High-Resolution Vertical Habitat Mapping of a Deep-Sea Cliff Offshore Greenland

Recent advances in deep-sea exploration with underwater vehicles have led to the discovery of vertical environments inhabited by a diverse sessile fauna. However, despite their ecological importance, vertical habitats remain poorly characterized by conventional downward-looking survey techniques. Here we present a high-resolution 3-dimensional habitat map of a vertical cliff hosting a suspension-feeding community at the flank of an underwater glacial trough in the Greenland waters of the Labrador Sea. Using a forward-looking set-up on a Remotely Operated Vehicle (ROV), a high-resolution multibeam echosounder was used to map out the topography of the deep-sea terrain, including, for the first time, the backscatter intensity. Navigational accuracy was improved through a combination of the USBL and the DVL navigation of the ROV. Multi-scale terrain descriptors were derived and assigned to the 3D point cloud of the terrain. Following an unsupervised habitat mapping approach, the application of a K-means clustering revealed four potential habitat types, driven by geomorphology, backscatter and fine-scale features. Using groundtruthing seabed images, the ecological significance of the four habitat clusters was assessed in order to evaluate the benefit of unsupervised habitat mapping for further fine-scale ecological studies of vertical environments. This study demonstrates the importance of a priori knowledge of the terrain around habitats that are rarely explored for ecological investigations. It also emphasizes the importance of remote characterization of habitat distribution for assessing the representativeness of benthic faunal studies often constrained by time-limited sampling activities. This case study further identifies current limitations (e.g., navigation accuracy, irregular terrain acquisition difficulties) that can potentially limit the use of deep-sea terrain models for fine-scale investigations

Monitoring ecological dynamics on complex hydrothermal structures: A novel photogrammetry approach reveals fine‐scale variability of vent assemblages

We set out to characterize the fine-scale processes acting on interannual dynamics of deep-sea vent fauna by using a novel approach involving a 5-yr time series of 3D photogrammetry models acquired at the Eiffel Tower sulfide edifice (Lucky Strike vent field, Mid-Atlantic Ridge). Consistently, with the overall stability of the vent edifice, total mussel cover did not undergo drastic changes, suggesting that they have been at a climax stage for at least 25 yr based on previous data. Successional patterns showed consistency over time, illustrating the dynamic equilibrium of the ecological system. In contrast, microbial mats significantly declined, possibly due to magmatic events. The remaining environmental variability consisted of decimeter-scale displacement of vent outflows, resulting from their opening or closure or from the progressive accretion of sulfide material. As a result, vent mussels showed submeter variability in the immediate vicinity of vent exits, possibly by repositioning in response to that fine-scale regime of change. As former studies were not able to quantify processes at submeter scales in complex settings, this pioneering work demonstrates the potential of 3D photogrammetry models for conducting long-term monitoring in the deep sea. We observed that the ability of mussels to displace may enable them to cope with changing local conditions in a stable system. However, the long-term stability of mussel assemblages questions their capacity to withstand large-scale disturbances and may imply a low resilience of these “climax” communities. This suggests that they may be particularly vulnerable to the negative effects of mining activities in hydrothermal ecosystems

Convolutional neural networks for hydrothermal vents substratum classification: An introspective study

The increasing availability of seabed images has created new opportunities and challenges for monitoring and better understanding the spatial distribution of fauna and substrata. To date, however, deep-sea substratum classification relies mostly on visual interpretation, which is costly, time-consuming, and prone to human bias or error. Motivated by the success of convolutional neural networks in learning semantically rich representations directly from images, this work investigates the application of state-of-the-art network architectures, originally employed in the classification of non-seabed images, for the task of hydrothermal vent substrata image classification. In assessing their potential, we conduct a study on the generalization, complementarity and human interpretability aspects of those architectures. Specifically, we independently trained deep learning models with the selected architectures using images obtained from three distinct sites within the Lucky-Strike vent field and assessed the models' performances on-site as well as off-site. To investigate complementarity, we evaluated a classification decision committee (CDC) built as an ensemble of networks in which individual predictions were fused through a majority voting scheme. The experimental results demonstrated the suitability of the deep learning models for deep-sea substratum classification, attaining accuracies reaching up to 80% in terms of F1-score. Finally, by further investigating the classification uncertainty computed from the set of individual predictions of the CDC, we describe a semiautomatic framework for human annotation, which prescribes visual inspection of only the images with high uncertainty. Overall, the results demonstrated that high accuracy values of over 90% F1-score can be obtained with the framework, with a small amount of human intervention

Workshop on 3D mapping of habitats and biological communities with underwater photogrammetry

For the past decades, photogrammetry has been increasingly used for monitoring spatial arrangement or temporal dynamics of submerged man-made structures and natural systems. As photogrammetry remains a nascent technique for data collection in the underwater environment, acquisition workflows have evolved constrained by specific methodological practicalities (e.g. euphotic environments vs. deep-sea waters). The annual GeoHab conference gathers a world-wide range of scientists interested in mapping and is, therefore, an adequate event to set up a state-of-the-art workshop on (underwater) photogrammetry. More specifically, a preliminary survey identified the overall lack of photogrammetry knowledge from the audience. A programme was conceptualised to explore within a day theoretical concepts, sampling design and practicalities and a wide range of case studies in various underwater environments. Furthermore, we provided manual training on data acquisition and processing. In overall, a post-survey demonstrated the audience’s satisfaction despite a remaining lack of confidence for implementing their own photogrammetry studies. As this workshop gathers a diversity of materials and a training relevant for a scientific audience, it sets the stage for a reproducible event and leaves room for future improvements. Finally, it provided relevant materials and discussions that enabled us to identify the aspects limiting photogrammetry methodology across scientific applications and institutes, in order to work towards standardisation

COBRA Master Class: Providing deep-sea expedition leadership training to accelerate early career advancement

Leading deep-sea research expeditions requires a breadth of training and experience, and the opportunities for Early Career Researchers (ECRs) to obtain focused mentorship on expedition leadership are scarce. To address the need for leadership training in deep-sea expeditionary science, the Crustal Ocean Biosphere Research Accelerator (COBRA) launched a 14-week virtual Master Class with both synchronous and asynchronous components to empower students with the skills and tools to successfully design, propose, and execute deep-sea oceanographic field research. The Master Class offered customized and distributed training approaches and created an open-access syllabus with resources, including reading material, lectures, and on-line resources freely-available on the Master Class website (cobra.pubpub.org). All students were Early Career Researchers (ECRs, defined here as advanced graduate students, postdoctoral scientists, early career faculty, or individuals with substantial industry, government, or NGO experience) and designated throughout as COBRA Fellows. Fellows engaged in topics related to choosing the appropriate deep-sea research asset for their Capstone “dream cruise” project, learning about funding sources and how to tailor proposals to meet those source requirements, and working through an essential checklist of pre-expedition planning and operations. The Master Class covered leading an expedition at sea, at-sea operations, and ship-board etiquette, and the strengths and challenges of telepresence. It also included post-expedition training on data management strategies and report preparation and outputs. Throughout the Master Class, Fellows also discussed education and outreach, international ocean law and policy, and the importance and challenges of team science. Fellows further learned about how to develop concepts respectfully with regard to geographic and cultural considerations of their intended study sites. An assessment of initial outcomes from the first iteration of the COBRA Master Class reinforces the need for such training and shows great promise with one-quarter of the Fellows having submitted a research proposal to national funding agencies within six months of the end of the class. As deep-sea research continues to accelerate in scope and speed, providing equitable access to expedition training is a top priority to enable the next generation of deep-sea science leadership

Etude par l'imagerie de la distribution spatio-temporelle multi-échelles des communautés benthiques associées au champ hydrothermal Lucky Strike

The multi-scale characterisation of ecosystem variability is fundamental to the conceptualisation of dynamic models. Since its discovery in 1993, the Lucky Strike vent field has been extensively studied, making it one of the most well-known hydrothermal area of the World’s ocean. However, remote access has limited -in space and time- the scope of the studies, preventing an integrated understanding of the ecosystem. Using new technologies, this thesis aims to unravel the relative role of processes driving the dynamics of biological communities at Lucky Strike over different spatial scales: at the assemblage, the edifice and the field scales. The monitoring of the faunal assemblages of the Eiffel Tower hydrothermal edifice were carried out at sub-annual scales through the EMSO Azores observatory and pluri-annually based on photogrammetric reconstructions. These surveys have revealed a limited intensity and number of disturbances to which the hydrothermal fauna is subjected. Decadal variability restricted to emission areas had little impact on the dominant engineer species Bathymodiolus azoricus, because of its mobility. Considering the stable distribution of species over a decade, the remarkable scale invariance (from m² to the edifice) could explain why this community has reached a climax stage maintained for at least 25 years. Finally, analysis of the factors controlling the distribution of benthic vent and peripheral communities at the scale of the field showed the importance of habitat heterogeneity over a hundred of metres. These results suggest a strong structuring and a low resilience of hydrothermal ecosystems to any potential large-scale disturbance on the Mid-Atlantic Ridge.La caractérisation multi-échelle de la variabilité d’un écosystème est fondamentale à la conceptualisation de modèles de dynamique. Depuis sa découverte en 1993, le champ hydrothermal profond Lucky Strike a fait l’objet d’un grand nombre d’études, ce qui en fait l’une des zones hydrothermales les mieux connues. La difficulté d’accès a toutefois limité la compréhension intégrée de l’écosystème dans le temps et l’espace. A l’aide de nouvelles technologies d’observation, cette thèse vise à comprendre l’influence des processus régissant la dynamique des communautés de Lucky Strike à différentes échelles spatiales : l’assemblage, l’édifice et le champ. Les suivis d’assemblages de faune de l’édifice Tour Eiffel ont été effectués aux échelles infra-annuelle grâce à l’observatoire EMSO Açores pluri-annuelle à partir de reconstructions photogrammétriques. Ils ont révélé l’intensité et le nombre limités des perturbations auxquelles est soumise la faune hydrothermale. La variabilité décimétrique restreinte aux zones d’émissions a peu d’impact sur l’espèce dominante Bathymodiolus azoricus, de par sa mobilité. La distribution des espèces n’ayant pas changé sur une décennie, cette invariance d’échelle (du m² à l’édifice) expliquerait que cette communauté ait atteint un stade de climax depuis au moins 25 ans. Enfin, à l’échelle du champ, l’analyse de la distribution préférentielle de la faune hydrothermale et périphérique a rendu compte de l’importante hétérogénéité de l’habitat sur une centaine de mètres. Ces résultats suggèrent une forte structuration et une faible résilience des écosystèmes hydrothermaux à de potentielles perturbations d’envergure sur la dorsale médio-Atlantique

Etude par l'imagerie de la distribution spatio-temporelle multi-échelles des communautés benthiques associées au champ hydrothermal Lucky Strike

The multi-scale characterisation of ecosystem variability is fundamental to the conceptualisation of dynamic models. Since its discovery in 1993, the Lucky Strike vent field has been extensively studied, making it one of the most well-known hydrothermal area of the World’s ocean. However, remote access has limited -in space and time- the scope of the studies, preventing an integrated understanding of the ecosystem. Using new technologies, this thesis aims to unravel the relative role of processes driving the dynamics of biological communities at Lucky Strike over different spatial scales: at the assemblage, the edifice and the field scales. The monitoring of the faunal assemblages of the Eiffel Tower hydrothermal edifice were carried out at sub-annual scales through the EMSO Azores observatory and pluri-annually based on photogrammetric reconstructions. These surveys have revealed a limited intensity and number of disturbances to which the hydrothermal fauna is subjected. Decadal variability restricted to emission areas had little impact on the dominant engineer species Bathymodiolus azoricus, because of its mobility. Considering the stable distribution of species over a decade, the remarkable scale invariance (from m² to the edifice) could explain why this community has reached a climax stage maintained for at least 25 years. Finally, analysis of the factors controlling the distribution of benthic vent and peripheral communities at the scale of the field showed the importance of habitat heterogeneity over a hundred of metres. These results suggest a strong structuring and a low resilience of hydrothermal ecosystems to any potential large-scale disturbance on the Mid-Atlantic Ridge.La caractérisation multi-échelle de la variabilité d’un écosystème est fondamentale à la conceptualisation de modèles de dynamique. Depuis sa découverte en 1993, le champ hydrothermal profond Lucky Strike a fait l’objet d’un grand nombre d’études, ce qui en fait l’une des zones hydrothermales les mieux connues. La difficulté d’accès a toutefois limité la compréhension intégrée de l’écosystème dans le temps et l’espace. A l’aide de nouvelles technologies d’observation, cette thèse vise à comprendre l’influence des processus régissant la dynamique des communautés de Lucky Strike à différentes échelles spatiales : l’assemblage, l’édifice et le champ. Les suivis d’assemblages de faune de l’édifice Tour Eiffel ont été effectués aux échelles infra-annuelle grâce à l’observatoire EMSO Açores pluri-annuelle à partir de reconstructions photogrammétriques. Ils ont révélé l’intensité et le nombre limités des perturbations auxquelles est soumise la faune hydrothermale. La variabilité décimétrique restreinte aux zones d’émissions a peu d’impact sur l’espèce dominante Bathymodiolus azoricus, de par sa mobilité. La distribution des espèces n’ayant pas changé sur une décennie, cette invariance d’échelle (du m² à l’édifice) expliquerait que cette communauté ait atteint un stade de climax depuis au moins 25 ans. Enfin, à l’échelle du champ, l’analyse de la distribution préférentielle de la faune hydrothermale et périphérique a rendu compte de l’importante hétérogénéité de l’habitat sur une centaine de mètres. Ces résultats suggèrent une forte structuration et une faible résilience des écosystèmes hydrothermaux à de potentielles perturbations d’envergure sur la dorsale médio-Atlantique

Étude comportementale de différentes espèces de poisson dans un modèle réduit de la passe à bassins multi-espèces de Rivière en Meuse belge

Dans le cadre de la restauration de la continuité écologique de la Meuse, un modèle réduit d’une passe à poissons a été construit à l’échelle 1 : 5, à la Direction des Recherches Hydrauliques du Service Public de Wallonie, dans le but de proposer des aménagements qui seront appliqués au dispositif de franchissement de Rivière. Faisant suite à une modélisation numérique de l’écoulement et à une expérimentation comportementale avec des salmonidés, cette étude a pour objectif d’évaluer la pertinence expérimentale d’utiliser diverses espèces dans un modèle réduit d’une passe afin de vérifier son caractère multispécifique souvent peu considéré par les critères de dimensionnement. Pour ce faire, diverses espèces mosanes (saumon, chevaine, ablette et chabot) ont été introduites dans le dispositif. Des caméras ont été placées au-dessus de quelques bassins au design standardisé dans le but de collecter des informations visuelles relatives au comportement des poissons dans ces bassins. L’élaboration d’un protocole de traitement d’image a permis de distinguer certaines zones préférentiellement occupées par les poissons, de déterminer certaines trajectoires réalisées par des individus ainsi que de quantifier les vitesses relatives des poissons dans les bassins. La difficulté des petits chabots à se maintenir dans l’écoulement a notamment été mise en avant. Par ailleurs, un système RFID a été disposé tout le long du modèle dans le but de retracer les déplacements des poissons dans la passe. L’objectif est d’évaluer la capacité spécifique de franchissement grâce à des indicateurs relatifs au processus de remontée. Les résultats montrent la capacité à remonter pour les chevesnes et les saumons, l’envisagent pour les ablettes mais la questionnent pour les chabots. En outre, les influences de la photopériode, de la répétition des remontées et de la longueur des poissons sur les franchissements sont aussi étudiées. Pour les chevesnes, des tendances à remonter durant la nuit avec un maximum d’activité après la fin du jour et à réaliser des remontées plus rapides après la première sont observées mais aucun effet marqué de la taille ne se démarque. Finalement, la méthode expérimentale utilisée montre des résultats plus satisfaisants pour les saumons et les chevaines que pour les ablettes et les chabots en raison de divers facteurs biologiques.Master [120] : ingénieur civil des constructions, Université catholique de Louvain, 201

Performance of a fish pass for multiple species: Scale model investigation

Artificial fish passes are often the most effective solution to restore the ecological continuity of a dammed river. Such a pass can be built for specifically targeted fish species, based on the existing knowledge on its swimming capacity and behaviour. Usually, a wider range of possible species are present in the river and may use the fish pass. In the present study, a vertical slot fish pass has been designed for salmonid fish (namely Atlantic salmon Salmo Salar). This fish pass layout was initially tested using a scale model where juvenile fish were introduced. The study has now been extended to other species, some of them having weaker swimming capacity: bleak (Alburnus alburnus); chub (Squalius cephalus); and bullhead (Cottus gobio). Fish behaviour in the pass was observed using PIT-tag and video. PIT-tag tracking enabled to characterise the capability of the fish to cross the whole fish pass. Video recording was used to analyse in more details the behaviour of the fish in a specific pool

Performance of a fish pass for multiple species: Scale model investigation

Artificial fish passes are often the most effective solution to restore the ecological continuity of a dammed river. Such a pass can be built for specifically targeted fish species, based on the existing knowledge on its swimming capacity and behaviour. Usually, a wider range of possible species are present in the river and may use the fish pass. In the present study, a vertical slot fish pass has been designed for salmonid fish (namely Atlantic salmon Salmo Salar). This fish pass layout was initially tested using a scale model where juvenile fish were introduced. The study has now been extended to other species, some of them having weaker swimming capacity: bleak (Alburnus alburnus); chub (Squalius cephalus); and bullhead (Cottus gobio). Fish behaviour in the pass was observed using PIT-tag and video. PIT-tag tracking enabled to characterise the capability of the fish to cross the whole fish pass. Video recording was used to analyse in more details the behaviour of the fish in a specific pool