Prokaryotic microorganisms, which are at the base of deep-sea hydrothermal vent food webs, adapt rapidly to environmental fluctuations. This study aimed at comparing bacterial communities in contrasting hydrothermal habitats to better understand compositional adaptations to local conditions. I first used small subunit (SSU) ribosomal RNA (rRNA) gene sequences to compare mat-forming bacterial communities associated with iron oxides at two hydrothermal vent sites on the Tonga Arc, southwest Pacific. Operational taxonomic units (OTUs), defined at 97% sequence similarity, were affiliated to a great diversity of autotrophic and heterotrophic groups. Metabolically diverse Gammaproteobacteria dominated the sample from Volcano 19, collected at 992 m depth. The sample from Volcano 1, collected at 197 m depth, was dominated by iron-oxidizing bacteria from the class Zetaproteobacteria. The depth of the sampling sites was proposed to explain clone library dissimilarities. In the following studies, I compared bacterial communities associated with the vestimentiferan tubeworm Ridgeia piscesae, a foundation species at the Juan de Fuca Ridge. Samples of the polychaete were collected from tubeworm habitats in contrasting flow regimes that influenced temperature and hydrogen sulphide concentrations. Free-living bacteria were analyzed using both sequencing and 454 pyrosequencing of the SSU rRNA gene. Statistical analyses suggested a predictable pattern of bacterial community composition for the two habitats, with higher proportions of sulphur and hydrogen oxidizers in High Flow and more heterotrophic groups in Low Flow environments. Temperature, available energy for metabolism, and stability of the habitat were suggested to explain these distinctive bacterial communities. Symbiotic assemblages were investigated using the same sequencing methods together with catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). Gammaproteobacteria dominated all sequence libraries, followed by Epsilonproteobacteria. CARD-FISH confirmed the co-occurrence of these groups within R. piscesae trophosomes. Statistical analyses indicated distinctive membership and structure of trophosome assemblages between sampling sites. Analysis of R. piscesae juvenile showed distinctive structural properties when compared to adult individuals, but similar membership, within sampling sites. These results suggested that the composition of trophosome assemblages might be affected by specific physical and chemical conditions at each vent site and that a selection process might occur during R. piscesae’s development. / Graduate / 0410 / 0416 / 0329 / nathalieforget@gmail.com

Vestimentiferan tubeworms of the eastern Pacific Ocean are often keystone species in vent communities. These polychaetes are host to intracellular Gammaproteobacteria symbionts. In this association, the siboglinid worms supply their symbionts with the compounds necessary to chemosynthesis while the sulfide oxidizing bacteria provide their host with the organic molecules necessary for their metabolism. The adult worms lack a digestive system and are therefore completely dependent on their symbionts for their nutrition. Given the obligate nature of the association for the host, it is surprising that the symbionts are not transmitted from parents to offspring but are acquired de novo from the environment at each generation. In other known cases of horizontally acquired mutualism (e.g. Rhizobium-legumes, dinoflagellates- corals), obtaining symbionts from the environment benefit the hosts by allowing for a degree of partner choice. According to the partner choice hypothesis, tubeworms that associate with the best-adapted partner(s) to a specific range of habitat conditions are in turn better adapted to this environment. Of course, this hypothesis assumes that there is diversity within the symbiotic partners. Phylogenetic analyses on the other hand seemed to indicate that nearly all species of vent tubeworms of the eastern Pacific were associated with the same species of symbionts: Candidatus Endoriftia persephone. However, these studies focussed on a few molecular markers. In this thesis, I used in situ hybridization and next generation sequencing to characterize the symbiont diversity at the species and strain level, as well as within individual hosts and across host species. I found that the intra-host symbiont populations are likely composed of multiple strains or lineages of the same bacterial species, that the symbiont populations separated by mid-ocean ridge discontinuities are vicariant, and that other factors such as local environmental conditions or host specificity might participate in shaping the genetic make-up of these populations. / Graduate / 0410 / 0307 / 0715 / 0306 / 0416 / 0329

In this dissertation, I use seismic imaging and waveform modeling methods to investigate melt migration processes and the structure of the magma plumbing system beneath the East Pacific Rise (EPR) and Endeavour segment of the Juan de Fuca Ridge, respectively. This work begins by studying shallow mantle reflections beneath the EPR. I find the amplitude versus offset and waveform characteristics of the reflections to be consistent with a sub-horizontal dunite channels located up to 20 km off-axis. The depth of the dunite channels correlate with patterns of mantle melt delivery and the predicted base of the thermal lithosphere, suggesting the channels are thermally controlled and may have formed in situ via dissolution by focused flow at the base of the lithosphere. This interpretation is consistent with field observations in ophiolites and numerical modeling of melt-focusing channels. The three-dimensional velocity structure of the Endeavour segment is then investigated to identify how patterns of mantle melt delivery influence the segment-scale distribution of crustal melt and crustal accretion. The results from this study indicate that the mantle magmatic system is skewed relative to the ridge-tracking crustal magmatic system and that this skew exerts primary control on magmatic, tectonic, and hydrothermal activity at the Endeavour segment. In regions where mantle melt delivery is axis-centered, mantle-derived melts are efficiently transported from the mantle to the crust, resulting in frequent crustal melt replenishment, associated seismogenic cracking, and enhanced crustal melt content that drives vigorous hydrothermal activity. Conversely, sites of off-axis melt delivery are characterized by less efficient vertical melt transport, resulting in infrequent crustal melt injection and hence, reduced crustal melt content and hydrothermal activity. Next, I focus on how along-axis variations in magma replenishment modulate crustal permeability and the intensity of hydrothermal circulation. Using full-waveform inversion, I show that sites of localized magma replenishment to the axial magma lens, along with induced seismogenic cracking, coincide with enhanced permeability. I conclude that the frequency of magma injection governs hydrothermal circulation patterns and heat flux at mid-ocean ridges. This dissertation includes previously published and unpublished coauthored material.

The biodiversity of two distinct marine environments was observed to describe the biogeocomplexity of these extreme ecological systems. A shallow-water hydrothermal vent in Papua New Guinea served as a study of a thermophilic ecosystem influenced by arsenic rich vent fluids while a 60 m deep offshore primarily anoxic karst sink served as a study of an anaerobic sulfur-influenced habitat. Both environments support unique biological communities that are influenced by the physical and chemical pressures imposed on them by the harsh conditions of these systems. In Tutum Bay, Ambitle Isle, Papua New Guinea, a transect was created from a shallow hydrothermal vent that extended 120 m away from the vent. Previous studies have shown that the geochemistry of the system is heavily influenced by arsenic which is toxic to most organisms. In this study, macro- and meiofauna were collected and scored and combined with bacterial sequence data collected along the length of the transect. It was found that near vent sites harbored biological communities more similar than sites further from the vent. Many species were found only at sites near the hydrothermal vent. Near-vent communities were less diverse than those away from the vent, and biodiversity generally increased as distance from the vent increased. Distinct correlations between thermophilic organisms and temperature were observed. The metabolic repertoire of the microbial communities suggests that many strategies are used to obtain energy and carbon. The relative abundance of bacteria containing genes to reduce arsenic was comparable to those able to reduce sulfur compounds. Primary production appeared to be a mix of chemo- and phototrophy. Food webs and association analysis suggest a complex interplay between macrofaunal, meiofaunal and bacterial communities. While the system is heavily influenced by arsenic, no specific correlation between the relative abundance of arsenic metabolizing organisms and the amount of arsenic in the system could be drawn. This is likely due to the fact that most of the arsenic produced by the system is readily adsorbed onto iron oxyhydroxides, reducing the arsenic's bioavailability. The anoxic conditions at Jewfish sink provide a different hurdle than the hot arsenic conditions found in Papua New Guinea. The anoxic conditions are shared by other pit features found in karst geography, but the metabolic processes between Jewfish sink and these other karst habitats are different. The blue holes and black holes of the Bahamas are some of the most well-studied of these karstic pits. In these features, which are large circular pits with diameters of over 300 m, light and sulfur are used as a means of energy acquisition. Jewfish sink, having an opening only 6 m in diameter, is light restricted compared to these systems. As a result, the strategy of organisms dwelling in the anoxic conditions of the sink is different than those found at the well-studied holes in the Bahamas. Geochemical measurements were recorded over two time periods spanning a combined total of 6 years. The anoxic bottom waters of Jewfish sink remain stable and contained high levels of sulfide throughout most of the seasons studies. Sequence analysis of prokaryotes within the sink showed that sulfur reducers had the highest relative abundance compared to other functional guilds. To monitor the changes of the microbial communities within the sink, bacterial communities were examined at 4 depths within the sink at 9 different intervals over a period of 685 days. Denaturing Gradient Gel Electrophoresis (DGGE) was used to fingerprint 16s rRNA bacterial communities and dissimilatory sulfite reducing communities by targeting the 16s rRNA bacterial gene and the dsr gene associated with dissimilatory sulfite reducing bacteria and archaea. The lowest depth studied within the sink (40 m) remained stable chemically and biologically until a turnover event occurred within the second winter of the study. This turnover event disrupted the biological communities at 40 m and led to a reestablished community comprised of different species that those found prior to the event. Upper waters within the sink show that clines establish themselves seasonally and partition zones that confine bacterial communities that are more similar to each other within these zones while excluding bacterial communities that are outside of these zones. Oxygenated water was shown to not contain prokaryotes containing the dsr gene. As the oxycline changed seasonally, dissimilatory sulfite reducing prokaryotes containing the dsr gene remained in the anoxic zone and required time to reestablish themselves whenever oxygenated water displaced them.

This thesis is an investigation into biogenic sulfide oxidation and sulfate reduction associated with hydrothermal systems at oceanic spreading centers. First, the production of sulfur floc and 'snowblower' events due to sulfide oxidizing bacteria is investigated. The effects of sulfur floc on the pososity is shown to be negligible. 'Snowblower' events are shown to be sulfur floc that is stored over long periods of time mixed with a component of sulfur floc being created in a bloom event. Secondly, biogenic sulfate reduction in hydrothermal recharge zones is investigated and the effects on the concentration profiles is considered.

Seafloor hydrothermal systems play a key role in Earth fs energy and geochemical budgets. They also support the existence and development of complex chemosynthetic biological ecosystems that use the mineral-laden fluids as a source of energy and nutrients. This dissertation focuses on two inter-related topics: (1) heat output and geochemical fluxes at mid-ocean ridges, and (2) structural deformation of oceanic lithosphere related to subsurface serpentinization in submarine settings. The determination of heat output is important for several reasons. It provides important constraints on the physics of seafloor hydrothermal processes, on the nature of the heat sources at mid-ocean ridges, and on nutrient transport to biological ecosystems. Despite its importance, measurements of hydrothermal heat outputs are still scarce and cover less than 5% of active hydrothermal vent sites. In this work, we report development of two new devices designed to measure fluid flow velocities from the submersible at temperatures of up to 450 C and depths 5,000 m. By using these instruments on 24 Alvin dives, new measurements of hydrothermal heat output have been conducted at the Juan de Fuca Ridge, including first measurements from the High Rise and Mothra hydrothermal fields. The collected data suggest that the high-temperature heat output at the Main Endeavour Field (MEF) may be declining since the 1999 eruption. The flow measurement results, coupled with in-situ geochemical measurements, yielded the first estimates of geochemical fluxes of volatile compounds at MEF and Mothra. Our findings indicate that geochemical flux from diffuse flows may constitute approximately half of the net geochemical flux from Juan de Fuca Ridge. It has recently been recognized that serpentinization of mantle peridotites, due to its exothermic nature, may be a mechanism contributing to the heat output at mid-ocean ridges. The tectonic response of the crust to serpentinization of extensively distributed peridotites at mid-ocean ridges and subduction zones could provide a means of characterizing serpentinized regions in the oceanic lithosphere. These regions are often associated with surface topographic anomalies that may result from the volume expansion caused by the serpentinization reactions. Although there is a clear correlation between tectonics and serpentinization, the link is complex and still not understood. In this dissertation, we calculated the transformation strain and surface uplift associated with subsurface serpentinization of variously shaped ultramafic inclusions. Application of the results to explain the anomalous topographic salient at the TAG hydrothermal field (Mid-Atlantic Ridge) suggests that this feature may result from a serpentinized body beneath the footwall of a detachment fault. Because the depth of the potential serpentinized region appears to be more than 1.5 times the size of the inclusion, the uplift profile is relatively insensitive to the exact location or shape of the serpentinized domain. The rate of exothermic heat release needed to produce the serpentinized volume may contribute to the ongoing diffuse flow. Application of the results to an uplift feature associated with the Kyushu ]Palau subduction zone in the western Pacific, shows that approximately 3% transformational strain in an inclined serpentinized region of the mantle wedge near the subducted Kyushu ]Palau Ridge may result in the observed uplift on the Miyazaki Plain. Using the uplift data may help to constrain the level of the subsurface serpentinization.

Shallow-water hydrothermal vents occur world-wide in regions of volcanic activity. The vents located at Tutum Bay, Ambitle Island, Papua New Guinea are unique in that the vent fluids and surrounding sediments contain some of the highest concentrations of arsenic in a natural system. This study addresses the effects of the vent system on the benthic communities, focusing on the eukaryotes, macrofauna, meiofauna and bacteria. Samples were collected in November 2003 and May/June 2005. Analysis of the 2003 macrofaunal samples indicated that pH, rather than arsenic was influencing the benthic community, and that the hydrothermal influence occurred at a greater distance than expected. Results of more intensive sampling carried out in 2005 are the primary focus of this dissertation. The pore water and sediment characteristics revealed distinct physical habitats corresponding with distance from the vent. There was a trend of decreasing temperature and arsenic concentration and increasing salinity and pH with distance from the vent. The vent sediment was poorly sorted volcanic gravel, while sediments along the transect showed a gradient from fine, well sorted volcanic sands to coarser carbonate sands farther away. The macrofauna showed a trend of increasing diversity with distance from the vent and similar taxa were present in both the 2003 and 2005 samples. The vent community was dominated by the polychaete Capitella cf. capitata. The inner transect from 30 m to 140 m had low diversity. Dominant taxa included thalassinid shrimp and the amphipod Platyischnopus sp.A. The 180 m to 300 m sites had significantly higher diversity. The Danlum Bay reference site had relatively higher diversity than the nearshore transect sites and was dominated by deposit feeding polychaetes. Macrofaunal community structure was influenced by the sediment characteristics, notably by CaCO3 content, sorting and median grain size. The meiofaunal community also showed changes with distance from the vent. Chromadorid nematodes were dominant at the vent site and were a major component of the meiofauna at most sites, along with copepods. The meiofaunal community at the reference site showed greater similarity to the vent community and both sites had low abundances. Nematodes were more abundant than copepods near the vent, but copepods were more abundant farther offshore and at the reference site. Meiofaunal community structure was influenced primarily by the pore water temperature and salinity. Biological interactions with the macrofaunal community through physical disturbance and predation may also influence the meiofaunal community.  The molecular analysis of eukaryotic and bacterial diversity also revealed changes with distance from the vent. The 0 m and reference sites grouped together due to the presence of fungal sequences and the 140 m and 300 m sites grouped together due to a common molluscan sequence. Metazoans and fungi dominated the eukaryote sequences. The most abundant eukaryotic OTUs included fungi matching Paecilomyces sp. and Cladosporium cladosporioides and metazoans matching Viscosia viscosa (Nematoda) and Astarte castanea represented by 24 phyla and was dominated by Actinobacteria and γ-Proteobacteria. More bacterial phyla were present near the vent, while more overall OTUs were found at the intermediate sites along the transect. The most distant site had much lower diversity dominated by Firmicutes. The macrofaunal community had the strongest correlation with environmental variables. Comparison between the meiofauna and the metazoan sequences showed the proportion of nematodes found in both datasets were comparable, but the meiofauna analysis found a higher proportion of arthropods, while the molecular results were disproportionally high for platyhelminthes. Overall, the vents increased the complexity of the system by creating unique habitats. The extreme environment created by the hydrothermal activity maintained the surrounding habitat at an early successional stage colonized by a few opportunistic species. There was a gradation in the benthic communities away from the vent towards a more carbonate based climax community. The low pH environment had an effect on the sediment composition, which in turn influenced the benthic community. These findings can serve as a model for studying the potential effects of ocean acidification and climate change on benthic communities and marine biocomplexity.

In March of 2000, March of 2001, and April of 2002, multibeam bathymetry and backscatter data were collected, which revealed several low-temperature hydrothermal submarine springs in the Mudhole Submarine Springs (MHSS) area that were investigated by SCUBA divers. High-resolution multibeam sonar provides a precise way of defining the geomorphology of the seafloor. The bathymetry data were used to understand (1) vent geomorphology and how it varied from vent to vent; (2) spatial patterns of active vents compared to extinct vents and known land springs identified by Kohout (1977) and Breland (1980); and (3) potential correlations between geochemical and geomorphological characteristics of the vents in the study area. SCUBA observations show that MHSS, Spring #3, New Spring, Northern Rusty, Rusty, and Near Rusty are active springs, while Dormant Spring and Sinister Spring were extinct or inactive at the time of the March 2001 cruise.During the April 2002 cruise the locations of Rusty Spring, New Spring and MHSS were confirmed. Two submarine springs, Creature Hole and Sparky Lee were also confirmed. Spring #3 is the deepest spring and Dormant Spring is the shallowest. There appears to be a rough spatial correlation between vents located on land and the vents on the seafloor, in which all known vents are either to the west or north of Lake Okeechobee. Vent distribution in the MHSS study area appears to correlate with the structural pattern of the local seafloor. Backscatter data and SCUBA observations show that fine to medium grain siliciclastic sediment bands overlie limestone hardbottom in a NE-SW orientation. Although vent geomorphologies are generally distinctive, vent activities generally correlate with the steepness of vent depressions.Most active vents had slopes of 6 degrees or greater, with the exception of Rusty Spring and Near Rusty Spring whose slopes ranged from 2.5 degrees and 6 degrees; whereas all the inactive vents had slopes of 5 degrees or less. Most active vents have "V"-shaped profiles versus the "U"-shaped profiles of most of the inactive vents. The inactive springs have shallower maximum depths and shallower ambient seafloor depths than the active vents.

<p>Genetic diversity, population structure, and connectivity influence interactions among communities and populations. At hydrothermal vents in the western pacific, population structure in vent-associated species could occur at spatial scales ranging from vent sites separated by a few hundred meters to oceanic basins separated by more than 3000 kilometers. The spatial scale of population structure has important conservation implications; species that are well-connected across large geographic regions are more resilient to natural and anthropogenic disturbance. This dissertation examines the genetic diversity, population structure, and connectivity of 3 vent-associated species in the western Pacific. It first presents results from the development of microsatellite primers for Ifremeria nautilei, a deep-sea vent associated snail, then uses mitochondrial COI sequences and a suite of microsatellite markers to examine the broader connectivity of three vent-associated species, Ifremeria nautilei, Chorocaris sp. 2, and Olgasolaris tollmanni, across three back-arc basins in the western Pacific. </p><p>Within Manus Basin, no significant genetic differentiation was detected in populations of Ifremeria nautilei (based on COI and microsatellite), Chorocaris sp. 2 (based on COI and microsatellite), or Olgasolaris tollmanni (based on COI). A previously documented low-abundance cryptic species, Chorocaris sp. 1, was detected from a single site, South Su (based on COI). The population of I. nautilei in Manus Basin was found to be significantly differentiated from a second population that appeared to be panmictic across North Fiji and Lau Basin (based on COI and microsatellites). Chorocaris sp. 2 was also found to be significantly differentiated between Manus and North Fiji Basin (based on COI). Both I. nautilei and Chorocaris sp. 2 showed signs of potential low-level migration between Manus and other southwestern Pacific basins. O. tollmanni was undifferentiated between Manus and Lau Basin (based on COI). It is likely that a variable impedance filter exists that limits the realized dispersal of some, but not all species between Manus Basin and other western Pacific back-arc basins. The presence of a variable filter has implications for the conservation and management of hydrothermal vents in Manus Basin, as it is unclear what effects sustained anthropogenic disturbance will have on isolated populations of I. nautilei and Chorocaris sp. 2.</p> / Dissertation

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