The mechanisms of recombination that have been shown for Lp include transformation and conjugation (reviewed in ref. 60). It is generally held that Lp1 strains that produce type IV pili are naturally competent for DNA transformation. While indigenous conjugative plasmids have been isolated from clinical and environmental Legionella and there is a recognized chromosome-based system for plasmid transfer, the majority of Lp1 strains do not contain these plasmids, as mentioned above, and are therefore unlikely to be necessary for virulence60. The CRISPR spacer analysis revealed that there is apparently a large ‘dark’ Legionella pan-genome, consisting of non-chromosomal DNA, presumably bacteriophage, suggesting that the true size of the pan-genome is considerably larger than the model-based estimation of 30,275. Interestingly, our GO and CRISPR findings for the monomorphic Lp serogroups, which are predicted to have an almost closed pan-genome and very few unique strain-specific genes, suggest that there is selective acquisition of genes that have enabled the organism to defend against phage attacks and to survive in both environmental and protozoan/eukaryotic hosts. These data indicate that the pool of foreign DNA in the environment able to be incorporated into the species is much greater than the number of genes that have actually been fixed in the chromosome.