Water column methane measurements have been used to understand both the global distribution of methane in the oceans and the local flux of methane from geologic sources on the continental margins, including methane vents and gas-hydrate-bearing sites. We have measured methane concentrations in 1607 water samples collected along the central California continental margin. Methane supersaturation of the surface mixed layer (0-50 msbsl) is widespread and above a well-defined subsurface particle maximum (~50 mbsl) that generally corresponds with the pycnocline. Local production of methane appears to be occurring in the surface mixed layer above the particle maximum and may not be particle-associated. Methane concentrations in water column CTD cast profiles and ROV-collected bottom waters obtained in Partington, Hueneme, Santa Monica, and Redondo submarine canyons increase towards the seafloor and are distinctly higher (up to 186 nM) compared to open-slope and shelf waters at similar depths. These values are in excess of measured surface water methane concentrations and could not be generated by mixing with surface water. Elevated methane concentrations in these submarine canyons and persistent mid-water methane anomalies in Ascension and Ano Nuevo Canyons could result from restricted circulation and/or proximity to gas vents, seafloor exposure of methane gas hydrates, recently-eroded methane-rich sediment, submarine discharge of methane-rich groundwater, or particle-associated methane production. On the Santa Barbara shelf water column methane profiles near known gas vents also increase in concentration with increasing depth. Thus, elevated bottom water methane concentrations observed in submarine canyons may not be diagnostic of proximity to methane vents and may be caused by other processes.

The natural instability of hydrothermal vents creates variable environmental conditions among habitat patches. Habitat differences correspond to phenotypic variation in Ridgeia piscesae, the only ‘vent tubeworm’ on the spreading ridges of the Northeast Pacific. Ridgeia piscesae that occupy high fluid flux habitats have rapid growth rates and high reproductive output compared to tubeworms in habitats with low rates of venting fluid delivery. As recruitment occurs in all settings, worms in the “optimal habitat” may act as source populations for all habitat types. Ridgeia piscesae is a foundation species in the Endeavour Hydrothermal Vents Marine Protected Area of the Juan de Fuca Ridge. The objective of this thesis was to assess fine scale population structure in Ridgeia piscesae within the Endeavour vent system using genetic data. Population structure was assessed by analysis of the mitochondrial COI gene in 498 individuals collected from three vent sites of the Juan de Fuca Ridge; Middle Valley (n=26), Endeavour Segment (n=444) and Axial Volcano (n=28). Genotyping using microsatellite markers was attempted but all loci developed for closely related tubeworm species failed to amplify microsatellites in Ridgeia piscesae. Sequence analysis identified 32 mitochondrial COI haplotypes; one dominant haplotype (68%), three common haplotypes (4%-7%) and the remainder were rare (<2%). Axial Volcano was differentiated from Middle Valley and Endeavour. Within Endeavour, genetic sub-structuring of Ridgeia piscesae occurred among vent fields (Clam Bed, Main Endeavour and Mothra) and habitat types < 10 km apart. Patterns of genetic variation and coalescent based models suggested that gene flow among vent fields moved in a north to south direction in individuals from high flux habitat but from south to north in individuals from low flux habitat. Tubeworms from low flux habitat had more nucleotide polymorphisms and haplotypes than those from high flux habitats. Estimates of the number of immigrants per generation moving from high flux to low flux subpopulations was four times higher than in the reverse direction. The effective population size was estimated to be three times greater in high flux habitat when the generation times for individuals from each habitat type were considered. Demographic tests for population equilibrium identified a recent and rapidly expanding metapopulation at Endeavour. Models of gene flow in Ridgeia piscesae reflected the general oceanographic circulation described at Endeavour. Genetic data illustrate that dispersing larvae exploit the bi-directional currents created through plume driven circulation within the Endeavour axial valley and suggest that adult position on or near chimneys may influence larval dispersal trajectories upon release. Building on known ecological and biological features, this study also showed that Ridgeia piscesae from limited and ephemeral high flux habitat act as sources to the overall metapopulation and that asymmetrical migration and habitat stability sustain high genetic diversity in low flux sinks. The overall metapopulation at Endeavour experiences frequent extinction and recolonization events, differences in individual reproductive success, and source-sink dynamics that decrease the overall effective size and genetic diversity within the population. These factors have important implications for the conservation of a foundation species. / Graduate / 0307 / 0329 / 0369 / lcpuetz@uvic.ca

Fish are not abundant at hydrothermal vents due to the toxicity of venting fluids. Those that are present usually roam the periphery of the vent field or visit occasionally to feed on the abundance of life supported by chemosynthesis. In the past decade, dense aggregations of a newly described flatfish, Symphurus n.sp, have been observed in association with hydrothermal vents in the western Pacific hydrothermal vent biogeographic province. In this thesis I provide evidence that Symphurus n.sp is a vent obligate and consider the ramifications that this association with hydrothermal vents may have for its distribution, population characteristics, behaviour and diet. Symphurus n.sp has a widespread but disjunct distribution throughout the western Pacific hydrothermal vent biogeographic province. Symphurus n.sp appears to be restricted to hydrothermally active, shallow, sulphur rich seamounts. Symphurus n.sp occurs on unconsolidated volcanoclastic ash and solid sulphur crusts and in close association with molten elemental sulphur. The obvious affinity that this species has for native sulphur is unusual and remains unexplained. Unlike most vent-associated fish, Symphurus n.sp occurs in close contact with point source venting and its distribution extends to the periphery of vent fields but not beyond. The density of flatfish on these seamounts surpasses density estimates of flatfish nursery grounds on the continental shelf. On Daikoku Seamount (Mariana Volcanic Arc), mean flatfish abundances were 100 and 66 individuals m-2 in 2005 and 2006 respectively. The prey items that support such high densities of flatfish vary over spatial scales. Differing prey, in turn, results in differing foraging modes. On Nikko Seamount (Mariana Volcanic Arc), Symphurus n.sp is a “sit and wait” predator that feeds exclusively on a vent endemic shrimp, Opaepele loihi. On other seamounts, Symphurus n.sp is an opportunistic forager that preys mostly on polychaetes and small crustaceans. By counting annuli on otoliths I constructed growth curves and determined that growth rates differ between seamounts. This difference in growth rates is likely due to differences in their diet and foraging strategies. Symphurus n.sp may be allocating more energy to growth when less energy is required to forage. Furthermore, size distributions also differ between populations, likely due to variability in growth rates as well as differences in strong recruitment years.

We investigated oceanic dissolved inorganic nitrogen (N) dynamics, focussing on processes removing bio-available N and ultimately affecting primary productivity, in sulfidic hydrothermal vent fluids discharging from the subsurface on the Juan de Fuca Ridge (northeast Pacific Ocean) and in anoxic bottom waters of Saanich Inlet, a British Columbia fjord, using a combination of geochemical and molecular microbial ecology techniques. During episodes of mixing with oxygenated sea-water, both systems can switch from anoxic to oxic conditions. Strong inter-site variations in the concentrations and δ15N of ammonium (NH4+) in high-T fluids suggested different N sources (deep-sea nitrate (NO3-) versus organic sediments) for hydrothermally discharged NH4+. Increase in the isotopic composition of NO3- (δ15N and δ18O), concomitant with decreased [NO3-], indicated NO3- assimilation or denitrification in the subsurface. NO3- isotope anomalies, i.e. deviations from the 15N:18O isotopic enrichment of 1:1 in marine environments, were observed and confirmed the occurrence of NO3- regeneration in vent fluids. Denitrification was the dominant N-loss pathway, suggesting that bacterial denitrification out-competes anaerobic NH4+ oxidation (anammox) in diffuse hydrothermal vent waters. The diversity of denitrifying bacteria encoding the nirS-form of nitrite reductase was low in vent fluids. Quantitative polymerase chain reaction (qPCR) analysis revealed that denitrifiers accounted for up to 38% (nirk-encoding γ-proteobacteria of the SUP05 cluster) and 8% (nirS-encoding bacteria) of the total bacterial abundance. Furthermore, nirS gene operational taxonomic units from two vent fields clustered into different groups in the phylogenetic tree, suggesting a link between denitrifying bacterial community membership and small-scale geographic isolation and/or fluid physico-chemical properties. Significant correlations existed between fixed N-loss rates and in-situ dissolved inorganic N deficits in the fluids. Based on our rate measurements, and on published data on hydrothermal fluid fluxes and residence times, we estimated that up to ~10 Tg N yr−1 could be removed globally in the subsurface biosphere. In Saanich Inlet, a gradual increase in both the δ15N and δ18O of NO3- associated with a decrease in [NO3-] and an increase in biological excess N2, was observed after bottom water renewal events in fall 2008, following NO3- consumption by denitrifiers in an expanding suboxic zone. N-to-O negative NO3- isotope anomalies were observed in surface and bottom waters, confirming the occurrence of NO3- regeneration and/or external NO3- input. Closed and open-system-model derived NO3- isotope effects in anoxic bottom waters were lower (as low as ~11‰) than the ~25‰ for water column denitrification reported in other studies, suggesting that ~50% of the denitrification could occur, with a highly suppressed isotope effect, in the sediments of the Inlet. / Graduate

Thesis (M.S.)--Miami University, Dept. of Geology, 2004. / Title from first page of PDF document. Includes bibliographical references (p. 126-129).

No description available.

Bathymodiolus azoricus est un bivalve endémique des sources hydrothermales de la dorsale Médio Atlantique qui présente une forte capacité à accumuler différents métaux dans ses tissus, la qualifiant comme espèce modèle en écotoxicologie. L’objectif de ce travail a consisté à décrire les mécanismes moléculaires de tolérance et de détoxication des métaux, que ce soit au sein des populations naturelles ou durant des expositions expérimentales, par le biais d’approches chimiques (quantification des métaux) et transcriptomiques (PCR quantitative et puces à ADN), afin de comprendre comment les facteurs environnementaux pouvaient influencer l’expression des gènes de B. azoricus et d’identifier des biomarqueurs potentiels utiles pour des études écotoxicologiques en environnement extrême. Les mesures de bioaccumulation de différents métaux (Cd, Cu, Fe, Pb,…) sur des individus provenant de sites aux caractéristiques contrastées ont révélé des patrons spécifiques aux populations et aux tissus examinés chez cette espèce, suggérant des phénomènes d’organotropisme. Nos résultats suggèrent également que les bactéries symbiotiques des branchies pourraient participer à la tolérance aux métaux et aux processus de détoxication. Des tendances comparables sont observées pour l’expression relative de certains gènes candidats impliqués dans la réponse au stress métallique, par exemple les métallothionéines, les superoxyde dismutases, les ferritines et les phytochélatines. Les réponses distinctes observées pour certaines populations ou certains tissus traduisent des différences d’état physiologique qui ne seraient pas directement reliées avec l’accumulation de métaux. En outre, l’analyse des puces à ADN à une échelle globale nous a permis d’identifier les réseaux métaboliques principaux pour chaque population et chaque tissu. / Bathymodiolus azoricus is an endemic bivalve from hydrothermal vents in the Mid-Atlantic ridge, which is known to accumulate different types of metals in various tissues at high concentrations, and has therefore been granted model species for exotoxicology. The objective of this work is to describe the mechanisms of metal tolerance and detoxification as they occur in natural populations and during experimental exposures, using both chemical (metal quantification) and transcriptomic (qPCR and microarrays) approaches to understand how environmental factors influence gene expression response in B. azoricus and to identify potential biomarkers useful for ecotoxicological studies in extreme environments. Bioaccumulation of different metals (Cd, Cu, Fe, Pb,…) was measured on individuals from contrasted vent sites, revealing specific population patterns and tissue differences for this species that could be related to processes of organotropism. Our results also suggest that the symbiotic bacteria in gills may be involved in metal tolerance and detoxification. Similar variation trends are observed in the relative expression of candidate genes involved in response to metal stress, e.g. metallothioneins, superoxide dismutase, ferritin, and phytochelatin, revealing contrasted responses at population and tissue level, and reflecting differences in physiological status not directly correlated with the accumulation of metals. In addition, global scale microarray analysis allowed us to identify the principal biological pathways representative of each population and tissues.

L'importance des symbioses dans l'évolution du vivant est désormais admise et les associations symbiotiques sont observées dans une grande diversité d'habitats. Notre étude porte sur une symbiose au sein d'un écosystème réduit, les sources hydrothermales de l'océan profond. Bathymodiolus azoricus est un bivalve hydrothermal vivant le long de la ride Médio-Atlantique, qui héberge dans des cellules branchiales spécialisées, deux types de γ-protéobactéries différentes : des méthanotrophes (MOX) et des sulfo-oxydantes (SOX). Ces dernières sont capables d'oxyder les composés réduits présents dans le fluide hydrothermal fournissant ainsi énergie et/ou source de carbone à leur hôte. Cette double endosymbiose est plastique ainsi, l'abondance relative du type de symbionte hébergé (SOX vs. MOX) varie en fonction des concentrations en composés réduits présent dans le milieu (H2S, CH4). L'objectif de ce travail de thèse est d'identifier les acteurs moléculaires impliqués dans l'acquisition, le maintien et la régulation des bactéries symbiotiques. Pour ce faire, une analyse OMICs globale (protéomique -nano LC-MS/MS- et transcriptomique -micro-array-) a été mise en ¿uvre sur des individus symbiotiques issus de population naturelle (site hydrothermal Lucky Strike, -1700m) et sur des individus ayant expérimentalement perdu ou maintenu leurs symbiotes. Suite à cette approche globale et exploratoire, une approche plus spécifique a été menée sur des familles de protéines impliquées dans des processus immunitaire et/ou d'interactions hôte/symbiotes. Cette thèse apporte un éclaircissement sur les mécanismes régissant les relations et la communication hôte/symbiote. / Hydrothermal vents are located on the mid-ocean ridges, and are characterized by challenging physico-chemical conditions. Despite these conditions dense hydrothermal communities develop down around hydrothermal fluid emissions. The presence of marine invertebrates relies on their capacity to cope with these challenging factors, and, for those forming most of the biomass, on their ability to live in symbiosis with chemoautotrophic bacteria. Bathymodiolus azoricus is one of these symbiotic species that harbors two types of γ-proteobacteria, a sulfide-oxidizing bacterium (SOX) (using the oxidation of H2S as the source of energy and CO2 as source of carbon) and a methane-oxidizing bacterium (MOX) (that uses the oxidation of CH4 as both a source of energy and carbon). These bacteria are located in specific epithelial cells in the gill tissue of the mussel. The proportion and number of these symbiont types (SOX vs. MOX) in B.azoricus can change in response to environmental conditions, and especially on the relative concentration of reduced compounds. The aim of our study is to understand the molecular mechanisms of acquisition, regulation and maintenance of the symbiotic charge in B .azoricus gills. We therefore, performed a global OMICs analysis (proteomics –nano LC-MS/MS and transcriptomics- micro-array) on mussels from natural population (Lucky Strike, -1700m) and on mussels that experimentally loose or maintain their symbiotic rate. This exploratory approach was followed by a more specific approach on family of proteins involved in immunity process and/or in host/symbiont interactions. This PhD provides hypotheses on the mechanisms governing the relationship and communication between host and symbionts.

Les novæ naines permettent, depuis presque 50 ans maintenant, de tester les modèles d’accrétion. Ces systèmes montrent des éruptions en optique d’une durée de l’ordre de la semaine avec des temps de récurrence de l’ordre du mois. Ces éruptions sont communément attribuées à une instabilité thermo-visqueuse au sein du disque d’accrétion entourant la naine blanche. Les temps caractéristiques de ces éruptions posent de fortes contraintes sur les mécanismes de transport de moment cinétique pilotant l’accrétion dans le disque, mécanismes qui constituent l’objet de cette thèse. Il est souvent admis que l’instabilité magnéto-rotationnelle (MRI) est responsable du transport de moment cinétique via la turbulence qu’elle produit. Cependant, je montre ici, à l’aide de simulations locales de disque d’accrétion avec transfert radiatif, que le transport turbulent produit par la MRI ne permet pas de reproduire les courbes de lumière. En quiescence, où le disque est peu ionisé, il est même peu probable que de la turbulence MRI puisse survivre. Un des résultats majeurs de cette thèse est d’avoir mis en lumière que la MRI ne participe pas qu’au transport turbulent mais peut également lancer des vents magnéto-hydrodynamiques (MHD) qui transportent également du moment cinétique, voire dominent le transport dans l’état quiescent. Ces vents MHD induisent un couple magnétique de surface sur le disque et ne peuvent être réduits à une turbulence effective, en partie car ceux-ci ne déposent pas d’énergie thermique localement mais en emportent contrairement au transport turbulent. Nous avons inclus le transport de moment cinétique dû au couple du vent MHD dans un modèle d’instabilité de disque, modèle classiquement utilisé pour reproduire les éruptions de novæ naines. Avec ce nouveau modèle, nous avons montré qu’il est possible de reproduire les courbes de lumière des éruptions de novæ naines, en utilisant un champ magnétique à la surface de la naine blanche compatible avec ce qui est attendu. C’est la première fois que les éruptions de novæ naines sont modélisées avec succès en utilisant des prescriptions pour le transport de moment cinétique basées sur des simulations MHD et non sur les observations. / Dwarf novæ have been used for almost 50 years now as a test for the theory of accretion. These systems exhibit eruptions in optical light lasting approximately a week with a recurrence time scale of a month. Eruptions are thought to be due to a thermal-viscous instability in the accretion disk surrounding the white dwarf. This model has long been known to put constraints on the mechanisms transporting angular momentum in the disk, which will be the subject of this thesis. Traditionally, transport is presumed to be turbulent where turbulence is due to the magneto-rotational instability (MRI). However, I show here, using local simulations of accretion disks with radiative transfer that there exists a discrepancy between observations and light curves obtained with MRI turbulence only. In quiescence, where the disk is poorly ionised, it is very unlikely that MRI can even survive. One of the key results of this thesis is that MRI do not participate to turbulent angular momentum transport only, but is also able to drive MHD outflows which extract angular momentum very efficiently, especially in quiescence. Wind-driven transport is, by nature, very different from turbulent transport, it induces a surface-torque on the disk and do not deposit thermal energy locally but extract energy from the disk instead. We included MHD wind-driven angular momentum transport in a disk instability model, model which is usually used to reproduce light curves of dwarf novæ. Using this new model, we were able to retrieve light curves looking alike observations, with a magnetic field consistent with what is expected from the dipolar magnetic field of a white dwarf. It is the first time that eruptions of dwarf novæ are modeled with success using prescriptions for angular momentum transport derived from first principles instead of ad hoc parameters.

Connaitre précisément la structure interne des corps célestes est indispensable pour, à la fois, comprendre la physique qui régit leur existence et le processus qui leur a donné naissance. La sismologie, d’abord appliquée à la Terre puis au soleil, s’est révélée être un outil très efficace pour sonder leurs intérieurs. Dans les années 70 (Vorontsov et al 1976), des premiers travaux théoriques ont étudié la possibilité d’une sismologie des planètes géantes gazeuses. Les premières tentatives de mesures d’oscillations ont eu lieu à la fin des années 80. La détection des modes d’oscillations de Jupiter s’est avérée une entreprise très délicate en raison de sa rotation rapide. Pour augmenter les chances de détection, un instrument spécifique a été construit au début des années 2000 à l’OCA. Cet instrument, appelé SYMPA, est un spectromètre imageur de type Mach-Zehnder capable de produire une carte de vitesse radiale de Jupiter. Une détection de modes d’oscillations sur Jupiter par cet instrument a été publiée par Gaulme et al en 2011. Une version améliorée de l’instrument (appelé DSI) a été proposée pour la mission spatiale JUICE à destination de Jupiter, et un nouveau prototype a été construit dans ce but. Par la suite, le projet s’est réorienté vers un programme d’observation depuis le sol sous la forme d’un réseau de trois télescopes répartis en longitude (USA, France, Japon) et financé par l’ANR à partir de 2015 (ANR JOVIAL). L’intérêt de la mise en réseau est d’assurer la continuité des données (météo mise à part). L’instrument étant capable de produire des cartes de vitesse radiales, le projet permet également l’étude de la dynamique atmosphérique des planètes géantes. Ce travail de thèse s’inscrit dans le contexte de préparation de JOVIAL, avec pour objectif de caractériser l’instrument en laboratoire et d’identifier les problèmes liés aux conditions réelles d’observation. Les mesures en laboratoires ont montré des performances conformes aux attentes, avec un bruit de mesure propre à l’instrument inférieur au bruit de photon attendu sur Jupiter. Les premières mesures sur le ciel avec un télescope ont mis en évidence une sensibilité de l’instrument au degré de polarisation de la lumière ainsi qu’une dérive de la vitesse mesurée liée aux instabilités de position de la pupille pendant les observations. Le design de l’instrument et de son interface avec le télescope a été revu pour résoudre ces problèmes. Plusieurs campagnes d’observations de Jupiter ont été réalisées, permettant de mettre sur pied une chaine complète de traitement des données, dont la validité a été vérifiée par des simulations réalistes. Les observations de Jupiter ont donné des résultats scientifiques particulièrement intéressants. L’analyse des données de deux campagnes de 2015 et 2016 a fourni des séquences temporelles de cartes de vitesses radiales de Jupiter. Une première étude a consisté à chercher dans ces cartes la signature des vents zonaux et de les comparer aux mesures réalisées par suivi des nuages sur des images résolues (cloud-tracking). Une telle mesure n’avait jamais été faite par effet Doppler. Le résultat, bien qu’affecté par des biais de mesures identifiés, montre des profils de vents stables d’une année sur l’autre et en cohérence avec les valeurs issues du cloud-tracking, sauf au niveau de la partie nord de la bande équatoriale de Jupiter. La mesure Doppler suggère en effet une vitesse de vent bien inférieure à la vitesse apparente dans cette zone, ce qui a potentiellement des implications sur les modèles de dynamique atmosphérique. Ces résultats sont très importants pour mieux comprendre les mesures de la sonde Juno, actuellement en orbite autour de Jupiter. L’analyse fréquentielle des données temporelles a été abordée en fin de thèse. Les analyses préliminaires ne semblent pas pour l’instant reproduire la détection de SYMPA. Une analyse plus poussée est nécessaire avant de conclure à une absence du signal. / To know precisely the internal structure of the celestial bodies is essential to both to understand the physics which governs their existence, and the process which gave them birth. First applied to the Earth and then to the sun, seismology has proven to be a very effective tool to sound their interiors. It has become natural and legitimate to question the possibility of seismology of gaseous giant planets. The first theoretical work was carried out in the 1970s (Vorontsov et al. 1976), and the first attempts to measure oscillations at the end of the 1980s. The detection of Jupiter's oscillating modes turned out to be very difficult (reduced flux, small apparent diameter, fast rotation ...). To increase the chances of detection, a specific instrument was built in the early 2000s at the OCA. This instrument, called SYMPA, is a Mach-Zehnder-type imaging spectrometer enable to produce radial velocity maps of Jupiter. A first detection of acoustic modes on Jupiter with this instrument was published by Gaulme et al in 2011. An improved version of the instrument (called DSI), based on the same principle, was built in the wake, with the primary objective of boarding a spacecraft to Jupiter. The project was finally reoriented towards an observation program from the ground in the form of a network of three telescopes equidistant in longitude (USA, France, Japan) and supported by the ANR fund starting in 2015 (ANR JOVIAL). The interest of the network is to ensure the continuity of data (weather apart). The instrument being able to produce radial velocity maps, the project also aims to study the atmospheric dynamics of giant planets. This thesis work is part of a preparation for JOVIAL, with the aim of characterizing the instrument and identifying the problems related to real observations conditions. Laboratory measurements showed expected performances with an instrumental noise level (related to thermal fluctuations) lower than expected photon noise on Jupiter. The first measurements on the sky with a telescope showed a sensitivity of the instrument to the degree of polarization of the light as well as drifts of the velocity measurements due the motions of the pupil position. Some adjustments of the design of the instrument and its interface with the telescope were necessary to solve these issues. Several Jupiter observation campaigns were carried out during the thesis, allowing the development of full data processing software. The complete procedure was tested against simulated data and validated. Two observations runs in 2015 and 2016 were analyzed to produce time sequences of radial velocity maps of Jupiter, providing very interesting scientific results. First, the maps were analyzed to look for the signature of the zonal winds and to compare them with the measurements made by cloud-tracking. Such measurements by Doppler effect were never made before. The result, albeit affected by measurement biases, showed stable year-to-year wind patterns and coherent results with cloud-tracking measurements, except at the northern part of the Jovian’s equatorial band. The Doppler measurement indeed suggests a wind speed well below the apparent speed in this area, which potentially has implications for the theory of atmospheric dynamics and will be helpful to interpret the Juno (a spacecraft presently orbiting Jupiter) measurements. Frequency analysis of temporal data was undertaken at the end of the thesis. The preliminary results do not seem for the moment to reproduce the SYMPA detection. Further analysis is necessary before concluding if the signal is absent or attenuated.