Fish schools are known to take a large number of different shapes and dimensions, in such a way that defining a school from its morphology is still an unanswered question. Nevertheless, some school typology and classification has been done successfully in different areas of the world using vertical echo sounding data. This implies that some morphological patterns may correspond to or reflect behavioural specificities. The objective of this paper is to take advantage of the 3D exhaustive observation capabilities of multibeam sonar to extract the morphological and internal characteristics of tropical clupeid schools. The main parameters measured are geometrical properties (overall dimensions, volume, surface, etc.) and relative distribution of densities inside the school (heterogeneity, existence of nuclei, etc.). The main results show that a school is usually formed of one or several nuclei of high density connected by less dense parts, including empty areas (vacuoles). The dimension of these sub-units is highly variable, but remains inside a diameter of 5-20 m. The reliability of these dimensions is evaluated, and some thoughts on the behavioural mechanisms constituting schools are presented.

Standard geostatistical techniques provide effective methods for estimating the global abundance and precision of a variable of interest, for mapping its spatial distribution and for describing its spatial structure. In the case of acoustic survey data, however, obtaining a measure of precision of the global abundance estimate is confounded by the combination of variances from the interpolation of both the acoustic data and the concomitant fish length data. Even if the global estimation variance could be calculated, the distribution of the estimation error is not known and so confidence intervals cannot be determined. Furthermore, kriged distribution maps, in minimising the estimation variance, tend to smooth out local details of the attribute’s spatial variation: small values can be overestimated and larger ones underestimated, such that the kriged map is smoother than reality. This can lead to serious shortcomings when trying to detect patterns of extreme attribute values, such as the high densities encountered in some fish schools. Stochastic geostatistical simulations, conditional on sampled locations, provide a solution to many of these problems. They can deliver a measure of uncertainty for local (density) estimates, a confidence interval estimation for the global mean density, and finally, reproduce global statistics, such as the sample histogram and variogram. In so doing, they also provide maps of the attribute, which are spatially realistic because the variogram is reproduced; these are generated as a number of equiprobable realisations. In the present paper, we apply these techniques to acoustic data from an acoustic survey of North Sea herring. Sequential gaussian simulations are used to generate realisations for fish length and values of the nautical area scattering coefficient. These are then combined to produce realisations of herring density. The combined set of multiple realisations is then used to provide confidence intervals for the global abundance estimate: 95% of the herring abundance estimates are between 5677 and 6271 millions of individuals. Although the method presented in this paper contributes to the assessment of total uncertainty for acoustic surveys, the approach may have suffered from bias due to the use of off-the-shelf data transformation algorithms on fisheries acoustic data, which are often very positively skewed. We discuss this limitation and propose corrections for future work.

Since the June 1995 ICES Symposium on Fisheries and Plankton Acoustics in Aberdeen (MacLennan and Holliday, 1996) the use of acoustics for studying zooplankton has seen important advances. Acoustical monitoring of small-scale zooplankton distributions can now be done at intervals of a fraction of a minute. Resolution at vertical spatial scales of tens of centimeters is now easily achieved with commercially available sensors. Multiple-frequency echo-ranging sensors (TAPS™) have been deployed in an up-looking mode on the bottom, and on moorings looking up, down and horizontally. Real-time telemetry provides data on plankton distributions at ranges up to tens of meters from the sensors for periods of weeks to months. These sensors allow one to estimate total zooplankton biomass and the size-abundance spectrum of the animals in the water column at different depths and times. When a profiling CTD and multi-spectral optical sensors were used to define the physical environment and phytoplankton distributions near an acoustical zooplankton profiler, bold relationships were observed between measured spatial and temporal patterns. New methods in zooplankton acoustics are illustrated with data collected from these sensors while monitoring thin, sub-meter thick layers of plankton and diel migrations of benthopelagic crustaceans.

Geostatistical conditional simulations are used to get a family of non-smoothed three-dimensional (3D) images of the St. Lawrence krill aggregation from echointegration data at 38 and 120 kHz on a systematic grid of transects. These maps respect the inherent patchiness of krill. Their ensemble gives an histogram of the krill density estimates at any point of the 3D grid, not only the mean density as in kriging. The spatially consistent simulations are conditional to match the observations and their histogram and variogram. The 3D problem is by-passed by transposing to a short series of 2D ones, which simplifies the modelling of the autocorrelation function and has the additional advantage of reducing by a factor of 5 the number of points to simulate. The spatially structured krill density profile is summarised by the first few factors of a principal component analysis, where the variables are the volume backscattering strength at 120 kHz for the integrated vertical bins along the profiles and the observations are the different profiles. The principal component scores are simulated over a 2D-grid and then used to reconstruct the full 3D-image. The method adequately reproduces the histogram, variogram and mean profile of krill density, and cross-validations replicate the observations. It is as precise as an alternative kriging approach to estimate the mean density, but has the additional advantages of requiring less computing time for our particular application. These conditional simulations enable estimating the probability density function of the krill density at any point, an essential information for predator-prey interactions and other ecosystem studies.

The size of pelagic fish schools depends on several parameters related to internal factors such as species, number of fish, fish swimming speed and physiological status and to external factors, such as hydrological factors and presence of predators. In order to better understand these relations, results coming from echosounder and multibeam sonar databases are analysed. Field data are collected during four acoustic surveys in the Mediterranean Sea in two different areas (Catalan and Adriatic Seas). The analysis shows differences between the two areas regarding size and position in the water column: schools are deeper and their mean size is lower in the Catalan Sea in comparison with Adriatic Sea. The differences in size of schools are mainly related to differences in school length. Moreover, the elongation of schools seen with the sonar is greater than one and half higher in the Adriatic Sea than in the Catalan Sea, whereas one would expect similar values for the two areas. The results are discussed in terms of environmental influence, avoidance reaction and acoustic capabilities of both tools. A hypothesis is proposed: the variation of school length and consecutively the variation of the correlated dimensions is first related to the strength of the avoidance reaction in front of the vessel and this effect can be reinforced depending on the environmental conditions. The model takes into account the effect of the boat, the vertical constraints undergone by the schools, and the internal requirements of the schools, such as the necessity for fish to keep visual contacts and the cohesion of the group.

The fisheries of Lake Victoria in East Africa must be managed effectively to ensure sustainable food supplies. This has been impossible in the past due to inadequate knowledge of commercially important fish stocks. Here we present the first acoustic abundance estimates of fish in Lake Victoria. Five lakewide acoustic surveys were conducted between 1999 and 2001, using the Simrad EY500 echo-integrator with a 120 kHz split-beam transducer. There are many species of fish in Lake Victoria, however, only limited identification of targets can be achieved by present methods. Broad categories were distinguished by visual examination of echo-traces. The echo-integrals were partitioned between four target groups: (1) the Nile perch (Lates niloticus), a top predator, (2) small pelagics comprising mainly the dagaa Rastrineobola argentea together with mixed species of haplochromines, (3) the crustacean Caridina nilotica and (4) other species. Spatial and temporal differences in the Standing Crop were observed between north and south, and between shallow and deep water. Most fish were found inshore but the spatial distribution varied between seasons. Mid-lake fish densities were higher in August compared to February. In August, the water column is well mixed while in February it is stratified with a low-oxygen layer inhospitable to fish near the bottom. There are consequent changes in the characteristics of observed echo-traces. Over the survey series, Nile perch biomass showed a consistent decline, while the stocks of small pelagic species increased. We emphasize the need for simple rules to identify species, and hydrographic monitoring to assist echo-trace classification. In the absence of any other source of comprehensive biomass estimates, the value of acoustic surveying in Lake Victoria is demonstrated.

Hydroacoustical estimation of fish abundance and distribution is performed in three reservoirs that are characterised by different levels of eutrophication. The Biosonics 101 dual beam echosounder with a frequency of 420 kHz and the ESP software for acoustical data analyses are used. A clear dependence between fish density and the level of eutrophication is observed. In the mesotrophic Solina reservoir, fish abundance is over an order of magnitude lower than that in the eutrophic Dobczyce and Sulejów reservoirs. Fish length distributions have different shapes in the three reservoirs, which indicates the changes in fish size structure due to eutrophication; however, the mean target strength of fish does not differ significantly. These results suggest that hydroacoustically collected data may help to assess the ecological state of inland waters and may be used together with other methods in monitoring the water quality.

A 200-kHz split-beam echosounder (BioSonics, DT6000) with a 6° circular-beam transducer was applied in a mangrove channel in Northern Brazil to study the migratory patterns of intertidal fish. Acoustic sampling was conducted horizontally across the channel perpendicular to the tidal current during two lunar cycles in the dry season 2000 and the wet season 2001. The complex acoustic environment of the mangrove channel was characterized by small target sizes (juvenile fish), multiple targets (aggregated fish), high reverberation and background noise levels due to sediment loads, plankton and mangrove litter transport. Dry seasons provided less noisy acoustic conditions resulting in clearer echo data than wet seasons. Neap tide data were less complex than spring tide data. During a tidal cycle, low water provided the clearest acoustic conditions. Mangrove leaves generated fish-like echoes. Analysis of two dry season wax moon cycles revealed fish flux maxima at low water, flood start and high water in the daytime and the night cycle. Night fish fluxes were significantly higher than at daylight. Throughout the tidal cycles, 60% of the fish traveled with the tide and 40% against, suggesting active foraging against the tide to be a major component of fish movements. Resident mangrove fish entered the intertidal creeks at early flood tide, leaving at late ebb tide at fairly shallow-water depths. Estuarine fish required a minimum water depth (about 2 m) for tidal migration. Since time delays during spring tides between immigration of resident and estuarine fish were reduced, foraging time and habitat accessibility would be enhanced and fish catches and fishes’ feeding success would be greater.

A 200 kHz digital echosounder (HTI) with two split-beam transducers was aimed horizontally to monitor the upstream migration activity of fish, from 24 April to 28 June, in Äijälänsalmi channel (mean width 35 m, length 700 m, and maximum depth 5 m) from large mesotrophic Lake Päijänne to small eutrophic Lake Jyväsjärvi. This study was part of a larger project which aims to analyse the movement of commercially unimportant fish species and reduce the abundance of these fish in L. Jyväsjärvi. Catch samples were collected with a trap net located immediately upstream from the acoustic beams. The most common species in the catch were roach (Rutilus rutilus), perch (Perca fluviatilis), bream (Abramis brama), ruffe (Gymnocephalus cernuus), and white bream (Abramis bjoerkna). The upstream migration of fish was correlated with water temperature (r = 0.40) with time lag of 1 d. In spring, L. Jyväsjärvi warmed faster than L. Päijänne, causing spawning migration from L. Päijänne to L. Jyväsjärvi. Clear diurnal rhythm in activity was observed. The migration rate through the channel peaked around dawn and dusk. Catch per unit effort of the trap net suggested that the peak of the spawning migration of different species was separate. Upstream migration was induced by the temperature difference between two lakes, and the activity of the migration was regulated by temperature changes and light rhythm.

Juvenile pelagic fishes are integral members of many coastal river communities. Many of these systems are boldly influenced by variable wind stress and freshwater inputs that can increase heterogeneity in estuarine habitat for fishes. We use mobile sonar surveys within the Neuse River Estuary System, NC, USA to assess the distribution and behavioral patterns of juvenile anchovies, Anchoa spp. 25-65 mm TL, over a broad range of spatial scales in relation to diel and seasonal changes in water quality including stratification, hypoxic events and copepod distribution. Results from our study indicate that episodic stratification-induced hypoxic events can reduce suitable habitat volume for anchovies by more than 50%. Furthermore, our sampling suggests that hypoxia causes spatial separation between plankton and the grazing fishes. Under stratified oxygen conditions, we observe higher densities of copepods in hypoxic bottom water. Finally, we report that reductions in available habitat caused an increase in local densities of fishes and may result in increased competition for resources. These spatially explicit data are critical for developing trophic dynamic models that predict the response of fish communities to natural and anthropogenic impacts on the system.

Fisheries management now extends from the stock to the ecosystem. The foundation for fisheries management on an ecosystem basis must lie in appropriate modelling of the ecosystems. A prerequisite for such models requires data on the two interactive components of the ecosystem: the biotope (physical environment), and the community of living species. In this context, acoustics become essential, as this tool can provide qualitative and quantitative data on various communities of species, and furthermore allows the seldom-attainable study of their interactions. In fact, acoustics allow the monitoring of entire communities, from plankton to large predators, as well as certain aspects of the physical environment, such as substratum characteristics. Acoustics have been used during the last two decades mainly to provide fishery-independent estimates of stocks. The intention of this paper is to promote the use of acoustics for studying marine ecosystems and to encourage the emergence of new generations of ecosystem models. As an example of integrative research based on acoustic data, we will present the approach and the results of a scientific programme (ECOTAP) carried out to study the tuna pelagic ecosystem in French Polynesia. We then discuss the use of acoustics as a tool for ecosystem-based studies and management.

Data from single and multi-frequency active acoustic surveys conducted annually in the vicinity of the South Shetland Islands, Antarctica were re-analyzed using updated procedures for delineating volume backscattering due to Antarctic krill, adjusting for signal contamination due to noise, and compensating for diel vertical migration of krill outside of the acoustic observation window. Intra-and inter-seasonal variations in krill biomass density and dispersion were derived from the re-processed data set for surveys conducted in the austral summers of 1991/1992 through 2001/2002. Estimated biomass density ranged from 1 to 60 g m–2, decreasing from mid-range levels in 1991/1992 to a minimum in 1992/1993–1993/1994, increasing to a peak in 1996/1997–1997/1998, and decreasing again through 2000/2001–2001/2002. Although this variability may be attributed to changes in the spatial distribution of krill relative to the survey area, comparisons with the proportion of juvenile krill in simultaneous net samples suggest that the changes in biomass density are consistent with apparent changes in reproductive success. A truncated Fourier series fit to the biomass density time series is dominated by an 8-year cycle and predicts an increase in krill biomass density in 2002/2003 and 2003/2004. This prediction is supported by an apparent association between cycles in the extent of sea ice cover and per-capita krill recruitment over the last 23 years and indications that ice cover in the winter of 2002 is seasonally early and extensive.

In order to monitor the recovery of vegetation from pollution and the success of re-seeding efforts, acoustic echoes from the sea floor, covered and uncovered by underwater vegetation, were collected in Puck Bay (southern Baltic sea) using a 208 kHz Biosonics DT 4200 scientific echo sounder. The echo envelopes were examined and several of their parameters were recommended for further analysis. The possibility of using these parameters to distinguish between a bare sea floor and underwater meadows was tested. The parameters may be helpful in the identification of the species composition of the meadows and in accurate biomass assessment.

Seagrass beds play an important role in coastal ecosystems as primary producers and providers of habitat and environmental structure. Therefore, mapping seagrass beds is indispensable in the management and conservation of sound littoral ecosystems, and in the development of sustainable fisheries in coastal waters. Multi-beam sonar is often used to map bottom topography. We developed a mapping method to quantify the volume of seagrass using a multi-beam sonar. Seagrass beds were scanned with the multi-beam sonar and quadrat sampled to verify the distribution of seagrasses. We used software to discriminate seagrass signals from echoes to obtain a topographic profile of the bottom without seagrass; this was then subtracted from the topography including the seagrass. We then mapped seagrass distribution, calculated seagrass volume, and estimated biomass using volume and quadrat samples. We applied these methods to map a seagrass bed of Zostera caulescens in Otsuchi Bay, on the Sanriku Coast of Japan, during the growing season of 2001. A transducer was attached to a boat (one gross ton) equipped with a differential-GPS, a motion sensor, and a gyrocompass. The vessel completed a grid survey scanning whole seagrass bed with an area of 115 m × 156 m at bottom depths between 2 and 8 m within about 40 min when traveling at a speed of 1.5 m s–1 (3 knots). The multi-beam sonar was able to visualize three-dimensional seagrass distribution without interpolation and easily to estimate area and volume occupied by the seagrass using hydrography software. The results indicated that Z. caulescens was distributed at bottom depths of 6–7 m with a surface area of 3 628 m2 and a volume of 1 368 m3. The mean biomass of above- and below-ground parts of seagrass were estimated to be 28.6 gDW m–2 (range 26.6–30.9) and 15.9 gDW m–2 (range 14.1–17.7). Our study demonstrated that multi-beam sonar is effective for mapping and quantifying the spatial distribution of seagrass beds, and for visualizing the landscape of the seagrass canopy.

The feeding behaviour of small tuna on the mesopelagic fish Vinciguerria nimbaria was studied in an equatorial area of the Atlantic Ocean (10–20° W, 0–5° N). Acoustic data (from a scientific cruise) and tuna stomach content data (from the tuna purse-seine fishery) were combined. V. nimbaria formed loose schools that occurred in clusters during daytime, and large aggregations during the night. The characteristics of the schools and clusters were analysed. The average length, size and packing density of the day-school were estimated at 48.5 m, 24400 individuals, and 5.8 fish m–3, respectively. The average length of clusters was close to 10 km. The packing density of night-school was estimated at 1.6 fish m–3. The preying of tuna on V. nimbaria was modelled as a stochastic process based on two Poisson processes. Daily rations of tuna were estimated at 3.5% and 7% of the body weight. Taking into account the swimming performance of the prey and the predator, we showed that tuna were able to feed on day-schools in a very short time, whereas feeding during the night by filtering was not competitive. Furthermore, a cluster is able to feed a single tuna school during 2 months, proving the sustainability of the biomass of small tuna in the area by V. nimbaria.

The most important pelagic artisanal fishery of the Colombian Caribbean Sea is the Atlantic thread herring (Opisthonema oglinum) and the associated species scaled herring (Harengula jaguana), round sardinella (Sardinella aurita), and scad (Decapterus punctatus). The largest aggregations of these small pelagics were found in the La Guajira area, where the local oceanography is modulated by seasonal upwelling intensity. We analysed the associations between the distribution of these small pelagic fishes and the environmental variables. A cumulative frequency method and a Monte Carlo randomization were used to detect associations between fish density and environmental variables. The adults of Atlantic thread herring were found in the upwelling area of La Guajira Peninsula and were associated to waters with temperature and salinity values higher than 25.5 and 36.7 °C, respectively. During December, a nursery area was found in the southern portion of the study area and the juveniles of Atlantic thread herring showed preference for temperatures higher than 27.4 °C. Scaled herring was found to be associated with temperatures (>25.7 °C) and salinities (>36.8). Scad and round sardinella were also associated to temperatures and salinities higher than 25 and 36.6 °C. Our results suggest that the dynamics of the upwelling area may influence the spatial distribution and abundance of small pelagics in the Colombian Caribbean Sea.

The Pacific herring Clupea pallasi population in Prince William Sound (PWS), Alaska, is both a valuable commercial resource and an important forage species for marine fish and wildlife. Historically, the herring were managed by a combination of age-structured models and egg deposition estimates. When these methods predicted a large return for spring 1993 that failed to materialize, we began surveying with echointegration–purse seine methods. After a decade of acoustic surveys, we show the new approach yields highly precise biomass estimates, which are consistent with historical measures of the miles of beach spawning. When compared, we show the traditional methods overestimated stock biomass, which resulted in harvest rates approaching 40%. In contrast, the acoustic methods are most likely to underestimate biomass. Since the acoustic estimates can be quickly obtained, we recommend their use to set harvest quotas for the fishery in the spring just prior to harvest. The shift from the traditional preseason to inseason management practices for herring in PWS is consistent with the Precautionary Principle by the fact that protection of the spawning population does not rely on the ability of science to predict how the population is changing. Furthermore, synoptic infrared measurements on our night-time acoustic surveys revealed herring to be the most important winter forage to marine birds and wildlife in PWS, including the endangered Steller sea lion Eumetopias jubatus. Given the importance of forage to marine birds and wildlife in the North Pacific during the extended winter conditions (October–March), the implementation of inseason management for herring using echointegration–purse seine techniques may be the most effective method to restore depressed populations of marine birds and mammals in the North Pacific.

The power of modern research vessels using diesel engines means significant levels of noise may be radiated underwater. At low frequencies a surveying vessel must not cause fish avoidance behaviour when it is using trawl or acoustic assessment methods. All the main mechanisms that form the essential propulsion system are described and discussed in terms of underwater radiated noise. Diesel engines, generators and propulsion motors contribute significantly to the low frequency spectrum and an illustration is given of underwater noise when an unsuitable propulsion system is used. Avoidance behaviour by a herring school is shown due to a noisy vessel, by contrast there is an example of no reaction of herring to a noise-reduced vessel. Propellers are major sources of both low and high frequency noise. The latter should not reduce echo sounder detection range, nor contaminate echo integrator recordings. Underwater noise levels from four vessels with different machinery and propulsion characteristics are seen in relation to ambient noise levels at 18 kHz. Fish detection is examined in relation to sea background noise and vessel self-noise. Calculated detection ranges for fish target strength classes from –30 to –60 dB at 38 kHz are shown for six vessels travelling at 11 knots, based on self-noise measurements. Echo sounder noise levels from several vessels at 120 and 200 kHz are tabulated. Beyond 100 kHz the effect of vessel-radiated noise is usually insignificant; levels up to that frequency are proposed in the International Council for the Exploration of the Sea (ICES) Cooperative Research Report No. 209 of 1995.

The reaction of fish induced by a trawling vessel was measured using the Bergen Acoustic Buoy. It is a free-floating buoy with a split beam echo sounder system. Individual fish trajectories were obtained by target tracking methods, and average swimming velocities as a function of depth and time before and after passage of the vessel was calculated. A measure for the change in behaviour was applied, showing a significant response during and after propeller passage. The change in horizontal displacement speed is significant at all depths, while the change in vertical displacement velocity is significant at all but one layer of depth. The horizontal reaction seems to occur a bit later than the diving reaction. After the main response, a slightly higher mean horizontal displacement speed was observed for the deepest layers. This indicates a change in the fish state after being exposed to the vessel/gear.