- Volume 67, Issue 12, 2017
Volume 67, Issue 12, 2017
- New Taxa
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- Proteobacteria
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Sphingomonas difficilis sp. nov., a difficultly cultivable bacterium that grows on solid but not in liquid medium, isolated from an abandoned lead–zinc mine
More LessA difficult to cultivate bacterial strain, designated 1PNM-26T, isolated from a lead–zinc mine, was investigated using a polyphasic taxonomic approach. The strain was able to grow on solid medium but not in liquid medium. Cells were Gram-reaction-negative, aerobic, non-spore-forming, non-motile and rod-shaped. It showed positive reactions for catalase and oxidase and hydrolysis of aesculin. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that strain 1PNM-26T represents a member of the genus Sphingomonas and forms a stable cluster with Sphingomonas morindae KCTC 42183T, Sphingomonas polyaromaticivorans JCM 16711T and Sphingomonas oligoaromativorans NBRC 105508T. The major fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. C14 : 0 2-OH was present as the major hydroxyl fatty acid. The major polyamine was sym-homospermidine, and ubiquinone 10 (Q-10) was the predominant respiratory quinone. The genomic DNA G+C content of strain 1PNM-26T was determined to be 66.3±0.3 mol%, and the polar lipids consisted of sphingoglycolipid, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidyldimethylethanolamine, phosphatidylmonomethylethanolamine, an unidentified glycolipid, three unidentified aminolipids and three unidentified lipids. The phenotypic, phylogenetic and chemotaxonomic results strongly supported the hypothesis that strain 1PNM-26T represents a novel species of the genus Sphingomonas , for which the name Sphingomonas difficilis sp. nov. is proposed. The type strain is 1PNM-26T (=GDMCC 1.664T=KCTC 42758T=DSM 27573T).
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Genome-based reclassification of Sphingopyxis ummariensis as a later heterotypic synonym of Sphingopyxis terrae, with the descriptions of Sphingopyxis terrae subsp. terrae subsp. nov. and Sphingopyxis terrae subsp. ummariensis subsp. nov.
More LessDuring the phylogenetic analysis of the genus Sphingopyxis , we found that an incorrect 16S rRNA gene sequence (accession number: D13727) was provided in the original description of Sphingopyxisterrae NBRC 15098T and the wrong sequence has been adopted and used for a long time. It should be replaced by the new correct 16S rRNA gene sequence (accession number: MF618306). The new sequence shared the highest similarity (99.8 %) with that of Sphingopyxisummariensis DSM 24316T. The average nucleotide identity (ANI) (96.87 %) and digital DNA–DNA hybridization (75.30 %) values based on the whole-genome sequences and almost the same phenotypic and chemotaxonomic characteristics of the two type strains revealed that Sphingopyxis ummariensis should be a later heterotypic synonym of Sphingopyxis terrae . However, the distinctions in the genome size, hydrolysis of aesculin, α-glucosidase and particularly the fatty acid profiles strongly support that strain DSM 24316T should be considered to represent a novel subspecies of Sphingopyxis terrae. Two novel subspecies are therefore proposed, namely Sphingopyxisterrae subsp. terrae subsp. nov. (type strain E-1-AT=NBRC 15098T=JCM 10195T=DSM 8831T=LMG 17326T) and Sphingopyxisterrae subsp. ummariensis subsp. nov. (type strain UI2T=DSM 24316T=CCM 7428T=MTCC 8591T).
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- Eukaryotic Micro-organisms
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Cyberlindnera xishuangbannaensis f.a., sp. nov., a yeast isolated from rotting wood
More LessThree strains representing a novel species of yeast were isolated from samples of rotting wood collected from Xishuangbanna Tropical Rainforest in Yunnan Province, PR China. Phylogenetic analysis based on the concatenated sequences of the internal transcribed spacer (ITS) region and the D1/D2 domains of the large subunit (LSU) rRNA gene revealed that the novel species is a member of the genus Cyberlindnera, although the formation of ascospores was not observed. The novel species was related most closely to the type strain of the species Candida pattaniensis, but they had a 0.5 % sequence divergence (3 substitutions, 0 gap) in the D1/D2 domain and a 5.4 % sequence divergence (21 substitutions, 10 gaps) in the ITS region. The novel species could also be differentiated from the closely related species by some biochemical and physiological characteristics. The species name Cyberlindnera xishuangbannaensis f.a., sp. nov. is proposed to accommodate these strains, with NYNU 16752T (=CICC 33163T=CBS 14692T) designated as the type strain. The MycoBank number is MB 822199.
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- Evolution, Phylogeny and Biodiversity
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Detection and identification of a novel subgroup 16SrII-V phytoplasma associated with Praxelis clematidea phyllody disease
More LessPraxelis clematidea is a very vigorous non-native weed in tropical and subtropical regions of China. P. clematidea plants showing symptoms of phyllody disease were found in an orchard located in Hainan province, PR China. The presence of phytoplasmas was confirmed by PCR of 16S rRNA gene using phytoplasma universal primers R16mF2/R16mR1 followed by R16F2n/R16R2. According to 16S rRNA gene sequence similarity, the P. clematidea phyllody (PCP) phytoplasma is a 'Candidatus Phytoplasma australasiae'-related strain (99.5 % similarity). The virtual RFLP pattern analyses of 16S rRNA gene sequences indicated that the PCP is a new subgroup within 16 Sr group II. The most similar RFLP pattern is the reference pattern of 16Sr group II, subgroup M, with a similarity coefficient of 0.94. These results were confirmed by phylogenetic analyses of the 16S rRNA gene. These findings suggest that P. clematidea phyllody disease is caused by a new phytoplasma considered to be a novel subgroup, 16SrII-V.
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- ICSP Matters
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Minimal standards for describing new species belonging to the families Campylobacteraceae and Helicobacteraceae: Campylobacter, Arcobacter, Helicobacter and Wolinella spp.
More LessOngoing changes in taxonomic methods, and in the rapid development of the taxonomic structure of species assigned to the Epsilonproteobacteria have lead the International Committee of Systematic Bacteriology Subcommittee on the Taxonomy of Campylobacter and Related Bacteria to discuss significant updates to previous minimal standards for describing new species of Campylobacteraceae and Helicobacteraceae . This paper is the result of these discussions and proposes minimum requirements for the description of new species belonging to the families Campylobacteraceae and Helicobacteraceae , thus including species in Campylobacter, Arcobacter , Helicobacter , and Wolinella . The core underlying principle remains the use of appropriate phenotypic and genotypic methods to characterise strains sufficiently so as to effectively and unambiguously determine their taxonomic position in these families, and provide adequate means by which the new taxon can be distinguished from extant species and subspecies. This polyphasic taxonomic approach demands the use of appropriate reference data for comparison to ensure the novelty of proposed new taxa, and the recommended study of at least five strains to enable species diversity to be assessed. Methodological approaches for phenotypic and genotypic (including whole-genome sequence comparisons) characterisation are recommended.
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Volumes and issues
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Volume 74 (2024)
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Volume 73 (2023)
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Volume 72 (2022 - 2023)
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Volume 71 (2020 - 2021)
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Volume 70 (2020)
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Volume 69 (2019)
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Volume 68 (2018)
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Volume 67 (2017)
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Volume 66 (2016)
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Volume 65 (2015)
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Volume 64 (2014)
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Volume 63 (2013)
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Volume 62 (2012)
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Volume 61 (2011)
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Volume 60 (2010)
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Volume 59 (2009)
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Volume 58 (2008)
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Volume 57 (2007)
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Volume 56 (2006)
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Volume 55 (2005)
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Volume 54 (2004)
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Volume 53 (2003)
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Volume 52 (2002)
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Volume 51 (2001)
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Volume 50 (2000)
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Volume 49 (1999)
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Volume 48 (1998)
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Volume 47 (1997)
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Volume 46 (1996)
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Volume 45 (1995)
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Volume 44 (1994)
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Volume 43 (1993)
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Volume 42 (1992)
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Volume 41 (1991)
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Volume 40 (1990)
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Volume 39 (1989)
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Volume 38 (1988)
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Volume 37 (1987)
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Volume 36 (1986)
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Volume 35 (1985)
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Volume 34 (1984)
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Volume 33 (1983)
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Volume 32 (1982)
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Volume 31 (1981)
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Volume 30 (1980)
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Volume 29 (1979)
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Volume 28 (1978)
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Volume 27 (1977)
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Volume 26 (1976)
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Volume 25 (1975)
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Volume 24 (1974)
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Volume 23 (1973)
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Volume 22 (1972)
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Volume 21 (1971)
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Volume 20 (1970)
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Volume 19 (1969)
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Volume 18 (1968)
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Volume 17 (1967)
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Volume 16 (1966)
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Volume 15 (1965)
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Volume 14 (1964)
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Volume 13 (1963)
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Volume 12 (1962)
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Volume 11 (1961)
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Volume 10 (1960)
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Volume 9 (1959)
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Volume 8 (1958)
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Volume 7 (1957)
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Volume 6 (1956)
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Volume 5 (1955)
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Volume 4 (1954)
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Volume 3 (1953)
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Volume 2 (1952)
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Volume 1 (1951)