DOI: 10.5061/dryad.zcrjdfnp3
title: Antarctic krill vertical migrations modulate seasonal carbon export

description: Vertical migrations by marine organisms contribute to carbon export by
 consumption of surface phytoplankton followed by defecation in the deep
 ocean. However, biogeochemical models lack observational data, leading to
 an oversimplified representation of carbon cycling by migrating organisms.
 Using a numerical model informed by one year of acoustic observations in
 the East Antarctic, we estimated Antarctic krill (Euphausia superba)
 contributions to particulate organic carbon flux. We estimated the total
 particulate organic carbon (POC) flux from krill faecal pellets to be 9.68
 mg C m-2 d-1. A maximum of 25% of krill migrated to depths over 200 m with
 a strong seasonality component, transporting less than 10% of the total
 krill POC flux (1.28 mg C m-2 d-1). Models that include vertical migration
 risk overestimating carbon export if this seasonality is not captured and
 accurate estimates are essential to inform climate policy and mitigation
 strategies.
description: # Antarctic krill vertical migrations modulate seasonal carbon export
 [https://doi.org/10.5061/dryad.zcrjdfnp3](https://doi.org/10.5061/dryad.zcrjdfnp3) ## Description of the data and file structure Files are stored in .csv or .rds format #### Data Files Processed echosounder data from the KOMBI mooring are divided into seasonal files. Each file includes data integrated over 1m depth bins and 1-hour intervals. Files include: * 'autumn_KOMBI03.csv' * 'winter_KOMBI03.csv' * 'spring_KOMBI03.csv' * 'summer_KOMBI03.csv' Target strength data used for krill lengths include: * 'krillTS.rds' Krill length frequency information collated from historical ship surveys and predator gut contents in the East Antarctic include: * 'seasonal_krill_LF_ships*_*predators.csv' * 'seasonal*_*LF*_*interp.csv' Interpolated chlorophyll data for Prydz Bay region: * 'bgcargo_zc.csv' ### Files and variables #### File: krillTS.rds **Description:** This file contains target strength data for Antarctic krill used by CCAMLR in biomass estimates for krill of lengths 10 - 67mm. ##### Variables * length: length of krill (mm) * TS038: Target strength of Antarctic krill at 38kHz (dB re 1m^2) * TS120: Target strength of Antarctic krill at 120kHz (dB re 1m^2) * TS200: Target strength of Antarctic krill at 200kHz (dB re 1m^2) #### File: bgcargo\_zc.csv **Description:** Depth of the chlorophyll zone (max depth where adjusted chlorophyll a concentration is &gt; 0.05 mg m^3) in Prydz Bay across a full year from BGC-Argo floats. ##### Variables * doy: day of the year * chla: depth of chlorophyll zone (m) * mld: mixed layer depth (m) * chla_2: depth of chlorophyll zone interpolated across NA days (m) * mld_2: mixed layer depth interpolated across NA days (m) #### File: seasonal\_krill\_LF\_ships\_predators.csv **Description:** Krill length frequency data for East Antarctica collected from ship surveys and the Scientific Committee for Antarctic Research SO-diet database.  ##### Variables: * Type: Krill lengths derived from Predator (gut contents), Ship (net haul), IGR (instantaneous growth rate experiment) * Method: Method for obtaining krill lengths from type * Cruise: Research cruise from which the samples were collected * Station_or_species: Prey species * Lat: Latitude (degrees) * Lon: Longitude (degrees) * Date: Date (dd/mm/YYYY) * Length (mm): Prey length (mm)  * Length method: Method used to measure length * Wet wt (g): Wet weight (g) * Maturity: Maturity stage * Trawl Type: Routine or target trawl (for net haul data) * Year: Year * Month: Month * Day: Day * Count: Number of individuals counted at that length per sample (predator/net haul) #### File: seasonal\_LF\_interp.csv **Description:** Monthly krill length frequency data interpolated over data poor length bins.  ##### Variables: * Length: krill length (mm) * Month: Month * Total: Total count at length bin * PrProp: Proportion of bin in monthly distribution #### File: autumn\_KOMBI03.csv **Description:** Krill classified acoustic data (processed in Echoview) from the KOMBI03 Nortek Signature100. Data integrated across 1m depth x 1-hour cells. Specific to autumn months. Definitions taken from Echoview Software help files on export variables and also see Urmy S.S., Horne J.K., and Barbee D.H. (2012) Measuring the vertical distributional variability of pelagic fauna in Monterey Bay. ICES Journal of Marine Science, 69(2), 184–196. ##### Variables: * Process_ID: Calculation identifier - Interval: Calculation identifier * Layer: Cell number - Sv_mean: (Mean) Volume Backscattering strength (dB re 1m-1) integrated for the cell (1 hour x 1 metre). - NASC: Nautical area scattering coefficient (m2 nmi-2) integrated for the cell (1 hour x 1 metre). - Height_mean: Height_mean is the projection of thickness_mean onto the vertical axis taking transducer geometry into account (m). - Depth_mean: It reports the mean depth of the domain which was analyzed (m). - Layer_depth_min: It reports the minimum depth of the cell (layer) that was analyzed (m). - Layer_depth_max: It reports the maximum depth of the cell (layer) that was analyzed (m). - Ping_S: number of the ping at the beginning of the bounding rectangle of the cell - Ping_E: number of the ping at the end of the bounding rectangle of the cell - Dist_M: It reports the distance from the start of the GPS source of the acoustic variable to the middle ping in the analysis domain. - Date_M: It reports the date of the middle ping in the domain that was analyzed (M for middle). - Time_M: It reports the time of the middle ping in the domain that was analyzed (M for middle). - Lat_M: It reports the Latitude (decimal degrees) of the middle ping in the domain that was analyzed (M for middle). - Lon_M:  It reports the Longitude (decimal degrees) of the middle ping in the domain that was analyzed (M for middle). - Noise_Sv_1m: It reports the value of Background noise at 1m value entered on the Analysis page of the Variable Properties dialog box for the variable that was analyzed (dB re 1m2/m3). Empty for this data (-999). - Minimum_Sv_threshold_applied: It has a value of 1 if a minimum Sv threshold was applied on the Data page of the Variable Properties dialog box for the variable that was analyzed, and 0 otherwise. - Maximum_Sv_threshold_applied: It has a value of 1 if a maximum Sv threshold was applied on the Data page of the Variable Properties dialog box for the variable that was analyzed, and 0 otherwise. - Standard_deviation: It reports the standard deviation of all sample values in the domain that was analyzed. This is calculated in the linear domain (not the dB domain). - Thickness_mean: It reports the mean thickness of the domain which was analyzed (m). - Range_mean: It reports the mean range of the domain which was analyzed (m). - Exclude_below_line_range_mean: It reports the mean range of the exclude-below line over the domain that was analyzed (m). Only line segments with line status good are used in this calculation. The special export value -9999 indicates the calculation was not possible no good line segment exists over the analyzed domain. - Exclude_above_line_range_mean: It reports the mean range of the exclude-above line over the domain that was analyzed (m). Only line segments with line status good are used in this calculation. The special export value -9999 indicates the calculation was not possible no good line segment exists over the analyzed domain. - Center_of_mass: It reports the center of "mass" (m) of the domain. It is calculated by considering the average of all sample depths weighted by sample sv values in the domain that was analyzed. The exported Center_of_mass is equivalent to the 'Centre of mass' as discussed by Urmy et al (2012). - Inertia: It reports the spread as the sum of squared distances from the Center_of_mass, weighted by the sv at each distance and normalized by the total sa of the domain. The exported Inertia is equivalent to the 'Inertia' as used by Urmy et al (2012). - Proportion_occupied: It reports the proportion of the water column with Sv above a threshold; and considers all samples of the domain. The exported Proportion_occupied is equivalent to the 'Proportion occupied' as used by Urmy et al (2012). - Equivalent_area: It reports the area (m) that would be occupied if all the samples had the mean Sv of the domain (Urmy et al (2012) citing (Woillez et al., 2007)). It is calculated by considering all the samples of the domain which was analyzed. The exported Equivalent_area is equivalent to the 'Equivalent area' as used by Urmy et al (2012). - Aggregation_index: It reports the aggregation index (m-1)of the domain. It is calculated by evaluating the reciprocal of the Equivalent area for the samples of the domain that was analyzed. The exported Aggregation_index is equivalent to the 'Index of Aggregation' as used by Urmy et al (2012). Urmy et al noted that the Index of aggregation values is "high when small areas are much denser than the rest of the distribution". #### File: spring\_KOMBI03.csv **Description:** Krill classified acoustic data (processed in Echoview) from the KOMBI03 Nortek Signature100. Data integrated across 1m depth x 1-hour cells. Specific to spring months. ##### Variables * Please see the variable descriptions above for autumn_KOMBI03.csv #### File: summer\_KOMBI03.csv **Description:** Krill classified acoustic data (processed in Echoview) from the KOMBI03 Nortek Signature100. Data integrated across 1m depth x 1-hour cells. Specific to summer months. ##### Variables * Please see the variable descriptions above for autumn_KOMBI03.csv #### File: winter\_KOMBI03.csv **Description:** Krill classified acoustic data (processed in Echoview) from the KOMBI03 Nortek Signature100. Data integrated across 1m depth x 1-hour cells. Specific to winter months. ##### Variables * Please see the variable descriptions above for autumn_KOMBI03.csv ## Code/software All code used in the KOMBI POC model and dependent scripts was developed in R (v4.2.0).