A Standardized Workflow Based on the STAVIRO Unbaited Underwater Video System for Monitoring Fish and Habitat Essential Biodiversity Variables in Coastal Areas

Essential Biodiversity Variables (EBV) related to benthic habitats and high trophic levels such as fish communities must be measured at fine scale but monitored and assessed at spatial scales that are relevant for policy and management actions. Local scales are important for assessing anthropogenic impacts, and conservation-related and fisheries management actions, while reporting on the conservation status of biodiversity to formulate national and international policies requires much broader scales. Measurements must account for the fact that coastal habitats and fish communities are heterogeneously distributed locally and at larger scales. Assessments based on in situ monitoring generally suffer from poor spatial replication and limited geographical coverage, which is challenging for area-wide assessments. Requirements for appropriate monitoring comprise cost-efficient and standardized observation protocols and data formats, spatially scalable and versatile data workflows, data that comply with the FAIR (Findable, Accessible, Interoperable, and Reusable) principles, while minimizing the environmental impact of measurements. This paper describes a standardized workflow based on remote underwater video that aims to assess fishes (at species and community levels) and habitat-related EBVs in coastal areas. This panoramic unbaited video technique was developed in 2007 to survey both fishes and benthic habitats in a cost-efficient manner, and with minimal effect on biodiversity. It can be deployed in areas where low underwater visibility is not a permanent or major limitation. The technique was consolidated and standardized and has been successfully used in varied settings over the last 12 years. We operationalized the EBV workflow by documenting the field protocol, survey design, image post-processing, EBV production and data curation. Applications of the workflow are illustrated here based on some 4,500 observations (fishes and benthic habitats) in the Pacific, Indian and Atlantic Oceans, and Mediterranean Sea. The STAVIRO’s proven track-record of utility and cost-effectiveness indicates that it should be considered by other researchers for future applications.publishedVersio

A predictive model based on multiple coastal anthropogenic pressures explains the degradation status of a marine ecosystem: Implications for management and conservation

International audienceDuring the last fifty years, there has been a dramatic increase in the development of anthropogenic activities, and this is particularly threatening to marine coastal ecosystems. The management of these multiple and simultaneous anthropogenic pressures requires reliable and precise data on their distribution, as well as information (data, modelling) on their potential effects on sensitive ecosystems. Focusing on Posidonia oceanica beds, a threatened habitat-forming seagrass species endemic to the Mediterranean, we developed a statistical approach to study the complex relationship between human multiple activities and ecosystem status. We used Random Forest modelling to explain the degradation status of P. oceanica (defined herein as the shift from seagrass bed to dead matte) as a function of depth and 10 anthropogenic pressures along the French Mediterranean coast (1700 km of coastline including Corsica). Using a 50 x 50 m grid cells dataset, we obtained a particularly accurate model explaining 71.3 % of the variance, with a Pearson correlation of 0.84 between predicted and observed values. Human-made coastline, depth, coastal population, urbanization, and agriculture were the best global predictors of P. oceanica's degradation status. Aquaculture was the least important predictor, although its local individual influence was among the highest. Non-linear relationship between predictors and seagrass beds status was detected with tipping points (i.e. thresholds) for all variables except agriculture and industrial effluents. Using these tipping points, we built a map representing the coastal seagrass beds classified into four categories according to an increasing pressure gradient and its risk of phase shift. Our approach provides important information that can be used to help managers preserve this essential and endangered ecosystem

Splanchnic Artery Stenosis and Abdominal Complaints: Clinical History Is of Limited Value in Detection of Gastrointestinal Ischemia

BACKGROUND: Splanchnic artery stenosis is common and mostly asymptomatic and may lead to gastrointestinal ischemia (chronic splanchnic syndrome, CSS). This study was designed to assess risk factors for CSS in the medical history of patients with splanchnic artery stenosis and whether these risk factors can be used to identify patients with high and low risk of CSS. METHODS: All patients referred for suspected CSS underwent a standardized workup, including a medical history with questionnaire, duplex ultrasound, gastrointestinal tonometry, and angiography. Definitive diagnosis and treatment advice was made in a multidisciplinary team. Patients with confirmed CSS were compared with no-CSS patients. RESULTS: A total of 270 patients (102 M, 168 F; mean age, 53 years) with splanchnic artery stenosis were analyzed, of whom 109 (40%) had CSS and 161 no CSS. CSS-patients more often reported postprandial pain (87% vs. 72%, p = 0.007), weight loss (85% vs. 70%, p = 0.006), adapted eating pattern (90% vs. 79%, p = 0.005) and diarrhea (35% vs. 22%, p = 0.023). If none of these risk factors were present, the probability of CSS was 13%; if all were present, the probability was 60%. Adapted eating pattern (odds ratio (OR) 3.1; 95% confidence interval (CI) 1.08-8.88) and diarrhea (OR 2.6; 95% CI 1.31-5.3) were statistically significant in multivariate analysis. CONCLUSIONS: In patients with splanchnic artery stenosis, the clinical history is of limited value for detection of CSS. A diagnostic test to detect ischemia is indispensable for proper selection of patients with splanchnic artery stenosis who might benefit from treatment

The Clinical Variability of Maternally Inherited Diabetes and Deafness Is Associated with the Degree of Heteroplasmy in Blood Leukocytes

Context: Maternally inherited diabetes and deafness (MIDD) is a rare form of diabetes with a matrilineal transmission, sensorineural hearing loss, and macular pattern dystrophy due to an A to G transition at position 3243 of mitochondrial DNA (mtDNA) (m.3243A>G). The phenotypic heterogeneity of MIDD may be the consequence of different levels of mutated mtDNA among mitochondria in a given tissue. Objective: The aim of the present study was thus to ascertain the correlation between the severity of the phenotype in patients with MIDD and the level of heteroplasmy in the blood leukocytes. Participants: The GEDIAM prospective multicenter register was initiated in 1995. Eighty-nine Europid patients from this register, with MIDD and the mtDNA 3243A>G mutation, were included. Patients with MELAS (mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes) or with mitochondrial diabetes related to other mutations or to deletions of mtDNA were excluded. Results: A significant negative correlation was found between levels of heteroplasmy and age of the patients at the time of sampling for molecular analysis, age at the diagnosis of diabetes, and body mass index. After adjustment for age at sampling for molecular study and gender, the correlation between heteroplasmy levels and age at the diagnosis of diabetes was no more significant. The two other correlations remained significant. A significant positive correlation between levels of heteroplasmy and HbA1c was also found and remained significant after adjustment for age at molecular sampling and gender. Conclusions: These results support the hypothesis that heteroplasmy levels are at least one of the determinants of the severity of the phenotype in MIDD. Heteroplasmy levels are at least one of the determinants of the severity of the phenotype of maternally inherited diabetes and deafness

Rapid Recruitment of Symbiotic Algae into Developing Scleractinian Coral Tissues

While the early acquisition of Symbiodiniaceae algae into coral host tissues has been extensively studied, the dynamics of the migration of algal cells into rapidly expanding coral tissues still lacks a systematic study. This work examined two Red Sea branching coral species, Pocillopora damicornis and Stylophora pistillata, as they were growing and expanding their tissue laterally on glass slides (January-June, 2014; 450 assays; five colonies/species). We measured lateral tissue expansion rates and intratissue dinoflagellate migration rates. Tissue growth rates significantly differed between the two species (with Stylophora faster than Pocillopora), but not between genotypes within a species. Using a "flow-through coral chamber" under the microscope, the migration of dinoflagellates towards the peripheral edges of the expanding coral tissue was quantified. On a five-day timescale, the density of the endosymbiotic dinoflagellate cells, presenting within a 90 mu m region of expanding coral tissue (outer edge), increased by a factor of 23.6 for Pocillopora (from 1.2 x 10(4) cells cm(-2) to 2.4 x 10(5) cells cm(-2)) and by a factor of 6.8 for Stylophora (from 3.6 x 10(4) cells cm(-2) to 2.4 x 10(5) cells cm(-2)). The infection rates were fast (5.2 x 10(4) and 4.1 x 10(4) algal cells day-1 cm(-2), respectively), further providing evidence of an as yet unknown pathway of algal movement within coral host tissues

Evaluation de l’état de santé des habitats et peuplements de poissons de la zone de Voh-Koné-Pouembout, Campagnes de stations vidéo rotatives STAVIRO 2007-2013. Annexe cartographique

Maps of the indicators analyzed in video-based assessment of status and trends in fish assemblages and habitats, Voh-Koné-PouemboutCartes des indicateurs analysés dans Evaluation par vidéo de l’état de santé des habitats et peuplements de poissons de la zone de Voh-Koné-Pouembout, Campagnes de stations vidéo rotatives STAVIRO 2007-2013

Etat de santé des habitats et peuplements de poissons des îles et récifs de l’Astrolabe, Pétrie et Walpole, Parc Naturel de la Mer de Corail. Evaluation initiale par stations vidéo rotatives STAVIRO

- The AMBIO project conducted a comprehensive video-based baseline assessment of coral reef fish communities and associated habitats in the New Caledonian lagoons. The survey relies on remote unbaited underwater video observations, using the STAVIRO rotating technique. - The study pertains to the reefs of Astrolabe, Pétrie and Walpole Island, located within the Coral Sea Natural Park. The survey conducted in 2014 covers the entire area, and the sampling design was stratified according to reef type. 95 stations were validated. They were analyzed to characterize the habitat surrounding each station, and fish communities, based on a list of 565 fish species (cf. AMBIO/A/1). - 28 indicators were computed and mapped (maps available on a Sextant server). Indicators were analyzed using the PAMPA computing tool. Outcomes were organized in a dashboard for each management objective (biodiversity conservation and fisheries management). - 171 fish species (and one turtle species), belonging to 33 families were observed. Two families were observed on more than 95% of stations: surgeonfish and wrasses. Eight other families were observed on 50% to 95% of stations: parrotfish, groupers, triggerfish, snappers, butterflyfish, goatfish, emperors and angelfish. - Coral health status is good with high living coral covers (62% on average), mostly in Astrolabe, but branch coral was scarce. Sharks and giant wrasse were frequently observed, as well as jacks. - Fish communities are diversified and very abundant, particularly in the Living Coral habitat; and generally more abundant than on the rest of the sites, particularly at Astrolabe. All trophic groups were abundant on the area, except for planktivorous species. Piscivorous species were very abundant. - Most fisheries-related metrics indicate highly abundant resources, particularly at Astrolabe. - The health status of coral habitat and associated fish communities appears exceptional at Astrolabe, and generally good at Pétrie and Walpole.  - Le projet AMBIO a conduit des évaluations des peuplements de poissons et habitats associés aux récifs coralliens sur l’ensemble  des lagons de Nouvelle-Calédonie, en s’appuyant sur la technique de vidéo rotative STAVIRO. - Cette campagne a été réalisée en 2014 sur les iles et récifs éloignés d’Astrolabe, Pétrie et Walpole, situés dans le périmètre du Parc Naturel de la Mer de Corail. Le plan d'échantillonnage couvre toute la zone avec une stratification en fonction des structures récifales présentes. 95 stations STAVIRO ont été validées. Leur analyse a permis de caractériser l’habitat environnant chaque station, ainsi que les communautés de poissons sur la base d’une liste de 565 espèces (cf. AMBIO/A/1). - 28 indicateurs ont été calculés et représentés sous forme de carte disponible sur un serveur Sextant. Ces indicateurs ont été analysés grâce à l’outil de calcul PAMPA. Les résultats sont synthétisés sous forme de tableau de bord par objectif de gestion relatif à la conservation de la biodiversité et la gestion des ressources de la pêche. - 171 espèces de poissons (et 1 espèce de tortue) appartenant à 33 familles ont été observées. Deux familles sont vues sur plus de 95% de stations : poissons-chirurgiens et labres. Huit autres familles sont vues sur 50 à 95% des stations : poissons-perroquets, loches, balistes, lutjans, poissons-papillons, rougets-barbets, bossus/becs et poissons-ange. - L’état de santé du corail est bon, avec des recouvrements en corail vivant élevés (62% en moyenne sur l’habitat Corail vivant), surtout à Astrolabe, mais quasiment pas de corail branchu. Les requins et le poisson-napoléon sont fréquemment observés, ainsi que les carangues. - Les peuplements de poissons sont diversifiés et très abondants, notamment sur l’habitat Corail vivant. Ils sont très généralement plus abondants que sur le reste de la Grande Terre, particulièrement pour les récifs d’Astrolabe. Tous les groupes trophiques sont abondants sur la zone, à l’exception des espèces planctonophages, dont l’abondance est moyenne. Les espèces piscivores sont très abondantes. - La plupart des métriques liées aux ressources de la pêche montrent des ressources abondantes, particulièrement sur les récifs d’Astrolabe. - L’état de santé de l’habitat corallien et des peuplements  associés apparaît exceptionnel à Astrolabe, et généralement bon à Pétrie et à Walpole.

Etat de santé des habitats et peuplements de poissons de la Réserve Merlet, zone inscrite au Patrimoine Mondial - Evaluation initiale par stations vidéo rotatives STAVIRO

Conducted within the AMBIO project, this work deals with coral reef fish communities and associated habitats, in the New Caledonian lagoons. It relies on remote unbaited underwater video observations, using the STAVIRO rotating technique. The field work was realized in 2013 in and around the Merlet Marine Reserve, in the south of New-Caledonia, and located within the “Grand Lagon Sud” world heritage area. The sampling design covers the entire area, and was stratified according to reef type (outer slope, reef flat, reef shallow terrace, lagoon, and fringing reef). 162 stations were validated within 6 days. They were analyzed to characterize the habitat surrounding each station, and fish communities, based on a list of 429 fish species (cf. AMBIO/A/1). 28 indicators were computed and mapped (maps available on a Sextant server). Indicators were analyzed using the PAMPA computing tool. Outcomes were organized in a dashboard for each management objective (biodiversity conservation and fisheries management). 165 fish species (and one turtle species), belonging to 20 families were observed. Two families were observed on more than 80% of stations: surgeonfish and parrotfish. Four other families were observed on 50% to 80% of stations: butterflyfish, wrasses, groupers and goatfish. Living coral habitat display a good ecological status, in particular on external slopes (on average over 35% on this habitat). A large diversity (26 species) and abundance of butterflyfish was observed. 2 shark species, 1 turtle species and 3 ray species were encountered, as well as giant wrasse. Fish communities display a good ecological status, in particular on external slopes in the Living Coral habitat, consistently with an ancient and strong protection. Emblematic species were regularly observed. Most fisheries-related metrics indicate relatively abundant resources, with higher occurrences abundances, and a greater proportion of large individuals. These results indicate lower anthropogenic pressures, especially fishing pressure,than at other coastal sites.    Cette étude conduite dans le cadre du projet AMBIO concerne les communautés de poissons et habitats associés aux récifs coralliens des lagons de Nouvelle-Calédonie. Elle s’appuie sur des données collectées par STAVIRO, une technique de vidéo rotative. Cette campagne a été réalisée en 2013 dans et autour de la réserve Yves Merlet, située dans le Grand Lagon Sud, bien inscrit au patrimoine mondial. Le plan d'échantillonnage couvre toute la zone avec une stratification en fonction des structures récifales (pente externe, fond lagonaire, récif frangeant, platier, plateau récifal). En 6 jours sur zone, 162 stations STAVIRO ont été validées. Leur analyse a permis de caractériser l’habitat environnant chaque station, ainsi que les communautés de poissons sur la base d’une liste de 429 espèces (cf. AMBIO/A/1). 28 indicateurs ont été calculés et représentés sous forme de carte disponible sur un serveur Sextant. Ces indicateurs ont été analysés grâce à l’outil de calcul PAMPA. Les résultats sont synthétisés sous forme de tableau de bord par objectif de gestion relatif à la conservation de la biodiversité et la gestion des ressources de la pêche. 165 espèces de poissons (et 1 espèce de tortue) appartenant à 20 familles ont été observées. Deux familles sont vues sur plus de 80% de stations : poissons chirurgiens et poissons perroquets. Quatre autres familles sont vues sur 50 à 80% des stations : poissons-papillons, labres, loches et rougets-barbets. L’état de santé du corail est bon, avec des recouvrements en corail vivant élevés (plus de 35% en moyenne sur l’habitat Corail vivant). Les poissons-papillons sont diversifiés (26 espèces) et abondants sur la zone. 2 espèces de requins, 1 espèce de tortue et trois espèces de raies sont observées, ainsi que le poisson napoléon. L’état de l’ichtyofaune est satisfaisant, notamment sur la pente externe, et cohérent avec le statut de protection intégrale ancien. Les espèces emblématiques sont régulièrement observées. Les résultats indiquent des pressions anthropiques, et notamment une pression de pêche, clairement plus faibles que sur d’autres sites côtiers, avec des espèces-cibles plus fréquentes, plus abondantes et plus de grands individus.  

Etat de santé des habitats et peuplements de poissons de la Corne Sud, zone inscrite au Patrimoine Mondial de l’Humanité - Evaluation initiale par stations vidéo rotatives STAVIRO

The AMBIO project conducted a comprehensive video-based baseline assessment of coral reef fish communities and associated habitats in the New Caledonian lagoons. The survey relies on remote unbaited underwater video observations, using the STAVIRO rotating technique. The present study deals with the Corne Sud area, in the south of New-Caledonia, and located within the “Grand Lagon Sud” World Heritage Property. The survey design covers the entire area. 155 stations were validated within 9 days. They were analyzed to characterize the habitat surrounding each station, and fish communities, based on a list of 429 fish species (cf. AMBIO/A/1). 27 indicators were computed and mapped (maps available on a Sextant server). Indicators were analyzed using the PAMPA computing tool. Outcomes were organized in a dashboard for each management objective (biodiversity conservation and fisheries management). 170 fish species (and one turtle species), belonging to 23 families were observed. Surgeonfish and parrotfish were observed on 95% of the stations. Wrasses, butterflyfish, goatfish and groupers were observed on 50% to 80% of the stations. Live coral habitat was dominant (almost 60% of stations). Coral cover status was very good on the external slope, good on fringing reefs. Branch coral cover was high in sheltered locations, islet fringing reefs and coral patches. Butterflyfish diversity was very high (26 species). Fish communities are among the most diversified in New Caledonia, particularly on barrier reef and lagoon coral patches. Fish abundance is heterogenous, high on the barrier reef and coral patches, and medium on islet fringing reefs. Turtles, sharks, rays and giant wrasse are regularly observed on their favorite habitats. Ressource status is good for fished species and species targeted by spearfishing and line. In particular, blue spine unicorn, coral trout and “picot kanak” (Acanthurus blochii, dussumieri and nigricauda) are both more frequent and more abundant than in the other sites studied.    Le projet AMBIO a conduit des évaluations des peuplements de poissons et habitats associés aux récifs coralliens sur l’ensemble  des lagons de Nouvelle-Calédonie, en s’appuyant sur la technique de vidéo rotative STAVIRO. Cette campagne a été réalisée en 2013 dans la Corne Sud, située dans le Grand Lagon Sud, bien inscrit au Patrimoine Mondial. Le plan d'échantillonnage couvre la totalité de cette vaste zone. En 9 jours sur zone, 155 stations STAVIRO ont été validées. Leur analyse a permis de caractériser l’habitat environnant chaque station, ainsi que les peuplements de poissons sur la base d’une liste de 527 espèces (cf. AMBIO/A/1). 27 indicateurs ont été calculés et représentés sous forme de cartes disponibles sur un serveur Sextant. Ces indicateurs ont été analysés grâce à l’outil de calcul PAMPA. Les résultats sont synthétisés sous forme de tableau de bord par objectif de gestion relatif à la conservation de la biodiversité et la gestion des ressources de la pêche. 170 espèces de poissons (et 1 espèce de tortue) appartenant à 23 familles ont été observées. Poissons chirurgiens et poissons perroquets sont observés sur plus de 95% des stations. Labres, poissons-papillons, loches et rougets-barbets sont observés sur 50 à 80% des stations. L’habitat corallien est largement dominant avec presque 60% des stations et un recouvrement en corail vivant très bon sur la pente externe, presque bon sur les frangeants d’îlot et un recouvrement élevé en corail branchu dans les zones lagonaires abritées, frangeantes et patates isolées. La diversité des poissons-papillons est très élevée (26 espèces observées). Le peuplement est un des plus diversifiés autour de la Grande Terre surtout sur le récif barrière et les patates lagonaires isolées. Son abondance est moyenne et hétérogène, élevée sur la barrière et les patates isolées, moyenne sur les frangeants d’îlot. Tortues, requins, raies et poissons-napoléons sont régulièrement observés sur leurs habitats préférés. L’état des ressources est satisfaisant pour les espèces commerciales, consommables et pour les cibles de la chasse, et celles de la ligne. En particulier, le dawa, la saumonée petits points et le picot kanak sont plus fréquents et plus abondants que sur les autres sites.  

A regionally scalable habitat typology for assessing benthic habitats and fish communities: Application to New Caledonia reefs and lagoons

Scalable assessments of biodiversity are required to successfully and adaptively manage coastal ecosystems. Assessments must account for habitat variations at multiple spatial scales, including the small scales (<100 m) at which biotic and abiotic habitat components structure the distribution of fauna, including fishes. Associated challenges include achieving consistent habitat descriptions and upscaling from in situ‐monitored stations to larger scales. We developed a methodology for (a) determining habitat types consistent across scales within large management units, (b) characterizing heterogeneities within each habitat, and (c) predicting habitat from new survey data. It relies on clustering techniques and supervised classification rules and was applied to a set of 3,145 underwater video observations of fish and benthic habitats collected in all reef and lagoon habitats around New Caledonia. A baseline habitat typology was established with five habitat types clearly characterized by abiotic and biotic attributes. In a complex mosaic of habitats, habitat type is an indispensable covariate for explaining spatial variations in fish communities. Habitat types were further described by 26 rules capturing the range of habitat features encountered. Rules provided intuitive habitat descriptions and predicted habitat type for new monitoring observations, both straightforwardly and with known confidence. Images are convenient for interacting with managers and stakeholders. Our scheme is (a) consistent at the scale of New Caledonia reefs and lagoons (1.4 million km2) and (b) ubiquitous by providing data in all habitats, for example, showcasing a substantial fish abundance in rarely monitored soft‐bottom habitats. Both features must be part of an ecosystem‐based monitoring strategy relevant for management. This is the first study applying data mining techniques to in situ measurements to characterize coastal habitats over regional‐scale management areas. This approach can be applied to other types of observations and other ecosystems to characterize and predict local ecological assets for assessments at larger scales