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Document Type

Open Access Dissertation

Degree Name

Doctor of Philosophy (PhD)

Degree Program


Year Degree Awarded

Spring 2014

First Advisor

Dr. James F. Holden

Subject Categories

Biogeochemistry | Environmental Microbiology and Microbial Ecology


This dissertation uses a combination of microbiology, mineralogy, and geochemistry to understand dissimilatory iron reduction in hyperthermophilic archaea and the role and potential impact of these and other vent microorganisms within active deep-sea hydrothermal vent chimneys. The central objective of the dissertation is to determine if mineral composition and chimney type are among the primary determinants of microbial community composition and hyperthermophilic, dissimilatory iron reducer growth, in addition to other environmental factors such as nutrient availability, temperature, pH, and chlorinity. This is done using samples and organisms collected from the Endeavour Segment of the Juan de Fuca Ridge in the northeastern Pacific Ocean. The goals of this dissertation are: 1) to correlate microbial community compositions within three Endeavour hydrothermal chimneys with their mineral compositions using mineral spectroscopic techniques that have not been applied previously to hydrothermal chimneys, 2) to characterize the growth and Fe2+ production rates and constraints of two novel hyperthermophilic iron reducers isolated from Endeavour hydrothermal chimneys, and 3) to determine the mineral end-products of these iron reducers using mineral spectroscopic techniques that have not been applied previously with hyperthermophiles.

This was first done by collecting three active hydrothermal chimneys and their associated high-temperature fluids from the Endeavour Segment, Juan de Fuca Ridge to evaluate the linkages among mineralogy, fluid chemistry, and microbial community composition within the chimneys. To identify mineralogy, Mössbauer, mid-infrared thermal emission, and VNIR spectroscopies were used for the first time on vent chimneys, in addition to thin-section petrography, x-ray diffraction (XRD) and elemental analyses. A chimney from the Bastille edifice was rich in Fe-sulfide and composed primarily of chalcopyrite, marcasite, sphalerite, and pyrrhotite (i.e., type I chimney) while chimneys from the Dante and Hot Harold edifices were rich in anhydrite (type II-III chimneys). The bulk emissivity and reflectance spectroscopies corroborated petrography, XRD, and elemental analyses, demonstrating the potential of these techniques for future shipboard analysis. The microbial community within the Bastille chimney was most closely related to mesophilic and thermophilic anaerobes of the deltaproteobacteria, especially sulfate reducers, and anaerobic hyperthermophilic archaea, while those within the Dante and Hot Harold chimneys were most closely related to mesophilic and thermophilic aerobes of the beta-, gamma- and epsilonproteobacteria. Numerical modeling of energy availability from redox reactions in vent fluids suggests that aerobic oxidation of sulfide and methane should be the predominant autotrophic microbial metabolisms at 25°C and 55°C and that anaerobic oxidation of methane should prevail at 80°C. While the microbial community compositions of all three chimneys show aerobic sulfide-oxidizing epsilonproteobacteria, the predominance of mesophilic sulfate reducers in the Bastille chimney suggests that type I chimneys may promote anaerobic metabolisms.

The next two goals, namely characterizing the growth and Fe2+ production rates and constraints of two novel hyperthermophilic iron reducers isolated from Endeavour hydrothermal chimneys, and determining their mineral end-products using mineral spectroscopic techniques that have not been applied previously with hyperthermophiles, were carried out in parallel.

Hyperthermophilic iron reducers are common in hydrothermal chimneys found along the Endeavour Segment in the northeastern Pacific Ocean based on culture-dependent estimates. However, information on the availability of Fe(III) (oxyhydr)oxides within these chimneys, the types of Fe(III) (oxyhydr)oxides utilized by the organisms, rates and environmental constraints of hyperthermophilic iron reduction, and mineral end products are needed to determine their biogeochemical significance and are addressed in this study. Thin-section petrography on the interior of a hydrothermal chimney from the Dante edifice at Endeavour showed a thin coat of Fe(III) (oxyhydr)oxide associated with amorphous silica on the exposed outer surfaces of pyrrhotite, sphalerite and chalcopyrite in pore spaces, along with anhydrite precipitation in the pores that is indicative of seawater ingress. The iron sulfide minerals were likely oxidized to Fe(III) (oxyhydr)oxide with increasing pH and Eh due to cooling and seawater exposure, providing reactants for bioreduction. Culture-dependent estimates of hyperthermophilic iron reducer abundances in this sample were 1,740 and 10 cells per gram (dry weight) of material from the outer surface and the marcasite-sphalerite-rich interior, respectively. Two hyperthermophilic iron reducers, Hyperthermus sp. Ro04 and Pyrodictium sp. Su06, were isolated from other active hydrothermal chimneys on the Endeavour Segment. Strain Ro04T grew on peptides, reduced poorly crystalline iron oxide to black ferromagnetic magnetite and produced acetate and minor amounts of ethanol. It did not grow on any other terminal electron acceptor or purely by fermentation. Strain Su06T also catabolized peptides but only when H2 was present and reduced poorly crystalline iron oxide to magnetite and nitrate to N2. They both grew between 82°C and 97°C (Topt 90-92°C) and pH 5.0 and 9.0, but strain Ro04T had a pH optimum of 8.0 while strain Su06T had a pH optimum of 5.0. 16S rRNA gene sequence similarity analysis indicated they are 98.4% identical to each other and are most closely related (>98%) to Hyperthermus butylicus DSM 5456T, Pyrodictium abyssi DSM 6158T, Pyrodictium occultum DSM 2709T and Pyrodictium brockii DSM 2708T. The complete genome for Strain Su06 was obtained and genome comparisons done in silico between Strain Su06T against Hyperthermus butylicus and Pyrolobus fumarii, revealed that Strain Su06 is a novel species. Strain Ro04T had growth characteristics most similar to H. butylicus while strain Su06 was more similar to P. abyssi. However, the ability of the strains to reduce iron and their inability to reduce sulfur compounds clearly distinguished them from all of their closest relatives. Phylogenetic, genomic, and phenotypic data indicate that strain Ro04T is novel species of Hyperthermus and strain Su06T is a novel species of Pyrodictium. The name Hyperthermus hephaesti is proposed for strain Ro04T and Pyrodictium delaneyi is proposed for Su06T. Mössbauer spectroscopy of the iron oxides before and after growth demonstrated that both organisms form nanophase (nm) magnetite [Fe3O4] from laboratory-synthesized ferrihydrite [Fe10O14(OH)2] with no detectable mineral intermediates. They produced up to 40 mM Fe2+ in a growth-dependent manner while all abiotic and biotic controls produced < 3 mM Fe2+. Hyperthermophilic iron reducers may have a growth advantage over other hyperthermophiles in hydrothermal systems that are mildly acidic where mineral weathering at elevated temperatures occurs.