Cross-ocean patterns and processes in fish biodiversity on coral reefs through the lens of eDNA metabarcoding

Increasing speed and magnitude of global change threaten the world's biodiversity and particularly coral reef fishes. A better understanding of large-scale patterns and processes on coral reefs is essential to prevent fish biodiversity decline but it requires new monitoring approaches. Here, we use environmental DNA metabarcoding to reconstruct well-known patterns of fish biodiversity on coral reefs and uncover hidden patterns on these highly diverse and threatened ecosystems. We analysed 226 environmental DNA (eDNA) seawater samples from 100 stations in five tropical regions (Caribbean, Central and Southwest Pacific, Coral Triangle and Western Indian Ocean) and compared those to 2047 underwater visual censuses from the Reef Life Survey in 1224 stations. Environmental DNA reveals a higher (16%) fish biodiversity, with 2650 taxa, and 25% more families than underwater visual surveys. By identifying more pelagic, reef-associated and crypto-benthic species, eDNA offers a fresh view on assembly rules across spatial scales. Nevertheless, the reef life survey identified more species than eDNA in 47 shared families, which can be due to incomplete sequence assignment, possibly combined with incomplete detection in the environment, for some species. Combining eDNA metabarcoding and extensive visual census offers novel insights on the spatial organization of the richest marine ecosystems

Comparaison de la biodiversité ichthyologique des lagons, récifs et monts sous-marins par ADN environnemental, stéréo-vidéos et apprentissage profond

Biodiversity is a concept at the heart of global issues in the face of human-induced changes, with a possible sixth mass extinction underway. Emphasis has always been made on regions that have been described as biodiversity hotspots, such as coral reefs. However, far fewer studies have focused on desert-like environments such as the inter-reef zone of the continental shelf, or difficult to access areas such as seamounts. This CIFRE PhD focuses on the use of two standardized methods: environmental DNA metabarcoding (eDNA) and baited stereo-cameras (S-BRUVS) to study and compare the diversity of coral reef fishes with the inter-reef, but also with deep environments including seamount summits and deep outer slopes up to 550 meters depth in New Caledonia. A new technology is also used, the automatic processing of images from S-BRUVS for the detection, identification and counting of deep water snappers through artificial intelligence (AI). The results showed that the inter-reef area had a diversity distributed along an inshore-offshore gradient, with levels of diversity and biomass at least equivalent to that of the coral reefs. The inter-reef is about ten times larger than coral reefs, shares some of its fauna with coral reefs, but is left virtually unprotected on a global scale. In contrast, levels of diversity on seamounts were much lower than those observed on coral reefs. However, biomass levels were highest on seamounts and slopes at depths between 50m and 250m. Depth was the primary factor governing the distribution of biodiversity and biomass. Shark biomass was 5 times higher on shallow seamounts (50m) than on coral reefs. Shallow seamounts turn out to be an oasis of biomass and a refuge for megafauna partly associated with coral reefs. The work of this thesis has made it possible to compare biodiversity in lesser-known environments, and to question the notions of hotspot, oasis and refuge through standardized measures of their biodiversity. The methods used have proven to be complementary for the comparative study of multiple ecosystems; they also show strong operational potential. For example, the deep learning algorithm demonstrated its ability to identify and count snapper species, heralding the upcoming incorporation of new technologies in underwater engineering.La biodiversité est un concept au cœur des enjeux globaux face aux changements causés par l’Homme, avec une possible sixième extinction de masse en cours. Une emphase a toujours été faite sur les régions qualifiées de Hotspot de biodiversité comme les récifs coralliens. Cependant, beaucoup moins d’études ont focalisé sur les environnements d’apparence désertique comme la zone inter-récifale du plateau continental, ou bien difficiles d’accès comme les monts sous-marins. Cette thèse en partenariat CIFRE se consacre à l’utilisation de deux méthodes standardisées : le metabarcoding de l’ADN environnemental (ADNe) et les stéréo-caméras appâtées (S-BRUVS) pour étudier et comparer la diversité des poissons des récifs coralliens avec l’inter-récif, mais aussi avec des environnements profonds incluant des sommets de monts sous-marins et des pentes externes allant jusqu’à 550 mètres de profondeur en Nouvelle Calédonie. Une nouvelle technologie est également utilisée, le traitement automatique par intelligence artificielle (IA) d’images issues de S-BRUVS pour la détection, l’identification et le comptage d’un groupe d’espèces commerciales profondes, les vivaneaux. Les résultats ont montré que la zone inter-récifale disposait d’une diversité répartie selon un gradient côte-large, avec des niveaux de diversité et de biomasse régionaux au moins équivalents à ceux des récifs coralliens. L’inter-récif est environ dix fois plus vaste que les récifs coralliens, partage également une partie de sa faune, mais n’est quasiment pas protégé à l’échelle mondiale. A l’opposé, les niveaux de diversité sur les monts sous-marins étaient très inférieurs à ceux observés dans les récifs coralliens. Cependant les niveaux de biomasse étaient supérieurs sur les monts sous-marins et pentes entre 50m et 250m de fond. La profondeur s’est révélée être le facteur principal régissant la distribution de la biodiversité et de la biomasse. La biomasse des requins était 5 fois plus élevée sur les monts peu profonds (50m) que sur les récifs coralliens. Les monts sous-marins peu profonds peuvent prétendre à un statut d’oasis de biomasse ainsi que de refuge pour une mégafaune qui est en partie associée aux récifs coralliens. Les travaux de cette thèse ont permis de comparer la biodiversité sur des environnements moins connus, et de questionner les notions de hotspot, oasis et refuge à travers des mesures standardisées de leurs biodiversités. Les méthodes utilisées se sont révélées complémentaires pour l’étude comparative de multiples écosystèmes ; elles montrent également un fort potentiel opérationnel. L’algorithme d’apprentissage profond a par exemple démontré sa capacité à identifier et compter les espèces de vivaneaux annonçant une incorporation prochaine des nouvelles technologies en ingénierie sous-marine

Comparaison de la biodiversité ichthyologique des lagons, récifs et monts sous-marins par ADN environnemental, stéréo-vidéos et apprentissage profond

Biodiversity is a concept at the heart of global issues in the face of human-induced changes, with a possible sixth mass extinction underway. Emphasis has always been made on regions that have been described as biodiversity hotspots, such as coral reefs. However, far fewer studies have focused on desert-like environments such as the inter-reef zone of the continental shelf, or difficult to access areas such as seamounts. This CIFRE PhD focuses on the use of two standardized methods: environmental DNA metabarcoding (eDNA) and baited stereo-cameras (S-BRUVS) to study and compare the diversity of coral reef fishes with the inter-reef, but also with deep environments including seamount summits and deep outer slopes up to 550 meters depth in New Caledonia. A new technology is also used, the automatic processing of images from S-BRUVS for the detection, identification and counting of deep water snappers through artificial intelligence (AI). The results showed that the inter-reef area had a diversity distributed along an inshore-offshore gradient, with levels of diversity and biomass at least equivalent to that of the coral reefs. The inter-reef is about ten times larger than coral reefs, shares some of its fauna with coral reefs, but is left virtually unprotected on a global scale. In contrast, levels of diversity on seamounts were much lower than those observed on coral reefs. However, biomass levels were highest on seamounts and slopes at depths between 50m and 250m. Depth was the primary factor governing the distribution of biodiversity and biomass. Shark biomass was 5 times higher on shallow seamounts (50m) than on coral reefs. Shallow seamounts turn out to be an oasis of biomass and a refuge for megafauna partly associated with coral reefs. The work of this thesis has made it possible to compare biodiversity in lesser-known environments, and to question the notions of hotspot, oasis and refuge through standardized measures of their biodiversity. The methods used have proven to be complementary for the comparative study of multiple ecosystems; they also show strong operational potential. For example, the deep learning algorithm demonstrated its ability to identify and count snapper species, heralding the upcoming incorporation of new technologies in underwater engineering.La biodiversité est un concept au cœur des enjeux globaux face aux changements causés par l’Homme, avec une possible sixième extinction de masse en cours. Une emphase a toujours été faite sur les régions qualifiées de Hotspot de biodiversité comme les récifs coralliens. Cependant, beaucoup moins d’études ont focalisé sur les environnements d’apparence désertique comme la zone inter-récifale du plateau continental, ou bien difficiles d’accès comme les monts sous-marins. Cette thèse en partenariat CIFRE se consacre à l’utilisation de deux méthodes standardisées : le metabarcoding de l’ADN environnemental (ADNe) et les stéréo-caméras appâtées (S-BRUVS) pour étudier et comparer la diversité des poissons des récifs coralliens avec l’inter-récif, mais aussi avec des environnements profonds incluant des sommets de monts sous-marins et des pentes externes allant jusqu’à 550 mètres de profondeur en Nouvelle Calédonie. Une nouvelle technologie est également utilisée, le traitement automatique par intelligence artificielle (IA) d’images issues de S-BRUVS pour la détection, l’identification et le comptage d’un groupe d’espèces commerciales profondes, les vivaneaux. Les résultats ont montré que la zone inter-récifale disposait d’une diversité répartie selon un gradient côte-large, avec des niveaux de diversité et de biomasse régionaux au moins équivalents à ceux des récifs coralliens. L’inter-récif est environ dix fois plus vaste que les récifs coralliens, partage également une partie de sa faune, mais n’est quasiment pas protégé à l’échelle mondiale. A l’opposé, les niveaux de diversité sur les monts sous-marins étaient très inférieurs à ceux observés dans les récifs coralliens. Cependant les niveaux de biomasse étaient supérieurs sur les monts sous-marins et pentes entre 50m et 250m de fond. La profondeur s’est révélée être le facteur principal régissant la distribution de la biodiversité et de la biomasse. La biomasse des requins était 5 fois plus élevée sur les monts peu profonds (50m) que sur les récifs coralliens. Les monts sous-marins peu profonds peuvent prétendre à un statut d’oasis de biomasse ainsi que de refuge pour une mégafaune qui est en partie associée aux récifs coralliens. Les travaux de cette thèse ont permis de comparer la biodiversité sur des environnements moins connus, et de questionner les notions de hotspot, oasis et refuge à travers des mesures standardisées de leurs biodiversités. Les méthodes utilisées se sont révélées complémentaires pour l’étude comparative de multiples écosystèmes ; elles montrent également un fort potentiel opérationnel. L’algorithme d’apprentissage profond a par exemple démontré sa capacité à identifier et compter les espèces de vivaneaux annonçant une incorporation prochaine des nouvelles technologies en ingénierie sous-marine

Comparison of ichthyologic biodiversity in lagoons, coral reefs and seamounts using environmental DNA, stereo videos and deep learning

La biodiversité est un concept au cœur des enjeux globaux face aux changements causés par l’Homme, avec une possible sixième extinction de masse en cours. Une emphase a toujours été faite sur les régions qualifiées de Hotspot de biodiversité comme les récifs coralliens. Cependant, beaucoup moins d’études ont focalisé sur les environnements d’apparence désertique comme la zone inter-récifale du plateau continental, ou bien difficiles d’accès comme les monts sous-marins. Cette thèse en partenariat CIFRE se consacre à l’utilisation de deux méthodes standardisées : le metabarcoding de l’ADN environnemental (ADNe) et les stéréo-caméras appâtées (S-BRUVS) pour étudier et comparer la diversité des poissons des récifs coralliens avec l’inter-récif, mais aussi avec des environnements profonds incluant des sommets de monts sous-marins et des pentes externes allant jusqu’à 550 mètres de profondeur en Nouvelle Calédonie. Une nouvelle technologie est également utilisée, le traitement automatique par intelligence artificielle (IA) d’images issues de S-BRUVS pour la détection, l’identification et le comptage d’un groupe d’espèces commerciales profondes, les vivaneaux. Les résultats ont montré que la zone inter-récifale disposait d’une diversité répartie selon un gradient côte-large, avec des niveaux de diversité et de biomasse régionaux au moins équivalents à ceux des récifs coralliens. L’inter-récif est environ dix fois plus vaste que les récifs coralliens, partage également une partie de sa faune, mais n’est quasiment pas protégé à l’échelle mondiale. A l’opposé, les niveaux de diversité sur les monts sous-marins étaient très inférieurs à ceux observés dans les récifs coralliens. Cependant les niveaux de biomasse étaient supérieurs sur les monts sous-marins et pentes entre 50m et 250m de fond. La profondeur s’est révélée être le facteur principal régissant la distribution de la biodiversité et de la biomasse. La biomasse des requins était 5 fois plus élevée sur les monts peu profonds (50m) que sur les récifs coralliens. Les monts sous-marins peu profonds peuvent prétendre à un statut d’oasis de biomasse ainsi que de refuge pour une mégafaune qui est en partie associée aux récifs coralliens. Les travaux de cette thèse ont permis de comparer la biodiversité sur des environnements moins connus, et de questionner les notions de hotspot, oasis et refuge à travers des mesures standardisées de leurs biodiversités. Les méthodes utilisées se sont révélées complémentaires pour l’étude comparative de multiples écosystèmes ; elles montrent également un fort potentiel opérationnel. L’algorithme d’apprentissage profond a par exemple démontré sa capacité à identifier et compter les espèces de vivaneaux annonçant une incorporation prochaine des nouvelles technologies en ingénierie sous-marine.Biodiversity is a concept at the heart of global issues in the face of human-induced changes, with a possible sixth mass extinction underway. Emphasis has always been made on regions that have been described as biodiversity hotspots, such as coral reefs. However, far fewer studies have focused on desert-like environments such as the inter-reef zone of the continental shelf, or difficult to access areas such as seamounts. This CIFRE PhD focuses on the use of two standardized methods: environmental DNA metabarcoding (eDNA) and baited stereo-cameras (S-BRUVS) to study and compare the diversity of coral reef fishes with the inter-reef, but also with deep environments including seamount summits and deep outer slopes up to 550 meters depth in New Caledonia. A new technology is also used, the automatic processing of images from S-BRUVS for the detection, identification and counting of deep water snappers through artificial intelligence (AI). The results showed that the inter-reef area had a diversity distributed along an inshore-offshore gradient, with levels of diversity and biomass at least equivalent to that of the coral reefs. The inter-reef is about ten times larger than coral reefs, shares some of its fauna with coral reefs, but is left virtually unprotected on a global scale. In contrast, levels of diversity on seamounts were much lower than those observed on coral reefs. However, biomass levels were highest on seamounts and slopes at depths between 50m and 250m. Depth was the primary factor governing the distribution of biodiversity and biomass. Shark biomass was 5 times higher on shallow seamounts (50m) than on coral reefs. Shallow seamounts turn out to be an oasis of biomass and a refuge for megafauna partly associated with coral reefs. The work of this thesis has made it possible to compare biodiversity in lesser-known environments, and to question the notions of hotspot, oasis and refuge through standardized measures of their biodiversity. The methods used have proven to be complementary for the comparative study of multiple ecosystems; they also show strong operational potential. For example, the deep learning algorithm demonstrated its ability to identify and count snapper species, heralding the upcoming incorporation of new technologies in underwater engineering

Seamounts_Oasis_New_Caledonia_BRUVS

<p>This dataset contains BRUVS (Baited Remote Underwater Video Station) data for 224 video stations collected in seamounts, continental slopes and coral reefs of New-Caledonia in 2019 and 2020. The data were collected under permits to Laurent Vigliola by the Government of New-Caledonia (permit N° 2019-733/GNC, 2020-503/GNC and 2020-1077/GNC), the Southern Province of New Caledonia (permit N° 898-2019/ARR/DENV, 3066-2019/ARR/DENV, 844-2020/ARR/DDDT and 1955-2020/ARR/DDDT) and the Northern Province of New Caledonia (permit N° 609011/2019/DEPART/JJC , 609011-18/2019/DEPART/JJC and 609011-39/2020/DEPART/JJC). Collection was performed during the SEAMOUNTS and REEF3.0 projects led by Laurent Vigliola. The data contains the outputs of BRUVS video analyses (species id, abundance, size, biomass) as described in Baletaud et al. 2023. The metadata contains information on the stations, sampling locations and associated environmental variables.</p&gt

Seamounts_Oasis_New_Caledonia_eDNA

<p>This dataset contains eDNA MOTUs for 192 water samples collected in seamounts, continental slopes and coral reefs of New-Caledonia in 2019 and 2020. The data were collected under permits to Laurent Vigliola by the Government of New-Caledonia (permit N° 2019-733/GNC, 2020-503/GNC and 2020-1077/GNC), the Southern Province of New Caledonia (permit N° 898-2019/ARR/DENV, 3066-2019/ARR/DENV, 844-2020/ARR/DDDT and 1955-2020/ARR/DDDT) and the Northern Province of New Caledonia (permit N° 609011/2019/DEPART/JJC , 609011-18/2019/DEPART/JJC and 609011-39/2020/DEPART/JJC). Collection was performed during the SEAMOUNTS and REEF3.0 projects led by Laurent Vigliola. The data contains the outputs of the bioinformatic process as described in Baletaud et al. 2023. The metadata contains information on the sampling filters, sampling locations and associated environmental variables.</p&gt

Comparing Seamounts and Coral Reefs with eDNA and BRUVS Reveals Oases and Refuges on Shallow Seamounts

Number: 11 Publisher: Multidisciplinary Digital Publishing InstituteSeamounts are the least known ocean biome. Considered biodiversity hotspots, biomass oases, and refuges for megafauna, large gaps exist in their real diversity relative to other ecosystems like coral reefs. Using environmental DNA metabarcoding (eDNA) and baited video (BRUVS), we compared fish assemblages across five environments of different depths: coral reefs (15 m), shallow seamounts (50 m), continental slopes (150 m), intermediate seamounts (250 m), and deep seamounts (500 m). We modeled assemblages using 12 environmental variables and found depth to be the main driver of fish diversity and biomass, although other variables like human accessibility were important. Boosted Regression Trees (BRT) revealed a strong negative effect of depth on species richness, segregating coral reefs from deep-sea environments. Surprisingly, BRT showed a hump-shaped effect of depth on fish biomass, with significantly lower biomass on coral reefs than in shallowest deep-sea environments. Biomass of large predators like sharks was three times higher on shallow seamounts (50 m) than on coral reefs. The five studied environments showed quite distinct assemblages. However, species shared between coral reefs and deeper-sea environments were dominated by highly mobile large predators. Our results suggest that seamounts are no diversity hotspots for fish. However, we show that shallower seamounts form biomass oases and refuges for threatened megafauna, suggesting that priority should be given to their protection

The aesthetic value of reef fishes is globally mismatched to their conservation priorities

International audienceReef fishes are closely connected to many human populations, yet their contributions to society are mostly considered through their economic and ecological values. Cultural and intrinsic values of reef fishes to the public can be critical drivers of conservation investment and success, but remain challenging to quantify. Aesthetic value represents one of the most immediate and direct means by which human societies engage with biodiversity, and can be evaluated from species to ecosystems. Here, we provide the aesthetic value of 2,417 ray-finned reef fish species by combining intensive evaluation of photographs of fishes by humans with predicted values from machine learning. We identified important biases in species’ aesthetic value relating to evolutionary history, ecological traits, and International Union for Conservation of Nature (IUCN) threat status. The most beautiful fishes are tightly packed into small parts of both the phylogenetic tree and the ecological trait space. In contrast, the less attractive fishes are the most ecologically and evolutionary distinct species and those recognized as threatened. Our study highlights likely important mismatches between potential public support for conservation and the species most in need of this support. It also provides a pathway for scaling-up our understanding of what are both an important nonmaterial facet of biodiversity and a key component of nature’s contribution to people, which could help better anticipate consequences of species loss and assist in developing appropriate communication strategies

The distribution of coastal fish eDNA sequences in the Anthropocene

Aim: Coastal fishes have a fundamental role in marine ecosystem functioning and contributions to people, but face increasing threats due to climate change, habitat degradation and overexploitation. The extent to which human pressures are impacting coastal fish biodiversity in comparison with geographic and environmental factors at large spatial scale is still under scrutiny. Here, we took advantage of environmental DNA (eDNA) metabarcoding to investigate the relationship between fish biodiversity, including taxonomic and genetic components, and environmental but also socio-economic factors. Location: Tropical, temperate and polar coastal areas. Time period: Present day. Major taxa studied: Marine fishes. Methods: We analysed fish eDNA in 263 stations (samples) in 68 sites distributed across polar, temperate and tropical regions. We modelled the effect of environmental, geographic and socio-economic factors on alpha-and beta-diversity. We then computed the partial effect of each factor on several fish biodiversity components using taxonomic molecular units (MOTU) and genetic sequences. We also investigated the relationship between fish genetic alpha-and beta-diversity measured from our barcodes, and phylogenetic but also functional diversity. Results: We show that fish eDNA MOTU and sequence alpha-and beta-diversity have the strongest correlation with environmental factors on coastal ecosystems worldwide. However, our models also reveal a negative correlation between biodiversity and human dependence on marine ecosystems. In areas with high dependence, diversity of all fish, cryptobenthic fish and large fish MOTUs declined steeply. Finally, we show that a sequence diversity index, accounting for genetic distance between pairs of MOTUs, within and between communities, is a reliable proxy of phylogenetic and functional diversity. Main conclusions: Together, our results demonstrate that short eDNA sequences can be used to assess climate and direct human impacts on marine biodiversity at large scale in the Anthropocene and can further be extended to investigate biodiversity in its phylogenetic and functional dimensions.ISSN:1466-822XISSN:1466-823

Circumglobal distribution of fish environmental DNA in coral reefs

DNAQUA International Conference : international Conference on the Use of DNA for Water Biomonitoring , [En ligne], , -Coral reefs host the highest fish diversity on Earth despite covering less than 0.1% of theocean’s seafloor. At the same time they are also extremely threatened. Data synthesesover decades of surveys estimate the total number of coral reef fishes to vary from 2,400 to8,000 species distributed among roughly 100 families. But this diversity remains largelyunknown