Comparison of conserved structural and regulatory domains within divergent 16S rRNA-23S rRNA spacer sequences of cyanobacteria

Kovacikia euganea sp. nov. (Leptolyngbyaceae, Cyanobacteria), a new chlorophyll f producing cyanobacterium from the Euganean Thermal District (Italy)

Hot springs are considered modern terrestrial environments analogous to Archean continental surfaces, where photosynthetic life could have evolved. In this habitat cyanobacteria dominate thanks to the adaptations to high temperature and the capability to acclimate to low light intensity and far-red enriched spectra typical of microbial biofilms. The isolation and characterization of new cyanobacterial species from these environments is fundamental to discover genetic and physiological traits allowing them to thrive under such unfavorable conditions, giving useful information to understand the evolution and plasticity of oxygenic photosynthesis as well as to assess their metabolic biodiversity for biotechnological purposes. In this study, we present the polyphasic characterization of a filamentous cyanobacterium, denominated strain ETS-13, isolated from mud biofilms collected in the Euganean Thermal District (Italy). The area is known since ancient times for the presence of thermal springs and muds exploited for the beneficial properties linked to heat, electrolytes, and organic compounds produced by the microbiota. The ETS-13 genome was assembled and annotated, while phylogenetic analyzes were performed using a combined approach based on the 16S rRNA sequence and considering the 16S-23S ITS secondary structures. In addition, morphological, biochemical, and physiological features of the organism were investigated, allowing its classification as a new species of the Kovacikia genus, named Kovacikia euganea, which formed a cluster with other species of Leptolyngbyaceae from thermal environments. Interestingly, the strain was the first isolated in Italy capable of performing Far-Red Light Photoacclimation (FaRLiP) when exposed to far-red light, a feature found in other species of the same genus so far tested for this acclimation and isolated form geographically distant and different environments.

Far-red light-driven photoautotrophy of chlorophyll f-producing cyanobacterium without red-shifted phycobilisome core complex

Chlorophyll (Chl) f production expands oxygenic photosynthesis of some cyanobacteria into the far-red light (FRL) region through reconstructed FRL-allophycocyanin (APC) cores and Chl f-containing photosystems. Presently, a unicellular cyanobacterium was isolated for studying FRL photoacclimation (FaRLiP) and classified as a new species Altericista leshanensis. It uses additional Chl f and FRL-APC cores, with retained white light (WL)-phycobiliproteins to thrive FRL conditions. Marker-less deletion of FaRLiP-apcE2 gene was constructed using CRISPR-Cpf1 system. This genetic manipulation has no significant effects on the expression of genes in the FaRLiP gene cluster, including adjacent apc genes under FRL conditions. The function-loss mutant cells cannot assemble FRL-APC cores, and show the decreased growth rate and Chl f production under FRL conditions. Interestingly, the expression levels of phycocyanin (PC) subunits (cpc) and photosystem II D1 proteins (psbA2) are significantly increased in mutant cells under FRL conditions. These results suggest that FRL acclimation in the mutant cells has a different photosynthetic apparatus due to the lack of FRL-APC cores. The alternative strategy of FaRLiP provides additional evidence of flexible pathways towards the potential application of Chl f and associated biotechnology.

A Pipeline for the Isolation and Cultivation of Microalgae and Cyanobacteria from Hypersaline Environments

Microorganisms in high-salinity environments play a critical role in biogeochemical cycles, primary production, and the biotechnological exploitation of extremozymes and bioactive compounds. The main challenges in current research include isolating and cultivating these microorganisms under laboratory conditions and understanding their complex adaptive mechanisms to high salinity. Currently, universally recognized protocols for isolating microalgae and cyanobacteria from salt pans, salterns, and similar natural habitats are lacking. Establishing axenic laboratory cultures is essential for identifying new species thriving in high-salinity environments and for exploring the synthesis of high-value metabolites by these microorganisms ex situ. Our ongoing research primarily focuses on photosynthetic microorganisms with significant biotechnological potential, particularly for skincare applications. By integrating data from the existing literature with our empirical findings, we propose a standardized pipeline for the isolation and laboratory cultivation of microalgae and cyanobacteria originating from aqueous environments characterized by elevated salt concentrations, such as solar salterns. This approach will be particularly useful for researchers working with microorganisms adapted to hypersaline waters.

Widespread distribution of chlorophyll f-producing Leptodesmis cyanobacteria

Chlorophyll (Chl) f was reported as the fifth Chl in oxygenic photoautotrophs. Chlorophyll f production expanded the utilization of photosynthetically active radiation into the far-red light (FR) region in some cyanobacterial genera. In this study, 11 filamentous cyanobacterial strains were isolated from FR-enriched habitats, including hydrophyte, moss, shady stone, shallow ditch, and microbial mat across Central and Southern China. Polyphasic analysis classified them into the same genus of Leptodesmis and further recognized them as four new species, including Leptodesmis atroviridis sp. nov., Leptodesmis fuscus sp. nov., Leptodesmis olivacea sp. nov., and Leptodesmis undulata sp. nov. These cyanobacteria had absorption peaks beyond 700 nm due to Chl f production and red-shifted phycobiliprotein complexes under FR conditions. All but L. undulata produced phycoerythrin and showed varying degrees of a reddish-brown to dark green color under white light conditions. However, the phycoerythrin contents were sharply decreased under FR conditions, and these three Leptodesmis species appeared green. In summary, the Leptodesmis genus contains diverse species with the capacity to synthesize Chl f and is likely a ubiquitous group of Chl f-producing cyanobacteria.

Life on the rocks: polyphasic evaluation of three epilithic cyanobacterial strains isolated from a single rock, with the description of Nostoc sikkimense sp. nov., from the northeastern region of India

Three epilithic cyanobacterial strains were isolated from the scrapings of a single rock surface from the Reshi River in Sikkim, India. At the time of sampling, the rock surface did not show any visible cyanobacterial growth; however, the surface of the rock was glistering. Subsequent morphological analysis indicated that two out of three strains exhibited typical Nostoc-like morphology and the third strain had cell division in multiple planes showing typical morphology of a member of the family Hapalosiphonaceae. Further, 16S rRNA gene phylogeny indicated the strains to be members of the genera Nostoc, Desmonostoc, and Westiellopsis. For species-level demarcation, additionally, 16S-23S ITS (Internal Transcribed Spacer) region analysis was performed, which indicated that the strain RESHI-1B-PS was a novel cyanobacterial lineage of the genus Nostoc, while the strains RESHI-1A-PS and RESHI-1C-PS were representatives of Desmonostoc sp. and Westiellopsis prolifica, respectively. Thus, in the current investigation, we have described an undocumented species of the cyanobacteria, which we named Nostoc sikkimense in accordance with the guidelines outlined in the International Code of Nomenclature for algae, fungi, and plants (ICN). The study also enumerates and illustrates different life cycle stages of N. sikkimense RESHI-1B-PS along with further expanding the geographic distribution of W. prolifica and its substantial ecological adaptability.

Expanding the cyanobacterial flora of India: Multiple novel species of Nostoc and Desmonostoc from Jammu and Kashmir, India using a polyphasic approach

This investigation reports the polyphasic characterization of six cyanobacterial strains that were isolated from Basantgarh village of district Udhampur in the union territory of Jammu and Kashmir, India. Morphological examination of the isolated strains indicated that the strains are members of the genus Nostoc or its morphotypes. Phylogenetic analyses using the 16S rRNA gene showed that five strains clustered in the Nostoc sensu stricto clade, whereas one strain clustered in the Desmonostoc clade. Further, comparative studies with their phylogenetically related taxa, based on morphology, folded secondary structures, phylogeny of the ITS rRNA region, and the percent genetic homology of 16S rRNA gene and ITS rRNA region clearly established the strains as novel taxa belonging to the genera Nostoc and Desmonostoc. Also, two strains 21A-PS and 2JNA-PS emerged as conspecific to each other, representing the same species of Nostoc. Hence, in accordance with the International code of Nomenclature for algae, fungi, and plants, this study describes Nostoc jammuense, Nostoc globosum, Nostoc breve, and Nostoc coriaceum, as novel species of the genus Nostoc, while Desmonostoc raii is described as a novel species of the genus Desmonostoc. This study adds novel species of Nostoc from Indian habitats and reinforces the need to explore the Nostoc sensu stricto clade for more novel taxa.

Novel oceanic cyanobacterium isolated from Bangaram island with profound acid neutralizing ability is proposed as Leptolyngbya iicbica sp. nov. strain LK

An acid-neutralizing, filamentous, non-heterocytous, marine cyanobacterium named 'LK' has been isolated from the seashore of Bangaram Island, an atoll of Lakshadweep, India, and is described here as a novel species. LK has been characterized using morphological, ecological, and genomic features. Based on 16S rRNA, whole-genome sequencing, and marker gene-based analysis, LK has been identified as a new species. LK clustered with Leptolyngbya-like strains belonging to the LPP group but diverged from Leptolyngbya sensu stricto, indicating the polyphyletic nature of the Leptolyngbya genus. Leptolyngbya sp. SIOISBB and Halomicronema sp. CCY15110 were identified as LK's two closest phylogenetic neighbors in various phylogenetic studies. The analysis of 16S rRNA, ITS secondary structures, and genome relatedness indices such as AAI, ANI, and gANI strongly support LK as a novel species of the Leptolyngbya genus. The mechanism behind acid neutralization in LK has been delineated, attributing it to a surface phenomenon most likely due to the presence of salts of calcium, magnesium, sodium, and potassium. We name LK as Leptolyngbya iicbica strain LK which is a novel species with prominent acidic pH-neutralizing properties.

Okeanomitos corallinicola gen. and sp. nov. (Nostocales, Cyanobacteria), a new toxic marine heterocyte-forming Cyanobacterium from a coral reef

Cyanobacterial mats supplanting coral and spreading coral diseases in tropical reefs, intensified by environmental shifts caused by human-induced pressures, nutrient enrichment, and global climate change, pose grave risks to the survival of coral ecosystems. In this study, we characterized Okeanomitos corallinicola gen. and sp. nov., a newly discovered toxic marine heterocyte-forming cyanobacterium isolated from a coral reef ecosystem of the South China Sea. Phylogenetic analysis, based on the 16S rRNA gene and the secondary structure of the 16S-23S rRNA intergenic region, placed this species in a clade distinct from closely related genera, that is, Sphaerospermopsis stricto sensu, Raphidiopsis, and Amphiheterocytum. The O. corallinicola is a marine benthic species lacking gas vesicles, distinguishing it from other members of the Aphanizomenonaceae family. The genome of O. corallinicola is large and exhibits diverse functional capabilities, potentially contributing to the resilience and adaptability of coral reef ecosystems. In vitro assays revealed that O. corallinicola demonstrates notable cytotoxic activity against various cancer cell lines, suggesting its potential as a source of novel anticancer compounds. Furthermore, the identification of residual saxitoxin biosynthesis function in the genome of O. corallinicola, a marine cyanobacteria, supports the theory that saxitoxin genes in cyanobacteria and dinoflagellates may have been horizontally transferred between them or may have originated from a shared ancestor. Overall, the identification and characterization of O. corallinicola provides valuable contributions to cyanobacterial taxonomy, offering novel perspectives on complex interactions within coral reef ecosystems.

Development of Leptolyngbya sp. BL0902 into a model organism for synthetic biological research in filamentous cyanobacteria

Cyanobacteria have great potential in CO2-based bio-manufacturing and synthetic biological studies. The filamentous cyanobacterium, Leptolyngbya sp. strain BL0902, is comparable to Arthrospira (Spirulina) platensis in commercial-scale cultivation while proving to be more genetically tractable. Here, we report the analyses of the whole genome sequence, gene inactivation/overexpression in the chromosome and deletion of non-essential chromosomal regions in this strain. The genetic manipulations were performed via homologous double recombination using either an antibiotic resistance marker or the CRISPR/Cpf1 editing system for positive selection. A desD-overexpressing strain produced γ-linolenic acid in an open raceway photobioreactor with the productivity of 0.36 g·m-2·d-1. Deletion mutants of predicted patX and hetR, two genes with opposite effects on cell differentiation in heterocyst-forming species, were used to demonstrate an analysis of the relationship between regulatory genes in the non-heterocystous species. Furthermore, a 50.8-kb chromosomal region was successfully deleted in BL0902 with the Cpf1 system. These results supported that BL0902 can be developed into a stable photosynthetic cell factory for synthesizing high value-added products, or used as a model strain for investigating the functions of genes that are unique to filamentous cyanobacteria, and could be systematically modified into a genome-streamlined chassis for synthetic biological purposes.

Igniting taxonomic curiosity: The amazing story of Amazonocrinis with the description of a new genus Ahomia gen. nov. and novel species of Ahomia, Amazonocrinis, and Dendronalium from the biodiversity-rich northeast region of India

Five cyanobacterial strains exhibiting Nostoc-like morphology were sampled from the biodiversity hotspots of the northeast region of India and characterized using a polyphasic approach. Molecular and phylogenetic analysis using the 16S rRNA gene indicated that the strains belonged to the genera Amazonocrinis and Dendronalium. In the present investigation, the 16S rRNA gene phylogeny clearly demarcated two separate clades of Amazonocrinis. The strain MEG8-PS clustered along with Amazonocrinis nigriterrae CENA67, which is the type strain of the genus. The other three strains ASM11-PS, RAN-4C-PS, and NP-KLS-5A-PS clustered in a different clade that was phylogenetically distinct from the Amazonocrinis sensu stricto clade. Interestingly, while the 16S rRNA gene phylogeny exhibited two separate clusters, the 16S-23S ITS region analysis did not provide strong support for the phylogenetic observation. Subsequent analyses raised questions regarding the resolving power of the 16S-23S ITS region at the genera level and the associated complexities in cyanobacterial taxonomy. Through this study, we describe a novel genus Ahomia to accommodate the members clustering outside the Amazonocrinis sensu stricto clade. In addition, we describe five novel species, Ahomia kamrupensis, Ahomia purpurea, Ahomia soli, Amazonocrinis meghalayensis, and Dendronalium spirale, in accordance with the International Code of Nomenclature for algae, fungi, and plants (ICN). Apart from further enriching the genera Amazonocrinis and Dendronalium, the current study helps to resolve the taxonomic complexities revolving around the genus Amazonocrinis and aims to attract researchers to the continued exploration of the tropical and subtropical cyanobacteria for interesting taxa and lineages.

Examination of Large Chromosomal Inversions in the Genome of Erwinia amylovora Strains Reveals Worldwide Distribution and North America-Specific Types

Erwinia amylovora is a relatively homogeneous species with low genetic diversity at the nucleotide level. However, phenotypic differences and genomic structural variations among E. amylovora strains have been documented. In this study, we identified 10 large chromosomal inversion (LCI) types in the Spiraeoideae-infecting (SI) E. amylovora strains by combining whole genome sequencing and PCR-based molecular markers. It was found that LCIs were mainly caused by homologous recombination events among seven rRNA operons (rrns) in SI E. amylovora strains. Although ribotyping results identified inter- and intra-variations in the internal transcribed spacer (ITS1 and ITS2) regions among rrns, LCIs tend to occur between rrns transcribed in the opposite directions and with the same tRNA content (tRNA-Glu or tRNA-Ile/Ala) in ITS1. Based on the LCI types, physical/estimated replichore imbalance (PRI/ERI) was examined and calculated. Among the 117 SI strains evaluated, the LCI types of Ea1189, CFBP1430, and Ea273 were the most common, with ERI values at 1.31, 7.87, and 4.47°, respectively. These three LCI types had worldwide distribution, whereas the remaining seven LCI types were restricted to North America (or certain regions of the United States). Our results indicated ongoing chromosomal recombination events in the SI E. amylovora population and showed that LCI events are mostly symmetrical, keeping the ERI less than 15°. These findings provide initial evidence about the prevalence of certain LCI types in E. amylovora strains, how LCI occurs, and its potential evolutionary advantage and history, which might help track the movement of the pathogen.

A multiplex Taqman PCR assay for MRSA detection from whole blood

Methicillin-resistant Staphylococcus aureus (MRSA) causes a wide range of hospital and community-acquired infections worldwide. MRSA is associated with worse clinical outcomes that can lead to multiple organ failure, septic shock, and death, making timely diagnosis of MRSA infections very crucial. In the present work, we develop a method that enables the positive enrichment of bacteria from spiked whole blood using protein coated magnetic beads, followed by their lysis, and detection by a real-time multiplex PCR directly. The assay targeted bacterial 16S rRNA, S. aureus (spa) and methicillin resistance (mecA). In addition, an internal control (lambda phage) was added to determine the assay's true negative. To validate this assay, staphylococcal and non-staphylococcal bacterial strains were used. The three-markers used in this study were detected as expected by monomicrobial and poly-microbial models of the S. aureus and coagulase-negative staphylococci (CoNS). The thermal cycling completed within 30 mins, delivering 100% specificity. The detection LoD of the pre-processing step was ∼ 1 CFU/mL from 2-5mL of whole blood and that of PCR was ∼ 1pg of NA. However, the combined protocol led to a lower detection limit of 100-1000 MRSA CFUs/mL. The main issue with the method developed is in the pre-processing of blood which will be the subject of our future study.

Polyphasic characterization of a novel hot-spring cyanobacterium Thermocoleostomius sinensis gen et sp. nov. and genomic insights into its carbon concentration mechanism

Thermophilic cyanobacteria play a crucial role as primary producers in hot spring ecosystems, yet their microbiological, taxonomic, and ecological characteristics are not extensively studied. This study aimed to characterize a novel strain of thermophilic cyanobacteria, PKUAC-SCTA174 (A174), using a combination of traditional polyphasic methods and modern genomic-based approaches. The study included 16S rRNA-based phylogeny, ITS secondary structure prediction, morphological and habitat analyses, as well as high-quality genome sequencing with corresponding phylogenomic analyses. The results of the 16S rRNA, 16S-23S ITS secondary structure, morphology, and habitat analyses supported the classification of the strain as a member of a novel genus within the family Oculatellaceae, closely related to Albertania and Trichotorquatus. Genomic analysis revealed the presence of a sophisticated carbon-concentrating mechanism (CCM) in the strain, involving two CO2 uptake systems NDH-I3, and NDH-I4, three types of bicarbonate transporters (BCT1, bicA, sbtA,) and two distinct putative carboxysomal carbonic anhydrases (ccaA1 and ccaA2). The expression of CCM genes was investigated with a CO2 shift experiment, indicating varying transcript abundance among different carbon uptake systems. Based on the comprehensive characterization, the strain was delineated as Thermocoleostomius sinensis, based on the botanical code. The study of the complete genome of strain A174 contributes valuable insights into the genetic characteristics of the genus Thermocoleostomius and related organisms and provides a systematic understanding of thermophilic cyanobacteria. The findings presented here offer valuable data that can be utilized for future research in taxogenomics, ecogenomics, and geogenomics.

Isolation of Pseudomonas syringae pv. Tomato strains causing bacterial speck disease of tomato and marker-based monitoring for their virulence

BACKGROUND

The bacterial speck disease of tomato caused by a bacterial pathogen Pseudomonas syringae pv. tomato is a most important disease causing severe crop losses.

METHODS AND RESULTS

Present study was conducted to investigate and characterize the population diversity of P. syringae pv. tomato pathogen isolated from infected tomato plants from various regions of Egypt. Significant variation among the isolates was observed which demonstrated considerable virulence. All isolates were pathogenic and the CFU population recovered from inoculate tomato leaves by isolate Pst-2 was higher than other isolates. Genetic disparity among the isolates was investigated by PCR analysis by amplifying hrpZ gene using random amplified polymorphic DNA (RAPD), sequence-related amplified polymorphism (SRAP), and inter-simple sequence repeats (ISSR) markers. The amplified products for ITS1 were found to have 810 bp length whereas 536 bp length was observed for hrpZ gene using primer pairs (1406-f/23S-r) and (MM5-F, MM5-R) respectively. The restriction analysis of amplified regions "ITS" and hrpZ by using 5 and 4 endonucleases respectively demonstrated slight variation among the bacterial isolates. The results of RAPD, ISSR and SRAP showed higher polymorphism (60.52%) within the isolates which may assist for successful characterization by unique and specific markers based on geographical distribution, origin and virulence intensity.

CONCLUSION

The results of present study suggested that the use of molecular approach may provide successful and valuable information to differentiate and classify P. syringae pv. tomato strains in future for the detection and confirmation of pathogenicity.

Chlorophyll f production in two new subaerial cyanobacteria of the family Oculatellaceae

Chlorophyll (Chl) f was recently identified in a few cyanobacteria as the fifth chlorophyll of oxygenic organisms. In this study, two Leptolyngbya-like strains of CCNU0012 and CCNU0013 were isolated from a dry ditch in Chongqing city and a brick wall in Mount Emei Scenic Area in China, respectively. These two strains were described as new species: Elainella chongqingensis sp. nov. (Oculatellaceae, Synechococcales) and Pegethrix sichuanica sp. nov. (Oculatellaceae, Synechococcales) by the polyphasic approach based on morphological features, phylogenetic analysis of 16S rRNA gene and secondary structure comparison of 16S-23S internal transcribed spacer domains. Both strains produced Chl a under white light (WL) but additionally induced Chl f synthesis under far-red light (FRL). Unexpectedly, the content of Chl f in P. sichuanica was nearly half that in most Chl f-producing cyanobacteria. Red-shifted phycobiliproteins were also induced in both strains under FRL conditions. Subsequently, additional absorption peak beyond 700 nm in the FRL spectral region appeared in these two strains. This is the first report of Chl f production induced by FRL in the family Oculatellaceae. This study not only extended the diversity of Chl f-producing cyanobacteria but also provided precious samples to elucidate the essential binding sites of Chl f within cyanobacterial photosystems.

Competitiveness and Phylogenetic Relationship of Rhizobial Strains with Different Symbiotic Efficiency in Trifolium repens: Conversion of Parasitic into Non-Parasitic Rhizobia by Natural Symbiotic Gene Transfer

In Uruguayan soils, populations of native and naturalized rhizobia nodulate white clover. These populations include efficient rhizobia but also parasitic strains, which compete for nodule occupancy and hinder optimal nitrogen fixation by the grassland. Nodulation competitiveness assays using gusA-tagged strains proved a high nodule occupancy by the inoculant strain U204, but this was lower than the strains with intermediate efficiencies, U268 and U1116. Clover biomass production only decreased when the parasitic strain UP3 was in a 99:1 ratio with U204, but not when UP3 was at equal or lower numbers than U204. Based on phylogenetic analyses, strains with different efficiencies did not cluster together, and U1116 grouped with the parasitic strains. Our results suggest symbiotic gene transfer from an effective strain to U1116, thereby improving its symbiotic efficiency. Genome sequencing of U268 and U204 strains allowed us to assign them to species Rhizobium redzepovicii, the first report of this species nodulating clover, and Rhizobium leguminosarun, respectively. We also report the presence of hrrP- and sapA-like genes in the genomes of WSM597, U204, and U268 strains, which are related to symbiotic efficiency in rhizobia. Interestingly, we report here chromosomally located hrrP-like genes.

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.

Insights into the phylogenetic inconsistencies of the genus Amazonocrinis and description of epilithic Amazonocrinis malviyae sp. nov. (Cyanobacteria, Nostocales) from Jammu and Kashmir, India

A dark-coloured thin film of cyanobacteria growing on the bottom of a submerged stone was isolated from Basantgarh village in Udhampur district, Jammu and Kashmir, India. The isolated strain (designated 19C-PS^T) was characterized using a polyphasic approach. The strain exhibited typical Nostoc-like morphology with a characteristic feature of having heterocytes in series. The 16S rRNA gene phylogeny placed the strain at a well-supported and distinct node. Notably, the recently described genus, Amazonocrinis, on the addition of more 16S rRNA gene sequences, reflected a critical split, which proved to be stable and well supported in all phylogenetic analyses of the 16S rRNA gene. Interestingly, Amazonocrinis nigriterrae CENA67^T (type species of the genus) clustered together with our strain 19C-PS^T in the 16S rRNA gene phylogenetic analysis while the rest of the members of the genus Amazonocrinis were placed at a separate and distant node. This clearly indicated that strain 19C-PS^T is a member of Amazonocrinis sensu stricto. However, the results of phylogenetic analysis of ITS sequences only, in strains purported to belong to Amazonocrinis did not agree with the 16S rRNA gene results and placed our strain 19C-PS^T in a sister clade to three strains that have not yet been speciated, UHCC 0702, NIES-4103 and SA22, with A. nigriterrae falling into a separate clade. Further, folded secondary structures of the D1-D1', V2, BoxB and V3 helices of strain 19C-PS^T were found to be significantly different from those of all the phylogenetically related taxa. The study revealed an interesting case where low taxon sampling and phylogenomic interpretations came across as points of attention in cyanobacterial taxonomy. Based on the morphological, phylogenetic, 16S-23S ITS secondary structure analyses, we describe our strain as Amazonocrinis malviyae sp. nov. in accordance with the International Code of Nomenclature for algae, fungi and plants. This work also illuminates the need for further research to resolve the taxonomic discrepancies among Amazonocrinis strains.

Mojavia aguilerae and M. dolomitestris - two new Nostocaceae (Cyanobacteria) species from the Americas

While nostocacean cyanobacteria are ubiquitous and play critical roles in terrestrial ecosystems, their taxonomy and biogeography still entail mysteries. We isolated two Nostoc-like cyanobacteria from biological soil crusts of the Atacama (Chile) and Mojave (USA) Deserts. An initial 16S rRNA gene phylogeny placed both in monophyly with Mojavia pulchra. Here, we describe two new species of the previously monotypic Mojavia using a polyphasic approach including morphology, 16S rRNA phylogenies, secondary structure, and percent similarity of the 16S-23S ITS region. Like M. pulchra, both new species produce compact microcolonies, arthrospore-like akinetes, and monocytes, traits characteristic of the genus. Mojavia aguilerae sp. nov. is morphologically distinct from both other species in producing bluntly conical end cells, abundant enlarged akinetes in multiseriate filaments, and gold-colored cells during senescence. Mojavia dolomitestris sp. nov. exhibited distinctly firm, light-colored, compartmentalized mucilage. M. dolomitestris is somewhat cryptic with M. pulchra, but has more densely packed microcolonies, rarity and later onset of brownish sheath pigmentation, and an origin from soils derived from dolomite. The two new species strengthened the position of Mojavia as a robust genus sister to Nostoc. Although 16S rRNA gene data could not separate the Mojavia species from each other, the three species showed distinct dissimilarities in secondary ITS structure and differed greatly from Nostoc sensu stricto. The high dissimilarities between their 16S-23S ITS regions suggest a long evolutionary history of the three species as separate lineages. Mojavia is an evolutionary and ecologically unique nostocacean genus, and its rarity and restricted habitat point to an urgent need for recognition and protection.

Kovacikia minuta sp. nov. (Leptolyngbyaceae, Cyanobacteria), a new freshwater chlorophyll f-producing cyanobacterium

A few groups of cyanobacteria have been characterized as having far-red light photoacclimation (FaRLiP) that results from chlorophyll f (Chl f) production. In this study, using a polyphasic approach, we taxonomically transferred the Cf. Leptolyngbya sp. CCNUW1 isolated from a shaded freshwater pond, which produces Chl f under far-red light, to the genus Kovacikia and named this taxon Kovacikia minuta sp. nov. This strain was morphologically similar to Leptolyngbya-like strains. The thin filaments were purplish-brown under white light but became grass green under far-red light. The 31-gene phylogeny grouped K. minuta CCNU0001 into order Synechococcales and family Leptolyngbyaceae. Phylogenetic analysis based on 16S rRNA gene sequences further showed that K. minuta CCNU0001 was clustered into Kovacikia with similarities of 97.2-97.4% to the recently reported type species of Kovacikia muscicola HA7619-LM3. Additionally, the internal transcribed spacer region between 16S-23S rRNA genes had a unique sequence and secondary structure compared with other Kovacikia strains and phylogenetically related taxa. Draft genome sequences of K. minuta CCNU0001 (8,564,336 bp) were assembled into one circular chromosome and two circular plasmids. A FaRLiP 20-gene cluster comprised two operons with the unique organization. In sum, K. minuta was established as a new species, and it is the first species reported to produce Chl f and for which a draft genome was produced in genus Kovacikia. This study expanded our knowledge regarding the diversity of Chl f-producing cyanobacteria in far-red light-enriched environments and provides important foundational information for future investigations of FaRLiP evolution in cyanobacteria.

Heterocyte production, gene expression and phylogeography in Raphidiopsis ( = Cylindrospermopsis) Raciborskii

Raphidiopsis ( = Cylindrospermopsis) raciborskii was described as a subtropical-tropical cyanobacterium, later reported expanding into temperate regions. Heterocyte presence used to distinguish Cylindrospermopsis from the very similar Raphidiopsis, but recently the two genera were recognized as one and unified. This study aimed to investigate how heterocyte production is related to nitrogen (N) limitation in heterocytous and non-heterocytous strains of R.raciborskii. High N-concentrations did not inhibit heterocyte development in some strains, while prolonged N-starvation periods never stimulated production in others. RT-qPCR was used to examine the genetic background, through the expression patterns of nifH, ntcA and hetR. While gene expression increased under N-restriction, N-sufficiency did not suppress nifH transcripts as previously observed in other diazotrophyc cyanobacteria, suggesting that heterocyte production in R. raciborskii is not regulated by N-availability. Heterocytous and non-heterocytous strains were genotypically characterized to assess their phylogenetic relationships,. In the phylogenetic tree, clusters were intermixed and confirmed Raphidiopsis and Cylindrospermopsis as the same genus. The tree supported previous findings of earlier splitting of American strains, while contesting the African origin hypothesis. The existence of two lines of Chinese strains, with distinct evolutionary patterns, is a significant addition that could lead to new hypotheses of the species biogeography.

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.

Introducing Petrachlorosaceae fam. nov., Petrachloros gen. nov. and Petrachloros mirabilis sp. nov. (Synechococcales, Cyanobacteria) Isolated from a Portuguese UNESCO monument

The Synechococcales is a large cyanobacterial order comprising both unicellular and filamentous forms, with parietal thylakoid arrangement. Previously, this order has been the subject of taxonomic revisions with new families being erected. During studies of the phototrophic communities on the limestone walls of the Old Cathedral of Coimbra (UNESCO monument), a coccoid Aphanocapsa-like cyanobacterium was isolated. It was characterized using a polyphasic approach, based on morphology, 16S rRNA phylogenetic and phylogenomic analyses, internal transcribed spacer (ITS) secondary structure, and ecology. The 16S rRNA phylogenetic analyses showed that this strain is placed in a separate and highly supported family-level clade, as part of a large group comprising the families Prochlorococcaceae and Prochlorotrichaceae, with Lagosinema as the closest (although quite distant) taxon. Additionally, the phylogenomic analysis also placed this strain in a separate lineage, situated distantly apart from the family Thermosynechococcaceae, but with strains assigned to Acaryochloris marina MBIC 11017 and Aphanocapsa montana BDHKU210001 as the closest taxa. Based on these data, as well as on the results from the secondary ITS structure, morphology, and ecology, we here propose the establishment of Petrachlorosaceae fam. nov., along with the description of Petrachloros gen. nov. and Petrachloros mirabilis sp. nov. We also address additional considerations regarding some cyanobacterial taxa within the order Synechococcales, which we believe deserve further revisions.

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.

High-resolution Spatiotemporal Dynamics of Harmful Algae in the Indian River Lagoon (Florida)-A Case Study of Aureoumbra lagunensis, Pyrodinium bahamense, and Pseudo-nitzschia

The Indian River Lagoon (IRL), located on the east coast of Florida, is a complex estuarine ecosystem that is negatively affected by recurring harmful algal blooms (HABs) from distinct taxonomic/functional groups. Enhanced monitoring was established to facilitate rapid quantification of three recurrent bloom taxa, Aureoumbra lagunensis, Pyrodinium bahamense, and Pseudo-nitzschia spp., and included corroborating techniques to improve the identification of small-celled nanoplankton (<10 μm in diameter). Identification and enumeration of these target taxa were conducted during 2015-2020 using a combination of light microscopy and species-specific approaches, specifically immunofluorescence flow cytometry as well as a newly developed qPCR assay for A. lagunensis presented here for the first time. An annual bloom index (ABI) was established for each taxon based on occurrence and abundance data. Blooms of A. lagunensis (>2×10⁸ cells L^-1) were observed in all six years sampled and across multiple seasons. In contrast, abundance of P. bahamense, largely driven by the annual temperature cycle that moderates life cycle transitions and growth, displayed a strong seasonal pattern with blooms (10⁵-10⁷ cells L^-1) generally developing in early summer and subsiding in autumn. However, P. bahamense bloom development was delayed and abundance was significantly lower in years and locations with sustained A. lagunensis blooms. Pseudo-nitzschia spp. were broadly distributed with sporadic bloom concentrations (reaching 10⁷ cells L^-1), but with minimal concentrations of the toxin domoic acid detected (<0.02 μg L^-1). In summer 2020, multiple monitoring tools characterized a novel nano-cyanobacterium bloom (reaching 10⁹ cells L^-1) that coincided with a decline in A. lagunensis and persisted into autumn. Statistical and time-series analyses of this spatiotemporally intensive dataset highlight prominent patterns in variability for some taxa, but also identifies challenges of characterizing mechanisms underlying more episodic yet persistent events. Nevertheless, the intersect of temperature and salinity as environmental proxies proved to be informative in delineating niche partitioning, not only in the case of taxa with long-standing data sets but also for seemingly unprecedented blooms of novel nanoplanktonic taxa.

A new cyanobacterial genus Altericista and three species, A. lacusladogae sp. nov., A. violacea sp. nov., and A. variichlora sp. nov., described using a polyphasic approach

Several strains of unicellular cyanobacteria from the culture collection of St. Petersburg State University, St. Petersburg, Russia (CALU), which were preliminary identified as Synechocystis sp., are reclassified in the new genus Altericista. Three new species are proposed, A. lacusladogae, A. violacea, and A. variichlora. The last species produces accessory chlorophylls d and f in cultures illuminated by far-red light, an attribute rarely observed in cyanobacteria, especially in unicellular strains. This genus is morphologically similar to Synechocysis having coccoid cells that divide in two successive planes at right angles, containing no sheath or capsule, and having the lamellar system represented by peripheral concentric thylakoids. Altericista shows ecological, biochemical, and physiological characters unlike those in Synechocystis and has the distinguishing phenotypic characters as follows: freshwater, non-halotolerant ecotype; palmitate and α-linoleate as major fatty acids; and the ability to photoacclimate, including several types of complementary chromatic adaptation. Genetic differences from Synechocystis sp. include 16S rRNA, rpoC1, and rbcL gene sequences, as well as sequence and folding of 16S-23S ITS.

Description, Taxonomy, and Comparative Genomics of a Novel species, Thermoleptolyngbya sichuanensis sp. nov., Isolated From Hot Springs of Ganzi, Sichuan, China

Thermoleptolyngbya is a newly proposed genus of thermophilic cyanobacteria that are often abundant in thermal environments. However, a vast majority of Thermoleptolyngbya strains were not systematically identified, and genomic features of this genus are also sparse. Here, polyphasic approaches were employed to identify a thermophilic strain, PKUAC-SCTA183 (A183 hereafter), isolated from hot spring Erdaoqiao, Ganzi prefecture, China. Whole-genome sequencing of the strain revealed its allocation to Thermoleptolyngbya sp. and genetic adaptations to the hot spring environment. While the results of 16S rRNA were deemed inconclusive, the more comprehensive polyphasic approach encompassing phenetic, chemotaxic, and genomic approaches strongly suggest that a new taxon, Thermoleptolyngbya sichuanensis sp. nov., should be delineated around the A183 strain. The genome-scale phylogeny and average nucleotide/amino-acid identity confirmed the genetic divergence of the A183 strain from other strains of Thermoleptolyngbya along with traditional methods such as 16S-23S ITS and its secondary structure analyses. Comparative genomic and phylogenomic analyses revealed inconsistent genome structures between Thermoleptolyngbya A183 and O-77 strains. Further gene ontology analysis showed that the unique genes of the two strains were distributed in a wide range of functional categories. In addition, analysis of genes related to thermotolerance, signal transduction, and carbon/nitrogen/sulfur assimilation revealed the ability of this strain to adapt to inhospitable niches in hot springs, and these findings were preliminarily confirmed using experimental, cultivation-based approaches.

Variability in microcystin quotas during a Microcystis bloom in a eutrophic lake

Microcystis is a bloom-forming genus of cyanobacteria with some genotypes that produce highly toxic microcystin hepatotoxins. In waterbodies where biological and physical factors are relatively homogenous, toxin quotas (the average amount of toxin per cell), at a single point in time, are expected to be relatively constant. In this study we challenged this assumption by investigating the spatial distribution of microcystin quotas at a single point in time on two separate occasions in a lake with a major Microcystis bloom. Microcystis cell concentrations varied widely across the lake on both sampling occasions (730- and 137-fold) together with microcystin quotas (148- and 362-fold). Cell concentrations and microcystin quotas were strongly positively correlated (R2 = 0.89, P < 0.001, n = 28; R2 = 0.67, P < 0.001, n = 25). Analysis of Microcystis strains using high-throughput sequencing of the 16S-23S rRNA intergenic spacer region showed no relationship between microcystin quota and the relative abundance of specific sequences. Collectively, the results of this study indicate an association between microcystin production and cell density that magnifies the potential for bloom toxicity at elevated cell concentrations.

Amazonocrinis nigriterrae gen. nov., sp. nov., Atlanticothrix silvestris gen. nov., sp. nov. and Dendronalium phyllosphericum gen. nov., sp. nov., nostocacean cyanobacteria from Brazilian environments

The cyanobacterial genus Nostoc is an important contributor to carbon and nitrogen bioavailability in terrestrial ecosystems and a frequent partner in symbiotic relationships with non-diazotrophic organisms. However, since this currently is a polyphyletic genus, the diversity of Nostoc-like cyanobacteria is considerably underestimated at this moment. While reviewing the phylogenetic placement of previously isolated Nostoc-like cyanobacteria originating from Brazilian Amazon, Caatinga and Atlantic forest samples, we detected 17 strains isolated from soil, freshwater, rock and tree surfaces presenting patterns that diverged significantly from related strains when ecological, morphological, molecular and genomic traits were also considered. These observations led to the identification of the evaluated strains as representative of three novel nostocacean genera and species: Amazonocrinis nigriterrae gen. nov., sp. nov.; Atlanticothrix silvestris gen. nov., sp. nov.; and Dendronalium phyllosphericum gen. nov., sp. nov., which are herein described according to the rules of the International Code of Nomenclature for algae, fungi and plants. This finding highlights the great importance of tropical and equatorial South American ecosystems for harbouring an unknown microbial diversity in the face of the anthropogenic threats with which they increasingly struggle.

The occurrence of Affixifilum gen. nov. and Neolyngbya (Oscillatoriaceae) in South Florida (USA), with the description of A. floridanum sp. nov. and N. biscaynensis sp. nov

South Florida (USA) has a subtropical to tropical climate with an extensive and diverse coastline that supports the growth of benthic cyanobacterial mats (BCMs). These BCMs are widespread and potentially house numerous bioactive compounds; however, the extent of the cyanobacterial diversity within these mats remains largely unknown. To elucidate this diversity, BCMs from select locations in South Florida were sampled and isolated into unicyanobacterial cultures for morphological and molecular studies. Phylogenetic relationships of isolated taxa were assessed using the markers 16S rRNA and 16S-23S rRNA ITS by both maximum likelihood and Bayesian inference. We propose Affixifilum gen. nov. based on morphological characteristics and the 16S rRNA phylogeny. Two species are included: Affixifilum granulosum comb nov. (=Neolyngbya granulosa) found in Brazil and Florida (USA) and A. floridanum sp. nov. Several other features, including pair-wise distance of 16S rRNA and 16S-23S rRNA ITS, 16S-23S rRNA ITS secondary structure, morphology, and ecology, provide support for Affixifilum. We also propose the transfer of Lyngbya regalis to Neolyngbya as N. regalis comb. nov. and include the description of one novel species, N. biscaynensis sp. nov.

Spatial and temporal variations in Synechococcus microdiversity in the Southern California coastal ecosystem

The Synechococcus cyanobacterial population at the Scripps Institution of Oceanography pier in La Jolla, CA, shows large increases in abundance, typically in the spring and summer followed, by rapid declines within weeks. Here we used amplicon sequencing of the ribosomal RNA internal transcribed spacer region to examine the microdiversity within this cyanobacterial genus during these blooms as well as further offshore in the Southern California coastal ecosystem (CCE). These analyses revealed numerous Synechococcus amplicon sequence variants (ASVs) and that clade and ASV composition can change over the course of blooms. We also found that a large bloom in August 2016 was highly anomalous both in its overall Synechococcus abundance and in terms of the presence of normally oligotrophic Synechococcus clade II. The dominant ASVs at the pier were found further offshore and in the California Current, but we did observe more oligotrophic ASVs and clades along with depth variation in Synechococcus diversity. We also observed that the dominant sequence variant switched during the peak of multiple Synechococcus blooms, with this switch occurring in multiple clades, but we present initial evidence that this apparent ASV switch is a physiological response rather than a change in the dominant population.

Revealing new sponge-associated cyanobacterial diversity: Novel genera and species

Cyanobacteria are often reported as abundant components of the sponge microbiome; however their diversity below the phylum level is still underestimated. Aiming to broaden our knowledge of sponge-cyanobacteria association, we isolated cyanobacterial strains from Aegean Sea sponges in previous research, which revealed high degree of novel cyanobacterial diversity. Herein, we aim to further characterize sponge-associated cyanobacteria and re-evaluate their classification based on an extensive polyphasic approach, i.e. a combination of molecular, morphological and ecological data. This approach resulted in the description of five new genera (Rhodoploca, Cymatolege, Metis, Aegeococcus, and Thalassoporum) and seven new species (R. sivonenia, C. spiroidea, C. isodiametrica, M. fasciculata, A. anagnostidisi, A. thureti, T. komareki) inside the order Synechococcales, and a new pleurocapsalean species (Xenococcus spongiosum). X. spongiosum is a baeocyte-producing species that shares some morphological features with other Xenococcus species, but has distinct phylogenetic and ecological identity. Rhodoploca, Cymatolege, Metis and Thalassoporum are novel well supported linages of filamentous cyanobacteria that possess distinct characters compared to their sister taxa. Aegeococcus is a novel monophyletic linage of Synechococcus-like cyanobacteria exhibiting a unique ecology, as sponge-dweller. The considerable number of novel taxa characterized in this study highlights the importance of employing polyphasic culture-dependent approaches in order to reveal the true cyanobacterial diversity associated with sponges.

Phylogeographic, toxicological and ecological evidence for the global distribution of Raphidiopsis raciborskii and its northernmost presence in Lake Nero, Central Western Russia

Raphidiopsis raciborskii is a freshwater, potentially toxigenic cyanobacterium, originally described as a tropical species that is spreading to northern regions over several decades. The ability of R. raciborskii to produce cyanotoxins - in particular the alkaloid cylindrospermopsin (CYN), which is toxic to humans and animals - is of serious concern. The first appearance of R. raciborskii in Russia was noted in Lake Nero in the summer of 2010. This is the northernmost (57°N) recorded case of the simultaneous presence of R. raciborskii and detection of CYN. In this study, the data from long-term monitoring of the R. raciborskii population, temperature and light conditions in Lake Nero were explored. CYN and cyr/aoa genes present in environmental samples were examined using HPLC/MS-MS and PCR analysis. A R. raciborskii strain (R104) was isolated and its morphology, toxigenicity and phylogeography were studied. It is supposed that the trigger factor for the strong development of R. raciborskii in Lake Nero in summer 2010 may have been the relatively high water temperature, reaching 29-30 °C. Strain R. raciborskii R104 has straight trichomes and can produce akinetes, making it morphologically similar to European strains. Phylogeographic analysis based on nifH gene and 16S-23S rRNA ITS1 sequences showed that the Russian strain R104 grouped together with R. raciborskii strains isolated from Portugal, France, Germany and Hungary. The Russian strain R104 does not contain cyrA and cyrB genes, meaning that it - like all European strains - cannot produce CYN. Thus, while recent invasion of R. raciborskii into Lake Nero has occurred, morphological, genetic, and toxicological data supported the spreading of this cyanobacterium from other European lakes. Detection of CYN and cyr/aoa genes in environmental samples indicated the cyanobacterium Aphanizomenon gracile as a likely producer of CYN in Lake Nero. The article also discusses data on the global biogeography of R. raciborskii. Genetic similarity between R. raciborskii strains isolated from very remote continents might be related to the ancient origin of the cyanobacterium inhabiting the united continents of Laurasia and Gondwana, rather than comparably recent transoceanic exchange between R. raciborskii populations.

Phylogenetic relationships and genetic divergence of paralytic shellfish toxin- and cylindrospermopsin- producing Cylindrospermopsis and raphidiopsis

Cylindrospermopsis and Raphidiopsis (C/R group) are closely related species responsible for cyanobacterial blooms worldwide. Paralytic shellfish toxins (PSTs) and cylindrospermopsins (CYNs) have been identified in different C/R group strains. However, the evolutionary relationship between PST- and CYN-producing strains has not been systematically evaluated. In this study, C/R group strains and their toxin biosynthesis genes were evaluated by phylogenetic analysis and sequence comparison. None of the tested strains are able to produce PSTs and CYNs simultaneously. The C/R group strains were clustered into five clades, including two non-toxic, two CYN-producing and one PST-producing clades. A high degree of similarity was observed for rpoC1 (> 96%) and ITS-L (> 97%) sequences within each clade with the exception of the ITS-L (87% to 100%) region in CYN-producing R. curvata, which has been shown to contain variable sequence insertions. Genomic analysis revealed that sxtY and sxtZ could be found in both toxic and non-toxic strains. The transposase gene IS4 was only observed in strains from the PST-producing clade. The sxt and cyr gene clusters share five gene families with similar functions. The amino acid sequences of the adenylyl-sulfate kinase genes, sxtO and cyrN, are more similar (45% to 81%) than other pairs of genes (8.0% to 40%). SxtO and CyrN proteins from C/R group strains forms an independent clade on the phylogenetic tree with a high degree of sequence similarity (78% to 100%). In conclusion, PST- and CYN- producing C/R group species can be classified into different clades based on their phylogenetic profile. The sxtO and cyrN genes have probably diverged from a single ancestral adenylyl-sulfate kinase gene, and may be specifically used for toxin biosynthesis in C/R group species.

Cell membrane fatty acid and pigment composition of the psychrotolerant cyanobacterium Nodularia spumigena CHS1 isolated from Hopar glacier, Pakistan

In the present study, cyanobacterium isolate CHS1 isolated from Hopar glacier, Pakistan, was analyzed for the first time for cell membrane fatty acids and production of pigments. Sequencing of the 16-23S intergenetic region confirmed identification of the isolate CHS1 as Nodularia spumigena. All chlorophyll and carotenoid pigments were quantified using high-performance liquid chromatography and experiments to test tolerance against a range of physico-chemical conditions were conducted. Likewise, the fatty acid profile of the cell membrane CHS1 was analyzed using gas chromatography and mass spectroscopy. The cyanobacterium isolate CHS1 demonstrated tolerance to 8 g/L% NaCl, 35°C and pH 5-9. The characteristic polyunsaturated fatty acid (PUFA) of isolate CHS1, C18:4, was observed in fatty acid methyl esters (FAMEs) extracted from the cell membrane. CHS1 was capable of producing saturated fatty acids (SFA) (e.g., C16:0), monounsaturated fatty acids (MUFA) (e.g., C18:1) and polyunsaturated fatty acids (e.g., C20:5) in the cell membrane. In this study, we hypothesize that one mechanism of cold adaptation displayed by isolate CHS1 is the accumulation of high amounts of PUFA in the cell membrane.

Toxicity of herbicides to cyanobacteria and phytoplankton species of the San Francisco Estuary and Sacramento-San Joaquin River Delta, California, USA

The herbicides glyphosate, imazamox and fluridone are herbicides, with low toxicity towards fish and invertebrates, which are applied to waterways to control invasive aquatic weeds. However, the effects of these herbicides on natural isolates of phytoplankton and cyanobacteria are unknown. Three species of microalgae found in the San Francisco Estuary (SFE)/Sacramento-San Joaquin River Delta (Delta) (Microcystis aeruginosa, Chlamydomonas debaryana, and Thalassiosira pseudonana) were exposed to the three herbicides at a range of concentrations in 96-well plates for 5-8 days. All three algal species were the most sensitive to fluridone, with IC₅₀ of 46.9, 21, and 109 µg L^-1 for M. aeruginosa, T. pseudonana and C. debaryana, respectively. Imazamox inhibited M. aeruginosa and T. pseudonana growth at 3.6 × 10⁴ µg L^-1 or higher, and inhibited C. debaryana growth at 1.0 × 10⁵ µg L^-1 or higher. Glyphosate inhibited growth in all species at ca. 7.0 × 10⁴ µg L^-1 or higher. Fluridone was the only herbicide that inhibited the microalgae at environmentally relevant concentrations in this study and susceptibility to the herbicide depended on the species. Thus, the application of fluridone may affect cyanobacteria and phytoplankton community composition in water bodies where it is applied.

Microcystins distribution, bioaccumulation, and Microcystis genotype succession in a fish culture pond

In freshwater aquaculture ponds, cyanobacterial blooms and microcystins (MCs) pollution have attracted considerable attention due to their toxic effects. To provide an insight into cyanobacterial problems in aquaculture ponds, MCs distribution, bioaccumulation, and Microcystis genotype succession in a fishpond were investigated from May 2017 to November 2017. The distribution of MCs in filtered water, seston, and sediment varied considerably among months. MCs concentrations in filtered water, seston, and sediment ranged from 1.16 to 3.66 μg/L, 0.64 to 13.98 μg/g DW, and 1.34 to 5.90 μg/g DW, respectively. In addition, chemical oxygen demand was positively correlated with sestonic MCs concentrations. MCs concentrations accumulated in different tissues of market-size fish were in the order of liver > kidney > intestine > muscle. MCs content in muscle was 4.3 times higher than the WHO recommended tolerable daily intake level. Twenty-four ITS genotypes of Microcystis were identified from a total of 653 sequences. During the survey period, considerable genotype variation and rapid genotype succession were observed and dominant genotype was absent. A redundancy analysis revealed that Microcystis genotypes could significantly influence the variations in the proportions of the potentially toxic Microcystis, which could in turn influence the MCs concentrations in seston.

Leptothoe, a new genus of marine cyanobacteria (Synechococcales) and three new species associated with sponges from the Aegean Sea

Cyanobacterial diversity associated with sponges remains underestimated, though it is of great scientific interest in order to understand the ecology and evolutionary history of the symbiotic relationships between the two groups. Of the filamentous cyanobacteria, the genus Leptolyngbya is the most frequently found in association with sponges as well as the largest and obviously polyphyletic group. In this study, five Leptolyngbya-like sponge-associated isolates were investigated using a combination of molecular, chemical, and morphological approach and revealed a novel marine genus herein designated Leptothoe gen. nov. In addition, three new species of Leptothoe, Le. sithoniana, Le. kymatousa, and Le. spongobia, are described based on a suite of distinct characters compared to other marine Leptolyngbyaceae species/strains. The three new species, hosted by four sponge species, showed different degrees of host specificity. Leptothoe sithoniana and Le. kymatousa hosted by the sponges Petrosia ficiformis and Chondrilla nucula, respectively, seem to be more specialized than Le. spongobia, which was hosted by the sponges Dysidea avara and Acanthella acuta. All three species contained nitrogen-fixing genes and may contribute to the nitrogen budget of sponges. Leptothoe spongobia TAU-MAC 1115 isolated from Acanthella acuta was shown to produce microcystin-RR indicating that microcystin production among marine cyanobacteria could be more widespread than previously determined.

In Situ Collection and Preservation of Intact Microcystis Colonies to Assess Population Diversity and Microcystin Quotas

Understanding of colony specific properties of cyanobacteria in the natural environment has been challenging because sampling methods disaggregate colonies and there are often delays before they can be isolated and preserved. Microcystis is a ubiquitous cyanobacteria that forms large colonies in situ and often produces microcystins, a potent hepatotoxin. In the present study a new cryo-sampling technique was used to collect intact Microcystis colonies in situ by embedding them in a sheet of ice. Thirty-two of these Microcystis colonies were investigated with image analysis, liquid chromatography-mass spectrometry, quantitative polymerase chain reaction and high-throughput sequencing to assess their volume, microcystin quota and internal transcribed spacer (ITS) genotype diversity. Microcystin quotas were positively correlated to colony volume (R² = 0.32; p = 0.004). Individual colonies had low Microcystis ITS genotype diversity and one ITS operational taxonomic unit predominated in all samples. This study demonstrates the utility of the cryo-sampling method to enhance the understanding of colony-specific properties of cyanobacteria with higher precision than previously possible.

Taxonomic resolution of the genus Cyanothece (Chroococcales, Cyanobacteria), with a treatment on Gloeothece and three new genera, Crocosphaera, Rippkaea, and Zehria

The systematics of single-celled cyanobacteria represents a major challenge due to morphological convergence and application of various taxonomic concepts. The genus Cyanothece is one of the most problematic cases, as the name has been applied to oval-shaped coccoid cyanobacteria lacking sheaths with little regard to their phylogenetic position and details of morphology and ultrastructure. Hereby we analyze an extensive set of complementary genetic and phenotypic evidence to disentangle the relationships among these cyanobacteria. We provide diagnostic characters to separate the known genera Cyanothece, Gloeothece, and Aphanothece, and provide a valid description for Crocosphaera gen. nov. We describe two new genera, Rippkaea and Zehria, to characterize two distinct phylogenetic lineages outside the previously known genera. We further describe 13 new species in total including Cyanothece svehlovae, Gloeothece aequatorialis, G. aurea, G. bryophila, G. citriformis, G. reniformis, Gloeothece tonkinensis, G. verrucosa, Crocosphaera watsonii, C. subtropica, C. chwakensis, Rippkaea orientalis, and Zehria floridana to recognize the intrageneric diversity as rendered by polyphasic analysis. We discuss the close relationship of free-living cyanobacteria from the Crocosphaera lineage to nitrogen-fixing endosymbionts of marine algae. The current study includes several experimental strains (Crocosphaera and "Cyanothece") important for the study of diazotrophy and the global oceanic nitrogen cycle, and provides evidence suggesting ancestral N₂ -fixing capability in the chroococcalean lineage.

Characterization of phototrophic microorganisms and description of new cyanobacteria isolated from the saline-alkaline crater-lake Dziani Dzaha (Mayotte, Indian Ocean)

The saline-alkaline crater-lake Dziani Dzaha (Mayotte, Indian Ocean) is dominated by the bloom-forming cyanobacterium Arthrospira. However, the rest of the phototrophic community remains underexplored because of their minute dimension or lower biomass. To characterize the phototrophic microorganisms living in this ecosystem considered as a modern analog of Precambrian environments, several strains were isolated from the water column and stromatolites and analyzed using the polyphasic approach. Based on morphological, ultrastructural and molecular (16S rRNA gene, 18S rRNA gene, 16S-23S internal transcribed spacer (ITS) region and cpcBA-IGS locus) methods, seven filamentous cyanobacteria and the prasinophyte Picocystis salinarum were identified. Two new genera and four new cyanobacteria species belonging to the orders Oscillatoriales (Desertifilum dzianense sp. nov.) and Synechococcales (Sodalinema komarekii gen. nov., sp. nov., Sodaleptolyngbya stromatolitii gen. nov., sp. nov. and Haloleptolyngbya elongata sp. nov.) were described. This approach also allowed to identify Arthrospira fusiformis with exclusively straight trichomes instead of the spirally coiled form commonly observed in the genus. This study evidenced the importance of using the polyphasic approach to solve the complex taxonomy of cyanobacteria and to study algal assemblages from unexplored ecosystems.

Global Metabolomic Characterizations of Microcystis spp. Highlights Clonal Diversity in Natural Bloom-Forming Populations and Expands Metabolite Structural Diversity

Cyanobacteria are photosynthetic prokaryotes capable of synthesizing a large variety of secondary metabolites that exhibit significant bioactivity or toxicity. Microcystis constitutes one of the most common cyanobacterial genera, forming the intensive blooms that nowadays arise in freshwater ecosystems worldwide. Species in this genus can produce numerous cyanotoxins (i.e., toxic cyanobacterial metabolites), which can be harmful to human health and aquatic organisms. To better understand variations in cyanotoxin production between clones of Microcystis species, we investigated the diversity of 24 strains isolated from the same blooms or from different populations in various geographical areas. Strains were compared by genotyping with 16S-ITS fragment sequencing and metabolite chemotyping using LC ESI-qTOF mass spectrometry. While genotyping can help to discriminate among different species, the global metabolome analysis revealed clearly discriminating molecular profiles among strains. These profiles could be clustered primarily according to their global metabolite content, then according to their genotype, and finally according to their sampling location. A global molecular network of all metabolites produced by Microcystis species highlights the production of a wide set of chemically diverse metabolites, including a few microcystins, many aeruginosins, microginins, cyanopeptolins, and anabaenopeptins, together with a large set of unknown molecules. These components, which constitute the molecular biodiversity of Microcystis species, still need to be investigated in terms of their structure and potential bioactivites (e.g., toxicity).

Polyphasic approach using multilocus analyses supports the establishment of the new aerophytic cyanobacterial genus Pycnacronema (Coleofasciculaceae, Oscillatoriales)

A new Phormidium-like genus was found during an investigation of Oscillatoriales diversity in Brazil. Eight aerophytic populations from south and southeastern regions were isolated in monospecific cultures and submitted to polyphasic evaluation. The populations presented homogeneous morphology with straight trichomes, not attenuated, and apical cell with thickened cell wall. Phylogenetic analyses based on 16S rRNA gene sequences showed that these populations, plus the Brazilian strain Phomidium sp. B-Tom from GenBank, formed a highly supported and distinctive clade, which corresponds to the new genus Pycnacronema, comprising six new species: P. brasiliensis (type species), P. arboriculum, P. conicum, P. marmoreum, P. rubrum, and P. savannensis. These results were confirmed and supported by rpoC1 and rbcL genes evaluated independently and by the concatenated analysis of 16S rRNA, rpoC1 and rbcL genes (for all species but P. savannensis). Secondary structures of the D1-D1', box-B, and V3 regions of the internal transcribed spacer were informative at specific level, being conserved in P. brasiliensis and variable among the other strains, also confirming the phylogenetic analyses. The generic name and specific epithets of the new taxa are proposed under the provisions of the International Code of Nomenclature of algae, fungi, and plants.

Cryptic diversity within the Scytonema complex: Characterization of the paralytic shellfish toxin producer Heterosyctonema crispum, and the establishment of the family Heteroscytonemataceae (Cyanobacteria/Nostocales)

Strains of the freshwater filamentous, benthic cyanobacterium Scytonema crispum Agardh isolated from six sites in subtropical south-east Queensland were characterised using a combination of phenotypic and genetic traits. Morphologically, the strains were consistent with the description of Scytonemataceae sensu stricto, and the description of Scytonema crispum. However, phylogenetic analysis of the 16S rRNA gene, the 16S-23S rRNA operon, and the nifH gene revealed that these strains and three others from outside Australia formed a monophyletic clade distinct from Scytonema and other species in the Scytonemataceae. Collectively, this data suggests this group is sufficiently evolutionarily distinct to be placed in a new family, Heteroscytonemataceae fam. nov. Accordingly, the taxon previously known as S. crispum has been transferred to a new genus Heteroscytonema gen nov., as H. crispum. Some strains of H. crispum exhibited facultative production of paralytic shellfish toxins (PSTs). The concentration of PSTs produced by individual strains varied widely, from 2.7 μg g^-1 to 171.3 μg g^-1, and included C toxins, decarbamoyl saxitoxin (dcSTX), gonyautoxins (GTX2, GTX3 and GTX5), saxitoxin (STX) and uncharacterised PSTs. The majority of the Australian strains produced dcSTX as the dominant saxitoxin analogue, a significant finding given that dcSTX has approximately half the relative toxicity of STX. The PST profile varied within and between Australian strains of H. crispum and in strains collected from New Zealand and the United States. The sxtA gene, one of the determinants for the production of PSTs, was present in all strains in which PSTs were detected. The discovery of PST-producing H. crispum in the headwaters of a major drinking water reservoir presents a serious risk for potential human and animal exposure to these neurotoxic compounds and further highlights the importance of monitoring benthic cyanobacteria populations for potentially toxigenic species.

Relationship of diversity and the secondary structure in 16S-23S rDNA internal transcribed spacer: a case in Vibrio parahaemolyticus

The 16S-23S rDNA internal transcribed spacer (ITS) sequence, located in the rrn operon, has been analyzed and evaluated for use in phylogenetic analysis and the detection target of bacteria. The ITS region displays a high level of diversity, being present in multiple copies and displaying variability in both length and sequence, and it carries more phylogenetic information than 16S rDNA. However, appropriately identifying ITS regions to use in analyses is challenging. To solve this problem, we analyzed the ITS regions in Vibrio parahaemolyticus and predicted the secondary structure of each analogous rrn transcript. The genomic DNA of V. parahaemolyticus contains approximately 8-14 rrns, making it more complex than the sequences of most other bacterial species. We analyzed 216 ITSs, of which 206 ITSs come from 18 complete genomes, and 10 ITSs were identified in the present study. The subunits of each ITS were distinguished by their predicted secondary structures. We propose a refined backbone model of the V. parahaemolyticus ITS that can be applied to the sequences of other bacteria. The backbone includes C, V, tDNA and linker blocks. These blocks, which may represent true functional units, may be used as potential targets for phylogenetic analysis or molecular detection.

Uncovering cryptic diversity of Lyngbya: the new tropical marine cyanobacterial genus Dapis (Oscillatoriales)

Cyanobacteria comprise an extraordinarily diverse group of microorganisms and, as revealed by increasing molecular information, this biodiversity is even more extensive than previously estimated. In this sense, the cyanobacterial genus Lyngbya is a highly polyphyletic group composed of many unrelated taxa with morphological similarities. In this study, the new genus Dapis was erected from the genus Lyngbya, based on a combined molecular, chemical, and morphological approach. Herein, two new species of cyanobacteria are described: D. pleousa and D. pnigousa. Our analyses found these species to be widely distributed and abundant in tropical and subtropical marine habitats. Seasonally, both species have the ability to form extensive algal blooms in marine habitats: D. pleousa in shallow-water, soft bottom habitats and D. pnigousa on coral reefs below depths of 10 m. Electron microscopy showed that D. pleousa contains gas vesicles, a character not previously reported in Lyngbya. These gas vesicles, in conjunction with a mesh-like network of filaments that trap oxygen released from photosynthesis, provide this species with an unusual mechanism to disperse in coastal marine waters, allowing D. pleousa to be present in both benthic and planktonic forms. In addition, both D. pleousa and D. pnigousa contained nitrogen-fixing genes as well as bioactive secondary metabolites. Several specimens of D. pnigousa biosynthesized the secondary metabolite lyngbic acid, a molecule that has also been isolated from many other marine cyanobacteria. Dapis pleousa consistently produced the secondary metabolite malyngolide, which may provide a promising chemotaxonomic marker for this species.

Extending the ecological distribution of Desmonostoc genus: proposal of Desmonostoc salinum sp. nov., a novel Cyanobacteria from a saline-alkaline lake

Cyanobacteria is an ancient phylum of oxygenic photosynthetic microorganisms found in almost all environments of Earth. In recent years, the taxonomic placement of some cyanobacterial strains, including those belonging to the genus Nostocsensu lato, have been reevaluated by means of a polyphasic approach. Thus, 16S rRNA gene phylogeny and 16S-23S internal transcribed spacer (ITS) secondary structures coupled with morphological, ecological and physiological data are considered powerful tools for a better taxonomic and systematics resolution, leading to the description of novel genera and species. Additionally, underexplored and harsh environments, such as saline-alkaline lakes, have received special attention given they can be a source of novel cyanobacterial taxa. Here, a filamentous heterocytous strain, Nostocaceae CCM-UFV059, isolated from Laguna Amarga, Chile, was characterized applying the polyphasic approach; its fatty acid profile and physiological responses to salt (NaCl) were also determined. Morphologically, this strain was related to morphotypes of the Nostocsensu lato group, being phylogenetically placed into the typical cluster of the genus Desmonostoc. CCM-UFV059 showed identity of the 16S rRNA gene as well as 16S-23S secondary structures that did not match those from known described species of the genus Desmonostoc, as well as distinct ecological and physiological traits. Taken together, these data allowed the description of the first strain of a member of the genus Desmonostoc from a saline-alkaline lake, named Desmonostoc salinum sp. nov., under the provisions of the International Code of Nomenclature for algae, fungi and plants. This finding extends the ecological coverage of the genus Desmonostoc, contributing to a better understanding of cyanobacterial diversity and systematics.

Characterization of Microcystis (Cyanobacteria) Genotypes Based on the Internal Transcribed Spacer Region of rRNA by Next-Generation Sequencing

Microcystis is one of the most common and dominant bloom-forming cyanobacteria in freshwater worldwide. The method for genotype detection based on traditional molecular cloning is expensive and time consuming and generates a limited number of sequences. In this study, a high-throughput sequencing (HTS) method was developed to detect the internal transcribed spacer (ITS) regions between 16S and 23S rRNA region of Microcystis populations along a typical water system in Yuqiao Reservoir-Haihe River in Tianjin, northern China. A total of 629,341 reads were obtained and clustered into 2005 operational taxonomic units (OTUs). Analysis of alpha diversity indices showed that the Haihe River is more diverse than Yuqiao Reservoir. In general, the two water areas exhibit a clear differentiation pattern in OTU abundance, sharing genotypes from a small part of Yuqiao Reservoir with those in the Haihe River. Phylogenetic analysis further indicated the possible flexible evolution of Microcystis genotypes occurring in the research areas. This study provides the first exhaustive description of HTS method for detection of ITS region to evaluate Microcystis intra-species diversity and relationship.