Cyanobacteria Phylogenetic Studies Reveal Evidence for Polyphyletic Genera from Thermal and Freshwater Habitats

Screening of Lipid-Reducing Activity and Cytotoxicity of the Exometabolome from Cyanobacteria

Cyanobacteria are rich producers of secondary metabolites, excreting some of these to the culture media. However, the exometabolome of cyanobacteria has been poorly studied, and few studies have dwelled on its characterization and bioactivity assessment. In this work, exometabolomes of 56 cyanobacterial strains were characterized by HR-ESI-LC-MS/MS. Cytotoxicity was assessed on two carcinoma cell lines, HepG2 and HCT116, while the reduction in lipids was tested in zebrafish larvae and in a steatosis model with fatty acid-overloaded human liver cells. The exometabolome analysis using GNPS revealed many complex clusters of unique compounds in several strains, with no identifications in public databases. Three strains reduced viability in HCT116 cells, namely Tolypotrichaceae BACA0428 (30.45%), Aphanizomenonaceae BACA0025 (40.84%), and Microchaetaceae BACA0110 (46.61%). Lipid reduction in zebrafish larvae was only observed by exposure to Dulcicalothrix sp. BACA0344 (60%). The feature-based molecular network shows that this bioactivity was highly correlated with two flavanones, a compound class described in the literature to have lipid reduction activity. The exometabolome characterization of cyanobacteria strains revealed a high chemodiversity, which supports it as a source for novel bioactive compounds, despite most of the time being overlooked.

Description of four new filamentous cyanobacterial taxa from freshwater habitats in the Azores Archipelago

Simple filamentous cyanobacteria comprise a diverse and polyphyletic group of species, primarily in the orders Leptolyngbyales and Oscillatoriales, that need more sampling to improve their taxonomy. Oceanic islands, such as the Azores archipelago, present unique habitats and biogeographic conditions that harbor an unknown range of diversity of microorganisms. Filamentous cyanobacteria isolated from aquatic habitats in the Azores and maintained in the BACA culture collection were described using morphology, both light and transmission electron microscopy, ecology, and genetic data of the 16S rRNA gene sequences and 16S-23S Internal Transcribed Spacer (ITS) rRNA region secondary structure. Our analyses revealed two new monophyletic genera: Tumidithrix elongata gen. sp. nov. (Pseudanabaenaceae) and Radiculonema aquaticum gen. sp. nov. (Leptolyngbyaceae). In addition, two new species Leptodesmis lacustris sp. nov. (Leptolyngbyaceae) and Pycnacronema lacustrum sp. nov. (Wilmottiaceae) are reported as the first aquatic species for these genera. The description of these new taxa and the genetic study of an isolate of Leptodesmis alaskaensis from the Azores followed the polyphasic approach, identifying diacritical features. Our results reinforce the need for taxonomic studies on cyanobacteria from less-studied habits and geographic regions, which have a potential for new taxa description.

Characterization of a novel thermophilic cyanobacterium within Trichocoleusaceae, Trichothermofontia sichuanensis gen. et sp. nov., and its CO2-concentrating mechanism

Thermophiles from extreme thermal environments have shown tremendous potential regarding ecological and biotechnological applications. Nevertheless, thermophilic cyanobacteria remain largely untapped and are rarely characterized. Herein, a polyphasic approach was used to characterize a thermophilic strain, PKUAC-SCTB231 (hereafter B231), isolated from a hot spring (pH 6.62, 55.5°C) in Zhonggu village, China. The analyses of 16S rRNA phylogeny, secondary structures of 16S-23S ITS and morphology strongly supported strain B231 as a novel genus within Trichocoleusaceae. Phylogenomic inference and three genome-based indices further verified the genus delineation. Based on the botanical code, the isolate is herein delineated as Trichothermofontia sichuanensis gen. et sp. nov., a genus closely related to a validly described genus Trichocoleus. In addition, our results suggest that Pinocchia currently classified to belong to the family Leptolyngbyaceae may require revision and assignment to the family Trichocoleusaceae. Furthermore, the complete genome of Trichothermofontia B231 facilitated the elucidation of the genetic basis regarding genes related to its carbon-concentrating mechanism (CCM). The strain belongs to β-cyanobacteria according to its β-carboxysome shell protein and 1B form of Ribulose bisphosphate Carboxylase-Oxygenase (RubisCO). Compared to other thermophilic strains, strain B231contains a relatively low diversity of bicarbonate transporters (only BicA for HCO₃^- transport) but a higher abundance of different types of carbonic anhydrase (CA), β-CA (ccaA) and γ-CA (ccmM). The BCT1 transporter consistently possessed by freshwater cyanobacteria was absent in strain B231. Similar situation was occasionally observed in freshwater thermal Thermoleptolyngbya and Thermosynechococcus strains. Moreover, strain B231 shows a similar composition of carboxysome shell proteins (ccmK1-4, ccmL, -M, -N, -O, and -P) to mesophilic cyanobacteria, the diversity of which was higher than many thermophilic strains lacking at least one of the four ccmK genes. The genomic distribution of CCM-related genes suggests that the expression of some components is regulated as an operon and others in an independently controlled satellite locus. The current study also offers fundamental information for future taxogenomics, ecogenomics and geogenomic studies on distribution and significance of thermophilic cyanobacteria in the global ecosystem.

Spatial and temporal dynamics at an actively silicifying hydrothermal system

Steep Cone Geyser is a unique geothermal feature in Yellowstone National Park (YNP), Wyoming, actively gushing silicon-rich fluids along outflow channels possessing living and actively silicifying microbial biomats. To assess the geomicrobial dynamics occurring temporally and spatially at Steep Cone, samples were collected at discrete locations along one of Steep Cone's outflow channels for both microbial community composition and aqueous geochemistry analysis during field campaigns in 2010, 2018, 2019, and 2020. Geochemical analysis characterized Steep Cone as an oligotrophic, surface boiling, silicious, alkaline-chloride thermal feature with consistent dissolved inorganic carbon and total sulfur concentrations down the outflow channel ranging from 4.59 ± 0.11 to 4.26 ± 0.07 mM and 189.7 ± 7.2 to 204.7 ± 3.55 μM, respectively. Furthermore, geochemistry remained relatively stable temporally with consistently detectable analytes displaying a relative standard deviation <32%. A thermal gradient decrease of ~55°C was observed from the sampled hydrothermal source to the end of the sampled outflow transect (90.34°C ± 3.38 to 35.06°C ± 7.24). The thermal gradient led to temperature-driven divergence and stratification of the microbial community along the outflow channel. The hyperthermophile Thermocrinis dominates the hydrothermal source biofilm community, and the thermophiles Meiothermus and Leptococcus dominate along the outflow before finally giving way to more diverse and even microbial communities at the end of the transect. Beyond the hydrothermal source, phototrophic taxa such as Leptococcus, Chloroflexus, and Chloracidobacterium act as primary producers for the system, supporting heterotrophic growth of taxa such as Raineya, Tepidimonas, and Meiothermus. Community dynamics illustrate large changes yearly driven by abundance shifts of the dominant taxa in the system. Results indicate Steep Cone possesses dynamic outflow microbial communities despite stable geochemistry. These findings improve our understanding of thermal geomicrobiological dynamics and inform how we can interpret the silicified rock record.

Using FlowCam and molecular techniques to assess the diversity of Cyanobacteria species in water used for food production

Globally, the occurrence of cyanobacteria in water currently remains an important subject as they produce cyanotoxins that pose threat to human health. Studies on the contamination of maize meals during mill grinding processes using cyanobacteria-contaminated water have not been conducted. The present study aimed to assess the diversity of cyanobacteria in the samples (process water, uncooked maize meal, and cooked maize meal (porridge)). Polymerized Chain Reaction (PCR) and Advanced digital flow cytometry (FlowCAM) were used to detect and identify cyanobacterial species available in these samples. 16S Primers (forward and reverse) tailed with Universal Sequences were used for amplification and sequencing of full-length 16S rRNA genes from cyanobacteria found in all samples. Cyanobacterial species from order Nostocales, Pseudanabaenales, Oscillatoriales Chroococcales, Synechococcales, and unclassified cyanobacterial order, some of which have the potential to produce cyanotoxins were amplified and identified in process water, raw maize meal and porridge samples using PCR. Images of the genus Microcystis, Phormidium, and Leptolyngbya were captured in process water samples using FlowCAM. These findings show the presence of cyanobacteria species in process water used for maize meal and the absence in cooked maize meal. The presence of cyanobacteria in process water is likely another route of human exposure to cyanotoxins.

Distribution and diversity of cyanobacteria in the Azores Archipelago: An annotated checklist

Background

Knowledge about cyanobacteria diversity in the Azores is spread over several publications, dating from 1874, with some of them not generally available to the scientific community due to their restricted access. The dispersion and sometimes inaccessibility of this information hinder a deeper analysis and a better understanding of the biodiversity of the Azores Islands and more general ecological processes in oceanic islands. Here we present the first checklist of cyanobacteria for the Azores Archipelago with updated taxonomy of all recorded taxa.

New information

This work provides a compiled and annotated checklist of all known cyanobacteria from the Azores Archipelago with morphological identification from preserved samples and cultures, based on published literature. All records of taxa known to occur in the Azores were taxonomically updated. The present checklist comprises 225 taxa distributed by six orders (Chroococcales, Nostocales, Oscillatoriales, Pleurocapsales, Spirulinales and Synechococcales). Our literature review reveals that the Azores Archipelago hosts a high diversity of cyanobacteria, despite several overlooked habitats that may present great potential regarding cyanobacteria diversity. Increasing efforts to study these neglected habitats could contribute to the knowledge of cyanobacteria taxonomy. This checklist provides the basis for future works on the taxonomy and taxa richness of cyanobacteria in the Azores and the Atlantic Islands, as also for understanding and monitoring non-indigenous and invasive species.

DNA sequence and taxonomic gap analyses to quantify the coverage of aquatic cyanobacteria and eukaryotic microalgae in reference databases: Results of a survey in the Alpine region

The taxonomic identification of organisms based on the amplification of specific genetic markers (metabarcoding) implicitly requires adequate discriminatory information and taxonomic coverage of environmental DNA sequences in taxonomic databases. These requirements were quantitatively examined by comparing the determination of cyanobacteria and microalgae obtained by metabarcoding and light microscopy. We used planktic and biofilm samples collected in 37 lakes and 22 rivers across the Alpine region. We focused on two of the most used and best represented genetic markers in the reference databases, namely the 16S rRNA and 18S rRNA genes. A sequence gap analysis using blastn showed that, in the identity range of 99-100%, approximately 30% (plankton) and 60% (biofilm) of the sequences did not find any close counterpart in the reference databases (NCBI GenBank). Similarly, a taxonomic gap analysis showed that approximately 50% of the cyanobacterial and eukaryotic microalgal species identified by light microscopy were not represented in the reference databases. In both cases, the magnitude of the gaps differed between the major taxonomic groups. Even considering the species determined under the microscope and represented in the reference databases, 22% and 26% were still not included in the results obtained by the blastn at percentage levels of identity ≥95% and ≥97%, respectively. The main causes were the absence of matching sequences due to amplification and/or sequencing failure and potential misidentification in the microscopy step. Our results quantitatively demonstrated that in metabarcoding the main obstacles in the classification of 16S rRNA and 18S rRNA sequences and interpretation of high-throughput sequencing biomonitoring data were due to the existence of important gaps in the taxonomic completeness of the reference databases and the short length of reads. The study focused on the Alpine region, but the extent of the gaps could be much greater in other less investigated geographic areas.

Roholtiella volcanica sp. nov., a New Species of Cyanobacteria from Kamchatkan Volcanic Soils

During a study of biodiversity of cyanobacteria in Gorely volcano soils (Kamchatka Peninsula), a strain of heterocytous, a false branching cyanobacterium with gradually tapered filaments, was isolated. Prominent features of the strain were purplish-grey trichomes and firm, distinct multilayered sheaths. Based on the results obtained from the morphological, ecological, and phylogenetic analysis using the 16S rRNA and 16S–23S ITS region, 16S–23S ITS secondary structure analysis, comparison of flanking regions of BoxB and V3 helices, and the p-distance between the 16S–23S ITS region, we describe our strain K7 as a novel species of the genus Roholtiella with the name Roholtiella volcanica sp. nov., in accordance with the International Code of Nomenclature for algae, fungi, and plants. This work continues the rapid expansion of the description of new taxa of cyanobacteria, and particularly demonstrates a coming phase in cyanobacterial taxonomy in which the discovery of new species in recently described genera rapidly increases our understanding of the diversity in this phylum.

Polyphasic Identification and Genomic Insights of Leptothermofonsia sichuanensis gen. sp. nov., a Novel Thermophilic Cyanobacteria Within Leptolyngbyaceae

Thermal environments are an important reservoir of thermophiles with significant ecological and biotechnological potentials. However, thermophilic isolates remain largely unrecovered from their habitats and are rarely systematically identified. In this study, we characterized using polyphasic approaches a thermophilic strain, PKUAC-SCTAE412 (E412 hereafter), recovered from Lotus Lake hot spring based in Ganzi prefecture, China. The results of 16S rRNA/16S-23S ITS phylogenies, secondary structure, and morphology comparison strongly supported that strain E412 represent a novel genus within Leptolyngbyaceae. This delineation was further confirmed by genome-based analyses [phylogenomic inference, average nucleotide/amino-acid identity, and the percentages of conserved proteins (POCP)]. Based on the botanical code, the isolate is herein delineated as Leptothermofonsia sichuanensis gen. sp. nov, a genus adjacent to recently delineated Kovacikia and Stenomitos. In addition, we successfully obtained the first complete genome of this new genus. Genomic analysis revealed its adaptations to the adverse hot spring environment and extensive molecular components related to mobile genetic elements, photosynthesis, and nitrogen metabolism. Moreover, the strain was capable of modifying the composition of its light-harvesting apparatus depending on the wavelength and photoperiod, showing chromatic adaptation capacity characteristic for T1 and T2 pigmentation types. Other physiological studies showed the strain’s ability to utilize sodium bicarbonate and various sulfur compounds. The strain was also shown to be diazotrophic. Interestingly, 24.6% of annotated protein-coding genes in the E412 genome were identified as putatively acquired, hypothesizing that a large number of genes acquired through HGT might contribute to the genome expansion and habitat adaptation of those thermophilic strains. Most the HGT candidates (69.4%) were categorized as metabolic functions as suggested by the KEGG analysis. Overall, the complete genome of strain E412 provides the first insight into the genomic feature of the genus Leptothermofonsia and lays the foundation for future global ecogenomic and geogenomic studies.

Characterization of a Novel Hot-Spring Cyanobacterium Leptodesmis sichuanensis sp. Nov. and Genomic Insights of Molecular Adaptations Into Its Habitat

The newly described genus Leptodesmis comprises several strains of filamentous cyanobacteria from diverse, primarily cold, habitats. Here, we sequenced the complete genome of a novel hot-spring strain, Leptodesmis sp. PKUAC-SCTA121 (hereafter A121), isolated from Erdaoqiao hot springs (pH 6.32, 40.8°C), China. The analyses of 16S rRNA/16S-23S ITS phylogenies, secondary structures, and morphology strongly support strain A121 as a new species within Leptodesmis, Leptodesmis sichuanensis sp. nov. Notably, strain A121 is the first thermophilic representative of genus Leptodesmis and more broadly the first Leptodesmis sp. to have its genome sequenced. In addition, results of genome-scale phylogenetic analysis and average nucleotide/amino acid identity as well as in silico DNA-DNA hybridization and patristic analysis verify the establishment of genus Leptodesmis previously cryptic to Phormidesmis. Comparative genomic analyses reveal that the Leptodesmis A121 and Thermoleptolyngbya sichuanensis A183 from the same hot-spring biome exhibit different genome structures but similar functional classifications of protein-coding genes. Although the core molecular components of photosynthesis, metabolism, and signal transduction were shared by the two strains, distinct genes associated with photosynthesis and signal transduction were identified, indicating that different strategies might be used by these strains to adapt to that specific niche. Furthermore, the complete genome of strain A121 provides the first insight into the genomic features of genus Leptodesmis and lays the foundation for future global ecogenomic and geogenomic studies.

Cyanobacteria derived compounds: Emerging drugs for cancer management

The wide diversity of cyanobacterial species and their role in a variety of biological activities have been reported in the previous few years. Cyanobacteria, especially from marine sources, constitutes a major source of biologically active metabolites that have gained great attention especially due to their anticancer potential. Numerous chemically diverse metabolites from various cyanobacterial species have been recognized to inhibit the growth and progression of tumor cells through the induction of apoptosis in many different types of cancers. These metabolites activate the apoptosis in the cancer cells by different molecular mechanisms, however, the dysregulation of the mitochondrial pathway, death receptors signaling pathways, and the activation of several caspases are the crucial mechanisms that got considerable interest. The array of metabolites and the range of mechanisms involved may also help to overcome the resistance acquired by the different tumor types against the ongoing therapeutic agents. Therefore, the primary or secondary metabolites from the cyanobacteria as well as their synthetic derivates could be used to develop novel anticancer drugs alone or in combination with other chemotherapeutic agents. In this study, we have discussed the role of cyanobacterial metabolites in the induction of cytotoxicity and the potential to inhibit the growth of cancer cells through the induction of apoptosis, cell signaling alteration, oxidative damage, and mitochondrial dysfunctions. Moreover, the various metabolites produced by cyanobacteria have been summarized with their anticancer mechanisms. Furthermore, the ongoing trials and future developments for the therapeutic implications of these compounds in cancer therapy have been discussed.

Genomic and transcriptomic insights into the habitat adaptation of the diazotrophic paddy-field cyanobacterium Nostoc sphaeroides

Nitrogen-fixing cyanobacteria are common in paddy fields, one of the most productive wetland ecosystems. Here, we present the complete genome of Nostoc sphaeroides, a paddy-field diazotroph used for food and medicine for more than 1700 years and deciphered the transcriptional regulation during the developmental transition from hormogonia to vegetative filaments with heterocysts. The genome of N. sphaeroides consists of one circular chromosome (6.48 Mb), one of the largest ever reported megaplasmids (2.34 Mb), and seven plasmids. Multiple gene families involved in the adaption to high solar radiation and water fluctuation conditions were found expanded, while genes involved in anoxic adaptation and phosphonate utilization are located on the megaplasmid, suggesting its indispensable role in environmental adaptation. Distinct gene expression patterns were observed during the light-intensity-regulated transition from hormogonia to vegetative filaments, specifically, genes encoding proteins involved in photosynthetic light reaction, carbon fixation, nitrogen metabolism and heterocyst differentiation were significantly upregulated, whereas genes related to cell motility were down-regulated. Our results provide genomic and transcriptomic insights into the adaptation of a filamentous nitrogen-fixing cyanobacterium to the highly dynamic paddy-field habitat, suggesting N. sphaeroides as an excellent system to understand the transition from aquatic to terrestrial habitats and to support sustainable rice production.

Cyanotoxin Screening in BACA Culture Collection: Identification of New Cylindrospermopsin Producing Cyanobacteria

Microcystins (MCs), Saxitoxins (STXs), and Cylindrospermopsins (CYNs) are some of the more well-known cyanotoxins. Taking into consideration the impacts of cyanotoxins, many studies have focused on the identification of unknown cyanotoxin(s)-producing strains. This study aimed to screen strains from the Azorean Bank of Algae and Cyanobacteria (BACA) for MCs, STX, and CYN production. A total of 157 strains were searched for mcy, sxt, and cyr producing genes by PCR, toxin identification by ESI-LC-MS/MS, and cyanotoxin-producing strains morphological identification and confirmation by 16S rRNA phylogenetic analysis. Cyanotoxin-producing genes were amplified in 13 strains and four were confirmed as toxin producers by ESI-LC-MS/MS. As expected Aphanizomenon gracile BACA0041 was confirmed as an STX producer, with amplification of genes sxtA, sxtG, sxtH, and sxtI, and Microcystis aeruginosa BACA0148 as an MC-LR producer, with amplification of genes mcyC, mcyD, mcyE, and mcyG. Two nostocalean strains, BACA0025 and BACA0031, were positive for both cyrB and cyrC genes and ESI-LC-MS/MS confirmed CYN production. Although these strains morphologically resemble Sphaerospermopsis, the 16S rRNA phylogenetic analysis reveals that they probably belong to a new genus.

Issues in cyanobacterial taxonomy: comprehensive case study of unbranched, false branched and true branched heterocytous cyanobacteria

The order Nostocales is represented by morphologically diverse forms with respect to the branching patterns and polarity of the filaments. With growing understanding of taxonomy and systematics, members of the order Nostocales have also undergone multiple taxonomic revisions. The last decade has seen a surge in the description of new genera and families within the order Nostocales. In this study, we discuss the taxonomic status of all the newly described and reclassified taxa of some of the prominent morphological forms within the order Nostocales by constructing comprehensive phylogenetic trees. Further, we propose certain strategies that would contribute to resolving the taxonomic complexities arising due to inadequate taxon sampling.