- Volume 61, Issue 12, 2011

A Gram-negative, oxidase- and catalase-positive, moderately halophilic strain, designated YCSA40T, was isolated from sediment of Daqiao saltern in Qingdao, on the east coast of China. Growth occurred at 10–45 °C, at pH 5–9 and with 1–15 % NaCl. Strain YCSA40T showed the highest 16S rRNA gene sequence similarity to Marinobacter segnicrescens SS011B1-4T (97 %) and M. gudaonensis SL014B61AT (96.9 %) and 16S rRNA gene sequence phylogenetic analysis assigned the isolate to the genus Marinobacter. Strain YCSA40T contained C18 : 1ω9c (34.8 %), C16 : 0 (11.6 %), C19 : 0 cyclo ω10c/C19 : 1ω6c (10.5 %), C16 : 1ω9c (8.4 %), C17 : 0 (6.3 %) and C12 : 0 3-OH (5.8 %) as the predominant fatty acids. The DNA G+C content was 60.8 mol% and the major ubiquinone was Q-9. These chemotaxonomic characters were all consistent with membership of the genus Marinobacter. DNA–DNA relatedness between the isolate and M. segnicrescens CGMCC 1.6489T, M. gudaonensis CGMCC 1.6294T and other type strains of species of the genus Marinobacter was ≤30 %. On the basis of the aforementioned data, it was concluded that strain YCSA40T represents a novel species of the genus Marinobacter, for which the name Marinobacter daqiaonensis sp. nov. is proposed. The type strain is YCSA40T ( = CGMCC 1.9167T  = NCCB 100308T  = LMG 25365T).

Two novel vibrio isolates (R-40492T and R-40493T) originating from the zoanthid Palythoa caribaeorum in Brazil in 2005 were taxonomically characterized by means of a polyphasic approach comprising multilocus sequence analysis (MLSA), DNA–DNA hybridization (DDH), ΔT m analysis and phenotypic characterization. Phylogenetic analysis based on 16S rRNA gene sequences showed that R-40492T and R-40493T fell within the genus Vibrio and were most closely related to each other with 99 % similarity; similarities of these two novel isolates towards Vibrio neptunius LMG 20536T, Vibrio coralliilyticus LMG 20984T, Vibrio nigripulchritudo LMG 3896T, Vibrio sinaloensis LMG 25238T and Vibrio brasiliensis LMG 20546T varied between 97.1 and 98.5 %. DDH experiments showed that the two isolates had less than 15 % relatedness to the phylogenetically most closely related Vibrio species. R-40492T and R-40493T had 55–57 % relatedness to each other. The ΔTm between R-40492T and R-40493T was 6.12 °C. In addition, MLSA of concatenated sequences (16S rRNA, ftsZ, gyrB, recA, rpoA, topA, pyrH and mreB; 6035 bp in length) showed that the two novel isolates formed a separate branch with less than 92 % concatenated gene sequence similarity towards known species of vibrios. Two novel species are proposed to accommodate these novel isolates, namely Vibrio variabilis sp. nov. (type strain, R-40492T = LMG 25438T = CAIM 1454T) and Vibrio maritimus sp. nov. (type strain, R-40493T = LMG 25439T = CAIM 1455T).

Phenotypic and phylogenetic studies were performed on eight Gram-negative-staining, rod-shaped bacteria isolated from seals. Biochemical and physiological studies showed identical profiles for all of the isolates and indicated that they were related to the family Pasteurellaceae. 16S rRNA gene sequencing demonstrated that the organism represented a distinct cluster with two sublines within the family Pasteurellaceae with <96 % sequence similarity to any recognized species. Multilocus sequence analysis (MLSA) including rpoB, infB and recN genes further confirmed these findings with the eight isolates forming a genus-like cluster with two branches. Genome relatedness as deduced from recN gene sequences suggested that the isolates represented a new genus with two species. On the basis of the results of the phylogenetic analysis and phenotypic criteria, it is proposed that these bacteria from seals are classified as Bisgaardia hudsonensis gen. nov., sp. nov. (the type species) and Bisgaardia genomospecies 1. The G+C content of the DNA was 39.5 mol%. The type strain of Bisgaardia hudsonensis gen. nov., sp. nov. is M327/99/2T ( = CCUG 43067T = NCTC 13475T = 98-D-690BT) and the reference strain of Bisgaardia genomospecies 1 is M1765/96/5 ( = CCUG 59551 = NCTC 13474).

We analysed the taxonomic position of the genus Listonella based on phylogenetic, genomic and phenotypic data. The species of the genus Listonella were nested within the genus Vibrio according to the 16S rRNA gene sequence-based phylogenetic tree. The closest neighbour of Vibrio (Listonella) anguillarum strains LMG 4437T and ATCC 68554 ( = strain 775) was Vibrio ordalii LMG 13544T, with more than 99.5 % 16S rRNA gene sequence similarity. Furthermore, Vibrio (Listonella) pelagius is highly related to Vibrio splendidus. According to average amino acid identity (AAI), multilocus sequence analysis (MLSA) and Karlin genome signature, the closest neighbour of L. anguillarum ATCC 68554 is V. ordalii LMG 13544T, with 95 % AAI, 98 % MLSA and 5 in Karlin. V. anguillarum ATCC 68554 and Vibrio cholerae N16961 had 77 % similarity in AAI, 85 % in MLSA and 14 in the Karlin signature. Phenotypic analyses of previously published data for V. (L.) anguillarum and V. (L.) pelagius revealed that the genus Listonella is extremely similar to the genus Vibrio. V. ordalii and L. anguillarum strains yielded up to 67 % DNA–DNA hybridization. There are only a few phenotypic features that might be used to discriminate these two species: L. anguillarum is positive for the Voges–Proskauer reaction, citrate utilization, starch hydrolysis, lipase activity and acid production from glycerol, sorbitol and trehalose, whereas V. ordalii is negative for these traits. We suggest that the genus Listonella is a later heterotypic synonym of the genus Vibrio and propose to use the names Vibrio anguillarum and Vibrio pelagius in place of Listonella anguillarum and Listonella pelagia, respectively.

A novel gammaproteobacterium, designated LnR5-47T, was isolated from soil of a ginseng field in Liaoning province, China. The isolate was a Gram-negative, aerobic, non-motile, non-spore-forming rod. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain LnR5-47T belonged to the genus Rhodanobacter. The isolate was most closely related to Rhodanobacter ginsengisoli GR17-7T, Rhodanobacter terrae GP18-1T, Dyella ginsengisoli Gsoil 3046T, Rhodanobacter soli DCY45T, Dyella soli JS12-10T and Dyella japonica IAM 15069T (98.0, 97.9, 97.7, 97.3, 97.2 and 97.1 % 16S rRNA gene sequence similarity, respectively). Chemotaxonomic data (Q-8 as the predominant ubiquinone, and iso-C16 : 0, iso-C17 : 1ω9c and iso-C15 : 0 as the major fatty acids) also supported the affiliation of strain LnR5-47T with the genus Rhodanobacter. However, DNA–DNA relatedness between strain LnR5-47T and its closest phylogenetic neighbours was <25.8 %. Moreover, physiological and biochemical tests phenotypically differentiated the isolate from other members of the genus Rhodanobacter. Therefore, strain LnR5-47T represents a novel species, for which the name Rhodanobacter panaciterrae sp. nov. is proposed; the type strain is LnR5-47T ( = KACC 12826T = KCTC 22232T = LMG 24460T).

A novel phytoplasma, designated strain SoyST1c1, associated with a newly emerging disease in soybean (Glycine max), known as soybean stunt (SoyST), was found in 2002 in a soybean plantation in Alajuela Province, Costa Rica. The same phytoplasma, or a very closely related strain, also infected sweet pepper (Capsicum annuum) with purple vein syndrome (SwPPV) and passion fruit vine (Passiflora edulis) with bud proliferation disease (PasFBP) in the same region. Sequence analysis of cloned 16S rRNA gene sequences (GenBank accession nos FJ226068–FJ226073 and HQ225624–HQ225635) indicated that all three affected plants were infected by phytoplasmas that shared <97.5 % sequence similarity with previously described phytoplasmas. The SoyST-causing phytoplasma represents a new taxon, most closely related to phytoplasma group 16SrI and 16SrXII strains. Virtual RFLP analysis indicated that the SoyST-causing phytoplasma and its closely related strains represent a novel 16Sr group, designated 16SrXXXI. Phylogenetic analysis of 16S rRNA gene sequences from the new phytoplasma strains, those previously described as ‘Candidatus Phytoplasma spp.’ and other distinct, as yet unnamed, phytoplasmas indicated that the SoyST-causing phytoplasma represents a distinct lineage within the aster yellows/stolbur branch on the phylogenetic tree. On the basis of its unique 16S rRNA gene sequence and biological properties, strain SoyST1c1 represents a novel taxon, for which the name ‘Candidatus Phytoplasma costaricanum’ is proposed with SoyST1c1 as the reference strain.

As part of a study of the diversity of planctomycetes, two novel strains, designated OJF2T and OJF8, were isolated from the sediments of a freshwater aquarium. The organisms were chemoheterotrophic, spherical and pink-pigmented, had an optimum growth temperature of about 30–35 °C and an optimum pH for growth of around 7.5–8.5. The predominant fatty acids were C18 : 1ω9c and C16 : 0. The two strains were able to assimilate several sugars and organic acids. 16S rRNA gene sequence analysis confirmed the affiliation of these organisms to the phylum ‘Planctomycetes’; they showed highest similarity to the type strains of Singulisphaera acidiphila (92.4 %) and Isosphaera pallida (91.9 %). On the basis of physiological, biochemical and chemotaxonomic characteristics, strains OJF2T and OJF8 are considered to represent a novel species of a new genus of the order Planctomycetales, for which the name Aquisphaera giovannonii gen. nov., sp. nov. is proposed. The type strain of Aquisphaera giovannonii is OJF2T ( = CECT 7510T  = DSM 22561T).

Caves have generally been found to host phototrophic micro-organisms from various taxonomic groups, with cyanobacteria comprising an important group that have adapted to these stable and highly specific environments. A polyphasic study based on aspects of classical morphology and molecular data revealed two new monospecific genera from fresh material of Greek and Spanish caves. Both taxa are characterized by obligatory true branching (T-type, V-type and false branching), the presence of heterocysts, and reproduction by hormocysts and akinetes. They shared some similarities in their morphological characteristics as revealed by light, scanning electron and transmission electron microscopy, but phylogenetic analysis based on 16S rRNA gene sequences showed that the two phylotypes were different (89.8 % similarity); this represents an example of shared morphology in genetically different strains of cave-adapted species. Phenotypic and genetic traits strongly support classification of the phylotypes as independent taxa in the order Stigonematales (the most differentiated and complicated group of cyanobacteria), family Loriellaceae Geitl 1925. Hence, the names Iphinoe spelaeobios Lamprinou and Pantazidou gen. nov., sp. nov. and Loriellopsis cavernicola Hernández-Mariné and Canals gen. nov., sp. nov. are proposed.

An obligate piezophilic anaerobic hyperthermophilic archaeon, designated strain CH1T, was isolated from a hydrothermal vent site named ‘Ashadze’, which is located on the Mid-Atlantic Ridge at a depth of 4100 m. Enrichment and isolation of the strain were carried out at 95 °C under a hydrostatic pressure of 42 MPa. Cells of strain CH1T were highly motile irregular cocci with a diameter of ~1–1.5 µm. Growth was recorded at 80–108 °C (optimum 98 °C) and at pressures of 20–120 MPa (optimum 52 MPa). No growth was observed under atmospheric pressures at 60–110 °C. Growth was observed at pH 6.0–9.5 (optimum 7.5–8.0) and in 2.5–5.5 % (w/v) NaCl (optimum 3.5 %). Strain CH1T was strictly anaerobic and grew on complex proteinaceous substrates, such as yeast extract, Peptone, and casein, as well as on sucrose, starch, chitin, pyruvate, acetate and glycerol without electron acceptors. The G+C content of the genomic DNA was 49.0±0.5 mol%. Analysis of 16S rRNA gene sequences revealed that strain CH1T belongs to the genus Pyrococcus. Based on its physiological properties and similarity levels between ribosomal proteins, strain CH1T represents a novel species, for which the name Pyrococcus yayanosii sp. nov. is proposed. The type strain is CH1T ( = JCM 16557). This strain is also available by request from the Souchothèque de Bretagne (catalogue LMBE) culture collection (collection no. 3310).

Two mesophilic methanogenic strains, designated TS-2T and GHT, were isolated from sediments of Tuosu lake and Gahai lake, respectively, in the Qaidam basin, Qinghai province, China. Cells of both isolates were rods (about 0.3–0.5×2–5 µm) with blunt rounded ends and Gram-staining-positive. Strain TS-2T was motile with one or two polar flagella and used only H2/CO2 for growth and methanogenesis. Strain GHT was non-motile, used both H2/CO2 and formate and displayed a variable cell arrangement depending on the substrate: long chains when growing in formate (50 mM) or under high pressure H2 and single cells under low pressure H2. Phylogenetic analysis based on 16S rRNA gene sequences placed the two isolates in the genus Methanobacterium. Strain TS-2T was most closely related to Methanobacterium alcaliphilum NBRC 105226T (96 % 16S rRNA gene sequence similarity). Phylogenetic analysis based on the alpha subunit of methyl-coenzyme M reductase also supported the affiliation of the two isolates with the genus Methanobacterium. DNA–DNA relatedness between the isolates and M. alcaliphilum DSM 3387T was 39–53 %. Hence we propose two novel species, Methanobacterium movens sp. nov. (type strain TS-2T = AS 1.5093T = JCM 15415T) and Methanobacterium flexile sp. nov. (type strain GHT = AS 1.5092T = JCM 15416T).

A novel, Gram-positive, rod-shaped, motile, endospore-forming, halophilic bacterial strain, J18T, was isolated from a traditional salt-fermented seafood made of gizzard shad in Korea. Colonies were convex, cream-coloured and 1.0–2.0 mm in diameter after incubation for 3 days on marine agar. Growth occurred at pH 7.0–11.0 (optimum, pH 10.0), at 4–40 °C (optimum, 37 °C) and in the presence of 0–30 % NaCl (optimum, 9–10 %). On the basis of 16S rRNA gene sequence analysis, strain J18T was related most closely to Virgibacillus byunsanensis ISL-24T (96.3 % similarity), Virgibacillus carmonensis LMG 20964T (96.2 %), Virgibacillus halodenitrificans DSM 10037T (96.0 %), Virgibacillus arcticus Hal 1T (95.5 %) and Virgibacillus necropolis LMG 19488T (95.5 %). The major fatty acids were anteiso-C15 : 0 and anteiso-C17 : 0. The DNA G+C content of strain J18T was 37.0 mol%. The cell-wall peptidoglycan was of the meso-diaminopimelic acid type. The major quinone was menaquinone 7 (MK-7). Based on phenotypic, chemotaxonomic and phylogenetic data, strain J18T is considered to represent a novel species of the genus Virgibacillus, for which the name Virgibacillus alimentarius sp. nov. is proposed. The type strain is J18T ( = KACC 14624T  = JCM 16994T).

A novel Gram-staining-positive, moderately halophilic, facultatively alkaliphilic, non-motile, catalase-positive, oxidase-negative, endospore-forming, facultatively anaerobic rod, designated JSM 076093T, was isolated from a sea urchin (Hemicentrotus pulcherrimus) collected from Naozhou Island in the South China Sea. Growth occurred with 0.5–25 % (w/v) NaCl (optimum 5–8 %) and at pH 6.0–10.5 (optimum pH 8.0) and 5–40 °C (optimum 30–35 °C). meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. The predominant respiratory quinone was menaquinone 7 and the polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and one unidentified phospholipid. The major cellular fatty acids (>10 % of the total) were anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and iso-C14 : 0. The genomic DNA G+C content was 38.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain JSM 076093T belonged to the genus Bacillus and was related most closely to Bacillus hwajinpoensis SW-72T (99.1 % 16S rRNA gene sequence similarity) and Bacillus algicola KMM 3737T (97.3 %). The combination of results from the phylogenetic analysis, DNA–DNA hybridization and phenotypic and chemotaxonomic characterization supported the conclusion that strain JSM 076093T represents a novel species of the genus Bacillus, for which the name Bacillus hemicentroti sp. nov. is proposed, with JSM 076093T ( = DSM 23007T = KCTC 13710T) as the type strain.

The taxonomic status of Paralactobacillus selangorensis is described and, based on evidence presented, transfer of the species to the genus Lactobacillus with the name Lactobacillus selangorensis comb. nov. is proposed. This reclassification is supported by multilocus sequence analysis of the 16S rRNA gene and portions of the cpn60, pheS and rpoA genes. Mode of cell division and existing phenotypic information also show that P. selangorensis cannot be differentiated from the genus Lactobacillus. The type strain of Lactobacillus selangorensis comb. nov. is ATCC BAA-66T ( = LMG 17710T  = CIP 106482T).

Two novel strains of marine lactic acid bacteria, isolated from decaying marine algae collected from a subtropical area of Japan, are described. The isolates, designated O24-2T and O25-2, were Gram-positive, non-sporulating and non-motile. They lacked catalase and quinones. Under anaerobic cultivation conditions, lactate was produced from glucose with the production of formate, acetate and ethanol in a molar ratio of approximately 2 : 1 : 1. Under aerobic cultivation conditions, acetate and lactate were produced from carbohydrates and related compounds. The isolates were slightly halophilic, highly halotolerant and alkaliphilic. They were able to grow in 0–17.0 % (w/v) NaCl, with optimum growth of strains O24-2T and O25-2 at 1.0–3.0 and 1.0–2.0 % (w/v) NaCl, respectively. Growth of strain O24-2T was observed at pH 7.5–9.5, with optimum growth at pH 8.0–8.5. Comparative 16S rRNA gene sequence analysis revealed that the isolates occupied a phylogenetic position within the genus Alkalibacterium, showing highest similarity (99.6 %) to Alkalibacterium putridalgicola T129-2-1T. Although sequence similarity was high, the DNA–DNA relatedness value between strain O24-2T and A. putridalgicola T129-2-1T was 27 %, indicating that they are members of distinct species. The DNA G+C contents of O24-2T and O25-2 were 43.7 and 44.4 mol%, respectively, and DNA–DNA relatedness between the isolates was 89 %. The cell-wall peptidoglycan was type A4β, Orn-d-Asp. The major cellular fatty acid components were C14 : 0, C16 : 0 and C16 : 1ω9c. Based on phenotypic characteristics and genetic distinctiveness, the isolates were classified as representatives of a novel species within the genus Alkalibacterium, for which the name Alkalibacterium subtropicum sp. nov. is proposed; the type strain is O24-2T ( = DSM 23664T = NBRC 107172T).

A Gram-negative, non-motile, non-sporulating bacterial strain, designated LYX05T, was isolated from coastal sediment of Qingdao, China, on the coast of the Yellow Sea. Strain LYX05T was aerobic and heterotrophic. The strain grew optimally at 37 °C and pH 7.5 and in the presence of 2 % (w/v) NaCl. Colonies were 1–2 mm in diameter, circular, reddish orange and shiny with entire edges on marine agar medium. Cells were rods (0.3–0.5 µm wide and 0.8–1.6 µm long). The dominant fatty acids were iso-C15 : 0 (40.82 %) and C16 : 0 (10.45 %). The DNA G+C content was 42.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain LYX05T was phylogenetically related to the members of the genus Algoriphagus and the closest relative was Algoriphagus hitonicola 7-UAHT (95.8 % 16S rRNA gene sequence similarity). On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain LYX05T was considered to represent a novel species of the genus Algoriphagus, for which the name Algoriphagus faecimaris sp. nov. is proposed. The type strain is LYX05T ( = JCM 16561T  = DSM 23095T  = LMG 25474T).

Two bacterial strains, 01-96T and 15-51T, isolated from rhizosphere soil of Chinese cabbage (Brassica campestris) were characterized by using a polyphasic approach. 16S rRNA gene sequence analysis showed that strain 01-96T was phylogenetically related most closely to Pedobacter suwonensis 15-52T and Pedobacter roseus CL-GP80T (96.7 and 96.7 % similarity, respectively), and strain 15-51T to Pedobacter borealis G-1T and P. suwonensis 15-52T (97.2 and 97.1 %, respectively). However, levels of DNA–DNA relatedness between strain 15-51T and P. borealis KACC 14287T and P. suwonensis KACC 11317T were low (<50 %). The G+C content of the genomic DNA was 37.8 mol% for strain 01-96T and 38.6 mol% for strain 15-51T. The major fatty acids of the two strains were iso-C17 : 0 3-OH, iso-C15 : 0 and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c). The results of DNA–DNA hybridization and phenotypic data showed that strains 01-96T and 15-51T could be distinguished from their closest phylogenetic relatives, and that these strains represented two novel species of the genus Pedobacter, for which the names Pedobacter rhizosphaerae sp. nov. (type strain 01-96T  = KACC 14938T  = NBRC 107690T) and Pedobacter soli sp. nov. (type strain 15-51T  = KACC 14939T  = NBRC 107691T) are proposed.

Three novel aerobic, elliptic bacteria, designated DQHS4T, DQHS8 and DQHS15, were isolated from sediment of a seashore pond for sea cucumber culture in Jimo, Qingdao, on the east coast of China. Cells were Gram-, oxidase- and catalase-negative. All three strains grew at 15–42 °C, pH 5–9 and NaCl concentrations between 0.5 and 10 %. DNA–DNA hybridization experiments revealed high (>85 %) relatedness among the three novel isolates and suggested that the strains constitute a single species. Comparative 16S rRNA gene sequence analysis indicated that these bacteria had less than 90 % similarity to all described species of the phylum Bacteroidetes; the closest relative of the three isolates was Prolixibacter bellariivorans F2T, sharing only 89.6 % sequence similarity. The major cellular fatty acids were iso-C17 : 0 3-OH (19.8–20.0 %), iso-C15 : 0 (16.9–17.3 %), anteiso-C17 : 1 B and/or iso-C17 : 1 I (7.4–8.7 %), C17 : 0 2-OH (8.4 %), anteiso-C15 : 0 (8.2–8.6 %) and C17 : 1ω6c (5.6–6.0 %). The major respiratory quinone was menaquinone-7 (MK-7) and the DNA G+C content was 41.8–43.5 mol%. Based on the distinct phylogenetic position and the combination of genotypic, phenotypic and chemotaxonomic characteristics, these three strains were considered to represent a novel species of a new genus in the phylum Bacteroidetes, for which the name Sunxiuqinia elliptica gen. nov., sp. nov. is proposed. The type strain of Sunxiuqinia elliptica is DQHS4T ( = CGMCC 1.9156T  = NCCB 100301T  = LMG 25367T).

Three strains were isolated from the nostrils of a koala and the surrounding environment in a Japanese zoological park. Sequence analysis of the nuclear rDNA internal transcribed spacer (ITS) region and the large subunit rDNA D1/D2 domains in addition to physiological and morphological studies indicated that the isolates represent a single novel species belonging to the basidiomycetous genus Cryptococcus (Tremellales, Tremellomycetes, Agaricomycotina). Phylogenetic analysis based on D1/D2 and ITS regions revealed that the novel species belongs to the Fuciformis clade. The name Cryptococcus yokohamensis sp. nov. is proposed to accommodate these isolates with strain JCM 16989T ( = TIMM 10001T = CBS 11776T = DSM 23671T) as the type strain.

A single strain, CLQCA-10-114T, representing a novel yeast species belonging to the genus Saturnispora was isolated from the fruit of an unidentified species of bramble (Rubus sp.), collected from the Maquipucuna cloud forest reserve, near Quito, in Ecuador. Sequence analyses of the D1/D2 domains of the large-subunit rRNA gene and ribosomal internal transcribed spacer region indicated that the novel species is most closely related to the recently described species Saturnispora gosingensis, isolated from the fruiting body of a mushroom collected in Taiwan, and Saturnispora hagleri, a Drosophila-associated yeast found in Brazil. The name Saturnispora quitensis sp. nov. is proposed to accommodate this strain; the type strain is CLQCA-10-114T ( = CBS 12184T = NCYC 3744T).