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. 2024 Jan 9:371:fnad136.
doi: 10.1093/femsle/fnad136.

Phylogenetic analysis of Nostocales (Cyanobacteria) based on two novel molecular markers, implicated in the nitrogenase biosynthesis

Affiliations

Phylogenetic analysis of Nostocales (Cyanobacteria) based on two novel molecular markers, implicated in the nitrogenase biosynthesis

Christos Giannakopoulos et al. FEMS Microbiol Lett. .

Abstract

The characterization of cyanobacteria communities remains challenging, as taxonomy of several cyanobacterial genera is still unresolved, especially within Nostocales taxa. Nostocales cyanobacteria are capable of nitrogen fixation; nitrogenase genes are grouped into operons and are located in the same genetic locus. Structural nitrogenase genes (nifH, nifK and nifD) as well as 16S rRNA have been shown to be adequate genetic markers for distinguishing cyanobacterial genera. However, there is no available information regarding the phylogeny of regulatory genes of the nitrogenase cluster. Aiming to provide a more accurate overview of the evolution of nitrogen fixation, this study analyzed for the first time nifE and nifN genes, which regulate the production of nitrogenase, alongside nifH. Specific primers were designed to amplify nifE and nifN genes, previously not available in literature and phylogenetic analysis was carried out in 13 and 14 TAU-MAC culture collection strains, respectively, of ten Nostocales genera along with other sequences retrieved from cyanobacteria genomes. Phylogenetic analysis showed that these genes seem to follow a common evolutionary pattern with nitrogenase structural genes and 16S rRNA. The classification of cyanobacteria based on these molecular markers seems to distinguish Nostocales strains with common morphological, ecological, and physiological characteristics.

Keywords: ecophysiological characters; nif genes; nitrogenase evolution; novel markers; phylogeny; taxonomy.

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Conflict of interest statement

None declared.

Figures

Figure 1.
Figure 1.
Agarose gel electrophoresis analysis of PCR amplification products of the nifE gene in cyanobacterial strains TAU-MAC 0515, 0699, 0599, 0799, 0899, 2510, 2610, and 2710. The observed bands demonstrate an approximate size of 1 250 base pairs (bp).
Figure 2.
Figure 2.
Agarose gel electrophoresis analysis of PCR amplification products of the nifN gene in cyanobacterial strains TAU-MAC MAC 2510, 2610, 2710, 1614 and 1714. The observed bands demonstrate an approximate size of 1 150 base pairs (bp).
Figure 3.
Figure 3.
Bayesian phylogenetic tree of nucleotide sequences of the nifE gene (1,272 bp) in cyanobacteria. The five labeled groups, as described in the text, represent distinct clades based on shared ecological and physiological characteristics. The numbers adjacent to the branches represent posterior probabilities obtained from the Bayesian Inference (BI) method and bootstrap values from the Maximum Likelihood (ML) method, respectively.
Figure 4.
Figure 4.
Bayesian phylogenetic tree of nucleotide sequences of the nifN gene (1,166 bp) in cyanobacteria. The five labeled groups, as described in the text, represent distinct clades based on shared ecological and physiological characteristics. The numbers adjacent to the branches represent posterior probabilities obtained from the Bayesian Inference (BI) method and bootstrap values from the Maximum Likelihood (ML) method, respectively.

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