Doctoral Dissertations

Date of Award

12-2018

Degree Type

Dissertation

Degree Name

Doctor of Philosophy

Major

Microbiology

Major Professor

Karen Lloyd

Committee Members

Alison Buchan, Terry Hazen, Jill Mickuki, Andrew Steen

Abstract

Marine sediments contain more microorganisms than all of the world’s oceans, with current of estimates of 1×1029 microorganisms. Despite marine sediments being replete with microbial cells, the majority of these microorganisms remain uncultured in the laboratory. At present, it is estimated that over 99% of all microorganisms have evaded culture, although truer estimates likely depend upon environment. Factors responsible for the intractability of these microorganisms include very slow doubling times, predicted to be on the orders of years to centuries, as well as special physiological needs of extremophiles. Unsuccessful laboratory growth of these microorganisms requires us to rely on culture-independent tools, including molecular techniques, metagenomics, and bioinformatic tools to glean insight into their ecological structure and function.This dissertation combines molecular and bioinformatic techniques to evaluate the biosphere within deeply buried sediments of the Baltic Sea and shallow sediments in Arctic fjords. Quantification of microbial biomass within marine sediments lays the groundwork for questions related to organic carbon and element cycling. Although essential, reliable and reproducible estimates of microbial biomass within deeply buried sediments has proved challenging. Here we present an interlaboratory comparison of quantification results from International Ocean Discovery Program Exp. 347 sediments that allowed us to define best practices that lead to meaningful quantification estimates. We then transferred these best practices to marine sediments in a Svalbard fjord (Van Keulenfjorden) to understand how glacial proximity influences microbial communities. Through 16S rRNA gene libraries, organic geochemistry, and genome reconstruction, we illustrate that cross-fjord trends in organic matter influence community structure in the sediment. In addition, we argue that biological iron and sulfur cycling facilitates rapid recycling of electron acceptors crucial for carbon oxidation. We delved deeper into their metabolic pathways with metagenomic sequencing and contig binning. We reconstructed several genomes of the Woeseiaceae clade that can act both as a sink and a source of carbon. Ultimately, our work provides a framework for understanding how glacial proximity influences microbial community composition and metabolic function, which is important and timely with ongoing climate change and a strong threat of severe glacial retreat in this region.

Comments

Portions of this document have been published in FEMS Microbiology Ecology and ASM Genome Announcements.

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