Date of Award

2021

Degree Type

Dissertation

Degree Name

Doctor of Philosophy in Oceanography

Specialization

Biological Oceanography

Department

Oceanography

First Advisor

Steven D’Hondt

Abstract

Over the last fifteen years, there has been a large increase in the literature on microbial community composition in marine sediment (Inagaki et al., 2006, 2015; Biddle et al., 2012; Briggs et al., 2012; Breucker et al., 2013; Lloyd, 2014; Teske et al., 2014; Nunoura et al., 2016; Walsh et al., 2016; Petro et al., 2017; Harrison et al., 2018; Hoshino et al., 2020), and seawater (Quaiser et al., 2011; Hamdan et al., 2013; Walsh et al., 2016; Medina-Silva et al., 2018; Mestre et al., 2018; Quero et al., 2019). As molecular study of these biomes progresses, and the tools available for detailed analyses expand, it has become important to evaluate those tools for their effectiveness and limitations. By combining environmental microbial investigations with evaluation of some of the most common genetic protocols, I have characterized microbial diversity and community composition in (i) Pacific, Atlantic, and Arctic seawater and (ii) Pacific and Atlantic sediment, and I have identified the common results obtainable using (i) two different 16S ribosomal RNA gene (rRNA) hypervariable regions of interest, and (ii) the two amplicon analysis pipelines most commonly used to determine microbial diversity and community composition.

My first manuscript, “Influence of 16S rRNA Hypervariable Region on Estimates of Bacterial Diversity and Community Composition in Seawater and Marine Sediment”, looks at the bacterial diversity and community composition of deep-ocean sediment and overlying seawater from one site in the Central North Atlantic and one site in the Equatorial Pacific. In each case, we amplified both the V4 and V6 hypervariable regions of the 16S rRNA gene of each sample and clustered the sequences into operational taxonomic units (OTUs) of 97% similarity. In doing so, we determined that while OTU-level diversity metrics and community composition are quite different between the two tags, (i) vertical patterns of relative diversity are broadly the same, (ii) community composition is very similar for both tags at the class level, and (iii) while the open ocean communities are very similar between the Pacific and Atlantic oceans, the sediment communities of each ocean differ greatly.

My second manuscript, “Patterns of Relative Bacterial Richness and Community Composition in Seawater and Marine Sediment are Robust for both Operational Taxonomic Units and Amplicon Sequence Variants”, examines how the choice of bioinformatic analysis pipeline affects characterization of taxonomic richness and community composition in seawater (from 12 sites in the North Atlantic Ocean and Canadian Arctic) and sediment (from two sites in the North Atlantic). For all samples, we amplified the V4-V5 hypervariable region of the 16S rRNA gene and analyzed each sample in two different ways: (i) by clustering its reads into 97%-similar OTUs, and (ii) by assigning sequences to unique amplicon sequence variants (ASVs). By comparing the results obtained with each method, we determined that (i) for both OTUs and ASVs, estimates of taxonomic richness depend on the number of sequences analyzed, (ii) bacterial community composition between the two methods is broadly similar in all samples at the taxonomic levels of phyla to families, and (iii) broad-scale patterns of relative richness and community composition are similar with both methods.

My third manuscript, “Microbial Community Composition of Canadian Arctic Seawater”, leverages the results of the first two manuscripts to characterize microbial community composition in the Northwest Passage of the Arctic Ocean and illustrate its connection to community composition in other major oceans. Here, we analyzed from three to six water-column depths at eleven locations throughout the Canadian Arctic and Davis Strait, as well as one site in the North Atlantic by amplifying the V4-V5 hypervariable region of the 16S rRNA gene and clustering the sequences into 97%-similar OTUs. While we report specifically on the OTU-based results, we also analyzed each sample with the ASV methods described in manuscript two to test our conclusions. Our results show that (i) vertical profiles of OTU-level richness (and ASV-level richness) in Arctic seawater are similar to those in other oceans, and (ii) the predominant primary producers in Northwest Passage communities appear to be eukaryotes, not bacteria. In the latter respect, the Northwest Passage communities resemble coastal communities of other ocean regions, rather than open-ocean communities of the North Atlantic and North Pacific.

Available for download on Saturday, August 13, 2022

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