Date of Award

Spring 2019

Document Type


Degree Name

Doctor of Philosophy (PhD)


Ocean & Earth Sciences



Committee Director

H. Rodger Harvey

Committee Member

Brook L. Nunn

Committee Member

P. Dreux Chappell

Committee Member

David Gauthier


Understanding how the functionality of marine microbial communities change over time and space, and which taxonomic groups dominate distinct metabolic pathways, are essential to understanding the ecology of these microbiomes and the factors contributing to their regulation of elemental cycles in the oceans. The primary goal of this dissertation was to investigate the community metabolic and taxonomic responses and the degradation potential of two compositionally distinct marine microbiomes within the shallow shelf ecosystem of the Chukchi Sea after rapid fluctuations in algal organic matter availability. Novel bioinformatics tools were collaboratively developed and used together with community proteomics (metaproteomics) to characterize and quantify changes in bacterial community functioning and taxonomic composition over time. 16S rRNA sequencing was employed to confirm bacterial taxonomic dynamics. These approaches were linked to particulate analyses for lipids and amino acids in order to track temporal changes in organic substrate composition. Results obtained using these improved methodological standards and the multidisciplinary approach demonstrated that organic perturbations within these systems stimulated changes to microbial taxonomic composition and functionality. The removal of organic particles seen within the control initiated a divergence between the two microbiomes while substrate abundance, as algal inputs, led to a convergence in community function. Despite the functional and taxonomic overlap seen as dominant features characterizing the responses to rapid influxes of algal organic matter, unique metabolic traits differentiated the major bacterial groups of each microbiome. This was most apparent in the recycling of nitrogen and carbon as well as substrate acquisition, suggesting that conditions which select for certain bacterial groups in the western Arctic Ocean may impact local chemical gradients. The large dataset of information obtained from this dissertation provides insight into the timing and characterization of Arctic bacterial community responses to environmental perturbations and in turn how they influence changes in substrate composition through selective degradation of labile lipid classes. In addition, this work demonstrates the applicability of trait-based methodologies to inform on how environmental conditions may drive niche formation within complex microbial communities.


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Materials and methods.docx (24 kB)
Materials and Methods

Dataset 1.xlsx (14293 kB)
Complete taxonomic inventory of peptide spectra for Bering Strait, algal organic matter (aOM) inputs

Dataset 2.xlsx (11464 kB)
Complete taxonomic inventory of peptide spectra for Bering Strait, particulate organic matter (POM) removal

Dataset 3.xlsx (7250 kB)
Complete taxonomic inventory of peptide spectra for Chukchi Sea, algal organic matter (aOM) inputs

Dataset 4.xlsx (5342 kB)
Complete taxonomic inventory of peptide spectra for Chukchi Sea, particulate organic matter (POM) removal

Dataset 5.xlsx (2978 kB)
Dataset 5 – Relative abundance of 16S rRNA sequences to the level of genus