Prokaryotes are the main actors in biogeochemical cycles that are fundamental in global nutrient cycling. The characterization of microbial communities and isolates can enhance the comprehension of such cycles. Potentially novel biochemical processes can be discovered in particular environments with unique characteristics. The Red Sea can be considered as a unique natural laboratory due to its peculiar hydrology and physical features including temperature, salinity and water circulation. Moreover the Red Sea is subjected to hydrocarbon pollution by both anthropogenic and natural sources that select hydrocarbon degrading prokaryotes. Due to its unique features the Red Sea has the potential to host uncharacterized novel microorganisms with hydrocarbondegrading pathways. The focus of this thesis is on the characterization at the metagenomic level of the water column of the Red Sea and on the isolation and characterization of novel hydrocarbon-degrading species and genomes adapted to the unique environmental characteristics of the basin. The presence of metabolic genes responsible of both linear and aromatic hydrocarbon degradation has been evaluated from a metagenomic survey and a meta-analysis of already available datasets. In parallel, water column-based microcosms have been established with crude oil as the sole carbon source, with aim to isolate potential novel bacterial species and provide new genome-based insights on the hydrocarbon degradation potential available in the Red Sea.

Hydrostatic pressure (HP) and low temperature are among the main parameters that affect the microbial activity in the deep sea. Especially in the event of an oil spill, the natural microbial degradation of hydrocarbons in the harsh conditions of the deep sea can be significantly impaired. In the Red Sea, the temperature in the deep (22°C) is much higher than in other oceans and may favor hydrocarbon degradation. Bacteria of the genus Alcanivorax, which are prominent and ubiquitous alkane degrading bacteria, have been extensively studied because of their high abundance in oil-contaminated shallow water, but have been shown to be absent in the deep sea because of their piezo-sensitivity. In the present thesis, the novel species Alcanivorax marisrubri isolated at 1000 m from the Southern Red Sea has been evaluated for its piezo-adaptation under different combinations of temperature, and HP. A. marisrubri showed a piezotolerance different from other Alcanivorax species. Furthermore, a positive compensation of growth inhibition was observed when the cells were exposed to mild HP (10 MPa) in combination with a relatively high temperature of 38°C. While growth was inhibited at lower temperatures (20 and 26°C) under mild-HP (5 and 10 MPa), the metabolic activity was triggered, possibly in response to cellular stress. This study showed that the growth and metabolic activity of A. marisrubri under HP depend on temperature, which exerts a positive compensation effect and may extend the growth of this bacterium to the depths of the Red Sea.