Understanding how diversity is partitioned along natural and anthropogenic gradients within ecosystems is important to predict the persistence of species and the ecological functions they provide. Dottybacks (Pseudochromidae) are a diverse group of mesopredators that feed on cryptic macroinvertebrates and newly recruited fishes. This diet behavior may modify the composition and abundance of cryptobenthic fauna within coral reef ecosystems. Understanding how mesopredators partition their diet and the functional role provided by available prey within reefs can assist in understanding the ecological role these predators contribute to coral reef trophodynamics and the effect of their population changes on the reef ecosystem. To assess the diet of three common Pseudochromis species and two distinct color morphs of P. flavivertex in the Red Sea, I used a combination of i) visual stomach content analysis, ii) stomach DNA metabarcoding (18S, COI), and iii) stable isotope analysis (δ15N, δ13C). I evaluated i) dietary niche breadth, ii) variation in diet composition, iii) degree of dietary specialization, and iv) trophic level. These techniques revealed partitioning in the dietary composition and resource use between P. flavivertex, P. fridmani, and P. olivaceus. Although the two technics used for stomach content analysis did not show differences in the dietary composition within color morphs of P. flavivertex, the isotopic signature showed marked differences in the isotopic niche and resource use between morphs. Resource partitioning appears to be driven by variation in resource availability in the fish habitat and by subtle differences in the ecology of these species. These findings provide evidence of species-specific differences in the trophic ecology of pseudochromids in the Red Sea and demonstrate their important role as predators of cryptic invertebrates and small fish, being key components in energy transfer in coral reef ecosystems by acting as a link between cryptofauna and higher trophic levels. This study highlights the importance of combining several approaches (short-term: visual analysis and DNA metabarcoding; and long-term: isotope analysis) when assessing the feeding habits of coral reef fish, as they provide different and complementary information necessary to delimit their niches and understand the role that small mesopredators play in coral reef ecosystems.

Palynology or the study of pollen, is essential understand the relationship between plants and their pollinators. Traditionally, pollen grains are identified by microscopy. The method has several shortcomings, such as being time-consuming and having low taxonomic resolution. DNA-barcoding-based sequencing can identify pollen at the genus and species levels without specialized paleontological expertise. Aim of this study is to assess which molecular approach can be the most effective tool and is the most cost-effective for the identification of pollen from mixed pollen samples. A DNA metabarcoding study was conducted using the rbcL barcode gene for pollen identification using two sequencing techniques: Sanger and MinION. DNA metabarcoding produced taxonomic data easily. For the analysis of Sanger and MinION sequencing data, BLAST and KRAKEN2 were used respectively. Pavian and KRONA were later used to visualize the MinION sequencing data. Various plant species native to Sweden were identified with this metabarcoding approach. However, the reference database failed to identify a few of them, thus indicating the need to expand the reference database.

Understanding factors that influence a species' distribution and abundance across their annual cycle is needed for range-wide conservation planning. Every year during spring migration, thousands of federally threatened (U.S.A.) and endangered (Canada) migratory Western Atlantic red knots (Calidris canutus rufa, 'red knot') use Virginia's barrier islands as stopover habitat to regain the fat required to continue flights to breeding grounds. Because the red knot completes one of the longest avian migrations in the world and relies on variable prey resources at its stopover grounds, the red knot exemplifies the challenges faced by long-distance migrant shorebirds. These challenges may be exacerbated by climate change, as long-distance migrants may be unable to adapt quickly to changing prey ranges and abundances, resulting in spatial and temporal mismatches between predators and prey. More specifically, as climate change causes ocean temperatures near Virginia's barrier islands to rise, organisms that live within the intertidal zone, like blue mussels (Mytilus edulis), are experiencing range shifts. Here, we 1) confirmed what prey red knots select in Virginia, 2) addressed the factors that affect red knot site selection, red knot flock size, and prey abundances across Virginia's barrier island intertidal shoreline during 2007 – 2018, and 3) predicted the origin of juvenile blue mussels, a key prey resource for red knots in Virginia. To determine which prey are most available to red knots in Virginia, we collected sand and peat substrate core samples from Virginia's ocean intertidal zone and counted the number of prey in each sample. We compared these prey availability data to prey DNA data obtained from fecal DNA metabarcoding analyses on red knot feces (n = 100) collected on peat and sand substrates between 2017 – 2019. Red knots consumed prey from Orders Veneroida (clams), Mytiloida (mussels), Diptera (flies), and Amphipoda/Calanoida (crustaceans). While crustaceans were the most abundant prey on both sand (70.80% of total prey counted) and peat (74.88%) substrates, red knots selected crustaceans less than expected given their availability. Red knots selected clams and mussels, supporting their status as bivalve specialists in Virginia. After determining which prey red knots consumed and selected in Virginia, we predicted the number of red knots using Virginia's barrier island stopover during their migratory stopover (May 14 – 27, 2007 – 2018) annually. We used confirmed prey, tide, distance to known roosts, and red knot winter counts from Tierra del Fuego to inform zero-inflated negative binomial mixed-effects regression models of red knot site selection and flock size in Virginia. We also used generalized linear mixed-effects regression models to determine how climatic and geomorphological factors affected prey abundances. Modeled red knot peak counts were highest in 2012 (11,644) and lowest in 2014 (2,792; x̄ = 7,055, SD = 2,841); the trend over time was variable but there was no evidence of a linear increase or decrease. Red knots selected foraging locations with more prey, though red knot flock size did not consistently relate to prey abundance. Tide, substrate, and water temperature affected prey availability. While different prey responded to these covariates in variable ways, prey generally were most abundant on peat banks at low tide. Given the importance of blue mussels in the red knot's diet and distribution in Virginia, if the blue mussel's range continues to contract northward, red knots could be faced with additional fat replenishment challenges. We analyzed the variation in blue mussels from 2010 – 2018 by collecting core samples on peat banks in Virginia and counting the number of blue mussels in the cores. To approximate the origin of Virginia's juvenile blue mussels and determine how continued ocean temperature warming may further affect the blue mussel's range contraction, we conducted oxygen stable isotope (δ¹⁸O_c) analyses on 74 blue mussel shell umbos (the first portion of the shell precipitated) and shell edges (the most recently precipitated shell) to compare and predict where different portions of the shell were formed. We compared blue mussel shell compositions to δ¹⁸O_c calculated in equilibrium with regional ocean water using recorded δ¹⁸O_w data and sea surface temperature data from ocean buoys between New Hampshire and Virginia. Blue mussel abundance/core sample declined over the duration of our study (Spearman's rank correlation coefficient: ρ(rho) = -0.31, p < 0.001), with the highest abundance in 2010 (x̄ blue mussels/core sample = 537.88, SE = 85.85) and lowest in 2016 (x̄ = 34.08 blue mussels/core sample, SE = 6.96). Blue mussel umbos (x̄ δ¹⁸O_c = -0.23‰, SE = 0.12) contained more positive δ18Oc than shell edges (x̄ δ¹⁸O_c = -0.53‰, SE = 0.20), suggesting that Virginia's blue mussels originated from ocean populations in more saline and/or colder water than that within Virginia's intertidal zone. Blue mussel umbo δ¹⁸O_c were not different than δ¹⁸O_c calculated in equilibrium with regional ocean water off the Virginia and Delaware coasts, suggesting that Virginia's blue mussels originated in ocean waters between Delaware and Virginia; however, they may have originated in waters as far north as New York in some years, potentially decreasing the risk of blue mussels being completely extirpated from Virginia in the near future. While red knots currently use spring migratory stopovers across the United States' Atlantic Coast, from Florida to New Jersey, the largest spring concentrations of knots are confined to the Delaware Bay and Virginia's barrier islands. Because these stopover grounds support large proportions of the red knot's migratory population, any changes in the factors that affect red knots at these stopover sites could have lasting implications for red knots. The blue mussel's range contraction and decline over time in Virginia, for example, is concerning from a conservation perspective. Red knots require easily accessible and abundant prey resources to efficiently replenish fat-stores needed for continued migration and breeding. Additionally, because red knots breed within a narrow period, any delays on stopover grounds could prevent red knots from breeding, even if they survive migration. Our research demonstrates that red knots use prey abundance as a determinant when selecting foraging locations, and that peat banks, while only sporadically available across the barrier islands at mid- to low-tides, contain higher prey abundances than sand. Thus, to continue maximizing the availability of prey in Virginia, measures should continue to be taken to allow natural island migration processes that encourage the presence of both sand and peat substrates. Beach nourishment and stabilization projects are often used on coastal beaches to prevent shoreline erosion; however, such actions prevent the formation of peat banks by blocking island migration processes. A reduction in peat banks could decrease the abundance of prey available to red knots, making weight gain during the critical stopover period more challenging for red knots. Additionally, beach nourishment through sand replenishment buries invertebrate prey, potentially causing mass prey mortality and reducing shorebirds' ability to access deeply buried prey. To prevent the loss of important peat banks on these islands, and to prevent disrupting predator-prey interactions, managers should continue their ongoing focus on allowing natural processes to occur on Virginia's barrier islands. / Doctor of Philosophy / Red knots (Calidris canutus rufa) are imperiled shorebirds that migrate thousands of kilometers each year from wintering grounds as far south as Argentina to breeding grounds in the Canadian Arctic. To migrate such long distances, red knots use stopover habitat, like Virginia's barrier islands, to regain the fat required to continue flights to breeding grounds. Climate change is causing the ranges of important red knot prey, such as blue mussels (Mytilus edulis), to shift. Red knots may be unable to quickly adapt to changes in prey abundances on stopover grounds, making it more challenging for them to gain the weight required for successful migration and breeding. Thus, understanding the factors that may affect red knots in Virginia are important for successful management of this shorebird. Here, we determined what prey red knots consume in Virginia, addressed the factors that affect red knots in Virginia, and predicted the origin of blue mussels, an important prey resource for red knots in Virginia. We collected sand and peat substrate samples from Virginia's ocean intertidal zone to determine what prey were available to red knots and collected red knot feces to determine what prey red knots consume. Red knots consumed clams, mussels, fly larvae, and crustaceans in Virginia and showed preference for clams and mussels over the more abundant crustaceans. Red knots selected foraging locations that had higher prey abundances than unused sites. The relationship between red knots and prey was affected by the tidal cycle, with the highest abundance of prey available and most birds foraging at low tide when peat banks were exposed. After confirming that red knots preferentially consume blue mussels, which is experiencing a northward range contraction due to increasing ocean temperatures, we analyzed how blue mussel numbers have changed over time in Virginia. Blue mussel numbers declined over the duration of our study. We also analyzed blue mussel shells to help determine where the blue mussels were spawned, as shells contain environmental clues that relate to the conditions within which the shell forms. The juvenile blue mussels red knots consumed on Virginia's peat banks likely originated in ocean waters between Delaware and Virginia, but potentially in waters as far north as New York, possibly using ocean currents to travel to Virginia's intertidal zone. Because migratory stopovers, like Virginia's barrier islands, support a large percentage of the total red knot migratory population, any changes in factors that affect red knots during their spring stopover, like prey availability, may negatively affect red knots. Because red knots need to quickly consume large quantities of prey to gain the weight needed for continued migration and breeding, managers should continue to prevent factors that negatively affect prey in Virginia. For example, we found that peat banks support high quantities of red knot prey; thus, continuing to ensure that peat banks are able to form on the islands is paramount. However, peat banks form through shoreline erosion and overwash, two natural processes which are often portrayed negatively. Beach nourishment and stabilization projects are commonly used in other coastal areas to prevent shoreline erosion and overwash along coastal beaches. If Virginia's barrier island beaches are nourished, natural processes like shoreline erosion may be less likely to occur. The absence of shoreline erosion on Virginia's barrier islands would preclude the formation of peat banks, likely decreasing prey availability for red knots. Beach nourishment also buries invertebrate prey, as sand is deposited along the beaches' intertidal zone. The disturbance caused by nourishment combined with the reduction in prey caused by it could negatively affect red knots in Virginia. Managers should continue to protect both peat and sand substrates by further allowing natural processes, like shoreline erosion, to occur on Virginia's barrier islands.

Bien que très peu explorés, les fonds des océans pourraient représenter le futur de l’industrie minière mondiale. L’impact écologique de ces activités reste encore inconnu, notamment sur les cibles privilégiées que sont les systèmes hydrothermaux et leurs écosystèmes. Ce travail s’intéresse à la crevette Rimicaris chacei et à sa potentielle symbiose avec des bactéries hydrothermales. R. chacei présente une alimentation mixte, nécrophagie et symbiose, plasticité alimentaire qui pourrait être un atout en cas de modification de son environnement. La proximité phylogénétique et écologique de C. chacei avec une autre crevette hydrothermale, Rimicaris exoculata, laisse supposer une possible histoire commune de leurs symbioses. Deux compartiments biologiques des crevettes ont été étudiés au cours de ce travail, le céphalothorax et le tube digestif, via deux approches complémentaires: l’imagerie et la biologie moléculaire. Nous souhaitions répondre à deux questions principales (1) Décrire le type d’association entre la crevette et ses « symbiontes » d’un point de vue morpho-anatomique et phylogénétique. (2) Evaluer le degré de similarité entre les symbiontes de C. chacei, et R. exoculata via une approche de métabarcoding. Notre but est de déterminer si une possible variation de la distribution des symbiontes existe chez ces deux espèces en fonction du site hydrothermal d’origine (facteur environnemental), en fonction de l’espèce de crevette étudiée (facteur hôte), ou une association de ces deux facteurs. La bioinformatique ayant une part importante dans l’analyse des données de barcoding/metabarcoding, une partie du manuscrit lui est dédiée pour « désacraliser » ce type d’analyse. / Deep-sea ocean may soon represent deep-sea mining industry future. However, these environments are still poorly explored. Therefore, mining issues on deep-sea ecosystems are not yet evaluated, mostly on their main target: the deep-sea hydrothermal vents. Our study focused on a shrimp, Rimicaris chacei and to its potential symbioses with chemoautotrophic microbial communities.This shrimp have a mixotrophic behaviour, mixed between necrophagy and symbiosis. It could therefore have a potential trophic plasticity in case of steep environmental modifications. Moreover, C. chacei is closely related to Rimicaris exoculata, in terms of both phylogeny and ecology. This could let suppose a common symbiosis history, presenting nowadays two different levels of association.Two potential symbiotic microbial communities have been studied here, one located in the cephalothorax and the other in the digestive tract, using two complementary approaches: microscopy and molecular analyses. Two main points have been focused in our work: (1) Describing the shrimp and its associated microbial communities in terms of morphology, repartition and phylogeny. (2) Using a metabarcoding approach to evaluate the similarity level shared between C. chacei and R. exoculata associated microbial communities. We intend to analyse a possible genetic variation among symbionts of the two hosts, whether it would be linked to the hydrothermal vent origin (geography), or to the studied shrimp (host), or both of them. As bioinformatics was an important part of my work to analyse barcoding/metabarcoding data, a part of my thesis is dedicated to explain these analyses as a tutorial for all future users.

L’exposition aux polluants environnementaux a été associée à de nombreux désordres métaboliques, immunitaires et reproductifs ainsi qu’à divers cancers. De plus en plus de travaux, indiquent que le microbiote intestinal, qui joue un rôle majeur dans l’immunité et le métabolisme de l’hôte, interagit avec les xénobiotiques dont les polluants organiques persistants (POPs) et les contaminants néoformés dans les aliments. Cette interaction peut avoir des conséquences toxicologiques importantes via la modification des fonctions du microbiote intestinal mais également via la métabolisation des xénobiotiques, entraînant une potentielle altération de l'homéostasie de l'hôte. Dans le cadre de cette thèse, nous avons démontré, en modèle in vitro, qu’une exposition aigüe du microbiote intestinal humain au benzo[a]pyrène (hydrocarbure aromatique polycyclique) a entraîné une altération des fonctions du microbiote intestinal au niveau du volatolome et du métatranscriptome microbien. Cependant, dans nos conditions expérimentales, aucun impact sur la structure microbienne n'a été observé. L’Homme étant continuellement exposé à un panel de composés chimiques environnementaux, nous avons par la suite étudié l'impact de divers POPs et produits néoformés dans les aliments sur le microbiote intestinal humain. Des familles de gènes ainsi que des composés volatiles microbiens ont été identifiés comme altérés après l’exposition, conduisant à une perturbation de l'activité microbienne. Nous avons finalement démontré que l'interaction microbiote-polluant pourrait conduire à l'établissement d'un état pro-inflammatoire modéré dans l'intestin avec une libération de cytokine IL-8 par les cellules épithéliales intestinales. Ces résultats appuient le concept émergent selon lequel les contaminants alimentaires pourraient altérer les activités du microbiote intestinal. / Exposure to environmental pollutants has been associated with various life-threatening disorders, including dysregulation of the immune and reproductive systems, metabolic diseases and various cancers. Growing evidences indicate that the gut microbiota, which plays major roles in host metabolic and immune functions, interacts with xenobiotics including persistent organic pollutants (POPs) and foodborne chemicals. The toxicological relevance of the gut microbiota-pollutant interplay is of great concern for the host since the chemicals may disrupt the gut microbiota functions leading to a potential impairment of the host homeostasis. During this PhD thesis, we demonstrated that in vitro acute exposure of the human gut microbiota with benzo[a]pyrene (polycyclic aromatic hydrocarbon) led to an impairment of the gut microbiota functions with a specific shift of the microbial volatolome and metatranscriptome. However, in our experimental conditions, no impact on the microbial structure was observed. Since humans are exposed to a wide range of environmental chemicals we investigated the impact of various POPs and foodborne chemicals on the human gut microbiota. We identified microbial volatiles and gene families that shifted after this exposure leading to an imbalance of the microbial activity. Furthermore, we demonstrated that the interaction between the pollutants and the gut microbiota lead to a significant release of pro-inflammatory IL-8 cytokine by the intestinal epithelial cells which may contribute to the establishment of a low-grade inflammatory state in the gut. All together, these data support the emerging concept that food pollutants could alter the gut microbiota activities.

Les feuilles hébergent une grande diversité de micro-organismes. Parmi les facteurs responsables de la structuration des communautés microbiennes foliaires, l’effet du processus de dispersion reste peu étudié. Les structures paysagères telles que les lisières ou l’hétérogénéité du paysage influencent la migration et la dispersion de nombreuses espèces de macro-organismes, mais l’effet de tels facteurs sur la composition des communautés microbiennes foliaires n’a jamais été testé.Nous faisons l’hypothèse que les parcelles forestières sont une source de champignons foliaires pour les vignes adjacentes. Nous avons comparé les communautés fongique foliaires et aériennes de la vigne et des forêts adjacentes au cours d’une saison de végétation, testé l’effet d’une lisière forestière sur ces communautés et évalué l’effet de la composition du paysage sur ces communautés. Les communautés fongiques ont été caractérisées par métabarcoding.Les communautés fongiques foliaires viticoles et forestières divergent au cours de la saison. Ni la distance à la lisière, ni la proportion de forêt dans le paysage n’affectent les communautés foliaires de la vigne, mais les communautés aériennes diffèrent en fonction de la distance à la lisière forestière. Ces résultats suggèrent que la dispersion ne joue qu’un rôle mineur dans la structure des communautés fongiques foliaires. De nombreuses pressions de sélection telles que les pratiques agricoles semblent en revanche avoir un effet fort sur ces communautés. Des études supplémentaires sont nécessaires pour vérifier la contribution relative de ces pressions de sélection, ainsi que le potentiel service de régulation fourni aux cultures par la forêt. / Plant leaves host a large diversity of microorganisms. Among the factors shaping foliar microbial community structure, the effect of the dispersal process remain understudied. Landscape elements, such as edges or landscape heterogenity, influence migration and dispersal of many macro-organism species. However, the effect of such factors on foliar microbial communities has never been studied. We hypothesized that forests are a source of foliar fungi for adjacent vineyards. We compared foliar and airborne fungal communities in vineyard and adjacent forests along a vegetative season, we examined the effect of a forest edge on these communities in a vineyard, and weassessed the effect of landscape composition on these communities. Fungal communities were characterized with a metabarcoding method. Foliar fungal communities in vineyards and forests diverge over the course of the vegetative season. Neither the distance to the edge nor the proportion of forest in the landscape affect foliar fungal communities in vineyards, while airborne communities change with the distance to the forest edge. These results suggest that dispersal is not dominant in shaping foliar fungal communities. Instead, many selective pressures such as agricultural practices seem to shape strongly these communities. Further investigations are required in order to estimate the relative contribution of those processes, and the potential ecosystem service provided by the forest to crops.

Gut microbiota is considered an important factor in the development of various diseases including inflammatory bowel disease (IBD, n = 127), Ulcerative colitis, Crohn's disease, and colorectal cancer (CRC, n = 64). A part of this thtesis is to prepare clinical material of different sorts (stool, biopsy) for sequencing on Illumina Miseq platform. This is achieved trough DNA isolation, amplification of 16S and internal transcribed spacer (ITS), normalization and ligation of sequencing adaptors. The aim of this project is to describe the differences between microbiota in healthy and diseased subjects in case of IBD or unimpaired and tumorous tissue for CRC patients. This research is also being based on cultivation, where a fresh stool samples (n = 3) are cultivated in a broad range of conditions, which enables us to obtain ecophysiological and species diversity of these samples by traditional and molecular methods. The cultivable fungi are also assigned reliable taxonomy by amplification of relevant genes (ITS1, β tubulin, second largest subunit of RNA polymerase II, RPB2) followed by both-sided Sanger sequencing. Selected species of fungi are processed into lysates, which are used for stimulation of mice macrofage cell line (RAW). Therefore the impact on immunity response is studied in vitro and...

La biodiversité englobe toute la diversité des éléments du vivant des molécules à la biosphère et différents niveaux de biodiversité peuvent être distingués. Les habitats coralligènes sont des constructions biogènes calcaires emblématiques de la mer Méditerranée principalement construits par des espèces d’algues rouges calcaires puis consolidés par les squelettes calcaires de différents invertébrés marins. La structure tridimensionnelle formée abrite de nombreuses espèces, faisant des habitats coralligènes un point chaud de biodiversité en mer Méditerranée. L’étude de la diversité génétique chez une algue rouge calcaire ingénieure a révélé la présence d’espèces cryptiques dont l’abondance relative varie en fonction de la localité et de la profondeur. Cette approche a aussi montré que la diversité génétique chez l’espèce cryptique la plus abondante est principalement structurée par des processus neutres de dérive et de migration eux-mêmes influencés par la courantologie. L’étude de la diversité en espèces des communautés, réalisée par une approche de métabarcoding, a révélé une forte diversité au sein des habitats coralligènes ainsi qu’une forte influence des variables environnementales sur la composition des communautés d’espèces. La comparaison des deux niveaux de diversité révèle que la diversité génétique et la diversité spécifique sont positivement corrélées pour la composante alpha et non corrélées pour la composante beta .Cette thèse contribue à améliorer nos connaissances de la biodiversité et du fonctionnement écologique des habitats coralligènes et a aussi permis le développement des certaines méthodes potentiellement applicable au monitoring de ces habitats / Biodiversity encompasses the diversities of all the living elements from the molecules to the biosphere and several levels of biodiversity can be distinguished. Coralligenous habitats are emblematic calcareous biogenic constructions of the Mediterranean Sea mainly built by calcareous red algae and consolidated by calcareous skeletons built by several mine invertebrates. The complex three-dimensional structure shelters for a huge variety of species, and coralligenous habitats are considered to be one of the biodiversity hotspot of the Mediterranean Sea. The study of the genetic diversity of a engineering calcareous red algae, by capture sequencing, revealed that this nominal species is actually composed of eight cryptic species which relative abundances vary among localities and depth. This approach also showed that genetic diversity in the most abundant cryptic species, is shaped by neutral processes of drift and migration strongly influenced by oceanic currents in Marseilles area. The species diversity in communities was studied using a metabarcoding approach. It revealed the high diversity found in these habitats and the important effect of environmental variables on the species communities composition. The comparison between both level of diversities established that that genetic diversity and species diversity are positively correlated for the alpha component of diversity and uncorrelated for the beta component.These work contribute to improve our knowledge of the biodiversity and ecological functioning of these habitats. Some of the methods developments and tuning implemented during this study could be used in monitoring applications of these habitats

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