- Volume 59, Issue 3, 2009

Five strains, NBRC 3271T, NBRC 3272, NBRC 3263, NBRC 3260 and NBRC 3269 were examined genetically, phylogenetically, phenotypically and chemotaxonomically. The DNA G+C contents of the five strains were 55.1–56.4 mol%. The five strains had low levels of DNA–DNA hybridization of 13–51 % to the type strains of Gluconobacter frateurii, Gluconobacter thailandicus, Gluconobacter oxydans, Gluconobacter cerinus, Gluconobacter albidus and Gluconobacter kondonii and formed a cluster that was separate from the type strains of the six Gluconobacter species given above in phylogenetic trees based on 16S rRNA gene and 16S–23S rRNA gene internal transcribed spacer sequences. The five strains weakly produced dihydroxyacetone from glycerol, but not 2,5-diketo-d-gluconate or a water-soluble brown pigment from d-glucose and contained ubiquinone-10. The five strains were assigned as representing a novel species of the genus Gluconobacter, for which the name Gluconobacter japonicus sp. nov. is proposed. The type strain is NBRC 3271T (=BCC 14458T=strain 7T, K. Kondo). Cells of the type strain are motile by means of polar flagella and the DNA G+C content is 56.4 mol%.

A Gram-negative, short rod-shaped bacterium, strain GA2-M15T, was isolated from a sea-sand sample at Homi Cape, Pohang city, Republic of Korea. 16S rRNA gene sequence analysis demonstrated that this isolate was unique, showing 95.9 % sequence similarity to the type strain of Thalassobacter stenotrophicus and similarities of 94.0–95.2 % to the type strains of species of the genera Octadecabacter (94.4–95.2 %), Jannaschia (94.0–94.4 %) and Thalassobius (94.0–94.7 %). Chemotaxonomic characteristics (diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine as the major polar lipids and C18 : 1 ω7c as the predominant fatty acid) and DNA G+C content (56 mol%) were also similar to those of Thalassobacter stenotrophicus. 16S rRNA gene sequence similarity, physiological properties and some fatty acid components showed that strain GA2-M15T could be differentiated from Thalassobacter stenotrophicus. On the basis of these results, strain GA2-M15T is considered to represent a novel species of the genus Thalassobacter, for which the name Thalassobacter arenae sp. nov. is proposed. The type strain is GA2-M15T (=KACC 12675T =DSM 19593T).

A novel Gram-negative, facultatively anaerobic, non-sporulating, non-motile, catalase- and oxidase-positive, rod-shaped bacterium (strain JSM 061001T) was isolated from a tidal flat in the South China Sea, China. Growth occurred with 0–5 % (w/v) NaCl [optimum, 0.5–1 % (w/v) NaCl], at pH 5.0–10.0 (optimum, pH 7.0) and at 4–35 °C (optimum, 25–30 °C). The major cellular fatty acids were C16 : 0, cyclo C17 : 0, C18 : 1 ω7c and C16 : 1. Strain JSM 061001T contained ubiquinone Q-8 as the predominant respiratory quinone, and phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid as the polar lipids. The genomic DNA G+C content was 65.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain JSM 061001T belongs to the family Alcaligenaceae and was related most closely to the type strains of the two recognized species of the genus Pigmentiphaga. The three strains formed a robust cluster in the neighbour-joining, maximum-parsimony and maximum-likelihood phylogenetic trees. Levels of DNA–DNA relatedness between strain JSM 061001T and the type strains of Pigmentiphaga daeguensis and Pigmentiphaga kullae were 15.8 and 10.5 %, respectively. The combination of phylogenetic analysis, DNA–DNA hybridization data, phenotypic characteristics and chemotaxonomic differences supported the view that strain JSM 061001T represents a novel species of the genus Pigmentiphaga, for which the name Pigmentiphaga litoralis sp. nov. is proposed. The type strain is JSM 061001T (=CCTCC AA207034T=KCTC 22165T).

Two floc-forming, nitrogen-fixing bacteria, strains EMB43T and EMB61, obtained from activated sludge of a domestic wastewater treatment plant in Korea, were characterized. The two strains were very closely related, sharing 99.7 % 16S rRNA gene sequence similarity and showing a level of DNA–DNA relatedness of 93 %, which suggests that they represent members of a single species. Phylogenetic analysis based on 16S rRNA gene sequences showed that the two novel isolates formed a distinct phyletic lineage within the genus Zoogloea and were related most closely to Zoogloea resiniphila DhA-35T and Zoogloea oryzae A-7T, with sequence similarities of 97.2 %. Levels of DNA–DNA relatedness between strain EMB43T and Z. resiniphila DhA-35T and Z. oryzae A-7T were 12.8 and 7.4 %, respectively. Cells of strains EMB43T and EMB61 were facultatively aerobic, rod-shaped, Gram-negative and motile by means of a polar flagellum. The strains grew at temperatures of 15–40 °C (optimum: 25–30 °C) and at pH 6.0–9.0 (optimum: pH 6.5–7.5). The predominant fatty acids were C16 : 0, C10 : 0 3-OH and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH), and the predominant polar lipid was phosphatidylethanolamine. The genomic DNA G+C content was 64.9–65.0 mol% and the major isoprenoid quinone was ubiquinone-8 (Q-8). On the basis of phenotypic, chemotaxonomic and molecular data, the isolates are considered to represent a novel species of the genus Zoogloea, for which the name Zoogloea caeni sp. nov. is proposed. The type strain is EMB43T (=KCTC 22084T=DSM 19389T).

A bright pink to red-coloured, phototropic, purple non-sulfur bacterium, designated strain TUT3530T, was isolated from pond water. Cells of the novel isolate were found to be Gram-negative, motile, budding rods. Cell extracts from phototrophically grown cultures had absorption maxima at 378, 482, 512, 550, 590, 800 and 850 nm, indicating the presence of bacteriochlorophyll a and carotenoids of the spirilloxanthin series. The intracytoplasmic membrane system was of the lamellar type. Anaerobic photo-organotrophy with simple organic acids such as pyruvate was the preferred mode of growth. Aerobic growth at full atmospheric oxygen tension and anaerobic denitrifying growth in darkness were also possible. Photolithotrophic growth occurred with thiosulfate, but not with sulfide or hydrogen, as the electron donor. No growth factors were required. The major whole-cell fatty acid was C18 : 1 ω7c. The major quinones were ubiquinone-10 and rhodoquinone-10. A phylogenetic analysis based on 16S rRNA gene sequences and studies involving DNA–DNA hybridization demonstrated that strain TUT3530T occupies a distinct taxonomic position within the genus Rhodoplanes. On the basis of these data, strain TUT3530T represents a novel species of the genus Rhodoplanes, for which the name Rhodoplanes serenus sp. nov. is proposed. The type strain is TUT3530T (=DSM 18633T=NBRC 102049T).

A bacterial strain, designated MS4T, was isolated from soil in the Ryukyu Archipelago, Japan. The bacterium grew with 3-methyl sulfolane as sole sulfur source. Phylogenetic analysis based on 16S rRNA gene sequences suggested that strain MS4T belonged to the genus Shinella; it was closely related to the type strains of Shinella granuli and Shinella zoogloeoides (16S rRNA gene sequence similarities of 98.2 and 96.7 %, respectively). Strain MS4T was a Gram-negative, non-motile, rod-shaped, aerobic bacterium. The major respiratory quinone was ubiquinone-10 and the predominant cellular fatty acid was C18 : 1 ω7c. The DNA G+C content was 66.4 mol%. Based on phylogenetic and phenotypic traits, it was concluded that the organism represents a novel species in the genus Shinella for which the name Shinella yambaruensis sp. nov. is proposed; the type strain is MS4T (=NBRC 102122T=DSM 18801T).

A Gram-negative, aerobic, neutrophilic, rod-shaped bacterium, designated strain CN85T, was isolated from a sediment sample collected from the East China Sea and was subjected to a polyphasic taxonomic characterization. This isolate grew in the presence of 0.5–6.0 % (w/v) NaCl and at 20–40 °C; optimum growth was observed with 3 % (w/v) NaCl and at 35 °C. Chemotaxonomic analysis showed that Q-8 was the predominant respiratory quinone and that iso-C15 : 0, iso-C11 : 0 3-OH, iso-C17 : 1 ω9c, iso-C17 : 0, iso-C11 : 0 and C16 : 0 were the major fatty acids. The G+C content of the genomic DNA was 57.8 mol%. On the basis of 16S rRNA gene sequence analysis, the isolate was affiliated to the genus Microbulbifer. Strain CN85T exhibited most phylogenetic affinity with respect to the type strain of Microbulbifer maritimus (97.0 % sequence similarity) and showed less than 97 % sequence similarity with respect to other described Microbulbifer species with known 16S rRNA gene sequences. The DNA–DNA hybridization between strain CN85T and M. maritimus JCM 12187T was 44 %. On the basis of phenotypic and genotypic data, strain CN85T represents a novel species of the genus Microbulbifer, for which the name Microbulbifer donghaiensis sp. nov. is proposed. The type strain is CN85T (=CGMCC 1.7063T =JCM 15145T).

A Gram-negative, heterotrophic, aerobic, pale orange-pigmented, non-endospore-forming and motile bacterial strain, designated strain SP8T, was isolated from a salty water sample from the solar salterns of Santa Pola, located on the Mediterranean coast of Spain. The strain grew optimally at 37 °C, pH 6.5 and in the presence of 10 % NaCl. A polyphasic taxonomic study was conducted in order to characterize the strain in detail. Phylogenetic analyses based on 16S rRNA gene sequence comparisons indicated that strain SP8T clustered within the branch constituted by species of the genus Halomonas. The closest phylogenetic neighbours of strain SP8T were Halomonas muralis LMG 20969T (96.0 % sequence similarity), Halomonas pantelleriensis AAPT (95.9 %) and Halomonas campaniensis 5AGT (95.8 %). Phenotypic features, the fatty acid profile and the DNA G+C content of the novel strain further supported its placement in the genus Halomonas. On the basis of phenotypic, chemotaxonomic and phylogenetic distinctiveness, it is suggested that strain SP8T represents a novel species for which the name Halomonas ilicicola sp. nov. is proposed. The type strain is SP8T (=CECT 7331T=CCM 7522T=DSM 19980T).

Strain D24TNT was enriched and isolated from sediment collected from a tar oil-contaminated aquifer at a former gasworks site located in Duesseldorf-Flingern, Germany. Cells of strain D24TNT were rod-shaped, non-spore-forming and stained Gram-negative. Thiosulfate was used as an electron donor. The organism was obligately chemolithoautotrophic and facultatively anaerobic, and grew with either oxygen or nitrate as electron acceptor. Growth was observed at pH values between 6.3 and 8.7 and at temperatures of −2 to 30 °C; optimum growth occurred at pH 7.5–8.3 and 25–30 °C. The DNA G+C content was 61.5 mol%. On the basis of the 16S rRNA gene sequence analysis, strain D24TNT clustered in the Betaproteobacteria and was most closely related to Thiobacillus denitrificans (97.6 %) and Thiobacillus thioparus (97.5 %). Based on the phenotypic, chemotaxonomic and phylogenetic data, strain D24TNT represents a novel species of the genus Thiobacillus, for which the name Thiobacillus thiophilus sp. nov. is proposed. The type strain is D24TNT (=DSM 19892T=JCM 15047T).

A Gram-negative, rod-shaped, strictly aerobic bacterium, designated strain CL-SK30T, was isolated from a culture of the marine ciliate Myrionecta rubra. 16S rRNA gene sequence analysis revealed that strain CL-SK30T was most closely related to Cucumibacter marinus (92.0 % similarity) and next to the type strains of species of the genus Devosia (89.8–91.3 % similarities) in the family Hyphomicrobiaceae. Phylogenetic analyses of the 16S rRNA gene sequences showed that strain CL-SK30T formed a robust clade together with C. marinus, but the sequence divergence value of 8 % between them indicated that the novel bacterium represented a distinct lineage. Strain CL-SK30T grew optimally in the presence of 2–5 % sea salts at 30–35 °C and pH 7.2–8.0. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, two unidentified glycolipids, an unidentified phospholipid and an unidentified lipid. Ubiquinone 10 was the major quinone. The DNA G+C content was 52.7 mol%. Based on its phenotypic, chemotaxonomic and phylogenetic characteristics, strain CL-SK30T represents a novel genus and species of the family Hyphomicrobiaceae, for which the name Maritalea myrionectae gen. nov., sp. nov. is proposed. The type strain is CL-SK30T (=KCCM 90060T=DSM 19524T).

Here, we report on two novel sexual basidiomycetous red yeast species of the genus Cystofilobasidium. Cystofilobasidium lacus-mascardii sp. nov. is based on sexually compatible strains isolated from Lake Mascardi, an ultraoligotrophic lake in north-western Patagonia, Argentina. Following the discovery of the first isolate of this species, additional (sexually compatible) strains were isolated using a selective medium containing erythritol as the sole source of carbon. The second novel species corresponds to the sexual state of Cryptococcus macerans. In spite of accounts over the last 20 years of sexually compatible strains of this species, the complete life has never been observed. We provide evidence of a Cystofilobasidium-like basidial stage with teliospores and slender holobasidia, based on the study of self-fertile (homothallic) and self-sterile (heterothallic) isolates of Cryptococcus macerans. A revised molecular phylogeny of the genus Cystofilobasidium is presented and the most salient features of Cystofilobasidium lacus-mascardii sp. nov. (type strain CBS 10642T =PYCC 5819T =CRUB 1046T) and Cystofilobasidium macerans sp. nov. (type strain CBS 10757T) are discussed and compared with those of the remaining species in the genus. Information on additional Patagonian isolates belonging to the Cystofilobasidiales is also included in this report.

Cryptococcus terrestris sp. nov. (Basidiomycota, Agaricomycotina, Tremellomycetes, Tremellales) is typified by CJDX4 Y23T (=CBS 10810T =NRRL Y-48451T), isolated from forest soil in Oklahoma, USA. This species is most readily identified by the sequence of the D1/D2 domain region of the 26S rDNA and ITS (internal transcribed spacer) region. Additional strains from Oklahoma (C107DX4 Y11 =CBS 10813 =NRRL Y-48452) and Brazil (Ep11c =CBS 10812 =NRRL Y-48454; 56e =CBS 10811 =NRRL Y-48453) either had identical sequences or differed minimally. C. terrestris differs physiologically from the most closely related species, Cryptococcus flavescens, by the weak or delayed assimilation of ribose and salicin, and differs from Cryptococcus aureus by the utilization of nitrate and nitrite and growth in vitamin-free medium.

The family Halobacteriaceae currently contains 96 species whose names have been validly published, classified in 27 genera (as of September 2008). In recent years, many novel species have been added to the established genera but, in many cases, one or more properties of the novel species do not agree with the published descriptions of the genera. Authors have often failed to provide emended genus descriptions when necessary. Following discussions of the International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Halobacteriaceae, we here propose emended descriptions of the genera Halobacterium, Haloarcula, Halococcus, Haloferax, Halorubrum, Haloterrigena, Natrialba, Halobiforma and Natronorubrum.