Methodology:

Underway acoustics

Multifrequency acoustic data were collected using a hull-mounted Simrad EK60 echosounder (18, 38, 70, 120, 200, and 333 kHz). The echosounders were calibrated using a 38.1 mm tungsten carbide sphere following the standard sphere method. The calibration performed on the RRS Discovery highlighted a malfunctioning of the 18 and 38 kHz transducers precluding the use of those frequencies. For this reason, the main frequency used for the analysis was 70 kHz (70 kHz was also used for the 2018 data for consistency). The settings and calibration parameters of the acoustic equipment used in the two expeditions are detailed in the associated manuscript. The acoustic data from the surface to a maximum depth of 600 m (below which the 70 kHz data were affected by absorption) were cleaned and processed using the software Echoview v10. The area immediately below the transducers (about 10 m below) was excluded from the analysis because it was affected by the near-field effect and surface noise (e.g., surface bubbles). Background noise, pulse noise and attenuated signals were removed using a series of tools integrated in the Echoview software. The Nautical Area Backscattering Coefficient (NASC) was exported from the 'clean' echograms and used for further analyses. NASC, also referred to as backscatter, was considered a proxy for relative biomass. The horizontal sampling unit used to export the NASC was 1 nm.

In order to discriminate different classes of acoustic target, a combination of thresholding and the difference in mean volume backscattering strength (DB differencing) was also used. The analysis consisted of two steps:

(i) Thresholding - Mean Volume Backscattering Strength (MVBS) at 70 and 120 kHz was summed and the resulting echogram was thresholded in order to separate two broad classes of targets (fish vs plankton). The difference in variability between fish and zooplankton was used to enhance the contrast between both types of organisms. The use of this approach is helpful when there is a high density of gas-bearing plankton that can easily be mistaken for fish if only dB-differencing is used. The threshold value used for the data collected during the day was empirically chosen at -140 dB. Values above the threshold were classified as fish and values below the threshold were identified as plankton. A Boolean mask was then used to assign the backscatter to fish and plankton;

(ii) DB differencing - the fish and plankton categories were further separated into four additional classes (fish with swimbladder, fish without swimbladder, fluid-like plankton, gas-bearing plankton). Identification of these classes was based on the differences of MVBS measured at 120 and 70 kHz (delta MVBS120-70). The NASC for the 'fish' and 'gas-bearing' plankton categories was exported at 70 kHz using a minimum Sv (Volume backscattering strength, dB re 1 m-1) threshold value of -70 dB. The NASC for the 'fish without swimbladder' and 'fluid-like plankton' categories was exported at 120 kHz using a minimum Sv (Volume backscattering strength, dB re 1 m-1) threshold value of -85 dB.

The spatial patterns of distribution of the different scatter categories were investigated using a set of spatial metrics calculated in a cell of 1 nm (horizontally) by 200 m (vertically). Specifically, we estimated center of gravity, equivalent area and inertia. The center of mass is the mean location of the backscatter in the water column; the inertia is a measure of the dispersion of the backscatter around its center of gravity; the equivalent area is an individual-based index of the area occupied by the backscatter and it is a measure of the evenness. The spatial metrics were estimated using the daytime data only to exclude the effects of vertical migrations within the water column. The spatial metrics and the NASC were grouped in 5 degree longitudinal classes an...(20)

Data collection:

For fisheries acoustics: Hull-mounted Simrad EK60 echosounder (18, 38, 70, 120, 200, and 333 kHz).