Patterns of marine microbial community composition are observable across ocean depths, with distinct ecological niches based on the environmental conditions at each depth. A fundamental biogeochemical role of microbes in the marine carbon cycle is the degradation of particulate organic matter. Identifying the microbes that are actively degrading organic matter in the deep sea is challenging. The main objective of this dissertation is to understand variations in vertical distributions of microbial communities and to develop methods that could allow us to understand which community members contribute actively to degradation of organic matter. Vertical gradients of marine bacterial diversity and overall abundances were characterized from the surface to the seafloor (Chapter 2), and the variability of deep sea sediment bacterial communities was identified through replicated sampling of sediments (Chapter 3). Flow cytometric cell enumeration showed that bacterial abundance decreased with increasing water depth regardless of the region studied or distance from shore. V1-V2 16S rRNA gene amplicon analyses at 100% nucleotide identity as amplicon sequence variants (ASVs) identified distinct bacterial communities in four defined zones: photic (0 – 200 m), mesopelagic (200 – 1000 m), bathypelagic (> 1000 m) and surface sediments (0 to 20 cmbsf). Bacterial communities of surface sediments >10 km apart were distinct from each other, while those sampled from within 1 m were similar. Phylogenetic approaches focusing on the ubiquitous pelagic bacteria, Alphaproteobacteria Pelagibacterales (SAR11 clade) and Deltaproteobacteria SAR324, expanded our evolutionary understanding about the diversity of these groups while also distinguishing potential ecological niches based on vertical depth distributions. Building on characterization of bacterial diversity, deep water in situ incubation experiments were performed to identify bacterial groups activity involved in phytodetrital organic matter degradation (Chapter 4). The addition of phytodetritus led to an increase in relative abundance of taxa known to degrade polysaccharides. The results provided in this thesis provide high-resolution analyses of marine bacterial community composition throughout the water column and into the upper 20 cm of deep sea sediments in the eastern North Pacific Ocean. Collectively, these studies provide a baseline for assessment of future changes, as the influences of global climate change reshape ocean communities.

Little is known about the molecular diversity of the phytoplankton inhabiting the fjords of the West Antarctic Peninsula (WAP), despite the status of this region as being among the most vulnerable to future warming. Additionally, there are many gaps in our knowledge of how polar phytoplankton will respond to the effects of climate change or about the unique life history strategies they may have evolved. The main objective of this dissertation is to develop an improved understanding of the physiology of a model polar phytoplankton species and to characterize phytoplankton community structure in terms of molecular diversity in a climate-sensitive polar environment. The phytoplankton community in a WAP fjord was surveyed by sequencing the V9 region of the 18S rRNA gene and the V1-V2 region of the plastid derived 16S rRNA gene (Chapter 2). In addition, photosynthetic cells were enumerated by flow cytometry. A novel cryptophyte was observed and the phylogeny and global distribution of this cryptophyte was then examined. Among other phytoplankton, the picoprasinophyte, Micromonas polaris, was also observed in these Antarctic samples. With the genome of M. polaris CCMP2099 newly in hand, we aimed to improve our understanding of how polar phytoplankton may respond to the future effects of climate change by examining M. polaris’ physiological and transcriptional responses to changing CO2 and nitrate conditions in continuous-flow photo-bioreactors (Chapter 3). Finally, we explored the potential survivability and transcriptional responses by this alga as it descends to the deep ocean, building on prior observations of M. polaris in North Atlantic Deep Water, using a series of in situ incubation experiments (Chapter 4). Collectively, these studies provide baseline information on polar phytoplankton community structure and physiological capability, which will help to guide future assessments of the phytoplankton in these regions under a changing climate.

The seasonal and geographical dynamics of phytoplankton have important implications for primary production, carbon sequestration, and predicting future ocean change. The distribution of phytoplankton is influenced by their environmental needs and preferences and can be examined at various levels, from strain or species to size class or broad taxonomic grouping. The first two chapters of this thesis focus on phytoplankton distribution by taxonomic group as determined by 16S and 18S rRNA gene amplicon sequencing. In chapter one, a time-series study of the seasonally oligotrophic northwestern Sargasso Sea underscores the importance of prasinophytes, a polyphyletic group of green algae. Prasinophytes (mostly Class II Mamiellophyceae) comprised approximately half the eukaryotic phytoplankton amplicons during the time of year where deep mixing brings nutrients to the surface. At the end of the deep mixing, the mixed layer shoaled quickly, which could lead to carbon export when the algae were trapped at depth. The focus of the second chapter is expanded to include other phytoplankton groups in addition to prasinophytes. This chapter explores the eukaryotic phytoplankton communities of various tropical habitats, from the green-algae-dominated salt ponds to the mangroves, reefs, and offshore habitats where stramenopiles become more relatively abundant. The Stramenopile group dictyochophytes were examined at high taxonomic resolution previously not reported for this region, with much of that group found to be comprised of uncultured environmental clades. The third chapter moves from the field to the laboratory, measuring the cell quotas of cultured representatives of Mamiellophyceae under nutrient replete, limiting, and starved conditions. Together, these chapters seek to increase the knowledge of prasinophytes across geographic areas and environmental parameters.

We describe the biogeography of two clades of Bathycoccus, a picoplanktonic group of marine green algae, that are phylogenetically distinct based on analysis of the ITS1/5.8S/ITS2 region of the nuclear rRNA operon, but identical across the 18S rRNA gene. QPCR assays were developed against the ITS1 to allow quantification of these taxa (clades BI and BII). These were used alongside prior 18S rRNA primer-probes for two Ostreococcus clades that have previously been classified as different ecotypes (clades OI and OII) to analyze 266 photic zone samples from the tropical Atlantic and North Pacific Oceans. Clades BI and OI were observed in mesotrophic locations, whereas BII and OII were found in oligotrophic regions. Bathycoccus ecotypes co-occurred more often than Ostreococcus ecotypes. In contrast to Ostreococcus ecotypes, the adaptive differences between Bathycoccus clades have yet to be resolved and both Bathycoccus ecotypes appear to be more flexible in their niche(s) than Ostreococcus.

Marine phytoplankton perform approximately half of global CO2 uptake. The phytoplankton communities that perform this photosynthesis are diverse and belong to different size classes. In many marine settings picophytoplankton (size) are abundant and among eukaryotic picoplankton the prasinophyte class Mamiellophyceae is particularly well-represented. Three Mamiellophyceae genera found in many marine settings are Micromonas, Ostreococcus and Bathycoccus. This thesis provides analyses of features shared by the Mamiellophyceae, features unique to an individual genus, and overall environmental distributions of the above genera. Specifically, Mamiellophyceae genome features were characterized quantitatively in Micromonas (Chapter 2, 3) and led to the detection of repetitive elements that can be used as tools for identifying Micromonas clades (Chapter 3). Application of these 'markers' to metagenomic data led to the discovery of Micromonas in the Southern Ocean and at salinities and depths it was previously not known to inhabit. In Ostreococcus and Bathycoccus different types of molecular markers were used to define distances between putative ecotypes within these genera (Chapter 4). This analysis showed two coastal Bathycoccus targeted metagenomes belong to the same clade as a cultured species, Bathycoccus prasinos, while sequences from a Tropical Atlantic Bathycoccus belong to a separate clade. Using this comprehension of Bathycoccus and Ostreococcus diversity, ecomarker genes were selected and used to analyze ecotypes of these genera in metatranscriptome and metagenome data. These analyses were combined with qPCR, flow cytometry and nutrient measurements (Chapter 4). The results provided in this thesis improve our knowledge of the diversity and biogeography of members of the Mamiellophyceae class. Collectively, these studies provide a baseline for future comparisons, as speciation and environmental adaptations are ongoing and may increase with global climate change.

Marine phytoplankton constitute the base of ocean food webs and are responsible for nearly half of the total annual carbon dioxide uptake on the planet acting as important players in biogeochemical cycles. Nitrogen is an essential nutrient that can limit phytoplankton growth. Eukaryotic phytoplankton within the prasinophytes are widespread in the ocean, found from polar to tropical regions under a wide range of environmental conditions, where nitrogen can be an essential nutrient limiting their growth. However, little is known about prasinophyte population dynamics, distributions, growth and abundance, as well as prasinophyte physiological strategies to cope with fluctuation in nitrogen availability in the ocean. Chapter 2 focuses primarily on phytoplankton population dynamics in offshore mesotrophic sites in the dynamic transition zone of the central California Current System. Based on hierarchical clustering of abiotic factors, two modalities were identified within the mesotrophic sites; each modality with distinct phytoplankton communities (determined by flow cytometry and high resolution 16S V1-V2 region rRNA gene amplicon sequencing) that appear to underlie the differences in phytoplankton growth and biomass production observed (determined by dilution experiments and 14C method). The highest biomass production (38.7 ± 8.1 µg C L-1 D-1 by 14C, 86% from photosynthetic eukaryotes) was found in a mesotrophic high modality (MHM) where nitrate was approximately 4-fold higher than in the MLM (mesotrophic low modality). The pico-prasinophyte Ostreococcus clade OI dominated the MHM, whereas in the MLM higher relative contributions of another prasinophyte (uncultured prasinophyte class VIII) and Pelagomonas (stramenopile) were found. Furthermore, the effects of nitrogen (N) depletion on growth, cellular parameters (Chapter 3) and whole-genome transcriptional responses (Chapter 4) of the pico-prasinophyte Micromonas, were investigated in laboratory experiments. This study showed common responses of three Micromonas species that come from three divergent and ecologically important clades. The main commonalities observed were that nitrogen depletion induced a pronounced decrease in growth rate compared to controls within 1 or 2 days and N-deplete treatments take longer to show signs of growth recovery than stationary phase control cells. One major difference was that M. pusilla under N-depletion exhibited a pronounced increase in mean FALS cell-1 (proxy of cell size). At a transcriptional level (RNA-seq), also several commonalities were observed for both two of the Micromonas species studied under N-depletion, such as a major decrease in the relative transcript abundance of genes related to the photosynthetic machinery, carbon transport and metabolism and fatty acid biosynthesis, and an increase in the relative transcript abundance of genes related to flagella and microtubule formation as well as an increase of a number of transcription factors (TFs). In addition, despite the slower growth recovery of N-deplete treatments after transferring to replete medium, a rapid transcriptional response was observed. The Micromonas species exhibited differences in the transcriptional patterns of genes related to nitrogen transport and assimilation. Under N-depletion, the majority of these genes increased in Micromonas commoda while results were more variable for homologous genes in Micromonas pusilla. Distinct transcriptional patterns were observed for ammonium transporter (AMT) homologous in each Micromonas species. In M. pusilla, one ammonium transporter (AMT1.3) appears to only increase under nitrogen depletion and may be a good marker of nutrient status in the field.