The phylogenetic relationship among Ectothiorhodospiraceae: a reevaluation of their taxonomy on the basis of 16S rDNA analyses

Sequences of the 16S rRNA gene were determined from all type strains of the recognized Ectothiorhodospira species and from a number of additional strains. For the first time, these data resolve the phylogenetic relationships of the Ectothiorhodospiraceae in detail, confirm the established species, and improve the classification of strains of uncertain affiliation. Two major groups that are recognized as separate genera were clearly established. The extremely halophilic species were removed from the genus Ectothiorhodospira and reassigned to the new genus Halorhodospira gen. nov., to recognize that the most halophilic eubacteria are species of this genus. These species are Halorhodospira halophila comb. nov., Halorhodospira halochloris comb. nov., and Halorhodospira abdelmalekii comb. nov. Among the slightly halophilic Ectothiorhodospira species, the classification of strains belonging to Ectothiorhodospira mobilis and Ectothiorhodospira shaposhnikovii was improved. Several strains that were tentatively identified as Ectothiorhodospira mobilis form a separate cluster on the basis of their 16S rDNA sequences and are recognized as two new species: Ectothiorhodospira haloalkaliphila sp. nov., which includes the most alkaliphilic strains originating from strongly alkaline soda lakes, and Ectothiorhodospira marina, describing isolates from the marine environment. Received: 12 October 1995 / Accepted: 1 December 1995     

Aspergillus osmophilus sp. nov., and a new teleomorph for A. proliferans

A new species of Aspergillus and a new teleomorph for A. proliferans, both isolated from cereals in Iran, are described using morphological and molecular data. A combined sequence dataset of the ITS region, partial β-tubulin and partial calmodulin genes resolved the relationships of members of section Aspergillus largely in concordance with morphological traits of ascospores. Aspergillus osmophilus sp. nov. is differentiated from the closest species, A. xerophilus by possessing larger ascospores, conidia and associated fruiting bodies. Both species are strongly xerophilic and possess ascospores with lobate-reticulate convex surfaces. The newly discovered teleomorph for A. proliferans is characterized by delicately roughened ascospores with a shallow or distinct furrow and finely roughened to irregular equatorial crests.     

Using the taxon-specific genes for the taxonomic classification of bacterial genomes

Background

The correct taxonomic assignment of bacterial genomes is a primary and challenging task. With the availability of whole genome sequences, the gene content based approaches appear promising in inferring the bacterial taxonomy. The complete genome sequencing of a bacterial genome often reveals a substantial number of unique genes present only in that genome which can be used for its taxonomic classification.

Results

In this study, we have proposed a comprehensive method which uses the taxon-specific genes for the correct taxonomic assignment of existing and new bacterial genomes. The taxon-specific genes identified at each taxonomic rank have been successfully used for the taxonomic classification of 2,342 genomes present in the NCBI genomes, 36 newly sequenced genomes, and 17 genomes for which the complete taxonomy is not yet known. This approach has been implemented for the development of a tool ‘Microtaxi’ which can be used for the taxonomic assignment of complete bacterial genomes.

Conclusion

The taxon-specific gene based approach provides an alternate valuable methodology to carry out the taxonomic classification of newly sequenced or existing bacterial genomes.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1542-0) contains supplementary material, which is available to authorized users.     

Phylogeny and molecular fingerprinting of green sulfur bacteria

The 16S rDNA sequences of nine strains of green sulfur bacteria (Chlorobiaceae) were determined and compared to the four known sequences of Chlorobiaceae and to sequences representative for all eubacterial phyla. The sequences of the Chlorobiaceae strains were consistent with the secondary structure model proposed earlier for Chlorobium vibrioforme strain 6030. Similarity values > 90.1% and K_nuc values < 0.11 indicate a close phylogenetic relatedness among the green sulfur bacteria. As a group, these bacteria represent an isolated branch within the eubacterial radiation. In Chlorobiaceae, a similar morphology does not always reflect a close phylogenetic relatedness. While ternary fission is a morphological trait of phylogenetic significance, gas vesicle formation occurs also in distantly related species. Pigment composition is not an indicator of phylogenetic relatedness since very closely related species contain different bacteriochlorophylls and carotenoids. Two different molecular fingerprinting techniques for the rapid differentiation of Chlorobiaceae species were investigated. The 16S rDNA fragments of several species could not be separated by denaturing gradient gel electrophoresis. In contrast, all strains investigated during the present work gave distinct banding patterns when dispersed repetitive DNA sequences were used as targets in PCR. The latter technique is, therefore, well suited for the rapid screening of isolated pure cultures of green sulfur bacteria. Received: 26 August 1996 / Accepted: 8 January 1997     

Ultrastructural and molecular analyses of Rhizophydiales (Chytridiomycota) isolates from North America and Argentina

The Rhizophydiales is the most recently circumscribed order in the Chytridiomycota. Past studies focused on soil chytrids from North America and Australia to determine the range of diversity within this clade of chytrids and established three families (Rhizophydiaceae, Terramycetaceae, and Kappamycetaceae) in the new order. Although Rhizophydiales contains seemingly simple chytrids morphologically, analyses of ribosomal gene sequences and zoospore characters have demonstrated unexpected genetic and ultrastructural diversity, highlighting the need for broader habitat and geographic sampling to reveal the actual diversity within this new order. To enlarge our sampling, in this study we investigated 38 newly cultured chytrids collected from aquatic habitats in Argentina, a territory under-explored for chytrid diversity. From analyses of thallus morphology, zoospore ultrastructure, and 28S and ITS1–5.8S–ITS2 ribosomal gene sequences, we expand the concept of Rhizophydiales, describing seven new families (Alphamycetaceae, Angulomycetaceae, Aquamycetaceae, Globomycetaceae, Gorgonomycetaceae, Pateramycetaceae, and Protrudomycetaceae) and eight new genera (Alphamyces, Angulomyces, Aquamyces, Globomyces, Urceomyces, Gorgonomyces, Pateramyces, and Protrudomyces). Results of this study underscore that even more extensive sampling from varied habitats and geographies is needed to adequately ascertain the diversity of chytrids in the Rhizophydiales.     

Two new species of Neosartorya isolated from soil in Xinjiang, China

Two new species, Neosartorya shendaweii and N. tsunodae, isolated from soil in Xinjing, China and in Pernambuco, Brazil, are described and illustrated. The first species is characterized by its ascospores with two widely separated equatorial crests and tuberculate to verrucose convex surfaces. This species has affinities with several known species of the genus, bearing ascospores with a similar ornamentation, but can be distinguished from these species by other morphological characteristics such as smaller cleistothecia and conidiophores, spathulate vesicles and rather ellipsoidal conidia. The second species is characterized by its unique ascospores with two low equatorial crests, an evident furrow as a deep depression, and finely reticulate convex surfaces. The validation of these new species is supported further by analyses of the β-tubulin, calmodulin and actin gene sequences.     

Phylogenetic basis for a taxonomic dissection of the genus Clostridium

The 16S rDNA-based phylogenetic analysis of the genus Clostridium has been completed by determination of the phylogenetic position of the type strains of 15 species and two non-validated species. These strains are members of phylogenetic clusters I, III, IV, V, IX, XIVa and XVIII as defined previously by Collins et al. [Int. J. Syst. Bacteriol. 44 (1994) 812-826]. Members of the genus Clostridium span a large evolutionary distance and the genus is not a phylogenetically coherent taxon but is intermixed with members of different genera, exhibiting a combination of Clostridium- and non-Clostridium-type properties. Anaerobacter polyendosporus, Syntrophococcus sucromutans and Acetivibrio multivorans also cluster within the radiation of Clostridium species. Although several taxa have been described for former Clostridium species with distinct phenotypic properties, the majority of Clostridium species, which are not members of the core cluster I, can at present not be reclassified as long as taxon-specific, phenotypic properties are not available.     

Molecular phylogeny of Drosophila based on ribosomal RNA sequences

Nucleotide sequences of 72 species of Drosophilidae were determined for divergent D1 and D2 domains (representing 200 and 341 nucleotides respectively in D. melanogaster) of large ribosomal RNA, using the rRNA direct sequencing method. Molecular phylogenetic trees were reconstructed using both distance and parsimony methods and the robustness of the nodes was evaluated by the bootstrap procedure. The trees obtained by these methods revealed four main lineages or clades which do not correspond to the taxonomical hierarchy. In our results, the genus Chymomyza is associated with the subgenus Scaptodrosophila of the genus Drosophila and their cluster constitutes the most ancient clade. The two other clades are constituted of groups belonging to the subgenus Sophophora of the genus Drosophila: the so-called Neotropical clade including the willistoni and saltans groups and the obscura-melanogaster clade itself split into three lineages: (1) obscura group + ananassae subgroup, (2) montium subgroup, and (3) melanogaster + Oriental subgroups. The fourth clade, the Drosophila one, contains three lineages. D. polychaeta, D. iri, and D. fraburu are branched together and constitute the most ancient lineage; the second lineage includes the annulimana, bromeliae, dreyfusi, melanica, mesophragmatica, repleta, robusta, and virilis groups. The third lineage is composed of the immigrans and the cardini, funebris, guaramunu, guarani, histrio, pallidipennis, quinaria, and tripunctata groups. The genera Samoaia, Scaptomyza, and Zaprionus are branched within the Drosophila clade. Although these four clades appear regularly in almost all tree calculations, additional sequencing will be necessary to determine their precise relationships.Correspondence to: M. Pelandakis     

The current status of the small subunit rRNA phylogeny of the coccidia (Sporozoa)

There is no current comprehensive assessment of the molecular phylogeny of the coccidia, as all recently published papers either deal with subsets of the taxa or sequence data, or provide non-robust analyses. Here, we present a comprehensive and consistent phylogenetic analysis of the available data for the small-subunit ribosomal RNA gene sequence, including a number of taxa not previously studied, based on a Bayesian tree-building analysis and the covariotide model of evolution. The assumptions of the analysis have been rigorously tested, and the benefits and limitations highlighted. Our results provide support for a number of prior conclusions, including the monophyly of the families Sarcocystidae (cyst-forming coccidia) and Eimeriidae (oocyst-forming coccidia), but with bird-host Isospora species in the Eimeriidae and mammal-host species in the Sarcocystidae. However, it is clear that a number of previously reported relationships are dependent on the evolutionary model chosen, such as the placements of Goussia janae, Lankesterella minimia and Caryospora bigenetica. Our results also confirm the monophyly of the subfamilies Toxoplasmatinae and Sarcocystinae, but only some of the previously reported groups within these subfamilies are supported by our analysis. Similarly, only some of the previously reported groups within the Eimeriidae are supported by our analysis, and the genus Eimeria is clearly paraphyletic. There are unambiguous patterns of host-parasite relationship within the coccidia, as most of the well-supported groups have a consistent and restricted range of hosts, with the exception of the Toxoplasmatinae. Furthermore, the previously reported groups for which we found no support all have a diverse range of unrelated hosts, confirming that these are unlikely to be natural groups. The most interesting unaddressed questions may relate to Isospora, which has the fewest available sequences and host-parasite relationships apparently not as straightforward as elsewhere within the suborder.     

Zopfochytrium is a new genus in the Chytridiales with distinct zoospore ultrastructure

While surveying chytrid diversity in lakes and streams, we found on cellulosic bait a chytrid that had both monocentric and polycentric thallus forms. We brought this chytrid into axenic culture from three sites in eastern North America, studied its thallus development and zoospore ultrastructure, and compared its 28S rDNA sequence with those of other members of the Chytridiomycota. Thallus morphology matched that described for the rare chytrid, Cladochytrium polystomum Zopf. Sporangia were spherical and produced numerous long discharge tubes. After discharge, zoospores remained in spherical clusters at the tips of the inoperculate openings of discharge tubes. After 10–30 min zoospores either swam away or encysted in place. Zoospore ultrastructural features included a cell coat, flagellar plug, and paracrystalline inclusion, features typical of members of the Chytridiales. However, the flagellar apparatus structure and organellar organization differed from that of zoospores previously described. Based on its molecular phylogeny and its zoospore ultrastructural features, we classify C. polystomum as a member of the Chytridiaceae in the Chytridiales. Because its thallus development and its ribosomal DNA sequences diverged decidedly from those of Cladochytrium tenue Nowak, the type species of Cladochytrium, we erected Zopfochytrium as a new genus for this chytrid.     

Coltriciella minuscula sp. nov., a new species of poroid fungus on Pinus merkusii from an Indonesian tropical forest

Coltriciella minuscula sp. nov. is described and illustrated from a specimen collected on Pinus merkusii from Bogor, Indonesia. This species is characterized by the size of its basidiocarp up to 4 mm in diam, with long hair on the stipe and with ornamented spores. Both morphological distinctiveness and phylogenetic separation based upon analyses of nrDNA ITS sequences support the establishment of this new species. Morphological dissimilarities between C. minuscula and closely related species are discussed.     

Botrytis sinoallii: a new species of the grey mould pathogen on Allium crops in China

A study was conducted to identify Botrytis spp. isolated from bulb onion, green onions, garlic, and garlic chives grown in Hubei Province of China. Based on colony morphology and conidial characteristics, 367 strains of Botrytis spp. were identified as five distinct species, namely, B. cinerea, B. squamosa, B. porri, B. byssoidea, and an undescribed Botrytis species (Botrytis sp.), which accounted for 64.3, 29.9, 3.3, 0.3, and 2.2%, respectively. The previously undescribed species is herein described as a new species, B. sinoallii sp. nov., which is characterized by production of numerous small sclerotia on potato dextrose agar. Phylogenetic analysis using partial sequences of three nuclear genes (G3PDH, HSP60, and RPB2) showed that B. sinoallii forms a unique lineage, which is closely related to B. squamosa, a well-known species on Allium crops, but distantly related to the other species of Botrytis on Allium crops, including B. cinerea, B. porri, B. aclada, B. allii, B. byssoidea, B. globosa, and B. sphaerosperma. Results of inoculation tests showed that B. sinoallii is a newly identified agent that can cause leaf blight of green onion, garlic, and garlic chives. Potential impact of B. sinoallii on production of Allium crops in China is discussed.     

Phylogeny and classification of the Asteroidea (Echinodermata)

Post-Palaeozoic asteroids share a large number of derived characters of the ambulacral column and the mouth frame, and constitute the crown group of the monophyletic group Asteroidea. This crown group is here called the Neoasteroidea (new subclass). The stem species of the crown group lived in the Permian or early Triassic and so the evolution of the asteroids parallels that of the echinoids. Character distribution within the Neoasteroidea, especially morphology of the skeleton, digestive system, larvae and tube feet, allows subdivision into four orders (Paxillosida, Notomyotida, Valvatida, Forcipulatida). The latter three orders possess the synapomorphy of suckered tube feet and are united as the Surculifera (new superorder); the Paxillosida are their primitive sister group. Palaeozoic asteroids represent the stem group of the class, and may be divided into plesions according to the order of appearance of synapomorphies with the crown group. Classification of Palaeozoic asteroids requires much further study. The appearance of new characters within the crown group asteroids, such as suckered tube feet, implies that these were absent in the stem group. The range of life-habits possible in Palaeozoic asteroids can thus be partly deduced from evidence provided by living asteroids. Palaeozoic asteroids are deduced to have lacked suckered tube feet and were presumably unable to evert the stomach; hence they were precluded from life on hard substrates and extraoral feeding on epifaunal organisms. It is suggested that they lived on soft substrates by deposit feeding, scavenging and predation on small benthos.     

Phylogenetic analyses of Japanese species of Phyllosticta sensu stricto

Although the genus concept of Phyllosticta s. str. (teleomorph: Guignardia) as defined by van der Aa is widely accepted, the species concept is still controversial because it is often based on the morphology on host plants. In this study, the culture characteristics within Phyllosticta s.str. were examined, and the phylogenetic relationships among Japanese species of Phyllosticta s.str. and its teleomorph Guignardia were analyzed using 18S rDNA sequences. Phyllosticta s. str. formed a monophyletic clade. ITS-28S rDNA sequences extracted from fungal cultures derived from various host plants were divided into two subgroups. The first group included cultures from a wide range of host plants and were mainly derived as endophytes from a symptom-less plant. In the second group, cultures from each host plant genus formed distinct clades; these were often isolated as leaf pathogens from diverse plants. Isolates belonging to the first lineage generally grew faster on oatmeal agar. To classify species of Phyllosticta it is necessary to consider an integrated approach such as molecular phylogeny, host plant, colony growth, symptoms, and morphological characteristics of the conidiomata.     

Two misconceptions of phylogeny and classification

A recent contribution embodies the assumptions that organisms may be excluded from relationship with others on the basis of autopomorphy, and that its position in a classification is an inherent characteristic of an organism. Both of these assumptions are fallacious.     

The celC gene, a new phylogenetic marker useful for taxonomic studies in Rhizobium

The celC gene codifies for a cellulase that fulfils a very significant role in the infection process of clover by Rhizobium leguminosarum. This gene is located in the celABC operon present in the chromosome of strains representing R. leguminosarum, Rhizobium etli and Rhizobium radiobacter whose genomes have been completely sequenced. Nevertheless, the existence of this gene in other species of the genus Rhizobium had not been investigated to date. In this study, the celC gene was analysed for the first time in several species of this genus isolated from legume nodules and plant tumours, in order to compare the celC phylogeny to those of other chromosomal and plasmidic genes. The results obtained showed that phylogenies of celC and chromosomal genes, such as rrs, recA and atpD, were completely congruent, whereas no relation was found with symbiotic or virulence genes. Therefore, the suitability and usefulness of the celC gene to differentiate species of the genus Rhizobium, especially those with closely related rrs genes, was highlighted. Consequently, the taxonomic status of several strains of the genus Rhizobium with completely sequenced genomes is also discussed.