How many species of cyanobacteria are there

Evolution studies on closely related bacteria show rapid and highly variable gene fluxes in evolving microbial genomes, suggesting that extensive gene loss and horizontal gene transfer leading to innovation are the dominant evolutionary processes Batut et al. CGT will solve the often-observed issue that even closely related genomes contain high gene content variation, that gives phenotypic variation. CGT is completely adjusting to the genomics era, addressing the needs of its users in microbial ecology and clinical microbiology, in a new paradigm of open access Beiko, CGT will provide a predictive operational framework for reliable automated and openly available identification and classification Thompson et al.

A main gap exists and is growing each day between the formal taxonomy of Cyanobacteria and the forest of acronyms and numbers in the different databases. There is a need to re-examine the Cyanobacteria prokaryote species, taking into account all recently developed concepts, e. The international initiatives of GEBA are currently working on determining the WGS of all type strains of known microbial species to shorten this gap more than eleven thousand genomes.

We strongly recommended that the modern taxonomy should be based on WGS. The enormous amount of unique gene sequences e. It will avoid the inclusion of the previously erroneous taxa on the analysis. Furthermore, the anxiety to give a new name should be reconsidered.

Proposes of new taxa where the phylogenetic relationship was not firmly established are frequently found e. Correlation analysis allowed us to characterize how the abundance of the analyzed genomes is associated with environmental parameters at both marine and freshwater habitats. These associations shed light on ecological interactions taking place within aquatic habitats that are responsible for delineating the ecological niches of Cyanobacteria.

Our results showed that taxonomic affiliation and niche occupancy are coherently linked, i. The identification of specific features responsible for defining niche occupancy among these organisms depends on extensive experimental data focusing on both physiological and morphological features, which is outside of our scope. Nevertheless, we speculate that some features are likely playing a role in this process:.

The cyanobacterial capacity for uptake and utilization of limiting nutrients e. 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. Species differ with regard their preferred light intensities and wavelengths which affects their photosynthetic efficiency Moore et al.

They also can be differentiated regarding their carboxysomes, sub-cellular structures where carbon fixation takes place Yeates et al. To our knowledge, no study has consistently compared the photosynthetic yields of all the strains analyzed here, therefore we cannot determine if the proposed ecogenomic groups differ regarding this parameter.

Nevertheless, distinctions regarding their requirements for efficient photosynthesis are likely linked to their patterns of niche occupancy. Over the past two centuries, human development has affected aquatic ecosystems due to nutrient over-enrichment eutrophication , hydrologic alterations, global warming and ocean acidification.

Temperature is one of the most important factors determining the taxonomic composition of marine microbial communities Sunagawa et al. Our data shows that temperature is central for regulating the composition and functioning of cyanobacterial communities. Global warming can affect growth rates and bloom potentials of many taxa within this phylum Fu et al.

Niche based models predict an increase in the absolute levels of organisms formerly classified as Prochlorococcus and Synechococcus due to global warming Flombaum et al.

Consequently, the functioning of the biogeochemical cycles in which these organisms are involved will also be affected Fu et al. Nevertheless, much less is known regarding how global warming could affect communities of Cyanobacteria aside from these two groups of organisms.

The ecogenomic groups identified and their associations with environmental parameters shed light into the potential changes that communities of Cyanobacteria will undergo following global climate changes. Our results indicate that an increase in temperature will lead to decreases in the relative abundances of Low Temperature and Low Temperature Copiotroph groups, while that of High Temperature Oligotroph group increases, especially those of species Eurycolium neptunis, E.

One major impact of this alteration is a possible effect on the degree of nitrogen fixation mediated by Cyanobacteria, as none of the species assigned to the High Temperature Oligotroph group are known to fix nitrogen Latysheva et al.

In fact, our data shows that higher temperatures are associated with lower relative abundances of nitrogen fixating Cyanobacteria of the genera Trichodesmium and Anabaena Zehr, Both beneficial and deleterious effects of the ocean warming and associated phenomena e. Rising temperatures might shift cyanobacterial community composition toward a state were diazotrophs are relatively less abundant. Because nitrogen is often a limiting nutrient to marine primary productivity Tyrrell, ; Moore et al.

Furthermore, our findings suggest that changes in temperature can affect the contributions of Cyanobacteria to the global carbon pump Flombaum et al. For example, the five strongest positive correlations with temperature between the High Temperature Oligotroph group involve the high-light adapted members of the Eurycolium genus i. These are high-light adapted strains that display lower photosynthetic efficiency than their low-light adapted counterparts Moore et al.

Our results suggest that the relative abundance of high-light adapted strains would increase induced by the rising temperatures.

In turn, these changes could affect the efficiency of carbon fixation in the ocean, a change that could also be influenced by the alterations in nitrogen fixation mentioned above. The present study proposes a first attempt toward integrating taxonomy and ecogenomics, offering a compelling new perspective for the development of Cyanobacteria studies. Our results show that closely related genomes often share a niche and can be assigned to the same ecogenomic group. End-users of Cyanobacteria taxonomy may benefit from a more reproducible and portable taxonomic scheme.

Future studies are needed to expand the evolutionary and physiological basis for the cyanobacterial niche occupancy, integrating other important ecological variables such as phage susceptibility, light utilization strategies, horizontal gene transfer, and inter-species interactions.

All authors contributed to the writing of the manuscript. JW and FC performed the bioinformatics analyses, analyzed the results, and compiled the data. All authors approved the final version of the manuscript. The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

This paper is part of the D. Figure S1. Ribosomal phylogenetic reconstruction of the Cyanobacteria phylum. The species cut-off was The percentages of replicate trees in which the associated taxa clustered together in the bootstrap test 1, replicates are shown next to the branches. Overwritten T indicates type strain or type species of validly published species to assess their correct phylogenetic assignations. Bold names indicate the additional type strains or type species only for 16S tree.

Gloeobacter violaceus PCC sequence was designated as outgroup. Figure S2. Heatmaps based on GGD metrics of specific cases.

The GGD values are associated with the respective thermal color scale located at the bottom left corner of the figure. The proposed new names were adopted in this figure. Figure S3. Abundance and distribution of ecogenomic clusters across global marine metagenomes. Figure S4. Abundance and distribution of ecogenomic clusters across freshwater metagenomes. B Non-metric multidimensional scaling NMDS analysis of the freshwater metagenomes and environmental parameters.

C Non-metric multidimensional scaling NMDS analysis of the freshwater metagenomes and environmental parameters Ordination plot of ecogenomic clusters. Table S1. Estimates of genome relatedness of cyanobacterium strains. Values at the matrix indicates the intergenomic distances i. The numbers of base substitutions per site between sequences are shown. Analyses were conducted accordingly Tamura et al.

The analysis involved nucleotide sequences. All positions containing gaps and missing data were eliminated. There were a total of positions in the final dataset. Evolutionary analyses were conducted in MEGA6. Table S2. Details of all cyanobacterial genomes included in this study.

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Hahnke, R. In less eutrophic waters, some species also form colonies, which are large dark dots in water samples and on filters after filtration.

Planktothrix agardhii forms long, slender, straight filaments that usually remain separate but form dense surface scums. Its presence may be revealed by a strong earthy odor and the filaments are easily detected visually in a water sample. The most commonly found cyanotoxins in the U. Microcystins are produced by Dolichospermum previously Anabaena , Fischerella , Gloeotrichia, Nodularia , Nostoc, Oscillatoria , members of Microcystis , and Planktothrix.

Microcystins are the most widespread cyanobacterial toxins and can bioaccumulate in common aquatic vertebrates and invertebrates such as fish, mussels, and zooplankton. Microcystins primarily affect the liver hepatotoxin , but can also affect the kidney and reproductive system.

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Cylindrospermopsin is usually produced by Raphidiopsis previously Cylindrospermopsis , raciborskii C. The primary toxic effects of this toxin are damage to the liver and kidney.

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