טכניון מכון טכנולוגי לישראל
הטכניון מכון טכנולוגי לישראל - בית הספר ללימודי מוסמכים  
Ph.D Thesis
Ph.D StudentFlores-Uribe Jose
SubjectCharacterization of Ocean Metagenomes: from
Phages to Proteins
DepartmentDepartment of Biology
Supervisor Professor Oded Beja
Full Thesis textFull thesis text - English Version


Abstract

Estimates indicate that only about 1% of the microorganisms in the environment can be cultured under standard laboratory conditions. Metagenomics allows the study of microbial communities by sequencing genetic material obtained directly from the environment. Metagenomic data can be analyzed to shed light into different biological questions by using bioinformatics.

            Recently projects like the Tara Oceans expedition have produced a large amount of metagenomic data from the marine environment, the rate at data is being generated requires the implementation of novel pipelines and analysis techniques. Here bioinformatic pipelines were developed to analyze metagenomes with focus in: (i) uncultured viruses and (ii) a the distribution of a rhodopsin protein family.

            In the first part Metagenome Assembled Genomes (MAGs) from a family of uncultured viruses infecting marine cyanobacteria (cyanophages) were identified. Cyanophages play an important role regulating microbial populations and nutrient cycling. The family described here prevails in several regions of the ocean, possess genes previously undescribed in marine viruses, and forms an uncharacterized lineage among cyanophages. Furthermore, this lineage is related to a genomic island in the marine cyanobacteria Synechococcus WH8016. The genomic island shares several genes in synteny with the MAGs and it?s flanked by tRNAs which might indicate a viral integration event into the WH8016 chromosome. However, our efforts to induce a lytic cycle from WH8016 in the laboratory were not successful. Our results suggest that the island might be a ?relic prophage? establishing a link between the novel viral family discovered and the elusive temperate marine cyanophages.

            The second part studies heliorhodopsins, a recently discovered rhodopsin family of unknown biological activity. Comparing heliorhodopsins to type-1 microbial rhodopsins their diversity, abundance, biogeography, and taxonomical distribution was revealed. Heliorhodopsins were found to be abundant in the photic zone, widespread in the environment, detected in viruses and across the three domains of life. Interestingly, our initial screening could not detect heliorhodopsins in Proteobacteria, one of the most abundant phylum in the environment. To address this observation, ~150 million proteins from metagenomes and cultured isolates were analyzed, looking for heliorhodopsins. The analysis indicated that heliorhodopsins are not present in Proteobacteria nor in any other Gram-negative bacteria, with a single Sphaerochaeta occurrence being the only exception. Our results help us to speculate on the putative role of heliorhodopsins in light-driven transport of amphiphilic molecules.

These studies could be a starting point to develop new metagenomic data-driven projects. Moreover, the methodologies employed here can be applied to other families of microbes, viruses, and proteins, helping to answer different biological questions.