טכניון מכון טכנולוגי לישראל
הטכניון מכון טכנולוגי לישראל - בית הספר ללימודי מוסמכים  
Ph.D Thesis
Ph.D StudentPhilosof Alon
SubjectA Day in the Life of the Red-Sea: A Metagenomic and
Metatranscriptomic Analysis
DepartmentDepartment of Biology
Supervisor Professor Oded Beja
Full Thesis textFull thesis text - English Version


Abstract

Marine viruses comprise the largest reservoir of genetic diversity in the ocean and are major players in oceanic processes. Phages carry a large repertoire of Auxiliary Metabolic Genes (AMGs), such as photosynthesis genes and phosphate metabolism genes. Their effect on bacterial populations by predation and the consequent release of dissolved organic matter along with the prevalence of AMGs at the genome level are well-studied aspects of virus-host interactions. However, the expression of such genes in the marine environment is not well documented, and it is hypothesized that phages may contribute to biogeochemical processes both indirectly by predation and directly by expressing and constantly tinkering with genes related to these processes.

To gain knowledge about the abundance of phage-harbored metabolic genes and the extent to which they are expressed in the marine environment, and to detect changes in viral and host populations as well as variations in gene expression, two sets of samples were collected from the Gulf of Aqaba. The first set of samples was collected in 2010 at a single time point and was sequenced using 454 pyrosequencing following rRNA depletion and mRNA amplification in the RNA fraction, and Multiple Displacement Amplification (MDA) of the vDNA fraction. The sequencing of this sample resulted in large vDNA and gDNA libraries and a poor cDNA library. Analysis of the samples revealed systemic biases that were found to be similar to other metagenomic and metaviriomic projects. Despite these biases, we report on the presence of proteorhodopsins of SAR11 and SAR 86 groups (bacteria), group II euryarchaeal group (archaea) and rhodopsins from giant viruses from the Red Sea. Multiple sequence analyses revealed that viral rhodopsin is possibly a sensory rhodopsin, and we suggest that the virus might change the behavior of its host (Pheocystis globosa) during infection.

Knowledge from the 2010 sampling has enabled us to design a new sampling and processing methodology, and a second set of samples (gDNA, vDNA and RNA) was collected in 2012 at four different time points over 24 hours. Using a unique approach, no amplification or enrichment methods were applied to any of the samples prior to sequencing limiting sample-specific biases. Following sequencing on the Illumina HISeq platform, an iterative assembly approach of pooled samples allowed the assembly of large contigs, and facilitated a quantitative comparison of the abundance of species and genes between fractions and time points.

Here, based on comparisons to known cultured genomes along with an analysis of assembled contigs of uncultured viruses from our samples, we provide evidence of a daily variation in the abundance of cyanobacteria and their phages. In addition, we report on variations in their gene expression and show evidence of phage-harbored photosynthesis genes highly expressed during the light hours. These expression signals have not been reported before. We also present the daily patterns of expression and abundance of Pelagibacter ubique and other heterotrophic bacteria, and show that the phages that infect them, such as the highly abundant SAR11 and SAR116 phages, are very diverse and poorly characterized.