Date of Award


Degree Type


Degree Name

Doctor of Philosophy in Biological and Environmental Sciences


Biological Sciences

First Advisor

Bethany Jenkins


This dissertation focuses on the molecular ecology of diatoms in the marine environment as it relates to co-occurring associated bacteria, spatial and temporal gradients of physical and chemical oceanographic parameters, and even biotoxin production. The study sites range from the polar habitat of the Southern Ocean (SO) surrounding the Western Antarctic Peninsula (WAP) to the productive estuary Narragansett Bay (NBay) in Rhode Island, USA. The WAP exhibits a naturally occurring gradient of a dissolved iron (Fe), which is an essential micronutrient that diatoms need for growth. Dissolved Fe is growth-limiting in the offshore area and replete in the nearshore areas. This provides a natural laboratory to examine how concentrations of dissolved Fe impact the native diatom communities, while also investigating the concentrations of Fe ligands produced by the co-occurring bacteria. The co-occurring bacteria may participate in a mutualism with the diatoms where bacteria produce Fe ligands to increase the bioavailability of iron to the diatom, increasing the diatoms’ growth while the diatoms in turn release additional dissolved organic carbon to support bacterial growth.

Chapter 1 focuses on the in situ communities of diatoms and particle-associated bacteria in the iron-limited Southern Ocean. Community composition was assessed with high-throughput amplicon sequencing and analysis was performed to examine regional patterns that correspond to dissolved Fe and other metal and nutrient concentrations in addition to correlations with diatom and bacteria amplicons, which may indicate mutualisms. While there was a strong pattern in dissolved Fe concentrations with low concentrations offshore and higher concentrations closer to landmasses, there was no geographical pattern in the concentrations of siderophores, a class of bacterially-produced Fe-ligands. Both diatom and particle-associated bacterial community composition were similar by region sampled, indicating that metals, nutrients, and salinity may drive these taxonomic compositional differences. The most common diatom sequences types observed were Thalassiosira and Fragilariopsis while the particle-associated bacteria were mostly Gammaproteobacteria and Bacteroidetes. From network analysis, there were species-specific positive associations between diatoms and particle-associated bacteria, which were unique between the offshore and nearshore regions indicating potential mutualisms in these two unique environments. This work improves our understanding of how naturally occurring gradients of metals and nutrients influence diatom-bacteria interactions.

Chapter 2 focuses on the genomes of four Gammaproteobacteria that may be equipped to interact closely with diatoms in the SO. These bacteria, along with 150+ other isolates mostly from the particle-associated size fraction, were cultured from the same research cruise effort surrounding the WAP as Chapter 1. All isolates were screened for the production of Fe ligands, which is an important characteristic to overcome Fe stress in the Fe-limited conditions of this region. Nearly all of the isolates displayed the ability to produce Fe-ligands. The four isolates chosen for genome sequencing were Colwellia sp., Moritella sp., Psychrobacter sp., and Pseudoalteromonas sp. All genomes contained siderophore transport genes, while three of the four contained genes related to siderophore biosynthesis. Other genes of interest related to microbial interactions included vitamin B biosynthesis, plant growth hormone (auxin) production, and chitin utilization. The screening of cultured isolates for siderophore production and the comparative analysis of bacterial genomes provides insights into Fe stress mechanisms and potential diatom-bacteria interactions.

Chapter 3 focuses on toxic diatoms, specifically Pseudo-nitzschia which can produce a potent neurotoxin called domoic acid (DA), in the temperate region of NBay. Harmful algal blooms (HABs) caused by Pseudo-nitzschia are a recent problem for NBay starting with a precautionary DA closure of shellfish harvest in 2016 and then a closure in 2017 due to DA exceeding action limits in shellfish meat for the first time since HAB monitoring began by the RI Department of Environmental Management. It is unknown what caused these closure events as Pseudo-nitzschia has been observed for over 50 years in NBay: whether an environmental factor caused endemic Pseudo-nitzschia to become toxic or a new toxic strain of Pseudo-nitzschia was introduced into NBay. We analyzed weekly samples from 2017-2019 for particulate DA, Pseudo-nitzschia species composition, and environmental metadata. The high-throughput sequencing methods of species composition yielded a detailed understanding of the seasonal succession of toxic and non-toxic Pseudo-nitzschia strains in NBay. In particular, we uncovered a potentially worrisome trend of the notorious toxin-producer P. australis present in all 2017 closure samples and infrequently in other 2017-2019 samples, which may indicate it is an important player in the toxin production and closures of NBay. Overall, there were recurring seasonally different Pseudo-nitzschia assemblages and increased DA production was correlated with low dissolved inorganic nitrogen concentrations. In summary, Chapter 3 provides previously unknown information about the resident and problematic Pseudo-nitzschia spp. in NBay and potential drivers of species composition and DA production which may help with future prediction and mitigation of Pseudo-nitzschia HABs and their impacts on NBay and fisheries.

All in all, this dissertation advances the knowledge of the ecological dynamics of diatoms experiencing different nutrient regimes while using cutting-edge molecular techniques. This work also furthers the molecular knowledge of bacteria associated with natural diatom communities. Collecting plankton field samples from globally important regions like the SO and NBay allowed us to examine in situ dynamics in relation to naturally occurring chemical and physical environmental gradients.

Available for download on Friday, August 11, 2023