טכניון מכון טכנולוגי לישראל
הטכניון מכון טכנולוגי לישראל - בית הספר ללימודי מוסמכים  
Ph.D Thesis
Ph.D StudentAtamna-Ismaeel Nof
SubjectEcological Diversity of Microbial Rhodopsins in Freshwater
Ecosystems; Sea Ice and in the Phyllosphere of
Terrestrial Plants
DepartmentDepartment of Biology
Supervisor Professor Oded Beja
Full Thesis textFull thesis text - English Version


Abstract

Proteorhodopsins (PRs) are bacterial, retinal-binding membrane pigments that function as light-driven proton pumps in the marine ecosystem. PRs were shown experimentally to exist in several marine environments with a worldwide distribution; these findings were also supported by metagenomic data retrieved from the Global Ocean Sampling (GOS) expedition sites. In this study we investigated the presence of microbial rhodopsins in various non-marine environments; freshwater, Sea Ice and a terrestrial environment; the phyllosphere, using both experimental approaches and metagenomics.

In order to investigate the presence of PRs in freshwater environments, we have designed several sets of primers targeting freshwater microbial rhodopsins, based on both GOS retrieved PR sequences and PR sequences from culture. We showed for the first time the presence of microbial rhodopsins in freshwater environments globally. Freshwater microbial rhodospins were found to cluster separately from the marine ones, forming unique phylogenetic groups. Phylogenomic analysis of genes found on these GOS scaffolds representatives suggests that some of the freshwater PRs are found in freshwater Proteobacteria, Actinobacteria, Flavobacteria and the Fibrobacteres, Chlorobi Bacteroidetes (CFB) groups.

Furthermore, we have investigated the presence of these microbial rhodopsins in the Antarctic Sea-Ice. We were able to present the first report of PR-bearing bacteria, both dormant and active, in Antarctic Sea-Ice from a series of sites in the Ross Sea using PR specific primers. Positive PR sequences were generated from genomic DNA and from cDNA reverse transcribed from RNA, at all depths in Sea-Ice. This finding indicates that these sequences were generated from metabolically active cells and suggests that the PR gene is functional within Sea-Ice.

Lastly we investigated the presence of PR genes in the phyllosphere; the above-ground surfaces of terrestrial plants. Based on metagenomic data, we were able to show the existence of diverse microbial rhodopsins in five distinct phyllospheres from Tamarix, soybean, Arabidopsis, clover and rice. Our findings, for the first time describe microbial rhodopsins from a non-aquatic habitat and show the coexistence of microbial rhodopsin-based phototrophy and plant chlorophyll-based photosynthesis, with the different pigments absorbing non-overlapping fractions of the light spectrum.

Microbial rhodopsins provide a new perspective on the nature of light use strategies in various non-marine and terrestrial habitats. Our data imply that there is a widespread distribution of several bacterial groups that use the PR-based phototrophy as a way to harvest additional energy in the terrestrial and the non-marine environments, which may have a significant impact on the global energy fluxes.