Biodiversité marine

Biodiversity loss and impacts on the functioning of marine ecosystems

Marine ecosystems are subject to multiple pressures related to human activities that disrupt food webs and threaten human health. The introduction of non-native species, in particular, modifies ecological dynamics, community structure, functions, and ecosystem services. 78 projects co-financed by the ANR, some using molecular approaches such as environmental DNA (eDNA) and genomics to improve species detection and understand adaptation mechanisms to disturbances, have led to major advances in monitoring and predictive modeling, facilitating early detection of changes in marine biodiversity and guiding management policies (Marine Protected Areas) towards the most sensitive areas. Among the research avenues to follow: the integration of cutting-edge technologies such as eDNA and artificial intelligence for better management of marine ecosystems, as well as concrete solutions to limit biodiversity loss, such as habitat restoration and biocontrol techniques.

Yunne-Jai Shin: IRD, Valérie Stiger: UBO and Line le Gall: MNHN

1- Scientific background:

Scientific evidence clearly shows that marine biodiversity is being impacted at unprecedented rates by human activities (fishing, coastal development, pollution) and human-induced climate change (ocean warming, acidification, sea level rise, extreme events). Over the last decade, 66% of the ocean has faced rising cumulative impacts, with only 3% remaining untouched by human pressure. While fishing has remained the most significant driver of biodiversity loss over the past 50 years, climate change effects continue to accelerate.

Coastal ecosystems are under increasing threat as coastal populations grow at a faster rate than the global average. With 75% of megacities now situated along coastlines, more than 2.6 billion people rely on these ecosystems for food, income, and protection. This growing pressure has contributed to the decline of vital ecosystems such as seagrass meadows, mangroves, and coral reefs.

Land-based pollution further compounds these challenges. Since 1980, marine plastic pollution has increased tenfold, harming wildlife through macroplastic ingestion, while microplastics infiltrate food webs, posing risks to human health. Coastal waters also suffer from high levels of metals and persistent organic pollutants, originating from industrial discharge and agricultural runoff, which contaminate marine populations. Excess fertilizers fuel nitrogen and phosphorus runoff, leading to eutrophication and the formation of hypoxic "dead zones." Moreover, ocean and airborne pollutant transport drives these harmful impacts — from plastics to heavy metals — to spread globally, with lasting consequences for both ecosystems and human health.

Biological invasions refer to the introduction and rapid proliferation of an exotic species in a new ecosystem, where it causes ecological imbalances and impacts biodiversity, the economy or human health. These invasions are often encouraged by human activities (for example, trade, aquaculture and transport) and the absence of natural predators in the area of introduction. Introduced species with significant ecological and/or economic consequences are referred to as invasive species. They represent a growing threat, amplified by globalisation and climate change.

The challenges posed by invasive species are manifold and concern four major dimensions: ecological, economic, health and regulatory.

Invasive species cause major disruption to ecosystems and contribute to a reduction in biodiversity (Molnar et al., 2008). Some non-native species modify the abundance and diversity of local populations, influence ecological interactions and accelerate evolutionary processes that alter ecosystem structure, functions and services (Simberloff et al., 2013; Dawson et al., 2017; Blakeslee et al., 2020). In the case of microbial invasive species, these disturbances can include the spread of pathogens affecting local flora and fauna. Moreover, their impact on native ecosystems leads to anthropogenic biotic homogenisation, a process whereby regional biological communities become similar over time (Olden et al., 2018), a phenomenon that is expected to intensify with climate change (Bennett et al., 2021).
The introduction of non-native species can also have major economic repercussions. According to Hulme et al (2009), biological invasions entail considerable costs for the agricultural, forestry and fisheries sectors. Globally, the economic costs of biological invasions have been estimated at US$1,288 billion over the period 1970-2017 (Diagne et al., 2021).

Some invasive species have a direct impact on human health. As disease vectors, they can transmit dangerous pathogens. Some are also highly allergenic, causing severe respiratory allergies and high costs for the healthcare system. In addition, some invasive microalgae produce toxins that can contaminate the food chain and affect human consumption.
In response to these threats, a number of laws and regulations have been introduced to limit the spread of invasive species. At international level, the Convention for the Control and Management of Ships' Ballast Water and Sediments (BWM Convention), adopted in 2004, establishes global rules aimed at reducing the transfer of alien species via ships' ballast water. At European level, Regulation 1143/2014 establishes a list of invasive alien species of concern for the European Union, banning their import, sale and transport in order to limit their spread. In France, the National Action Plan (PNA) sets out strategies for the prevention, early detection and eradication of certain invasive species, based on monitoring and management actions tailored to the different environments concerned.

Despite these initiatives, the fight against invasive species remains a major challenge, requiring international coordination and ongoing efforts. In Europe, more than 14,000 non-native species have been introduced and established over the centuries as a result of trade and human transport (EASIN, 2022).

A new approach with the challenges of understanding marine biodiversity and the contribution of eDNA and genomics. Marine biodiversity is an immense reservoir of biological diversity, playing an essential role in the functioning of ecosystems and the maintenance of ecosystem services. With 240,000 species currently described, our knowledge of this biodiversity remains incomplete, and around 2,000 new species are described each year. The extent of underestimated genetic and specific diversity limits our ability to develop effective conservation strategies. Environmental DNA (eDNA) and genomics are the tools of choice for filling these gaps. eDNA makes it possible to identify the presence of organisms from genetic traces left in the environment (water, sediment, ice, etc.), without having to physically capture them. This approach is particularly valuable for detecting rare, cryptic or low-abundance species, and facilitates the temporal and spatial monitoring of marine communities. However, to be able to assign a molecular sequence to an organism, it is essential to have a reference database with a robust taxonomy, which is currently far from the case for most organisms.
Genomics approaches, favoured by the advent of high-throughput sequencing technologies, provide access to the genetic information of individual species, revealing little-known biological functions. They also make it possible to study the mechanisms of adaptation to changing environmental conditions, in particular by analysing mutations and genetic variations influencing resistance to stress, reproduction and population dynamics. This knowledge is essential both for understanding the relationships between marine organisms and for anticipating the impact of climate change and human pressures on marine ecosystems.

2- Main Contributions of the French Communities through ANR co-funding:

Scientific advancements, by showing that all facets of biodiversity are impacted by human pressures and do matter for ecosystem functioning, have been pivotal in shaping how the Convention on Biological Diversity (CBD) addresses biodiversity conservation across genetic, species, and ecosystem levels.

For addressing marine genetic diversity, genomic research and techniques like environmental DNA (eDNA) and genetic sequencing allow scientists to monitor marine species’ genetic variation, which is essential for understanding their adaptation capacity to changing ocean conditions, such as ocean acidification and warming, and emerging diseases and pollution. These technics are used in the ongoing DockEvol project, specifically haplotagging genome sequencing, combined with condition index assessments, and microbiome profiling, alongside characterization of abiotic and biotic environmental factors through eDNA metabarcoding. These data will inform the construction of fitness landscape models in highly anthropized port environments where exotic and native species sometimes hybridize and interbreed, hence changing population dynamics and demography (Touchard et al. 2024). Based on massive eDNA sampling and analyses, the ATLASea research programme is one of the winners of the PEPR (Priority Research Projects and Equipment) exploratory programmes, aimed at structuring emerging scientific communities. Co-piloted by CNRS and CEA and funded by France 2030 over 8 years, ATLASea aims to sequence the genomes of 4,500 eukaryotic marine species, including molluscs, crustaceans, annelids, cnidarians, ascidians, unicellular and multicellular algae, sponges and fish. This represents around a third of known marine species in France and the overseas territories. The data collected will be made freely available, enriching biodiversity inventories and contributing to international sequencing efforts under the aegis of the Earth Biogenome Project (EBP). Integrating these technologies into marine biodiversity research presents a number of challenges. On the one hand, standardisation of methods and accessibility to reference databases are essential to guarantee reliable identifications. Secondly, managing and analysing massive volumes of genomic data requires advances in bioinformatics and artificial intelligence. Finally, the use of these techniques raises ethical and legal questions about the protection of genetic resources and the equitable sharing of knowledge.In short, eDNA and genomics are essential tools for improving our understanding of marine biodiversity, better assessing its conservation status and anticipating the impact of global change on ocean ecosystems. Their development and integration into marine research and monitoring programmes are therefore priorities for sustainable ocean management.

The focus on genetic diversity is reflected in the CBD’s Target 13, which aims to prevent genetic erosion in both wild marine species and aquaculture species, ensuring their long-term resilience.

At the species level, scientific innovations such as satellite tracking, underwater acoustic monitoring, and AI-powered biodiversity assessments have significantly improved our ability to study the dynamics of marine species in relation to their biotic and abiotic environment. The deployment of novel observation technics at different spatio-temporal scales has helped to better explain ecological processes, and has increased inference capacities in varying and perturbed environments. Satellite tracking allows scientists to follow the migratory patterns of vulnerable marine animals, such as sea turtles, birds, whales, and sharks, which is vital for protecting migratory routes and critical habitats. Underwater acoustic monitoring provides key data on species abundance and behavior, especially in hard-to-reach marine areas. The project TOPINEME innovated by combining different layers of data from the physics, plankton up to fish, fishers and top predators, for example using GPS data loggers for tracking seabirds foraging trajectories, acoustic backscattering data for modelling prey abundance and schooling behaviour. They showed how the variability in the physical environment can change the accessibility of prey to seabirds, hence changing seabird species composition by bottom-up control (Boyd et al. 2015). The TOPP-PATCHES project used accelerometers coupled with a new generation of Argos CTD tags recording dissolved oxygen concentration to assess fine-scale feeding success of elephant seals as a function of oceanographic conditions (Vacquié-Garcia et al. 2015). Artificial intelligence (AI) has also revolutionized marine biodiversity monitoring by processing vast amounts of data from sensors, underwater cameras, and remote sensing tools (Future-OBS, FISH-PREDICT). AI algorithms can identify and track species in real time, helping decision-makers and managers to meet the goals of halting extinctions and restoring threatened marine populations (Goal A, Target 4 of the CBD).

For marine ecosystem diversity, advances in remote sensing and ecosystem modelling have enhanced our ability to monitor and assess the health of marine environments, regarding habitat degradation, carbon storage, foodweb maintenance and ecosystem connectivity. Remote sensing through satellites and drones allows for the large-scale assessment of marine ecosystems, providing valuable insights into marine productivity, habitat degradation, water quality, and temperature changes. For example, the APEX project proposes an innovative automatic prey observation system using drones equipped with an echo sounder to map the spatio-temporal distribution of prey for seabirds. Integrated ecosystem and ocean modelling is crucial in predicting the impacts of climate change on marine ecosystems, including shifts in species distributions and abundances, coral bleaching, and the expansion of hypoxic “dead zones.” These models are essential in guiding restoration efforts, such as the CBD ambitious “30 by 30” target, aiming to protect 30% of of the ocean by 2030.

In the last decade, biodiversity science has made considerable progress in building integrated models and scenarios that link multiple drivers of global change to ecosystem functioning from the physics, through biogeochemistry, plankton up to fish biodiversity and fisheries. These models and scenarios provide decision-makers with visions for the future, and exploration of actionable management, economic, policy options for the future of the ocean. The development of state-of-the art end-to-end modelling tools makes the core of the CIGOEFF, SOMBEE and MEDIATION projects. Significantly, two of the developed models (APECOSM, OSMOSE) have been selected in the top ten models (out of 62) by an independent expert study tendered by the European Commission, for the implementation of the European Digital Twin of the Ocean that aims to support decision-making capabilities to implement EU policies like the Marine Strategy Framework Directive (DGRI and AZTI, 2022). In addition, the french IPSL and APECOSM ocean models have been used in a major ensemble modelling endeavour reported in IPBES and IPCC latest reports, showing that, by the end of the century, climate change is projected to decrease net primary production (by ca. 1.9% under the low greenhouse gas emission scenario, RCP2.6 and ca. 7.5% in the high emission scenario, RCP8.5), and secondary production up to fish biomass (by 7% and 19% under RCP2.6 and RCP8.5, respectively) (Tittensor et al. 2021).

By integrating the scientific findings, tools and data into its framework, the CBD ensures that its marine conservation strategies remain data-driven, evidence-based, and adaptive to the challenges posed by climate change and human impacts. These advancements enable more targeted, effective conservation measures and provide the necessary information to monitor and adjust efforts to protect marine biodiversity in the face of an accelerating global environmental crisis.

The ANR DockEvol project explores the concept of biological portuarisation, which refers to the evolution of marine species in port environments that have been heavily modified by human activities. This project aims to understand how these specific conditions influence the adaptation and evolution of species, with a particular focus on ascidians (Touchard et al., 2024).

This research shows that climate change and anthropogenic modifications to ecosystems favour invasive species, threatening native biodiversity and sustainably transforming coastal and port ecosystems.

Invasive species are a key topic in research funded by the French National Research Agency (ANR), which supports projects aimed at better understanding and limiting their impacts. As part of this, the ANR is funding a number of studies focusing on the following themes:

• Understanding the mechanisms by which invasive species are introduced, established and spread, taking into account global change. The ANR DEVODIVERSITY project, which studies the invasive potential of chordates, explores the role of colonial and solitary ascidians, some species of which have developed reproductive and regenerative strategies that enhance their invasive capacity. The ANR DockEvol project is looking at the identification and adaptive evolution of species, both native and introduced, in port environments, with a focus on ascidians living in these anthropized environments. The ANR REMOVE DISEASE project has demonstrated that rats, mice and cats introduced to oceanic islands are vectors of pathogens, affecting the health of seabirds. Finally, the impact of climate change on invasive macro-algae has been studied, in the ANR INVASIVES project, which studied the ecophysiology and chemical ecology of invasive marine macroalgae in Europe, from Portugal to Norway. The results highlighted a chemical adaptation of these species, influencing their expansion in a context of climate change (Surget et al., 2017). This ANR-funded research is helping to improve our understanding of the dynamics of biological invasions, to anticipate how they will evolve in the face of environmental change, and to identify solutions for limiting their impact on biodiversity and ecosystems.
• Assessing the impact of invasive species on ecosystems, biodiversity and ecosystem services is based on experimental approaches. Researchers manipulate ecosystems by eradicating invasive species, then observe the consequences for native species and ecological balances. As part of the ANR INVASIVES project, removal experiments were carried out on several species of invasive macroalgae present in rocky intertidal environments. The results showed an increase in floristic diversity on the manipulated sites, underlining the negative role of invasive species in the decline of biodiversity. However, these effects vary depending on the environment. In intertidal mudflats, the presence of the red macroalga Gracilaria vermiculophylla has, on the contrary, favoured the diversity of burrowing animals and modified the food web, benefiting species that consume the invasive alga (Davoult et al., 2017).

Two other ANR projects are looking at the impact of invasive mammals on island ecosystems: ANR REMOVE_DISEASE is studying the eradication of rats, mice and cats and its effects on the health of seabirds. Similarly, ANR InvEcoF is analysing the impact of invasive rats on the functional role of land crabs and seabirds in the atolls of French Polynesia. These two projects have shown that reducing populations of invasive mammals contributes to the preservation and health of seabird populations.

The ANR SEAPROLIF project focused on chemical interactions between invasive macroalgae and native species. It studied the impact of metabolites produced by the invasive red alga Asparagopsis taxiformis on the microbiota of native species (Greff et al., 2014). He also highlighted a change in the metabolome of A. taxiformis when it comes into contact with the native coral Astroides calycularis (Greff et al., 2017), highlighting the complex chemical interactions influencing local biodiversity.

This research shows that invasive species have variable impacts on ecosystems, potentially reducing biodiversity or, in some cases, altering food webs in unexpected ways. It also highlights the importance of chemical interactions in invasion mechanisms and the impact of invasive mammals on island fauna.

Developing monitoring and management tools to limit the spread of invasive species is a major challenge.

In the ANR DockEvol project, biomonitoring tools based on environmental DNA are being developed. These approaches make it possible to design a model of fitness landscapes, adjusted to genotype-phenotype maps that take account of environmental variations.
A key advance in this field is the study by Milián-García et al (2025), which constitutes the first molecular biomonitoring research applied to international shipping containers. Carried out in Canada, this study aims to detect and identify invasive species before they are dispersed, paving the way for better prevention of biological invasions.

Studying the fate of invasive species in the context of global change. Global warming is a key factor in the expansion of invasive species. Because of their ability to adapt rapidly to new environmental conditions, these species benefit from global change, unlike native species, which are generally specialised in their original habitat and less resilient to disturbance, as has been shown in marine macroalgae (Le Lann et al., 2012; Tanniou et al., 2014).

In the ANR INVASIVES project, experiments in thermostatically controlled tanks were carried out on pairs of invasive/native species, testing different temperatures and salinities. The results showed that the invasive brown macroalga Sargassum muticum is highly resistant to increases in temperature and dilution of seawater, unlike the native species Cystoseira baccata, which does not tolerate these environmental variations. These observations confirm that climate change could favour the expansion of invasive species to the detriment of local species.

The ANR DockEvol project explores the concept of biological portuarisation, which refers to the evolution of marine species in port environments that have been heavily modified by human activities. This project aims to understand how these specific conditions influence the adaptation and evolution of species, with a particular focus on ascidians (Touchard et al., 2024).

This research shows that climate change and anthropogenic modifications to ecosystems favour invasive species, threatening native biodiversity and sustainably transforming coastal and port ecosystems.

All of this research and the many results obtained are helping to guide public conservation policies and strengthen strategies to combat biological invasions. Faced with the growing challenges of climate change and globalisation, this work is essential to anticipate, manage and mitigate the impact of invasive species on biodiversity and ecosystems.

3- Research perspectives:

Invasive species are a major scientific challenge, requiring interdisciplinary approaches to better understand, anticipate and manage their spread. Current and future research into these species is divided into several strategic areas:

• Understanding invasion mechanisms. The study of invasion dynamics is based on three main areas: a) identifying the factors favouring the establishment and dispersal of invasive species, which is made possible by analysing the biological and ecological traits of invasive species and comparing them with native species. b) assessing the effects of global warming on the expansion of invasive species into new regions. And c) to identify the influence of human activities on invasions, which means studying the vectors of introduction (maritime transport, international trade, aquariology, urbanisation). A focus on port ecosystems, where species evolve in a specific abiotic environment and cohabit with a novel assemblage of invasive and indigenous species, is a promising avenue.
• Genetic and biotechnological approaches. Technological advances offer new tools for detecting and monitoring invasive species. Environmental DNA (eDNA) is an area of interest because it enables early detection of invasive species before they become a problem. Genomics and epigenetics can also be used to analyse the rapid adaptation of invasive species to their new environment.
• New management and control strategies. Several solutions are being developed to limit the impact of invasive species: Starting with biocontrol methods, in which natural predators, pathogens or competitors are sought out and used to regulate invasive populations. There is also ecological restoration, which enables degraded ecosystems to be rehabilitated after an invasive species has been eradicated.
• Integration of the social and economic sciences. Biological invasions are not just an ecological issue; they also have economic and societal repercussions. It is important to assess the economic costs of invasions: analysis of losses in the agricultural, fisheries and forestry sectors, and in terrestrial and marine environments. Another priority is the social acceptability of control measures, as some invasive species are perceived differently by managers and the general public, which can make their management more complex. In conclusion, research into invasive species is not limited to their current management; it aims to anticipate future invasions, develop innovative tools and integrate the economic and social dimensions into control strategies. Against a backdrop of climate change and increasing global trade, the prevention and monitoring of biological invasions are essential to preserve ecosystems, reduce their economic impact and protect human health. Finally, informing the public and raising awareness remains a priority, to encourage good practice and limit accidental introductions.

Given the complexity of marine ecosystems and their deep interconnections with human societies — now recognized as socio-ecosystems — along with the multiple drivers of biodiversity loss and the need to address biodiversity at genetic, species, and ecosystem levels, scientific research is inevitably moving toward more interdisciplinary, integrated approaches. These approaches combine diverse techniques and tools, from environmental genomics and remote sensing to social science methods, to capture the full complexity of these systems and design more effective, adaptive conservation strategies.

Facing increasing human pressures, long-term observation of coastal socio-ecosystems is essential to understand their dynamics, manage risks, and assess public policies. Despite progress in ocean observation, disciplinary fragmentation still prevents a holistic understanding of these complex systems. Twenty years ago, the CHALOUPE project was a pioneer in integrating different disciplines, tools, and data types into its analysis of marine biodiversity loss, looking not only at historical data analyses but also at prospective viability analyses. The recent ongoing FUTURE-Obs project aims to develop multi-scale, multi-disciplinary observation strategies, combining traditional methods with innovations like environmental genomics, in situ imaging for biodiversity, and social media data for human activity analysis. The diversity and heterogeneity of the data will support the development of new indicators using AI tools.

Developing transdisciplinary approaches — where scientists collaborate with stakeholders such as decision-makers, managers, fishers, tourism operators, renewable energy developers, and coastal communities — can greatly enhance the planning and implementation of ocean-related measures. By merging ecological data, oceanographic modelling, and socioeconomic insights with local and sector-specific knowledge, these inclusive approaches can support complex processes such as marine spatial planning that better balances conservation (e.g., marine protected areas), exploitation, marine renewable energy development, and potential sectoral conflicts like those between tourism and fisheries. Even though transdisciplinary projects have been developed for a long time, they were either led by social scientists, or were specific to a marine sector of activities (fishing for example). Recent projects such as FUTURISKS, MaHeWa, REMOVE_DISEASE, SOMBEE develop significant stakeholder engagement activities, in a way that integrates different scientific disciplines and a diversity of stakeholders. Engaging stakeholders throughout the scientific process fosters co-produced knowledge, ensuring measures are not only scientifically robust but also reflect local realities. It eventually aims to improve the quality and legitimacy of decisions and thus to increase stakeholder buy-in, fostering a sense of ownership and responsibility. As a result, management measures are more likely to be respected and effectively implemented, ensuring both ecological and socio-economic goals are met.