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

Exploring the vertebrate fauna of the Bird’s Head Peninsula (Indonesia, West Papua) through DNA barcodes

Biodiversity knowledge is widely heterogeneous across the Earth's biomes. Some areas, due to their remoteness and difficult access, present large taxonomic knowledge gaps. Mostly located in the tropics, these areas have frequently experienced a fast development of anthropogenic activities during the last decades and are therefore of high conservation concerns. The biodiversity hotspots of Southeast Asia exemplify the stakes faced by tropical countries. While the hotspots of Sundaland (Java, Sumatra, Borneo) and Wallacea (Sulawesi, Moluccas) have long attracted the attention of biologists and conservationists alike, extensive parts of the Sahul area, in particular the island of New Guinea, have been much less explored biologically. Here, we describe the results of a DNA-based inventory of aquatic and terrestrial vertebratecommunities, which was the objective of a multidisciplinary expedition to the Bird's Head Peninsula (West Papua, Indonesia) conducted between 17 October and 20 November 2014. This expedition resulted in the assembly of 1005 vertebrate DNA barcodes. Based on the use of multiple species-delimitation methods (GMYC, PTP, RESL, ABGD), 264 molecular operational taxonomic units (MOTUs) were delineated, among which 75 were unidentified and an additional 48 were considered cryptic. This study suggests that the diversity of vertebrates of the Bird's Head is severely underestimated and considerations on the evolutionary origin and taxonomic knowledge of these biotas are discussed.Fieldwork and laboratory activities were supported by the Lengguru 2014 Project (www.lengguru.org), conducted by the French National Research Institute for Sustainable Development (IRD), the Indonesian Institute of Sciences (LIPI) with the Research Centre for Biology (RCB), and the Politeknik KP Sorong, with the help of the Institut Français in Indonesia (IFI) and the French embassy in Jakarta, with corporate sponsorship from COLAS SA Company (Environment Department), Total Foundation, ABS, Wasco, Veolia Eau, SDV-Bolloré,Peer reviewe

L'usage du CCR par la science : vers de nouvelles perspectives

National audienceThe conquest of new spaces, spatial as submarine, promotes the technological progress. The corollary is that some scientific advances are directly related to the available resources and technologies.By way of illustration, in the coral reef environment, the scientific studies (...)La conquête de nouveaux espaces, spatial comme sous-marin, favorise les progrès technologiques. Le corollaire est que certaines avancées de la science sont directement liées aux moyens et technologies mobilisables.Pour l’illustrer, en milieu corallien, les études (…

ReefTEMPS est un réseau de capteurs de température, pression et salinité dans le domaine côtier

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SI-TEC-PSO: retour d'expérience sur le système d'information dédié capteurs et reconstitution de séries temporelles de ReefTEMPS.

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Le système d’information du « réseau de capteurs de température des eaux côtières dans la région du Pacifique Sud et Sud-Ouest »

National audienceLe Grand Observatoire de l’environnement et de la biodiversité terrestre et marine du Pacifique Sud (GOPS) informe de l’ouverture du nouveau Système d’Information du « réseau de capteurs de Température des eaux Côtières dans la région du Pacifique Sud et Sud-Ouest (ReefTEMPS) » à la fin du 1er trimestre 2013

Collection des Données de Biodiversité marine de l’Indo Pacifique IRD Nouméa

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A European competency level applied to the use of the closed circuit rebreather in scientific diving at work. First step. Highlighting the best practice

International audienceThe use of the closed circuit rebreather (CCR) for scientific diving activities is growing. During the last 10 years more and more scientists and scientific projects did take advantage of the furtive behaviour CCR offers together with the very efficient gas management, optimized decompression and enhanced diving safety. Many applications exists, among others, the exploration of the mesophotic zone or the fishes sensing, sampling, study of their vocal communication. The use of rebreather in sciences exploration constitutes a new technological paradigm.The American Academy of Underwater Science (AAUS) in the USA established a standard for the use of rebreathers in scientific diving some 10 years ago and such document is lacking in Europe. Today in Europe the use of rebreather is generally not permitted by existing national legislation. If accepted in Belgium, France is currently undergoing changes to its laws and should allow the use of closed circuit rebreather early 2017. These national legislations need to evolve and adapt to the new technique used for scientific diving but that takes time. So it is time to establish at European level a competency level for the use of CCR at work. Taking advantage of the existing European norm for that respiratory equipment will permit to put more emphasis on the best practice rules aiming at inferring adapted and unified training around Europe using a common reference frame. This paper is a first step on that process and will highlight all the points that will need to be addressed in this future new competency level

Transmission de données océanographiques via le réseau IoT LoRaWAN sur une bouée instrumentée du Service National d'Observation ReefTEMPS

International audienceIn the event of extreme events, such as cyclones, tropical storms or coral bleaching episodes, being able to access In case of extreme events, such as cyclones, tropical storms or coral bleaching episodes, having access to real-time data on swell, temperature salinity data is invaluable for decision making in the spirit of early warning systems, but also for the study of but also for the study of these events.The National Observation Service (SNO) ReefTEMPS has deployed a hundred autonomous underwater sensors sensors, in coastal areas and lagoons of several countries and island states of the South Pacific. As data access is only possible when the sensors are relieved, we have initiated to transmit data in real time.For this, we acquired in 2020 a LoRaWAN gateway for the IRD Center (Institute of Research for Development) in New Caledonia. (Institut de Recherche pour le Développement) in New Caledonia with the objective of using the of things (IoT) technology between the sensor network and the oceanographic database. oceanographic database.A prototyping buoy has been set up in the Anse Vata bay in Noumea. The device includes a Sea Bird SBE16 type temperature sensor immersed at a depth of 3 m and a surface buoy a surface buoy for signaling and data transmission. The sensor is connected to the surface by a cable to an autonomous nano computer equipped with a radio antenna. The embedded system proceeds to the transmission of information through the IoT network.In this article we will detail the communication system realized by the students of the Lycée of Mont-Dore as well as the complete assembly realized by our care. This prototype demonstrates the feasibility and genericity of a LoRaWAN IoT solution to transmit in real time in situ oceanographic data from sensors immersed at depth in the coastal area. coastal domain.Translated with www.DeepL.com/Translator (free version)En cas d'événements extrêmes, comme des cyclones, des tempêtes tropicales ou des épisodes de blanchissement corallien, pouvoir accéder en temps réel à des données de houle, de température, de salinité est précieux pour permettre les prises de décisions dans l’esprit de systèmes d'alerte précoce mais également pour l’étude de ces événements.Le Service National d’Observation (SNO) ReefTEMPS a déployé une centaine de capteurs immergés autonomes, en zone littorale et dans les lagons de plusieurs pays et États insulaires du Pacifique Sud. L’accès aux données n’étant possible qu’à la relève des capteurs, nous avons initié une expérimentation de transmission de données en temps réel.Pour cela, nous avons acquis en 2020 une passerelle LoRaWAN pour le Centre IRD (Institut de Recherche pour le Développement) de Nouvelle-Calédonie avec comme objectif l’utilisation de la technologie Internet of things (IoT) entre le réseau de capteurs et la base de données océanographique.Une bouée de prototypage a été mise en place dans la baie de l’Anse Vata à Nouméa. Le dispositif comprend un capteur de température de type Sea Bird SBE16 immergé à une profondeur de 3 m et une bouée de surface permettant sa signalisation et la transmission des données. Le capteur est relié à la surface par un câble de connexion jusqu’à un nano ordinateur autonome muni d’une antenne radio. Le système embarqué procède à la transmission des informations par le réseau IoT.Dans cet article nous détaillerons le système de communication réalisé par les étudiants du Lycée technologique du Mont-Dore ainsi que le montage complet réalisé par nos soins. Ce prototype démontre la faisabilité et la généricité d’une solution IoT LoRaWAN pour transmettre en temps réel des données océanographiques in situ issues de capteurs immergés en profondeur dans le domaine côtier

MARBEC-Obs : towards a virtual observatory of marine and coastal ecosystems, mainly in Mediterranean and tropical areas

International audienceMARBEC is the largest French research unit in marine biodiversity (IRD IFREMER CNRS and University of Montpellier) with many international partnerships.MARBEC-Obs is in charge of 20 durable observatories, contributing to research and expertise on the state of coastal and marine ecosystems, biodiversity and the impact of human activities exploiting this biodiversity. The services and functionalities offered by the information systems combine modeling, statistical analysis, data management and data visualisation.MARBEC-Obs can evolve towards a virtual observatory of marine and coastal ecosystems, mainly in Mediterranean and tropical areas