Title: Seamounts as critical habitats for marine biodiversity. Oases of biodiversity, seamounts are among the least known habitats on Earth. Human impact is rapidly extending with major threats on marine vertebrates so species may disappear from seamounts without realizing it. SEAMOUNTS proposes to illuminate the 3-dimensional distribution of vertebrate diversity and abundance on New Caledonian seamounts combining environmental DNA metabarcoding, seascape genomics, machine learning and baited video. The overreaching goal is to better understand the influence of human, environmental and geomorphological variables on seamounts fauna to inform conservation and management. SEAMOUNTS will be articulated around four hypotheses: (H1) benthic-pelagic coupling promotes biodiversity on seamounts, (H2) vertebrates find refuge in the deepest part of their range, (H3) residual populations of the most threatened vertebrate species (e.g. sharks) are present even close to humans, (H4) seamounts are key to connect remote wilderness reefs to more impacted reefs. Keywords: Seamounts, Biodiversity, eDNA

Atmospheric and oceanic warming is currently accelerating at an unprecedented rate, with consequences for biodiversity as the modification of species geographic distribution, hereafter range shift. Fish, as marine ectotherms, are particularly sensitive to these temperature changes. These modifications in species assemblages can induce functional reorganizations with disturbances on ecosystem processes, which ultimately affect ecosystem services, and thus human well-being. The polar regions (Arctic and Antarctic) are the scene of the most profound changes, with the arrival of new species from lower latitudes or the local disappearance of species for which cold conditions are no longer guaranteed. The low latitudes (tropics) are also threatened by local extinctions that are difficult to observe in the vast ocean. These difficulties to monitor fish biodiversity in the ocean has created significant gaps in knowledge, both in species occurrences and in models of species distribution. New approaches are urgently needed to better quantify and anticipate species shifts and future assemblage compositions. SHIFTeDNA aims to i) model the distributions of marine fish species, even the rarest, from available OBIS occurrence data in response to climate, habitat and human pressures, and to predict future species range shifts under several climate change scenarios; ii) evaluate predictions of modelled distributional shifts using a global, independent and recent database of environmental DNA (eDNA) occurrences sampled from the tropics to the poles to detect early arrivals of species in cold regions (colonization) or local extinctions in warm regions; iii) adjust predictions of species range shifts till the end of the 21st century, taking into account eDNA occurrences; iv) study the influence of species characteristics (mobile or not, mating type, trophic level and others), conservation status (IUCN status, vulnerability to fishing) and phylogeny on species range shifts to better understand the underlying processes. To address these objectives, we will exploit publicly available occurrence data of marine fishes via OBIS, and the largest eDNA-derived occurrence database available from a project carried out by a Franco-Swiss consortium involving the project partners (MARBEC-ETH-CEFE) over the past four years across all oceans. To improve the analysis of eDNA data, we will also complete the genetic reference base with >2000 fish samples from aquariums and museums. This new metabarcoding reference database will produce the most complete eDNA occurrence data to date. The resulting eDNA occurrences will be used to update predictions of species shifts at the poles, and extinctions in the tropics, and to feed new models of marine fish species distribution. These results will be made possible through the original application of the most up-to-date advances in artificial intelligence on both metabarcoding bioinformatics pipelines and species distribution models. We will then be able to characterize the factors that influence species range shifts in order to better understand their mechanisms and anticipate their effects. The success of the project relies on a consortium of 4 highly qualified French-Swiss partners with complementary skills (environmental genomics, bioinformatics, modeling, marine ecology, molecular genomics).

Depredation by toothed whales of Patagonian toothfish on demersal longline and tuna and swordfish on pelagic longlines is a growing problem internationally and the main problem exposed the French longline fisheries operated from Reunion Island. Pelagic and demersal longline fishery operated from Réunion Island is the first French fishery in terms of economic value and the second merchant economic sector of Réunion Island (100 M d'€/yr). These fisheries are highly affected by this depredation with an estimated financial loss of € 65 million over the 2003-2013 period. The observed depredation levels raise both economic and conservation issues. Indeed the artificial supply of food helps in creating an imbalance between these populations of cetaceans and their natural resources. Longlining is one of the fishing methods with the lowest environmental effect. The objectives of OrcaDepred are firstly to better understand the depredation behaviour of and ecology of cetacean species involved to offer fishing companies operational and technological solutions to depredation. Technological approaches tested to this day, namely the use of pots, acoustic repellents are ineffective. Under the OrcaDepred four Work Packages (WP) will be implemented to study and solve the depredation issue. - WP1 aims at better understanding the natural feeding and interaction behaviours with the fishery cetaceans interacting with the lines, and in the case of pelagic longlines identify the cetacean species involves. For this two dimensions tracking movements (tracks and dives) of these cetaceans will be studied using i) a new generation of satellite tags processing on-board the pressure and acceleration data and ii) by passive acoustic monitoring using hydrophones deployed along pelagic longline or a dedicated acoustic vertical array to the demersal fishery. The interactions of cetaceans with the lines will be studied using an experimental line on which the hooks are equipped with accelerometers to assess when fish are caught and depredated. - WP2 is devoted to assessments of the bio-economic consequences of depredation through an ecological economic for sustainable management of these fisheries taking into-account depredation. Finally, ecosystem modelling based on trophic links between species will be carried out to assess the ecological consequences of fishing-depredation at the ecosystem level. - WP3 will consider whether changes in levels of interaction between cetaceans and ships are related to fishing practice differences between captains and/or vessel characteristics, with a special focus on acoustic noise generated. These analyses are essential to guide the fishing companies in their strategic choices: training their fishing captains and/or conducting technical changes on their vessels. - WP4 will implement a technological approach to remove depredation. In partnership with industry, new prototypes of fish protection devices on the lines and not harmful to cetaceans and possibly limiting the levels of accessory catch such as skate on demersal long line will be tested and operational systems will be patented. OrcaDepred federates the complete French scientific community currently involved in addressing the longline depredation issue. Other fisheries at both national and international levels should benefit directly from the OrcaDepred as this problem is expending worldwide. Orcadepred outcomes will lead to mitigation solutions and should generate a strong national and international audience.

Mediterranean coastal ecosystems are facing unprecedented anthropogenic disturbances that synergistically threaten their unique biodiversity and the ecosystem services they provide to human populations. The ongoing expansion of herbivorous fishes from the genus Siganus, which entered the Mediterranean Sea from the Red Sea after Suez Canal opening, is one of the most critical issues. Indeed, in the Oriental basin of the Mediterranean Sea (from Turkey to Tunisia) Siganus populations tend to exclude the single native herbivorous species (Sarpa salpa) and to cause a widespread depletion of macrophytes, including seagrass meadows that serve as habitat and/or food for many animal species and play key roles in nutrient cycles. As sea warming is accelerating, it is likely that these tropical exotic species will colonize the Occidental basin of the Mediterranean Sea and establish populations in coastal ecosystems of South-Western Europe in a near future. However, although some aspects of Siganus ecology have received attention, there are still knowledge gaps about the causes and consequences of this invasion. EXOFISHMED project will thus address two questions (1) which factors explain how exotic fishes are supplanting the native species ? (2) what are the consequences of this species replacement on the functioning of ecosystems ? To answer these questions we will conduct a multidisciplinary approach to compare the biological attributes and ecological roles of native and exotic herbivorous fish species. We will collect this information on Siganus luridus and Sarpa salpa using two complementary approaches: (i) sample juvenile and adult individuals from 4 locations around the Mediterranean basin, and (ii) conduct a mesocosm experiment under controlled environmental conditions. Four biological features will be examined on these fish individuals: diet using stable isotope ratios, food acquisition strategy using morphology, growth rates using sclerochronology on otoliths, and nutrient storage in body using tissue nitrogen and phosphorus content. These data will permit to assess intraspecific variability of each feature between life-stages and between populations of each species, and to test for differences between the two species. In addition to these biological features, we will assess the diversity of microbial communities present in fish gut, which is a poorly known but a key feature of herbivorous fishes. More precisely, we will assess gut microbial diversity accounting for the three microbial domains (archaea, bacteria, eukaryotes) and for all their respective diversity facets (taxonomic, phylogenetic and functional) using high-throughput DNA sequencing methods and complementary biodiversity indices. Intra- and interspecific variability of gut microbial diversity will be measured and compared to intra- and interspecific variability of the four biological features to provide the first multi-faceted assessment of the differences between the two species. Then, based on these fish data and measures during mesocosms experiment we will assess the contribution of native and exotic fish species to two key processes in coastal ecosystems: trophic control of macrophytes (macroalgae, seagrass) through grazing activity, and nutrient recycling through excretion of metabolic wastes. The unknown effects of these two roles of herbivorous fishes on the abundance and diversity of planktonic and benthic microbes (microalgae, bacteria, archaea, eukaryotes) will also be measured to provide the first overall assessment of the consequences of Siganus invasion on ecosystem functioning. These objectives will be reached within 3 years thanks to the complementary skills of the research consortium. The outputs of the project will be communicated to scientists, policy makers and ecosystem managers and to the general public and will help set relevant prevention and mitigation measures against this invasion.

Oceanic ecosystems cover more than 70% of the Earth surface and provide major ecosystem services. They are responsible for most of the carbon transfer to the deep ocean, thus having a major influence on atmospheric CO2 and climate. They host a rich biodiversity with emblematic large predatory fishes whose exploitation supports livelihood and supplies animal protein for hundreds of millions of people worldwide. Amongst them, tunas are the major part with annual catches reaching more than 7.7 million tons and an economical value around 40 billion US$. But climate change is threatening these ecosystems and precious ecological services. Climate change impacts ocean temperature, stratification and circulation. It may trigger the expansion of anoxic “dead zones” over vast regions of the global ocean and the absorption of anthropogenic carbon leads to a marked seawater acidification. It has negative consequences on primary production, which fuels food chains and biodiversity, and potentially important effects on the structure of ecosystems. Climate change pushes oceanic ecosystems toward new states, with unknown consequences for essential services such as fisheries and associated economies, and potential feedbacks to the climate system through alteration of the biological carbon pump. Achieving sustainability of oceanic ecosystems in this context is a fundamental issue, and there is an urgent need for clear political strategies toward this aim. In this perspective, an inclusive socio-ecological analysis is urgently needed to anticipate climate-change threats and opportunities, and integrate complex processes into policy-relevant scenarios, in support of sustainable governance of oceanic resources and adaptation to climate change. The purpose of this project is to address these urgent challenges from a scientific perspective, analyzing and projecting the global oceanic socio-ecological system each step of the way from climate to fish markets. To advance toward the achievement of such an ambitious goal, CIGOEF will build on recent developments in coupled numerical modeling (ANR project MACROES) to simulate and analyze the cumulative effects of multiple climatic and non-climatic stressors on oceanic socio-ecosystems. MACROES initiated the incorporation of a marine ecosystem component into one of the French Earth System Models. The resulting global model presently couples climate and related atmospheric and oceanic processes, marine biogeochemistry, marine ecosystem, and fishing effort distribution components. It doesn’t have any equivalent worldwide. CIGOEF will explicit bacteria and gelatinous organisms in the system, two components of critical functional importance that were previously overlooked. It will also improve and integrate components that were developed but not coupled in the system for representing exploited oceanic tuna populations, fishing fleet bio-economy and global tuna markets. The coupled models will be used for both process studies and scenarios development. First CIGOEF will study the effects of climate change on the bacterial loop and jellyfish populations at the global scale, and quantify their feedbacks to the carbon cycle and the climate system. Second it will study the impacts of climate change on tuna resources, fisheries and markets, quantify their vulnerability and study alternative adaptation strategies through the development of integrated model-based scenarios, jointly with the CLIOTOP Scenario Task Team. To ensure their wide availability, simulated scenarios will be provided online. This would constitute a major contribution to IPCC and IPBES endeavors.