2.1. Research topics and challenges

2.1.1. Marine Geosciences

The scientific challenges to be highlighted in the coming years reveal not only society’s concern for the ocean, coasts and associated hazards but also the progress of our knowledge on how the present Earth’s system works on a geological time scale.

Among society’s concerns, the main challenges are to:

  •  Encourage coastal studies and earth-sea pairings, particularly in terms of tsunami/seismic/gravitational hazards and underground continent/ocean exchanges;
  •  Understand the dynamics of the pollutants (metal, metal-organic and organic) tied in with the hydro-sedimentary forcings and exploit the historical sediment archives to characterise the transformations and the persistence of pollutants in geological reservoirs depending on environmental conditions;
  •  Characterise the morphological response from the coastline and follow how the sedimentary construction of shelves and coastal zones change in response to rising sea levels, weather-climate forcings or anthropic disruptions (migration, construction/erosion, etc.) that modify the flux of available matter;
  • Determine tolerable disruption thresholds for the substrate (physical habitat) to maintain or restore the biological habitat (tied in with anthropic impacts);
  •  Decrypt marine archives (sediment and biological fossils), in high resolution, to better restrict climate change and the anthropic impacts and better date catastrophic, atmospheric or telluric events; improve comprehension and quantification of proxies to help reconstruct past oceanic changes;
  •  Improve assessment of major oceanic earthquakes, past and present, from mechanisms at source and their recurrences up to the characterisation of ruptures linked to the oceanic floor.
  •  Study the oceanic methane cycle, from genesis to storage in the sedimentary column and from there its influence on the water column and its potential contribution to the atmosphere as a greenhouse gas.


Among the research on the present Earth’s system and on a geological time scale, the following objectives were more particularly identified:

  • Restrict the circulation of fluids under the oceanic floor and the marine sediments (hydrothermal circulation, cold seeps, gas, etc.) in space and time in relation to the magmatic, tectonic, sedimentary activity and its impact on the diversity of deep ecosystems and the balance of chemical elements in the ocean;
  • understand the magmatism/tectonic relations on slow and ultra-slow moving ridges, as well as the volcanic structures (e.g. arcs, underwater mounts…) where a large number of processes and structures remain unknown (deformation linked to transforming faults, tectonic exhumation along the detachments and in amagmatic extension zones, very variable hydrothermal systems), with their impact on the structure, the composition and the thermal regime of the oceanic lithosphere that remain to be determined;
  • understand the tectonic/magmatism/sedimentation relations on the passive continental margins, a non-negligible geological element on a global scale and essentially not very well known. In the deep-sea margin area, in a diverging and/or transforming context, the exhumation of the lower crust all along the crustal detachment zone or sub-continental mantle exhumation zone and how it relates to setting up hydrothermal systems in transitional areas are still studied very little. What are the impacts of passing between a continental lithosphere and an oceanic lithosphere on the structure, the composition and the thermal regime of the lithosphere?
  • understand the “mud to mantle - source to sink” interconnected relationship, meaning the relationship between the deep-sea processes and the surface processes, or even determine the weight of the structural heritage of the pedestal on the sedimentation (architecture and type of deposits), as far as quantifying the complete sedimentary balance taking into account: (1) role of chemical alteration (e.g. dissolution of silicates) versus how relief is changing, (2) impact of climate variations, (3) determination of continental sources, (4) quantification of continental capture and (5) deposit in a more or less closed system;
  • make progress on tracing the source of marine sediments, by developing geochemical proxies on the mineralogical and/or fossil archive phase;
  •  for digital modelling, provide dating and constraints from environments of deposits and include the geochemical data from the sedimentary archive and fossils that help assess the erosion of the catchment basins and the origin of the sediments, on a geological time scale;
  • study the nonlinear processes in the ocean-atmosphere-biosphere-internal Earth coupled systems;
  • continue multi-disciplinary research work by coupling geodynamics, geology, biology and chemistry on characterising sea mounts in the oceans that are still studied very little;
  • the other major topics tackled in MG remain current such as the chemistry and the dynamics of the mantle, volcanic construction - time and space scale, the structure of the oceanic lithosphere, and its evolution from formation in diverging continent margins up to subduction.


It is important to highlight that these numerous challenges require physical and chemical seabed instrumentation to be developed in order to obtain long series of high-resolution data and to tackle the process dynamics on a local scale. This implies not only increasing the number of instruments to widen the number of observations but also strengthening R&D to better automate data processing and make it easier to extract useful information.


2.1.2. Oceanic physics and dynamics, Carbon cycles and elements, ecosystems

The major issues of these topics are still observing, understanding modelling the oceanic processes, their variability, their responses to climate change and anthropic pressure and their interactions with other compartments of the “Earth” system. The coastal area, in synergy with environmental issues (potentially high-impact, over-populated areas, such as concerning contribution to pollutants) and society issues (ecosystemic services, resources) are also a major concern for the scientific community. It is urgent to understand the combined issues of marine and atmospheric, physical-chemical and ecological dynamics and contributions from the coastal catchment basins on the natural variability of coastal environments (trophic networks, algae efflorescence) that are connected to each other and to the ocean and land environments.

More specific issues were identified for the coming years.


Physical Processes

The physical processes that control the oceanic dynamic on a large scale and its variability, are currently facing the following fundamental questions:

  • What are the mechanisms (seen as physical, geochemical and ecosystemic sequencing and interactions of multiple scale processes) by which the ocean is going to prioritise the space and time structures of their low frequency variations, regardless of whether they are forced by the atmosphere or intrinsic? One of the issues concerns the integration of small-scale space-time processes for large climate variability time scales, particularly in pertinent processes for thermohaline circulation and for the physical (and biological) pumping of carbon as well as for very long pertinent scales for paleo-oceanography;
  • How does the ocean redistribute or dilute climate change (i.e. changes in thermal and salt content, CO2, oxygen or even methane) towards the depths and between the major regions of the ocean? And how do these changes affect and interact with the different ecosystems?
  • What particular role is played by the dynamics of major oceanic crossroads (west coast current, thermocline, topographical thresholds, inter-gyre zones, etc.) in these mechanisms? This question is crucial in regions that are as varied as the bifurcation of currents zone in the South-West Pacific or in the Gulf Stream region of the North Atlantic;
  • What are the determinisms of the El Niño phenomenon for which the occurrence, dependence on equatorial conditions and “Warm Pool” coastal dynamics are still not understood?
  • Which processes determine the genesis of cyclones (dynamics, air-sea exchanges, etc.)?

Lack of knowledge on these matters is a barrier to understanding variations and changes to the climate and to quantify the ocean’s energy balance. The dynamics being studied are complex and often have a strong non-linear character, originating from strong scale interactions, and can have a stochastic dimension. In this context, it is now primordial to develop high resolution measurements to get databases that cover a large range of scales.


Chemical elements

 Chemical elements in the ocean can be beneficial for the biota (these are the nutritional and micro-nutritional elements) but are also potentially toxic (such as certain metals and metalloids, other organic pollutants or others). The study of their cycle is therefore intrinsically linked to studying their physical transport, by considering interactions with the matrices such as particles and organic matter, and to studying ecosystems.

  • How is the structure and the diversity of biological communities regulated by and/or does it regulate the flux of minor and trace elements? What is the importance of nitrogen fixers, particularly in the South-West Pacific?
  • How is the biological pump modulated by these exchanges?
  • What are the sources of these minor and trace elements, the factors of their bioavailability and their variability?
  • What is the feedback towards the atmosphere and particularly, can we improve the quantifications of emissions to the atmosphere of certain greenhouse gases (methane and nitrous oxide)?


High latitudes

Still largely unknown, polar oceans and ice fields are responsible for significant uncertainties in our understanding of the future climate and its impact on the ecosystems and the global sea level (Antarctic polar ice cap melting is the origin of the strongest uncertainty concerning global sea level). Furthermore, they are the scenario for the fastest and most violent climate changes that we know about right now in the world:

  • Evolution of ice caps in Greenland and the Antarctic.
  • Role of ocean-ice interactions in this evolution.
  • Role of the Arctic and Austral oceans in the global carbon sink.
  • Evolution of Arctic and Antarctic ice fields.
  • Acidification with ecosystems potentially at risk more quickly than in other regions of the globe.
  • Change in the distribution of freshwater with impacts on the stratification and the renewal of oceanic seabed waters...

 It is therefore fundamental for the national polar research community to be able to access these regions. This implies specialised infrastructures that are crucially missing in France right now and thinking about long-lasting solutions that meet the major challenges posed in these regions.



 Emerging studies, where the French community is a driving force, look at micro-plastics which are present in all regions of the ocean and their impact on the biota, out at sea or along the coast. As coastal environments are particularly interesting for humans (aquaculture, fishing, tourism), better assessment should be urgently run on how this pollution is transferred to the ocean, to better determine the origin and quantify the flows of pollutants and assess their impact on the quality of water and ecosystems.

In conclusion, acquisition of more in situ observations, often at high resolution, combining fine biogeochemical (e.g. trace elements), physical and biological parameters (provided by automated sensors) in contrasted regions of the ocean is necessary to improve the capacity of the models combining physics-chemistry and biology to represent how life develops at different scales of time (from the extreme event to the scale of the “paleo” recording via the description of a bloom or a ten-year trend) and space (model on a basin scale or on a global scale). These improvements are necessary to reduce uncertainties on climate projections provided by these models, to improve our understanding of changes to cycles, ecosystems, habitats of organisms and ecological niches of species under the effect of climate change and anthropic pressure. And in fine this will give us a better quantification of the impact of these changes on the biological pump and therefore on the carbon cycle.

One important challenge will also be to control observation systems on multiple scales, that will also require the use and development of dedicated instrumentation and vectors allowing regular and suitable observation, whether this is in the field (such as adapted gliders, appropriate vessels, etc.) or remotely (satellites, radars, etc.).


2.1.3. Biology-Ecology-Biodiversity

In the field of ecology, we can identify different communities with specific priorities.

  • A strong community is concentrated on the coastal and shore area (including internal and medium shelf), on the mainland and in overseas territories. It mainly uses station vessels, the coastal fleet and two multi-purpose intermediate-sized RV dedicated to tropical regions. Regardless of the site, current research is looking at benthic-pelagic coupling and the earth-sea continuum and leaning towards encompassing an ecosystemic scale with a fine space and time resolution in order to complete integrative modelling. The impact of anthropic uses (ecotoxicology, eutrophication, introduced species, development of renewable marine energies) and the context of global change (heating, modifications of oceanic circulation, acidification of oceans, changing biogeography of marine species, erosion of the biodiversity and habitats) furthermore imposing multi-parameter studies, coupled with studies from physicist oceanographers and biogeochemists, requiring more ambitious campaigns in terms of equipment and human resources;
  • In the pelagic open-sea area, the breadth of the taxonomic (protists) or metabolic (prokaryotes) diversity brought to light over the last few years implies reviewing certain functional diagrams and including in them the key role of long-lasting biological interactions by identifying a few site zones in contrasted contexts where these processes will be re-examined in detail;
  • Access to the dynamics of the planktonic, coastal and high sea communities, in real time, and at fine space and time resolution, in view of the use of sensors and (semi-)automated collection systems, will allow better characterisation of the structure and the operation of coastal and oceanic ecosystems;
  • In the study of deep-sea benthic ecosystems, the French community has been widely acknowledged internationally, particularly thanks to its research resources (submersibles: HOV, ROV, AUV). The perspective of future deep-sea energy or mining exploitations nevertheless increases the urgency of expanding our knowledge of these environments and beyond the inventory that remains largely outstanding (explorations in or outside the EEZ), expanding studies on functional dynamics of potentially-affected communities, and on the biogeography and connectivity of species and populations to be preserved. As an example, conservation of deep-sea coral habitats in the Bay of Biscay will be subject to European-scale negotiations in the years to come, following their classification as a Natura 2000 site. Trawling and dragging, likely to cause significant destruction, is increasingly less tolerated by the authorities even within scientific research. Resorting to use of the ROV (SCAMPI type or other) is going to be generalised for sampling;
  • Although this activity is “Public Service”, the demand from the public sector to monitor and characterise the ecological condition of benthic and pelagic ecosystems in connection with biodiversity condition describers and trophic networks, as well as the different associated pressures (MSFD), puts a growing constraint on the use of vessels.


2.1.4. Fisheries

Although the ‘classic’ aspect of fisheries remains, marked by an operational purpose of evaluating stocks for fish management, for several years, the fishery research framework has been moving towards the ecosystem approach to fish and more recently for all human activities. This framework has been developed for around twenty years. On the one hand, it relies on improving knowledge in a variety of scientific areas (biology, ecology, physical oceanography, meteorology, etc.) and modern opportunities for modelling and on the other hand, on the resolutions from world summits (Cancun 1992, Reykjavik 2001, Johannesburg 2002…) and the resulting policies (PCP 1992, DCSMM 2008). Therefore, there are many fishery topics: relations between populations and environment (biology-water mass dynamic coupling), identification of essential habitats for renewing resources, multi-scale interactions between fishing and marine biodiversity, impacts of the economic and governance determining factors on fishing work and catch capacities... Use of the FOF to acquire this fishery data coupled with the environmental data, impossible or very difficult to obtain on professional boats, is more than justified here. It is expected that this data collection will be completed in the future from other platforms (fixed stations, gliders, etc.).

Among the scientific challenges and barriers, the most outstanding can be mentioned:

  • Integration of geographical and biological scales for a real ecosystemic approach;
  • The effects (additive, synergetic, antagonist) of multiple stress factors within global change (global warming, acidification, eutrophication, pollution, biological invasions, alterations to habitats, modification of the biodiversity, over-exploitation, other uses, etc.) on the different organisation levels (individuals, populations, communities, ecosystems);
  • Taking into account compromises between ecosystem compartments and between uses/sectors when managing human activities and conserving marine ecosystems;
  • Development of observation methods that are not or are barely invasive (replacing trawling, for example, which kills species and destroys habitats).


2.1.5. Questions regarding scientific community interfaces

The ocean is one of the Earth’s compartments that constantly exchanges with the others (atmosphere, ice, continent). Quantifying these exchange flows is key for an optimum description of how the “Earth system” works. Furthermore, the whole planet is affected by global changes, regardless of the scale of time and space under consideration: the study of interfaces between oceans, atmosphere and continents should therefore be strengthened over the coming years. Furthermore, recent discoveries regarding the importance of hydrothermal flows of micro-nutritional elements (Fe, Zn, Co, Cu…) plus the role of oceanic margins on their budgets have led to more intense research in these environments. Finally, these interface questions are crucial between disciplines to lift cognitive barriers. This chapter looks at both interfaces between compartments of the earth system and also important “mechanistic” questions between (for example) living and mineral aspects.

Ocean-atmosphere coupling

  • Quantify the effects of atmospheric flux on the oceanic dynamic and ecosystems as well as feedback towards the atmosphere (marine emissions, radiative impact, impact on cloud formation and climate) will help improve climate models. Our knowledge on marine biogenic emissions into the atmosphere is very fragmented and this feedback has not been quantified for the time being. One of the issues is to take these coupled measurements of the different flows through this interface to understand the effect of these emissions and their physical-chemical or biological origin.
  • Furthermore, the effects of “Black Carbon” on biogeochemical and microbial functioning of the pelagic ecosystem remain too scarcely documented. Measurements exist on continents and occasionally in the coastal area but not in the open-sea. One recommendation is to develop this type of measurement more systematically.
  • The role of the Austral Ocean in ocean-atmosphere CO2 exchanges, the fragility of its biology with regard to acidification of surface waters, micro-nutrition dynamics and identification of factors limiting primary production in these high latitudes are still unresolved points. It is strongly recommended to give the community the means to explore the Austral Ocean to a greater extent.


Continent-ocean transition

  • The systems generated between the continental and marine waters in estuaries and plumes and within the shelves and margins (dilution fronts, thermal fronts, currents, tide) permanently or temporarily, complexly structure the different pelagic ecosystems, their inter-connection and their connections with the benthic systems: these mechanisms condition and sometimes limit biological production and the diversity of the communities present. Restricting these highly variable physical mechanisms is complex. They require high-resolution monitoring over time and space;
  • Quantification of transfers of chemical species (contaminating or natural) between continents and oceans is as essential as it is unknown. It refers to identifying flux released from matter discharged by the rivers and/or sediments from margins and/or even by the discharges from underground water and understanding why certain contaminants clog up for a long time whilst others are released from the solid matter when it meets the saline front. The physical mechanisms that favour release of chemical species by putting sediment back in suspension are theoretically intermittent processes (run-off in fracture zones, canyons, pockmarks, small scale whirlwinds, internal waves and mixture, gravitational events, etc.).  Studying these mechanisms and the catchment basin-ocean continuum (particularly in flooding periods, vectors from the majority of the annual sedimentary deposits) require stronger collaboration between physicists and geochemists, between scientific communities, but also vessels capable of fast reactions (during extreme weather events, for example);
  • There are crucial questions relating to the dynamics and the preservation of marine habitats. In a balanced system, the sediment and the mudflats provide a physical habitat that is modified in return by biological activity (diggers, ecosystem engineers, etc.). In the same way, if we see a forcing of sea-grass beds on the substrate, the inverse is also happening. In tropical zones, the coral reefs play the role of substrate construction and house ecological niches. Climate change and rising sea levels, storms and induced erosions cause a reduction in these habitats, with major consequences on marine resources, particularly the coastal economy in the inter-tropical zone;
  • Management overseeing port activities and marine and coastal resources, both in terms of fishing, shellfish farming or marine energies, requires a systemic approach, integrating the physical and biological environments and socio-economic aspects. The recent and booming topic of coastal nurseries requires specific data acquisition work to improve knowledge. For example, too little research is being run today on the ecological impact of exploiting marine granulate: the studies are too short, too localised and do not tackle the medium-term effects of turbidity on the nurseries for example. The intensification of surface and deep mining (P, Ni, Cd, metals, etc.) and the disruptions caused by these activities, particularly on the trophic chain (accumulation-detoxification) make these quantifications urgent;
  • More generally, the quality of the water, the biodiversity and how the ecosystems work are transverse problems and essential conditions for preserving ecosystems and human activities that depend on this. These are major management issues integrated at the earth-sea interface (WFD, MSFD).


For all these questions affecting the coastal environment, long-range planning discussion has highlighted the importance of working on an ecosystemic scale: very few studies on ecosystems produce a mass balance, involving primary and secondary producers at an ecosystem scale. As field studies are often occasionally in space, the change of scale to the ecosystemic scale should be able to link in using remote detection. New satellites actually have a spatial and spectral resolution that should allow coastal ecosystems (spatial resolution) to be studied using a wider set of parameters (dissolved and particulate organic matter, phytoplankton taxa, spectral resolution), linked in with new sensors and automated collection systems.

Suitable dynamic constraints are required to control the flux of sediment towards the water or of sediment into the air (intertidal zone) and towards the ocean.


The essential development of these ecosystemic studies must be accompanied by vessels allowing multidisciplinary work. Furthermore, vessels should be equipped with resources to deal with the impact of extreme events (floods, storms, coastal submersion). The fleet’s resources and vessel programming do not always allow this type of reaction. The observation services (SOMLIT, MOOSE, Coast-HF), the “ferrybox” deployed on the Brittany Ferry vessels are equivalent resources to “surprise” a sudden event. It is therefore recommended to develop automated sensors to be deployed on the vessels, linked in with development of satellite sensors.


Deep earth-ocean interface: marine hydrothermalism

Hydrothermal circulation is the result of seawater percolating through marine sediments and the oceanic lithosphere. The physical-chemical composition of the water is drastically modified by water-rock interactions. The initial seawater is transformed into a hydrothermal fluid presenting chemical characteristics: either acid, reductive and strongly enriched in metals for high temperature hydrothermalism, or hyperalkaline, reductive and strongly alkaline-enriched for low temperature hydrothermalism (<120°C). Over the last 50 years, research has demonstrated the wide diversity and breadth of these phenomena, at both high and low temperatures, in basaltic, dacitic and peridotitic substrates, in accretion and subduction contexts. The hydrothermal dynamics not only affect the chemical composition of the oceanic lithosphere and the deep ocean but also how the diversity of the deep ecosystems works. To sum up, quantification of transfers of matter and heat linked to the hydrothermal dynamics remains relatively unknown in time and space and needs to be constrained. In this wide multidisciplinary field, the main questions revolve around the future of these hydrothermal flows in the ocean and their role in the biogeochemical balance reports and cycles, the origin and nature of the ligands that may or may not stabilise the micro-nutrients in seawater, their distribution among the dissolved and particulate phases and therefore their bioavailability for deep and surface ecosystems, particularly for diazotrophs in the Pacific Ocean or, by means of circulation, a partial fertilisation of the Austral ocean.

Qualification of the hydrothermal flows, involving characterisation of circulation geometry and whatever is driving this circulation (thermal? tectonic?) and understanding water-rock interaction mechanisms, is one of the major issues of the study of transfers of matter and energy between large geochemical reservoirs. These studies require access to deep-sea exploration machinery, recurring campaigns, multidisciplinary campaigns and therefore they need to use large ocean-going vessels.


Chemistry-biology-physics interface (all compartments)

“Micro-nutritional” trace metals are recognised as nutritional elements because, without them, there is no life. However, understanding the conditions that make them bioavailable, their behaviour during remineralisation of organic matter, and their sources (inside and outside the ocean) are also barriers that imply working on the boundary between transport, fine chemical speciation and biological development. Our understanding of the processes in play between the living cells and the chemical substances is still in its infancy. This is a major “mechanistic” boundary that uses the very latest observation techniques on the matter and to identify the chemical and biological speciation.

Biogeochemical studies are indissociable from questions on the ocean’s dynamics and the air-sea interface exchanges. In particular, the oceanic meso and sub-meso scale processes affect the major scales through energy exchanges (and particularly vertical flows on a small scale) and one of the issues consists of quantifying their impacts on stratification, on the vertical flux of carbon and all nutriments, that are key factors in climate change. The critical role of sub-mesoscale circulation and vertical mixture in regulation of structuring of planktonic microbial communities, of primary production and of exporting organic carbon is increasingly clear, as shown in recent satellite observations, the field measurements and modelling simulations. Combining these observations with optical instruments will provide a unique glimpse of particle distribution and exports of particles to unprecedented scales. We might also mention the potential impact of primary production (particularly phytoplankton) on the oceanic heat balance via its impact on light penetration in the mixture layer. This type of parameter (Chla, pigments) must therefore be considered and measured more often. This has been done systematically on the PIRATA-Fr campaigns for the last 6 years for example and with Argo floats via the development of the BGC-Argo component.

It will also refer to quantifying the flows of interesting biogeochemical or toxic elements, to understand and quantify exchanges between the particulate and dissolved phases depending on the environment’s biogeochemical conditions (T, pH, type and quantity of MOD) and the associated microbial dynamic that will help identify the bioavailability of these elements.

Only multidisciplinary studies bringing together chemists, biologists and ecologists with specialist small scale physicians and their associated equipment at sea (own sampling systems, incubations, particle collection, etc.) will help make progress on these questions.


2.1.6. Challenges from Overseas Territories

The French Oceanographic Fleet is capable of meeting the issues and challenges of the French overseas territory. Although the overseas territories are essential regions for studying global relevance processes illustrated in the preceding chapters (2.1.1 to 2.1.5), more specific questions are tackled in collaboration with emerging countries:

  • Biodiversity: from the gene to populations/connectivity/inventories of biodiversity in distant zones that are rarely visited, studies on how the associated ecosystems work;
  • Bioresources: research into new natural substances (venom, anti-cancerous molecules, etc.), new bacterial species, etc. 
  • Monitoring coral and associated ecosystems (reefs, sea-grass beds and mangroves) in parallel with the different impacts of global change (coral bleaching crisis, proliferation of predator starfish on the coral, invasive species, relation to marine bird population, etc.
  • Analysis of the effects of over-exploitation (small and large pelagic fish, sharks, coral fish, etc.);
  • Impact of other human pressure (habitat destruction, pollution, contamination, etc.);
  • Improvement of knowledge on open-sea pelagic ecosystems (tunas, sharks, cetaceans, etc.);
  • Continue discovering, exploring and studying exceptional singular environments:
    • Ultrabasic source of shallow Hydroprony in New Caledonia;
    • Coral reef on the volcanic island of Ambitle exposed to a simulation of climate change (higher temperature and concentration of CO2);
    • “Sentry” islands with no human impact to assess the variations of habitats and associated communities with the different components of global change.


Target sites in overseas territory are being developed in the Atlantic (Guiana, Antilles, West Africa) and Indian Ocean (Mozambique) and the Pacific. These questions can affect both the coastal, inland environments and the open sea. In the case of the Pacific, the pressure of research and the length of the obligatory transits make it necessary to keep a vessel available such as the RV Alis based in Nouméa.