THEMISTO

Type	Set of cruises
Chief scientist(s)	COTTE Cédric
Project manager	COTTE Cédric
DOI	10.18142/288
Objective	The main objective of THEMISTO is to study the 3-D distribution of zooplankton and micronekton in relation to physical physical features and climate. The project proposes to use active acoustics as a tool to measure the distribution and densities of organisms. Through the continuous collection of measurements by the EK80 echosounder (at 5 frequencies, from more than 1000m depth for the 18kHz to 200m for the 200kHz) during the Reunion-Crozet-Kerguelen-Amsterdam-Reunion transits, the purposes are to i) distinguish groups and species of zooplankton and micronekton and ii) characterize the variability of their distribution in 3-D over a large latitudinal gradient (from tropical to polar regions). Physical processes is studied simultaneously (mainly in-situ thermosalinograph data and satellite image analysis), allowing to define critical multi-scale habitats of key species of the southern Indian Ocean ecosystems. Including a methodological development part to take the best advantage of the new onboard equipment and benefiting from collaborations (including REPCCOAI and OISO on the Obsaustral campaigns at the national level and MOBYDICK and MESOPP (Mesopelagic Southern Ocean Prey and Predators) at the international level), the results obtained allow a better understanding of the pelagic ecosystems but also the contribution of these informations in terms of assimilation into trophic models and conservation through spatial planning.

Scientific context

Main results

The results presented last year did not satisfy the commission, which had "great difficulty in understanding in the information provided what was relevant to THEMISTO or MOBYDICK". In the first evaluation document, it was specified that the valorisation should only concern the THEMISTO 2016 and 2017 campaigns. However, after clarification with the committee, it is indeed the valorisation of the entire series that is concerned, from 2016 to 2019, thus also including the year 2018 when the THEMISTO and MOBYDICK programs were associated (moreover referred to as such by the DOI: 10.17600/18000403). In order to facilitate the understanding of the commission on the valorisation of this double configuration, the presentation of the results will be in two parts: the THEMISTO program alone from 2016 to 2019, and then the valorisation of the joined MOBYDICK-THEMISTO program/campaign.

The major results strictly related to the THEMISTO program 2016-2019 are presented first. Contrary to what was proposed last year on the presentation of the valorisation of the previous acoustic campaigns because of their coherence with THEMISTO, the results obtained recently on the acoustic data linked to the previous MyctO-3D-MAP program are no longer presented here. The results obtained in the 2018 MOBYDICK-THEMISTO program will then be presented, presenting only the studies carried out in relation to the intermediate trophic levels addressed by THEMISTO.

1. Main results of the THEMISTO campaigns 2016-2019

Study of zooplankton abundance variations in the Indian part of the Southern Ocean: influence of nycthemeral migrations and environmental parameters (Master Claire Godet)

The Joint MDCPR/REPCCOAI and MyctO/THEMISTO campaigns (from 2013 to 2016) have quantified zooplankton densities using two methods: the "Continuous Plankton Recorder" (CPR), which samples at the surface, and acoustics, which allows the visualization of zooplankton densities on the water column. Generalized linear mixed models were performed in order to analyze whether the variations in abundance of zooplankton collected by CPR could be explained by the nychtemeral cycles observed using acoustics, and to analyze whether environmental parameters could explain these fluctuations in abundance on CPR samples at night, the time of day when zooplankton abundance at the surface is at a maximum. By coupling the CPR data with the acoustic data, the fluctuations in abundance could be explained by the nycthemeral migrations. The bioregionalization of the South Indian and the comparison with zooplankton communities studied by the CPR collection could thus be carried out (Fig. ? from Godet et al. 2020), as well as the ecoregionalization of euphausiids and myctophids conducted in the framework of the REPCCOAI program.

Fig. 3. Map of the six bioregions and position of the three main fronts (from north to south: subtropical, subantarctic and polar front). Bioregions are defined based on abiotic parameters (SST, EKE and bathymetry) and Chl a concentration. From Godet et al. 2020

Spatial structuring of pelagic ecosystems in the South Indian Ocean and the Indian zone of the Southern Ocean (Master Camille Merland)

The aim was to study the spatial structuring of micronektonic organisms in the South Indian zone, and particularly the scales at which they structure, and to highlight possible similarities with the scales at which top predators concentrate their foraging activity. In a first step, a functional approach allowed to regionalize and identify the patterns of variability of the micronekton. The regionalization obtained is consistent with that previously presented by Béhagle et al. 2016. It allowed us to take an additional step by prioritizing the patterns of variability. In two out of three years, the day/night distinction is the factor that predominantly structures the data. Spatial variability of densities is the second parameter that explains the difference between acoustic profiles. In contrast, we show an inverse trend in the third year in which the effect of spatial variability dominates over the effect of day/night variability. Next, we compared the scales of horizontal structuring between micronekton (prey) densities and predator foraging from telemetry monitoring. Common scales of the order of 20 km were revealed, suggesting the importance of the (sub-)mesoscale (attributed to oceanic fronts). This first approach combining trophic links and environmental forcing complements the approaches usually used to define areas of high conservation concern and will be further developed to reinforce the results obtained.

"Switching off the Sun" to observe the twilight zone spatial dynamics across Saint-Paul and New-Amsterdam Islands, Southern Indian Ocean (PhD candidate Lloyd Izard)

Information on micronekton (> 2 cm organisms) are globally scarce in the open ocean and its vertical and horizontal distribution in relation to oceanographic structures is poorly known. The complex biodiversity compositing micronektonic functional groups leads to even more challenging interpretations of their spatial dynamics. Active acoustics is a non-intrusive observation method allowing high-frequency monitoring of micronektonic organism in the water column. Advanced generations of echosounders emit simultaneously several acoustic signals (multi-frequency device), allowing to gain a more representative view of the micronektonic community. While data becomes more abundant and complex, it is crucial to develop statistical tools aiming to objectively extract key components of its variability. In this study, we developed a Multivariate Functional Data Analysis method to determine patterns in micronekton structures across Saint-Paul and New-Amsterdam economic exclusive zone, at the boundary between large oceanic domains. Our results show a clear latitudinal acoustic pattern in concordance with hydrological features and biological samples (THEMISTO and REPCCOAI programs) (Fig. 4). This study proposes an objective method to analyse the vertical variability and quantify temporal or spatial modes of variability in multivariate acoustic data. Such methods could be implemented in any regions and allow 3-D modelling of micronektonic structuring.

Fig. 4. Classification of 2016 acoustic profiles (MD206) overlaid on maps of (from left to right) chlorophyll a concentrations (mg.m^-3), temperature (°C) and surface salinity.

Ecoregionalisation of the subantarctic region (20°W - 120°E)

Amongst a compilation of data in the framework of an international programme, the active acoustic data were obtained with an EK80 echo sounder on board the Marion Dufresne during the THEMISTO 2018 campaign. The transect extends over 7766 km in the southwest Indian Ocean over an area ranging from 25 to 52° South and 51 to 77° East. The data were recorded from 05 January 2018 to 01 February 2018. Poor quality data due to unfavourable weather conditions were removed from the data set. After cleaning the data, an echo-integration was applied on the water column from 20 to 1000 m depth with a thickness of 10 m and a path length of 1 km. Maps of the distribution of average densities were thus created for the daytime and nighttime data and for each frequency studied. Similarly, the evolution of these density distributions was studied as a function of longitude and latitude along the entire route.

Contribution to the program "Mesopelagic Southern Ocean Prey and Predators (MESOPP, H2020)"

The concept of MESOPP is the creation of a collaborative network and associated e-infrastructure (marine ecosystem information system) between European and Australian research teams/institutes with similar interests in the Southern Ocean and Antarctic, the functioning of its marine ecosystems and the rapid changes occurring with global warming and marine resource exploitation. The THEMISTO acoustic measurements integrated the MESOPP reference datasets comprising 67 transects of 38 kHz volume backscatter intensity measurements (Sv, dB re 1 m-1) collected by 6 vessels (research and fishing) (Fig. 5). The reference data sets also contain calibrated and post-processed data from 18 kHz of 3 transits, 70 kHz of 2 transits, 120 kHz of 4 transits and 200 kHz of 2 transits. These reference data sets are from three areas of the Southern Ocean (South Atlantic, South Indian and South Pacific).

Fig. 5. MESOPP transits of calibrated and post-process acoustic backscatter

Post-processing of the data was undertaken using a combination of in-house tools developed by CSIRO, BAS and/or IRD and used to facilitate data management, data subset identification and post-processing. These tools used software packages including Java, Matlab, Movies 3D and Echoview. A preliminary comparison indicated that two of the three post-processing methods used generated similar values of water column NASC integrated from 0 to 800 m. There were some differences between biases with depth, although all still low. SEAPODYM LMTL modelling is optimised using the ratio between layers and therefore this discrepancy in bias with depth may cause greater uncertainty when using data post-processed with different methods. As a result it is clear that to ensure good data quality and assurance processes, data processing techniques should be compared on common data sets. Estimates of uncertainty to highlight precision and accuracy of the measurements and whether those variances matter in models need to be assessed so that potential errors are identified, and new and emerging methods are evaluated, in order to recommend best practice.

From the database referenced on the MESOPP website (https://www.mesopp.eu/), including THEMISTO data, analyses are underway and articles are being evaluated for publication in high-citation journals. THEMISTO contributes to the effort of sharing data for (meta)analysis at regional (Austral) or global scale.

2. Main results of the MOBYDICK-THEMISTO campaign (2018)

Macrozooplankton/micronekton diversity, content and active carbon flux in contrasting environments of the Kerguelen region

Given the dominant role of the Southern Ocean in the global carbon cycle, it is important to consider estimates of active carbon flux relative to the global carbon budget. It is fundamental to assess the contribution of the active biological community of zooplankton and micronekton on the biological carbon pump. Our study provides new information on the response of the macrozooplankton and micronekton (MM) community under contrasting production regimes (oligotrophic vs. biologically enriched zones) found in the naturally fertilized Kerguelen Plateau site. Using a combination of trawl sampling and acoustic measurements, we demonstrated a vertical three-layer system at both the HNLC and fertilized stations (Fig. 6). However, different communities and biomasses and complex patterns of vertical distribution of MM and associated carbon fluxes were identified. This study provides new information on the importance of migrating biomasses and size structure in the biological pump of Southern Ocean regions under the influence of complex topography and land mass effects.

Fig. 6. Acoustic profiles and biomasses corresponding to the different taxa for the 4 stations of the MOBYDICK-THEMISTO program. From Cotté et al. in revision

Pelagic food web structure in high nutrient low chlorophyll (HNLC) and naturally iron fertilized waters in the Kerguelen Islands region, Southern Ocean

Simultaneous collection of WP2, WP3, trawl and acoustic data was used to study the diversity, abundance and biomass of pelagic communities, as well as ecosystem dynamics in different primary production regimes in the Kerguelen region.
We found that the pelagic macrozooplankton/micronekton communities differed under distinct production conditions despite a clearly visible vertical three-layer system. As a result, HNLC waters upstream of the Kerguelen shelf, dominated by pico and nanophytoplankton, had mesozooplankton/macrozooplankton communities that were > 0.6 trophic positions higher than on the naturally iron-enriched shelf that supports large summer diatom blooms (Fig. 7). This suggests that the efficiency of biomass accumulation in iron-enriched regions depends on the presence of large zooplanktonic grazers that can efficiently consume and assimilate diatoms, such as the crustaceans that were abundant on the shelf. Salps accounted for almost half of the micronekton biomass and the population dynamics of this abundant gelatinous organism responded to the contrasting production regimes of the area. Complex models of the vertical distribution of macrozooplankton/micronekton and estimates of carbon flux mediated by migratory myctophids helped to provide insight into the main components and mechanisms of active carbon export in the region and how these are modulated by the complex topography and land mass effects.

Fig. 7.

Demography, population growth rates and vertical migrations of salps (Salpa thompsoni) on the Kerguelen Plateau.

S. thompsoni are important grazers in the Southern Ocean, and have been shown to perform diel vertical migration to 500 m. However, estimates of their size and stage specific migration patterns are lacking. This work is both novel and timely as it provides the first insights into S. thompsoni size and stage migration patterns in the Kerguelen plateau region. This study provides the first information (from trawls and acoustics) on the vertical distribution of blastozooids and oozoids across day and night; identifying that the smallest individuals are the strongers migrators, and that larger individuals may occur at a deeper daytime residence depth than previously considered (> 800 m).

This study also aimed to obtain first estimates of S. thompsoni population dynamics and growth rates on the Kerguelen Plateau (southern Indian Ocean) at contrasting hydrological stations on the Kerguelen Plateau. Environmental conditions were important in determining the density and development of S. thompsoni populations. Growth rates (0.5-7.0% d-1 ) were higher than previously reported on the Antarctic Peninsula (0.3-4.6% d-1 ), but lower than near the Antarctic Polar Front (APF; 3.7-20.7% d-1 ). Despite warm surface waters (4-5°C), low chlorophyll a concentrations prevented salp populations from growing as rapidly as populations near the APF. The Kerguelen Plateau region diverts a branch of warm water southwards towards Antarctica. Further studies on the population dynamics of S. thompsoni over several seasons are needed to fully understand their importance on the Kerguelen Plateau and their potential to invade to higher latitudes.

3. Contributions of the THEMISTO program

- The EU-IUCN BEST initiative aims to support projects for biodiversity and ecosystem services in overseas territories. The SEECTOR program (Significant Ecological areas for pElagic species and ConservaTion challenge in the sOutheRn Indian Ocean, PI C. Cotté) has focused on the sub-Antarctic zone of the Indian Ocean to identify trophic hotspots, i.e. where the highest densities of pelagic organisms of intermediate trophic levels and top predators occur. The aim is to provide (i) a better understanding of the prey-predator link and the environmental phenomena at their origin and (ii) to better delimit these hotspots according to their dynamical characteristics.

- Within the framework of Lloyd Izard PhD thesis obtained at SU and the collaboration with the French Southern and Antarctic Territories (TAAFs), MyctO/THEMISTO data are involved in the scientific support of the file of extension of the marine reserve in the St Paul - Amsterdam EEZ and announced in February 2022 (https://www.outre-mer.gouv.fr/emmanuel-macron-annonce-lextension-de-la-reserve-naturelle-des-terres-australes-francaises-la).

- Contribution to dissemination activities in the framework of THEMISTO:

THEMISTO program blog during the 2019 Obsaustral sea campaign: https://www.ipsl.fr/Actualites/A-decouvrir/Carnet-de-campagne-THEMISTO-campagne-oceanique-hydroacoustique-dans-l-ocean-indien

Participation to an exhibition, "MYCTOPHIDAE, voyage en eau profonde", organized at the Institut Universitaire Européen de la Mer (Brest), and to a journal, La Lanterne, during the Festival Ressac (Fig. 8)

Fig. 8: Illustration of the exhibition "MYCTOPHIDAE, voyage en eau profonde"

References (selection of references on the THEMISTO program aims from the list of all publications automatically associated by SGC with the THEMISTO and MOBYDICK-THEMISTO campaigns)

- Cotté Cedric, Ariza A., Berne Adrien, Habasque Jeremie, Lebourges-Dhaussy Anne, Roudaut Gildas, Espinasse B., Hunt B.P.V., Pakhomov E.A., Henschke N., Péron C., Conchon A., Koedooder C., Izard L., Cherel Y. (2022). Macrozooplankton and micronekton diversity and associated carbon vertical patterns and fluxes under distinct productive conditions around the Kerguelen Islands. Journal Of Marine Systems, 226, 103650 (18p.). https://doi.org/10.1016/j.jmarsys.2021.103650

- Hunt Brian P.V., Espinasse Boris, Pakhomov Evgeny A., Cherel Yves, Cotté Cedric, Delegrange Alice, Henschke Natasha (2021). Pelagic food web structure in high nutrient low chlorophyll (HNLC) and naturally iron fertilized waters in the Kerguelen Islands region, Southern Ocean. Journal Of Marine Systems, 224, 103625 (10p.). https://doi.org/10.1016/j.jmarsys.2021.103625

- Henschke Natasha, Cherel Yves, Cotté Cedric, Espinasse Boris, Hunt Brian P.V., Pakhomov Evgeny A. (2021). Size and stage specific patterns in Salpa thompsoni vertical migration. Journal Of Marine Systems, 222, 103587 (5p.). https://doi.org/10.1016/j.jmarsys.2021.103587

- Henschke Natasha, Blain Stéphane, Cherel Yves, Cotte Cedric, Espinasse Boris, Hunt Brian P.V., Pakhomov Evgeny A. (2021). Population demographics and growth rate of Salpa thompsoni on the Kerguelen Plateau. Journal Of Marine Systems, 214, 103489 (10p.). Publisher's official version : https://doi.org/10.1016/j.jmarsys.2020.103489 , Open Access version : https://archimer.ifremer.fr/doc/00659/77147/

- Godet Claire, Robuchon Marine, Leroy Boris, Cotté Cedric, Baudena Alberto, Da Silva Ophélie, Fabri-Ruiz Salomé, Lo Monaco Claire, Sergi Sara, Koubbi Philippe (2020). Matching zooplankton abundance and environment in the South Indian Ocean and Southern Ocean. Deep-sea Research Part I-oceanographic Research Papers, 163, 103347 (12p.). Publisher's official version : https://doi.org/10.1016/j.dsr.2020.103347 , Open Access version : https://archimer.ifremer.fr/doc/00643/75474/

Data acquired and analyses carried out at sea and on shore

The study of macrozooplankton and micronekton patterns and their variability was conducted using continuous EK80 acoustic data acquisition on transits and at stations during the 2016-2019 campaigns and the in-situ oragnisms sampling.

1. Acoustic acquisition with the EK80 echosounder and in-situ sampling

The EK80 sounder has 5 frequencies (18-38-70-120-200 kHz). The depth sampled decreases as the frequency increases. The recordings constitute a large volume of data (about 2-3 TB for a 40-day campaign). All operations and events were reported and synchronized to the recordings because of possible interference with the acoustic recordings.

Depending on the campaign, the ADCP 75 and 150kHz was used. In this case, the K-Sync synchronization unit was used. The software had malfunctions, including a "Timeout" problem (reported in the THEMISTO 2016 and 2017 campaign reports) that required the system to be restarted very regularly.

The instruments are located in an appendix positioned under the hull of the ship dedicated to the acoustic instruments. This installation allowed to reduce the bubbling problem, important in rough sea conditions. Globally, the quality of the data depends on 3 factors whose optimal combination must be found: Weather conditions / Speed and direction of the ship / Weight and trim of the ship.

The transits were covered at an average speed of 12 knots. The ping rate was set at 3-4 s for all the campaigns, i.e. one data every 20-25 m during the transit phase.

The echosounder was generally used in narrow band, except during experimental acquisition in wide band which will allow the exploration of the frequency response of organisms whose acoustic signature corresponded with important specific samples taken by trawl (during the Mobydick campaign).

Concerning the acoustic data only, the processing on board consisted in the parameterization linked to the acquisition.

Concerning the physical oceanography measurements, the thermosalinograph data were acquired simultaneously with the acoustic measurements. Temperature, salinity and fluorometry profiles at the stations (OISO for obsaustral and the dedicated Mobydick campaign) were also integrated into the data set to describe the physical and biological environment.

Macrozooplankton and micronekton were collected during the day and night during the MOBYDICK-THEMISTO cruise using the Mesopelagos trawl, designed by Ifremer (Laboratoire de Biologie et Technologie des Pêches, LTBH, Lorient, France) (Meillat, 2012). This non-closing trawl has a vertical opening of 7 m and a horizontal opening of 12 m, and a length of 44 m. The trawl has a mesh size of 30 mm in the wings and 4 mm in the codend, so it was used to target organisms ranging in size from about 1 to 30 cm. The depth of the trawl was monitored in real time using a Scanmar depth sensor (Åsgårdstrand, Norway) attached to the trawl head. We adopted a semi-stratified/adaptive strategy in sampling to sample 3 layer depths of the water column based on the observed real-time acoustic detections.

2. Analyses of acoustic data

The data were cleaned and processed with the Matecho tool developed by the LEMAR IRD acoustic team (Perrot et al., 2018), interfaced with Movies3D software developed by Ifremer (Trenkel et al., 2009).

Each study conducted with THEMISTO data used analyses adapted to the question addressed:

- C. Godet (Master 2 SU, "Etude des variations d'abondance du zooplancton dans la partie indienne de l'océan Austral : influence des migrations nycthémérales et des paramètres environnementaux"): Generalized linear mixed models were performed to test the effect of nycthemeral cycles from vertical variations of acoustic densities on abundance variations of zooplankton collected by CPR.

- C. Merland (Master 2 SU, "Structuration spatiale des écosystèmes pélagiques dans l'Océan Indien Sud et la zone indienne de l'Océan Austral"): A functional approach (Principal Component Analysis) allowed to regionalize and identify the patterns of micronekton variability on the latitudinal transect between La Reunion and Kerguelen.

- L. Izard (Thèse SU, "Structuration spatiale et variabilité des écosystèmes mésopélagiques dans l'Océan Indien Sud"): The purpose of this study is to develop statistical tools aiming to objectively extract key components of micronekton distribution variability. We developed a Multivariate Functional data analysis (FDA) method to classify acoustic observations in Saint-Paul and Amsterdam economic exclusive zone. This study proposes a novative method to analyse the vertical variability and quantify temporal or spatial modes of variability in multivariate acoustic data (Fig. 1).

Fig. 1. From statistical classification to spatial patterns. (A) Matrix representation of multivariate acoustique data. An acousitc observation corresond to the simultaneous information sampled at a time t. (B) Curve representation of acoustic data; S v is soly represented as a function of depth. (C) FPCA result allows to identifiy the principal modes of variability of AO. Interpretation of the CP allows to atribute it to a temporal of spatial dynamic. (D) Statistical classification of AO depending of the CP kept and spatial representation of the clusters. From Izard et al. in prep.

- MOBYDICK-THEMISTO: The Sv profiles were compared to the biomasses of the different families of organisms. The "RGB" representation (representation of frequency differences by a color scale on the same echogram) was used to better visualize the different acoustic structures and their variability in time and space. We used the E-score method, developed by the IRD acoustic team. It is a semi-supervised method of classification of echoes based on 3 differences in frequency (thus 4 frequencies, Fig. 2). As the classification parameters are relative responses, the classification is independent of the absolute acoustic density. The correspondence of the acoustic groups formed with the biology can be done after the classification, on the one hand with trawls and on the other hand with the acoustic response models (swimbladder like, fluid like, ...).

Fig.2. Ellipsoids of 50% confidence around the groups formed by the hierarchical classification in the E-score analysis. 3D representation according to the 3 Sv differences.

Published data

Metzl Nicolas, Fin Jonathan, Lo Monaco Claire, Mignon Claude, Alliouane Samir, Antoine David, Bourdin Guillaume, Boutin Jacqueline, Bozec Yann, Conan Pascal, Coppola Laurent, Douville Eric, Durrieu De Madron Xavier, Gattuso Jean-Pierre, Gazeau Frédéric, Golbol Melek, Lansard Bruno, Lefèvre Dominique, Lefèvre Nathalie, Lombard Fabien, Louanchi Férial, Merlivat Liliane, Olivier Léa, Petrenko Anne, Petton Sébastien, Pujo-Pay Mireille, Rabouille Christophe, Reverdin Gilles, Ridame Céline, Tribollet Aline, Vellucci Vincenzo, Wagener Thibaut, Wimart-Rousseau Cathy (2023). A synthesis of ocean total alkalinity and dissolved inorganic carbon measurements from 1993 to 2022: the SNAPO-CO2-v1 dataset. https://doi.org/10.17882/95414

Bibliography

Publications

Izard L., Fonvieille N., Merland C., Koubbi P., Nerini D., Habasque Jeremie, Lebourges-Dhaussy Anne, Lo Monaco C., Roudaut Gildas, D’ovidio F., Charrassin J.-B., Cotté Cedric (2024). Decomposing acoustic signal reveals the pelagic response to a frontal system between oceanic domains. Journal Of Marine Systems, 243, 103951 (19p.). https://doi.org/10.1016/j.jmarsys.2023.103951

Uitz J., Roesler C., Organelli E., Claustre H., Penkerc'h C., Drapeau Serge, Leymarie E., Poteau A., Schmechtig C., Dimier C., Ras J., Xing X., Blain S. (2023). Characterization of Bio‐Optical Anomalies in the Kerguelen Region, Southern Indian Ocean: A Study Based on Shipborne Sampling and BioGeoChemical‐Argo Profiling Floats. Journal Of Geophysical Research-oceans, 128(12), e2023JC019671 (33p.). Publisher's official version : https://doi.org/10.1029/2023JC019671 , Open Access version : https://archimer.ifremer.fr/doc/00868/98001/

Zhang Rui, Debeljak Pavla, Blain Stéphane, Obernosterer Ingrid (2023). Seasonal shifts in Fe-acquisition strategies in Southern Ocean microbial communities revealed by metagenomics and autonomous sampling. Environmental Microbiology, 25(10), 1816-1829. https://doi.org/10.1111/1462-2920.16397

Debeljak Pavla, Bayer Barbara, Sun Ying, Herndl Gerhard J., Obernosterer Ingrid (2023). Seasonal patterns in microbial carbon and iron transporter expression in the Southern Ocean. Microbiome, 11(1), 187 (12p.). Publisher's official version : https://doi.org/10.1186/s40168-023-01600-3 , Open Access version : https://archimer.ifremer.fr/doc/00849/96098/

Amano Chie, Zhao Zihao, Sintes Eva, Reinthaler Thomas, Stefanschitz Julia, Kisadur Murat, Utsumi Motoo, Herndl Gerhard J. (2022). Limited carbon cycling due to high-pressure effects on the deep-sea microbiome. Nature Geoscience, 15(12), 1041-1047. Publisher's official version : https://doi.org/10.1038/s41561-022-01081-3 , Open Access version : https://archimer.ifremer.fr/doc/00808/91962/

Petit Flavien, Uitz Julia, Schmechtig Catherine, Dimier Céline, Ras Joséphine, Poteau Antoine, Golbol Melek, Vellucci Vincenzo, Claustre Hervé (2022). Influence of the phytoplankton community composition on the in situ fluorescence signal: Implication for an improved estimation of the chlorophyll-a concentration from BioGeoChemical-Argo profiling floats. Frontiers In Marine Science, 9, 959131 (16p.). Publisher's official version : https://doi.org/10.3389/fmars.2022.959131 , Open Access version : https://archimer.ifremer.fr/doc/00796/90786/

Smolina Irina, Espinasse Marina, Amundsen Cesilie Røtnes, Espinasse Boris (2022). The complete mitochondrial genome of the southern calanoid copepod Calanus simillimus Giesbrecht, 1902. Mitochondrial Dna Part B-resources, 7(7), 1260-1262. Publisher's official version : https://doi.org/10.1080/23802359.2022.2093678 , Open Access version : https://archimer.ifremer.fr/doc/00783/89480/

Remize Marine, Planchon Frederic, Loh Ai Ning, Grand Fabienne Le, Bideau Antoine, Puccinelli Eleonora, Volety Aswani, Soudant Philippe (2022). Origin and fate of long-chain polyunsaturated fatty acids in the Kerguelen Islands region (Southern Ocean) in late summer. Journal Of Marine Systems, 228, 103693 (17p.). Publisher's official version : https://doi.org/10.1016/j.jmarsys.2021.103693 , Open Access version : https://archimer.ifremer.fr/doc/00741/85281/

Cotté Cedric, Ariza A., Berne Adrien, Habasque Jeremie, Lebourges-Dhaussy Anne, Roudaut Gildas, Espinasse B., Hunt B.P.V., Pakhomov E.A., Henschke N., Péron C., Conchon A., Koedooder C., Izard L., Cherel Y. (2022). Macrozooplankton and micronekton diversity and associated carbon vertical patterns and fluxes under distinct productive conditions around the Kerguelen Islands. Journal Of Marine Systems, 226, 103650 (18p.). Publisher's official version : https://doi.org/10.1016/j.jmarsys.2021.103650 , Open Access version : https://archimer.ifremer.fr/doc/00729/84089/

Hunt Brian P.V., Espinasse Boris, Pakhomov Evgeny A., Cherel Yves, Cotté Cedric, Delegrange Alice, Henschke Natasha (2021). Pelagic food web structure in high nutrient low chlorophyll (HNLC) and naturally iron fertilized waters in the Kerguelen Islands region, Southern Ocean. Journal Of Marine Systems, 224, 103625 (10p.). Publisher's official version : https://doi.org/10.1016/j.jmarsys.2021.103625 , Open Access version : https://archimer.ifremer.fr/doc/00718/82993/

Henschke Natasha, Cherel Yves, Cotté Cedric, Espinasse Boris, Hunt Brian P.V., Pakhomov Evgeny A. (2021). Size and stage specific patterns in Salpa thompsoni vertical migration. Journal Of Marine Systems, 222, 103587 (5p.). Publisher's official version : https://doi.org/10.1016/j.jmarsys.2021.103587 , Open Access version : https://archimer.ifremer.fr/doc/00697/80925/

Sun Ying, Debeljak Pavla, Obernosterer Ingrid (2021). Microbial iron and carbon metabolism as revealed by taxonomy-specific functional diversity in the Southern Ocean. Isme Journal, 15(10), 2933-2946. Publisher's official version : https://doi.org/10.1038/s41396-021-00973-3 , Open Access version : https://archimer.ifremer.fr/doc/00693/80483/

Leblanc Karine, Lafond Augustin, Cornet Veronique, Legras Justine, Marie Barbara, Queguiner Bernard (2021). Deep particle stocks following the summer bloom around the Kerguelen islands: Insights into diatoms physiological state, community structure and mortality modes. Journal Of Marine Systems, 222, 103609 (17p.). Publisher's official version : https://doi.org/10.1016/j.jmarsys.2021.103609 , Open Access version : https://archimer.ifremer.fr/doc/00704/81648/

St John Glew Katie, Espinasse Boris, Hunt Brian P. V., Pakhomov Evgeny A., Bury Sarah J., Pinkerton Matt, Nodder Scott D., Gutiérrez‐rodríguez Andres, Safi Karl, Brown Julie C. S., Graham Laura, Dunbar Robert B., Mucciarone David A., Magozzi Sarah, Somes Chris, Trueman Clive N. (2021). Isoscape Models of the Southern Ocean: Predicting Spatial and Temporal Variability in Carbon and Nitrogen Isotope Compositions of Particulate Organic Matter. Global Biogeochemical Cycles, 35(9), e2020GB006901 (18p.). Publisher's official version : https://doi.org/10.1029/2020GB006901 , Open Access version : https://archimer.ifremer.fr/doc/00722/83389/

Irion Solène, Christaki Urania, Berthelot Hugo, L’helguen Stéphane, Jardillier Ludwig (2021). Small phytoplankton contribute greatly to CO2-fixation after the diatom bloom in the Southern Ocean. Isme Journal, 15(9), 2509-2522. Publisher's official version : https://doi.org/10.1038/s41396-021-00915-z , Open Access version : https://archimer.ifremer.fr/doc/00684/79595/

Hernandez-Magana Alejandra Elisa, Liu Yan, Debeljak Pavla, Crispi Olivier, Marie Barbara, Koedooder Coco, Obernosterer Ingrid (2021). Prokaryotic diversity and activity in contrasting productivity regimes in late summer in the Kerguelen region (Southern Ocean). Journal Of Marine Systems, 221, 103561 (12p.). Publisher's official version : https://doi.org/10.1016/j.jmarsys.2021.103561 , Open Access version : https://archimer.ifremer.fr/doc/00694/80583/

Christaki Urania, Skouroliakou Ioli-Dimitra, Delegrange Alice, Irion Solène, Courcot Lucie, Jardillier Ludwig, Sassenhagen Ingrid (2021). Microzooplankton diversity and potential role in carbon cycling of contrasting Southern Ocean productivity regimes. Journal Of Marine Systems, 219, 103531 (16p.). Publisher's official version : https://doi.org/10.1016/j.jmarsys.2021.103531 , Open Access version : https://archimer.ifremer.fr/doc/00689/80068/

Henschke Natasha, Blain Stéphane, Cherel Yves, Cotte Cedric, Espinasse Boris, Hunt Brian P.V., Pakhomov Evgeny A. (2021). Population demographics and growth rate of Salpa thompsoni on the Kerguelen Plateau. Journal Of Marine Systems, 214, 103489 (10p.). Publisher's official version : https://doi.org/10.1016/j.jmarsys.2020.103489 , Open Access version : https://archimer.ifremer.fr/doc/00659/77147/

Christaki Urania, Gueneugues Audrey, Liu Yan, Blain Stéphane, Catala Philippe, Colombet Jonathan, Debeljak Pavla, Jardillier Ludwig, Irion Solène, Planchon Frederic, Sassenhagen Ingrid, Sime Ngando Telesphore, Obernosterer Ingrid (2021). Seasonal microbial food web dynamics in contrasting Southern Ocean productivity regimes. Limnology And Oceanography, 66(1), 108-122. Publisher's official version : https://doi.org/10.1002/lno.11591 , Open Access version : https://archimer.ifremer.fr/doc/00649/76109/

Godet Claire, Robuchon Marine, Leroy Boris, Cotté Cedric, Baudena Alberto, Da Silva Ophélie, Fabri-Ruiz Salome , Lo Monaco Claire, Sergi Sara, Koubbi Philippe (2020). Matching zooplankton abundance and environment in the South Indian Ocean and Southern Ocean. Deep-sea Research Part I-oceanographic Research Papers, 163, 103347 (12p.). Publisher's official version : https://doi.org/10.1016/j.dsr.2020.103347 , Open Access version : https://archimer.ifremer.fr/doc/00643/75474/

Lafond Augustin, Leblanc Karine, Legras Justine, Cornet Véronique, Quéguiner Bernard (2020). The structure of diatom communities constrains biogeochemical properties in surface waters of the Southern Ocean (Kerguelen Plateau). Journal Of Marine Systems, 212, 103458 (22p.). Publisher's official version : https://doi.org/10.1016/j.jmarsys.2020.103458 , Open Access version : https://archimer.ifremer.fr/doc/00654/76599/

Irion Solène, Jardillier Ludwig, Sassenhagen Ingrid, Christaki Urania (2020). Marked spatiotemporal variations in small phytoplankton structure in contrasted waters of the Southern Ocean (Kerguelen area). Limnology And Oceanography, 65(11), 2835-2852. Publisher's official version : https://doi.org/10.1002/lno.11555 , Open Access version : https://archimer.ifremer.fr/doc/00635/74746/

Sassenhagen Ingrid, Irion Solène, Jardillier Ludwig, Moreira David, Christaki Urania (2020). Protist Interactions and Community Structure During Early Autumn in the Kerguelen region (Southern Ocean). Protist, 171(1), 125709 (25p.). https://doi.org/10.1016/j.protis.2019.125709

References of Technical Reports

Lehodey, P. Kloser R., Ariza A., Brierley A., Conchon A., Constable A., Cotté C., Fielding S., Fulton B., Handegard N.O., Haris K., Koubbi P., Kunath H., Proud R. (2019). MESOPP roadmap. MESOPP-19-0004: 20 pp. www.mesopp.eu/documents/

Fielding, S. (2018) Report of acoustic processing routines & quality checking methods. France, Collection Location Satellites (CLS) 9pp. (MESOPP-18-0003 [D.1]). DOI: http://dx.doi.org/10.25607/OBP-442

Koubbi P., Godet C., Robuchon M., Leroy B., Serandour B., Cotté C. (2018). Atlas of the main mesopelagic fish in the Southern Ocean. Report from the EU-H2020 MESOPP project, MESOPP-18-0010, 47 pp.

Lehodey P., Conchon A. (2018). Characterizing large scale micronekton assemblages based on acoustic data, in situ sampling and oceanic variables. Report from the EU-H2020 MESOPP project, MESOPP-18-0048, 25 pp.

Conchon A. (2017). Collocated NASC and oceanographic variables. Report from the EU-H2020 MESOPP project No 692173, MESOPP-17-0006, 8 pp.

Conchon A. (2017). Reference dataset of 38 kHz acoustic backscatter for South Indian ocean sector. Report from the EU-H2020 MESOPP project No 692173, MESOPP-17-0004, 10 pp.

References of International Seminar Communications

- C. Cotté, F. d'Ovidio , Y. Cherel, C. Guinet, C.-A. Bost, P. Koubbi, G. Duhamel, N. Behagle, G. Roudaut, A. Lebourges-Dhaussy, E. Josse, P. Bremher, P. Lehodey, B. Queguiner, S. Blain, I. Obernosterer. Lumière sur les écosystèmes mésopélagiques de Kerguelen, du carbone aux prédateurs. 16 émes Journées Scientifiques du CNFRA, La Rochelle France. 22-23 septembre 2020

- C. Cotté, F. d'Ovidio , M. Lévy, Y. Cherel, C. Guinet, C.-A. Bost, G. Duhamel, N. Behagle, G. Roudaut, E. Josse, P. Bremher, P. Lehodey, B. Queguiner, S. Blain, I. Obernosterer, L. Boehme, M. Hindell, M. Fedak. Pelagic spatial planning for the eastern subantarctic region (CCAMLR Domains 4, 5 and 6), Environmental forcing of the multiscale mesopelagic variability and trophic interactions. Cape Town South Africa, 26 - 30th August 2019

- Espinasse B., B.P.V. Hunt, E.A. Pakhomov, N. Henschke, Y. Cherel, C. Cotté, A. Delegrange, F. Planchon. Estimating food chain length and trophic transfer efficiency across contrasting productivity regimes in the Kerguelen region. IMBER Future Ocean, Brest France, 17-21 June 2019

- Quéguiner B., I. Obernosterer, S. Blain, U. Christaki, K. Leblanc, C. Cotté, A. Delegrange, Y. Cherel, C. Guinet, M. Zhou, B.P.V. Hunt, E.A. Pakhomov, F. Planchon. Pelagic ecosystem functioning in the vicinity of the Kerguelen Islands (Southern Ocean): Towards an end-to-end approach. IMBER Future Ocean, Brest France, 17-21 June 2019

- F. d'Ovidio, Y. Lehahn, C. Cotté, M. Lévy, C. Guinet, P. Koubbi. 25 Years of progress in radar altimetry symposium. Progresses of Altimetry for Marine Ecology: from a Dataset for Biophysical Studies, to a Tool for Conservation Policies. 24-29 September 2018, Ponta Delgada, São Miguel Island, Azores Archipelago, Portugal.

- O'Toole M, Cotté C, Cherel Y, Bost CA, Guinet C, Weimerskirch H, Hindell MA, d?Ovidio F. Use of thermal structure of the water column by multiple predator species. In: Where the poles come together. A SCAR & IASC Conference, Davos, Switzerland, 15-26 June 2018

- Conchon A., Titaud O., Lehodey P. & Cotté C. Acoustic data assimilation in a micronekton model: a method to study species assemblage. The 12th SCAR biology symposium, Leuven, Belgium, July 2017

- Cotté C., O'Toole M., d'Ovidio F., Lévy M., Guinet C., Bost CA., Behagle N., Roudaut G., Brehmer P. & Cherel Y.vOcean physics and its impact on trophic interactions within the Antarctic Circumpolar Current. 2nd international Symposium on the Kerguelen Plateau, Hobart, Australia, Nov. 2017

- Cotté C, d'Ovidio F, Béhagle N, Roudaut G, Brehmer P, Guinet C, Cherel Y. An integrative approach to understand a rich ecosystem in the Southern Ocean from carbon to top predators. Ocean Sciences Meeting, New Orleans, USA, February 21-26

References of National Seminar Communications

C. Cotté, F. d'Ovidio , Y. Cherel, C. Guinet, C.-A. Bost, P. Koubbi, G. Duhamel, N. Behagle, G. Roudaut, A. Lebourges-Dhaussy, E. Josse, P. Bremher, P. Lehodey, B. Queguiner, S. Blain, I. Obernosterer. Lumière sur les écosystèmes mésopélagiques de Kerguelen, du carbone aux prédateurs. 16 émes Journées Scientifiques du CNFRA, La Rochelle France. 22-23 septembre 2020

DEA or MASTER 2 using campaign data

Camille Merland, Master 2 SU (2019)

Claire Godet, Master 2 SU (2017)

Thesis using campaign data

Izard Lloyd (2023). Spatial structuring and variability of mesopelagic ecosystems in the southern Indian ocean. PhD Thesis, Université Sorbonne.

Sergi Sara (2021). Apport en nutriments par les monts sous-marins et les vents hydrothermaux dans l’océan Austral : effets sur les écosystèmes pélagiques et implications pour la conservation / Nutrient input from seamounts and hydrothermal vents in the Southern Ocean : impacts on the pelagic ecosystems and implications for conservation. PhD Thesis, Université Sorbonne.

Thèse de Lloyd Izard (2020-2023), "Structuration spatiale et variabilité des écosystèmes mésopélagiques dans l'Océan Indien Sud". PhD Thesis, Sorbonne Université