Ecogenomics and Taxonomy of Cyanobacteria Phylum

Abstract

Cyanobacteria are major contributors to global biogeochemical cycles. The genetic diversity among Cyanobacteria enables them to thrive across many habitats, although only a few studies have analyzed the association of phylogenomic clades to specific environmental niches. In this study, we adopted an ecogenomics strategy with the aim to delineate ecological niche preferences of Cyanobacteria and integrate them to the genomic taxonomy of these bacteria. First, an appropriate phylogenomic framework was established using a set of genomic taxonomy signatures (including a tree based on conserved gene sequences, genome-to-genome distance, and average amino acid identity) to analyse ninety-nine publicly available cyanobacterial genomes. Next, the relative abundances of these genomes were determined throughout diverse global marine and freshwater ecosystems, using metagenomic data sets. The whole-genome-based taxonomy of the ninety-nine genomes allowed us to identify 57 (of which 28 are new genera) and 87 (of which 32 are new species) different cyanobacterial genera and species, respectively. The ecogenomic analysis allowed the distinction of three major ecological groups of Cyanobacteria (named as i. Low Temperature; ii. Low Temperature Copiotroph; and iii. High Temperature Oligotroph) that were coherently linked to the genomic taxonomy. This work establishes a new taxonomic framework for Cyanobacteria in the light of genomic taxonomy and ecogenomic approaches.

Insights on the taxonomy and ecogenomics of theSynechococcuscollective

“…To the best of our knowledge, there is not a consensus on whether the Synechococcus form a monophyletic clade. This may be the case for specific marine or freshwater lineages, but when examined in the context of the Cyanobacteria phylum, the genus as presently classified is paraphyletic or polyphyletic as demonstrated here (Walter et al 2017). Our advanced genomic taxonomy analyses demonstrate the heterogeneous nature of the SC collective.…”

“…The new nomenclature also highlighted the genetic difference between marine Parasynechococcus and freshwater Synechococcus. Walter et al (2017) further elucidates this difference and propose 12 genera for the SC. However, the limited number genomes examined in this previous study hampered a more fine-grained taxonomic analysis of the Synechococcus collective.…”

“…Names for each genera were maintained the same as in Walter et al (2017). An exception to that are the newly-named Synechospongium gen. nov. and Lacustricoccus gen. nov.…”

“…Heterogeneous genera are mostly marine lineages, and display the highest number of genomes (47 and 41, respectively) (Table 1). They are considered oceanic generalists, living in both low and high temperature environments(Walter et al 2017). In contrast, the…”

Unlocking the genomic taxonomy of theProchlorococcuscollective

“…Strains of the same species form monophyletic groups on the basis of MLSA [16]. Walter et al [18] further split the Prochlorococcus collective into three new genera: (1) the genus Eurycolium (type species Eurycolium pastoris with the type strain MED4 T (= CCMP 1986 T ), E. chisholmii with its type strain AS9601 T , E. ponticus with its type strain MIT9301 T , E. nereus with its type strain MIT9202 T ), E. neptunius with its type strain MIT9312 T , E. ponticus with its type strain MIT 9301 T , and E. tetisii with its type strain MIT9515 T ; (2) the genus Prolificoccus, with Prolificoccus proteus as the type species and NATL2A T as its type strain; and (3) the genus Thaumococcus, with Thaumococcus swingsii as the type species and the type strain MIT9313 T . The current (type) genus Prochlorococcus contains two species: the type species Prochlorococcus marinus and its type strain SS120 T (= CCMP 1375 T ) and P. ceticus with its type strain MIT9211 T .…”