Date of Award


Degree Type


Degree Name

Doctor of Philosophy in Biological and Environmental Sciences


Integrative and Evolutionary Biology (IEB)


Cell & Molecular Biology

First Advisor

Bethany D. Jenkins


Atmospheric CO2 has risen dramatically since the industrial revolution. This rise in atmospheric and oceanic pCO2 has perturbed ocean carbonate chemistry and led to ocean acidification. Diatoms are phytoplankton that account for 40% of oceanic primary production through photosynthetic carbon fixation, which is aided by their carbon concentrating mechanism (CCM). The CCM uses the bicarbonate transporters (BCTs) and carbonic anhydrases (CAs). Our current understanding of how diatoms might respond to ocean acidification is based on experiments using model diatoms or assessing the response of the bulk diatom community, rather than assessing a diversity of diatoms in a complex environment. This dissertation aims to expand our knowledge regarding diatom response to CO2 in ecologically important, non-model diatoms and their response in laboratory experiments and field mesocosms to alterations in CO2 concentration.

Diatoms’ primary production is a function of their growth, which is constrained by the availability of nutrients in the surface ocean. Silicon is a nutrient that is particularly important for diatoms, as they are unique in their requirement for silicon to build their cell walls. Silicon limitation has been observed in low iron high nutrient low chlorophyll (HNLC) regions and the North Atlantic Ocean, although these studies have focused on the whole diatom community rather than specific diatom groups that may not uniformly experience silicon limitation. Genetic markers have been used to probe species-specific iron status in the field, and similar molecular markers of silicon status could be powerful tools to probe the silicon status of different co-existing diatom species. However, current studies of silicon limitation have relied on model diatoms rather than species that are likely to be found in HNLC regions or the North Atlantic Ocean, limiting the ability to develop appropriate molecular markers. This dissertation aimed to fill in these knowledge gaps using transcriptomic studies of Thalassiosiroid diatom isolate cultures as well as incubations of mixed diatom assemblages.

Chapter 1 of this thesis examined the transcriptomes of two closely related Thalassiosira diatoms to better understand the silicon limitation gene expression response of diatoms found in ecosystems where their growth may be constrained by silicon availability, toward the goal of developing appropriate molecular markers of silicon status. This study found a gene family encoding putative ATP-grasp domain proteins that were upregulated in silicon-limited T. oceanica and T. weissflogii. The upregulation of these genes is unique to silicon limitation and its expression is not induced in nitrate or iron limitation conditions. The members of this gene family were also upregulated in response to silicon limitation in previously published T. pseudonana transcriptome studies and homologs were found across a diversity of diatoms, suggesting that it might be useful as a silicon limitation marker in many diatoms, in addition to Thalassiosira spp. diatoms.

Chapter 2 of this thesis adds to our knowledge of the diversity of CCM and high CO2 response in different species of the Thalassiosira genus of diatoms. CO2 manipulation experiments were conducted with four Thalassiosira species – T. pseudonana, T. rotula, T. weissflogii, and T. oceanica, and transcriptomes were sequenced from the latter 3 species. These species displayed a range of growth rate changes across CO2conditions, from no change across conditions (T. pseudonana), slower growth in lower CO2 (T. weissflogii), slower growth in higher CO2 (T. oceanica), and faster growth in higher CO2 (T. rotula). The accompanying transcriptome evidence for T. rotula, T. weissflogii, and T. oceanica indicate that these differences in CO2 responses boil down to the ability to dynamically regulate the carbon concentrating mechanism while maintaining internal redox and ion homeostasis, as well as trade-offs between funneling excess CO2 into internal storage pools versus a higher growth rate.

Chapter 3 uses a metatranscriptome approach to generalize about how the CCM of Thalassiosira spp. differs from that of Skeletonema spp. diatoms. This study involved CO2 manipulation experiments of a plankton assemblage collected from Massachusetts Bay during March of 2014. We show evidence of distinct enzymatic strategies for N and P uptake and scavenging in these two diatom genera. There is also evidence of distinct strategies in their CCMs – while Thalassiosira spp. diatoms seem to use the α, δ, and ζ carbonic anhydrases and the substrate-specific SLC4 and non- specific SLC26 bicarbonate transporters, Skeletonema spp. diatoms rely on the γ and ζ carbonic anhydrases and the SLC26 bicarbonate transporters or diffuse CO2 uptake. This suggests that the co-existence of Skeletonema spp. and Thalassiosira spp. might be partially due to a CCM that uses distinct forms of inorganic carbon (CO2 or HCO3-) and CA isozymes that use different metal cofactors for their enzymatic activity (γ can substitute iron, δ can substitute cobalt). Furthermore, if Skeletonema does rely on diffusive CO2 uptake rather than active transport of HCO3- using SLC4 or SLC26 transporters, Thalassiosira may have a competitive advantage in high CO2 as it downregulates these active transporters.

Available for download on Monday, July 27, 2020