Asterotremella meifongana sp. nov. and Asterotremella nantouana sp. nov., two anamorphic basidiomycetous yeasts isolated from soil and mushrooms

Two novel yeast species, Asterotremella meifongana sp. nov. and Asterotremella nantouana sp. nov., belonging to Asterotremellaceae within the Trichosporonales, are proposed to accommodate five strains isolated from Taiwanese samples of soil and basidiocarps during 2006-2007. Sequence analysis of the D1/D2 domains of the large subunit rRNA gene revealed that the two species are phylogenetically closely related to species of the genus Asterotremella, which indicates that they are members of the genus. The two species can be further differentiated from other Asterotremella species based on their internal transcribed spacer sequences, as well as on a few physiological test responses. The type strains are A. meifongana SN4S04(T) (=CBS 11424(T) = BCRC 23196(T)) and A. nantouana SN5S06(T) (=CBS 10890(T) = BCRC 23135(T)).     

Asterotremella gen. nov. albida, an anamorphic tremelloid yeast isolated from the agarics Asterophora lycoperdoides and Asterophora parasitica

Using a genotypic approach (PCR-fingerprinting, DNA/DNA reassociation, partial sequences of the 26S rDNA gene, complete sequences of the 18S rDNA gene, and sequences of the internal transcribed spacers) five tremelloid yeast isolates from the agarics Asterophora lycoperdoides and A. parasitica were shown to be conspecific with Cryptococcus ramirezgomezianus. It was not possible to distinguish the yeast strains from A. lycoperdoides and A. parasitica using sequences from the intergenic spacer (IGS1). Phylogeny based on the 26S (D1/D2-domain), ITS1-5.8S-ITS2 and complete 18S rDNA demonstrated that C. ramirezgomezianus is closely related to several additional Cryptococcus species (C. humicola, C. longus, C. musci, C. pseudolongus) within the Trichosporonales. A new genus, Asterotremella, and a new family, Asterotremellaceae were introduced for Cryptococcus species clustering within the Trichosporonales having a ubiquinone Q-9. Cryptococcus ramirezgomezianus is a synonym of Asterotremella albida.     

Blastobotrys serpentis sp. nov., isolated from the intestine of a Trinket snake (Elaphe sp., Colubridae)

Asporogenus yeast strains W113AT and W113B were isolated from the intestine of a dead Trinket snake. The two isolates showed 100% sequence similarity in the D1/D2 domain of the large-subunit (LSU) rRNA gene, internal transcribed spacer (ITS) 1-5.8S rRNA gene-ITS2 region and mitochondrial small-subunit rRNA gene and the cytochrome oxidase II gene sequence and also showed similar phenotypic characteristics. The nearest phylogenetic neighbors of W113AT and W113B based on the sequence of the D1/D2 domain of the LSU rRNA gene were Blastobotrys chiropterorum NRRL Y-17017T and Blastobotrys terrestris NRRL Y-17704T with about 98% similarity. The close affiliation of W113AT and W113B with B. chiropterorum NRRL Y-17017T and B. terrestris NRRL Y-17704T was also evident from the high similarity observed in the nucleotide sequences of the mitochondrial small subunit rRNA (96-97.8%) and the cytochrome oxidase II (95.5-95.6%) genes. In the neighbor-joining phylogenetic trees constructed based on the D1/D2 domain or cytochrome oxidase gene, the isolates clustered with the above-mentioned species. However, the isolates showed a number of differences in their phenotypic properties with B. chiropterorum NRRL Y-17017T and B. terrestris NRRL Y-17704T and hence are regarded as representing a novel member of the genus Blastobotrys, for which the name Blastobotrys serpentis sp. nov. is proposed.     

Cryptococcus arboriformis Sp. Nov., a novel anamorphic basidiomycetous yeast species isolated from a patient's urine

A basidiomycetous yeast strain isolated from the urine of a 73-year-old Japanese patient with chronic renal failure was revealed to be a novel species by sequencing the D1/D2 26S rDNA and ITS regions of the rRNA gene. The name Cryptococcus arboriformis sp. nov. is proposed for the isolate, with IFM 54862(T) (=CBS 1044(T) =JCM 14201(T)) as the type strain. A phylogenetic analysis positioned Cryptococcus arboriformis in the Trichosporonales lineage and showed that it is closely related to C. haglerorum.     

Dysgonomonas mossii sp. nov., from human sources

Phenotypic and phylogenetic studies were performed on seven unidentified gram-negative, facultatively anaerobic, coccobacillus-shaped organisms isolated from human clinical specimens. Comparative 16S rRNA gene sequencing demonstrated that four of the strains corresponded to Dysgonomonas capnocytophagoides whereas the remaining three isolates represent a new sub-line within the genus Dysgonomonas, displaying greater than 5% sequence divergence with Dysgonomonas capnocytophagoides and Dysgonomonas gadei. The three novel isolates were readily distinguished from D.capnocytophagoides and D. gadei by biochemical tests. The DNA base composition of the novel species was consistent with its assignment to the genus Dysgonomonas. Based on phylogenetic and phenotypic evidence it is proposed that the unknown species, be classified as Dysgonomonas mossii sp. nov. The type strain of Dysgonomonas mossii is CCUG 43457T (= CIP 107079T).     

Candida dajiaensis sp. nov., Candida yuanshanicus sp. nov., Candida jianshihensis sp. nov., and Candida sanyiensis sp. nov., four anamorphic, ascomycetous yeast species isolated from soil in Taiwan

Nine anamorphic, ascomycetous yeast strains belonging to the Pichia anomala clade were recovered from forest soil in 2006 in Taiwan. The nine yeast strains represent four novel yeast species based on the sequences of their D1/D2 domain of the large subunit (LSU) rRNA gene and their physiological characteristics. The scientific names of Candida dajiaensis sp. nov., Candida yuanshanicus sp. nov., Candida jianshihensis sp. nov., and Candida sanyiensis sp. nov. are proposed for these novel yeast species. The type strains are C. dajiaensis SM11S03(T) (=CBS 10590(T)=BCRC 23099(T)), C. yuanshanicus SY3S02(T) (=CBS 10589(T)=BCRC 23100(T)), C. jianshihensis SM8S04(T) (=CBS 10591(T)=BCRC 23096(T)), and C. sanyiensis SA1S06(T) (=CBS 10592(T)=BCRC 23094(T)). Sequence analysis of the D1/D2 of the LSU rRNA gene revealed that the three species, C. dajiaensis, C. yuanshanicus and Pichia onychis, shared a separate branch in the phylogenetic tree, C. jianshihensis is phylogenetically related to Candida ulmi and Pichia alni, and the phylogenetically closest relative of C. sanyiensis is Pichia populi.     

Geminicoccus roseus gen. nov., sp. nov., an aerobic phototrophic Alphaproteobacterium isolated from a marine aquaculture biofilter

A Gram-negative, strictly aerobic, diplococcoid bacterium (strain D2-3^T) was isolated from the biofilter of a recirculating marine aquaculture system. Phylogenetic analysis of the 16S rRNA gene sequence of D2-3^T indicated that the new organism occupied a novel lineage within the -1 subclass of Proteobacteria and was related to the genera Rhodothalassium, Azospirillum, Craurococcus, Acidiphilium, and Tistrella. The highest sequence similarity (90.8%) of the 16S rRNA gene sequence of D2-3^T was to that of Candidatus “Alysiosphaera europaea”. D2-3^T was mesophilic, heterotrophic, required sea salt, and had a pH optimum of 8.0. Growth in the presence of light resulted in the formation of pink colonies, a 25% increased cell yield, and a slightly increased growth rate. D2-3^T contained carotenoids and low amounts of bacteriochlorophyll a. Membranes of D2-3^T contained b-type cytochromes. The G+C content of the DNA was 60.3±0.1 mol%. Phylogenetic, morphological, physiological, and biochemical analyses demonstrated that D2-3^T represented a new aerobic phototrophic genus, for which the name Geminicoccus roseus gen. nov., sp. nov. is proposed for the type species (D2-3^T=DSM 18922^T=ATCC BAA-1445^T).     

Ogataea thermophila sp. nov., the teleomorph of Candida thermophila

Ascospore formation was observed in the type strain of Candida thermophila Shin K-S, Shin YK, Yoon and Park on some yeast sporulation media. In addition, a further sporulating strain was found that proved to be conspecific with C. thermophila on the basis of sequences of the D1/D2 domain of the large-subunit (26S) rRNA gene and the internal transcribed spacer (ITS)1-5.8S rRNA gene - ITS2 region. Therefore, Ogataea thermophila Péter, Tornai-Lehoczki, Shin K-S & Dlauchy sp. nov. is proposed as the teleomorph of C. thermophila. The type strain is Y94(T)=JCM 10994(T)=KCCM 50661(T)=KCTC 17233(T).     

Natronobacillus azotifigens gen. nov., sp. nov., an anaerobic diazotrophic haloalkaliphile from soda-rich habitats

Gram-positive bacteria capable of nitrogen fixation were obtained in microoxic enrichments from soda soils in south-western Siberia, north-eastern Mongolia, and the Lybian desert (Egypt). The same organisms were obtained in anoxic enrichments with glucose from soda lake sediments in the Kulunda Steppe (Altai, Russia) using nitrogen-free alkaline medium of pH 10. The isolates were represented by thin motile rods forming terminal round endospores. They are strictly fermentative saccharolytic anaerobes but tolerate high oxygen concentrations, probably due to a high catalase activity. All of the strains are obligately alkaliphilic and highly salt-tolerant natronophiles (chloride-independent sodaphiles). Growth was possible within a pH range from 7.5 to 10.6, with an optimum at 9.5–10, and within a salt range from 0.2 to 4 M Na⁺, with an optimum at 0.5–1.5 M for the different strains. The nitrogenase activity in the whole cells also had an alkaline pH optimum but was much more sensitive to high salt concentrations compared to the growing cells. The isolates formed a compact genetic group with a high level of DNA similarity. Phylogenetic analysis based on 16S-rRNA gene sequences placed the isolates into Bacillus rRNA group 1 as a separate lineage with Amphibacillus tropicus as the nearest relative. In all isolates the key functional nitrogenase gene nifH was detected. A new genus and species, Natronobacillus azotifigens gen. nov., sp. nov., is proposed to accommodate the novel diazotrophic haloalkaliphiles. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. The GenBank accession numbers for the 16S rRNA gene of the novel strains are EU143681-EU143690 and EU850814-EU850816; for the nifH gene the accession numbers are EU542601, EU563380-EU563386 and EU850817-EU850819.     

Bullera koratensis sp. nov. and Bullera lagerstroemiae sp. nov., two new ballistoconidium-forming yeast species in the Trichosporonales clade isolated from plant leaves in Thailand

Seven strains of ballistoconidiogenous yeasts that contain xylose, form Q-10 ubiquinone, propagate by budding and don't produce stalk conidia were isolated from plant leaves collected in Thailand and were found to represent two new species. The taxonomic properties of the two species coincided with the genus Bullera so they are described as Bullera koratensis sp. nov. and Bullera lagerstroemiae sp. nov. In phylogenetic trees based on the nucleotide sequences of 18S ribosomal DNA and the D1/D2 domain of 26S rDNA, these two species are located in the Trichosporonales clade (Cryptococcus humicola-Trichosporon lineage).     

Torulaspora maleeae sp. nov., a novel ascomycetous yeast species from Japan and Thailand

Nine strains of a new Torulaspora species were isolated from natural samples collected in Japan and Thailand including one strain obtained from a leaf of Rhizophora stylosa (NBRC 11061T), one strain from soil (NBRC 11062), six strains from mosses (ST-14, ST-266, ST-510, ST-511, ST-513 and ST-581) and one strain from sediment in mangrove forest (RV-51). On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics, and the sequence analyses of the D1/D2 domain of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) (ITS1-5.8S rRNA gene-ITS2) region, the nine strains were found to represent a single novel species of the genus Torulaspora, which were named Torulaspora maleeae sp. nov. The type strain is NBRC 11061T (BCC 25515T=CBS 10694T). In the phylogenetic trees based on the sequences of the D1/D2 domain of the LSU rRNA gene, T. maleeae showed a close relationship with the five recognized species of the genus Torulaspora, Torulaspora delbrueckii, Torulaspora franciscae, Torulaspora globosa, Torulaspora microellipsoides and Torulaspora pretoriensis. Torulaspora maleeae differed from the five recognized species of the genus Torulaspora by six to 12 nucleotide substitutions (1.1-2.1%) in the D1/D2 domain of the LSU rRNA gene and by 6.4-11.7% nucleotide substitutions in the ITS (ITS1-5.8S rRNA gene-ITS2) region.     

Neoscardovia arbecensis gen. nov., sp. nov., isolated from porcine slurries

Three Gram-positive, anaerobic, pleomorphic strains (PG10(T), PG18 and PG22), were selected among five strains isolated from pig slurries while searching for host specific bifidobacteria to track the source of fecal pollution in water. Analysis of the 16S rRNA gene sequence showed a maximum identity of 94% to various species of the family Bifidobacteriaceae. However, phylogenetic analyses of 16S rRNA and HSP60 gene sequences revealed a closer relationship of these strains to members of the recently described Aeriscardovia, Parascardovia and Scardovia genera, than to other Bifidobacterium species. The names Neoscardovia gen. nov. and Neoscardovia arbecensis sp. nov. are proposed for a new genus and for the first species belonging to this genus, respectively, and for which PG10(T) (CECT 8111(T), DSM 25737(T)) was designated as the type strain. This new species should be placed in the Bifidobacteriaceae family within the class Actinobacteria, with Aeriscardovia aeriphila being the closest relative. The prevailing cellular fatty acids were C(16:0) and C(18:1)ω9c, and the major polar lipids consisted of a variety of glycolipids, diphosphatidyl glycerol, two unidentified phospholipids, and phosphatidyl glycerol. The peptidoglycan structure was A1γmeso-Dpm-direct. The GenBank accession numbers for the 16S rRNA gene and HSP60 gene sequences of strains PG10(T), PG18 and PG22 are JF519691, JF519693, JQ767128 and JQ767130, JQ767131, JQ767133, respectively.     

Hymenobacter perfusus sp. nov., Hymenobacter flocculans sp. nov. and Hymenobacter metalli sp. nov. three new species isolated from an uranium mine waste water treatment system

Three red-pink pigmented strains, designated A1-12(T), A2-50A(T) and A2-91(T), were recovered from two different sites in a uranium mine. For all strains, the optimum growth temperature was 25°C, the optimum pH was 6.0-6.5 and the DNA G+C contents were between 60 and 63.4 mol%. The major respiratory quinone was menaquinone 7 (MK-7) and the fatty acid profiles contained iso- and anteiso-branched C15 fatty acids, summed feature 3 (16:1 ω6c and/or ω7c and/or 15:0 iso 2-OH), summed feature 4 (17:1 anteiso B and/or iso I) and the unsaturated fatty acid 16:1 ω5c as the major components. Phylogenetic analysis of the 16S rRNA gene sequences showed that these organisms represented three distinct branches within the family Flexibacteraceae most closely related to the members of the genus Hymenobacter. Strain A1-12(T) formed a distinct phylogenetic line along with H. rigui KCTC 12533(T) and they shared approximately 98.9% 16S rRNA gene sequence similarity. However, these two strains shared only 14.7% pairwise similarity in their genomic DNA. Strains A2-50A(T) and A2-91(T) formed two distinct lineages, related to the species H. soli KCTC 12607(T), sharing about 95.5% 16S rRNA gene sequence similarity between themselves, and 88.3 and 92.0% with other members of the genus Hymenobacter. Based on the phylogenetic analysis and physiological and biochemical characteristics, these isolates were considered to represent three novel species for which we propose the names Hymenobacter perfusus for strain A1-12(T) (=CIP 110166=LMG 26000), Hymenobacter flocculans for strain A2-50A(T) (=CIP 110139=LMG 25699) and Hymenobacter metalli for strain A2-91(T) (=CIP 110140=LMG 25700).     

Candida ogatae sp. nov., an anamorphic member of the Kuraishia clade

Three methanol-assimilating yeast strains representing a hitherto undescribed species were isolated from rotten wood and freshwater samples collected in Hungary. Analysis of the D1/D2 large subunit rRNA gene sequences placed the strains in the Kuraishia clade; however, no ascospore formation was observed. These strains differ from Candida hungarica , the genetically most closely related recognized species, by four and five substitutions in D1/D2 and by >1% and 4% differences in the internal transcribed spacer and in the mitochondrial small subunit rRNA gene regions, respectively. Some phenotypic differences were also observed. Candida ogatae , a novel yeast species, is proposed to accommodate these isolates. The type culture is NCAIM Y.01845^T (CBS 10924, NRRL Y-48474).     

Selenihalanaerobacter shriftii gen. nov., sp. nov., a halophilic anaerobe from Dead Sea sediments that respires selenate

We isolated an obligately anaerobic halophilic bacterium from the Dead Sea that grew by respiration of selenate. The isolate, designated strain DSSe-1, was a gram-negative, non-motile rod. It oxidized glycerol or glucose to acetate + CO2 with concomitant reduction of selenate to selenite plus elemental selenium. Other electron acceptors that supported anaerobic growth on glycerol were nitrate and trimethylamine-N-oxide; nitrite, arsenate, fumarate, dimethylsulfoxide, thiosulfate, elemental sulfur, sulfite or sulfate could not serve as electron acceptors. Growth on glycerol in the presence of nitrate occurred over a salinity range from 100 to 240 g/l, with an optimum at 210 g/l. Analysis of the 16S rRNA gene sequence suggests that strain DSSe-1 belongs to the order Halanaerobiales, an order of halophilic anaerobes with a fermentative or homoacetogenic metabolism, in which anaerobic respiratory metabolism has never been documented. The highest 16S rRNA sequence similarity (90%) was found with Acetohalobium arabaticum (X89077). On the basis of physiological properties as well as the relatively low homology of 16S rRNA from strain DSSe-1 with known genera, classification in a new genus within the order Halanaerobiales, family Halobacteroidaceae is warranted. We propose the name Selenihalanaerobacter shriftii. Type strain is strain DSSe-1 (ATCC accession number BAA-73).     

Dimorphic cycle in Candida citri sp. nov., a novel yeast species isolated from rotting fruit in Borneo

Five dimorphic yeast strains were isolated from rotting lime fruits in Borneo. The sequences of the D1/D2 domains of the 26S rRNA genes, the internal transcribed spacer (ITS) chromosomal regions and the 18S rRNA genes were identical in the isolates and differed from the corresponding sequences of all known yeast species. Based on the sequence differences (12-15% in the D1/D2 domain) from the closest relatives and the different pattern of taxonomic traits, the new isolates are assigned the status of a new species, for which the name Candida citri sp. nov. is proposed. Its type strain is 11-469(T) , which has been deposited in Centralbureau voor Schimmelcultures (Utrecht, the Netherlands) as CBS 11858(T) , Culture Collection of Yeasts (Bratislava, Slovakia) as CCY 29-181-1(T) and the National Collection of Agricultural and Industrial Microorganisms (Budapest, Hungary) as NCAIM Y.01978(T) . MycoBank number: MB 519100. The GenBank accession numbers for nucleotide sequences of its D1/D2 domain, ITS and 18S regions are HM803241, HM803242 and HM803243, respectively. Candida citri produces invasive mycelium composed of true septate hyphae that grow towards nutrient-rich parts of the medium and develop large vacuoles at the nongrowing ends of their cells. The hyphae produce blastoconidia, which can establish satellite yeast colonies in the invaded solid substrate.     

Arcobacter bivalviorum sp. nov. and Arcobacter venerupis sp. nov., new species isolated from shellfish

A group of ten Arcobacter isolates (Gram negative, slightly curved motile rods, oxidase positive) was recovered from mussels (nine) and from clams (one). These isolates could not be assigned to any known species using the molecular identification methods specific for this genus (16S rDNA-RFLP and m-PCR). The aim of this study is to establish the taxonomic position of these isolates. The 16S rRNA gene sequence similarity of mussel strain F4(T) to the type strains of all other Arcobacter species ranged from 91.1% to 94.8%. The species most similar to the clams' strain F67-11(T) were Arcobacter defluvii (CECT 7697(T), 97.1%) and Arcobacter ellisii (CECT 7837(T), 97.0%). On the basis of phylogenetic analyses with 16S rRNA, rpoB, gyrB and hsp60 genes, the mussel and clam strains formed two different, new lineages within the genus Arcobacter. These data, together with their different phenotypic characteristics and MALDI-TOF mass spectra, revealed that these strains represent two new species, for which the names Arcobacter bivalviorum (type strain F4(T)=CECT 7835(T)=LMG 26154(T)) and Arcobacter venerupis (type strain F67-11(T)=CECT 7836(T)=LMG 26156(T)) are proposed.     

Trichosporon vanderwaltii sp. nov., an asexual basidiomycetous yeast isolated from soil and beetles

During a survey of unidentified yeast isolates deposited in the UNESCO-MIRCEN Biotechnological Yeast Culture Collection housed at the Department of Microbial, Biochemical and Food Biotechnology of the University of the Free State, one isolate obtained from soil in South Africa showed 100 % identity in D1/D2 rDNA sequence with undescribed basidiomycetous yeasts isolated from the gut of beetles from the United States of America and forest soil from Taiwan in the NCBI sequence database. Phylogenetic analyses using sequences of the D1/D2 rDNA and ITS regions indicated that all these isolates form a well-supported sub-clade that is the sister clade to the Brassicae plus Porosum clades of Trichosporon in the order Trichosporonales. Subsequent phenotypic tests revealed that asexual reproduction by budding is rare but dominated by arthroconidia resulting from segmentation of hyphae and that fusiform giant cells are characterized by budding from a broad base. These findings further suggest that these isolates belong to a single tremellomycetous yeast species for which the name Trichosporon vanderwaltii CBS 12124^T (=NRRL Y-48732^T, =UOFS Y-1920^T) is proposed.