DOI: 10.5061/dryad.wstqjq2rd
title: First description of in situ chlorophyll fluorescence signal within East Antarctic coastal polynyas during fall and winter

description: Antarctic coastal polynyas are persistent and recurrent regions of open
 water located between the coast and the drifting pack-ice. In spring, they
 are the first polar areas to be exposed to light, leading to the
 development of phytoplankton blooms, making polynyas potential ecological
 hotspots in sea-ice regions. Knowledge on polynya oceanography and ecology
 during winter is limited due to their inaccessibility. This study
 describes i) the first in situ chlorophyll fluorescence signal (a proxy
 for chlorophyll-a concentration and thus presence of phytoplankton) in
 polynyas between the end of summer and winter, ii) assesses whether the
 signal persists through time and iii) identifies its main oceanographic
 drivers. The dataset comprises 698 profiles of fluorescence, temperature
 and salinity recorded by southern elephant seals in 2011, 2019–2021 in the
 Cape-Darnley (CDP;67˚S-69˚E) and Shackleton (SP;66˚S-95˚E) polynyas
 between February and September. A significant fluorescence signal was
 observed until April in both polynyas. An additional signal occurring at
 130m depth in August within CDP may result from in situ growth of
 phytoplankton due to potential adaptation to low irradiance or remnant
 chlorophyll-a that was advected into the polynya. The decrease and
 deepening of the fluorescence signal from February to August were
 accompanied by the deepening of the mixed layer depth and a cooling and
 salinification of the water column in both polynyas. Using Principal
 Component Analysis as an exploratory tool, we highlighted previously
 unsuspected drivers of the fluorescence signal within polynyas. CDP shows
 clear differences in biological and environmental conditions depending on
 topographic features with higher fluorescence in warmer and saltier waters
 on the shelf compared with the continental slope. In SP, near the
 ice-shelf, a significant fluorescence signal in April below the mixed
 layer (around 130m depth), was associated with fresher and warmer waters.
 We hypothesize that this signal could result from potential ice-shelf
 melting from warm water intrusions onto the shelf leading to iron supply
 necessary to fuel phytoplankton growth. This study supports that Antarctic
 coastal polynyas may have a key role for polar ecosystems as biologically
 active areas throughout the season within the sea-ice region despite inter
 and intra-polynya differences in environmental conditions.
description: The dataset is composed of <em>in
 situ</em> profiles of temperature, salinity and fluorescence
 recorded by nine post-moulting male southern elephant seals (SES) equipped
 with CTD-Fluo-SRDLs (Conductivity-Temperature-Depth-Fluorescence Satellite
 Relay Data Loggers) (Boehme et al., 2009; Guinet et al., 2013) between 2011 and 2021. All SES visit a coastal polynya in East Antarctica at least once. Individual seals were anesthetized with an intravenous injection of a 1:1 combination of tiletamine and zolazepam (Zoletil 100) (McMahon et al., 2000; Field et al., 2002) to attach the instrumentation. The data loggers were glued to the seals heads using quick-setting epoxy (Araldite AW 2101, Ciba; Field et al., 2012). Data on seal’s diving behavior as well as <em>in situ</em> hydrographic conditions were transmitted when the seal surfaces to breathe through communication with polar-orbiting Argos satellites (Harcourt et al., 2019).  Fluorescence measurements are used as a proxy to estimate the concentration of chlorophyll-a in the water (Guinet et al., 2013). In this study, we have chosen not to convert chlorophyll-a fluorescence into chlorophyll-a concentration, as conversion ratios are highly variable in the Southern Ocean (Schallenberg et al., 2022), which could affect the validity of results interpretations. However, although quantitative assessments of phytoplankton biomass can hardly be reached with the sole use of fluorometers (Roesler et al., 2017; Petit et al., 2022), <em>in vivo</em> chlorophyll-a fluorescence is a commonly used method to detect presence of living phytoplanktonic organisms and study their dynamics in terms of concentration (IOCCG, 2011).  Each profile of fluorescence, salinity and temperature had a vertical resolution of one meter after interpolation. No fluorescence data were available above 10 m and below 170 m. The mixed layer depth (MLD) was computed from temperature and salinity profiles using a density criteria Δρ = 0.03kg.m<sup>-3</sup>, with density at 10 m depth used as the reference value following de Boyer Montégut et al. (2004). Fluorescence profiles can be corrected for non-photochemical quenching (NPQ) with a correction algorithm developed by Xing et al. (2018). The NPQ effect is induced by photo-inhibition in phytoplankton cells exposed to high light levels. This method aims at correcting the depression observed in the fluorescence signal (generally in the surface layer) resulting from the NPQ effect. As all profiles start at 10 m depth and the study focuses on autumn and winter, the effect of NPQ is negligible. However, when light was available, which is the case for profiles recorded in 2020 and 2021 (236 profiles out of 766), a correction was still applied. The correction is based on the definition of a “NPQ-layer”. Upper and lower boundaries are, respectively, the ocean surface, and the shallowest value between MLD and a light-threshold depth fixed at 15 <em>μ</em>mol. <em>m</em><sup>-2</sup><em>s</em><sup>-1</sup> (PAR15, expressed in m). The maximum fluorescence value in the so-called NPQ-layer is then extrapolated up to 10 m depth which, as a result, discards the fluorescence depression due to NPQ (for details, see Xing et al. (2018)). Moreover, background noise from the fluorescence sensor detected at 170 m depth (where it is assumed that the fluorescence signal should be null) was removed from all the 766 fluorescence profiles. The geographical positions transmitted <em>via</em> the Argos system use the Doppler shift of the signal frequency received during the passing of one of the polar-orbitting satellites and depending on the position of the satellite relative to the transmitting tags, errors from 0.5 to 10 km may be observed. To provide the best location estimates we (i) filter the trajectories of individuals in order to (ii) interpolate the position of the CTD profiles from the filtered trajectory. The method used is based on a continuous-time state-space model presented in Jonsen et al. (2020) and implemented using the R package <em>foieGras</em> (now known as <em>Animotum</em> (Jonsen et al., 2019; Jonsen et al., 2020; Jonsen et al., 2023)). Each profile was assigned to a broad regional area based on its location. These three areas: the continental shelf, the continental slope and the pelagic zone, were determined from the GEBCO_2021 Grided bathymetry (Gebco, 2021). The latitudinal limits of the continental slope were determined by graphic visualization every 0.5˚ longitudes (between -0.5˚E and 158°E) by plotting bathymetry against latitude. The beginning of the slope corresponds to the latitude where bathymetry starts to decrease drastically while the end of the slope corresponds to the first latitude where bathymetry is deeper than 2,900 m.
description: The data are in a .txt format and the codes are in R and Matlab.
 See Readme.md for details. Please do not hesite to
 contact the corresponding author (Lucie Bourreau, lucie.bourreau.1@ulaval.ca) if you have any questions.