The discovery of deep-sea hydrothermal vents in 1977 revealed an ecosystem supported by chemosynthesis with a rich diversity of invertebrates, Archaea and Bacteria. While the invertebrate vent communities are largely composed of endemic species and exist in different biogeographical provinces, the possible factors influencing the distribution patterns of free-living Archaea and Bacteria are still being explored. In particular, how differences in the geologic setting of vent fields influence microbial communities and populations associated with active vent deposits remains largely unknown. The overall goal of the studies presented in this dissertation was to examine the links between the geologic setting of hydrothermal vent fields and microorganisms associated with actively venting mineral deposits at two levels of biological organization. At the community level, bar-coded pyrosequencing of a segment of the archaeal and bacterial 16S rRNA gene was employed to characterize and compare the microbial communities associated with numerous deposits from several geochemically different vent fields. Results from these studies suggest that factors influencing end-member fluid chemistry, such as host-rock composition and degassing of magmatic volatiles, help to structure the microbial communities at the vent field scale. At the population level, targeted cultivation-dependent and -independent studies were conducted in order to expand our understanding of thermoacidophily in diverse hydrothermal environments. Results of these studies expanded the phylogenetic and physiological diversity of thermoacidophiles in deep-sea vent environments and provided clues to factors that are influencing the biogeography of an important thermoacidophilic archaeal lineage. Overall, these studies have increased our understanding of the interplay between geologic processes and microorganisms in deep-sea hydrothermal environments.

Univ., Diss.--Sydney. / Literaturverz. S. [237] - 268.

Thesis (Ph. D.)--Rutgers University, 2007. / "Graduate Program in Microbiology and Molecular Genetics." Includes bibliographical references (p. 102-114).

Three gastropods occupy a range of habitats along gradients in hydrothermal flux at Juan de Fuca Ridge vents. I examined how these species co-exist and identified mechanisms driving their abundances. First, I measured temperatures and spatial patterns in adult densities of the three species at three distances from vents to test if thermal regime relates to their habitat selection. Lepetodrilus fucensis and Depressigyra globulus were most dense in-vent (0-25 cm) at variable temperatures (10+5°C): 2100 and 240 incl. dm -2 (respectively). Provanna variabilis was most abundant far-vent (51-75 cm: 60 ind. dm 2) at stable temperatures (3±0.5°C). Thermal conditions are key in their habitat selection: behavioural experiments showed that these gastropods select fluid temperatures<18°C. L.fucensis and D. globulus preferred 5-15°C, while P. variabilis preferred 4-12°C. The next studies sought to explain how Lepetodrilus fucensis reaches order of magnitude higher densities in comparison to other gastropods. First. I quantified L. fucensis recruitment and sex ratio patterns to identify innovative life history traits. I meaured size structure and density at in- and far-vent locations. Early postlarval juveniles occupied far-vent at remarkable densities (2419 ind. dm-2). To test for sex ratio biases, I sexed animals from different habitats and sizes. Populations nearest vents hosted the largest females (>6.0 mm), while peripheral habitats were male-biased. A transplant experiment showed that female survivorship and gonad fullness were significantly lower than males in far-vent locations. Sex ratio biases are driven by two mechanisms: females maximize their reproductive output by selecting optimal habitats and suffer relatively higher mortality in low flux. Next, I hypothesized that the Lepetodrilus fucensis gill symbiosis is a key adaptation. I used multiple approaches to determine if the prevalence of the association and relationship to the limpets condition support this hypothesis. FISH probes specific to the 16S rRNA molecule of a gamma-Proteobacteria hybridized where bacteria were present. Direct sequencing using symbiont-specific primers gave a single unambiguous sequence. indicating high specificity. Light and TEM micrographs of gill tissue from a range of species also showed that the symbiosis is ubiquitous. In addition, the gills of in-vent animals had high surface area. dense symbiont populations and healthy tissues, while far-vent animals showed the reverse trend, suggesting that the symbiosis benefits L. fucensis. Carbon fixation by gill tissues was stimulated by inorganic sulfide and related to the abundance of bacteria on the gill. These data indicate a persistent and specific symbiosis that is dependent on access to sulphide. I further examined feeding by Lepetodrilus fucensis to determine if the bacteria contribute to their host's nutrition. The morphology of feeding structures were compared among Lepetodrilus species. L. fucensis exhibited specialized features: the gill is enlarged. the lamellae are free of the mantle. do not narrow and are stabilized by ciliary junctions. The radula and stomach of L. fucensis are also reduced. Shipboard observations confirmed suspension feeding by L. fucensis. In addition, the symbiont may be ingested because its phylotype was well-represented in food material on the gill. The limpet's morphological specializations are consistent with dependence on suspension feeding and/or symbiont farming; however, L. fucensis also grazes. a mechanism likely important in peripheral locations. Lepetodrilus fucensis populations are partitioned by size and sex along environmental gradients near vents. Peripheral populations are dominated by recruits and adults tend to be male: grazing is likely their primary feeding mode. Larger animals form stacks in venting fluids and are female-biased. These populations access suspended particles for food and sulphide, which generates dense symbiont populations for ingestion. Multiple feeding modes sustain high L. fucensis densities in a space-limited environment and may be an innovative strategy that drives its remarkable abundances.

Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Biology; and the Woods Hole Oceanographic Institution), 2016. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 145-161). / Chemoautotrophic ecosystems at deep-sea hydrothermal vents were discovered in 1977, but not until 1995 were free-living autotrophic Epsilonproteobacteria identified as important microbial community members. Because the deep-sea is food-starved, the autotrophic metabolism of hydrothermal vent Epsilonproteobacteria may be very important for deep-sea consumers. However, quantifying their metabolic activities in situ has remained difficult, and biochemical mechanisms underlying their autotrophic physiology are poorly described. To gain insight into environmental processes, an approach was developed for incubations of microbes at in situ pressure and temperature (25 MPa, 24°C) with various combinations of electron donors/acceptors (H₂ , O₂ and NO₃- and ¹³HCO₃-) as a tracer to track carbon fixation. During short (18-24 h) incubations of low-temperature vent fluids from Crab Spa (9°N East Pacific Rise), the concentration of electron donors/acceptors and cell numbers were monitored to quantify microbial processes. Measured rates were generally higher than previous studies, and the stoichiometry of microbially-catalyzed redox reactions revealed new insights into sulfur and nitrogen cycling. Single-cell, taxonomically-resolved tracer incorporation showed Epsilonproteobacteria dominated carbon fixation, and their growth efficiency was calculated based on electron acceptor consumption. Using these data, in situ primary productivity, microbial standing stock, and average biomass residence time of the deep-sea vent subseafloor biosphere were estimated. Finally, the population structures of the most abundant genera Sulfurimonas and Thioreductor were shown to be strongly influenced by pO₂ and temperature respectively, providing a mechanism for niche differentiation in situ. To gain insights into the core biochemical reactions underlying autotrophy in Epsilonprotebacteria, a theoretical metabolic model of Sulfurimonas denitrificans was developed. Validated iteratively by comparing in silico yields with data from chemostat experiments, the model generated hypotheses explaining critical, yet so far unresolved reactions supporting chemoautotrophy in Epsilonproteo bacteria. For example, it provides insight into how energy is conserved during sulfur oxidation coupled to denitrification, how reverse electron transport produces ferredoxin for carbon fixation, and why aerobic growth yields are only slightly higher compared to denitrification. As a whole, this thesis provides important contributions towards understanding core mechanisms of chemoautrophy, as well as the in situ productivity, physiology and ecology of autotrophic Epsilonproteobacteria. / by Jesse Christopher McNichol. / Ph. D.

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2008. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Includes bibliographical references. / Ecological processes at deep-sea hydrothermal vents on fast-spreading mid-ocean ridges are punctuated by frequent physical disturbance. Larval dispersal among disjunct vent sites facilitates the persistence of sessile invertebrate species in these geologically and chemically dynamic habitats despite local extinction events. Regional population extension and rapid recolonization by the siboglinid tubeworm Riftia pachyptila have been well documented along the East Pacific Rise and the Galápagos Rift. To analyze spatial and temporal population genetic patterns and the processes governing them at ephemeral and disjunct habitats, a suite of 12 highly variable microsatellite DNA markers were developed for this species. Eight of these loci were used to assess the regional and within-ridge genetic structure of recent colonists and resident adults collected from nine sites in the eastern Pacific Ocean over period of three to seven years. A significant seafloor eruption during the seven-year sampling period allowed investigation into the role of local extinction in population genetic diversity at the Tica vent site at 9°N EPR, while collections within two and five years of an eruption that created the Rosebud vent field at 86°W GAR provided insights into genetic diversity input over population establishment. For the first time, this thesis demonstrated significant genetic differences between Riftia populations on the East Pacific Rise and Galápagos Rift. Moreover, the separate treatment of colonist and resident subpopulations revealed a high potential for local larval retention at vent sites. This mechanism for recruitment likely sustains disjunct populations and supports the recolonization of locally extinct areas after disturbance events, while episodic long-distance dispersal maintains genetic coherence of the species. / (cont.) Temporal population genetic consideration at the Tica site on the East Pacific Rise suggests that the 2005-2006 seafloor eruption had little to no discernable effect on local population genetic composition. Yet local populations appear to exhibit a small degree of genetic patchiness, with a high degree of relatedness (half-sibs) among subsets of individuals within both colonist and resident cohorts. This thesis broadens the application of recently developed molecular techniques to study the effect of ridge-crest processes and offers new perspectives into marine dispersal, gene flow, and population differentiation. / by Abigail Jean Fusaro. / Ph.D.

As part of a large study aimed at searching for patterns of diversity in the genus Persephonella along the north to south geochemical gradient of the ELSC, ten novel strains of Alphaproteobacteria were isolated unexpectedly. Using defined media under microaerophilic conditions to enrich for Persephonella from chimney samples collected at the seven vent fields on the ELSC and the dilution to extinction by serial dilution method to purify cultures, a total of ten strains belonging to the Alphaproteobacteria were isolated. Two of these isolates, designate MN-5 and TC-2 were chosen for further characterization and are proposed as two new species of a novel genus to be namedThermopetrobacter. Both strains are aerobic, capable of chemoautotrophic growth on hydrogen and grow best at 55°C, pH 6 and 3.0% NaCl. Strain MN-5 is capable of heterotrophic growth on pyruvate and malate and TC-2 is only able to grow heterotrophically with pyruvate. The GC content of MN-5 is 69.1 and TC-2 is 67 mol%. GenBank BLAST results from the 16S rRNA gene reveal the most closely related sequence to MN-5 is 90% similar and the most closely related sequence to strain TC-2 is 89% similar. Sampling at a shallow marine vent on the coast of Vulcano Island, Italy in 2007 led to the isolation of a novel species of Hydrogenothermus, a genus within the Hydrogenothermaceae family. This isolate, designated NV1, represents the secondHydrogenothermusisolated from a shallow marine vent. NV1 cells are rod-shaped, approximately 1.5μm long and 0.7μm wide, motile by means of a polar flagellum and grow singularly or in short chains. Cells grow chemoautotrophically using hydrogen or thiosulfate as electron donors and oxygen as the sole electron acceptor. Growth was observed between 45 and 75°C with an optimum of 65°C (doubling time 140 min), pH 4.0-6.5 and requires NaCl (0.5-6.0% w/v). The G+C content of total DNA is 32 mol%.