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Abstract Small-scale turbulent mixing drives the upwelling of deep water masses in the abyssal ocean as part of the global overturning circulation¹. However, the processes leading to mixing and the pathways through which this upwelling occurs remain insufficiently understood. Recent observational and theoretical work^2–5has suggested that deep-water upwelling may occur along the ocean’s sloping seafloor; however, evidence has, so far, been indirect. Here we show vigorous near-bottom upwelling across isopycnals at a rate of the order of 100 metres per day, coupled with adiabatic exchange of near-boundary and interior fluid. These observations were made using a dye released close to the seafloor within a sloping submarine canyon, and they provide direct evidence of strong, bottom-focused diapycnal upwelling in the deep ocean. This supports previous suggestions that mixing at topographic features, such as canyons, leads to globally significant upwelling^3,6–8. The upwelling rates observed were approximately 10,000 times higher than the global average value required for approximately 30 × 10⁶m³s⁻¹of net upwelling globally⁹. 

We contend that ocean turbulent fluxes should be included in the list of Essential Ocean Variables (EOVs) created by the Global Ocean Observing System. This list aims to identify variables that are essential to observe to inform policy and maintain a healthy and resilient ocean. Diapycnal turbulent fluxes quantify the rates of exchange of tracers (such as temperature, salinity, density or nutrients, all of which are already EOVs) across a density layer. Measuring them is necessary to close the tracer concentration budgets of these quantities. Measuring turbulent fluxes of buoyancy (J_b), heat (J_q), salinity (J_S) or any other tracer requires either synchronous microscale (a few centimeters) measurements of both the vector velocity and the scalar (e.g., temperature) to produce time series of the highly correlated perturbations of the two variables, or microscale measurements of turbulent dissipation rates of kinetic energy (ϵ) and of thermal/salinity/tracer variance (χ), from which fluxes can be derived. Unlike isopycnal turbulent fluxes, which are dominated by the mesoscale (tens of kilometers), microscale diapycnal fluxes cannot be derived as the product of existing EOVs, but rather require observations at the appropriate scales. The instrumentation, standardization of measurement practices, and data coordination of turbulence observations have advanced greatly in the past decade and are becoming increasingly robust. With more routine measurements, we can begin to unravel the relationships between physical mixing processes and ecosystem health. In addition to laying out the scientific relevance of the turbulent diapycnal fluxes, this review also compiles the current developments steering the community toward such routine measurements, strengthening the case for registering the turbulent diapycnal fluxes as an pilot Essential Ocean Variable. 

The transition from winter to spring represents a major shift in the basal energy source for the Antarctic marine ecosystem from lipids and other sources of stored energy to sunlight. Because sea ice imposes a strong control on the transmission of sunlight into the water column during the polar spring, we hypothesized that the timing of the sea ice retreat influences the timing of the transition from stored energy to photosynthesis. To test the influence of sea ice on water column microbial energy utilization we took advantage of unique sea ice conditions in Arthur Harbor, an embayment near Palmer Station on the western Antarctic Peninsula, during the 2015 spring–summer seasonal transition. Over a 5-week period we sampled water from below land-fast sea ice, in the marginal ice zone at nearby Palmer Station B, and conducted an ice removal experiment with incubations of water collected below the land-fast ice. Whole-community metatranscriptomes were paired with lipidomics to better understand how lipid production and utilization was influenced by light conditions. We identified several different phytoplankton taxa that responded similarly to light by the number of genes up-regulated, and in the transcriptional complexity of this response. We applied a principal components analysis to these data to reduce their dimensionality, revealing that each of these taxa exhibited a strikingly different pattern of gene up-regulation. By correlating the changes in lipid concentration to the first principal component of log fold-change for each taxa we could make predictions about which taxa were associated with different changes in the community lipidome. We found that genes coding for the catabolism of triacylglycerol storage lipids were expressed early on in phytoplankton associated with aFragilariopsis kerguelensisreference transcriptome. Phytoplankton associated with aCorethron pennatumreference transcriptome occupied an adjacent niche, responding favorably to higher light conditions thanF. kerguelensis. Other diatom and dinoflagellate taxa had distinct transcriptional profiles and correlations to lipids, suggesting diverse ecological strategies during the polar winter–spring transition.