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Phylogenetic complexities of the members of Rivulariaceae with the re-creation of the family Calotrichaceae and description of Dulcicalothrix necridiiformans gen nov., sp nov., and reclassification of Calothrix desertica
Abstract
A freshwater dwelling, tapering, heterocytous cyanobacterium (strain V13) was isolated from an oligotrophic pond in the Shrirampur taluka, Ahmednagar district of Maharashtra in India. Initial morphological examination indicated, that strain V13 belonged to the genus Calothrix. Subsequent molecular and phylogenetic assessment based on 16S rRNA gene, led us to describe the freshwater/terrestrial clade of Calothrix strains without terminal hairs as a new genus Dulcicalothrix gen. nov., with the type species Dulcicalothrix necridiiformans sp. nov. (Strain V13) on the basis of the necridia forming ability of the strain. Also, the 16S-23S ITS secondary structure analysis clearly differentiated strain V13 from the other members of the clade. Past studies and the current state of knowledge makes it imperative to separate the groups Calothrix (marine/freshwater Calothrix), Macrochaete and Dulcicalothrix (freshwater/terrestrial Calothrix) into separate genera in accordance with the International Code of Nomenclature for Algae, Fungi and Plants. Robust phylogenetic evidence and previous reports strongly support the re-erection of the family Calotrichaceae distinct from the existing family Rivulariaceae.
... Key index words: 16S-23S ITS; Calothrix; Calotrichaceae; heteropolarity; isopolarity; Nostocales; Rivulariaceae Nostocales, among the eight orders of the phylum cyanobacteria (Kom arek et al. 2014), consist of thalli containing specialized cells (heterocytes and akinetes) in filaments that may be isopolar or heteropolar, tapering or untapering, or false branched or true branched. With the emergence of the polyphasic approach, the taxonomy of cyanobacteria has been moving at a fast pace, particularly in the Nostocales, but with phylogenetic inconsistencies being reported within the order at both family and genus levels (Hauer et al. 2014, Kom arek et al. 2014, Berrendero et al. 2016, Saraf et al. 2018, 2019. New families such as Gloeotrichiaceae (Kom arek et al. 2014), Tolypothrichaceae (Hauer et al. 2014), Godleyaceae (Hauer et al. 2014), and Cyanomargaritaceae (Shalygin et al. 2017) have been recently described. ...
... The family Calotrichaceae currently contains the type genus Calothrix (Agardh ex Bornet and Flahault 1886), as well as Macrochaete (Berrendero et al. 2016) and Dulcicalothrix (Saraf et al. 2019). The genus Calothrix is probably the most difficult genus among tapering taxa based on both morphological and phylogenetic complexities (Whitton 1987, Berrendero et al. 2016, Saraf et al. 2019. ...
... The family Calotrichaceae currently contains the type genus Calothrix (Agardh ex Bornet and Flahault 1886), as well as Macrochaete (Berrendero et al. 2016) and Dulcicalothrix (Saraf et al. 2019). The genus Calothrix is probably the most difficult genus among tapering taxa based on both morphological and phylogenetic complexities (Whitton 1987, Berrendero et al. 2016, Saraf et al. 2019. Calothrix exhibits heteropolar filaments having a basal heterocyte with the apical ends terminating slightly into narrow but chlorophyllous apical cells or into achlorophyllous, hyaline hairs. ...
Three novel strains in Calotrichaceae from tropical habitats were isolated and characterized with regards to their morphology, phylogenetic placement, and secondary structures of conserved domains in the 16S‐23S internal transcribed spacer (ITS). The strains fell into two clades formerly identified as Calothrix from freshwater and brackish habitats. Based on both morphology and ecology, they differed from the type species of Calothrix, C. confervicola, which is marine, has wide trichomes with short cells, and narrows abruptly to a hyaline hair. The first clade grouped species with heteropolar filaments widened at the base and narrowed gradually toward the apex but not ending in a hair, with basal heterocytes that are formed in series as the apically placed heterocytes senesce; this clade is being named Fulbrightiella gen. nov., with two named species, F. bharadwajae sp. nov. and F. oahuensis sp. nov. The second clade was comprised of a single species with isopolar trichomes that are untapering as hormogonia, but which widen midfilament and taper towards both ends following growth. These trichomes develop pairs of heterocyte mid‐filament, causing fragmentation into heteropolar trichomes with basal heterocytes and ends that taper, but not to a hair. This clade consists of a single species at present, Sherwoodiella mauiensis. With this action, four clades in the Calotrichaceae have been named: Macrochaete, Dulcicalothrix, Fulbrightiella and Sherwoodiella. Calothrix sensu stricto is truly marine, morphologically distinct, and unsequenced; finding and sequencing the generitype for Calothrix remains as the most important and unfinished task in the revision of the Calotrichaceae.
... Furthermore, the authors also emphasized the importance of polyphasic approach in the taxonomic and systematic studies of cyanobacteria. With more clarity and increased understanding in the usage of polyphasic approach, the last 6 years has seen a surge in the description of new families and genera along with taxonomic revisions at the family level (Hentschke et al. 2016;Rigonato et al. 2016;Hašler et al. 2017;Shalygin et al. 2017;Kilgore et al. 2018;Sendall and McGregor 2018;Saraf et al. 2019c are some of the examples). More than 80 new genera and nine new families have been described after the classification system proposed by Komárek et al. ...
... Furthermore, the phylogenetic analysis based on 16S rRNA gene, cpcBA-IGS, and nifD indicated Calothrix to be polyphyletic (Henson et al. 2004;Sihvonen et al. 2007;Berrendero et al. 2011;Domínguez-Escobar et al. 2011;Komárek et al. 2012;Whitton and Mateo 2012). Moreover, the absence of the sequence corresponding to the type species of Calothrix has further contributed to the taxonomic complexity hovering around the genus (Saraf et al. 2019c). Unlike the genus Nostoc, there have been comparatively fewer polyphasic studies on Calothrix-like taxa and this is evident from the fact that till date only two Calothrix-like genera have been described (Berrendero et al. 2016;Saraf et al. 2019c). ...
... Moreover, the absence of the sequence corresponding to the type species of Calothrix has further contributed to the taxonomic complexity hovering around the genus (Saraf et al. 2019c). Unlike the genus Nostoc, there have been comparatively fewer polyphasic studies on Calothrix-like taxa and this is evident from the fact that till date only two Calothrix-like genera have been described (Berrendero et al. 2016;Saraf et al. 2019c). Berrendero et al. in their study on Calothrix-like strains isolated from different ecological habitats observed that all the strains included in their study formed a separate monophyletic clade, and therefore, the authors characterized their strains as species of novel genus Macrochaete (Berrendero et al. 2016). ...
Cyanobacteria are oxygen-producing, photosynthesizing, gram-negative prokaryotes, which played a major role in the development of the atmosphere of the present earth. Despite being so old and omnipresent, it is surprising that proper and correct identification of cyanobacteria is still a challenge and has often created confusing patterns. The primary reason for all this confusion is the morphological plasticity of these organisms, which eventually creates confusion during long-term studies. This fact makes the study of cyanobacteria both challenging and interesting too. The taxonomy of cyanobacteria for a long time was based only on the morphological criterion, which, in the modern times, has raised many questions, which need to be answered by adopting an approach that respects both the classical morphology and the modern methods based on genetic information and phylogeny. The amalgamation of both the classical and the modern methods has led to the development of the polyphasic approach. Unfortunately, at the present moment what all constitutes a polyphasic approach is still under scrutiny, thus making the taxonomy of cyanobacteria complicated and challenging. Modern taxonomists must solve all the abovementioned problems by adopting an approach that reflects in a considerate way the morphology, ecology, and the molecular phylogeny. Unequal, biased preference or convenience-based methods are posing hindrances and thus lead to ambiguities that are tough to resolve. The future of cyanobacterial taxonomy may lie in the proper usage of the polyphasic approach with more revisionary works being anticipated.KeywordsCyanobacteriaTaxonomySystematicsPolyphasic approach
Nostoc
Calothrix
... Cyanobacterial researchers all over the world are adopting a polyphasic approach, according to which, information obtained from morphological observation is integrated with molecular and ecological data in order to resolve taxonomic dilemmas (Wilmotte & Golubic 1991;Wilmotte 1994;Komárek & Kaštovský 2003;Castenholz & Norris 2005;Taton et al. 2006;Berrendero et al. 2008;Garcia-Pichel et al. 2013). Following this approach, Saraf et al. (2019), reestablished family Calotrichaceae and described new genus and species Dulcicalothrix necridiiformans Saraf et al. based on 16S rRNA phylogeny. In this study, many "Calothrix'' species, including Calothrix desertica Schwabe, were assigned to Dulcicalothrix (Saraf et al. 2019). ...
... Following this approach, Saraf et al. (2019), reestablished family Calotrichaceae and described new genus and species Dulcicalothrix necridiiformans Saraf et al. based on 16S rRNA phylogeny. In this study, many "Calothrix'' species, including Calothrix desertica Schwabe, were assigned to Dulcicalothrix (Saraf et al. 2019). "Recreation" of the family Calotrichaceae seems to be premature in Saraf et al. (2019) since Calotrichaceae was established based on Dulcicalothrix sequence, and not based on type material of marine Calothrix confervicola Agardh ex Bornet et Flahault. ...
... In this study, many "Calothrix'' species, including Calothrix desertica Schwabe, were assigned to Dulcicalothrix (Saraf et al. 2019). "Recreation" of the family Calotrichaceae seems to be premature in Saraf et al. (2019) since Calotrichaceae was established based on Dulcicalothrix sequence, and not based on type material of marine Calothrix confervicola Agardh ex Bornet et Flahault. Hence, the "true" Calotrichaceae remain unknown and family level taxonomy of Dulcicalothrix should be clarified. ...
new species of heterocytous cyanobacterium Dulcicalothrix alborzica sp. nov. (Calotrichaceae) was isolated from Iran and described following a polyphasic approach. Morphological examination indicated that the strain, initially called "Alborzica", belonged to the genus Calothrix. Nonetheless, 16S rRNA gene analysis showed that "Alborzica" were within the Dulcicalothrix cluster. In order to confirm the taxonomic position of this new taxon, rbcL and rpoC1 phylogenies were inferred. Results confirmed identity of "Alborzica" supporting the 16S rRNA phylogeny. Analysis of the secondary structures of 16S-23S Internal Transcribed Spacer (ITS) revealed that "Alborzica" had unique structure compared with known Dulcicalothrix spp. Therefore, based on the morphology and thorough molecular analysis, "Alborzica'' should be considered a novel species in the genus Dulcicalothrix.
... Dulcicalothrix sp. (Saraf et al. 2019). Dulcicalothrix sp. ...
... nov. (Saraf et al. 2019). The authors based on the current state of knowledge suggested that several genera including Calothrix, Macrochaetae and Dulcicalothrix should be distinguished from the Rivulariaceae family to the Calothrichaceae family (Berrendero et al. 2016;Saraf et al. 2019). ...
... (Saraf et al. 2019). The authors based on the current state of knowledge suggested that several genera including Calothrix, Macrochaetae and Dulcicalothrix should be distinguished from the Rivulariaceae family to the Calothrichaceae family (Berrendero et al. 2016;Saraf et al. 2019). Calothrix and Dulcicalothrix cyanobacteria exhibited different morphologic and ecological features with the majority of Calothrix strains being reported from marine habitat while Dulcicalothrix strains were reported from freshwater and terrestrial habitats (Berrendero, Perona andMateo 2011, 2016;Saraf et al. 2019). ...
Cyanobacteria are able to synthesize a high diversity of natural compounds that account for their success in the colonization of a variety of ecological niches. Many of them have beneficial properties. The mud from the thermal baths of Balaruc-Les-Bains, one of the oldest thermal baths in France, has long been recognized as a healing treatment for arthro-rheumatic diseases. To characterize the cyanobacteria living in these muds, several strains were isolated from the water column and biofilms of the retention basin and analyzed using a polyphasic approach. Morphological, ultrastructural and molecular (16S rRNA gene and 16S-23S ITS region sequencing) methods were employed to identify nine cyanobacterial strains belonging to the orders Chroococcales, Synechococcales, Oscillatoriales and Nostocales. The combination of morphological and genetic characteristics supported the description of a new genus and species with the type species as Pseudochroococcus coutei. The taxonomic diversity in the muds from Thermes de Balaruc-Les-Bains appears higher than previously documented, providing new candidate taxa for their observed therapeutic properties.
... The aquatic taxa often form macroscopic epilithic mucilaginous colonies (Rivularia, Nunduva, Dichothrix), sometimes incrusted by calcium carbonate, or even live endolithically (Mastigocoleus, Kyrtuthrix) in the marine tidal zones (Shalygin et al. 2018, Johansen et al. 2021 Richelia (including Calothrix rhizosoleniae), a facultative nitrogen-fixing endosymbiont of marine diatoms (Foster et al. 2009), exhibits a simplified morphology with very short filaments, basal heterocytes, but only indistinct sheath and mild trichome tapering. Recently, Saraf et al. (2021) suggested resurrection of the family name Calotrichaceae to harbor Dulcicalothrix, Macrochaete, and putatively also Calothrix, based on their 16S rRNA gene analysis. While the two clades of Rivulariaceae and Calotrichaceae have often appeared separated in 16S rRNA gene trees, including ours (Fig. S1), they were clearly grouped as sister clades in our phylogenomic and combined analyses (Figs. 4 and S2). ...
... While the two clades of Rivulariaceae and Calotrichaceae have often appeared separated in 16S rRNA gene trees, including ours (Fig. S1), they were clearly grouped as sister clades in our phylogenomic and combined analyses (Figs. 4 and S2). Because both clades formed a group at similar level of branching to other hereby suggested nostocalean families, and the analysis of typical Calothrix material is still pending (Saraf et al. 2021), we prefer to merge the families under the name Rivulariaceae for now. 20.6. ...
Cyanobacterial taxonomy is facing a period of rapid changes thanks to the ease of 16S rRNA gene sequencing and established workflows for description of new taxa. Since the last comprehensive review of the cyanobacterial system in 2014 until 2021, at least 273 species in 140 genera were newly described. These taxa were mainly placed into previously defined orders and families although several new families were proposed. However, the classification of most taxa still relied on hierarchical relationships inherited from the classical morphological taxonomy. Similarly, the obviously polyphyletic orders such as Synechococcales and Oscillatoriales were left unchanged. In the current study, the rising number of genomic sequences of cyanobacteria and well described reference strains allowed us to reconstruct a robust phylogenomic tree for taxonomic purposes. A less robust but better sampled 16S rRNA gene phylogeny was mapped to the phylogenomic backbone. Based on both these phylogenies, a polyphasic classification throughout the whole phylum of Cyanobacteria was created, with ten new orders and fifteen new families. The proposed system of cyanobacterial orders and families relied on a phylogenomic tree but still employed phenotypic apomorphies where possible to make it useful for professionals in the field. It was, however, confirmed that morphological convergence of phylogenetically distant taxa was a frequent phenomenon in cyanobacteria. Moreover, the limited phylogenetic informativeness of the 16S rRNA gene, resulting in ambiguous phylogenies above the genus level, emphasized the integration of genomic data as a prerequisite for the conclusive taxonomic placement of a vast number of cyanobacterial genera in the future.
... After the classification system by Komárek et al. (2014), at least 10 new families have been described along with 80 new genera. Alone in India, many new genera have been described by using polyphasic approach and some of them include -Desertifilum (Dadheech et al. 2012), Aliinostoc (Bagchi et al. 2017), Leptoelongatus, Euryhalinema (Chakraborty et al. 2019), Desikacharya, Dulcicalothrix, (Saraf et al. 2019a(Saraf et al. , 2019b, Constrictifilum (Chavadar et al. 2021) etc. Family level revision was also done in Calotrichaceae (Saraf et al. 2019b), which now includes 3 genera-Dulcicalothrix, Calothrix and Macrochaete. We bring herein, some of the major taxonomic studies performed in India, in which new taxa were described using a polyphasic approach. ...
... After the classification system by Komárek et al. (2014), at least 10 new families have been described along with 80 new genera. Alone in India, many new genera have been described by using polyphasic approach and some of them include -Desertifilum (Dadheech et al. 2012), Aliinostoc (Bagchi et al. 2017), Leptoelongatus, Euryhalinema (Chakraborty et al. 2019), Desikacharya, Dulcicalothrix, (Saraf et al. 2019a(Saraf et al. , 2019b, Constrictifilum (Chavadar et al. 2021) etc. Family level revision was also done in Calotrichaceae (Saraf et al. 2019b), which now includes 3 genera-Dulcicalothrix, Calothrix and Macrochaete. We bring herein, some of the major taxonomic studies performed in India, in which new taxa were described using a polyphasic approach. ...
... (Hauer et al. 2014;Bohunická et al. 2015;Berrendero Gómez et al. 2016, McGregor andSendall 2017a,b;Shalygin et al. 2017;Kabirnataj et al. 2018;Saraf et al. 2018a,b;Saraf et al. 2019a,b;Kabirnataj et al. 2020). Five families have been newly described after the classification scheme provided by Komárek et al. in 2014(Hentschke et al. 2016Shalygin et al. 2017;Sendall and McGregor 2018;Kilgore et al. 2018;Saraf et al. 2019a). The aim of this minireview is to perform a phylogenetic assessment of three taxonomic groups in the order Nostocales that have seen considerable number of revisionary works in the recent few years. ...
... Based on our phylogenetic analysis we anticipate new families being created from the family Scytonemataceae in the future. Similar family level revisions have already taken place in the other false branching families-Microchaetaceae and Rivulariaceae(Hauer et al. 2014;Saraf et al. 2019a). According to our knowledge, this is the most comprehensive phylogenetic tree for the family Scytonemataceae and we recommend that all the sequences included in this tree should be used in the future for describing Scytonema-like taxa to avoid further creation of taxonomic complexities. ...
The order Nostocales is represented by morphologically diverse forms with respect to the branching patterns and polarity of the filaments. With growing understanding of taxonomy and systematics, members of the order Nostocales have also undergone multiple taxonomic revisions. The last decade has seen a surge in the description of new genera and families within the order Nostocales. In this study, we discuss the taxonomic status of all the newly described and reclassified taxa of some of the prominent morphological forms within the order Nostocales by constructing comprehensive phylogenetic trees. Further, we propose certain strategies that would contribute to resolving the taxonomic complexities arising due to inadequate taxon sampling.
... Sequence identity between OTU1 and the remaining OTUs belonging to this family was as low as approximately 90%, ranging from 90.73 to 93.41%, and when it was compared with other Rivulariaceae from the databases, in the different clusters of the phylogenetic tree, this value ranged from 87.12 to 93.90%. A large difference between the sequences of this gene was also found in other studies on Rivulariaceae [15][16][17]29,58 . In fact, several new genera are emerging on the basis of these differences [15][16][17] . ...
... A large difference between the sequences of this gene was also found in other studies on Rivulariaceae [15][16][17]29,58 . In fact, several new genera are emerging on the basis of these differences [15][16][17] . Comparisons of phylogenies using other markers, such as the phycocyanin operon and the intervening intergenic spacer (cpcBA-IGS) with the 16S rRNA gene in previous studies in Rivulariaceae, have shown largely consistent results, with a high level of divergence between the components of this family 11 . ...
Attached or floating macroscopic cyanobacteria can be found in shallow waters and can be easily hand-collected, but their identification is often challenging due to their high morphological variability. In addition, many members of environmental samples lose their morphological adaptations under controlled conditions, making the integration of analyses of field populations and derived isolated cultures necessary in order to evaluate phenotypic plasticity for identification purposes. Therefore, in this study, twenty-nine macroscopic field samples were analyzed by Illumina sequencing and parallel optical microscopy. Some colonies showed the typical morphological characteristics of Rivularia biasolettiana , and others showed those of Rivularia haematites . However, other Rivularia -like colonies showed ambiguous morphologies, and some of them showed the phenotypic features of the new genus Cyanomargarita , which is virtually indistinguishable from Rivularia in the field. In all of the colonies, phylotype composition was highly heterogeneous, with abundances varying depending on the analyzed sample. Some colonies were dominated (97–99%) by a single phylotype, while in others, the percentage of the dominant phylotype decreased to approximately 50–60%. Surprisingly, the same dominant phylotype was found in R. biasolettiana and R. haematites colonies. The relationships between environmental and/or biological factors and morphological variability in these colonies are discussed.
... Hence, some taxonomical researchers with similar data suggested modifying the family Calotrichaceae by putting Dulcicalothrix, Calothrix, and Macrochaete under it. Together, they strongly recommend the reclassification of C. desertica to Dulcicalothrix desertica (41). ...
Calothrix desertica having a semilunar apical heterocyst is proficient at excreting 1.2 g/L of extracellular polymers (EPsC) in 45 days. The refined EPsC constitutes 430 mg/g of glycogen, 390 mg/g of protein, and 14.6 mg/g of glycoproteins (GPs). The glycoprotein estimation of EPsC was performed by two step hydrolysis methods with H2SO4. The peak between 10 mAU to 20 mAU in HPLC, 1400 cm-1 to 1700 cm-1 in FTIR, and 40kDa- 35kDa bands in SDS-PAGE authenticates the presence of glycoproteins in the EPsC. The EPsC agglomerate of 1000 nm to 3000 nm size with a Zeta potential of -20 mV to 5 mV was determined using DLS. Further EPsC of nanosizes of 30 nm to 150 nm in 50,000 X and 20 nm to 40 nm in 60,000 X was measured using FE- SEM. The DPPH assay and H2O2 scavenging assay showed 73.1% and 70.8% of anti-oxidant activity in EPsC, which is coequally efficient as standard gallic acid. EPsC biopolymer can also be used as a potential reducing agent, as per the anti-nutrient activity studies.
... On rocks, plants, or soil particles in both marine and nonmarine environments; worldwide. Most of the terrestrial species will be probably transferred to recently established, morphologically similar genus Dulcicalothrix [61]. ...
... These include addition of new genera and also transfer of existing genera of the family to a new family [4,5,7,8]. Further, with the advent of the polyphasic approach many new families have been separated from the traditional Scytonemataceae, Rivulariaceae and Microchaetaceae due to phylogenetic inconsistencies [9][10][11][12]. The family Microchaetaceae was established by Lemmermann and included members with uniseriate, heteropolar filaments with frequent basal heterocyte and the hormogonia were liberated from the apical end of the trichome. ...
Cyanobacterial strain PS4G was isolated from seepage soil sampled at Pachmarhi, Madhya Pradesh, India, and was characterized using a polyphasic approach. The results of morphological analysis showed that strain PS4G had unique morphological characteristics which were not observed in the other described species of the genus Fortiea. In the 16S rRNA gene phylogenetic analysis inferred using Bayesian inference, maximum-likelihood and neighbour-joining methods, strain PS4G clustered within the clade consisting of the members of the genus Fortiea. Furthermore, in the secondary structure analysis using the D1-D1′ helix and BoxB regions of 16S-23S ITS, strain PS4G showed marked differences in comparison with other members of the genus Fortiea. Overall, the morphological, phylogenetic and folded 16S-23S ITS secondary structure examination indicated that strain PS4G represents a novel species of the genus Fortiea. In accordance with the International Code of Nomenclature of Algae, Fungi and Plants we describe a novel species of Fortiea with the name Fortiea necridiiformans sp. nov.
... A common taxonomic misconception is the identification of genera/species regardless of their ecology, despite several recognized polyphyletic genera containing species from different habitats [21,22]. This problem was resolved, for instance, in the Lyngbya genus, where marine species were genetically recognized as distinct (Moorea) [23] and more recently in the Calothrix cluster genus with the description of freshwater/terrestrial genus Dulcicalothrix [24]. Many other studies address this problem, but most of them do not consider other habitats, such as brackish or thermal habitats, mainly due to the lack of available cultured strains. ...
Cyanobacteria are among the most diverse morphological microorganisms that inhabit a great variety of habitats. Their presence in the Azores, a volcanic archipelago of nine islands in the middle of the North Atlantic Ocean, has already been reported. However, due to the high diversity of cyanobacteria habitats, their biodiversity is still understudied, mainly in extreme environments. To address this, a total of 156 cyanobacteria strains from Azores lakes, streams, thermal and terrestrial habitats were isolated. Identification was made based on a polyphasic approach using classical taxonomy (morphological characteristics and environmental data) and phylogeny among 81 strains assessed by maximum likelihood and Bayesian analysis of 16S rDNA partial sequences. The 156 isolates showed a high genera diversity (38) belonging to the orders Chroococcales, Nostocales, Oscillatoriales, and Synechococcales. Eleven new genera for the Azores habitats are here reported, reinforcing that cyanobacteria biodiversity in these islands is still much understudied. Phylogenetic analysis showed 14 clusters associated with these cyanobacteria orders, with evidence for six new genera and valuable information towards Microchaete/Coleospermum taxonomic revision that better reflects species environmental distribution. These results emphasize the need for cyanobacteria taxonomy revisions, through polyphasic studies, mainly in Synechococcales order and in the Microchaete/Coleospermum, Nostoc, and Anabaena genera.
... nov., and recognition of four rather than five species within Visia: . Similarly, molecular analysis of a distinct clade of Batrachospermum by Necchi, Garcia Fo, Paiano, and Vis (2019) (Saraf, Suradkar, et al., 2019). The analysis led to the re-erection of the family Calotrichaceae, distinct from the family Rivulariaceae Bornet et Flahault. ...
Highlights of new, interesting, and emerging research findings on substratum‐associated microbiota covered from a survey of 2019 literature from primarily freshwaters provide insight into research trends of interest to the Water Environment Federation and others interested in benthic, aquatic environments. Coverage of topics on bottom‐associated or attached algae and cyanobacteria, though not comprehensive, includes new methods, taxa new‐to‐science, nutrient dynamics, auto‐ and heterotrophic interactions, grazers, bioassessment, herbicides and other pollutants, metal contaminants, and nuisance, and bloom‐forming and harmful algae. Coverage of bacteria, also not comprehensive, focuses on the ecology of benthic biofilms and microbial communities, along with the ecology of microbes like Caulobacter crescentus , Rhodobacter , and other freshwater microbial species. Bacterial topics covered also include metagenomics and metatranscriptomics, toxins and pollutants, bacterial pathogens and bacteriophages, and bacterial physiology. Readers may use this literature review to learn about or renew their interest in the recent advances and discoveries regarding substratum‐associated microbiota.
Practitioner points
This review of literature from 2019 on substratum‐associated microbiota presents highlights of findings on algae, cyanobacteria, and bacteria from primarily freshwaters.
Coverage of algae and cyanobacteria includes findings on new methods, taxa new to science, nutrient dynamics, auto‐ and heterotrophic interactions, grazers, bioassessment, herbicides and other pollutants, metal contaminants, and nuisance, bloom‐forming and harmful algae.
Coverage of bacteria includes findings on ecology of benthic biofilms and microbial communities, the ecology of microbes, metagenomics and metatranscriptomics, toxins and pollutants, bacterial pathogens and bacteriophages, and bacterial physiology.
Highlights of new, noteworthy and emerging topics build on those from 2018 and will be of relevance to the Water Environment Federation and others interested in benthic, aquatic environments
The taxonomic identification of cyanobacteria is essential for researchers or/and competent authorities to know their diversity and detect, manage, and control potentially toxic cyanobacteria. Microbiologists and botanists agree that polyphasic approaches are a powerful tool to identify cyanobacteria. This chapter describes the polyphasic approach, the steps to follow, and some recommendations for its correct application. The changes in taxonomy using this methodology are also explained. Finally, the applications of a polyphasic approach on genomic and metabarcoding biodiversity studies are described. The polyphasic approach is a well defined and standard tool for classifying cyanobacteria, which researchers accept, but it is continuously being revised.
Cyanoprokaryotes (or cyanobacteria), the most ancient photoautotrophs on Earth, and eukaryotic algae are present nearly in all biomes across the globe. Besides their key role in the production of most of the global net oxygen, they also play multiple pivotal ecological roles in the environments they colonize. Most cyanoprokaryotes and algal species present a high degree of morphological and physiological adaptation to their biotopes. During recent decades, with the affirmation of the polyphasic approach and robust support from molecular phylogenetics, cyanoprokaryotes and algae have undergone extensive taxonomic revisions, resulting in the discovery and description of many new species, genera, families, and orders. In this chapter, we discuss the foundations and modern criteria of cyanobacterial and algal classification. Habitats of cyanoprokaryotes and algae, including extremophiles from hot springs, are presented with a focus on biogeographically and environmentally restricted flagship morphotaxa.
Cyanobacteria are photo-oxygenic prokaryotes present in nearly all ecosystems, where they are important in global oxygen, carbon, and nitrogen cycles. They are often recognized as the harbingers of eutrophication in freshwater systems and are increasingly being noted as nuisance species in marine ecosystems such as coral reefs. In recent years, cyanobacteria have been intensely studied due to their toxicity, harmful bloom formation, and because their distribution and abundance are expected to increase with climate change. Nevertheless, for all of their importance, many gaps in our knowledge of cyanobacteria remain: the distribution, dispersal, and biogeography of these microorganisms are still not understood. Until 1994 little attention was paid to tropical cyanobacteria and their diversity, despite some harmful invasive species having their putative origins in tropical habitats. However, more practiced articulation and research has recently uncovered previously undescribed biodiversity, and in turn changed our knowledge of the evolutionary relationships within the Cyanobacteria. The purpose of this paper is to describe the challenges of working with the cyanobacteria and to review what we know of them from tropical habitats.
A number of heterocytous, mat-forming, tapering cyanobacteria in the Rivulariaceae have recently been observed in both the Atlantic and Pacific coasts in the rocky intertidal and supratidal zones. These belong to the genera Nunduva, Kyrtuthrix, and Phyllonema, and have been the subject of several recent papers. Herein, two new species of Nunduva (N. komarkovae, N. sanagustinensis) and two new species of Kyrtuthrix (K. munecosensis, K. totonaca) are characterized and described from the coasts Mexico. Genetic separation based on the 16S-23S ITS region was pronounced (>10% in all comparisons). Morphological differences between all existing species in these two genera were also observed, but the group is morphologically complex and these taxa are considered pseudocryptic. Nunduva and Kyrtuthrix remain morphologically and phylogenetically separate even with the addition of new species. However, how long will this remain the case? Many new genera and species of cyanobacteria have recently been described. Will the taxonomy of cyanobacteria eventually become saturated? Will we start to see multiple populations for the same cryptic species, or will future taxonomists collapse multiple species into fewer species, or multiple genera into single genera. The description of even more Nunduva and Kyrtuthrix species causes us to pause and evaluate the future of cyanobacterial taxonomy. These same questions are faced by algal taxonomists studying other phyla, and the resolution may ultimately be similar.
A freshwater dwelling cyanobacterium (strain MKW3) was isolated from a sample collected from a water logged sugarcane field located in Malkapur, Karad, Maharashtra, India, and was characterized using a polyphasic approach. In the 16S rRNA gene phylogenetic analysis, strain MKW3 clustered with two misidentified strains—Nostoc sp. CENA239 and Calothrix sp. NIES2100. The phylogenetically related members included strains identified as Nostoc, Aulosira, Calothrix, Tolypothrix, Camptylonemopsis and Microchaete. The phylogenetic and the morphological analysis of the strain MKW3 indicated that it does not belong to any of the above mentioned genera. Furthermore, the 16S-23S ITS secondary structure analysis provided clear evidence indicating that strain MKW3 is different from Nostoc sp. CENA239 and Calothrix sp. NIES2100. Based on the morphological, phylogenetic and 16S-23S ITS secondary structure analysis we describe our strain as Constrictifilum karadense gen. et sp. nov. in accordance with the International Code of Nomenclature for algae, fungi and plants.
Fungi represent one of the most diverse and ancient branches of the tree of life and have a worldwide distribution. They successfully colonize every biome, including extreme environments such as polar and desert regions, playing a pivotal role in global biogeochemical processes. In the fungal kingdom, “black fungi” (or microcolonial fungi or meristematic fungi) are a slow-growing group that reproduces mostly asexually; it includes ascomycetous taxa that are phylogenetically quite heterogeneous in the classes Dothideomycetes, Eurotiomycetes, and Arthoniomycetes.
In contrast to the majority of fungi, which live more or less comfortably inside their hosts or substrates, few black fungal lineages have evolved and adapted to thrive on bare naked rock surfaces (e.g., in the Mediterranean basin or in hot and cold dry deserts) and are therefore referred to rock-inhabiting fungi (RIF). For their ability to
thrive in harshest conditions such as drought, temperature and pH extremes, excessive radiation, and oligotrophy, RIF are accounted as the most resistant eukaryotic organisms known to date. In this chapter, we will provide an overview of the diversity, taxonomy, occurrence, and ecology of RIF colonizing both worldwide natural rocks and stone monuments, also exploring the future perspectives, including their biotechnological, bioremediation, and radioprotection potential.
Cyanobacteria are common members of epilithic communities, contributing fixed carbon and nitrogen, providing UV light shielding pigments, helping to retain water, and in general stabilizing particles. Conversely, biofouling by cyanobacteria is of great concern in the U.S. and abroad. The epilithic growth of cyanobacteria on cultural monuments has been long noted, yet the basic systematics and diversity of these organisms is poorly understood. This paper describes two novel cyanobacteria isolated from cemetery tombstones from Jacksonville, Florida (USA). Using a total evidence approach of ecology, morphology, ITS structure, and molecular data we present two taxa new to science: Brasilonema geniculatum and Calothrix dumus. We note that tombstones represent an intriguing habitat for sampling cyanobacteria due to their ubiquity, stability, and cultural importance.
Two Nostoc-like strains have been isolated, purified, cultured and identified on the basis of the polyphasic approach using morphological, ecological, molecular and phylogenetic methods. Both strains were found to have morphology similar to the genus Nostoc, but clustered strongly in a group distant from the Nostocsensu stricto clade. Further analysis, using the folded structures of the 16S-23S ITS region revealed strong differences from closely related members of the genus Nostoc. Distinct phylogenetic clustering and strong tree topologies using Bayesian inference, maximum-likelihood and maximum-parsimony methods indicated the need to revisit the taxonomy of the members of this particular clade with a clear need for giving a generic status distinct from the genus Nostoc. In accordance with the International Code of Nomenclature for Algae, Fungi and Plants, the name Desikacharya gen. nov. is proposed for the new genus along with the description of two new species, Desikacharya nostocoides sp. nov. and Desikacharya soli sp. nov., and reclassification of Nostoc thermotolerans to Desikacharya thermotolerans comb. nov.
Several populations of a non–tapering and tapering, fasciculated, single and geminate false branching heterocytous cyanobacterium were collected from rocky shores in the Pacific Ocean and Gulf of Mexico. The populations were provisionally placed in Brasilonema based on morphology, but upon sequencing of both environmental and culture material it was discovered that the populations/cultures belonged to the Rivulariaceae, in a marine subclade of the family containing Kyrtuthrix huatulcensis. In culture, the taxon exhibited tapering in isopolar filaments, providing further evidence that it was a member of the rivulariacean clade. Based on molecular data for other cyanobacteria within the rivulariacean clade, we identified at least three more species morphologically distinguishable from the Brasilonema-like material, all of which show more pronounced tapering. These cyanobacteria include not only tropical marine strains, but also a strain isolated from the English coastline in the Atlantic Ocean. We propose a new genus and four species for members of this distinctive clade, Nunduva fasciculata gen. nov., sp. nov., N. kania sp. nov., N. biania sp. nov., and N. britannica sp. nov. Other strains that others and we have isolated are sister to Nunduva and may eventually be placed within this genus, but at present, we consider the evidence for inclusion in Nunduva to be insufficient.
Six strains of Cyanobacteria sampled in the Brazilian Atlantic rainforest and one strain from Kauai, Hawaii, were studied using morphological and molecular approaches, including 16S rRNA gene phylogenies and 16S–23S ITS secondary structures, and are herein described as Komarekilla atlantica gen. et sp. nov.. Morphologically they are similar to Nostoc, Desmonostoc, Halotia, and Mojavia and indistinguishable from Chlorogloeopsis. The parsimony and Bayesian phylogenies of the 16S rDNA show that these strains are close to nostocacean strains, in strongly supported clades and separated from all other genera. The secondary structures of the 16S–23S ITS were very consistent between strains of K. atlantica, but distinctly different from structures in other close taxa. Of special note, the Hawaiian strain of K. atlantica had 16S sequence identities of 99.5– 100% to the Brazilian strains, and 16S–23S ITS sequence identities of 99.4–99.8% to the Brazilian strains, and consequently likely represents a very recent introduction of the species to Kauai from South America, the geographic source of many of the non–native plants in the Hawaiian Archipelago.
A filamentous, soil dwelling cyanobacterial strain (9C-PS) was isolated from Mandsaur, Madhya Pradesh, India and is being described as new species of Nostoc. Extensive morphological and molecular characterization along with thorough assessment of ecology was performed. The style of filament orientation, type and nature of the sheath (e.g., distribution and visibility across the trichome), and vegetative and heterocyte cell dimensions and shape were assessed for more than a year employing both culture and naturally occurring samples. Sequencing of the 16S rRNA gene showed 94% sequence similarity with Nostoc piscinale CENA21 while the analyses of the secondary structures of the 16S-23S ITS region showed unique folding patterns that differentiated this strain from other species of Nostoc. The rbcl and rpoC1 sequence was 91% and 94% similar to Nostoc sp. PCC 7524 and Nostoc piscinale CENA21 respectively, while the nifD gene sequence similarity was found to be 99% with Nostoc piscinale CENA21. The phenotypic, ecological, genetic, and phylogenetic observations indicate that strain 9C-PS is a new species in the genus Nostoc with the name proposed being Nostoc thermotolerans, sp. nov. according to the International Code of Nomenclature for Algae, Fungi, and Plants.
Benthie marine heteroeytous eyanoprokaryotes of Mexieo’s tropieal eoast are being reeognized as an important and eon-spieuous eomponent of the supralittoral and intertidal zones usually deseribed as an extreme and low diversity biotope. Although Kyrtuthrix has been reported from different eoasts worldwide, its eomplex morphology has led to differing taxo-nomie interpretations and positioning. Ten marine supra and intertidal populations of Kyrtuthrix were analyzed using a detailed morphologieal approaeh, eomplemented with eeologieal and geographieal information as well as DNA sequenee data of the 16S rRNA gene and assoeiated 16S-23S ITS. Kyrtuthrix huatulcensis is deseribed as a new speeies, different from K. dalmatica Ereegovie and K. maculans (Gomont) Umezaki based primarily on morphologieal data. Our material has smaller dimensions in thalli, filaments, triehomes and eells, and possesses differenees in qualitative eharaeters as well. Our material is epilithie as in K. maculans but not endolithie as in K. dalmatica. The analysis of moleeular data, mainly 16S rRNA gene sequenee, show that this genus is within the Rivulariaeeae elade, and outside of the Seytonemataeeae elade. ITS seeondary strueture eomparison with some of the eloser representatives of Rivulariaeeae shows eonsiderable differenees with these related genera. Based on the evidenee gathered in this study, inelusion of Kyrtuthrix within the Rivulariaeeae, rather than the Seytonemataeeae, is fully supported.
Historically, the genus Calothrix included all noncolonial, tapered, heterocytous filaments within the Cyanobacteria. However, recent molecular phylogenies show that "Calothrix" defined in this sense represents five distinct clades. The type species of Calothrix is marine, with solitary basal heterocytes, no akinetes, and distal ends tapering abruptly into short hairs. We examined the morphology and phylogeny of 45 tapering cyanobacteria in the Rivulariaceae, including freshwater and marine representatives of both Calothrix (35 strains) and its sister taxon Rivularia (10 strains). The marine Calothrix fall into two lineages, but we lack the generitype and so cannot identify the clade corresponding to the type species. The freshwater and soil Calothrix fall into the C. parietina clade and are characterized by having a basal heterocyte, no akinetes, and gradual tapering - but not into a long hyaline hair. Macrochaete gen. nov. is a freshwater taxon sister to the Calothrix lineages but clearly separated from Rivularia. The species in this genus differ morphologically from Calothrix by ability to produce two heteromorphic basal heterocytes and specific secondary structures of the 16S-23S ITS. An additional feature present in most species is the presence of a distal, long hyaline hair, but this character has incomplete penetrance due to its expression only under specific environmental conditions (low phosphate), and in one species appears to be lost. We recognize three species - M. psychrophila (type species) from cold environments (high mountains, Antarctica), M. santannae from wet walls of subtropical South America, and M. lichenoides, a phycobiont of lichens from Europe. This article is protected by copyright. All rights reserved.
Cyanobacteria dwelling on the salt-excreting leaves of the mangrove tree Avicennia schaueriana were isolated and characterized by ecological, morphological, and genetic approaches. Leaves were collected in a mangrove with a history of oil contamination in the coastline of São Paulo state, Brazil, and isolation was achieved by smearing leaves on the surface of solid media or by submerging leaves in liquid media. Twenty-nine strains isolated were shown to belong to four cyanobacterial orders (thirteen Synechococcales, seven Nostocales, seven Pleurocapsales, one Chroococcales, and one Oscillatoriales) according to morphological and 16S rDNA sequence evaluations. More detailed investigations pointed six Rivulariacean and four Xenococcacean strains as novel taxa. These strains were classified as Phyllonema gen. nov. (type-species P. aviceniicola sp. nov.) and Foliisarcina gen. nov. (type-species F. bertiogensis sp. nov.) according to the International Code of Nomenclature for Algae, Fungi, and Plants. This investigation shows some of the unique cyanobacteria inhabiting the phyllosphere of A. schaueriana can be retrieved by culturing techniques, improving current taxonomy and providing new insights into the evolution, ecology, and biogeography of this phylum.
A total of 16 strains phylogenetically placed within the Nostocaceae were found to possess morphological features of the Rivulariaceae and Tolypothrichaceae (tapering trichomes and single false branching, respectively) in addition to their typical Nostocacean features (production of arthrospores in series). These strains formed a strongly supported clade separate from other strains that are phylogenetically and morphologically close. We describe four new species within the genus Roholtiella gen. nov. The four species include three distinguishable morphotypes. Roholtiella mojaviensis and R. edaphica are morphologically distinct from each other and from the other two species, R. fluviatilis and R. bashkiriorum. Roholtiella fluviatilis and R. bashkiriorum are cryptic species with respect to each other. All four species are easily distinguished based on the sequence of the 16S-23S ITS regions, in particular the flanking regions to the conserved Box-B and V3 helices. The species are further established by the elevated p-distance between species that is much reduced among strains within the same species. Calochaete cimrmanii, a recently described tapering species from tropical biomes, is the most likely sister taxon to Roholtiella.
The whole classification of cyanobacteria (species, genera, families, orders) has undergone exten-sive restructuring and revision in recent years with the advent of phylogenetic analyses based on molecular sequence data. Several recent revisionary and monographic works initiated a revision and it is anticipated there will be further changes in the future. However, with the completion of the monographic series on the Cyanobacteria in Süsswasserflora von Mitteleuropa, and the recent flurry of taxonomic papers describing new genera, it seems expedient that a summary of the modern taxonomic system for cyanobacteria should be published. In this review, we present the status of all currently used families of cyanobacteria, review the results of molecular taxonomic studies, descriptions and characteristics of new orders and new families and the elevation of a few subfamilies to family level. All recently defined cyanobacterial genera (some still invalid) are listed in the family to which they are likely to belong and an indication is given of their taxonomic validity and level of polyphasic characterization of each genus.
The family Microchaetaceae is a large group of heterocytous cyanobacteria, whose members bear typical morphological features of uniseriate heteropolar filaments never terminated by thin hairs and with simple false branching. However, phylogenetic analyses of the gene for 16S rRNA showed that members of this traditionally morphologically delimited family form several distant groups and therefore the current concept is hereafter indefensible. In this study, we provide reassessment of the status of the family Microchaetaceae based on morphology, ecology, biogeography and phylogeny of 16S rRNA gene. Thorough examination of strains of the nominate genus Microchaete revealed their affiliation to two groups, Nostocaceae and Rivulariaceae, and their distant position to other traditional members of Microchaetaceae such as Tolypothrix, Hassallia, and Coleodesmium. To reflect the phylogenetic relationships and to accommodate members of the traditional family Microchaetaceae that are clearly not related to any of the Microchaete representatives, we propose establishment of two new families, Tolypothrichaceae and Godleyaceae. Based on both molecular and morphological evidence, we also provide a description of three new species of the genus Fortiea.This article is protected by copyright. All rights reserved.
Publicly available sequence databases of the small subunit ribosomal RNA gene, also known as 16S rRNA in bacteria and archaea, are growing rapidly, and the number of entries currently exceeds 4 million. However, a unified classification and nomenclature framework for all bacteria and archaea does not yet exist. In this Analysis article, we propose rational taxonomic boundaries for high taxa of bacteria and archaea on the basis of 16S rRNA gene sequence identities and suggest a rationale for the circumscription of uncultured taxa that is compatible with the taxonomy of cultured bacteria and archaea. Our analyses show that only nearly complete 16S rRNA sequences give accurate measures of taxonomic diversity. In addition, our analyses suggest that most of the 16S rRNA sequences of the high taxa will be discovered in environmental surveys by the end of the current decade.
A new tapered and false branched morphotype of filamentous heterocytous cyanobacterium was isolated from soil material collected on a massif of Chirripó Mountain, Costa Rica. The strain was analyzed morphologically and a sequence of its 16S rRNA gene was compared with available 16S rDNA sequences of organisms with similar morphology, especially those with heteropolar tapering filaments. Phylogenetic analyses revealed that the strain was significantly different from Rivulariaceae, but was closely related to several strains designated as Tolypothrix. However, according to the original descriptions in the literature, members of the genus Tolypothrix possess only very slightly tapering filaments. With regard to all these differences, we decided to describe a new genus—Calochaete gen. nov. with type species C. cimrmanii.
On the basis of data presented here and in earlier studies, Desmonostoc gen. nov. is described. The new genus includes the traditional species Nostoc muscorum Agardh ex Bornet et Flahault 1888, and several other strains previously assigned to the genus Nostoc, which present similar morphology and phylogenetic placement within the Desmonostoc lineage. The Desmonostoc clade is phylogenetically coherent according to 16S rRNA gene sequence analysis performed with four distinct approaches. In all phylogenetic trees, Desmonostoc formed a supported group separated from strains belonging to the related taxa Nostoc, Trichormus, and Mojavia. We also suggest that other clusters hosting strains which for their morphology resemble Nostoc, but are more distant from Nostoc commune cluster than Desmonostoc, should be reclassified into new
genera in the future. Strains belonging to Desmonostoc form long vegetative filaments embedded in diffluent mucilaginous envelopes, except for primordial stages they never form a firm periderm, and the filaments are never densely coiled with compact trichomes as found in Nostoc. Both terminal and intercalary heterocytes occur, and mostly elliptical akinetes were
differentiated apoheterocytically in long chains. Desmonostoc strains can be usually found in moist or wet meadow, field and forest soils, more rarely in periphyton, but to our knowledge, they are missing or very rare in desert areas. Some of these strains have been found to grow in association with mosses or as symbionts of cycadean plants and of Gunnera sp.
Four Nostocacean species from desert soils of the western United States, including the phycobiont of the lichen Collema tenax, were studied. Our strains could be forced into morphospecies previously described from Europe, but phylogenetic analysis indicated that they belonged in separate, distinct, and previously undescribed taxa. Partial 16S rRNA sequences of the strains CM1-VF10, CM1-VF14, CNP-AK1 and JT2-VF2 were determined and aligned with published Nostoc sequences from GenBank and our lab, as well as other Nostocales. All aligned sequences were analysed using parsimony, distance, and maximum likelihood methods, and trees based on three separate data sets were generated. Full 16S-23S internal transcribed spacer (ITS) regions were also characterized for our strains, and secondary structures of the ITS region were compared among these and N. commune and N. punctiforme. Intragenomic variability was documented among ITS regions in different operons for these taxa. One of the four strains (JT2-VF2) is distinct from Nostoc by both morphological and molecular criteria and is described as Mojavia pulchra gen. et sp. nov. Two other strains (CM1-VF10 and CM1-VF14) are described as Nostoc indistinguendum sp. nov. and Nostoc desertorum sp. nov., respectively. According to both morphological and molecular characteristics, the phycobiont of C. tenax is not N. commune, N. sphaericum or N. punctiforme as variously suggested in the lichenological literature, and the older name for this taxon, Nostoc lichenoides, is consequently validated in this paper.
A new cyanobacterial genus and species, Spirirestis rafaelensis, is described from soils of a semi-arid Utah juniper community in the San Rafael Swell, Utah, U.S.A. Multiple isolates of the organism have only been recovered from well-crusted, protected, and totally undisturbed soils at this site; it has not been recovered from any of the other 40 sites we have examined in the Sonoran, Mojave, Chihuahuan, Colorado Plateau, or Great Basin deserts during the last eight years. Spirirestis shares morphological characters with members of both the Scytonemataceae and Microchaetaceae, principally heterocyte formation, false branching, and presence of sheath. However, unlike the trichomes of all previously described genera in these families, most trichomes of Spirirestis are tightly spiraled. 16S rRNA sequence data suggest that Spirirestis is more closely related to members of the Microchaetaceae than to members of the Scytonemataceae or Rivulariaceae. The data also support the maintenance of Microchaetaceae and Scytonemataceae as separate families.
Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d(N)/d(S) rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.
Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version 5 (MEGA5), which is a user-friendly software for mining online databases, building sequence alignments and phylogenetic trees, and using methods of evolutionary bioinformatics in basic biology, biomedicine, and evolution. The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models (nucleotide or amino acid), inferring ancestral states and sequences (along with probabilities), and estimating evolutionary rates site-by-site. In computer simulation analyses, ML tree inference algorithms in MEGA5 compared favorably with other software packages in terms of computational efficiency and the accuracy of the estimates of phylogenetic trees, substitution parameters, and rate variation among sites. The MEGA user interface has now been enhanced to be activity driven to make it easier for the use of both beginners and experienced scientists. This version of MEGA is intended for the Windows platform, and it has been configured for effective use on Mac OS X and Linux desktops. It is available free of charge from http://www.megasoftware.net.
Among the stone monumental assets, artistic fountains are particularly affected by microbial colonization due to constant contact with water, giving rise to biodegradation processes related with physical-chemical and aesthetical alterations. In this paper, we make an overview of reported biodiversity of the phototrophic patina developed in various fountains of Italy and Spain. The microbial composition of four fountains (two from Florence, Italy and two from Granada, Spain) was investigated using traditional and/or molecular techniques. The results indicated many common similarities with regard the phototrophic biodiversity for all the investigated fountains. Automated ribosomal RNA intergenic spacer analysis (ARISA), a molecular fingerprint tool, was used to examine the eubacterial and cyanobacterial community for two of the investigated fountains. The principal component analysis of ARISA profiles strengthens the results obtained by traditional methods and revealed separate clusters, as a consequence of the differences of micro-environmental conditions for each fountain.
Using a set of synthetic oligonucleotides homologous to broadly conserved sequences in-vitro amplification via the polymerase
chain reaction followed by direct sequencing results in almost complete nucleotide determination of a gene coding for 16S
ribosomal RNA. As a model system the nucleotide sequence of the 16S rRNA gene of M.kansasii was determined and found to be
98.7% homologous to that of M.bovis BCG. This is the first report on a contiguous sequence information of an entire amplified
gene spanning 1.5 kb without any subcloning procedures.
The abbreviated name, ‘mfold web server’, describes a number of closely related software applications available on the World
Wide Web (WWW) for the prediction of the secondary structure of single stranded nucleic acids. The objective of this web server
is to provide easy access to RNA and DNA folding and hybridization software to the scientific community at large. By making
use of universally available web GUIs (Graphical User Interfaces), the server circumvents the problem of portability of this
software. Detailed output, in the form of structure plots with or without reliability information, single strand frequency
plots and ‘energy dot plots’, are available for the folding of single sequences. A variety of ‘bulk’ servers give less information,
but in a shorter time and for up to hundreds of sequences at once. The portal for the mfold web server is http://www.bioinfo.rpi.edu/applications/mfold. This URL will be referred to as ‘MFOLDROOT’.
Three strains of Limnothrix (Cyanobacteria) isolated from Lake Kastoria, Greece, were characterized based on their morphological features and 16S rRNA gene sequences. The Limnothrix isolates 007a, 165a, and 165c can morphologically be assigned to Limnothrix redekei (Van Goor) Meffert. The 16S rRNA gene of the Limnothrix strains showed a 99% similarity to the 16S rRNA gene of Planktothrix sp. FP1. Limnothrix redekei strains 165a, 165c, 007a and Planktothrix sp. FP1 formed a separate cluster in the cyanobacterial 16S rRNA gene tree. It was distinct from the Pseudanabaena cluster, which included the other Limnothrix strains isolated from northern temperate lakes. This is the first report on the phylogeny of L. redekei strains originating from a Mediterranean lake (southern Europe) and provides new data about the genus Limnothrix.
In this study, a polyphasic approach was adopted to investigate natural freshwater (river and stream) samples of Rivularia colonies and isolated strains of cyanobacteria with a high degree of trichome tapering (genera Rivularia and Calothrix). Analysis of the phycocyanin (PC) operon and the intervening intergenic spacer (cpcBA-IGS) and 16S rRNA gene sequences were used for genetic characterization. In addition, a molecular fingerprinting method, temperature-gradient gel electrophoresis, which allows sequence-dependent separation of PCR products, was used to assess genotypic diversity in environmental samples and isolated strains. The results showed a high variability of the PC-IGS among the genotypes that was not associated with the morphologies observed. This study underlines the importance of choosing a low-nutrient-content culture medium, especially one with a low phosphorus concentration, for studying typical morphological features of Rivularia for taxonomic purposes. Molecular fingerprinting methods and morphological analyses confirmed the diversity in Rivularia colonial structure and trichome features corresponding to genetic diversity within a single colony. Phylogenetic analysis of cpcBA-IGS was largely consistent with that obtained from 16S rRNA gene sequence analysis and confirmed the high level of divergence between genotypes. The sequences of Rivularia and Calothrix from this study and database sequences showed great heterogeneity and were clearly not monophyletic. The results of this genetic and morphological study of field samples and fresh isolates indicated that the current classification of these genera needs to be revised.
A false branching cyanobacterium (strain 10A1_PS) was isolated from a freshwater body of the Pachmarhi Biosphere Reserve, India and was characterized using the polyphasic approach. The detailed morphological examination indicated that the strain belonged to the complex genus Scytonema as it exhibited typical false branching character whose frequency increased with age of the culture. As the family Scytonemataceae and the genus Scytonema has been shown to be polyphyletic in many studies, we provide deep insights into the phylogenetic complexities within the family Scytonemataceae based on 16S rRNA gene phylogeny along with complete morphological, molecular and phylogenetic characterization of the strain. The 16S rRNA gene phylogenetic tree inferred by Bayesian Inference, Neighbor-Joining and Maximum Parsimony methods showed that the strain clustered within the Scytonema sensu stricto clade. The phylogenetic distance and the positioning of the strain clearly indicated it to be different from other Scytonema species. Further analysis using rbcL phylogeny, folded secondary structures of the 16S-23S ITS, p-distance and percentage pairwise similarity matrix clearly distinguished the strain 10A1_PS from the other closely related species. In accordance with the International Code of Nomenclature of Algae, Fungi and Plants we propose the name of the new species to be Scytonema pachmarhiense.
Nostoc is a complex and tough genus to differentiate, and its morphological plasticity makes it taxonomically complicated. Its cryptic diversity and almost no distinguishable morphological characteristics make this genus incredibly heterogeneous to evaluate on taxonomic scales. The strain NOS, isolated from a eutrophic water body, is being described as a new genus Aliinostoc with the strain showing motile hormogonia with gas vesicles as an atypical feature, which is currently considered as the diacritical feature of the genus but should be subjected to critical evaluation in the near future. The phylogenetic placement of Aliinostoc along with some other related sequences of Nostoc clearly separated this clade from Nostoc sensu stricto with high bootstrap support and robust topology in all the methods tested, thus providing strong proof of the taxa being representative of a new genus which morphologically appears to be Nostoc-like. Subsequent phylogenetic assessment using the rbcL, psbA, rpoC1 and tufA genes was done with the aim of facilitating future multi-locus studies on the proposed genus for better taxonomic clarity and resolution. Folding of the 16S-23S internal transcribed spacer region and subsequent comparisons with members of the genera Nostoc, Anabaena, Aulosira, Cylindrospermum, Sphaerospermopsis, Raphidiopsis, Desmonostoc and Mojavia gave entirely new secondary structures for the D1-D1' and box-B helix. Clear and separate clustering from Nostoc sensu stricto supports the establishment of Aliinostoc gen. nov. with the type species being Aliinostoc morphoplasticum sp. nov. in accordance with the International Code of Nomenclature for algae, fungi and plants.
The recently-developed statistical method known as the "bootstrap" can be used to place confidence intervals on phylogenies. It involves resampling points from one's own data, with replacement, to create a series of bootstrap samples of the same size as the original data. Each of these is analyzed, and the variation among the resulting estimates taken to indicate the size of the error involved in making estimates from the original data. In the case of phylogenies, it is argued that the proper method of resampling is to keep all of the original species while sampling characters with replacement, under the assumption that the characters have been independently drawn by the systematist and have evolved independently. Majority-rule consensus trees can be used to construct a phylogeny showing all of the inferred monophyletic groups that occurred in a majority of the bootstrap samples. If a group shows up 95% of the time or more, the evidence for it is taken to be statistically significant. Existing computer programs can be used to analyze different bootstrap samples by using weights on the characters, the weight of a character being how many times it was drawn in bootstrap sampling. When all characters are perfectly compatible, as envisioned by Hennig, bootstrap sampling becomes unnecessary; the bootstrap method would show significant evidence for a group if it is defined by three or more characters.
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. This article is protected by copyright. All rights reserved.
Using a set of synthetic oligonucleotides homologous to broadly conserved sequences in-vitro amplification via the polymerase chain reaction followed by direct sequencing results in almost complete nucleotide determination of a gene coding for 16S ribosomal RNA. As a model system the nucleotide sequence of the 16S rRNA gene of M.kansasii was determined and found to be 98.7% homologous to that of M.bovis BCG. This is the first report on a contiguous sequence information of an entire amplified gene spanning 1.5 kb without any subcloning procedures.
On the basis of a comparative study of 178 strains of cyanobacteria, representative of this group of prokaryotes, revised definitions of many genera are proposed. Revisions are designed to permit the generic identification of cultures, often difficult through use of the field-based system of phycological classification. The differential characters proposed are both constant and readily determinable in cultured material. The 22 genera recognized are placed in five sections, each distinguished by a particular pattern of structure and development. Generic descriptions are accompanied by strain histories, brief accounts of strain properties, and illustrations; one or more reference strains are proposed for each genus. The collection on which this analysis was based has been deposited in the American Type Culture Collection, where strains will be listed under the generic designations proposed here.
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