Phylogeny of the genus Pythium and description of new genera

Phylogeny of the genus Pythium is analyzed based on sequences of the large subunit ribosomal DNA D1/D2 region and cytochrome oxidase II gene region of Pythium isolates and comprehensive species of related taxa belonging to the Oomycetes. The phylogenetic trees show that the genus Pythium is a highly divergent group and divided into five well- or moderately supported monophyletic clades. Each clade is characterized by sporangial morphology such as globose, ovoid, elongated, or filamentous shapes. Based on phylogeny and morphology, the genus Pythium (s. str.) is emended, and four new genera, Ovatisporangium, Globisporangium, Elongisporangium, and Pilasporangium, are described and segregated from Pythium s. lato.     

Actinomycetospora atypica sp. nov., a novel soil actinomycete and emended description of the genus Actinomycetospora

A novel actinomycete, designated strain NEAU-st4^T, was isolated from a soil sample collected from Shaanxi province, Northwest China and characterized using a polyphasic approach. 16S rRNA gene sequence analysis revealed that strain NEAU-st4^T has the highest sequence similarities with Actinomycetospora rishiriensis RI109-Li102^T (99.4 %), Actinomycetospora corticicola 014-5^T (99.1 %), Actinomycetospora chiangmaiensis YIM 0006^T (98.8 %) and Actinomycetospora iriomotensis IR73-Li102^T (98.2 %). However, the low level of DNA–DNA relatedness differentiated strain NEAU-st4^T from its closest phylogenetic neighbours. The main chemotaxonomic properties of strain NEAU-st4^T, such as the diamino acid of the peptidoglycan, the whole-cell hydrolysates, the predominant menaquinones and the phospholipid profile, supported its classification within the genus Actinomycetospora. The distinctive morphology of this strain compared with that of other members in the genus Actinomycetospora is the formation of sporangia directly on the substrate hyphae. Phenotypic and genotypic differences also allowed the distinction of the strain from closely related species. Consequently, strain NEAU-st4^T represents a new species of the genus Actinomycetospora, for which the name Actinomycetospora atypica sp. nov. is proposed. The type strain is NEAU-st4^T (=CGMCC 4.7093^T = DSM 45873^T).     

Transfer of members of the genus Falcivibrio to the genus Mobiluncus, and emended description of the genus Mobiluncus

It has long been thought that the genera Mobiluncus and Falcivibrio contain the same organisms. Using a polyphasic approach, it was found that Mobiluncus curtisii and Mobiluncus mulieris were the same as Falcivibrio vaginalis and Falcivibrio grandis, respectively. As the genus name Mobiluncus takes precedence, it is proposed that F. vaginalis and F. grandis be transferred to the genus Mobiluncus. In agreement with previous studies, results from phenotypic tests did not support the separation of M. curtisii strains into its two subspecies, M. curtisii subsp. curtisii and M. curtisii subsp. holmesii. Phenotypic complexity within M. curtisii dictates that the species should be treated as a complex until more in-depth analyses of the species have been performed. Phylogenetic analyses, based on 16S rRNA gene sequences, demonstrated that the genus Mobiluncus was associated with Varibaculum cambriense and the two subspecies of Actinomyces neuii, and that A. neuii is only distantly related to Actinomyces sensu stricto.     

The taxonomic and ecological status of the environmentally restricted spongillid species of North America. I. Spongilla sponginosa Penney 1957

The taxonomic validity, present distribution, and specific threats to the existence of the freshwater sponge,Spongilla sponginosa Penney were investigated. This species, reported only from the type locality, Week's Pond, Sumter County, South Carolina, has apparently been extirpated due to highly acidic pH levels in the pond water. Examination of holotype materials indicate some question of the validity of S. sponginosa as a distinct species.     

The taxonomic and ecological status of the environmentally restricted spongillid species of North America. IV. Spongilla heterosclerifera Smith 1918

The taxonomic status, present distribution and specific threats to the existence of the environmentally restricted freshwater sponge, Spongilla heterosclerifera Smith 1918 were investigated. This species, collected only from Oneida Lake, New York, has not colonized other habitats and continues to exhibit typical diagnostic characteristics, thus qualifying as a valid environmentally restricted species. Although the sponge presently colonizes two sites in the lake, both near the northwestern shore, the total absence of sponge fauna from other lake regions near more heavily populated areas of this species. Physicochemical data from Oneida Lake greatly extend the known environmental parameters of Spongilla heterosclerifera.     

A new genus and species of the subtribe Leptopsaltriina (Hemiptera: Cicadidae: Leptopsaltriini) from Vietnam,with a key to the genera of Leptopsaltriina

Vietanna Lee & Pham, gen. nov. and Vietanna hanoiensis Pham & Lee, sp. nov. are described based on a cicada specimen from Hanoi, Vietnam and placed in the subtribe Leptopsaltriina Moulton, 1923 of the tribe Leptopsaltriini Moulton, 1923 in the subfamily Cicadinae Latreille, 1802 (Hemiptera: Cicadidae). This new genus is morphologically similar to Tanna Distant, 1905 but distinguished from Tanna by the timbal cover exposing the inner part of timbal, the male abdominal epipleurite 3 with a distinct oblique linear fold, the male abdominal sternites without tubercle-like projections, and the aedeagus bifurcate at the apex. A key to the genera of Leptopsaltriina is provided.www.zoobank.org/urn:lsid:zoobank.org:pub:3B9CBC95-B54A-4BDE-A488-0DEAB69114BD.     

A new species and three new combinations in Cyphellophora, with a note on the taxonomic affinities of the genus, and its relation to Kumbhamaya and Pseudomicrodochium.

Cyphellophora guyanensis sp. nov., isolated from leaf litter in French Guyana, is described and illustrated. This fungus is characterized by ampulliform to flask-shaped phialides, with a conspicuous, funnel-shaped collarette, and nearly straight to falcate or slightly sigmoid, (2−)3–6 septate conidia. Cyphellophora guyanensis is compared to the other Cyphellophora species, and the latter genus is compared to Kumbhamaya and Pseudomicrodochium. Kumbhamaya indica, P. fusarioides, and P. suttonii are transferred to Cyphellophora. The phylogenetic relationships of Cyphellophora with other genera of ascomycetes and related mitosporic fungi were inferred from the analysis of the partial nuclear ribosomal DNA SSU sequences data. The analysis supports a placement of Cyphellophora in Chaetothyriales, and probably in the Herpotrichiellaceae This revised version was published online in August 2006 with corrections to the Cover Date.     

The taxonomic and ecological status of the environmentally restricted Spongillid species of North America. II. Anheteromeyenia biceps (Lindenschmidt, 1950)

The taxonomic validity, present distribution, and specific threats to the existence of the freshwater sponge, Anheteromeyenia biceps (Lindenschmidt, 1950) were investigated. The species, reported only from the type locality, Bessey Creek and Maple River, two streams flowing into Douglas Lake, Michigan, is relegated to synonomy with Ephydatia mülleri. Habitat data from Bessey Creek and Maple River, particularly physicochemical data, greatly extend the known environmental parameters of Heteromeyenia tubisperma and Ephydatia mülleri.     

An emended description of Amphidiniopsis arenaria Hoppenrath 2000, based on material from the Sea of Japan

Cells of a taxon similar to the type species of Amphidiniopsis, Amphidiniopsis kofoidii, were found during the course of a study of marine sand-dwelling dinoflagellates in Peter the Great Bay, Sea of Japan, Russia. These specimens were examined in detail using light and scanning electron microscopy and were identified as Amphidiniopsis arenaria, a species known so far only from the North Sea, Germany. Morphological variability within the species and details of its sulcal construction are described here for the first time.     

Molecular study of the genus Astraeus

The aim of the present work was to determine phylogenetic relationships among Astraeus species and to support macroscopic and microscopic characters of Astraeus with analysis of the ITS rDNA region. Collections of Astraeus basidiomes were made from different geographical areas in Thailand and compared with existing collections made worldwide. The marriage of observations on morphological features, including basidiospore ornamentation and molecular data demonstrated the presence of several Astraeus species. Sequences for 41 Astraeus collections were compared and the phylogenetic analyses grouped Thai Astraeus collections into two distinct groups. One contained A. odoratus and an Asian species described herein as A. asiaticus. There are at least two additional species: A. pteridis, and one so far un-named from North America. Our results show that molecular data can be used in combination with traditional morphological characteristics to resolve taxonomic uncertainties in the genus Astraeus.     

Effects of porphyrins and inorganic iron on the growth of Prevotella intermedia

We demonstrated earlier that hemin-iron-containing compounds which include hemin, human hemoglobin, bovine hemoglobin, and bovine catalase stimulate the growth of Prevotella intermedia [Leung, Subramaniam, Okamoto, Fukushima, Lai, FEMS Microbiol. Lett. 162 (1998) 227-233]. However, the contributions of tetrapyrrole porphyrin ring in these hemin-iron sources as well as inorganic iron for the growth of this organism have not been determined. The purpose of this study was to examine the effects of porphyrins, host iron-binding proteins, and various inorganic iron sources on the growth of hemin-iron depleted P. intermedia. Protoporphyrin IX and protoporphyrin IX-zinc, either in the presence or absence of supplemented ferrous or ferric iron, promoted the growth of P. intermedia at a rate that was comparable to that of the hemin control. On the other hand, neither the host iron proteins, transferrin and lactoferrin, nor the inorganic iron sources which included ferrous chloride, ferric chloride, ferric citrate, ferric nitrate, and ferric ammonium citrate at concentrations up to 200 microM stimulated the growth of hemin-iron-restricted P. intermedia. The results suggest that P. intermedia only use iron in a specific form and that the porphyrin-ring structure is essential for the growth of P. intermedia as in the case of other related organisms.     

A taxonomic review of Korean Hydroglyphus Motschulsky (Coleoptera: Dytiscidae: Hydroporinae) with a description of new species

A taxonomic study of Hydroglyphus Motschulsky in Korea is presented. Four species are recognized including a new species, Hydroglyphus coreanus sp. nov. Hydroglyphus flammulatus (Sharp) is reported for the first time in the Korean peninsula and H. geminus (Fabricius) is a new addition to the South Korean fauna. Habitus and SEM photographs, distribution maps, and key to the Korean species are provided.     

Genome-based taxonomic classification of the closest-to-Comamonadaceae group supports a new family Sphaerotilaceae fam. nov. and taxonomic revisions

Many genera closest to the family Comamonadaceae have not been classified into any family; moreover, some of them are not monophyletic groups beyond the genus level. To resolve the taxonomic uncertainty of the closest-to-Comamonadaceae (CTC) group, we performed 16S rRNA gene- and genome-based phylogenetic analyses combined with genome relatedness indices and phenotypic traits comparison. Phylogenies based on the 16S rRNA gene and genome sequences demonstrated that the CTC group formed a coherent and robust monophyletic lineage and was sister to the family Comamonadaceae, thereby proposing the CTC group as a novel family, Sphaerotilaceae fam. nov. The resolved genus- and species-level taxonomic relationships of this new family were then validated by the phylogenomic reconstruction and comparisons of genome relatedness indices including digital DNA-DNA hybridization and average nucleotide identity (ANI) as well as comprehensive phenotypic analysis for type strains. Finally, we reclassified all misidentified genera and species, resulting in 19 new combinations, and proposed Sphaerotilaceae-specific thresholds of ANI and average amino acid identity for genus delineation. Collectively, this study has established a sound taxonomic framework of the novel family Sphaerotilaceae and will help guide future taxonomic efforts and prevent the propagation of taxonomic errors.     

A rapid method for preparation of rough and smooth lipopolysaccharide from Bacteroides, Porphyromonas and Prevotella

Abstract We describe a new method for lipopolysaccharide (LPS) preparation by water extraction at 100°C and subsequent digestion with proteinase K. The crude LPS could be reliably used for immunoblotting since it retained a high level of antigenicity, and was free of SDS and proteinase K, both of which can cause problems. Two monoclonal antibodies which failed to react with LPS prepared by two conventional methods reacted well with our preparation. We used the new method to prepare LPS from 44 strains of bacteria formerly classified as Bacteroides , some of which have been reclassified as Porphyromonas or Prevotella . In general, yields were good, and electrophoretic profiles obtained with SDS-PAGE and silver staining enabled strains to be rated rough, semi-rough, or smooth.     

Meiothermus rufus sp. nov., a new slightly thermophilic red-pigmented species and emended description of the genus Meiothermus

Four red-pigmented isolates, with optimum growth temperatures of approximately 55–60 °C and an optimum pH for growth between 7.5 and 8.5, were recovered from hot springs in Central France. Phylogenetic analysis of the 16S rRNA gene sequences showed that these organisms represented a new species of the genus Meiothermus. The new isolates could be distinguished from other strains of the species of the genus Meiothermus primarily by the glycolipid profile and fatty acid composition because these organisms lacked the hydroxy fatty acids and the glycolipid variant GL-1a found in all other isolates of the species of Meiothermus examined. On the basis of the results presented here we propose the name Meiothermus rufus for the new species, which is represented by strains CAL-4^T (=DSM 22234^T=LMG 24878^T) and CAL-12 (=DSM 22235=LMG 24879). We also propose emending the genus Meiothermus to include strains that have only one glycolipid instead of two glycolipid variants.