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Front Microbiol. 2017 Nov 14;8:2132. doi: 10.3389/fmicb.2017.02132. eCollection 2017.

Ecogenomics and Taxonomy of Cyanobacteria Phylum.

Author information

1
Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
2
Radboud Institute for Molecular Life Sciences, Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, Netherlands.
3
Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands.
4
Laboratory of Microbiology, Ghent University, Ghent, Belgium.
5
Center of Technology - CT2, SAGE-COPPE, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.

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.

KEYWORDS:

charting biodiversity; ecological niches; genome-based microbial taxonomy; high-throughput sequencing technology; metagenome; microbial ecology

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