laurentian Great Lakes (LGL) constitute one of the largest freshwater systems in the world while providing social and economic value to two powerful nations. The spatial scale of these inland seas falls between two endpoints: small lakes and oceans. Lacustrine in many characteristics, the LGL often require a scientific approach with attributes similar to those of oceanography. There is a strong sense that within the LGL support for scientific research has not kept pace with the need for process-oriented research and that we lack basic information needed to forecast change, mitigate impacts and restore and preserve the LGL. Consequently, 58 researchers met in September 2014 and identified five “Grand Challenges for Research in the LGL”: (1) How has this vast inland freshwater system responded to shifting climate in the past, and how will it respond in the future? (2) What is the current status of the most important ecosystem processes, including their variability in space and time? (3) What processes are characteristic only of large lakes, and how do the distinct habitats integrate into a whole? (4) What are the ecosystem responses to major anthropogenic forces such as nutrients and invasive species, and are these reversible? and (5) What are the small to large-scale linkages and feedbacks among societal decisions, biological systems, and physicochemical dynamics? An urgent need exists for a unified scientific voice that articulates the Grand Challenges for research in the LGL and the need for associated funding. This treatise describing the Grand Challenges develops that voice.

Water movement can influence the distribution of benthos, in part, by increasing food delivery; however, the impact of advective transport and turbulent diffusion on organic matter flux to nearshore benthic communities is not well quantified. In this study, we measured the vertical particulate organic carbon (POC) and particulate phosphorus (PP) flux in nearshore Lake Michigan using two naturally occurring daughter/parent radionuclide pairs (234Th/238U and 90Y/90Sr) and compared these fluxes to coincident benthic chamber estimates of respiration and total phosphorus efflux by quagga mussels on the lakebed. We found that advective onshore transport and vertical convective mixing increased POC and PP flux to the nearshore benthos by a factor of ∼ 15 and ∼ 30 over offshore trap‐derived estimates of flux. From these results, we hypothesize that high benthos population densities are related to an edge effect created when the dominant mechanism of particle delivery transitions from gravitational settling to convection.

Green Bay, while representing only ~7% of the surface area and ~1.4% of the volume of Lake Michigan, contains one-third of the watershed of the lake, and receives approximately one-third of the total nutrient loading to the Lake Michigan basin, largely from the Fox River at the southern end of the bay. With a history of eutrophic conditions dating back nearly a century, the southern portion of the bay behaves as an efficient nutrient and sediment trap, sequestering much of the annual carbon and nitrogen input within sediments accumulating at up to 1 cm per year. Depositional fluxes of organic matter varied from ~0.1 mol C m22 yr21 to >10 mol C m−2 yr−1 and were both fairly uniform in stoichiometric composition and relatively labile. Estimates of benthic recycling derived from pore-water concentration gradients, whole-sediment incubation experiments, and deposition-burial models of early diagenesis yielded an estimated 40% of the carbon and 50% of the nitrogen recycled back into the overlying water. Remineralization was relatively rapid with ~50% of the carbon remineralized within ~15 yr of deposition, and a mean residence time for metabolizable carbon and nitrogen in the sediments of 20 yr. On average, organic carbon regeneration occurred as 75% CO2, 15% CH4, and 10% dissolved organic carbon (DOC). Carbon and nitrogen budgets for the southern bay were based upon direct measurements of inputs and burial and upon estimates of export and production derived stoichiometrically from a coupled phosphorus budget. Loadings of organic carbon from rivers were ~3.7 mol m−2 yr−1, 80% in the form of DOC and 20% as particulate organic carbon. These inputs were lost through export to northern Green Bay and Lake Michigan (39%), through sediment burial (26%), and net CO2 release to the atmosphere (35%). Total carbon input, including new production, was 4.54 mol m−2 yr−1, equivalent to ~10% of the gross annual primary production. Nitrogen budget terms were less well quantified, with nitrogen export ~54% of total inputs and burial ~24%, leaving an unquantified residual loss term in the nitrogen budget of ~22%.

A low-cost self-contained underwater particle image velocimetry (UWPIV) system has been developed to measure small-scale turbulent flow structures in situ. The UWPIV employs a compact continuous-wave laser and an optical scanner to deliver a light sheet that illuminates naturally occurring particles. Particle images are taken by a CCD camera along with an ultra-compact PC. The nontethered and compact design can be fit in two small underwater housings with all components powered by batteries: an ideal design for a variety of in situ deployments. The system has been field-tested in the coastal zone of Lake Michigan. Turbulent flow structures of the wave-current bottom boundary layer are measured right above the nearshore lakebed, which is densely covered by quagga mussels (Dreissena bugensis). Vertical profiles of mean velocity, Reynolds stresses, dissipation rate of the turbulent kinetic energy, turbulent viscosity, plankton particle concentration, and the turbulent flux of particles are presented and discussed.

Measured port-water concentration profiles for dissolved ammonium, phosphate, total inorganic carbon, and sulfate show a distinct seasonal cycle in response to the temperature dependence of rates of microbially mediated organic matter oxidation in sediments at Cape Lookout Bight, N.C. The depth and temperature dependence of measured production and consumption rates, adsorption coefficients, apparent diffusion cocllicients, and sediment porosities were combined to construct a diagenetic model of ammonium production, ZCOz production, and sulfate reduction that was timetcmpcraturc- and depth-dependent. Numerical predictions of pore-water concentrations from a set of initial spring conditions agree well with measured port-water profiles through summer and fall-the period of greatest change in reaction rates in response to seasonal fluctuations in temperature. Modeling also indicates that inclusion of complex, porosity-dependent terms, even in the time- and tcmperaturc-depcndcnt cast, is probably unnecessary in these sediments; simpler, constant-porosity models give results that generally deviate ~4% from the predictions of complex models.