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Two new species of Dulcicalothrix, D. adhikaryi sp. nov. and D. iyengarii sp. nov., were discovered in India and are characterized and described in accordance with the rules of the International Code of Nomenclature for algae, fungi, and plants (ICN). As a result of phylogenetic analysis, Calothrix elsteri is reassigned to Brunnivagina gen. nov. During comparison with all Dulcicalothrix for which sequence data were available, we observed that the genus has six ribosomal operons in three orthologous types. Each of the three orthologs could be identified based upon indels occurring in the D1-D1' helix sequence in the ITS rRNA region between the 16S and 23S rRNA genes, and in these three types, there were operons containing ITS rRNA regions with and without tRNA genes. Examination of complete genomes in Dulcicalothrix revealed that, at least in the three strains for which complete genomes are available, there are five ribosomal operons, two with tRNA genes and three with no tRNA genes in the ITS rRNA region. Internal transcribed spacer rRNA regions have been consistently used to differentiate species, both on the basis of secondary structure and percent dissimilarity. Our findings call into question the use of ITS rRNA regions to differentiate species in the absence of efforts to obtain multiple operons of the ITS rRNA region through cloning or targeted PCR amplicons. The ITS rRNA region data for Dulcicalothrix is woefully incomplete, but we provide herein a means for dealing with incomplete data using the polyphasic approach to analyze diverse molecular character sets. Caution is urged in using ITS rRNA data, but a way forward through the complexity is also proposed., (© 2024 The Author(s). Journal of Phycology published by Wiley Periodicals LLC on behalf of Phycological Society of America.)

The rapid expansion of whole genome sequencing in bacterial taxonomy has revealed deep evolutionary relationships and speciation signals, but assembly methods often miss true nucleotide diversity in the ribosomal operons. Though it lacks sufficient phylogenetic signal at the species level, the 16S ribosomal RNA gene is still much used in bacterial taxonomy. In cyanobacterial taxonomy, comparisons of 16S-23S Internal Transcribed Spacer (ITS) regions are used to bridge this information gap. Although ITS rRNA region analyses are routinely being used to identify species, researchers often do not identify orthologous operons, which leads to improper comparisons. No method for delineating orthologous operon copies from paralogous ones has been established. A new method for recognizing orthologous ribosomal operons by quantifying the conserved paired nucleotides in a helical domain of the ITS, has been developed. The D1' Index quantifies differences in the ratio of pyrimidines to purines in paired nucleotide sequences of this helix. Comparing 111 operon sequences from 89 strains of Brasilonema, four orthologous operon types were identified. Plotting D1' Index values against the length of helices produced clear separation of orthologs. Most orthologous operons in this study were observed both with and without tRNA genes present. We hypothesize that genomic rearrangement, not gene duplication, is responsible for the variation among orthologs. This new method will allow cyanobacterial taxonomists to utilize ITS rRNA region data more correctly, preventing erroneous taxonomic hypotheses. Moreover, this work could assist genomicists in identifying and preserving evident sequence variability in ribosomal operons, which is an important proxy for evolution in prokaryotes., (© 2024 The Author(s). Journal of Phycology published by Wiley Periodicals LLC on behalf of Phycological Society of America.)

Two populations of Rivularia-like cyanobacteria were isolated from ecologically distinct and biogeographically distant sites. One population was from an unpolluted stream in the Kola Peninsula of Russia, whereas the other was from a wet wall in the Grand Staircase-Escalante National Monument, a desert park-land in Utah. Though both were virtually indistinguishable from Rivularia in field and cultured material, they were both phylogenetically distant from Rivularia and the Rivulariaceae based on both 16S rRNA and rbcLX phylogenies. We here name the new cryptic genus Cyanomargarita gen. nov., with type species C. melechinii sp. nov., and additional species C. calcarea sp. nov. We also name a new family for these taxa, the Cyanomargaritaceae., (© 2017 Phycological Society of America.)

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. [ABSTRACT FROM AUTHOR]

The Nostocales is a monophyletic, heterocytous lineage of cyanobacteria capable of akinete production and division in multiple planes, depending upon family‐level clade. While present in a variety of ecosystems, the diversity of the Nostocales has been poorly elucidated. Due to environmentally ‐induced phenotypic plasticity, morphology alone is often insufficient to determine the true phylogenetic placement of these taxa. In order to bridge this gap, taxonomists now employ the polyphasic approach, combining methods such as morphological analysis, phylogenetic analysis based on DNA sequence and genetic identity based on ribosomal genes, and secondary structure of the 16S‐23S ITS and 16S rRNA gene sequences, as well as ecological characterization. Using this combined approach, a new genus and species (Reptodigitus chapmanii gen. et sp. nov.) isolated from the St. Johns River (Jacksonville, Florida, USA) within the Nostocales is herein described. Phylogenetic analyses place this taxon within the Hapalosiphonaceae, sister to the clade containing Fischerella, Hapalosiphon, and Westiellopsis. The 16S‐23S ITS secondary folding structure analysis also supports the erection of this new genus. [ABSTRACT FROM AUTHOR]

Filamentous nonhelerocytous cyanobacteria have been recognized as key ecosystem players in terms of soil stabilization, carbon sequestration, and water retention. Although the ecological importance of this group is well understood, its taxonomy is understudied. Microcoleus, Schizothrix, and Leptolyngbya, the most common cyanobacterial genera reported from soils, have all been found to be polyphyletic and in need of revision. In this study, strains morphologically corresponding to M. steenstrupii were isolated from North American desert soils. This species has been found to be polyphyletic, forming several distinct clades in numerous analyses. Three desert soil strains were analysed using ecological and geographical information, detailed morphological investigations, and DNA sequence data of the 16S rRNA gene and associated 16S-23S internal transcribed spacer. On the basis of this polyphasic characterization, we concluded that they represented the genus Symplocastrum. Until now, this cyanobacterial genus was poorly understood and lacked molecular definition. A more precise description of Symplocastrum is provided, including its phylogenetic position based on 16S rRNA gene sequence. Two new species are described (S. flechtnerae, S. torsivum) and Schizothrix californica is transferred to Symplocastrum. Phylogenetic placement of Symplocastrum is a critical component of the revisionary work underway in the nonheterocytous filamentous cyanobacteria and will lead tofurther revisionary work in this problematic group. Furthermore, with increasing taxonomic clarification of these filamentous taxa, ecological studies will have greater resolution and accuracy. [ABSTRACT FROM AUTHOR]

Twenty-six strains morphologically identified as Cylindrospermum as well as the closely related taxon Cronbergia siamensis were examined microscopically as well as phylogenetically using sequence data for the 16S r RNA gene and the 16S-23S internal transcribed spacer (ITS) region. Phylogenetic analysis of the 16S r RNA revealed three distinct clades. The clade we designate as Cylindrospermum sensu stricto contained all five of the foundational species, C. maius, C. stagnale, C. licheniforme, C. muscicola, and C. catenatum. In addition to these taxa, three species new to science in this clade were described: C. badium, C. moravicum, and C. pellucidum. Our evidence indicated that Cronbergia is a later synonym of Cylindrospermum. The phylogenetic position of Cylindrospermum within the Nostocaceae was not clearly resolved in our analyses. Cylindrospermum is unusual among cyanobacterial genera in that the morphological diversity appears to be more evident than sequence divergence. Taxa were clearly separable using morphology, but had very high percent similarity among ribosomal sequences. Given the high diversity we noted in this study, we conclude that there is likely much more diversity remaining to be described in this genus. [ABSTRACT FROM AUTHOR]

The diatom genusDiprora(Bacillariophyceae) was described from a cave on Kauaʻi, Hawaiʻi. Due to its lack of a raphe system and bilateral symmetry, the genus was first assigned to the Fragilariophycidae (‘araphid diatoms’), but its systematic affinities were undetermined. We present a three-gene phylogeny, based on nuclear (SSU rDNA) and chloroplast (rbcL,psbC) genes, to determine the phylogenetic relationships ofDiprorain the diatom tree of life. The concatenated multi-gene phylogenies, and the individual genes trees showDiprorato nest deep within the raphid diatoms, and in different analyses (of one-, two- and three-gene sequences) this diatom is shown to be most closely allied with taxa referred currently to the Sellaphoraceae, includingSellaphoraorFallacia. Hypothesis testing of the likelihood ofDiprorabeing an ‘araphid’ diatom indicates rejection of the hypothesis that the phylogenetic position ofD. haenaensisis within the araphid diatoms. Loss of the raphe system and reduction of other features may be related to its cave-dwelling habit. [ABSTRACT FROM PUBLISHER]

The cyanobacteria are a diverse, ancient lineage of oxygenic, phototrophic bacteria. Ubiquitous in nearly all ecosystems, the alpha-level diversity of these organisms lags behind other algal lineages due to a perceived dearth of phylogenetically useful characters. Recent phylogenetic studies of species within the genus Leptolyngbya have demonstrated that this is a polyphyletic assemblage. One group of strains that fits within the current circumscription of Leptolyngbya is genetically and phylogenetically distinct from Leptolyngbya sensu stricto. Members of this clade possess both a morphological synapomorphy and shared 16S-23S internal transcribed spacer (ITS) secondary structure, allowing the diagnosis of the new cyanobacterial genus Nodosilinea. Members of this genus are united by the unique ability to form nodules along the length of the filament. This trait has been previously observed only in the species Leptolyngbya nodulosa Z. Li et J. Brand, and we have chosen this species as the generitype of Nodosilinea. We currently recognize four species in the genus, N. nodulosa (Z. Li et J. Brand) comb. nov., N. bijugata (Kong.) comb. nov., N. conica sp. nov., and N. epilithica sp. nov. [ABSTRACT FROM AUTHOR]

Aulosira bohemensis sp. nov. was isolated from a wet meadow soil in South Bohemia, Czech Republic. It shares all the features of the majority of other Aulosira species, including isopolar development with intercalary heterocytes and apoheterocytic akinete development. It differs from all other species through the production of hormogonia perpendicular to the trichome axis following akinete germination. Morphologically the genus Aulosira appears closest to Nodularia, however, phylogenetic placement of A. bohemensis based on 16S rRNA was distant from that taxon. Aulosira falls within the Nostocaceae, with possible sister taxa in Trichormus, Mojavia and Nostoc. Despite the variety of phylogenetic analyses performed, we were unable to obtain bootstrap support for its position in any tree, and its correct phylogenetic position within the Nostocaceae remains unresolved. [ABSTRACT FROM AUTHOR]

Species currently classified within the cyanobacterial genus Microcoleus were determined to fall into two distinct clades in a 16S rDNA phylogeny, one containing taxa within the Oscillatoriaceae, the other containing taxa within the Phormidiaceae. The two lineages were confirmed in an analysis of the 16S–23S internal transcribed spacer (ITS) region sequences and secondary structures. The type species for Microcoleus is M. vaginatus Gomont, and this taxon belongs in the Oscillatoriaceae. Consequently, Microcoleus taxa in the Phormidiaceae must be placed in separate genera, and we propose the new genus Coleofasciculus to contain marine taxa currently placed in Microcoleus. The type species for Coleofasciculus is the well-studied and widespread marine mat-forming species Microcoleus chthonoplastes (Mert.) Zanardini ex Gomont. Other characters separating the two families include type of cell division and thylakoid structure. [ABSTRACT FROM AUTHOR]

The morphology, ecology, life cycles, ultrastructure and sequences of the 16S rRNA gene of four cyanobacteria strains from different localities putatively identified as Mastigocladus laminosus were studied. Our strains fall into three separate clades, and conclusions based on "classical" taxonomical methods correspond with conclusions based on sequences of the 16S rRNA gene. According to all methods used, M. laminosus sensu stricto includes true branching strains from thermal springs only, and the genus Mastigocladus is separated from all soil species in the genus Fischerella. The genera Mastigocladus and Fischerella have a confused taxonomic history because the generitype of both taxa was collected from Karlovy Vary Hot Spring within 15 years of the description of each. Strains with other ecological (nonthermal locality) or morphological characteristics (thermal habitat but unbranched forms) belong to different genera. We begin the revision process by moving Mastigocladus laminosus var. indica to Fischerella indica stat. nov., comb. nov. Full resolution of the taxonomic confusion surrounding Mastigocladus and Fischerella will likely require a proposal for designation of a new type species for the genus Fischerella. [ABSTRACT FROM AUTHOR]

Thirty-one strains of Microcoleus were isolated from desert soils in the United States. Although all these taxa fit the broad definition of Microcoleus vaginatus (Vaucher) Gomont in common usage by soil algal researchers, sequence data for the 16S rRNA gene and 16S–23S internal transcribed spacer (ITS) region indicated that more than one species was represented. Combined sequence and morphological data revealed the presence of two morphologically similar taxa, M. vaginatus and Microcoleus steenstrupii Boye-Petersen. The rRNA operons of these taxa were sufficiently dissimilar that we suspect the two taxa belong in separate genera. The M. vaginatus clade was most similar to published sequences from Trichodesmium and Arthrospira. When 16S sequences from the isolates we identified as M. steenstrupii were compared with published sequences, our strains grouped with M. chthonoplastes (Mertens) Zanardini ex Gomont and may have closest relatives among several genera in the Phormidiaceae. Organization within the 16S–23S ITS regions was variable between the two taxa. Microcoleus vaginatus had either two tRNA genes (tRNAIle and tRNAAla ) or a fragment of the tRNAIle gene in its ITS regions, whereas M. steenstrupii had rRNA operons with either the tRNAIle gene or no tRNA genes in its ITS regions. Microcoleus vaginatus showed no subspecific variation within the combined morphological and molecular characterizations, with 16S similarities ranging from 97.1% to 99.9%. Microcoleus steenstrupii showed considerable genetic variability, with 16S similarities ranging from 91.5% to 99.4%. In phylogenetic analyses, we found that this variability was not congruent with geography, and we suspect that our M. steenstrupii strains represent several cryptic species. [ABSTRACT FROM AUTHOR]

Thirty-one strains of Microcoleus were isolated from desert soils in the United States. Although all these taxa fit the broad definition of Microcoleus vaginatus (Vaucher) Gomont in common usage by soil algal researchers, sequence data for the 16S rRNA gene and 16S–23S internal transcribed spacer (ITS) region indicated that more than one species was represented. Combined sequence and morphological data revealed the presence of two morphologically similar taxa, M. vaginatus and Microcoleus steenstrupii Boye-Petersen. The rRNA operons of these taxa were sufficiently dissimilar that we suspect the two taxa belong in separate genera. The M. vaginatus clade was most similar to published sequences from Trichodesmium and Arthrospira. When 16S sequences from the isolates we identified as M. steenstrupii were compared with published sequences, our strains grouped with M. chthonoplastes (Mertens) Zanardini ex Gomont and may have closest relatives among several genera in the Phormidiaceae. Organization within the 16S–23S ITS regions was variable between the two taxa. Microcoleus vaginatus had either two tRNA genes (tRNAIle and tRNAAla ) or a fragment of the tRNAIle gene in its ITS regions, whereas M. steenstrupii had rRNA operons with either the tRNAIle gene or no tRNA genes in its ITS regions. Microcoleus vaginatus showed no subspecific variation within the combined morphological and molecular characterizations, with 16S similarities ranging from 97.1% to 99.9%. Microcoleus steenstrupii showed considerable genetic variability, with 16S similarities ranging from 91.5% to 99.4%. In phylogenetic analyses, we found that this variability was not congruent with geography, and we suspect that our M. steenstrupii strains represent several cryptic species. [ABSTRACT FROM AUTHOR]

The effects of temperature, ionic composition, and conductivity on growth rates of ten strains of Chaetoceros muelleri Lemmerman (mostly var. subsalsum Johan. & Rushf.) were studied. Lipid content of stressed and unstressed cells and fatty acid composition were also determined. Considerable physiological variability was also observed in the ten strains, although principal components analysis of physiological data indicated that all strains fell into one of two major groups: C. muelleri (var. muelleri and var. subsalum) and an undescribed Chaetoceros species morphologically close to C. muelleri var. subsalsum. A high degree of agreement was found among morphological, physiological, and biochemical data sets, indicating that physiological and biochemical data may be helpful in making taxonomic decisions in diatoms, particularly in taxa with few morphological characters. We also conclude that nonmorphological characters such as those employed in the present study can be used to test phylogenetic hypothesis formulated from traditional morphological data. [ABSTRACT FROM AUTHOR]

The Nostocales is a monophyletic, heterocytous lineage of cyanobacteria capable of akinete production and division in multiple planes, depending upon family‐level clade. While present in a variety of ecosystems, the diversity of the Nostocales has been poorly elucidated. Due to environmentally ‐induced phenotypic plasticity, morphology alone is often insufficient to determine the true phylogenetic placement of these taxa. In order to bridge this gap, taxonomists now employ the polyphasic approach, combining methods such as morphological analysis, phylogenetic analysis based on DNA sequence and genetic identity based on ribosomal genes, and secondary structure of the 16S‐23S ITS and 16S rRNA gene sequences, as well as ecological characterization. Using this combined approach, a new genus and species (Reptodigitus chapmanii gen. et sp. nov.) isolated from the St. Johns River (Jacksonville, Florida, USA) within the Nostocales is herein described. Phylogenetic analyses place this taxon within the Hapalosiphonaceae, sister to the clade containing Fischerella, Hapalosiphon, and Westiellopsis. The 16S‐23S ITS secondary folding structure analysis also supports the erection of this new genus. [ABSTRACT FROM AUTHOR]