Proposal of fifteen new species of Parasynechococcus based on genomic, physiological and ecological features

Coutinho, Felipe H.; Dutilh, BE; Thompson, Cristiane C.; Thompson, Fabiano L.

doi:10.1007/s00203-016-1256-y

Cited by 8 publications

(10 citation statements)

References 31 publications

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“…Nutrient uptake and utilization: Throughout the aquatic environment a myriad of gradients of nutrient abundance are formed (Stocker and Seymour, 2012 ). The cyanobacterial capacity for uptake and utilization of limiting nutrients (e.g., P, N and Fe) is associated with their ecological niches occupancy (Thompson et al, 2013a ; Coutinho et al, 2016b ; Farrant et al, 2016 ). Considering that significant associations were detected between the abundance of the analyzed genomes and the nutrients sources (phosphorus and nitrogen), we assume that the diversity and efficiency of their nutrient transporters plays a major role in defining the cyanobacterial affiliation to the proposed ecogenomic groups.…”

Section: Discussionmentioning

confidence: 99%

“… h Outgroup used in the phylogenetic analysis . • New taxonomic identification proposed by Coutinho et al ( 2016a , b ) . ○ New taxonomic classification proposed by Thompson et al ( 2013a ) Δ Number of contigs, total length and GC content values were obtained using QUAST tool .…”

Section: Methodsmentioning

confidence: 99%

“…Up-to-date, while several groups have been analyzed through a genomic-wide view (Gupta et al, 2015 ; Adeolu et al, 2016 ; Hahnke et al, 2016 ; Ahn et al, 2017 ; Amin et al, 2017 ; Waite et al, 2017 ), many others have faced hurdles, such as Cyanobacteria. However, a genomic taxonomy approach has successfully been applied to elucidate the taxonomic structure of the two cyanobacterial genera, Prochlorococcus and Synechococcus (Thompson et al, 2013a ; Coutinho et al, 2016a , b ). As genomic taxonomy postulates numeric, non-subjective, cut-offs for taxa delimitation, strains were considered to belong to the same species when share at least 98.8% 16S rRNA gene sequence similarity, 95% of AAI, and 70% GGD (Konstantinidis and Tiedje, 2005a ; Thompson et al, 2013a , b ), while species from the same genus form monophyletic branches (Yarza et al, 2008 ; Qin et al, 2014 ).…”

Section: Introductionmentioning

confidence: 99%

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Ecogenomics and Taxonomy of Cyanobacteria Phylum

et al. 2017

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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.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Ecogenomics and Taxonomy of Cyanobacteria Phylum

et al. 2017

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“…All strains included in S. elongatus clade had high genetic identities (>99.9%). Coutinho et al (2016b) published a separated cluster (with support of phylogenetic position), designated by the name Synechococcus elongatus with the strains PCC 6301 and PCC 7942 and a sister clade Synechococcus sp. with seven other strains.…”

Section: Order Synechococcales Family Synechococcaceaementioning

confidence: 99%

Phylogeny and taxonomy of Synechococcus-like cyanobacteria

Komárek¹,

Johansen²,

Šmarda³

et al. 2020

Fottea

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Unicellular cyanobacteria constitute a substantial, ecologically important part of freshwater and marine microflora. Solitary, elongated cyanobacterial cells without apparent slime envelopes and dividing in a single plane perpendicular to the longitudinal axis were traditionally classified into the genus Synechococcus. The type species originates from a freshwater benthic habitat while a number of other Synechococcus-like species were described from diverse environments. Morphologically similar, unicellular populations of "Synechococcus" belong to the most abundant oxygen evolving prokaryotes inhabiting freshwater and oceanic picoplanktic communities. Other species from extreme thermal habitats were described from temperatures over 70 °C. Recent molecular analyses, particularly the 16S rRNA gene and other multi-locus gene based phylogenies of Synechococcus-like species reveal the polyphyly and phylogenetic diversity of such simple cyanobacteria emphasizing the necessity of their accurate polyphasic taxonomic re-classification. To better understand the phylogeny of different Synechococcus-like species, we constructed a genome-derived phylogenetic tree using 133 cyanobacterial and eubacterial genomes as well as a 16S rRNA gene phylogenetic tree. Both trees indicate existence of deep splits between individual Synechococcus lineages corresponding with indistinct ecological and cytomorphological differences. The generic units derived from the traditional concept of the genus Synechococcus based on the combined traits and markers must be defined and validly described. The comparative taxonomic classification of phylogenetic clusters corresponding to various morphotypes and genotypes similar to the genus Synechococcus (Cyanobium, Parasynechococcus, Picosynechococcus, Prochlorococcus, Thermosynechococcus, Thermostichus) are discussed in the article.

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“…A robust classification system for the SC is still lacking. Coutinho and colleagues (2016a) and Coutinho and colleagues (2016b) made a first attempt to unlock the taxonomy of SC. They compared 24 Synechococcus genomes by using an alignment of 607 orthologous proteins.…”

Section: Introductionmentioning

confidence: 99%

A new genomic taxonomy system for the Synechococcus collective

Salazar

Tschoeke

Swings

et al. 2020

Environmental Microbiology

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Summary Cyanobacteria of the genus Synechococcus are major contributors to global primary productivity and are found in a wide range of aquatic ecosystems. This Synechococcus collective (SC) is metabolically diverse, with some lineages thriving in polar and nutrient‐rich locations and others in tropical or riverine waters. Although many studies have discussed the ecology and evolution of the SC, there is a paucity of knowledge on its taxonomic structure. Thus, we present a new taxonomic classification framework for the SC based on recent advances in microbial genomic taxonomy. Phylogenomic analyses of 1085 cyanobacterial genomes demonstrate that organisms classified as Synechococcus are polyphyletic at the order rank. The SC is classified into 15 genera, which are placed into five distinct orders within the phylum Cyanobacteria: (i) Synechococcales (Cyanobium, Inmanicoccus, Lacustricoccus gen. Nov., Parasynechococcus, Pseudosynechococcus, Regnicoccus, Synechospongium gen. nov., Synechococcus and Vulcanococcus); (ii) Cyanobacteriales (Limnothrix); (iii) Leptococcales (Brevicoccus and Leptococcus); (iv) Thermosynechococcales (Stenotopis and Thermosynechococcus) and (v) Neosynechococcales (Neosynechococcus). The newly proposed classification is consistent with habitat distribution patterns (seawater, freshwater, brackish and thermal environments) and reflects the ecological and evolutionary relationships of the SC.

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Proposal of fifteen new species of Parasynechococcus based on genomic, physiological and ecological features

Cited by 8 publications

References 31 publications

Ecogenomics and Taxonomy of Cyanobacteria Phylum

Ecogenomics and Taxonomy of Cyanobacteria Phylum

Phylogeny and taxonomy of Synechococcus-like cyanobacteria

A new genomic taxonomy system for the Synechococcus collective

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