The Acinetobacter venetianus pan-genome: clues on microbial hydrocarbon degradation

Some strains of the species Acinetobacter venetianus were demonstrated to be able to degrade alkanes of various chain length and were shown to possess genomic distinctness from the other strains belonging to the genus. In particular, some of them, namely A. venetianus VE-C3, RAG1T, LUH5627, LUH8758 and LUH7437 were shown to be able to grow on C10, C14 and C20, although with sensibly different efficiency. Moreover, fragmentation of diesel fuel drops at the cell wall was observed (although likely carried out with peculiar molecular strategies for each strain), thus suggesting their strong bioemulsifying activity. These physiological properties led us to choose these strains as a candidates for the determination of their genome sequences in order to gain more insights into the molecular mechanisms responsible for the degradation of n-alkanes and the genetic features representative for the species A. venetianus. Genome sequencing was performed with both Illumina and Roche 454 technologies and preliminary analysis of genome assemblies allowed us to identify important differences among both all the A. venetianus representatives and among the other, publically available, Acinetobacter genomes, thus revealing the possible genetic basis of observed different phenotypic traits (i.e. different efficiency/strategies in fuel degradation). Obtained sequences revealed a strong genomic distinctness both at inter- and intra-genus levels as, for example, gene predictions resulted in the identification of higly variable gene sets for each genome, ranging from 3307 (A. venetianus RAG-1T) to 3744 (A. venetianus VE-C3). Furthermore, the predicted genes were clustered in COG categories allowing the identification of putative niche-adaptation and fuel-degradation specific gene sets. The study of the A. venetianus pan-genome affords an opportunity for the analysis and manipulation of genes and gene products, and paves the way for a future analysis of metabolic transformations in the environment.