טכניון מכון טכנולוגי לישראל
הטכניון מכון טכנולוגי לישראל - בית הספר ללימודי מוסמכים  
Ph.D Thesis
Ph.D StudentYutin Natalya
SubjectDiversity and Biogeography of Marine Aerobic Anoxygenic
Photosynthetic Bacteria
DepartmentDepartment of Biology
Supervisor Professor Oded Beja


Abstract

Anoxygenic photosynthesis is the most ancient form of photosynthesis, as known to date. Since their discovery in the marine environment, Aerobic Anoxygenic Phototrophic bacteria (AAnP) were reported to be present in a variety of coastal and oceanic environments. Recent reports suggest that AAnPs compose a significant fraction of marine bacterioplankton communities and represent up to 11% of the total surface water microbial community. However, the relative abundance and importance of AAnPs to the flow of energy and carbon in the ocean is still controversial. 

The pufM gene encodes the M subunit of anoxygenic photosynthetic reaction centers. Until now, the diversity of marine AAnP was mainly estimated by amplifying the pufM gene from environmental samples, bacterial artificial chromosome (BAC) clones or cultured representatives. These studies brought the discovery of novel AAnPs that belong to different groups of Alpha- and Gammaproteobacteria. However, these results are influenced by the ability of primers to target diverse sequences, and by the resistance of the majority of marine bacteria to cultivation.

The general goal of this study was to investigate the genetic variability of marine AAnPs and to characterize distribution and composition of AAnP populations in different marine environments. The research was mainly based on culture-independent and metagenomic approaches.

Using genomic data from the GenBank, we checked the potential of most widely used pufM primers to target diverse environmental sequences. We revealed that previously used primers did not assess comprehensively the diversity of marine AAnPs.  We have designed and tested a new set of pufM primers and identify several new AAnP variants in environmental DNA samples and genomic libraries.

We identified examples of the puf-operon from cultured bacteria and environmental BAC sequences currently available in GenBank and from two metagenomic shotgun projects, the Sargasso Sea project and the Global Ocean Sampling (GOS) project. We found diverse operon organizations of puf-operons that reflected structural differences of the core complex in marine AAnPs.

We have studied AAnP diversity, abundance and population composition using the GOS data. New, previously undetected groups of AAnPs were found prevalent in the majority of open-sea AAnP communities. Furthermore, we show, for the first time, that the composition of AAnP assemblages changes between different oceanic regions with specific bacterial assemblages adapted to open ocean or coastal areas, respectively. Our results support the notion that marine AAnP populations are complex and dynamic and compose a significant portion of bacterioplankton assemblages in certain oceanic areas.