טכניון מכון טכנולוגי לישראל
הטכניון מכון טכנולוגי לישראל - בית הספר ללימודי מוסמכים  
Ph.D Thesis
Ph.D StudentHevroni Gur
SubjectFrom Unique Genes to Seasonal and Diel Patterns:
A Metagenomic Study of Marine Viruses
DepartmentDepartment of Biology
Supervisor Professor Oded Beja
Full Thesis textFull thesis text - English Version


Abstract

Microbial communities living in the oceans are major drivers of global biogeochemical cycles, where marine phytoplankton are responsible for nearly half of the global net primary production, while accounting for only 0.2% of the global primary producers’ biomass.  These microbial populations are outnumbered by predatory viruses, with estimates of 10^28 viral infections per day in the oceans. While viruses often lyse their host, driving the export of organic carbon from the surface to deep ocean, accumulating evidence shows that viruses also participate in biogeochemical processes by manipulating host metabolism using auxiliary metabolic genes (AMGs). Ubiquitous photoautotrophs in the ocean photic zone are Cyanobacteria, dominated by Synechococcus and Proclorococcus. Their cycles of gene expression and cell division exhibit a diel pattern regulated by sunlight. In recent decades many cyanophages (viruses infecting Cyanobacteria) have been found to carry photosynthetic genes and other AMGs, displaying oscillating gene expression patterns similar to their hosts. While such virus-host interactions have been studied in detail for many years in cultured model systems, a community-wide ecological perspective on these interactions are scarce.

In this work we applied molecular and bioinformatic approaches to detect unique photosynthetic viral AMGs, and used multi-omics tools to study the abundance of marine viruses and host interaction on a community level. In the first part, we designed and applied a PCR assay targeting a unique gene organization of a photosystem-I gene cassette from a recently discovered cyanophage. Using this targeted screen, we revealed 6 subgroups viral photosystem-I genes varying in their level of similarity, suggesting that the diversity of cyanophage photosystem-I genes is greater than originally thought.

In the second part, we collected highly-resolved time-series samples over 24-hours, during two distinct seasons in the Red Sea (summer and winter), while fractionating the microbial community based on their physical parameters (e.g. size, density) and nucleic content (i.e. DNA, RNA). This approach allowed us to study the identity and gene expression patterns of co-occurring communities in a diel and seasonal time-scales. We show a seasonal change in the microbial community composition, both on the genotype level as well as a succession of top-ranking members of the community. Moreover, we show that while the community is undergoing a seasonal change, the community-level transcriptional and functional activity remain similar, an indication of functional redundancy among distinct marine microbial communities.

In the third part we look at the seasonal and diel abundance patterns of viruses to better understand seasonal and diel effects on the viral community. We show that the viral community is undergoing a change in rank abundance across seasons, suggesting a seasonal succession of viruses in the Red Sea. Additionally, we use abundance patterns in the different sample types to classify viral populations, showing differences which might indicate different interaction with their host. Finally, we show how similar virus groups can differ in their hourly resolved intracellular abundance, which might indicate on a different infection cycle.