Date of Award

2023

Degree Type

Dissertation

Degree Name

Doctor of Philosophy in Oceanography

Specialization

Biological Oceanography

Department

Oceanography

First Advisor

Tatiana Rynearson

Abstract

Southern Ocean (SO) phytoplankton are foundational to Antarctic marine food webs and global carbon and silica cycling. As polar ocean environments continue to rapidly evolve, it is important to assess the extent to which these communities can successfully respond. Adaptation to novel conditions will be particularly important here, as shifts in biogeography to track temperature preferences are unlikely where communities already inhabit the coldest surface waters in the Southern Hemisphere. This work employs high throughput physiological and genomic methods to better understand how three important attributes, thermal trait diversity, standing genetic diversity, and repetitive genomic elements, assessed at a multiple taxonomic scales (community, population and individual genomes), all help shape the adaptive potential of Southern Ocean phytoplankton.

Physiological trait variability is crucial to successful and efficient adaptation to novel environmental conditions. As the SO warms, the degree to which traits related to temperature preference and tolerance vary inter- and intra-specifically will be particularly important. Given how poorly characterized traits such as optimal temperature for growth (Topt), maximum temperature for growth (Tmax) and maximum growth rate (μmax) are for cold-adapted phytoplankton (especially from SO), we applied a high throughput phenotyping method to determine growth rates for 43 SO diatom strains representing seven diverse lineages across eight ecologically relevant temperatures. We found these traits to meaningfully vary both among and within species, and that when applied to estimating species-specific thermal fundamental niches, intraspecific differences in observed Tmax values led to large differences (almost 2-fold greater for some taxa) in tolerable geographic range.

Ultimately, standing genetic variation underpins the thermal trait variation observed in Chapter 2. Marine phytoplankton, especially diatoms, are well-documented as being genetically diverse and have exhibited a range of spatial population structures elsewhere in the global ocean. Yet, this is still poorly understood for SO phytoplankton, which in addition to their global relevance, are difficult to sample. To address this, we sequenced 31 recently collected isolates of the endemic SO diatom Actinocyclus actinochilus and assessed genetic diversity levels and population structure. We found that standing genetic diversity in this taxon is remarkably high, more so than for previously analyzed temperate phytoplankton. We also identified a complete lack of population subdivision among the sampled strains. These findings suggest the presence of genetically diverse, large panmictic phytoplankton populations in the productive high latitudes of the Southern Ocean.

While phenotypic and genotypic diversity estimates are vital for any assessment or modeling of adaptive success, many other genomic features are thought to play an important role in rapid adaption. The repetitive fraction of a genome (its “repeatome") and how it varies is increasingly relevant in this context. For this final chapter, we take ad- vantage of recent innovations in sequencing technology and computational power and analyze the abundance and composition of two specific repetitive genomic attributes: transposable elements (TEs) and highly similar protein-coding genes. We constructed a new partial genome assembly for A. actinochilus and found its genomic content to be exceptionally repetitive, with over 53% of total length annotated as TEs. When compared to 10 other marine eukaryotic phytoplankton genomes, we determined TE pro- portion of genome to be significantly associated with genome size. We also found that protein-coding gene richness, as well as proportion of genes that are highly similar, both significantly scale with genome size. For each result, polar genomes were statistically distinguishable from temperate counterparts. Taken together, this research demonstrates the varied resources that SO phytoplankton may have at their disposal as they confront rapid, multi-faceted environmental change. These findings suggest that SO phytoplankton may be relatively, or even uniquely resilient to such change.

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