Document Type


Degree Name



Div. of Environmental & Biomolecular Systems


Oregon Health & Science University


This research characterizes microbial dynamics in dark, oligotrophic volcanic environments. The objective of this thesis is to provide new understanding to community succession at hydrothermal vents, what mechanisms are used for primary productivity in dark, oligotrophic environments, and what are the metabolic strategies of the primary producing populations in these communities. As introduced in Chapter 1, dark oligotrophic volcanic systems are ubiquitous, understudied ecosystems which have a tremendous influence on the biogeochemical cycles on earth. Community succession of primary producing bacteria in these ecosystems is shown in Chapter 2 using a long-term ecological study of microbial mat communities from Loihi Seamount which have been disturbed by an eruptive event. This microbial community succession closely mirrors that of models of hydrothermal fluid evolution following an eruptive event. Chapter 3 explores the great explosion of diversity information from genomic data of autotrophic isolates and presents a review of known carbon fixation pathways along with the phylogenetic diversity of key enzymes used in each pathway. Chapter 4 details the carbon fixation mechanisms and biodiversity of primary producers at multiple microbial mat communities at Loihi Seamount using both PCR-based and metagenome-based analyses. This study also proposes a novel syntrophic model consisting of hydrogen production from anaerobic iron oxidizing bacteria feeding methanogenic archaea and sulfur/iron reducing bacteria. Chapter 5 explores the microbial diversity and metabolic potential of a fumarolic sediment community from Warren Cave, Antarctica using metagenomic data. This chapter shows these communities are supported primary production via the Calvin Cycle which is fueled by high affinity hydrogenases and/or carbon monoxide dehydrogenase enzymes. Chapter 6 discusses some general considerations about sample collection, processing, and inherent biases of the methods used in this thesis. This is followed by a general summary and future directions for research for each chapter. Taken together, this thesis presents new understanding of mechanisms for community succession, carbon fixation, and metabolic strategies of microbes living in dark, oligotrophic volcanic systems.




Division of Environmental & Biomolecular Systems


School of Medicine



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