Applying meta-’omics to marine microbial ecophysiology
- Author(s): Kolody, Bethany
- Advisor(s): Allen, Eric E
- Allen, Andrew E
- et al.
Phytoplankton and associated microbial communities are essential for sustaining marine ecosystems. However, the structure and function of these communities is largely driven by dynamic physical forcing (e.g. upwelling, subduction) and micro-scale interactions (e.g. viral infection, trophic interactions, symbioses) that are difficult to capture. This dissertation applies recent molecular tools to these complex systems in order to resolve the physiology of key microbial players in the context of environmental forcing and community interactions.
In Chapter 1, a semi-Lagrangian drifter was deployed to capture the transcriptional dynamics of a phytoplankton community across diel cycles. Apart from fungi and archaea, all groups (dinoflagellates, ciliates, haptophytes, pelagophytes, diatoms, cyanobacteria, prasinophytes) exhibited 24-h periodicity in some transcripts. Larger portions of the transcriptome oscillated in phototrophs. Functional groups of genes, including photosynthetic machinery, had conserved timing across diverse lineages. In addition to responding to low-iron, many taxa were also being persistently infected by viruses.
Chapter 2 applied metatranscriptomics to a simulated upwelling experiment to examine the response of blooming phytoplankton to nitrogen and iron, the most common nutrients limiting marine phytoplankton growth in nature. Regulation of metabolism and light harvesting machinery changed in a conserved manner across diverse lineages. Viral activity was widespread and increased under nutrient limitation. The relative expression of NRT2 to GSII and iron starvation induced proteins (ISIP1, ISIP2, ISIP3) to the thiamin biosynthesis gene, ThiC, were identified as robust markers of diatom cellular nitrogen and iron status.
Chapter 3 applied high-resolution amplicon sequencing to a ship-based transect of the South Pacific along a gradient of water ages spanning newly subducted Antarctic water to subtropical water with a residence time >1,000 years. 16S and 18S rRNA diversity analyses were performed using both DNA and cDNA reverse-transcribed from RNA, providing an estimate of the breadth of deep-ocean microbial diversity that can be attributed to active cells. Microbial communities differed across size classes and were ultimately structured by physical properties of water masses and residence time in the deep ocean. These results highlight the utility of ‘omics techniques for capturing the response of marine microbes to physical dynamics and resolving relationships between key community members.