Environmental DNA provides quantitative estimates of Pacific hake abundance and distribution in the open ocean.

All species inevitably leave genetic traces in their environments, and the resulting environmental DNA (eDNA) reflects the species present in a given habitat. It remains unclear whether eDNA signals can provide quantitative metrics of abundance on which human livelihoods or conservation successes depend. Here, we report the results of a large eDNA ocean survey (spanning 86 000 km2 to depths of 500 m) to understand the abundance and distribution of Pacific hake (Merluccius productus), the target of the largest finfish fishery along the west coast of the USA. We sampled eDNA in parallel with a traditional acoustic-trawl survey to assess the value of eDNA surveys at a scale relevant to fisheries management. Despite local differences, the two methods yield comparable information about the broad-scale spatial distribution and abundance. Furthermore, we find depth and spatial patterns of eDNA closely correspond to acoustic-trawl estimates for hake. We demonstrate the power and efficacy of eDNA sampling for estimating abundance and distribution and move the analysis eDNA data beyond sample-to-sample comparisons to management relevant scales. We posit that eDNA methods are capable of providing general quantitative applications that will prove especially valuable in data- or resource-limited contexts.

Field measurements of acoustic absorption in seawater from 38 to 360 kHz.

Accurate estimates of acoustic absorption in seawater are crucial to the acoustic estimation of aquatic biomass. Estimates of acoustic absorption were obtained via a "pulse-echo" method, implemented using commonly available scientific echosounders and spherical calibration targets over a range of discrete frequencies. Below about 200 kHz, the absorption estimates were not significantly different from those of existing formulas, but at around 333 kHz, the measured absorption was 15 dB km-1 higher than estimated from existing formulas. Measurement variability was about ±2 dB km-1 for all frequencies. This is consistent with an observed anomaly between modelled and measured frequency-dependent biological backscatter. Allowing for this deviation will avoid incorrect spectral-based classification of acoustic targets and improve uncertainty in aquatic biomass estimation.

ZooScatR-An r package for modelling the scattering properties of weak scattering targets using the distorted wave Born approximation.

A thorough understanding of the scattering characteristics of marine organisms is a prerequisite for robust quantitative fisheries acoustic data processing or interpretation. Target strength models, such as the distorted wave Born approximation (DWBA) can be used to improve the understanding of field recordings of weakly scattering targets. With acoustic methods now being used by a wide audience, allowing access to such models becomes a necessity. To ease access to the DWBA model, an r package (zooscatr) which includes a web application and the ability to parameterise the model either through the web application, text files, or pure scripting has been developed and is now freely available on Github.

Estimation of biological parameters of marine organisms using linear and nonlinear acoustic scattering model-based inversion methods.

The linear inversion commonly used in fisheries and zooplankton acoustics assumes a constant inversion kernel and ignores the uncertainties associated with the shape and behavior of the scattering targets, as well as other relevant animal parameters. Here, errors of the linear inversion due to uncertainty associated with the inversion kernel are quantified. A scattering model-based nonlinear inversion method is presented that takes into account the nonlinearity of the inverse problem and is able to estimate simultaneously animal abundance and the parameters associated with the scattering model inherent to the kernel. It uses sophisticated scattering models to estimate first, the abundance, and second, the relevant shape and behavioral parameters of the target organisms. Numerical simulations demonstrate that the abundance, size, and behavior (tilt angle) parameters of marine animals (fish or zooplankton) can be accurately inferred from the inversion by using multi-frequency acoustic data. The influence of the singularity and uncertainty in the inversion kernel on the inversion results can be mitigated by examining the singular values for linear inverse problems and employing a non-linear inversion involving a scattering model-based kernel.

Calibration of a broadband acoustic transducer with a standard spherical target in the near field.

This paper investigates the applicability of calibrating a broadband acoustic system in the near field. The calibration was performed on a single transducer with a mono-static configuration using a single standard target, a 25-mm tungsten carbide sphere in the nearfield of both the transducer and the sphere. A theoretical model was developed to quantify the nearfield effect. Numerical simulations revealed that the frequency responses at different distances varied significantly, the null positions were essentially invariant-a unique characteristic for determination of the compressional and shear wave speeds in the calibration sphere. The calibration curves obtained in the near field could be applied to farfield once the nearfield effects were accounted for. Since the transducer was located in the near field, the signal-to-noise ratio was high, resulting in a much wider useable bandwidth than the nominal bandwidth. The resultant calibration uncertainty, i.e., root-mean-square uncertainty over the entire usable frequency band was 1.05 dB and reduces to 0.33 dB when the regions corresponding to nulls were excluded. The methods reported here could potentially be applied to the calibration of multibeam and broadband echosounder/sonar systems since it is difficult to meet the farfield condition for outermost beams when shipboard calibrations are needed.

Target strengths of two abundant mesopelagic fish species.

Mesopelagic fish of the Myctophidae and Sternoptychidae families dominate the biomass of the oceanic deep scattering layers and, therefore, have important ecological roles within these ecosystems. Interest in the commercial exploitation of these fish is growing, so the development of techniques for estimating their abundance, distribution and, ultimately, sustainable exploitation are essential. The acoustic backscattering characteristics for two size classes of Maurolicus muelleri and Benthosema glaciale are reported here based on swimbladder morphology derived from digitized soft x-ray images, and empirical (in situ) measurements of target strength (TS) derived from an acoustic survey in a Norwegian Sea. A backscattering model based on a gas-filled prolate spheroid was used to predict the theoretical TS for both species across a frequency range between 0 and 250 kHz. Sensitivity analyses of the TS model to the modeling parameters indicate that TS is rather sensitive to the viscosity, swimbladder volume ratio, and tilt, which can result in substantial changes to the TS. Theoretical TS predictions close to the resonance frequency were in good agreement (±2 dB) with mean in situ TS derived from the areas acoustically surveyed that were spatially and temporally consistent with the trawl information for both species.

Comparisons among ten models of acoustic backscattering used in aquatic ecosystem research.

Analytical and numerical scattering models with accompanying digital representations are used increasingly to predict acoustic backscatter by fish and zooplankton in research and ecosystem monitoring applications. Ten such models were applied to targets with simple geometric shapes and parameterized (e.g., size and material properties) to represent biological organisms such as zooplankton and fish, and their predictions of acoustic backscatter were compared to those from exact or approximate analytical models, i.e., benchmarks. These comparisons were made for a sphere, spherical shell, prolate spheroid, and finite cylinder, each with homogeneous composition. For each shape, four target boundary conditions were considered: rigid-fixed, pressure-release, gas-filled, and weakly scattering. Target strength (dB re 1 m(2)) was calculated as a function of insonifying frequency (f = 12 to 400 kHz) and angle of incidence (θ = 0° to 90°). In general, the numerical models (i.e., boundary- and finite-element) matched the benchmarks over the full range of simulation parameters. While inherent errors associated with the approximate analytical models were illustrated, so were the advantages as they are computationally efficient and in certain cases, outperformed the numerical models under conditions where the numerical models did not converge.

Acoustic scattering by gas-bearing cyanobacterium Microcystis: Modeling and in situ biomass assessment.

Cyanobacterial harmful algal blooms (HABs) are increasing in a growing number of aquatic ecosystems around the world due to eutrophication and climatic change over the past few decades. Quantitative monitoring of HABs remains a challenge because their distributions are spatially heterogeneous and temporally variable. Most of the standard biological sampling methods are labor intensive and time consuming. In this paper, we present an efficient acoustic method to assess the biomass (biovolume) concentration of the cyanobacterium Microcystis in aquatic ecosystems. Acoustic backscattering vertical profiles from a gas-bearing Microcystis population were measured with echosounders at three frequencies (70, 120, and 333 kHz) in Lake Kinneret (case study). Concurrently, the volume concentration of Microcystis colonies and cyanobacteria-related Chlorophyll a were evaluated. We developed a partially coherent acoustic scattering model to quantify the cyanobacterium biomass based on depth-dependent acoustic backscattering signals. We also evaluated empirical regression models to obtain the Microcystis biomass from acoustically measured volume backscattering strength, Sv. It is demonstrated that both methods can convert the Sv to Microcystis biovolume concentrations reasonably well. Pro and cons of these methods are discussed. The results suggest that the presented methods may have a potential to be used for broader applications to monitor and quantify the gas-containing plankton in large aquatic ecosystems.

Calibration of broadband active acoustic systems using a single standard spherical target.

When calibrating a broadband active acoustic system with a single standard target such as a sphere, the inherent resonances associated with the scattering by the sphere pose a significant challenge. In this paper, a method is developed which completely eliminates the source of resonances through isolating and exploiting the echo from the front interface of a sphere. This echo is relatively insensitive to frequency over a wide range of frequencies, lacking resonances, and is relatively insensitive to small changes in material properties and, in the case of spherical shells, shell thickness. The research builds upon the concept of using this echo for calibration in the work of Dragonette et al. [J. Acoust. Soc. Am. 69, 1186-1189 (1981)]. This current work generalizes that of Dragonette by (1) incorporating a pulse compression technique to significantly improve the ability to resolve the echo, and (2) rigorously accounting for the scattering physics of the echo so that the technique is applicable over a wide range of frequencies and material properties of the sphere. The utility of the new approach is illustrated through application to data collected at sea with an air-filled aluminum spherical shell and long broadband chirp signals (30-105 kHz).

Acoustic diffraction by deformed edges of finite length: theory and experiment.

The acoustic diffraction by deformed edges of finite length is described analytically and in the frequency domain through use of an approximate line-integral formulation. The formulation is based on the diffraction per unit length of an infinitely long straight edge, which inherently limits the accuracy of the approach. The line integral is written in terms of the diffraction by a generalized edge, in that the "edge" can be a single edge or multiple closely spaced edges. Predictions based on an exact solution to the impenetrable infinite knife edge are used to estimate diffraction by the edge of a thin disk and compared with calculations based on the T-matrix approach. Predictions are then made for the more complex geometry involving an impenetrable thick disk. These latter predictions are based on an approximate formula for double-edge diffraction [Chu et al., J. Acoust. Soc. Am. 122, 3177 (2007)] and are compared with laboratory data involving individual elastic (aluminum) disks spanning a range of diameters and submerged in water. The results of this study show this approximate line-integral approach to be versatile and applicable over a range of conditions.

Higher-order acoustic diffraction by edges of finite thickness.

A cw solution of acoustic diffraction by a three-sided semi-infinite barrier or a double edge, where the width of the midplanar segment is finite and cannot be ignored, involving all orders of diffraction is presented. The solution is an extension of the asymptotic formulas for the double-edge second-order diffraction via amplitude and phase matching given by Pierce [A. D. Pierce, J. Acoust. Soc. Am. 55, 943-955 (1974)]. The model accounts for all orders of diffraction and is valid for all kw, where k is the acoustic wave number and w is the width of the midplanar segment and reduces to the solution of diffraction by a single knife edge as w-->0. The theory is incorporated into the deformed edge solution [Stanton et al., J. Acoust. Soc. Am. 122, 3167 (2007)] to model the diffraction by a disk of finite thickness, and is compared with laboratory experiments of backscattering by elastic disks of various thicknesses and by a hard strip. It is shown that the model describes the edge diffraction reasonably well in predicting the diffraction as a function of scattering angle, edge thickness, and frequency.

Improved parameterization of Antarctic krill target strength models.

There are historical discrepancies between empirical observations of Antarctic krill target strength and predictions using theoretical scattering models. These differences are addressed through improved understanding of key model parameters. The scattering process was modeled using the distorted-wave Born approximation, representing the shape of the animal as a bent and tapered cylinder. Recently published length-based regressions were used to constrain the sound speed and density contrasts between the animal and the surrounding seawater, rather than the earlier approach of using single values for all lengths. To constrain the parameter governing the orientation of the animal relative to the incident acoustic wave, direct measurements of the orientation of krill in situ were made with a video plankton recorder. In contrast to previous indirect and aquarium-based observations, krill were observed to orient themselves mostly horizontally. Averaging predicted scattering over the measured distribution of orientations resulted in predictions of target strength consistent with in situ measurements of target strength of large krill (mean length 40-43 mm) at four frequencies (43-420 kHz), but smaller than expected under the semi-empirical model traditionally used to estimate krill target strength.

Protocols for calibrating multibeam sonar.

Development of protocols for calibrating multibeam sonar by means of the standard-target method is documented. Particular systems used in the development work included three that provide the water-column signals, namely the SIMRAD SM2000/90- and 200-kHz sonars and RESON SeaBat 8101 sonar, with operating frequency of 240 kHz. Two facilities were instrumented specifically for the work: a sea well at the Woods Hole Oceanographic Institution and a large, indoor freshwater tank at the University of New Hampshire. Methods for measuring the transfer characteristics of each sonar, with transducers attached, are described and illustrated with measurement results. The principal results, however, are the protocols themselves. These are elaborated for positioning the target, choosing the receiver gain function, quantifying the system stability, mapping the directionality in the plane of the receiving array and in the plane normal to the central axis, measuring the directionality of individual beams, and measuring the nearfield response. General preparations for calibrating multibeam sonars and a method for measuring the receiver response electronically are outlined. Advantages of multibeam sonar calibration and outstanding problems, such as that of validation of the performance of multibeam sonars as configured for use, are mentioned.

On the acoustic diffraction by the edges of benthic shells.

Recent laboratory measurements of acoustic backscattering by individual benthic shells have isolated the edge-diffracted echo from echoes due to the surface of the main body of the shell. The data indicate that the echo near broadside incidence is generally the strongest for all orientations and is due principally to the surface of the main body. At angles well away from broadside, the echo levels are lower and are due primarily to the diffraction from the edge of the shell. The decrease in echo levels from broadside incidence to well off broadside is shown to be reasonably consistent with the decrease in acoustic backscattering from normal incidence to well off normal incidence by a shell-covered seafloor. The results suggest the importance of the edge of the shell in off-normal-incidence backscattering by a shell-covered seafloor. Furthermore, when considering bistatic diffraction by edges, there are implications that the edge of the shell (lying on the seafloor) can cause significant scattering in many directions, including at subcritical angles.

Three-dimensional modeling of acoustic backscattering from fluid-like zooplankton.

Scattering models that correctly incorporate organism size and shape are a critical component for the remote detection and classification of many marine organisms. In this work, an acoustic scattering model has been developed for fluid-like zooplankton that is based on the distorted wave Born approximation (DWBA) and that makes use of high-resolution three-dimensional measurements of the animal's outer boundary shape. High-resolution computerized tomography (CT) was used to determine the three-dimensional digitizations of animal shape. This study focuses on developing the methodology for incorporating high-resolution CT scans into a scattering model that is generally valid for any body with fluid-like material properties. The model predictions are compared to controlled laboratory measurements of the acoustic backscattering from live individual decapod shrimp. The frequency range used was 50 kHz to 1 MHz and the angular characteristics of the backscattering were investigated with up to a 1 degree angular resolution. The practical conditions under which it is necessary to make use of high-resolution digitizations of shape are assessed.