Modern taxonomic revision of planktic nostocacean cyanobacteria: a short review of genera

The taxonomy of cyanobacteria has been substantially modified in the last few decades, particularly after application of modern ultrastructural and molecular methods. The group of heterocytous cyanobacteria (Nostocales) was found to be monophyletic, but the concept and content of different genera must be continually corrected and revised. The widespread introduction of the molecular approach (especially 16S rRNA gene sequencing) has confirmed almost all traditional genera based on distinct and morphologically recognizable type species, but indicated also broader diversity resulting in separation of more genetic and generic entities in several genera. The combination of molecular and phenotype analyses enables also a better and more objective definition of criteria for describing newly researched generic units, discovered from various habitats in the biosphere. Here, the nostocacean generic taxa are reviewed after recent necessary taxonomic corrections. Nostocacean cyanobacteria are filamentous, heterocytous, not branched and not polarized morphotypes, classified traditionally into one family (Nostocaceae). The main part of the review focuses on the genera containing planktic species.     

Planktic oscillatorialean cyanoprokaryotes (short review according to combined phenotype and molecular aspects)

This review presents the main genera and species of the oscillatorialean cyanobacteria, that can be observed in freshwater planktic biotopes. The taxa are classified according to combined modern, ultrastructural and molecular criteria. The review is organised in form of subsequent tables.     

Taxonomic studies of planktic species of Anabaena based on morphological characteristics in cultured strains

Fifty (50) strains of planktic species of Anabaena (cyanobacteria), including collections from Japan and China and from different culture collections, were induced to form akinetes at low temperature (15 °C). Their morphologies were then observed and described. Fourty seven strains successfully formed akinetes and these were classified into 20 species comprising seven with straight trichomes and 13 with coiled trichomes. Three strains, which did not form akinetes, were separated into two taxonomic groups, but could not be identified to any described species. In addition, a key to the planktic species of Anabaena described in the study is presented.     

Stability and change in Tethyan planktic foraminifera across the Paleocene–Eocene transition

Examination of planktic foraminifera in the Tethys basin during the Paleocene–Eocene transition reveals two stasis intervals that are separated by a major saltation event coincident with the P–E short-term perturbation in global climate and oceanography. Changes occurred at many spatial and temporal scales as well as many taxonomic and ecologic hierarchical levels, though with various rates and magnitudes. The stasis intervals are marked by slow changes at the species level and account for 50% of the observed first and last appearances during a 2.5 Myr interval. The saltation event is marked by rapid changes at the species and morpho-guild levels and accounts for the remaining 50% of first and last appearances during an interval of about 100–200 kyr. Despite these changes, many taxonomic and ecologic units, such as the depth assemblages and genera, and faunal parameters, such as species richness and turnover rates, are stable with respect to the P–E perturbation. This coexistence of change and stability marks the crisis of Tethyan planktic foraminifera across the P–E transition and reveals the possible dynamics of ecological evolution.     

Reconstruction of phylogenetic relationships within Grapsidae (Crustacea: Brachyura) and comparison of trans-isthmian versus amphi-atlantic gene flow based on mtDNA

Following taxonomic revisions in recent years, the originally large family Grapsidae MacLeay, 1838 has become a relatively small and morphologically homogeneous family in terms of adult and larval morphology. Most available molecular studies including more than one genus of the family have also suggested monophyly of the corresponding taxa. However, no single phylogenetic study has ever included all constituent genera of the Grapsidae. In the current study, a molecular phylogeny based on sequences of the mitochondrial 16S rRNA gene from all eight grapsid genera and 34 species is presented and suggests that up to four genera are not monophyletic. This is mainly due to the polyphyletic nature of the genus Pachygrapsus which can be found in six different lineages of the phylogeny, suggesting that the genus currently does not represent a single evolutionary lineage and is in need of taxonomic revision. Amphi-atlantic and trans-isthmian species pairs or populations in four genera are compared and reveal relatively constant and pronounced divergences across the Panama Isthmus as opposed to moderate divergences across the Atlantic Ocean, thereby suggesting occurrence of gene flow across the Atlantic Ocean during the past three million years.     

Generic characters of the simplest cyanoprokaryotes Cyanobium,Cyanobacterium and Synechococcus

The cytomorphological features (cell morphology, type of cell division, cell structure, structure of photosynthetic apparatus) were studied in the type strains of the cyanoprokaryotic genera Cyanobium and Cyanobacterium, and in the reference strain of the traditional genus Synechococcus (Synechococcus PCC 6301; = “Anacystis nidulans” sensu auct.). They were originally described by Rippka & Cohen-Bazire, based on the mean DNA-base composition (moles % G + C) and on the resistance to various cyanophages. The phenotypic diacritical characters were found to coincide well with the molecular markers, and thus, the genera Cyanobium and Cyanobacterium are acceptable also according to the traditional (botanical) taxonomic criteria. The integrated molecular, cytomorphological and ecophysiological approaches to the solution of taxonomic problems in cyanobacteria are therefore inevitable for taxonomic evaluation, from the methodological point of view. The lists of species within the revised genera Cyanobium and Cyanobacterium are reviewed.     

Diversity,taxonomy and autecology of autochtonous epipelic cyanobacteria of the genus <Emphasis Type="Italic">Komvophoron</Emphasis> (Borziaceae,Oscillatoriales): a study on populations from the Czech Republic and British Isles

Epipelic cyanobacteria were studied in bottom sediments from ponds and lakes in the United Kingdom and the Czech Republic, covering a trophic gradient from deep, oligotrophic, glacial lakes to shallow, eutrophic, urban manmade ponds. Although many planktic species were observed, the most frequently occurring cyanobacteria were the motile filamentous genera Oscillatoria, Phormidium, Pseudanabaena and Komvophoron. These genera represent autochtonous epipelic assemblages, occurring in upper surface layers of the sediments throughout the year and exhibiting seasonal variation in their abundancy. The occurrence of individual Komvophoron species was influenced by sediment quality, particularly the proportions of fine mud and organic detritus. A new species Komvophoron hindakii sp. nov. is described. Morphological features, autecology and occurrence of all the Komvophoron-like morphospecies found are discussed.     

THE CYANOBACTERIAL GENUS BRASILONEMA,GEN. NOV., A MOLECULAR AND PHENOTYPIC EVALUATION1

Twelve populations of filamentous, heterocytous scytonematoid cyanobacteria from subaerophytic (mainly epiphytic) habitats in subtropical and tropical Brazil (São Paulo) were studied. The populations form a uniform cluster, which differs from the traditional scytonematoid genera genetically and by several indistinct, but typical morphological characters (fasciculation of filaments, rare false branching). Two strains were isolated in monospecific cultures. Molecular analyses were performed on these strains from natural populations taken from bromeliad leaves and iron water pipes. Because the results from 16S rRNA gene sequencing indicated the separate position of this cyanobacterium at the generic level, a new genus, Brasilonema, is proposed with the type species Brasilonema bromeliae. The new genus is described using combined molecular and cytomorphological criteria, in accordance with the nomenclatorial recommendations of both the Bacteriological Code and the Botanical Code of Nomenclature (cf. Oren 2004 ). The ultrastructure of the type species was studied, and vacuole‐like structures in the cells were explained. The genus Brasilonema is commonly distributed, particularly in subaerophytic habitats from southeastern Brazil. The type species (B. bromeliae) has a rather curious ecology, living epiphytically (in phytothelmes) inside the vase‐shaped leaf rosettes of bromeliads.     

Re-assessment of the Oligocene genera Prosotherium and Propachyrucos (Hegetotheriidae,Notoungulata)

Several systematic revisions of the Hegetotheriidae have been published in the last twenty years, but some important taxonomic work remains limited to unpublished studies. In one such thesis, the late Oligocene genera Prosotherium and Propachyrucos were revised, so that Prosotherium garzoni and Propachyrucos smithwoodwardi were considered the only valid species for each genus. Later authors loosely accepted these informal revisions, but recent phylogenetic coding has yet to accurately reflect these revisions, with character states often at odds with the known material for these genera. This study re-examines most of the fossil material assigned to Propachyrucos and Prosotherium, including both published and unpublished fossils, and contributes to a better understanding of the systematics, taxonomic diversity and early morphological evolution of the pachyrukhines. We conclude that Prosotherium garzoni and Propachyrucos smithwoodwardi are indeed the only valid species for each genus, confirming the influential but unpublished revisions that have become widely accepted. The known material for these species is clarified to aid future phylogenetic studies. At the same time, Propachyrucos aequilatus and Pr. robustus are herein considered nomina dubia. Additionally, Miocene species originally ascribed to Propachyrucos, along with unpublished material loosely assigned to the same genus, are here synonymized with other genera. Finally, several fossils previously recognized as Prosotherium sp. are here recognized as P. garzoni.     

Outer membrane efflux protein (OMEP) is a suitable molecular marker for resolving the phylogeny and taxonomic status of closely related cyanobacteria

Taxonomy of Cyanobacteria, the oldest phototrophic prokaryotes, is problematic for many years due to their simple morphology, high variability and adaptability to diverse ecological niches. After introduction of the polyphasic approach, which is based on the combination of several criteria (molecular sequencing, morphological and ecological), the whole classification system of these organisms is subject to reorganization. The aim of this study was to evaluate whether the outer membrane efflux protein (OMEP) sequences can be used as a molecular marker for resolving the phylogeny and taxonomic status of closely related cyanobacteria. We have performed phylogenetic analyses based on the amino acid sequences of the OMEP and the DNA sequences of the 16S rRNA gene from 86 cyanobacterial species/strains with completely sequenced genomes. Phylogenetic trees based on the OMEP showed that most of the cyanobacterial species/strains belonging to different genera are clustered in separate clades supported by high bootstrap values. Comparing the OMEP trees with the 16S rDNA tree clearly showed that the OMEP is more suitable marker in resolving phylogenetic relationships within Cyanobacteria at generic and species level.     

An evaluation of the systematic value of skull morphology in the Trimeresurus radiation (Serpentes: Viperidae: Crotalinae) of Asian pitvipers

Trimeresurus (in its widest sense) is a very diverse and widespread radiation of Asian pitvipers, which has been subject to numerous taxonomic revisions, some of which have been based on characteristics of the skull. In order to evaluate the taxonomic utility of such characters, we conducted a comparison of the skulls of 57 specimens representing nine genera, and two currently unassigned species that are very closely related to each other. A canonical variate analysis reveals three distinct phenetic groups: the Protobothrops group, a group containing Ovophis monticola , ' Ovophis ' okinavensis , and ' Trimeresurus ' gracilis , and finally a group comprising the remaining species and characterized by considerable overlap between most genera with the exception of the monotypic Peltopelor and Himalayophis . Agreement between phenetic similarity based on skull characteristics and phylogenetic relationships based on molecular evidence varies between different groups: the morphological similarity of the skull of Protobothrops sieversorum to the other Protobothrops species is congruent with their recent synonymization while the phenetic similarity among the species within the second group does not reflect current molecular phylogenetic relationships and indicates that convergent or parallel evolution may be responsible for at least some of the phenetic similarity detected among skulls of the Asian pit vipers examined. A test of phylogenetic independence, however, indicates that there is still a significant phylogenetic signal that can be recovered from several skull characteristics. Thus, we conclude that skull morphology can contribute to an overall understanding of pitviper taxonomy, but that it would be unwise to rely on skull characteristics alone.     

Species composition of ichthyofauna of the Kuibyshev reservoir

Data on species composition of ichthyofauna of the Kuibyshev reservoir for its period of existence (1957–2012) are presented. The list of fish of the reservoir compiled on the basis of materials of studied of recent years with consideration of new taxonomic revisions and reports (13 orders, 19 families, 46 genera, and 58 species) is cited. For the period from the moment of formation of the reservoir, its ichthyofauna has been supplemented by 17 new species, nine of which have formed self-reproducing populations.     

Genus age,provincial area and the taxonomic structure of marine faunas

Species are unevenly distributed among genera within clades and regions, with most genera species-poor and few species-rich. At regional scales, this structure to taxonomic diversity is generated via speciation, extinction and geographical range dynamics. Here, we use a global database of extant marine bivalves to characterize the taxonomic structure of climate zones and provinces. Our analyses reveal a general, Zipf–Mandelbrot form to the distribution of species among genera, with faunas from similar climate zones exhibiting similar taxonomic structure. Provinces that contain older taxa and/or encompass larger areas are expected to be more species-rich. Although both median genus age and provincial area correlate with measures of taxonomic structure, these relationships are interdependent, nonlinear and driven primarily by contrasts between tropical and extra-tropical faunas. Provincial area and taxonomic structure are largely decoupled within climate zones. Counter to the expectation that genus age and species richness should positively covary, diverse and highly structured provincial faunas are dominated by young genera. The marked differences between tropical and temperate faunas suggest strong spatial variation in evolutionary rates and invasion frequencies. Such variation contradicts biogeographic models that scale taxonomic diversity to geographical area.     

Sugarcane moth borers (Lepidoptera: Noctuidae and Pyraloidea): phylogenetics constructed using COII and 16S mitochondrial partial gene sequences

Sugarcane moth borers are a diverse group of species occurring in several genera, but predominately within the Noctuidae and Pyraloidea. They cause economic loss in sugarcane and other crops through damage to stems and stalks by larval boring. Partial sequence data from two mitochondrial genes, COII and 16S, were used to construct a molecular phylogeny based on 26 species from ten genera and six tribes. The Noctuidae were found to be monophyletic, providing molecular support for the taxonomy within this subfamily. However, the Pyraloidea are paraphyletic, with the noctuids splitting Galleriinae and Schoenobiinae from the Crambinae. This supports the separation of the Pyralidae and Crambinae, but does not support the concept of the incorporation of the Schoenobiinae in the Crambidae. Of the three crambine genera examined, Diatraea was monophyletic, Chilo paraphyletic, and Eoreuma was basal to the other two genera. Within the Noctuidae, Sesamia and Bathytricha were monophyletic, with Busseola basal to Bathytricha. Many species in this study (both noctuids and pyraloids) had different biotypes within collection localities and across their distribution; however the individual biotypes were not phylogenetically informative. These data highlight the need for taxonomic revisions at all taxon levels and provide a basis for the development of DNA-based diagnostics for rapidly identifying many species at any developmental stage. This ability is vital, as the species are an incursion threat to Australia and have the potential to cause significant losses to the sugar industry.     

Description of six new cyanobacterial species from soil biocrusts on San Nicolas Island,California, in three genera previously restricted to Brazil

As the taxonomic knowledge of cyanobacteria from terrestrial environments increases, it remains important to analyze biodiversity in areas that have been understudied to fully understand global and endemic diversity. This study was completed as part of a larger algal biodiversity study of the soil biocrusts of San Nicholas Island, California, USA. Among the taxa isolated were several new species in three genera (Atlanticothrix, Pycnacronema, and Konicacronema) which were described from, and previously restricted to, Brazil. New taxa are described herein using a polyphasic approach to cyanobacterial taxonomy that considers morphological, molecular, ecological, and biogeographical factors. Morphological data corroborated by molecular analysis including sequencing of the 16S rRNA gene, and the associated 16S–23S ITS rRNA region was used to delineate three new species of Atlanticothrix, two species of Pycnacronema, and one species of Konicacronema. The overlap of genera from San Nicolas Island and Brazil suggests that cyanobacterial genera may be widely distributed across global hemispheres, whereas the presence of distinct lineages may indicate that this is not true at the species level. Our data suggest that based upon global wind patterns, cyanobacteria in both Northern and Southern hemispheres of the Americas may have a more recent common ancestor in Northern Africa, but this common ancestry is distant enough that speciation has occurred since transatlantic dispersal.     

论中国早寒武世原牙形类和牙形状化石——分类评述和地层意义

原牙形类和牙形状化石是早寒武世微小骨骼化石中非常特征的一个类群。自二十世纪70年代以来,这些齿状的微型磷质骨片化石在中国下寒武统含小壳化石地层中被大量发现,据统计已描述有25属52种。通过文中的评述和讨论,证实其中的一些属种是次异名或属于无效的分类名称,还有一些在归属上尚存在疑问。通过对原牙形类和牙形状化石定义的讨论,将先前指定为原牙形类的13个属进行了分类评述。表明其中的5个属是次异名,还有2个属是未知的节肢动物。其它的12个牙形状化石属中也有5个属是次异名,它们不仅显示了有多种动物亲缘的牙形状形态,而且大多属于绝灭生物,只有Beshtashella和Paraformitchella(=Beshtashella)被指定为软体动物。文中还简要地讨论了大多数属的时空分布,包括3个阶段的原牙形类地层分布,这不仅具有划分对比地层的意义,而且还反映了原牙形类的演化趋势。     

Molecular (PCR-DGGE) versus morphological approach: analysis of taxonomic composition of potentially toxic cyanobacteria in freshwater lakes

Background

The microscopic Utermöhl method is commonly used for the recognition of the presence and taxonomic composition of potentially toxic cyanobacteria and is especially useful for monitoring reservoirs used as drinking water, recreation and fishery resources. However, this method is time-consuming and does not allow potentially toxic and nontoxic cyanobacterial strains to be distinguished. We have developed a method based on denaturing gradient gel electrophoresis (DGGE) of the marker gene ITS and the mcy-gene cluster, and DNA sequencing. We have attempted to calibrate the DGGE-method with a microscopic procedure, using water samples taken in 2011 from four lakes of the Great Mazurian Lakes system.

Results

Results showed that the classic microscopic method was much more precise and allowed the classification of the majority of cyanobacterial taxa to the species or genus. Using the molecular approach, most of the sequences could only be assigned to a genus or family. The results of DGGE and microscopic analyses overlapped in the detection of the filamentous cyanobacteria. For coccoid cyanobacteria, we only found two taxa using the molecular method, which represented 17% of the total taxa identified using microscopic observations. The DGGE method allowed the identification of two genera of cyanobacteria (Planktothrix and Microcystis) in the studied samples, which have the potential ability to produce toxins from the microcystins group.

Conclusions

The results confirmed that the molecular approach is useful for the rapid detection and taxonomic distinction of potentially toxic cyanobacteria in lake-water samples, also in very diverse cyanobacterial communities. Such rapid detection is unattainable by other methods. However, with still limited nucleotide sequences deposited in the public databases, this method is currently not sufficient to evaluate the entire taxonomic composition of cyanobacteria in lakes.     

中国高等植物多样性编目进展

中国高等植物多样性编目是“中国生物物种名录”项目中的重要组成部分, 旨在后植物志时代对中国高等植物的物种名录进行修订和年度更新。自2017年深圳国际植物学大会以来, 中国高等植物物种名录已进行了5次年度更新。名录参考最新的植物分类学研究进展, 对各大类群全面采用有分子证据的新分类系统, 收录5年来发表的中国植物新类群和新记录, 补充往年遗漏的部分类群, 并依据新的专科专属的修订结果对发生属间分类变动的类群进行了更新。目前的中国高等植物物种名录包含角苔类4科9属27种, 苔类62科170属1,081种94个种下等级, 藓类94科453属2,006种154个种下等级, 石松类3科12属165种4个种下等级, 蕨类38科177属2,215种228个种下等级, 裸子植物10科45属291种118个种下等级, 被子植物272科3,409属32,708种6,909个种下等级, 共计483科4,275属38,493种7,507个种下等级, 较5年前增加了19科270属2,334种。     

Species concept and nomenclatural changes within the genera Elliptochloris and Pseudochlorella (Trebouxiophyceae) based on an integrative approach

The genera Elliptochloris and Pseudochlorella were erected for Chlorella‐like green algae producing two types of autospores and cell packages, respectively. Both genera are widely distributed in different soil habitats, either as free living or as photobionts of lichens. The species of these genera are often difficult to identify because of the high phenotypic plasticity and occasional lack of characteristic features. The taxonomic and nomenclatural status of these species, therefore, remains unclear. In this study, 34 strains were investigated using an integrative approach. Phylogenetic analyses demonstrated that the isolates belong to two independent lineages of the Trebouxiophyceae (Elliptochloris and Prasiola clades) and confirmed that the genera are not closely related. The comparison of morphology, molecular phylogeny, and analyses of secondary structures of SSU and ITS rDNA sequences revealed that all of the strains belong to three genera: Elliptochloris, Pseudochlorella, and Edaphochlorella. As a consequence of the taxonomic revisions, we propose two new combinations (Elliptochloris antarctica and Pseudochlorella signiensis) and validate Elliptochloris reniformis, which is invalidly described according to the International Code for Nomenclature (ICN), by designating a holotype. To reflect the high phenotypic plasticity of P. signiensis, two new varieties were described: P. signiensis var. magna and P. signiensis var. communis. Chlorella mirabilis was not closely related to any of these genera and was, therefore, transferred to the new genus Edaphochlorella. All of the taxonomic changes were highly supported by all phylogenetic analyses and were confirmed by the ITS‐2 Barcodes using the ITS‐2/CBC approach.