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International audience; Ecosystem engineering species alter the physical structure of their environment and can create or modify habitats , having a massive impact on local biodiversity. Coralligenous reefs are highly diverse habitats endemic to the Mediterranean Sea built by calcareous benthic organisms among which Crustose Coralline Algae are the main engineering species. We analyzed the diversity of Lithophyllum stictiforme or L. cabiochiae in coralligenous habitats combining a multiple barcode and a population genomics approach with seascape features. Population genomics allowed disentangling pure spatial effects from environmental effects. We found that these taxa form a complex of eight highly divergent cryptic species that are easily identifiable using classic barcode markers (psbA, LSU, COI). Three factors have a significant effect on the relative abundances of these cryptic species: the location along the French Mediterranean coast, depth and Photosynthetic Active Radiation (PAR). The analysis of around 5000 SNPs for the most abundant species revealed genetic differentiation among localities in the Bay of Marseille but no differentiation between depths within locality. Thus, the effect of depth and PAR on cryptic species communities is not a consequence of restricted connectivity but rather due to differential settlement or survival among cryptic species. This differential is more likely driven by irradiance levels rather than by pressure or temperature. Both the genetic and species diversity patterns are congruent with the main patterns of currents in the Bay. Ecological differentiation among these engineering cryptic species, sensitive to ocean warming and acidification, could have important consequences on the diversity and structure of the coralligenous communities .

The coralligenous habitat was studied at the large Mediterranean scale, by applying a standardized, non-destructive photo-sampling protocol, developed in the framework of the CIGESMED project. the results provided evidence to support the following statements: (a) the assemblage pattern is not homogeneously distributed across the four Mediterranean ecoregions studied (biotic gradients hypothesis); and (b) the assemblage pattern does not change significantly when the information is aggregated to higher taxonomic levels (taxonomic sufficiency hypothesis). Surrogate taxonomic categories higher than species, such as genus and family, can be used to reveal the multivariate pattern of the coralligenous assemblages. Although preliminary at the pan-Mediterranean scale, these outcomes set the scene for future comparisons as more data sets become available but also for comparisons between taxonomic and functional patterns. 1.2.3.4., CNRS - ANRFrench National Research Agency (ANR)Centre National de la Recherche Scientifique (CNRS) [12-SEAS-0001-01, 12-SEAS-0001-02, 12-SEAS-0001-03]; General Secretariat for Research and TechnologyGreek Ministry of Development-GSRT [12SEAS-2-C2]; Turkiye Bilimsel ve Teknolojik Arastirma KurumuTurkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [112Y393], CNRS - ANR, Grant/Award Numbers: 12-SEAS-0001-01, 12-SEAS-0001-02, 12-SEAS-0001-03; General Secretariat for Research and Technology, Grant/Award Number: 12SEAS-2-C2; Turkiye Bilimsel ve Teknolojik Arastirma Kurumu, Grant/Award Number: 112Y393

In the field of marine environment, observation protocols developed in many settings produce a large volume of heterogeneous data, which are difficult to aggregate since they focus on the use that is often specific to a profession. However, access and sharing of data on a large scale is essential to better understand the challenges behind protecting biodiversity and marine resources, and to anticipate their irreversible deterioration. To address these challenges, there is a need to strengthen the effectiveness of knowledge acquisition systems, and to organise data access for all potential users. Improving the consistency between observational systems and informational systems is the main objective of this work. Effective implementation of large-scale observational systems requires an inventory of knowledge, available skills and locks to be lifted. Monitoring networks for environmental protection become multi-user and must produce sufficient reliable descriptors to develop an effective reporting.The present work proposes to develop i) methods, protocols and recommendations to build and / or support the establishment of networks for monitoring biodiversity (from gene to species to habitats), operational and sustainable at all scales, (ii) innovative usage of data, their conservation and the organisation of their permanent access.Two case studies were chosen: coralligenous habitats at the Mediterranean scale and the colonisation of artificial reefs (ARMS) in various regional seas, focusing on: the construction of sustainable monitoring and observational networks; efficient sharing and inter-operability of long-term knowledge along with data analysis methods exploiting advances in the field of Big Data, and the analysis of heterogeneous data in the form of graphs.The testing of the proposed protocols developed during this thesis shows that a large-scale experiment must be described very explicitly in standardised terms beyond the disciplinary field of marine ecology and to be based on the simplest possible measurement methods. These tests also demonstrated the importance of operator’s training and iterative intercalibration.The work on the architecture of informational systems highlights the inevitability of a modular management system, business-oriented and decentralised. A mechanism for coupling data of different origins accessible in the form of parameterisable and open flows is proposed (field observations and data describing the contexts). It is based on the requalification of heterogeneous descriptive factors built on a collaborative arbitration between specialists. Thanks to the development of a prototype, a method of analysis and data mining based on graph theory has been experimented. Diverse types of possible demonstrations based on the data were constructed through the organisation of multidisciplinary curation and graphical data visualszation workshops.In conclusion, we recommend that the information produced is iteratively controlled in real time and that the curation processes of the data is implemented at the same time as the design of the observational processes. Standard definitions and access to context data require collaborative, interdisciplinary, iterative, long-term, international work. They must be considered for all their possible uses.In perspective, the use of the computation grid to carry out graph mining in a parallel way was prepared during the workshops, with the challenge of scaling up distributed and very heterogeneous data and forming graphs with more than one billion nodes and several hundred billions links., Dans le domaine de l’environnement marin, des protocoles d’observation développés dans de nombreux cadres produisent un grand volume de données hétérogènes, difficiles à agréger car centrées sur l’utilisation souvent spécifique à un métier. L’accès et le partage des données à large échelle est pourtant incontournable pour mieux cerner les enjeux de protection de la biodiversité et des ressources marines, et anticiper leur détérioration irréversible. Pour répondre à ces enjeux, il est nécessaire de renforcer l’efficacité des systèmes d’acquisition de connaissances, et d’organiser l’accès aux données pour tous les utilisateurs potentiels. Améliorer la cohérence entre systèmes d’observation et systèmes d’information est l’objectif cadre de ce travail. La mise en place efficace de systèmes d’observation à large échelle nécessite un état des lieux des connaissances, des compétences disponibles et des verrous à lever. Les réseaux de suivi pour la protection environnementale deviennent multi-usagers et doivent produire suffisamment de descripteurs fiables pour élaborer une indication et un reportage performants.Ce travail propose i) des méthodes, protocoles et recommandations pour construire et/ou soutenir la mise en place de réseaux de suivis de la biodiversité (du gène aux espèces et aux habitats), opérationnels et pérennes à toutes les échelles, ii) des utilisations novatrices des données, de leur conservation et de l’organisation de leurs accès permanent.Deux cas d’étude ont été choisis : les habitats coralligènes à l’échelle de la Méditerranée et la colonisation de récifs artificiels (ARMS) dans différentes mers régionales, en focalisant sur : la construction de réseaux de suivi et d’observation pérennes, le partage efficace et l’inter-opération des connaissances à long terme et les méthodes d’analyses de données exploitant les avancées dans le domaine du Big Data, et de l’analyse de données hétérogènes sous forme de graphes.Le test des protocoles élaborés dans le cadre de cette thèse montre qu’une expérimentation à large échelle doit être décrite très explicitement dans des termes standardisés au-delà du champ disciplinaire de l’écologie marine et se baser sur des méthodes de mesures les plus simples possibles. Ces tests ont aussi montré l’importance de la formation des opérateurs et d’une intercalibration itérative.Le travail sur l’architecture des systèmes d’information met en évidence l’inévitabilité d’un système de gestion modulaire, orienté “métier” et décentralisé. Un mécanisme de couplage de données de différentes origines accessibles sous forme de flux paramétrables et ouverts est proposé (observations de terrain et données décrivant les contextes). Il s’appuie sur la requalification des facteurs descriptifs hétérogènes reposant sur un arbitrage collaboratif entre spécialistes. Grâce au développement d’un prototype, une méthode d’analyse et de fouille de données basé sur la théorie des graphes a été expérimentée. Différents types de démonstrations possibles partant des données ont été construits grâce à l’organisation d’ateliers multidisciplinaires de curation et de visualisation de données sous forme de graphes.En conclusion, nous recommandons que l’information produite soit contrôlée par itérations en temps réel et que les processus de curation de la donnée soient mis en œuvre en même temps que la conception des procédés d’observation. Les définitions de standards et les accès aux données de contextes nécessitent un travail collaboratif, interdisciplinaire, itératif produit sur le long terme sur un plan international. Ils doivent être considérés pour toutes leurs utilisations possibles.En perspective, l’utilisation de la grille de calcul pour faire de la fouille de graphes de manière parallélisée a été préparée lors des ateliers, avec le challenge d’un passage à l’échelle avec des données distribuées et très hétérogènes formant des graphes de plus d’un milliard de nœuds et plusieurs centaines de milliards de liens.

WOS: 000449618200117, PubMed ID: 27932909, Background Over the last decade, inventorying and monitoring of marine biodiversity has significantly benefited from the active engagement of volunteers. Although several Citizen Science projects concern tropical reef ecosystems worldwide, none of the existing initiatives has yet specifically focused on their Mediterranean equivalents. Mediterranean coralline reefs, known as "coralligenous", are bioherms primarily built by calcifying rhodophytes on hard substrates under dim-light conditions; they are considered hotspots of biodiversity and are extremely popular among divers due to their complex structure, conspicuous biological wealth and high aesthetic value. Nevertheless, data on their distribution, structure and conservation status is lacking for several Mediterranean areas while they are vulnerable to an increasing number of threats. New information In the framework of CIGESMED SeasEra (ERAnet) project a specialized Citizen Science project was launched, aiming to engage enthusiast divers in the study and monitoring of Mediterranean coralligenous assemblages through the gathering of basic information regarding their spatial occurrence, assemblage structure and associated pressures or threats. For its active implementation, a data collection protocol and a multilingual website were developed, comprising an educational module and a data submission platform. Georeferenced data reporting focuses on: (a) basic topographic and abiotic features for the preliminary description of each site, and the creation of data series for sites receiving multiple visits; (b) presence and relative abundance of typical conspicuous species, as well as (c) existence of pressures and imminent threats, for the characterization and assessment of coralligenous assemblages. A variety of tools is provided to facilitate end users, while divers have the choice to report additional information and are encouraged to upload their photographs. The long-term goal is the development of an active community of amateur observers providing widespread and ecologically significant data on coralligenous assemblages.

http://www.iemss.org/sites/iemss2016/; International audience; Data produced by the SeasEra CIGESMED project (Coralligenous based Indicators to evaluate and monitor the "Good Environmental Status" of the MEDiterranean coastal waters) have a high potential to be used by several stakeholders involved in environmental management. A new consortium called IndexMed whose task is to index Mediterranean biodiversity data, makes it possible to build graphs in order to analyse the CIGESMED data and develop new ways for data mining of coralligenous data. This paper presents the prototypes under development that test the ability of graphs dataBases and tools to connect biodiversity objects with non-centralized data. This project explores the ability of two scientific communities to work together. The uses of data from coralligenous habitat demonstrate the prototype functionalities and introduce new perspectives to analyse environmental and societal responses.; Les données produites par le projet SeasEra CIGESMED (Indicateurs d'évaluation des habitats coralligènes et de surveillance du «Bon état écologique» des eaux côtières méditerranéennes) ont un fort potentiel d'utilisation par de nombreux acteurs impliqués dans la gestion environnementale. Un nouveau consortium appelé IndexMed dont la tâche est d'indexer les données sur la biodiversité méditerranéenne, permet de construire des graphes dans l'objectif d'analyser les données CIGESMED et développer de nouvelles méthodes pour l'extraction de données sur les habitats coralligènes. Cet article présente les prototypes en cours de développement qui testent la capacité des bases de données "graphe" et des outils permettant de relier des objets de biodiversité à partir de données non centralisées. Ce projet explore la capacité de deux communautés scientifiques à travailler ensemble. Les utilisations des données provenant de l'habitat coralligène permettent de présenter les fonctionnalités du prototype et proposent de nouvelles approches pour analyser les réponses environnementales et sociétales.

International audience; Coralligenous habitats are part of the most important Mediterranean marine ecosystems in terms of complexity and biodiversity. They provide protection, feeding and reproduction areas for more than 1600 species. This biodiversity is essential for economic activities such as fishing and scuba diving. The European program CIGESMED (ERA-NET funding), involving France, Greece and Turkey, investigates the “Good Environmental Status” of these habitats in the framework of the MFSD (Marine Strategy Framework Directive). One major objective of CIGESMED is to propose an operational, long-term, large-scale protocol to monitor coralligenous habitats in the Mediterranean Sea. This protocol is currently tested in French sites: the effects of (sampling) methods, materials and operators are studied in order to evaluate the influence of protocol implementation, and to find the easiest and most reliable procedure that could be implemented by and for a large public, also consisting of non-scientists, and would provide workable data for longterm monitoring. This protocol is based on photo-quadrats observations. The analyses are done on occurrences, relative abundances, species associations and species’ favourite environmental profile. In parallel, complementary protocols are implemented: one concerns the cartography of coralligenous habitats, and two are about population genetics of significant habitat-forming species Myriapora truncata (Pallas, 1766) and Lithophyllum cabiochiae ((Areschoug) Hauck, 1877)). All the data and results are organized as a non-centralized information system, with configurable plugins that can be installed free by all new partners