Monitoring Marine Habitats With Photogrammetry: A Cost-Effective, Accurate, Precise and High-Resolution Reconstruction Method

Underwater photogrammetry has been increasingly used to study and monitor the three-dimensional characteristics of marine habitats, despite a lack of knowledge on the quality and reliability of the reconstructions. More particularly, little attention has been paid to exploring and estimating the relative contribution of multiple acquisition parameters on the model resolution (distance between neighbor vertices), accuracy (closeness to true positions/measures) and precision (variability of positions/measures). On the other hand, some studies used expensive or cumbersome camera systems that can restrict the number of users of this technology for the monitoring of marine habitats. This study aimed at developing a simple and cost-effective protocol able to produce accurate and reproducible high-resolution models. Precisely, the effect of the camera system, flying elevation, camera orientation and number of images on the resolution and accuracy of marine habitat reconstructions was tested through two experiments. A first experiment allowed for testing all combinations of acquisition parameters through the building of 192 models of the same 36 m2 study site. The flying elevation and camera system strongly affected the model resolution, while the photo density mostly affected bundle adjustment accuracy and total processing time. The camera orientation, in turn, mostly affected the reprojection error. The best combination of parameters was used in a second experiment to assess the accuracy and precision of the resulting reconstructions. The average model resolution was 3.4 mm, and despite a decreasing precision in the positioning of markers with distance to the model center (0.33, 0.27, and 1.2 mm/m Standard Deviation (SD) in X, Y, Z, respectively), the measures were very accurate and precise: 0.08% error ± 0.06 SD for bar lengths, 0.36% ± 0.51 SD for a rock model area and 0.92% ± 0.54 SD for its volume. The 3D geometry of the rock only differed by 1.2 mm ± 0.8 SD from the ultra-high resolution in-air reference. These results suggest that this simple and cost-effective protocol produces accurate and reproducible models that are suitable for the study and monitoring of marine habitats at a small reef scale

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

Spatially Explicit Seagrass Extent Mapping Across the Entire Mediterranean

The Posidonia oceanica seagrass is the foundation species of the coastal Mediterranean, whose meadows support significant ecosystem services: food security, coastal protection, biodiversity maintenance, carbon sequestration, amongst others. This endemic in the basin seagrass features the largest carbon storage among seagrasses globally, contributing substantially to global blue carbon stocks.  However, climate change, coastal development, and decreasing water quality all render this slow-growing species at risk of area loss, functional extinction, and, hence, its provided services. This risk is further complicated by the current knowledge gaps in its bioregional extent, necessitating accurate, efficient and spatially explicit mapping and accounting of its distribution and trajectories at a high spatial resolution. Here, we leveraged recent Earth Observation advances—cloud computing, open satellite data, and machine learning—with field data via a cloud-based ecosystem accounting framework to map the spatially-explicit ecosystem extent of P. oceanica seagrass across the whole Mediterranean, at 10m resolution.  Employing 279,186 Sentinel-2 satellite images between 2015-2019, and a human-labelled training dataset of 62,928 pixels, we mapped 19,020 km2 of P. oceanica seagrass area in 22 countries across 56,783 km2 of mapped seabed between 0-25 m of depth. Based on 2,480 independent field-based points, we observe an overall accuracy of 72%. Using a Tier 2 assessment, we estimated the bioregional blue carbon storage of P. oceanica beds to be 722.2 million MgC.  As reference data collections, remote sensing technology and biophysical modelling improve and coalesce, such extent accounts could support physical and monetary accounting of seagrass condition and ecosystem services. We envisage that such holistic seagrass ecosystem accounts could enable effective policy uptake in national climate, biodiversity and protection strategies and necessary financing. This in turn could accelerate transparent natural climate solutions and coastal resilience, beyond the physical location of seagrass beds and the 21th century

Ecologie de la transmission de parasites (virus, nématodes) au sein d'une communauté de rongeurs cycliques. Conséquences pour la santé humaine.

Several rodent species exhibit cyclic variations of their population densities. These demographic cycles, by increasing contacts between humans and animals, can influence the emergence of zoonoses. This thesis takes part in conservation medicine. This approach aims to study human health by considering also animal health and ecosystem dynamics. In this context, I studied a community of parasites found in a community of cyclic rodents to identify the reservoirs of zoonosis agents and the parasites, which may have a role in rodent demographic cycles. I focused on a rodent community including the fossorial water voles, the common voles, the bank voles, the yellow necked mice and the wood mice in Franche-Comté (East of France). The results and the epizootiologic surveys presented here bring insights into the biotic and abiotic risks associated with emergence of zoonoses.Three zoonosis agents were detected: two hantaviruses (Puumala virus and Tula virus) and Cowpox virus. Host dispersal and social behaviour are important for the transmission of the specific hantaviruses and of the non specific Cowpox virus. These viruses are principally detected in forest area. Rodents from forested areas present a different parasite community from rodents found in meadows. Infestations with helminths are more frequent in meadows than in forest. An immunogenetic study revealed susceptibility or resistance alleles for viral infections. Helminths and mites could also have a protective or an enhancing role in viral infections. One of these helminths could have a role in its host dynamics. Using experimental work and modelling, I demonstrate the impact of the non specific nematode T. arvicolae on common vole fecundity and its regulator role for arvicoline populations. This thesis provides essential knowledge to evaluate the importance of biodiversity and community ecology in the management of human zoonosis risk factors.De nombreuses espèces de rongeurs montrent des variations cycliques de leurs densités. Ces cycles ont un rôle important dans l'émergence de zoonoses en augmentant les contacts entre l'Homme et l'animal. Cette thèse s'inscrit dans le domaine de l'écologie de la santé qui étudie les interactions entre santé humaine, santé animale et dynamique des écosystèmes. Dans ce cadre, j'ai étudié la communauté de parasites d'une communauté de rongeurs à dynamique cyclique afin d'identifier les réservoirs d'agents de zoonoses et les parasites potentiellement impliqués dans les cycles de cette communauté. Je me suis intéressée à trois espèces de campagnols et à deux espèces de mulots en Franche-Comté. Les résultats et les suivis épizootiologiques réalisés permettent d'inférer les facteurs de risques biotiques et abiotiques associés à l'émergence de ces zoonoses.Trois agents de zoonoses sont présents : deux hantavirus (virus Puumala et Tula) et le virus Cowpox. La dispersion et le comportement social des rongeurs sont importants pour la transmission de ces virus spécifiques (hantavirus) et non spécifique (virus Cowpox). Ces virus sont majoritairement trouvés en milieu forestier. Les communautés de parasites détectées en forêt et en prairie sont différentes. Les infestations par des helminthes sont plus nombreuses en prairie qu'en forêt. Une étude immunogénétique montre l'existence d'allèles de susceptibilité et de résistance aux agents de zoonoses étudiés. Des helminthes ou des acariens pourraient aussi intervenir dans l'infection par ces virus. Un de ces helminthes pourrait être impliqué dans la dynamique de ses hôtes. Mes travaux expérimentaux et de modélisation montrent l'impact du nématode non spécifique Trichuris arvicolae sur la reproduction du campagnol des champs et son rôle régulateur pour les populations d'arvicolinés. Cette thèse contribue à montrer l'importance de la biodiversité et de l'écologie des communautés pour évaluer et gérer les risques pour l'Homme vis-à-vis de zoonoses

Les récifs coralligènes, un habitat sous-marin riche en biodiversité mais vulnérable

International audienceMots-clefs : biodiversité marine, méditerranée, plongée, bio-concrétions, DCSMM Mis en ligne le 11 Avril 2016 sur https://www.sfecologie.org/regard/r66-recifs-coralligeneshabitat-marin-riche-biodiversite-vulnerable-f-holon-j-deter

Parasitisme

National audienc

Identifying key-conservation areas for Posidonia oceanica seagrass beds

International audienc

Dynamique et diversité des habitats coralligènes et des herbiers de posidonie en Méditerranée

International audienc

Evolutionary landscape epidemiology

International audienceInfectious diseases have long been studied by scientists and public managers from clinical points of view, including causes of diseases, prevention of illness, or means to facilitate recovery. These last decades, our understanding of disease occurrence and dynamics has been improved by the recognition of an unequal distribution of parasites in space and of relationships between environmental factors and disease cases. This has led to the development of ‘landscape or spatial epidemiology’, a fi eld of research which can be traced back to John Snow’s work on cholera in London (Snow 1855 ) . By projecting case reports on maps, Snow highlighted that all cases were clustered around a street pump and deduced that cholera was a water-borne pathogen. Later, considering the infl uence of biotic and abiotic factors on ecological processes, Pavlovsky ( 1966 ) stated that landscape strongly affects the spatiotemporal distribution, abundance, and dispersal of hosts and parasites. Landscape epidemiology was then proposed as an integrative approach that aimed to understand the spatial spread of disease agents by analysing both spatial patterns and environmental risk factors (Pavlovsky 1966 ) . The ‘BAM diagram’ introduced for host–parasite interactions by Soberon and Peterson ( 2005 ) provides a useful conceptual framework for understanding the geography of diseases at the scale of the landscape (Fig. 13.1a ) . It predicts that the distribution of a species (i.e. a parasite) is the overlap between favourable biotic conditions (i.e. presence of competent hosts and other interacting parasites), abiotic factors (i.e. temperature) controlling the survival of free-living stages, and mobility capacities allowing the presence of the species in the appropriate areas. These last years, landscape epidemiology and the modelling of disease dynamics have largely benefi ted from two scientifi c breakthroughs. New computing technologies such as geographic information systems or remote sensing have allowed important advances in infectious disease epidemiology. They are described in Part V of this book. Besides this, the combination of metapopulation theory (proposed by Levins 1969 ) and epidemiological models has greatly improved our understanding of disease dynamics. In these models, a metapopulation of parasites is described as a set of populations distributed over distinct patches represented by either host individuals or host populations, and connected to varying degrees by dispersal (Hess 2002 ; Fig. 13.1b ) . This framework has provided fundamental predictions about the probability of disease diffusion or persistence in different situations (e.g. Ostfeld et al . 2005 f or a r eview)

Mieux connaître la biodiversité européenne pour mieux la protéger : l’exemple des récifs coralligènes méditerranéens

Article publié sur le site de la Fondation pour la Recherche sur la Biodiversité https://www.fondationbiodiversite.fr/wp-content/uploads/2019/06/FRB-biodiversite-corail.pdfInternational audienceA l’instar des récifs coralliens des pays tropicaux, les récifs coralligènes, dénommés ainsi pour le corail rouge qu’ils abritent, ont tout pour devenir un emblème pour les pays côtiers Méditerranéens. En effet, la riche et belle biodiversité qu’ils abritent présente un intérêt de conservation en soi, mais aussi des avantages pour la pêche et le tourisme. Les connaissances sur ces écosystèmes sont longtemps restées par-cellaires, mais se développent aujourd’hui, soulignant la beauté et la vulnérabilité de ces habitats