Cold-adapted yeasts from Antarctica and the Italian Alps—description of three novel species: Mrakia robertii sp. nov., Mrakia blollopis sp. nov. and Mrakiella niccombsii sp. nov.

Worldwide glaciers are annually retreating due to global overheating and this phenomenon determines the potential lost of microbial diversity represented by psychrophilic microbial population sharing these peculiar habitats. In this context, yeast strains, all unable to grow above 20°C, consisting of 42 strains from Antarctic soil and 14 strains isolated from Alpine Glacier, were isolated and grouped together based on similar morphological and physiological characteristics. Sequences of the D1/D2 and ITS regions of the ribosomal DNA confirmed the previous analyses and demonstrated that the strains belong to unknown species. Three new species are proposed: Mrakia robertii sp. nov. (type strain CBS 8912), Mrakia blollopis sp. nov. (type strain CBS 8921) and a related anamorphic species Mrakiella niccombsii sp. nov. (type strain CBS 8917). Phylogenetic analysis of the ITS region revealed that the new proposed species were closely related to each other within the Mrakia clade in the order Cystofilobasidiales, class Tremellomycetes. The Mrakia clade now contains 8 sub-clades. Teliospores were observed in all strains except CBS 8918 and for the Mrakiella niccombsii strains.     

Neokomagataea gen. nov., with Descriptions of Neokomagataea thailandica sp. nov. and Neokomagataea tanensis sp. nov., Osmotolerant Acetic Acid Bacteria of the α-Proteobacteria

Isolates AH11^T and AH13^T were isolated from flowers of lantana and candle bush respectively collected in Thailand. In phylogenetic trees based on 16S rRNA gene sequences, the two isolates formed an independent cluster, which was then connected to the type strain of Saccharibacter floricola. The calculated pair-wise 16S rRNA gene sequence similarities of isolate AH11^T were 95.7–92.3% to the type strains of the type species of the 12 genera of acetic acid bacteria. The DNA base composition was from 51.2 to 56.8 mol % G+C, with a range of 5.6 mol %. When isolate AH11^T was labeled, DNA-DNA similarities were 100, 12, 4, 5, and 4% respectively to isolates AH11^T and AH13^T and the type strains of Saccharibacter floricola, Gluconobacter oxydans, and Acetobacter aceti. The two isolates were non-motile and did not oxidize either acetate or lactate. No growth was found in the presence of 0.35% acetic acid w/v. The two isolates were not osmophilic but osmotolerant, produced 2,5-diketo-D-gluconate from D-glucose, and did not oxidize lactate, thus differing from strains of Saccharibacter floricola, which showed weak lactate oxidation. The two isolates contained unsaturated C_18:1ω7c fatty acid as the major fatty acid, and were unique in the presence of a considerable amount of straight-chain C_18:12OH fatty acid. Q-10 was present as the major isoprenoid quinone. Neokomagataea gen. nov. was proposed with the two species, Neokomagataea thailandica sp. nov. for isolate AH11^T (=BCC 25710 ^T =NBRC 106555^T), which has 56.8 mol % G+C, and Neokomagataea tanensis sp. nov. for isolate AH13^T (=BCC 25711^T=NBRC 106556^T), which has 51.2 mol % G+C.     

Neokomagataea gen. nov., with descriptions of Neokomagataea thailandica sp. nov. and Neokomagataea tanensis sp. nov., osmotolerant acetic acid bacteria of the α-Proteobacteria

Isolates AH11(T) and AH13(T) were isolated from flowers of lantana and candle bush respectively collected in Thailand. In phylogenetic trees based on 16S rRNA gene sequences, the two isolates formed an independent cluster, which was then connected to the type strain of Saccharibacter floricola. The calculated pair-wise 16S rRNA gene sequence similarities of isolate AH11(T) were 95.7-92.3% to the type strains of the type species of the 12 genera of acetic acid bacteria. The DNA base composition was from 51.2 to 56.8 mol % G+C, with a range of 5.6 mol %. When isolate AH11(T) was labeled, DNA-DNA similarities were 100, 12, 4, 5, and 4% respectively to isolates AH11(T) and AH13(T) and the type strains of Saccharibacter floricola, Gluconobacter oxydans, and Acetobacter aceti. The two isolates were non-motile and did not oxidize either acetate or lactate. No growth was found in the presence of 0.35% acetic acid w/v. The two isolates were not osmophilic but osmotolerant, produced 2,5-diketo-D-gluconate from D-glucose, and did not oxidize lactate, thus differing from strains of Saccharibacter floricola, which showed weak lactate oxidation. The two isolates contained unsaturated C(18:1)ω7c fatty acid as the major fatty acid, and were unique in the presence of a considerable amount of straight-chain C(18:1)2OH fatty acid. Q-10 was present as the major isoprenoid quinone. Neokomagataea gen. nov. was proposed with the two species, Neokomagataea thailandica sp. nov. for isolate AH11(T) (=BCC 25710(T)=NBRC 106555(T)), which has 56.8 mol % G+C, and Neokomagataea tanensis sp. nov. for isolate AH13(T) (=BCC 25711(T)=NBRC 106556(T)), which has 51.2 mol % G+C.     

Corynebacterium antarcticum sp. nov., Corynebacterium marambiense sp. nov., Corynebacterium meridianum sp. nov., and Corynebacterium pygosceleis sp. nov., isolated from Adélie penguins (Pygoscelis adeliae)

A taxonomic study was conducted on 16 bacterial strains isolated from wild Adélie penguins (Pygoscelis adeliae) from Seymour (Marambio) Island and James Ross Island. An initial screening by repetitive sequence-based PCR fingerprinting divided the strains studied into four coherent groups. Phylogenetic analysis based on 16S rRNA gene sequences assigned all groups to the genus Corynebacterium and showed that Corynebacterium glyciniphilum and Corynebacterium terpenotabidum were the closest species with 16S rRNA gene sequence similarities between 95.4 % and 96.5 %. Further examination of the strains studied with ribotyping, MALDI-TOF mass spectrometry, comprehensive biotyping and calculation of average nucleotide identity and digital DNA–DNA hybridisation values confirmed the separation of the four groups from each other and from the other Corynebacterium species. Chemotaxonomically, the four strains P5828^T, P5850^T, P6136^T, P7210^T representing the studied groups were characterised by C_16:0 and C_18:1 ω9c as the major fatty acids, by the presence of meso-diaminopimelic acid in the peptidoglycan, the presence of corynemycolic acids and a quinone system with the predominant menaquinone MK-9(H₂). The results of this study show that the strains studied represent four new species of the genus Corynebacterium, for which the names Corynebacterium antarcticum sp. nov. (type strain P5850^T = CCM 8835^T = LMG 30620^T), Corynebacterium marambiense sp. nov. (type strain P5828^T = CCM 8864^T = LMG 31626^T), Corynebacterium meridianum sp. nov. (type strain P6136^T = CCM 8863^T = LMG 31628^T) and Corynebacterium pygosceleis sp. nov. (type strain P7210^T = CCM 8836^T = LMG 30621^T) are proposed.     

Isolation and Crystallization of Extracellular 3β-Hydroxysteroid Oxidase of Brevibacterium sterolicum nov. sp.

Among about 500 strains tested, a newly isolated soil bacterium, Brevibacterium sterolicum nov. sp. KY 3463 (ATCC 21387) showed the highest potency in production of 3β-hydroxysteroid oxidase in the culture fluid.

The 3β-hydroxysteroid oxidase was purified from the culture filtrate by a procedure involving ammonium sulfate fractionation, DEAE-cellulose and hydroxyapatite column chromatographies and Sephadex G–75 gel filtration. Crystals of the enzyme were obtained from solutions of the purified preparation by the addition of ammonium sulfate. The crystals appeared as fine rods, with a bright yellow color.

The enzyme is homogeneous by disc gel electrophoresis and ultracentrifugation. Sedimentation velocity yields a value of . It exhibits a typical flavoprotein spectrum of absorption maxima at 280, 390, and 470 mμ.     

Morphological Studies of Rhaphidopteris hsüi sp. nov

The present paper deals with the cuticular structure of Rhaphidopteris hsüi sp. nov. The specimens were collected from the Upper Triassic cos series of Liuzhi district, Guizhou Province. Based on the shape and cuticular structure of leaf and segments, this new species is assigned to Corystospermaceae of Cycadofilicales. According to the assemblage of the fossil plants, the writers consider that the geological age of this flora is assigned to the middle Keuper-Rhaetic stage of Late Triassic.     

Ambrosiozyma kamigamensis sp. nov. and A. neoplatypodis sp. nov., two new ascomycetous yeasts from ambrosia beetle galleries

Two new yeast species of the genus Ambrosiozyma are described on the basis of comparison of nucleotide sequences of large subunit of ribosomal DNA D1/D2 region. Ambrosiozyma kamigamensis and Ambrosiozyma neoplatypodis differ from Ambrosiozyma ambrosiae by 17 nucleotides (3.0%) and 16 nucleotides (2.8%), respectively, out of 565. The two species differ from each other by 13 nucleotides. Ambrosiozyma kamigamensis was isolated from galleries of the ambrosia beetle, Platypus quercivorus, in specimens of Quercus laurifolia and Castanopsis cuspidata located in the southern part of Kyoto, Japan. Ambrosiozyma neoplatypodis was isolated from similar material, but only in Q. laurifolia. Ambrosiozyma kamigamensis can be distinguished from the other Ambrosiozyma species by the inability to assimilate erythritol, whereas A. neoplatypodis can be distinguished by the ability to assimilate both L: -arabinose and nitrate. The type strains of A. kamigamensis and A. neoplatypodis are JCM 14990(T) (=CBS 10899(T)) and JCM 14992(T) (=CBS 10900(T)), respectively. This is the first report of new Ambrosiozyma species since the genus was proposed.     

Morphology and molecular phylogeny of Nitzschia bizertensis sp. nov.—A new domoic acid-producer

A new toxin-producing marine diatom, Nitzschia bizertensis sp. nov., isolated from the Bizerte Lagoon (Tunisia, Southwest Mediterranean Sea) is, based on studies on eight different strains, characterized morphologically by light microscopy, transmission and scanning electron microscopy, and phylogenetically using the nuclear rDNA regions: SSU, ITS1, 5.8S, ITS2 and D1–D3 of the LSU. The species belongs to the sections Lanceolatae or Lineares as defined by Cleve and Grunow (1880). These sections are characterized by species having linear-lanceolate valves with an eccentric raphe where the fibulae does not extend into the valve, and are otherwise famous for the lack of characters useful for delineation of species. Nitzschia bizertensis differs from most other species in these sections by having a high density of interstriae. The morphological and phylogenetic studies and comparisons with previously described Nitzschia species showed Nitzschia bizertensis sp. nov. to be a new species. Batch culture experiments were conducted for estimations of maximum growth rate and production of domoic acid (DA). Maximum cellular DA content of the examined strains ranged from 2 × 10⁻⁴ to 3.6 × 10⁻² pg cells⁻¹. The total DA concentration (pg mL⁻¹) was high already in exponential growth phase maybe due to reinoculation of “old” stationary phase cells, and increased into stationary growth phase where it reached a stationary level varying among the strains from ca. 4500 to 9500 pg mL⁻¹. Nitzschia bizertensis represents a new domoic acid-producing diatom and is the second toxin producing Nitzschia species. The resolution of Nitzschia bizertensis and Nitzschia navis-varingica in different parts of the LSU phylogenetic tree, and the recovery of the Pseudo-nitzschia species phylogenetically distant from those two species suggests that the ability to produce DA either evolved multiple times independently or was lost multiple times.     

Pyrenomycetes of the Russian Far East—Additions and corrections. 1.Rossmania ukurunduensis gen. et sp. nov.

Rossmania ukurunduensis gen. and sp. nov. collected in the reverve Bolshekhekhtsirsky (Khabarovsk Territory, Russian Far East) is described and illustrated.Rossmania aculeata comb. Nov. is indicated as the second species of the genus.     

Two new Cladophialophora species,C. tumbae sp. nov. and C. tumulicola sp. nov., and chaetothyrialean fungi from biodeteriorated samples in the Takamatsuzuka and Kitora Tumuli

During dismantling and relocation of the Takamatsuzuka Tumulus stone chamber, many Cladophialophora and chaetothyrialean black fungi, such as Exophiala and Phialophora, were isolated from samples taken from the joints between the stone walls. However, inside the stone chamber of the Kitora Tumulus, after intermittent UV irradiation in 2009, these black fungi were also isolated from samples taken from the stone walls. Molecular phylogenetic analyses based on only nrLSU and the concatenated (nrLSU D1/D2 + ITS) sequences revealed that the 35 Takamatsuzuka and Kitora Tumuli isolates of Cladophialophora and the chaetothyrialean black fungi were divergent. Two new species of Cladophialophora are described herein: C. tumulicola from the viscous gels and various substrates on the stone walls of the Takamatsuzuka and Kitora Tumuli and C. tumbae from black substances on the plastic cover over the “thief hole,” soil and plaster pieces between the stone walls, and the exterior of the Takamatsuzuka Tumulus chamber. Also, molecular phylogenetic placements for the remaining eight Takamatsuzuka and Kitora Tumuli isolates of chaetothyrialean black fungi have been determined or suggested.     

‘Candidatus Dichloromethanomonas elyunquensis’ gen. nov., sp. nov., a dichloromethane-degrading anaerobe of the Peptococcaceae family

Taxonomic assignments of anaerobic dichloromethane (DCM)-degrading bacteria remain poorly constrained but are important for understanding the microbial diversity of organisms contributing to DCM turnover in environmental systems. We describe the taxonomic classification of a novel DCM degrader in consortium RM obtained from pristine Rio Mameyes sediment. Phylogenetic analysis of full-length 16S rRNA gene sequences demonstrated that the DCM degrader was most closely related to members of the genera Dehalobacter and Syntrophobotulus, but sequence similarities did not exceed 94% and 93%, respectively. Genome-aggregate average amino acid identities against Peptococcaceae members did not exceed 66%, suggesting that the DCM degrader does not affiliate with any described genus. Phylogenetic analysis of conserved single-copy functional genes supported that the DCM degrader represents a novel clade. Growth strictly depended on the presence of DCM, which was consumed at a rate of 160 ± 3 μmol L^?1 d^?1. The DCM degrader attained 5.25 × 10⁷ ± 1.0 × 10⁷ cells per μmol DCM consumed. Fluorescence in situ hybridization revealed rod-shaped cells 4 ± 0.8 μm long and 0.4 ± 0.1 μm wide. Based on the unique phylogenetic, genomic, and physiological characteristics, we propose that the DCM degrader represents a new genus and species, ‘Candidatus Dichloromethanomonas elyunquensis’.     

‘Candidatus Megaira polyxenophila’ gen. nov., sp. nov.: Considerations on Evolutionary History,Host Range and Shift of Early Divergent Rickettsiae

“Neglected Rickettsiaceae” (i.e. those harboured by non-hematophagous eukaryotic hosts) display greater phylogenetic variability and more widespread dispersal than pathogenic ones; yet, the knowledge about their actual host range and host shift mechanism is scarce. The present work reports the characterization following the full-cycle rRNA approach (SSU rRNA sequence, specific in situ hybridization, and ultrastructure) of a novel rickettsial bacterium, herewith proposed as ''Candidatus Megaira polyxenophila'' gen. nov., sp. nov. We found it in association with four different free-living ciliates (Diophrys oligothrix, Euplotes octocarinatus, Paramecium caudatum, and Spirostomum sp., all belonging to Alveolata, Ciliophora); furthermore it was recently observed as intracellular occurring in Carteria cerasiformis and Pleodorina japonica (Chlorophyceae, Chlorophyta). Phylogenetic analyses demonstrated the belonging of the candidate new genus to the family Rickettsiaceae (Alphaproteobacteria, Rickettsiales) as a sister group of the genus Rickettsia. In situ observations revealed the ability of the candidate new species to colonize either nuclear or cytoplasmic compartments, depending on the host organism. The presence of the same bacterial species within different, evolutionary distant, hosts indicates that ''Candidatus Megaira polyxenophila'' recently underwent several distinct host shifts, thus suggesting the existence of horizontal transmission pathways. We consider these findings as indicative of an unexpected spread of rickettsial infections in aquatic communities, possibly by means of trophic interactions, and hence propose a new interpretation of the origin and phylogenetic diversification of rickettsial bacteria.     

Ougandatherium napakense nov. gen. nov. sp., le plus ancien Rhinocerotidae Iranotheriinae d’Afrique

Ougandatherium napakense nov. gen. nov. sp., the earliest Rhinocerotidae Iranotheriinae from Africa. The Uganda Palaeontology Expedition discovered an exceptionally rich fossiliferous channel deposit at Napak I, Karamoja, in 1999, which yielded two partial skeletons of a new genus and species of early Miocene Rhinocerotidae, together with various other mammals and gastropods typical of Faunal Set I of East Africa. The age of the deposits on the basis of both faunal correlation (biochronology) and radio-isotopic dating is ca 19–20 Ma. The new genus and species is a hornless rhinoceros about the size of a small horse, with long slender limb bones and metapodials and hypsodont upper cheek teeth whose enamel is undulate, and fossettes cement-filled. Upper premolars possess an inner wall; this is clearly an iranotheriine morphology. As such it is the earliest known African member of this subfamily, close to the oldest member of the subfamily recently discovered at Bugti in Pakistan, a site whose age is about the same.     

‘Candidatus ferrigenium straubiae’ sp. nov., ‘Candidatus ferrigenium bremense’ sp. nov., ‘Candidatus ferrigenium altingense’ sp. nov., are autotrophic Fe(II)-oxidizing bacteria of the family Gallionellaceae

Iron(II) [Fe(II)] oxidation coupled to denitrification is recognized as an environmentally important process in many ecosystems. However, the Fe(II)-oxidizing bacteria (FeOB) dominating autotrophic nitrate-reducing Fe(II)-oxidizing enrichment cultures, affiliated with the family Gallionellaceae, remain poorly taxonomically defined due to lack of representative isolates. We describe the taxonomic classification of three novel FeOB based on metagenome-assembled genomes (MAGs) acquired from the autotrophic nitrate-reducing enrichment cultures KS, BP and AG. Phylogenetic analysis of nearly full-length 16S rRNA gene sequences demonstrated that these three FeOB were most closely affiliated to the genera Ferrigenium, Sideroxydans and Gallionella, with up to 96.5%, 95.4% and 96.2% 16S rRNA gene sequence identities to representative isolates of these genera, respectively. In addition, average amino acid identities (AAI) of the genomes compared to the most closely related genera revealed highest AAI with Ferrigenium kumadai An22 (76.35–76.74%), suggesting that the three FeOB are members of this genus. Phylogenetic analysis of conserved functional genes further supported that these FeOB represent three novel species of the genus Ferrigenium. Moreover, the three novel FeOB likely have characteristic features, performing partial denitrification coupled to Fe(II) oxidation and carbon fixation. Scanning electron microscopy of the enrichment cultures showed slightly curved rod-shaped cells, ranging from 0.2-0.7 μm in width and 0.5–2.3 μm in length. Based on the phylogenetic, genomic and physiological characteristics, we propose that these FeOB represent three novel species, ‘Candidatus Ferrigenium straubiae’ sp. nov., ‘Candidatus Ferrigenium bremense’ sp. nov. and ‘Candidatus Ferrigenium altingense’ sp. nov. that might have unique metabolic features among the genus Ferrigenium.     

Methanopyrus kandleri,gen. and sp. nov. represents a novel group of hyperthermophilic methanogens,growing at 110°C

A novel group of hyperthermophilic rod-shaped motile methanogens was isolated from a hydrothermally heated deep sea sediment (Guaymas Basin, Gulf of California) and from a shallow marine hydrothermal system (Kolbeinsey ridge, Iceland). The grew between 84 and 110°C (opt: 98°C) and from 0.2% to 4% NaCl (opt. 2%) and pH 5.5 to 7 (opt: 6.5). The isolates were obligate chemolithoautotrophes using H₂/CO₂ as energy and carbon sources. In the presence of sulfur, H₂S was formed and cells tended to lyse. The cell wall consisted of a new type of pseudomurein containing ornithin in addition to lysine and no N-acetylglucosamine. The pseudomurein layer was covered by a detergent-sensitive protein surface layer. The core lipid consisted exclusively of phytanyl diether. The GC content of the DNA was 60 mol%. By 16S rRNA comparisons the new organisms were not related to any of the three methanogenic lineages. Based on the physiological and molecular properties of the new isolates, we describe here a new genus, which we name Methanopyrus (the methane fire). The type species is Methanopyrus kandleri (type strain: AV19; DSM 6324).This paper is dedicated to Otto Kandler on the occasion of his 70th birthday     

库蚊一新种(Culex cheni sp.nov.)

在1957年7月,作者在广州市郊夏收后稻田积水,采集库蚊幼虫一批,经隔离培养获得羽化成虫、蛹皮及幼虫皮,另保存四龄幼虫一批,经研究后认为是库蚊属的一新种。现将其中雌蚊10个,雄蚊9个及其幼虫皮,并将幼虫形态描述如下: 一、成虫 雌蚊 头部复盖有淡色至棕色弯窄鳞及直竖叉状鳞片,头顶部两侧有扁平淡色鳞     

The first survey of Cystobasidiomycete yeasts in the lichen genus Cladonia; with the description of Lichenozyma pisutiana gen. nov., sp. nov.

The view of lichens as a symbiosis only between a mycobiont and a photobiont has been challenged by discoveries of diverse associated organisms. Specific basidiomycete yeasts in the cortex of a range of macrolichens were hypothesized to influence the lichens' phenotype. The present study explores the occurrence and diversity of cystobasidiomycete yeasts in the lichen genus Cladonia. We obtained seven cultures and 56 additional sequences using specific primers from 27 Cladonia species from all over Europe and performed phylogenetic analyses based on ITS, LSU and SSU rDNA loci. We revealed yeast diversity distinct from any previously reported. Representatives of Cyphobasidiales, Microsporomycetaceae and of an unknown group related to Symmetrospora have been found. We present evidence that the Microsporomycetaceae contains mainly lichen-associated yeasts. Lichenozyma pisutiana is circumscribed here as a new genus and species. We report the first known associations between cystobasidiomycete yeasts and Cladonia (both corticate and ecorticate), and find that the association is geographically widespread in various habitats. Our results also suggest that a great diversity of lichen associated yeasts remains to be discovered.