טכניון מכון טכנולוגי לישראל
הטכניון מכון טכנולוגי לישראל - בית הספר ללימודי מוסמכים  
Ph.D Thesis
Ph.D StudentFeingersch Roi
SubjectEnvironmental Genomics of Eastern Mediterranean
DepartmentDepartment of Biology
Supervisor Professor Oded Beja
Full Thesis textFull thesis text - English Version


Abstract

Offshore waters of the eastern Mediterranean Sea are one of the most oligotrophic regions on Earth in which the primary productivity is phosphorus (P) limited. To study the unexplored function and physiology of microbes inhabiting this system, we have analyzed a genomic library from the eastern Mediterranean Sea surface waters by sequencing both termini of nearly 5000 clones. Genome recruitment strategies showed that the majority of high-scoring pairs corresponded to genomes from the Alphaproteobacteria (SAR11-like and Rhodobacterales), Cyanobacteria (Synechococcus and high-light adapted Prochlorococcus) and diverse uncultured Gammaproteobacteria. The community structure observed, as evaluated by both protein similarity scores or metabolic potential, was similar to that found in the euphotic zone of the ALOHA station off Hawaii but very different from that of deep aphotic zones in both the Mediterranean Sea and the Pacific Ocean. In addition, a strong enrichment toward phosphate and phosphonate (Pn) uptake and utilization metabolism was also observed.

Studies have indicated that Bacterial Artificial Chromosomes (BAC) and fosmid libraries contain biases against the relative proportion of certain phyla’s when trying to analyze their sequence identity and more specific in the representation of the SAR11 group. Here we discuss those biases and that the SAR11 group might be under-represented in fosmid and BAC libraries due to possible bias against toxic effects of some of their proteins and not as a result of the very low GC content of the SAR11 core genomes.

Pn are diverse organic P compounds containing C-P bonds and comprise up to 25% of the high-molecular-weight dissolved organic P pool (DOP) in the open ocean. Pn bioavailability was suggested to markedly influence bacterial primary production in low-P areas. Using metagenomic data from the Global Ocean Sampling expedition we show that the main microbial player of Pn utilization in oceanic surface water is the globally important marine primary producer Prochlorococcus. Moreover, a number of Prochlorococcus ecotypes harness two distinct Pn uptake operons coding for ABC-type Pn transporter. Based on microcalorimetric measurements, we find that each of the two different Pn-binding proteins (PhnD) transcribed by these operons possesses different Pn- as well as inorganic phosphite-binding specificities. Our results suggest that Prochlorococcus adapt to low P environments by increasing the number of Pn transporters with different specificities to different Pns and phosphite (HPn).