Genomic taxonomy of the genus prochlorococcus.

The genus Prochlorococcus is globally abundant and dominates the total phytoplankton biomass and production in the oligotrophic ocean. The single species, Prochlorococcus marinus, comprises six named ecotypes. Our aim was to analyze the taxonomic structure of the genus Prochlorococcus. We analyzed the complete genomes of 13 cultured P. marinus type and reference strains by means of several genomic taxonomy tools (i.e., multilocus sequence analysis, amino acid identity, Karlin genomic signature, and genome to genome distance). In addition, we estimated the diversity of Prochlorococcus species in over 100 marine metagenomes from all the major oceanic provinces. According to our careful taxonomic analysis, the 13 strains corresponded, in fact, to ten different Prochlorococcus species. This analysis establishes a new taxonomic framework for the genus Prochlorococcus. Further, the analysis of the metagenomic data suggests that, in total, there may only be 35 Prochlorococcus species in the world's oceans. We propose that the dearth of species observed in this study is driven by high selective pressures that limit diversification in the global ocean.

Towards a genome based taxonomy of Mycoplasmas.

Mycoplasmas are Gram-positive wall-less bacteria with a wide environmental and host distribution, causing disease in man and in (wild and farmed) animals. The aim of this study was to analyze the usefulness of a genomic taxonomic approach in Mycoplasma systematics. Multilocus Sequence Analysis (MLSA), average amino acid identity (AAI), and Karlin genomic signature allowed a clear identification of species. For instance, Mycoplasma pneumoniae and Mycoplasma genitalium had only 71% MLSA similarity, 67% AAI, and 88 for Karlin genomic signature. Codon usage (Nc) of the phylogenetically distantly related species Mycoplasma conjunctivae and Mycoplasma gallisepticum was identical, in spite of clear differences in MLSA, AAI, and Karlin, suggesting that these two species were subjected to convergent adaptation due to similar environmental conditions. We suggest that a Mycoplasma species may be better defined based on genomic features. In our hands, a Mycoplasma species is defined as a group of strains that share ≥ 97% DNA identity in MLSA, ≥ 93.9% AAI and ≤ 8 in Karlin genomic signature. This new definition may be useful to advance the taxonomy of Mycoplasmas.