[1] Shear instability is the dominant mechanism for converting fluid motion to mixing in the stratified ocean and atmosphere. The transition to turbulence has been well characterized in laboratory settings and numerical simulations at moderate Reynolds number-it involves "rolling up", i.e., overturning of the density structure within the cores of the instabilities. In contrast, measurements in an energetic estuarine shear zone reveal that the mixing induced by shear instability at high Reynolds number does not primarily occur by overturning in the cores; rather it results from secondary shear instabilities within the zones of intensified shear separating the cores. This regime is not likely to be observed in the relatively low Reynolds number flows of the laboratory or in direct numerical simulations, but it is likely a common occurrence in the ocean and atmosphere.

Environmental DNA (eDNA) analysis from water samples is a promising new method to identify both targeted species and whole communities of aquatic organisms. However, the current literature regarding eDNA shedding rates primarily focuses on fish and most decay rate constants are reported for warm sunlit waters. Here, we conducted experiments to investigate how eDNA shedding differs between animal forms and how long eDNA can persist in waters of varying temperature and light conditions. We designed quantitative PCR assays for one fish (mummichog, Fundulus heteroclitus), one crustacean (grass shrimp, Palaemon spp.), and two scyphomedusae (moon jelly, Aurelia aurita and nettle, Chrysaora spp.) to estimate eDNA shedding and decay rates. We found that shedding rates were highly variable for all organisms, but grass shrimp had the lowest shedding rate. We quantified eDNA decay rate constants at 6, 15, and 23°C and found that decay rate constants of mummichog and grass shrimp were larger at higher temperatures, while those of scyphomedusae did not show clear temperature dependence. We also found that higher‐order decay models with tails fit the data better than first‐order log‐linear models, suggesting temporal variability in eDNA decay rates. Results indicate that different animal forms shed different types of eDNA, impacting both shedding and decay rates. These findings fill critical knowledge gaps regarding variation in eDNA shedding and decay across animal forms under a range of realistic marine temperature conditions. These data will be useful for interpreting field studies that utilize eDNA to investigate ocean habitats that are otherwise difficult to access.

High-frequency acoustic scattering techniques have been used to investigate dominant scatterers in mixed zooplankton populations. Volume backscattering was measured in the Gulf of Maine at 43, 120, 200, and 420 kHz. Zooplankton composition and size were determined using net and video sampling techniques, and water properties were determined using conductivity, temperature, and depth sensors. Dominant scatterers have been identified using recently developed scattering models for zooplankton and microstructure. Microstructure generally did not contribute to the scattering. At certain locations, gas-bearing zooplankton, that account for a small fraction of the total abundance and biomass, dominated the scattering at all frequencies. At these locations, acoustically inferred size agreed well with size determined from the net samples. Significant differences between the acoustic, net, and video estimates of abundance for these zooplankton are most likely due to limitations of the net and video techniques. No other type of biological scatterer ever dominated the scattering at all frequencies. Copepods, fluid-like zooplankton that account for most of the abundance and biomass, dominated at select locations only at the highest frequencies. At these locations, acoustically inferred abundance agreed well with net and video estimates. A general approach for the difficult problem of interpreting high-frequency acoustic scattering in mixed zooplankton populations is described.

Lavery, A. C., Chu, D., and Moum, J. N. 2010. Measurements of acoustic scattering from zooplankton and oceanic microstructure using a broadband echosounder. – ICES Journal of Marine Science, 67: 379–394. In principle, measurements of high-frequency acoustic scattering from oceanic microstructure and zooplankton across a broad range of frequencies can reduce the ambiguities typically associated with the interpretation of acoustic scattering at a single frequency or a limited number of discrete narrowband frequencies. With this motivation, a high-frequency broadband scattering system has been developed for investigating zooplankton and microstructure, involving custom modifications of a commercially available system, with almost complete acoustic coverage spanning the frequency range 150–600 kHz. This frequency range spans the Rayleigh-to-geometric scattering transition for some zooplankton, as well as the diffusive roll-off in the spectrum for scattering from turbulent temperature microstructure. The system has been used to measure scattering from zooplankton and microstructure in regions of non-linear internal waves. The broadband capabilities of the system provide a continuous frequency response of the scattering over a wide frequency band, and improved range resolution and signal-to-noise ratios through pulse-compression signal-processing techniques. System specifications and calibration procedures are outlined and the system performance is assessed. The results point to the utility of high-frequency broadband scattering techniques in the detection, classification, and under certain circumstances, quantification of zooplankton and microstructure.

Increasingly, researchers are using innovative methods to census marine life, including identification of environmental DNA (eDNA) left behind by organisms in the water column. However, little is understood about how eDNA is distributed in the ocean, given that organisms are mobile and that physical and biological processes can transport eDNA after release from a host. Particularly in the vast mesopelagic ocean where many species vertically migrate hundreds of meters diurnally, it is important to link the location at which eDNA was shed by a host organism to the location at which eDNA was collected in a water sample. Here, we present a one-dimensional mechanistic model to simulate the eDNA vertical distribution after its release and to compare the impact of key biological and physical parameters on the eDNA vertical and temporal distribution. The modeled vertical eDNA profiles allow us to quantify spatial and temporal variability in eDNA concentration and to identify the most important parameters to consider when interpreting eDNA signals. We find that the vertical displacement by advection, dispersion, and settling has limited influence on the eDNA distribution, and the depth at which eDNA is found is generally within tens of meters of the depth at which the eDNA was originally shed from the organism. Thus, using information about representative vertical migration patterns, eDNA concentration variability can be used to answer ecological questions about migrating organisms such as what depths species can be found in the daytime and nighttime and what percentage of individuals within a species diurnally migrate. These findings are critical both to advance the understanding of the vertical distribution of eDNA in the water column and to link eDNA detection to organism presence in the mesopelagic ocean as well as other aquatic environments.

High-frequency broadband acoustic scattering techniques have enabled the remote, high-resolution imaging and quantification of highly salt-stratified turbulence in an estuary. Turbulent salinity spectra in the stratified shear layer have been measured acoustically and by in situ turbulence sensors. The acoustic frequencies used span 120-600 kHz, which, for the highly stratified and dynamic estuarine environment, correspond to wavenumbers in the viscous-convective subrange (500-2500 m À1 ). The acoustically measured spectral levels are in close agreement with spectral levels measured with closely co-located micro-conductivity probes. The acoustically measured spectral shapes allow discrimination between scattering dominated by turbulent salinity microstructure and suspended sediments or swim-bladdered fish, the two primary sources of scattering observed in the estuary in addition to turbulent salinity microstructure. The direct comparison of salinity spectra inferred acoustically and by the in situ turbulence sensors provides a test of both the acoustic scattering model and the quantitative skill of acoustical remote sensing of turbulence dissipation in a strongly sheared and salt-stratified estuary.

Acoustic scattering techniques provide a unique and powerful tool to remotely investigate the physical properties of the ocean interior over large spatial and temporal scales. With high-frequency acoustic scattering it is possible to probe physical processes that occur at the microstructure scale, spanning submillimeter to centimeter scale processes. An acoustic scattering model for turbulent oceanic microstructure is presented in which the current theory, which only accounts for fluctuations in the sound speed, has been extended to include fluctuations in the density as well. The inclusion of density fluctuations results in an expression for the scattering cross section per unit volume, v , that is explicitly dependent on the scattering angle. By relating the variability in the density and sound speed to random fluctuations in oceanic temperature and salinity, v has been expressed in terms of the temperature and salinity wave number spectra, and the temperature-salinity co-spectrum. A Batchelor spectrum for temperature and salinity, which depends on parameters such as the dissipation rates of turbulent kinetic energy and temperature variance, has been used to evaluate v . Two models for the temperature-salinity co-spectrum have also been used. The predictions indicate that fluctuations in the density could be as important in determining backscattering as fluctuations in the sound speed. Using data obtained in the ocean with a high resolution vertical microstructure profiler, it is predicted that scattering from oceanic microstructure can be as strong as scattering from zooplankton.

Animal biodiversity in the ocean’s vast mesopelagic zone is relatively poorly studied due to technological and logistical challenges. Environmental DNA (eDNA) analyses show great promise for efficiently characterizing biodiversity and could provide new insight into the presence of mesopelagic species, including those that are missed by traditional net sampling. Here, we explore the utility of eDNA for identifying animal taxa. We describe the results from an August 2018 cruise in Slope Water off the northeast United States. Samples for eDNA analysis were collected using Niskin bottles during five CTD casts. Sampling depths along each cast were selected based on the presence of biomass as indicated by the shipboard Simrad EK60 echosounder. Metabarcoding of the 18S V9 gene region was used to assess taxonomic diversity. eDNA metabarcoding results were compared with those from net-collected (MOCNESS) plankton samples. We found that the MOCNESS sampling recovered more animal taxa, but the number of taxa detected per liter of water sampled was significantly higher in the eDNA samples. eDNA was especially useful for detecting delicate gelatinous animals which are undersampled by nets. We also detected eDNA changes in community composition with depth, but not with sample collection time (day vs. night). We provide recommendations for applying eDNA-based methods in the mesopelagic including the need for studies enabling interpretation of eDNA signals and improvement of barcode reference databases.