- Volume 64, Issue Pt_6, 2014

A novel, red–pink-pigmented strain, designated R2-4T, was isolated from a till sample near Ny-Alesund, Svalbard Archipelago, Norway. Cells were aerobic, Gram-stain-negative and rod-shaped. Growth occurred at 4–30 °C (optimum, 20–22 °C), at pH 6.0–9.0 (optimum, pH 7.0) and with 0–1 % NaCl added to R2A agar. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain R2-4T belonged to the genus Hymenobacter . 16S rRNA gene sequence similarity between strain R2-4T and the type strains of related species of the genus ranged from 94.51 to 96.05 %. Strain R2-4T contained iso-C15 : 0, anteiso-C15 : 0, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), summed feature 4 (C17 : 1 anteiso B and/or iso I) and C16 : 1ω5c as the major cellular fatty acids, MK-7 as the major respiratory quinone, and phosphatidylethanolamine, unknown aminophospholipids, unknown aminolipids and unknown lipids as the main polar lipids. The polyamine was sym-homospermidine. The DNA G+C content of strain R2-4T was 61.6 mol%. On the basis of phylogenetic, physiological and chemotaxonomic data, strain R2-4T is considered to represent a novel species of the genus Hymenobacter , for which the name Hymenobacter arcticus sp. nov. is proposed. The type strain is R2-4T ( = CCTCC AB 2012104T = KACC 16881T).

A novel nitrite-oxidizing bacterium (NOB), strain LbT, was isolated from a nitrifying bioreactor with a high loading of ammonium bicarbonate in a mineral medium with nitrite as the energy source. The cells were oval (lancet-shaped) rods with pointed edges, non-motile, Gram-positive (by staining and from the cell wall structure) and non-spore-forming. Strain LbT was an obligately aerobic, chemolitoautotrophic NOB, utilizing nitrite or formate as the energy source and CO2 as the carbon source. Ammonium served as the only source of assimilated nitrogen. Growth with nitrite was optimal at pH 6.8–7.5 and at 40 °C (maximum 46 °C). The membrane lipids consisted of C20 alkyl 1,2-diols with the dominant fatty acids being 10MeC18 and C18 : 1ω9. The peptidoglycan lacked meso-DAP but contained ornithine and lysine. The dominant lipoquinone was MK-8. Phylogenetic analyses of the 16s rRNA gene sequence placed strain LbT into the class Thermomicrobia of the phylum Chloroflexi with Sphaerobacter thermophilus as the closest relative. On the basis of physiological and phylogenetic data, it is proposed that strain LbT represents a novel species of a new genus, with the suggested name Nitrolancea hollandica gen. nov., sp. nov. The type strain of the type species is LbT ( = DSM 23161T = UNIQEM U798T).

Acidobacteria constitute an abundant fraction of the soil microbial community and are currently divided into 26 subdivisions. Most cultivated members of the Acidobacteria are affiliated with subdivision 1, while only a few representatives of subdivisions 3, 4, 8, 10 and 23 have been isolated and described so far. Two novel isolates of subdivision 4 of the Acidobacteria were isolated from subtropical savannah soils and are characterized in the present work. Cells of strains A22_HD_4HT and Ac_23_E3T were immotile rods that divided by binary fission. Colonies were pink and white, respectively. The novel strains A22_HD_4HT and Ac_23_E3T were aerobic mesophiles with a broad range of tolerance towards pH (4.0–9.5 and 3.5–10.0, respectively) and temperature (15–44 and 12–47 °C, respectively). Both showed chemo-organoheterotrophic growth on some sugars, the amino sugar N-acetylgalactosamine, a few amino acids, organic acids and various complex protein substrates. Major fatty acids of A22_HD_4HT and Ac_23_E3T were iso-C15 : 0, summed feature 1 (C13 : 0 3-OH/iso-C15 : 1 H), summed feature 3 (C16 : 1ω7c/C16 : 1ω6c) and anteiso-C17 : 0. The major quinone was MK-8; in addition, MK-7 occurred in small amounts. The DNA G+C contents of A22_HD_4HT and Ac_23_E3T were 53.2 and 52.6 mol%, respectively. The closest described relative was Blastocatella fastidiosa A2-16T, with 16S rRNA gene sequence identity of 93.2 and 93.3 %, respectively. Strains A22_HD_4HT and Ac_23_E3T displayed 16S rRNA gene sequence similarity of 97.4 % to each other. On the basis of the low DNA–DNA hybridization value, the two isolates represent different species. Based on morphological, physiological and molecular characteristics, the new genus Aridibacter gen. nov. is proposed, with two novel species, the type species Aridibacter famidurans sp. nov. (type strain A22_HD_4HT = DSM 26555T = LMG 27985T) and a second species, Aridibacter kavangonensis sp. nov. (type strain Ac_23_E3T = DSM 26558T = LMG 27597T).

A thermophilic, filamentous, heterotrophic bacterium, designated strain JAD2T, a member of an as-yet uncultivated lineage that is present and sometimes abundant in some hot springs worldwide, was isolated from sediment of Great Boiling Spring in Nevada, USA. Cells had a mean diameter of 0.3 µm and length of 4.0 µm, and formed filaments that typically ranged in length from 20 to 200 µm. Filaments were negative for the Gram stain reaction, spores were not formed and motility was not observed. The optimum temperature for growth was 72.5–75 °C, with a range of 67.5–75 °C, and the optimum pH for growth was 6.75, with a range of pH 6.5–7.75. Peptone, tryptone or yeast extract were able to support growth when supplemented with vitamins, but no growth was observed using a variety of defined organic substrates. Strain JAD2T was microaerophilic and facultatively anaerobic, with optimal growth at 1 % (v/v) O2 and an upper limit of 8 % O2. The major cellular fatty acids (>5 %) were C16 : 0, C19 : 0, C18 : 0, C20 : 0 and C19 : 1. The genomic DNA G+C content was 69.3 mol%. Phylogenetic and phylogenomic analyses using sequences of the 16S rRNA gene and other conserved genes placed JAD2T within the phylum Chloroflexi , but not within any existing class in this phylum. These results indicate that strain JAD2T is the first cultivated representative of a novel lineage within the phylum Chloroflexi , for which we propose the name Thermoflexus hugenholtzii gen. nov., sp. nov., within Thermoflexia classis nov., Thermoflexales ord. nov. and Thermoflexaceae fam. nov. The type strain of Thermoflexus hugenholtzii is JAD2T ( = JCM 19131T = CCTCC AB-2014030T).

Two thermophilic, strictly anaerobic, Gram-negative bacteria, designated strains AZM34c06T and AZM44c09T, were isolated from terrestrial hot springs in Japan. The optimum growth conditions for strain AZM34c06T were 60 °C, pH 7.4 and 0 % additional NaCl, and those for strain AZM44c09T were 70 °C, pH 7.4 and 0 % additional NaCl. Complete genome sequencing was performed for both strains, revealing genome sizes of 2.19 Mbp (AZM34c06T) and 2.01 Mbp (AZM44c09T). Phylogenetic analyses based on 16S rRNA gene sequences and the concatenated predicted amino acid sequences of 33 ribosomal proteins showed that both strains belonged to the genus Thermotoga . The closest relatives of strains AZM34c06T and AZM44c09T were the type strains of Thermotoga lettingae (96.0 % similarity based on the 16S rRNA gene and 84.1 % similarity based on ribosomal proteins) and Thermotoga hypogea (98.6 and 92.7 % similarity), respectively. Using blast, the average nucleotide identity was 70.4–70.5 % when comparing strain AZM34c06T and T. lettingae TMOT and 76.6 % when comparing strain AZM44c09T and T. hypogea NBRC 106472T. Both values are far below the 95 % threshold value for species delineation. In view of these data, we propose the inclusion of the two isolates in the genus Thermotoga within two novel species, Thermotoga profunda sp. nov. (type strain AZM34c06T = NBRC 106115T = DSM 23275T) and Thermotoga caldifontis sp. nov. (type strain AZM44c09T = NBRC 106116T = DSM 23272T).

A mesophilic, obligately anaerobic, lactate-, alcohol-, carbohydrate- and amino-acid- degrading bacterium, designated strain 7WAY-8-7T, was isolated from an upflow anaerobic sludge blanket reactor treating high-strength organic wastewater from isomerized sugar production processes. Cells of strain 7WAY-8-7T were motile, curved rods (0.7–1.0×5.0–8.0 µm). Spore formation was not observed. The strain grew optimally at 37 °C (range for growth was 25–40 °C) and pH 7.0 (pH 6.0–7.5), and could grow fermentatively on yeast extract, glucose, ribose, xylose, malate, tryptone, pyruvate, fumarate, Casamino acids, serine and cysteine. The main end-products of glucose fermentation were acetate and hydrogen. In co-culture with the hydrogenotrophic methanogen Methanospirillum hungatei DSM 864T, strain 7WAY-8-7T could utilize lactate, glycerol, ethanol, 1-propanol, 1-butanol, l-glutamate, alanine, leucine, isoleucine, valine, histidine, asparagine, glutamine, arginine, lysine, threonine, 2-oxoglutarate, aspartate and methionine. A Stickland reaction was not observed with some pairs of amino acids. Yeast extract was required for growth. Nitrate, sulfate, thiosulfate, elemental sulfur, sulfite and Fe (III) were not used as terminal electron acceptors. The G+C content of the genomic DNA was 61.4 mol%. 16S rRNA gene sequence analysis revealed that the isolate belongs to the uncultured environmental clone clade (called ‘PD-UASB-13’ in the Greengenes database) in the bacterial phylum Synergistetes , showing less than 90 % sequence similarity with closely related described species such as Aminivibrio pyruvatiphilus and Aminobacterium colombiense (89.7 % and 88.7 %, respectively). The major cellular fatty acids were iso-C13 : 0, iso-C15 : 0, anteiso-C15 : 0, C18 : 1, C19 : 1, C20 : 1 and C21 : 1. A novel genus and species, Lactivibrio alcoholicus gen. nov., sp. nov. is proposed to accommodate strain 7WAY-8-7T ( = JCM 17151T = DSM 24196T = CGMCC 1.5159T).

Eight strains with identical sequences of the D1/D2 domains of the large subunit rRNA genes were isolated from fallen fruits in two distant localities in Laos. These strains represent a novel dimorphic budding yeast species producing invasive pseudohyphae and a brown pigment when growing on media containing quinic acid as the sole carbon source or tryptophan as the sole nitrogen source. Phylogenetic analysis of the sequences of the D1/D2 domains, the internal transcribed spacer (ITS) regions and the 18S rRNA genes placed the novel species in the Metschnikowia clade close to Candida torresii, Metschnikowia drosophilae and C andida danieliae. The taxonomic name Metschnikowia laotica f.a., sp. nov., reflecting the geographical origin of the isolates, is proposed for the novel species. The type strain is 11-524T ( = CBS 12961T = NCAIM Y.02124T = CCY 64-4-1T). The Mycobank number is MB 807383.

Several independent surveys of yeasts associated with different plant materials and soil led to the proposal of a novel yeast species belonging to the Tremellales clade (Agaricomycotina, Basidiomycota). Analysis of the sequences of the D1/D2 domains and internal transcribed spacer region of the large subunit of the rRNA gene suggested affinity to a phylogenetic lineage that includes Hannaella coprosmaensis, Hannaella oryzae and Hannaella sinensis. Thirty-two isolates were obtained from different sources, including bromeliads, nectar of Heliconia psittacorum (Heliconiaceae), flowers of Pimenta dioica (Myrtaceae), roots and leaves of sugar cane (Saccharum spp.) in Brazil, leaves of Cratoxylum maingayi, Arundinaria pusilla and Vitis vinifera in Thailand, soil samples in Taiwan, and prairie soil in the USA. Sequence analysis of the D1/D2 domains of the large subunit of the rRNA gene showed that the novel species differs from Hannaella coprosmaensis and Hannaella oryzae by 36 and 46 nt substitutions, respectively. A novel species is suggested to accommodate these isolates, for which the name Hannaella pagnoccae sp. nov. is proposed. The type strain is BI118T ( = CBS 11142T = ATCC MYA-4530T).

Two novel species, Wickerhamiella kiyanii f.a., sp. nov. (type strain FB1-1DASPT = CBS 12905T = CBMAI 1613T) and Wickerhamiella fructicola f.a., sp. nov. (type strain H10YT = CBS 12902T = CBMAI 1614T) are proposed in the Wickerhamiella clade (Saccharomycetes, Saccharomycetales) to accommodate three strains isolated from flowers and fruits typical of the Brazilian Atlantic rainforest. The novel status of these yeast species was established by sequence divergence observed in the D1/D2 domains of the LSU rRNA gene from the most closely related, described species as well as by phylogenetic analysis. Wickerhamiella kiyanii sp. nov. differs from its nearest phylogenetic neighbours W. pagnoccae CBS 12178T, Candida jalapaonensis CBS 10935T and Candida drosophilae CBS 8459T by 2.2–4.2 % in the D1/D2 sequences. By contrast, a sequence divergence of 13.2–13.8 % was observed between W. fructicola sp. nov. and its closest, described phylogenetic relative Candida kazoui JCM 12558T and Candida hasegawae JCM 12559T. Taxonomic descriptions of the two novel species are given.

A novel ustilaginomycetous yeast isolated from the intestinal tract of an insect pest of sugarcane roots in Ribeirão Preto, São Paulo State, Brazil, represents a novel species of the genus Pseudozyma based on molecular analyses of the D1/D2 rDNA large subunit and the internal transcribed spacer (ITS1+ITS2) regions. The name Pseudozyma brasiliensis sp. nov. is proposed for this species, with GHG001T ( = CBS 13268T = UFMG-CM-Y307T) as the type strain. P. brasiliensis sp. nov. is a sister species of Pseudozyma vetiver, originally isolated from leaves of vetiver grass and sugarcane in Thailand. P. brasiliensis sp. nov. is able to grow well with xylan as the sole carbon source and produces high levels of an endo-1,4-xylanase that has a higher specific activity in comparison with other eukaryotic xylanases. This enzyme has a variety of industrial applications, indicating the great biotechnological potential of P. brasiliensis.

Three yeast strains related to members of the genus Saccharomycopsis were isolated. One strain (CLIB 1310) was isolated from olive brines of fermented black olives in France and two strains (CLIB 1454 and CLIB 1455) were isolated from a plant in French Guiana. Sequence analyses based on the D1/D2 domains of the nuclear large subunit rRNA gene, small-subunit rRNA gene and partial EF-1α gene revealed that the strains represented two novel taxa exhibiting extensive sequence divergence from the previously described species of the genus Saccharomycopsis. Two novel species are described to accommodate these newly isolated strains: Saccharomycopsis olivae sp. nov. (type strain CLIB 1310T = CBS 12701T) and Saccharomycopsis guyanensis sp. nov. (type strain CLIB 1455T = CBS 12914T and strain CLIB 1454). Both strains CLIB 1454 and CLIB 1455T displayed identical sequences but differed in their ability to metabolize sorbitol and in their morphology on agar medium. Candida amapae, Candida lassensensis and Arthroascus babjevae belonging to the Saccharomycopsis clade, are reassigned to Saccharomycopsis as novel combinations.