PhD student: Sandrine Fanfard, Thesis directors : Jean-Marc Guarini et François Charles
Thesis defended the 13th of December 2016

Either adrift or submerged, coarse debris derived from terrestrial plants provide energy and nutrients for marine ecosystems. By considering this allochtonous organic material, the goals of my PhD were to describe the assembly process of macrobenthic communities around food sources and to consider the feedback effect of the observed communities on the geochemical fate of the resource. To do so, I combined in situ experiments and modelling with the intention to build a consistent, quantitative description of the ecogeochemical link between biodiversity and ecosystem functioning. Using leaf litter and dead wood, this approach allowed: (i) to show the importance of biotic interactions from the beginning of the community assembly process, (ii) to make the explicit connection between the resource consumption and the population dynamics of the consumers, and (iii) and to test how resource processing is affected by the specific diversity of the communities.
PhD student: Claudia Maturana Martínez, Thesis directors: Pierre Galand et Umberto Gonzáles
Thesis defended the 19th of January 2022

Southern high latitudes marine ecosystems (HLME) are highly sensitive to climate change, impacting physical, chemical, and biological processes, however, their prominent role in climate modulation and water masses circulation, contrast with the relatively low number of studies on their functioning. Relatively few studies on bacterioplankton community structure have been reported for southern Chilean Patagonia and for the Southern Ocean (SO) on a large scale, and none have targeted the active fraction of the bacterioplankton community. We used 16S rRNA sequencing to analyze and describe the community structure of the active bacterioplankton communities in southern HLME. The main objective of this thesis was to characterize de diversity and abundance of bacterioplankton communities along environmental and geographical gradients in southern HLME. First, we investigated whether nearby fjords of the southern Chilean Patagonia, with similar climate and location but different freshwater inflows, had different communities. Second, we investigated interannual changes experienced by the bacterioplankton community of the Yendegaia fjord. Third, we examined the large-scale spatial structure of the bacterioplankton community along a transect across the Pacific sector of the SO. Ours results show that southern polar bacterioplanktonic communities are structured according to physical, chemical, and biological parameters characteristic of the area. In addition, we also demonstrated that changes in environmental, spatial, and temporal parameters affect the structure of bacterioplanktonic communities. Thus, highlighting the importance of microbial ecology studies in areas sensitive to global climate change such as southern HLME.
PhD student: Victor Le Layec, Thesis director : Stéphane Hourdez
Thesis defended

The Polynoidae (polychaeteous annelids) are found in all marine environments: in polar, temperate and tropical environments, and in coast areas, as well as in the great abyssal depths, including at deep hydrothermal vents and cold seeps. This diversity of habitats and the great number of specie represent a very good opportunity for comparative approaches to study adaptation in a controlled phylogenetic context. If all known species possess neuroglobin, only hydrothermal ones have hemoglobin circulating freely within their coelomic fluid. These hemoglobins exhibit a diversity of structures (tetradomaine or single-domain subunits) and a diversity of properties. The hemoglobins possess a high affinity for oxygen, which allows polynoids to extract oxygen from the environment, even when environmental concentrations are very low. This capacity allows hydrothermal vent species to maintain a stable oxygen consumption rate at low environmental concentrations (oxyregulators) while littoral species are oxyconformers. The presence of hemoglobin also represents an oxygen storage allowing the polynoids to withstand periods of anoxia experienced near deep-sea hydrothermal vents. They also likely play a role in the physiological temperature tolerance of hydrothermal species by allowing sufficient oxygen supply to meet the temperature-related increase in metabolism.

Keywords : Polynoidae, hemoglobins, deep-sea hydrothermal vents, hypoxia, comparative physiology, respiration.
PhD student: Elise Wissenaekens, Thesis director: Katell Guizien
Thesis defended the 19th of January 2022

To give sound management advice, the connectivity in coastal areas must be thoroughly understood. The red thread throughout this PhD is analysing the uncertainty of the SYMPHONIE2015 model and its effect on larval dispersal simulations. In the first chapter, the robustness of the model to assumption violation was tested. This was done by calculating six relative and absolute statistical indicators during and outside of wind, wave and stratification events. The results showed that the model’s performance is not affected by these events. In the second chapter, the instant error was calculated. Then, the cumulative error distributions were compared to each other in space and time. In time, the intraseasonal differences in error distributions were smaller than the interseasonal ones. In space, eight groups of error distributions could be formed. No link was found between the model’s performance and stratification, water depth, resolution and bathymetry slope. However, a strong correlation between the current speed and the error distributions was found. In chapter three, the instant error was added as noise to the Lagrangian dispersal simulations and compared to the original run to assess the effect of the models’ error on connectivity. The median difference in transfer rate between the runs with and without noise around zero. However, the relative difference in transfer rate can vary from -100% to 100%. Knowing the uncertainties in dispersal simulations can aid in using them for management advice.
PhD student: Corentin Hochard, Thesis director : Pierre Galand
Thesis defended the 30th of may 2023

Tropical coral reefs depend on complex microbial communities that drive biogeochemical cycles, maintain host health, and support ecosystem homeostasis. Understanding the complex ecology of coral reef microorganisms is essential for the preservation of these precious ecosystems. However, the precise functional role of the reef microbial communities remains poorly known. In particular, the association between corals and bacteria of the Endozoicomonadaceae family, believed to be a crucial coral bacterial symbiont, is still not well defined. Microorganisms such as Endozoicomonadaceae appear essential for the survival of the adult coral host, but larval settlement is another important element for the corals’ fitness. The success of larval recruitment has recently been shown to depend on the Crustose Coraline Algae (CCA) on which they settle. More precisely, microbial communities associated with CCAs may play a crucial role, yet we know very little about these communities. The overall objectives of this thesis were to study the species diversity and the functional potential of the microbial communities associated with tropical corals and crustose coralline algae (CCA). Chapter 2 focused on Endozoicomonadaceae associated to three coral species across the Pacific Ocean. It revealed that different coral species exhibit distinct strategies of host-symbiont relationships. We identified three new symbiont species, each with distinct functional adaptations that may drive the host-symbiont relationship. The environment had generally only a small effect on Endozoicomonadaceae community composition, while the genetic lineage of the host was important in some corals. We suggest that the relation between Endozoicomonadaceae and the coral can range from stable co-dependent relationships to opportunistic associations. In Chapter 3, we described the microbial communities associated to different CCA species across spatial scales and defined the factors controlling their composition. We also tested if their were some links between the CCA and coral larvae microbial communities. Our results suggest that the CCA microbiome does not act as a microbial reservoir for the developing coral larvae. However, we observed that the microbial communities of coral recruits differed depending on their association with different types of algae. We conclude that CCAs and their associated bacteria influence the composition of the coral recruits’ microbiome. Additionally, we showed that different CCA species exhibit distinct microbial communities, with potential signal of phylosymbiosis, suggesting adaptability of the microbiome through evolutionary time. In Chapter 4, we studied the functional potential of CCA microbial communities. We demonstrate that CCA harbor distinct functional communities despite sharing a strong core functional metabolisms. The microbial community of the two CCA species that we targeted did not show clear differences in their ability to produce coral larvae inducers. However, inducing functional capabilities were not homogenous across microbial genera between CCA species. We suggest that microbial communities do not directly determine the behaviour of larvae settlement, but rather enhance or mitigate the response induced by the CCA and the environment.