SeaQUEST post cruise report

SeaQUEST oceanographic campaign 6-10 April 2016 Meso- and Sub-mesoscale Physico-biogeochemical Dynamics in a Coastal NW Mediterranean Sea: Quantifying and Understanding Ecosystem Structure and Transport

Oliver N. Ross1, Andrea M. Doglioli1, Dorian Guillemain1, Katja Klun2, Louise Rousselet1, Iva Talaber2, Leo Berline1, Loic Guilloux1, Christel Pinazo1, Christophe Yohia3 1

Mediterranean Institute of Oceanography OSU Pytheas, CNRS/IRD/BLA Aix-Marseille University Marseille, France

2

National Institute of Biology Marine Biology Station Piran Fornače 41 6330 Piran, Slovenia

3

OSU Institute Pytheas Aix-Marseille University, CNRS/INSU/IRD Toulon University Marseille, France

CRUISE REPORT In its final version from 18 May 2016

Brief overview Name of Campaign:

SeaQUEST

P.I.:

Oliver Ross

Campaign website:

http://mio.pytheas.univ-amu.fr/SEAQUEST/

Other scientists on board:

Andrea Doglioli (physics), Yoan Fremon (MVP operator), Dorian Guillemain (rosette and plankton net sampling), Katja Klun (biogeochemical sampling and analyses), Louise Rousselet (physics), Iva Talaber (biogeochemical sampling and analyses)

Scientists providing support on land:

Leo Berline (analyses of LOPC & LISST data), François Carlotti (expertise on zooplankton), Frederic Cyr (glider deployment), Loic Guilloux (analyses of in situ plankton samples), Anne Petrenko (expertise on physics), Christel Pinazo (3D coupled biogeochemical forecast modelling), Christophe Yohia (3D operational and predictive modelling, weather forecasts, general IT support)

Vessel name:

R/V Tethys II

Cruise period:

6-10 April 2016

Geographical area:

NW Mediterranean/Eastern Entrance to Gulf of Lion/area between about 42° 30’ – 43° 30’ N and 5° 30’ – 8° E

In situ data acquired/instruments deployed (F=fixed station, U=underway):

         



CTD (F,U) LOPC (F) LISST (F) ADCP (U) TSG (U) Down-welling irradiance (F) Fluorescence (F,U) Oxygen (F) Plankton concentration (vertical tows with a 200µm net) (F) Niskin water samples (F,U) for later analyses of: Chl-a, nutrients (DIN, PO4), particulate organic matter (C/P/N), dissolved organic carbon (DOC), total dissolved nitrogen and phosphorus (TDN, TDP), flow cytometry, taxonomy Meteorological conditions (atmospheric pressure/air temperature/relative humidity/wind direction and velocity/solar irradiance) (U)

How to cite This report may be cited as: Ross, O.N. et al. 2016, “SeaQUEST campaign from 6-10 April 2016 aboard R/V Tethys II: Cruise Report”, Mediterranean Institute of Oceanography, Aix-Marseille University, 34 pp, DOI: 10.13140/RG.2.1.2253.7846/2


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Acknowledgements The SeaQUEST campaign was made possible through financial support from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme FP7/2007-2013/ under REA grant agreement n° 624170 and through a collaboration with the NIB - Marine Biology Station Piran. Our particular thanks go to Captain Joel Perrot and the entire crew of R/V Tethys II for hosting us on board, for their fantastic help during the campaign and their enthusiasm and flexibility, while sometimes working in adverse weather conditions. Genavir and Yoan Fremon, in particular, are acknowledged for providing and operating the MVP. The MVP and associated captors are the property of IFREMER. We also wish to thank Isabelle Pujol (CLS) for her help with satellite tracks and Madeleine Goutx and Frederic Cyr for information on the glider deployment. Special thanks go also to the land based support of DT-INSU in La Seyne-sur-Mer. In particular, we would like to thank Malika Oudia for her help in the administrative work and Céline Heyndrickx and Frédéric Le Moal for their technical support. We acknowledge the IT Service of OSU Pythéas for their support in computing and networking.

Scientific Background The SeaQUEST campaign was the central observational component of the Marie Curie project of the same name. Its main purpose was to investigate the role of the Northern Current (NC), a slope current that passes along the continental slope off the Gulf of Lion (GoL), where it bounds and controls shelf circulation, and in particular its role as a physical barrier for cross-shelf exchanges between the plateau and the open ocean. This typically results in three biogeochemically distinct areas: (1) the coastal zone where production is typically driven by river run-off and/or upwelling; (2) the current itself, which typically carries a very distinct temperature and biogeochemical signature; and (3) the open Mediterranean. The cruise was specifically targeted for the spring season when these contrasts are often most pronounced. The original campaign objectives were: (i)

(ii)

(iii)

Carry out several transects by criss-crossing the NC in various places using underway sampling with a towed undulating profiler (carrying a CTD, LOPC, and fluorimeter) in conjunction with the ship’s own ADCP, TSG, and fluorescence probe to identify the location and characterize the strength and extent of the NC. Using information from (i) and also by making use of supporting information from remote sensing data: to carry out fixed station sampling in all 3 distinct bio-regions, collecting both physical (CTD, ADCP) and biogeochemical (LOPC, LISST, Fluorescence, Chl-a, nutrients, DOM, POM, oxygen) data. Recover a glider that was sampling the study area at the same time

Two days prior to the cruise, the original campaign design had to be severely modified due to the French Military which did not grant permission to sample most of the planned stations. In addition, in (i) we could only use a smaller profiler equipped with a CTD due to technical issues. Objective (iii) had to be abandoned due to lacking permissions from the military (see above).


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Contents Brief overview ........................................................................................................................................ 1 How to cite .............................................................................................................................................. 1 Acknowledgements ................................................................................................................................. 2 Scientific Background ............................................................................................................................. 2 List of Figures ......................................................................................................................................... 4 List of Tables .......................................................................................................................................... 4 1

Scientific Personnel ........................................................................................................................ 5

2

Cruise Itinerary ............................................................................................................................... 5

3

Introduction ..................................................................................................................................... 7

4

Cruise Planning and Strategy ........................................................................................................ 10 4.1

Satellite imagery ................................................................................................................... 10

4.2

Coastal Radar ........................................................................................................................ 11

4.3

Numerical Modelling ............................................................................................................ 11

4.3.1

WRF (Christophe Yohia) .............................................................................................. 11

4.3.2

MARS3D-ECO3M (Christel Pinazo & Christophe Yohia) .......................................... 12

4.4

Wave Forecasting.................................................................................................................. 13

4.5

Cruise Strategy and the French Navy.................................................................................... 14

5

Cruise Narrative and Daily Log .................................................................................................... 15

6

Instruments deployed and data collected ...................................................................................... 18 6.1

ADCP – Acoustic Doppler Current Profiler ......................................................................... 18

6.2

TSG – Thermosalinograph and Fluorimeter ......................................................................... 19

6.3

MVP – Moving Vessel Profiler ............................................................................................ 20

6.4

CTD Rosette including LOPC, LISST, and Plankton Net .................................................... 23

7

Water samples – collection and preparation ................................................................................. 25

8

Future Work and Planned Analyses .............................................................................................. 29

9

8.1

Biogeochemical analyses ...................................................................................................... 29

8.2

Analyses of Zooplankton Samples and LOPC/LISST data .................................................. 29

References ..................................................................................................................................... 31


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List of Figures Figure 1: Summary of the work carried out during the SeaQUEST campaign. The background image shows MODIS sea surface chlorophyll for the last day of the campaign and arrows the AVISO current velocities. Remote sensing images for all other days of the campaign are available at the campaign website at http://mio.pytheas.univ‐amu.fr/SEAQUEST/. ......................................................................................................... 7 Figure 2: Schematic of the study area. ................................................................................................................... 8 Figure 3: Satellite (MERIS) image of chlorophyll‐a concentration. The dashed area shows the location of the NC. The sharp drop in Chl concentration near the shelf edge (arrows) indicates how the horizontal dispersal of Chl beyond the shelf edge is blocked by the NC. ........................................................................................................... 9 Figure 4: Example output from the SPASSO software package showing (a) Modis Chl‐a, (b) AVISO current velocities, (c) Finite size Lyapunov exponents, and (d) L3 sea surface temperature. All images are for10 April 2016, the last day of the campaign. ..................................................................................................................... 10 Figure 5: Example image of surface current strength and direction from the HF Radar station at Cap Ferrat. ... 11 Figure 6: Example wind forecast from the WRF model for 8 April 2016 11:00h clearly illustrating the Mistral event. .................................................................................................................................................................... 12 Figure 7: Example model output from MARS3D/glxl‐ECO3M for 10 April 201612:00h showing (a) SST and surface currents, and (b) surface Chl‐a. Compared to the satellite images from Figure 4, the current appears to be well represented but the chlorophyll is clearly too high in the current and too low further offshore. ............ 13 Figure 8: Previmer forecast of significant wave height for 8 April 2016. .............................................................. 13 Figure 9: Original cruise plan submitted to the Flotte Cotiere and the French Navy. Grey boxes indicate the military ZONEX sectors (requires permission from French Navy to carry out any sampling activity). The background colour shows L4 SST from 31 March 2016. Grey arrows show the predicted AVISO current velocities from 31 March 2016. ............................................................................................................................................ 14 Figure 10: Strategy meeting to plan the cruise track for the following day, based on supporting information from satellite imagery, weather/weave forecasts and numerical modelling. ...................................................... 15 Figure 11: Processing the water samples. ............................................................................................................ 16 Figure 12: Recovery of the CTD/LOPC/LISST rosette ............................................................................................. 17 Figure 13: Summary of ADCP surveys. .................................................................................................................. 18 Figure 14: Summary of all data from TSG measurements, obtained between the 6th and 10th of April 2016 .... 19 Figure 16: Deploying the MVP during the SeaQUEST campaign. ......................................................................... 20 Figure 17: MVP data collected on 10 April 2016. ................................................................................................. 21 Figure 18: Calculation of steric sea surface height from MVP data acquired along parts of the SARAL/AltiKa satellite track 973 on 6 April 2016. ....................................................................................................................... 22 Figure 19: Photo plate showing the plankton net and the rosette Carousel Sampler. ......................................... 23

List of Tables Table 1: Scientific personnel on board .................................................................................................................... 5 Table 2: Scientific personnel providing support from land ..................................................................................... 5 Table 3: Summary of cruise itinerary (see section Cruise Narrative for more verbose version). A map is provided with Figure 1. .......................................................................................................................................................... 5 Table 4: Summary of all waypoints and their locations (cf. Figure 1). .................................................................... 6 Table 5: Summary of ZONEX permissions requested and the permissions granted by the French Navy 2 days prior to embarking. ............................................................................................................................................... 15 Table 6: Summary of MVP deployment ................................................................................................................ 20 Table 7: Summary of all CTD/LOPC/LISST and plankton net stations (cf. Figure 1). ............................................. 24 Table 8: Summary of fixed station and underway water sampling. ..................................................................... 26


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1 Scientific Personnel There were a total 14 people on board R/V Tethys II, including seven scientific personnel and seven crew under the command of Captain Joel Perrot. The table below provides a summary of the scientific personnel and their roles on board. Table 1: Scientific personnel on board

Name Oliver Ross Andrea Doglioli Yoan Fremon Dorian Guillemain Katja Klun Louise Rousselet Iva Talaber

Affiliation MIO MIO Genavir MIO NIB-MBP MIO NIB-MBP

Role on board Principal Scientist Scientist (physics) Tech (MVP) Tech (sampling) Scientist (biogeochemistry) Scientist (physics) Scientist (biogeochemistry)

The cruise was also supported from land through provision of real time satellite images, 3D operational modelling, and weather forecasting for the study area. The following table lists the land based scientific personnel and their roles prior to, during, and/or after the campaign. Table 2: Scientific personnel providing support from land

Name Leo Berlin François Carlotti Frederic Cyr Vesna Flander-Putrle Janja France Christian Grenz Loic Guilloux Anne Petrenko Christel Pinazo Tinkara Tinta Christophe Yohia

Affiliation MIO MIO MIO NIB-MBP NIB-MBP MIO MIO MIO MIO NIB-MBP OSU Pytheas

Role Analyses of LOPC and LISST data Expertise on zooplankton Glider support HPLC phytoplankton pigment analyses Expertise on phytoplankton taxonomy SAM oceanographic equipment pool Post-cruise analyses of plankton net samples Expertise on Northern Current 3D coupled biogeochemical forecast modelling Expertise on bacterial plankton taxonomy Operational modelling & forecasting, IT support

2 Cruise Itinerary (all times are UTC) Table 3: Summary of cruise itinerary (see section Cruise Narrative for more verbose version). A map is provided with Figure 1.

Date Day 0 (5 April) Day 1

Ship track Departure from La Seyne at 1900h toward T1 Start of transect from T2 toward T5 and for overnight shelter at T6


Work carried out/data acquired ADCP, TSG, fluorimeter along the way - ADCP, TSG, fluorimeter along the way - 4 CTD/LOPC/LISST stations (T2-T5) with water samples taken at various depths - MVP between T2&T3 and T4&T5 - Plankton net at T2, T4 & T5

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Day 2

Due to adverse wave conditions South of 43°N and West of 6.5°E, transect from T6-T7-T8

Day 3

Due to adverse weather (100 km/h winds) and sea (>4m weaves) conditions, no work could be carried out and the boat remained at T8 Adverse conditions persisted. In preparation for sampling on the following day, the boat transited from T8 to T9. Departure from anchor point T9 at 0300h to begin transect T10-T18 at 0415h. Arrival at quay in La Seyne (T18) at 1700h.

Day 4

Day 5

- ADCP, TSG, fluorimeter along the way - Surface water samples at regular intervals from ship’s intake -

- ADCP, TSG, fluorimeter along the way - ADCP, TSG, fluorimeter along the way - Surface water samples at regular intervals between T10-T14 - MVP between T11-T12 - 3 CTD/LOPC/LISST stations (T14T16) with water samples taken at various depths - Plankton net at T11, T14, T16

Table 4: Summary of all waypoints and their locations (cf. Figure 1).

Station name T0 T1 T2

Position 43.10600°N 5.88458°E 42.6700°N 6.2162°E 42.66654°N 6.45664°E

T3

42.78336°N 6.41768°E

T4

42.9958°N 6.3463°E

T5

43.0735°N

T6

43.269°N

T7 T8

42.979183°N 7.7623°E 43.27726°N 6.66829°E

T9

43.10161°N 5.93986°E

T10 T11

43.04310°N 5.81650°E 42.94072°N 5.81650°E

T12

42.78453°N 5.81650°E

T13 T14

42.70782°N 5.81650°E 42.78453°N 5.81650°E

T15

42.86574°N 5.81650°E

T16

42.92650°N 5.81488°E

6.3182°E 6.61983°E


Arrival (a)/Departure (d) (UTC) 05 April 2016 1700h (d) 05 April 2016 2351h (a,d) 06 April 2016 0507h (a) 06 April 2016 0826h (d) 06 April 2016 1009h (a) 06 April 2016 1049h (d) 06 April 2016 1400h (a) 06 April 2016 1432h (d) 06 April 2016 1554h (a) 06 April 2016 1629h (d) 06 April 2016 1918h (a) 07 April 2016 0500h (d) 07 April 2016 1152h (a,d) 07 April 2016 1821h (a) 09 April 2016 0700h (d) 09 April 2016 1140h (a) 10 April 2016 0310h (d) 10 April 2016 0418h (a,d) 10 April 2016 0503h (a) 10 April 2016 0538h (d) 10 April 2016 0754h (a) 10 April 2016 0757h (d) 10 April 2016 0834h (a,d) 10 April 2016 0907h (a) 10 April 2016 0958h (d) 10 April 2016 1038h (a) 10 April 2016 1117h (d) 10 April 2016 1150h (a)

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T17 T18

42.94060°N 6.04500°E 43.10600°N 5.88458°E

10 April 2016 1245h (d) 10 April 2016 1356h (a,d) 10 April 2016 1500h (a)

Figure 1: Summary of the work carried out during the SeaQUEST campaign. The background image shows MODIS sea surface chlorophyll for the last day of the campaign and arrows the AVISO current velocities. Remote sensing images for all other days of the campaign are available at the campaign website at http://mio.pytheas.univ-amu.fr/SEAQUEST/.

3 Introduction SeaQUEST aims to examine the role of the Northern Current as a physical barrier to cross-shelf transport in the Gulf of Lion (NW Mediterranean) and the effect of its seasonal variability on the local biogeochemistry and plankton dynamics at meso- and sub-mesoscales. Shelf and coastal seas are at the interface between continents (impacted by human activities) and the open ocean (the main regulator of our planet’s climate and its biogeochemical cycles). They are regions of exceptionally high biological productivity and biogeochemical cycling and play a crucial role in earth system functioning (Le Tissier et al., 2006). On a global scale, coastal and shelf seas only account for 8% of the ocean surface area but for up to 30% of oceanic primary production (Walsh et al. 1988, 1991; Longhurst et al. 1995), 80% of the organic matter burial, 90% of the sedimentary mineralization, and 50% of the deposition of calcium carbonate (Walsh et al. 1988; Mantoura et al. 1991; Pernetta and Milliman 1995; Gattuso et al. 1998). In addition, they provide a wide range of ecosystem services such as food and energy supply, natural resources as well as cultural services (tourism). It has been widely recognised, however, that shelf and coastal seas are subject to increasing pressure from human activities with detrimental effects on the ecosystem which include habitat loss and degradation, pollution, climate change, overexploitation of fish stocks and natural hazards (EEA, 2010 and 2012). At the same time, ocean general circulation models (OGCMs) struggle to represent the processes and scales relevant to coastal seas and satellite estimates of primary production are invariably contaminated by the non-biotic influence on optical properties. In order to study these important


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oceanic regions we therefore need in situ observations in combination with a localised (i.e. high resolution 3D regional) modelling approach, paying particular attention to the accurate implementation of the high resolution bathymetry and the forcing at the open boundaries. Primary production draws down atmospheric CO2, but unlike in the open ocean, where particulate carbon can sink directly to the deep ocean and be removed from contact with the atmosphere, the shelf-sea carbon pump (Tsunogai et al. 1999) often requires lateral transport to remove carbon from the ventilated surface waters. A good understanding of the physical transport processes in coastal regions and how they impact on the ecosystem is thus not only important for predicting climate change but also at a more local level for policy makers, stake holders, and managers. The interaction between local currents, run-off from land, winds and vertical mixing affects everything from the dispersal of nutrients and urban pollutants, the transport of plankton (incl. fish eggs) and sediments and the overall biogeochemical state of the coastal zone. Within this context, SeaQUEST will study the horizontal transport and cross-shelf exchange processes including their effect on the biogeochemistry in the coastal zone around the Gulf of Lion (GoL, Figure 1) in the NW Mediterranean. The Mediterranean Sea belongs to a group of oceanographic regions (together with the polar oceans) known to be particularly sensitive to climate change (Giorgi, 2006). Despite its small size (0.82% of the world’s oceans) it contains up to 18% of the global marine biodiversity (Bianchi and Morri, 2000). It is subject to increasing anthropogenic Figure 2: Schematic of the study area. pressure due to growing economic activities and receives up to 200 million tourists annually, making it the most popular tourist destination worldwide (www.newper.eu). The impact of climate change on the physical forcing (brought about mainly by meteorological regime shifts in wind, rainfall, temperature, cloud cover) is expected to impact directly on the functioning of food webs, ultimately leading to significant changes in the planktonic and nektonic community structure. The Rhône River/GoL area offers a typical system for studying river/shelf-sea interactions. The GoL is one of the most productive areas in a mostly oligotrophic Mediterranean Sea (Durrieu de Madron et al., 2011) and is home to the French Mediterranean fishing fleet, with over 500 aquaculture farms in the Sète region alone (EC 2011). Its high productivity is due to Rhône River inputs and coastal upwelling activity. It therefore is an important feeding area for fish, birds, and mammals, both resident and migratory. The circulation in the GoL is forced mainly by wind, freshwater run-off and seasonal heating–cooling (Millot, 1990). The dominant circulation feature is the Northern Current (NC, Figure 1), a slope current that passes along the continental slope off the GoL, where it bounds and controls shelf circulation. In fact, the NC can constitute an effective dynamical barrier to crossshelf transport, locking the coastal waters in the GoL (Figure 2). It originates from the confluence of the Eastern and Western Corsican Currents and flows from the Ligurian to the Balearic Sea forming part of the general cyclonic circulation in the Western Mediterranean (cf. Figure 3). The NC exhibits a seasonally variable flux (maximal in winter) between 1-2Sv (1Sv=106 m3 s-1) which is comparable to the fluxes through the Strait of Gibraltar (Albérola et al, 1995). The NC is wider and shallower in summer (50km and 250m respectively) when it flows further off-shore. In winter, it moves in-shore where it narrows and deepens (ca. 30km and 450m) reaching maximal velocities of over 50cm s-1 (André et al, 2009). Particularly in winter, the NC also becomes baroclinically unstable and produces


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important mesoscale meanders which can penetrate onto the shelf and into the GoL (Millot 1999, Petrenko 2003, Rubio et al 2009). The position and dynamics of these meanders and associated submesoscale features (e.g. mesoscale eddies, Kersalé et al, 2013) are crucial for a large part of the exchanges between the deep ocean and coastal regions (Petrenko et al, 2005), however, the dynamics are complex and highly variable (Petrenko et al, 2008) due to the strong temporal and spatial variability in the forcing occurring in the eastern part of the GoL (Allou et al, 2010). The biogeochemical functioning of the study site is complex and largely driven by hydrodynamics. The primary forcing components are the two dominant winds: (i) north-northwesterly winds (Mistral (M) and Tramontane (N) in Figure 1), which favour upwelling (Millot, 1990), and (ii) south-easterly winds, which favour downwelling. In addition, the dominant hydrodynamic force is the typically oligotrophic NC (Figure 1). During an upwelling event, cold, nutrient-rich waters are brought up to the euphotic zone (e.g. El Sayed et al, 1994), which can lead to an increase in primary production. A case study performed by Minas (1968) showed that primary production tripled at a coastal station influenced by upwelling compared with a reference offshore station. An area of particular interest is the eastern entrance to the GoL near Toulon, a region of frequent upwelling events where the NC can intrude onto the GoL shelf leading to meandering and eddy shedding (Figure 3). The shelf off the GoL area has also been recognised as a location for dense shelf water formation in winter due to rapid wind-induced cooling (Millot, 1990). These events often coincide with the winter phytoplankton bloom in the area and once these dense water masses cascade off the shelf, significant quantities of nutrients and organic matter, including living phytoplankton, are transported to the intermediate or deep-water layers on the slope (Canals et al, 2006) providing an important food source for the deep ecosystems (Danovaro et al, 1999). The interplay between these processes is quite complex and can have direct impacts on the transport of nutrients and pollutants as well as the ecosystem dynamics. Most of the relevant features have scales of the order of one to tens of kilometres (eddy diameters and width of the NC) and are thus considered to be at the meso- or sub-mesoscale. Their influence on the biology, biogeochemistry and many socio-economic activities are a major concern for the scientific community (DEWEX-MERMEX campaigns, Durrieu de Madron et al, 2011). Sub-mesoscale coastal structures such as eddies and filaments play an important role because they control the coastal transport and transport barriers may contribute to the determination of ecological niches (D'Ovidio et al, 2010). While satellite data of ocean colour can allow detection of these structures, the elevation data are not always reliable (Bouffard et al, 2008). This limitation is an obstacle to the analysis of transport and coastal dispersion, and therefore the understanding of ecosystem Figure 3: Satellite (MERIS) image of chlorophyll-a concentration. The dashed area shows the functioning and location of the NC. The sharp drop in Chl concentration near the shelf edge (arrows) indicates how the horizontal dispersal of Chl beyond the shelf edge is blocked by the NC. biogeochemical cycles.


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4 Cruise Planning and Strategy The cruise design was based on a combination of transects with underway sampling of the surface layer in conjunction with fixed stations where vertical profiles could be obtained. The layout and timing of each transect was based on information from remote sensing data (satellites, HF radar), as well as operational modelling and forecasting. The following sections will briefly explain each component and how it was used.

4.1 Satellite imagery We obtained near-real time images of sea surface temperature (SST), ocean colour (converted to chla), and altimetry data (AVISO) to obtain information on sea surface height and associated geostrophic currents. These data were processed using the SPASSO software package (Software Package for an Adaptive Satellite-based Sampling for Oceanographic campaigns http://www.mio.univamu.fr/~doglioli/spasso.htm). The tool implements several diagnostics to identify physical structures of biogeochemical interest (fronts, eddies, filaments) which can be used to guide the in-situ sampling strategy as well as aid in the interpretation of the data collected (d’Ovidio et al. 2009, Nencioli et al. 2011). Adaptive strategies based on these diagnostics have been successfully implemented during several oceanographic campaigns such as LATEX (2010), KEOPS2 (2011), STRASSE (2012), and - more recently - OUTPACE (2015) and OSCAHR (2015). The daily plots created by SPASSO for each day of the cruise can be found at http://mio.pytheas.univamu.fr/SEAQUEST/#spasso. The data was first treated on land and then transmitted to the ship to help plan the strategy for the following day. An example of the type of available images is included in Figure 4. The altimetry data are the AVISO Mediterranean regional product (http://www.aviso.altimetry.fr/index.php?id=1275). The derived currents are processed by SPASSO to derive Eulerian and Lagrangian diagnostics of ocean circulation: OkuboWeiss parameter, particle retention time and advection, Lagrangian Coherent Structures. Sea surface temperature (level 3 and 4, 1 km resolution) and chlorophyll concentration (level 3, 1 km resolution, MODIS Aqua and NPPVIIRS sensors) have been provided by CMEMS (Copernicus Marine Environment Monitoring Service - http://marine.copernicus.eu).

Figure 4: Example output from the SPASSO software package showing (a) Modis Chl-a, (b) AVISO current velocities, (c) Finite size Lyapunov exponents, and (d) L3 sea surface temperature. All images are for10 April 2016, the last day of the campaign.


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4.2 Coastal Radar Part of the SeaQUEST study area is covered by one HF radar system that operates from Cap Ferrat as part of the French Mediterranean observatory system (MOOSE : http://www.moose-network.fr/ and http://hfradar.univ-tln.fr). The instrument is a CODAR Seasonde operated at 13.5 MHz, allowing for an 80-100 km spatial coverage with hourly estimations of surface radial velocities. Figure 5 shows an example here high radial velocities (~ 60 cm/s) plausibly show the location, extent, and direction of the surface velocity of the Northern Current. HF radar data from the cruise period will be treated in conjunction with other current measurement (ADCP, buoys-derived Lagrangian current) to assess the system and to help with model validation.

4.3 Numerical Modelling

Figure 5: Example image of surface current strength and direction from the HF Radar station at Cap Ferrat.

The atmospheric numerical model WRF provided meteorological forecasts as well as forcing fields for the physical-biogeochemical coupled model MARS3D/ECO3M used for the forecast of surface physical and biogeochemical tracers. A short description of the implementation of these models is included below.

4.3.1 WRF (Christophe Yohia) The WRF (Weather Research & Forecasting, Skamarock et al. 2008) system contains two dynamical solvers, referred to as the ARW (Advanced Research WRF) core and the NMM (Nonhydrostatic Mesoscale Model) core. WRF has been implemented at the OSU Institut Pytheas (Marseille) as an operational model. The NMM core configuration uses 2 nested Arakawa-E grids for a horizontal resolution varying from 10km to 2km and 38 vertical σ−P levels. The ARW core configuration uses an Arakawa-C grid with a 2km resolution and 28 vertical σ levels. The open boundary conditions are obtained from the output of the GFS (Global Forecast System) by NCAR/NCEP (National Center Atmospheric Research/National Centers Environmental Prediction). Both cores have had three runs per day starting at 5:00, 17:00 and 22:00 ; the output of the 05:00 WRFARW run provided the meteorological forcing for the oceanographic model MARS3DECO3M. An example wind forecast is shown in Figure 6.


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Figure 6: Example wind forecast from the WRF model for 8 April 2016 11:00h clearly illustrating the Mistral event.

4.3.2 MARS3D‐ECO3M (Christel Pinazo & Christophe Yohia) Operational modelling was provided using the free-surface, three-dimensional circulation MARS3D model (3D hydrodynamic Model for Applications at Regional Scale, IFREMER) (Lazure & Dumas 2008) in conjunction with the biogeochemical mechanistic model ECO3M (Baklouti et al., 2006). The high resolution MARS3D/glxl configuration, which forms part of the MENOR (MEditerranné NORd occidentale) configuration, was used to forecast the oceanic circulation in the Gulf of Lion and the Gulf of Genoa, with a horizontal resolution of 1.2 km in 463x262 grid cells and 30 vertical sigma levels. The time step was fixed at 50 s. The initial and boundary forecast conditions provided by PREVIMER (http://www.previmer.org) were imposed using a downscaling method of grid nesting (Andre et al., 2005). The North Western Mediterranean Sea circulation model MENOR forecast was forced by the MFS (Mediterranean Forecasting System) 1/16° regional model daily outputs of temperature, salinity, current, and sea surface elevation spatially and temporally interpolated onto the MENOR grid. The MENOR modelling was validated for the years 2005–2006 in the Gulf of Lion by comparing the main characteristics of the simulated shelf slope circulation with in situ (Andre et al., 2009) and satellite observations (Andre et al., 2005), and for the years 2001–2008 with satellite observations and drifter trajectories in the Gulf of Lion by Nicolle et al. (2009). The ECO3M biogeochemical platform in the Massilia configuration (Fraysse et al, 2013; 2014; Ross et al., 2016) has 17 state variables and implements mechanistic formulations to describe the carbon, nitrogen and phosphorus cycles in five compartments: (i) phytoplankton, (ii) bacteria, (iii) detrital particulate organic matter, (iv) dissolved organic matter, and (v) dissolved inorganic matter including ammonium, nitrate, and oxygen. Chlorophyll-a is a diagnostic variable related to the variable phytoplankton ratios. A more detailed description of the model can be found in Fraysse et al. (2013).


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Figure 7: Example model output from MARS3D/glxl-ECO3M for 10 April 201612:00h showing (a) SST and surface currents, and (b) surface Chl-a. Compared to the satellite images from Figure 4, the current appears to be well represented but the chlorophyll is clearly too high in the current and too low further offshore.

Every day, the coupled system was used to produce a 24hour forecast for currents, SSH, temperature, salinity, and biogeochemistry (chlorophyll, nitrate, phosphate) with outputs every hour at the sea surface, at 10m, and at 50m depths.

4.4 Wave Forecasting The cruise planning also heavily relied on forecast of significant wave height, provided by Previmer (http://www.previmer.org/previsions/vagues/modeles_mediterranee). This was important as we had an episode of strong Mistral winds during the campaign and the R/V Tethys cannot safely operate (deploy any instruments) if the wave height exceeds about 1.25 to 1.5m. Forecasts were therefore obtained twice daily in order to gauge the viability of the planned sampling and to find alternatives in case the original area could not be sampled. An example forecast for one of the two days during which no sampling was possible is shown in Figure 8.

Figure 8: Previmer forecast of significant wave height for 8 April 2016.


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4.5 Cruise Strategy and the French Navy The Tethys II is no 24h working vessel. The crew only works from 0700h till 2100h (local time) although night time cruising (using the MVP and/or ADCP/TSG) are possible. Bearing this in mind, and also based on satellite images from the weeks leading up to the cruise, a campaign strategy was devised (Figure 9) which consisted of 4 daytime transects with fixed-station CTD and underway MVP/ADCP/TSG sampling, crossing the Northern Current (NC) in various places, plus several night time crossings using the MVP/ADCP/TSG only. The plan also foresaw to follow 2 satellite tracks (SARAL/AltiKa tracks 057 and 973) which were crossing the study area during the cruise period with the intention to obtain data of the sea surface height which could then be compared against the satellite data.

Figure 9: Original cruise plan submitted to the Flotte Cotiere and the French Navy. Grey boxes indicate the military ZONEX sectors (requires permission from French Navy to carry out any sampling activity). The background colour shows L4 SST from 31 March 2016. Grey arrows show the predicted AVISO current velocities from 31 March 2016.

In order to sample this part of the Mediterranean, permissions need to be obtained from the French Navy. A military committee which decides on these permissions meets once weekly and cruise leaders are typically advised with only 1-2 days’ notice prior to embarking whether they can actually carry out the original cruise design. And so it happened for SeaQUEST: two working days prior to embarking, we were informed that we effectively only had permission to carry out about 15% of the original cruise plan. Table 5 summarises the ZONEX permissions requested and the permissions obtained.


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Table 5: Summary of ZONEX permissions requested and the permissions granted by the French Navy 2 days prior to embarking.

Date

ZONEX sectors requested

ZONEX permissions obtained

6 April 2016

3, 9, 10, 11, 12, 13, 14, 15, 16, 17

3, 17

7 April 2016

5, 6, 9, 14, 30, 31, 32, 40

3, 17

8 April 2016

5, 6, 9, 14, 30, 31, 32, 40

3, 17, 31, 32

9 April 2016

5, 6, 9, 14, 30, 31, 32, 40

3, 9, 17, 31, 32

10 April 2016

5, 6, 9, 14, 30, 31, 32, 40

3, 9, 17, 31, 32

This represented a severe limitation on the cruise and our ability to pursue the original cruise objectives, as the centre of the Northern Current was effectively off limits for vertical sampling except in sector 9 during the last 2 days of the cruise. We also did not obtain permission to sample to the West (outside) of Sector 32 (the AltiKa 057 satellite track on 9 April) and could only sample those parts of the AltiKa 973 track (on 6 April) that were in sectors 3 and 17, lacking permissions for the crucial central part (sectors 12 and 13). The cruise layout thus had to be adapted and re-designed at the last minute.

Figure 10: Strategy meeting to plan the cruise track for the following day, based on supporting information from satellite imagery, weather/weave forecasts and numerical modelling.

5 Cruise Narrative and Daily Log (all times are UTC) Day 0 (5 April 2016) – We arrived in La Seyne-sur-Mer at about 1300h. The team from Slovenia arrived at 1500h. Loading of all material was finished by about 1600h and the ship left quay at 1700h to steam toward waypoint T1 (cf. Fig. 1) which we passed just before midnight.


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Day 1 – Today’s cruise track followed the track #973 of the SARAL/AltiKa satellite which had passed along this track at 0305h on the same day. We arrived at T2, our first station for the day, at 0507h. The sea state showed some small waves of about 1m and the sky was 7/8 overcast. The sun had just risen above the horizon. The CTD/LOPC/LISST rosette was deployed at 0517h and was lowered to a depth of 2500m. The CTD/LOPC/LISST was recovered at 0653h. At 0733h we deployed the plankton net to carry out a vertical upward tow from 200m. The net was back on deck at 0749h. Before being able to deploy the MVP, the cable needed to be completely unrolled and tested. This test began at 0756h. The test was completed by 0820h and we began the transect with the MVP toward the next waypoint T3 at 0826h. We arrived at T3 with a light 0.75m swell and mostly clear skies (1/8). Once the boat was on station (1007h), the MVP was recovered (1009h) and the CTD/LOPC/LISST deployed (1012h) down to a depth of 2470 m. Once the CTD/LOPC/LISST was recovered (1148h), the sky had become more overcast (5/8) and we steamed toward our next waypoint T4. As we had no permission from the French Navy to carry out any vertical sampling in this stretch, we could only do surface sampling, using the ship’s ADCP and TSG. At 1400h, the ship arrived at the coastal station T4, where we found a calm sea state and mostly (2/8) clear skies. The CTD/LOPC/LISST entered the water at 1403h and was back on deck by 1417h, having been lowered to a depth of 76m. At 1426h the plankton net was lowered and raised up from 70m to be recovered on board by 1431h. As we were now entering an area for which we had again permission to sample the water column, the MVP was deployed at 1438h and we steamed toward our last station for the day. We reached the last station T5 at 1554h in calm seas and clear skies. The MVP was recovered by 1556h and the plankton net deployed at 1601h. The tow was performed over the entire depth of the water column of 40m. The plankton net was recovered at 1605h and at 1615h the CTD/LOPC/LISST was deployed to be recovered by 1628h. During the day we had received the latest wave- and weather forecasts. The predictions for the following day were such that no sampling could be carried out south of about 43°N and west of about 6.5°E (waves up to 4m and wind speeds reaching 100 km/h). As the latest AVISO satellite image suggested the existence of a small anticyclonic gyre with its centre at about 43.269°N/6.61983°E, the decision was made to steam toward T6 in St. Tropez Bay as this would allow us to take shelter for the night and also be close to the starting point for this new transect on the following day. Day 2 – We left our overnight mooring point T6 at 0500h to begin the transect from 43° 17.83’ N/6° 40.58’N at 0524h. Due to lacking permissions from the French Navy, we could only perform surface sampling. We therefore steamed toward T7 using only the ship’s ADCP/TSG while taking regular water samples from the ship’s water intake for later nutrient, POM, DOM and chl-a analyses. We arrived at T7 at 1152h and were back at T8 at 1821h. During the entire transect, the sea was mostly calm and the skies clear with only some high cirrus clouds (1/8).

Figure 11: Processing the water samples.


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Day 3 – No work could be performed due to high waves and strong winds throughout our study area. The boat therefore remained anchored in St Tropez harbour and the time was used to start analysing the data obtained during the two previous days. Day 4 – Adverse weather conditions persisted but the forecast suggested an improvement for Day 5. As we had permission from the French Navy for ZONEX sector 9 (cf. Fig 1), a decision was taken to make for La Seyne in order to be close to the starting point of the transect for the following day. We therefore left T8 in St Tropez at 0700h and steamed toward T9 where we were going to shelter for the remainder of the day and overnight. During this crossing, the sea was very choppy, even close to the coast, and we only could deploy the ADCP and TSG. We arrived at T9 by 1140h. Day 5 – We left T9 at 0310h with waves of about 1-1.5m and while it was still dark. By 0418h we arrived at station T10 where we began the transect toward T11 and eventually all the way out to T13 (which, based on the latest satellite data, was supposed to lie just outside the Northern Current). We took surface samples along the way as we had no permission to perform any vertical profiles except for Zonex sector 9. We arrived at T11 – the northern edge to sector 9 – during sun rise at 0503h. The sea state was still choppy with 1.5m waves and mostly clear skies (1/8). We immersed the plankton net at 0506 and recovered it at 0521. Due to the considerable swell, the boat was pitching about 20° to each side. As a result, the secondary wheel on the hydraulic arm from which the net was lowered into the water (cf. Figure 18), did not accurately count the amount of cable paid out during the deployment of the plankton net as the cable would sometimes slide across the wheel without turning it. This occurred whenever the boat pitched starboard. We therefore only lowered the net to 170m (as counted by the wheel), estimating that this would correspond to roughly 200m. Once the net was recovered, the sea state was deemed too rough by the commanding officer to deploy the CTD/LOPC/LISST. We therefore continued by deploying the MVP (at 0538h) and steaming toward T12 (skipping the station which had originally been planned at the centre of sector 9) with the intention to return to these stations later during the day, when the waves were forecast to be Figure 12: Recovery of the CTD/LOPC/LISST rosette smaller. We arrived at T12 in choppy seas with 1.5m swell and mostly clear skies (1/8) at 0754h. As we only had permission for sector 9, we had to recover the MVP at this point (0756h) and continue toward T13 with only the ADCP/TSG and continuing to take surface water samples. By 0834h we arrived at the end of the transect at T13 and turned the ship around, heading toward T14 which was at the same location as T12. By now the waves were slightly smaller (1m) and the sky had cleared completely (0/8). We arrived at T14 at 0907h with 1m swell and clear skies (0/8). By now the sea state had improved sufficiently for us to attempt a CTD deployment. We deployed the CTD/LOPC/LISST at 0913h sampling down to 500m and it was recovered by 0938h. The plankton net was deployed down to 200m at 0942 and recovered at 0957h and we continued toward the next station.


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Upon arriving at T15 at 1042h, the sea state was 1m waves and the skies clear (0/8). We deployed the CTD/LOPC/LISST down to 500m at 1042h and it was recovered at 1116h. We left the station at 1117h and headed toward our final station for the day. We arrived at our T16 at 1150h in light swell and clear skies (0/8). The CTD/LOPC/LISST was deployed at 1150h and recovered at 1216h. The plankton net was deployed at 1223h. During the ascent, the cable jumped of the secondary wheel and got stuck. It took 4 minutes to resolve this issue, a time during which the net remained suspended at 120m. The net was finally recovered at 1244h. We then returned to La Seyne via T17 while finishing the processing of water samples and deploying the ADCP/TSG. Our arrival at quay in La Seyne was at 1500h.

6 Instruments deployed and data collected 6.1 ADCP – Acoustic Doppler Current Profiler Ocean current data was obtained throughout the entire cruise from a hull-mounted RDI Ocean Sentinel 75 kHz ADCP. The configuration used during the whole cruise was: 60 cells, 8 m sized bins, an ensemble average of 1 minute, and bottom tracking whenever possible. The sampled depth range thus extended from 18.5 m to 562.5 m. The initial ADCP data analysis was carried out using the CASCADE software (v7.0 http://wwz.ifremer.fr/lpo%29/Boite-a-outils/Logiciels/ADCP-de-coque). A total of 6 files (*.STA) covering the entire cruise track were analysed. The Matlab-based LATEXtools were then used in order to visualize the ADCP data in near real-time (see Figure 13). This yielded the position and extent of the Northern Current which in turn allowed us to adapt the cruise plan accordingly (planning the locations of fixed stations at the edge or the centre of the current, etc.).

Figure 13: Summary of ADCP surveys.


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6.2 TSG – Thermosalinograph and Fluorimeter The TSG provides high frequency measurements of temperature, salinity and fluorescence from the ship’s water intake system which draws water from 2m depth with a flow rate of 60 L min-1 (Error! Reference source not found.). This system was also used to obtain water samples for later analyses in those areas where vertical sampling was forbidden by the French Navy. The CT sensor on the TSG

Figure 14: Summary of all data from TSG measurements, obtained between the 6th and 10th of April 2016


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consisted of an SBE21 temperature-conductivity probe and fluorescence was obtained using a Turner Designs 10-AU-005-CE field fluorimeter. TSG measurements were obtained continuously throughout the cruise with 1 data point every 15 seconds. Due to an issue to with the TSG software, GPS positional data were not recorded correctly into the same file but had to be added during postcruise treatment by synchronising the TSG files with the ship’s own navigational GPS record (courtesy of Celine Heyndrickx).

6.3 MVP – Moving Vessel Profiler We used an MVP200 equipped with a SSFFF I (SingleSensor Free Fall Fish Type I) containing a microCTD, sampling at 25Hz. A total of 135 casts have been performed along about 35km km of cruise track. Although we would have liked to deploy the MVP along the entire length of each transect, we only had very restrictive permissions from the French Navy, which limited the use of the MVP to 3 small sectors. All sampling was carried out while the ship was maintaining a constant cruising speed of 4 knots with the profiler being allowed to fall to depths of up to 360m (bathymetry permitting) which yields in a horizontal resolution (distance between subsequent profiles) of about half a nautical mile (or less in shallower regions). Table 6 contains a summary of the MVP deployments made, while Figure 16 and Figure 17 show some preliminary data and results.

Figure 15: Deploying the MVP during the SeaQUEST campaign.

Table 6: Summary of MVP deployment

Dive number

Start of dive (UTC) End of dive (UTC) Duration

Max depth

Ship speed

Observations

PL01

06/04/2016 08:23:34

06/04/2016 09:55:00

01:32:00

360 m

4 kn

RAS

PL02

06/04/2016 14:39:47

06/04/2016 15:51:09

01:12:00

45 m

4 kn

RAS

PL03

10/04/2016 05:40:30

10/04/2016 07:49:29

02:09:00

45 m

4 kn

RAS


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Figure 16: MVP data collected on 10 April 2016.


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Figure 17: Calculation of steric sea surface height from MVP data acquired along parts of the SARAL/AltiKa satellite track 973 on 6 April 2016.


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6.4 CTD Rosette including LOPC, LISST, and Plankton Net Vertical profiles were conducted with an SBE 32 Carousel Water Sampler rosette containing 12 Niskin bottles (with 12L each) with two vertical extensions fixed immediately below the carousel sampler. The first extension stand (fixed directly below the carousel) carried a CTD SBE 911 Plus for conductivity/temperature/pressure measurements, an SBE 43 dissolved oxygen sensor, a Chelsea Aquatracka III fluorimeter for in situ detection of Chlorophyll-a, a Wetlabs Cstar transmissometer for underwater measurements of beam transmittance, a Tritech PA500 altimeter for bottom detection, and a PAR - Luminous intensity sensor. The second extension stand (fixed below the first one) carried two instruments for in situ measurements of particle size distribution: a LISST (Laser In situ Scatterometer and

Figure 18: Photo plate showing the plankton net and the rosette Carousel Sampler.


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Transmissometer) Deep type B (particle size range: 1.25-250μm) and an LOPC (Laser Optical Plankton Counter, Herman & Harvey, 2006; particle size range: 100-1920μm). In order to calibrate the automated measurements, six vertical net hauls were carried out with a WP2 net with 200μm mesh size. The net samples were preserved in formalin for further analysis with Zooscan and taxonomic identification. A total of 7 vertical CTD/LIST/LOPC profiles were taken using the rosette, with water samples from between 4 to 6 depths. At all stations, the CTD/LOPC/LISST was lowered with a velocity of 0.5 m s-1 in the top 200m to have better data for the optical instruments and then at 1 m s-1 for greater depths. The plankton net was deployed 6 times. Table 7 details the station locations and the depths at which the Niskin water samples were obtained. Table 7: Summary of all CTD/LOPC/LISST and plankton net stations (cf. Figure 1).

Station name and location T2 42.6665°N 6.4566° E

Time of CTD

Niskin depths (m) 06/04/2016 5, 15, 0518h (in) 30, 106, 0653h (out) 115, 500

Time of Weather & sea plankton net state 06/04/2016 0733h (in) 0749h (out)

06/04/2016 5, 46, T3 42.7836°N 1012h (in) 80, 260, 6.41768°E 1148h (out) 400, 2362

_

T4 42.9958°N 6.3463°E

06/04/2016 5, 25, 1403h (in) 30, 35, 1417h (out) 45, 55

06/04/2016 1426h (in) 1431h (out)

T5 43.0735°N 6.3182°E

06/04/2016 5, 15, 1615h (in) 23, 30, 1628h (out) 35

06/04/2016 1601h (in) 1605h (out)

T11 42.94072°N 5.81650°E T14 42.7845°N 5.8165°E

‐ See footnote (1) 10/04/2016 5, 55, 0913h (in) 90, 180 0938h (out)

10/04/2016 0506h (in) 0525h (out) 10/04/2016 0942h (in) 0957h (out)

10/04/2016 5, 28, T15 42.86574°N 1042h (in) 35, 60 5.81650°E 1116h (out)

_


observations

1m swell, over‐cast 7/8, 15.5°C, 1010.2 hPa, 84% rel. hum., 6kn winds from 343° 1m swell, mostly clear 1/8, 15.3°C, 1011.3 hPa, 89% rel. hum., 6kn winds from 328° 0.5m swell, some scattered clouds 2/8, 16.3°C, 1010.1 hPa, 85% rel. hum., 4kn winds from 270° 0.5m swell, high cirrus 1/8, 17.7°C, 1009.3 hPa, 74% rel. hum., 7kn winds from 250° 1.5m waves, mostly clear 1/8,

Boat drifted about 2 nautical miles between CTD and plankton net. Total depth: 2500m Boat drifted about 0.5 mile between beginning and end of CTD. Total depth: 2470m. Negligible drift. Total depth: 76m. Net cast down to 70m.

1m swell, clear 0/8, 14.3°C, 1010.7hPa, 64% rel. hum., 3kn winds from 30°

Boat had drifted about 1.5 miles since beginning of CTD. Total depth: 2317m. Boat drifted