- Volume 69, Issue 9, 2019
Volume 69, Issue 9, 2019
- New taxa
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- Proteobacteria
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Acidithiobacillus sulfuriphilus sp. nov.: an extremely acidophilic sulfur-oxidizing chemolithotroph isolated from a neutral pH environment
More LessThe genus Acidithiobacillus currently includes seven species with validly published names, which fall into two major groups, those that can oxidize ferrous iron and those that do not. All seven species can use zero-valent sulfur and reduced sulfur oxy-anions as electron donors, are obligately chemolithotrophic and acidophilic bacteria with pH growth optima below 3.0. The 16S rRNA gene of a novel strain (CJ-2T) isolated from circum-neutral pH mine drainage showed 95–97 % relatedness to members of the genus Acidithiobacillus . Digital DNA–DNA hybridization (dDDH) values between strains and whole-genome pairwise comparisons between the CJ-2T strain and the reference genomes available for members of the genus Acidithiobacillus confirmed that CJ-2Trepresents a novel species of this genus. CJ-2T is a strict aerobe, oxidizes zero-valent sulfur and reduced inorganic sulfur compounds but does not use ferrous iron or hydrogen as electron donors. The isolate is mesophilic (optimum growth temperature 25–28 °C) and extremely acidophilic (optimum growth pH 3.0), though its pH optimum and maximum were significantly higher than those of non-iron-oxidising acidithiobacilli with validly published names. The major fatty acids of CJ-2T were C18 : 1ω7c, C:16 : 1ω7c/iso-C15 : 0 2-OH, C16 : 0 and C19 : 0 cyclo ω8c and the major respiratory quinone present was Q8. The name Acidithiobacillus sulfuriphilus sp. nov. is proposed, the type strain is CJ-2T (=DSM 105150T=KCTC 4683T).
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Sphingomonas flavalba sp. nov., isolated from a procymidone-contaminated soil
More LessA novel Gram-stain-negative, strictly aerobic, non-spore-forming, motile with one polar flagellum and short rod-shaped bacterium, designated strain ZLT-5T, was isolated from procymidone-contaminated soil sampled in Nanjing, Jiangsu, PR China. Growth occurred at 26–37 °C (optimum, 37 °C), at pH 6.0–9.0 (pH 7.0) and in the presence of 0–1.5 % NaCl (0.5 %). Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain ZLT-5T belonged to the genus Sphingomonas , with the highest sequence similarity to Sphingomonas kyeonggiensis THG-DT81T (96.6 %), followed by Sphingomonas dokdonensis DSM 21029T (96.5 %) and Sphingomonas silvisoli RP18T (96.3 %). The G+C content of strain ZLT-5T was 68.0 mol% (draft genome sequence). The average nucleotide identity value of the draft genomes between strain ZLT-5T and S. kyeonggiensis THG-DT81T was 75.4 %. Strain ZLT-5T contained ubiquinone-10 as the predominant isoprenoid quinone and sym-homospermidine as the major polyamine. The major polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphoaminolipid and sphingoglycolipid. The main cellular fatty acids (>10 % of the total fatty acids) of strain ZLT-5T were C17 : 1ω6c, summed feature 3 (C16 : 1ω7c and/or C15 : 0 ISO 2-OH) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). Based on phylogenetic analysis and physiological and biochemical characterization, strain ZLT-5T is described as a novel species of the genus Sphingomonas , for which the name Sphingomonas flavalba sp. nov. is proposed. The type strain is ZLT-5T (=CCTCC AB 2018188T=KCTC 62840T).
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Iodobacter ciconiae sp. nov., a bacterium isolated from feces of oriental stork, Ciconia boyciana
A novel Gram-stain-negative, facultatively anaerobic, non-motile, non-violet-pigmented, rod-shaped bacterium, designated strain H11R3T, was isolated from the feces of Oriental stork, Ciconia boyciana, collected from Seoul Grand Park Zoo, Republic of Korea. Phylogenetic analysis of the 16S rRNA gene sequence revealed that H11R3T formed a monophyletic clade with Iodobacter fluviatilis DSM 3764T, Iodobacter arcticus DSM 100243T, and Iodobacter limnosediminis DSM 103822T, with sequence similarities of 98.8, 98.6 and 98.4 %, respectively. H11R3T grew optimally at 15 °C, pH 8, with 0.5 % (w/v) NaCl. The predominant isoprenoid quinone was ubiquinone-8 (Q-8), and polar lipids included phosphatidylethanolamine, three unidentified lipids, four unidentified phospholipids, and two unidentified aminophospholipids. The major fatty acids were summed feature 3 and C16 : 0, and the DNA G+C content of the genome is 48.0 mol%. The average nucleotide identity (ANI) value between strains H11R3T and I. fluviatilis NCTC 11159T (=DSM 3764T) is 83.7 %. On the basis of phenotypic, genotypic, phylogenetic and chemotaxonomic characteristics, strain H11R3T represents a novel species of the genus Iodobacter for which the name Iodobacter ciconiae sp. nov. is proposed. The type strain is H11R3T (=KCTC 62666T=JCM 33283T).
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Diaphorobacter polyhydroxybutyrativorans Qiu et al. 2015 is a later heterotypic synonym of Diaphorobacter nitroreducens Khan and Hiraishi 2003
Yang Liu and Hong-Hui ZhuComparative analyses of Diaphorobacter polyhydroxybutyrativorans SL-205T and Diaphorobacter nitroreducens NA10BT were conducted for clarifying their taxonomic relationship. The sequences of the 16S rRNA gene and nine housekeeping genes of SL-205T and NA10BT shared high similarities, above 98.8 %. Whole-genomic comparison between the two strains revealed a digital DNA–DNA hybridization estimate of 85.1 % and an average nucleotide identity of 98.3 % that were well above respective recognized thresholds for bacterial species delineation, strongly indicating that they represent the same genomospecies. The metabolic, physiological and chemotaxonomic features of SL-205T were also shown to be congruent with those of NA10BT. Therefore, we conclude that Diaphorobacter polyhydroxybutyrativorans Qiu et al. 2015 is a later heterotypic synonym of Diaphorobacter nitroreducens Khan and Hiraishi 2003.
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- Eukaryotic Micro-Organisms
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Saturnispora galanensis sp. nov., a yeast species isolated from rotting wood
More LessThree strains of a novel yeast species were isolated from rotting wood in the Xishuangbanna Tropical Rainforest, Yunnan Province, PR China. Sequence analysis of the D1/D2 domains of the large subunit rRNA gene and the internal transcribed spacer (ITS) regions showed that the novel species represents a member of the genus Saturnispora. It differed from its closest known species, Saturnispora sekii CBS 10931T, by 1.3 % nucleotide substitutions in the D1/D2 domains and by 2.2 % nucleotide substitutions in the ITS regions, respectively. In contrast to Saturnispora sekii, the novel yeast species was unable to assimilate glycerol, dl-lactate, succinate and citrate, and grow at 37 °C. The name Saturnispora galanensis sp. nov. is proposed to accommodate these strains, with NYNU 1797 as the holotype.
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Candida xylosifermentans sp. nov., a d-xylose-fermenting yeast species isolated in Thailand
Three strains, representing a novel anamorphic and d-xylose-fermenting yeast species, were isolated from moss (ST-302T), seawater (ST-1169) and peat (DMKU-XE12) collected from the southern part of Thailand. The three strains had identical sequences of the D1/D2 regions of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) regions. Candida flosculorum CBS 10566T and Candida sharkiensis CBS 11368T were the most closely related species with 7.9 % nucleotide substitutions in the D1/D2 regions of the LSU rRNA gene, and 10.3 and 12.6% nucleotide substitutions in the ITS regions, respectively. Phylogenetic analysis based on the concatenated sequences of the ITS and the D1/D2 regions confirmed that the three strains represented a distinct anamorphic species in the Clavispora clade. Therefore, the three strains were described as a novel species, for which we propose the name Candida xylosifermentans sp. nov.
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Candida yunnanensis sp. nov. and Candida parablackwelliae sp. nov., two yeast species in the Candida albicans/Lodderomyces clade
More LessDuring studies on the yeast communities associated with rotting wood in the Xishuangbanna Tropical Rainforest in PR China, four novel yeast strains were found. Phylogenetic analysis based on the concatenated sequences of the D1/D2 domains of the large subunit rRNA gene and the ITS regions showed that these strains represented two novel species in the Candida albicans/Lodderomyces clade. The novel species, represented by strains NYNU 17948 and NYNU 17981, formed a clade with Candida maltosa and Candida baotianmanensis, with 1–1.8% sequence divergence in the D1/D2 domains and 8.9–10% sequence divergence in the ITS regions. The other novel species, represented by NYNU 17105 and NYNU 17763, is most closely related to Candida blackwelliae with 0.7 % sequence divergence in the D1/D2 domains and 6.9 % sequence divergence in the ITS regions. The two novel species could be distinguished from their closest described species in terms of physiological traits. The two novel species are described as Candida yunnanensis sp. nov. (holotype NYNU 17948) and Candida parablackwelliae sp. nov. (holotype NYNU 17763).
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Heterocephalacria mucosa sp. nov., a new basidiomycetous yeast species isolated from a mangrove forest in Thailand
Strains of yeast were isolated under a nitrogen-depleted culture condition from decaying tree bark (strain N-12.1) and from mangrove forest water (strain 1–7W.1) sampled at different locations within a mangrove forest site in Ranong province, Thailand. They were found to be genetically and phenotypically different from any currently recognised yeast species. Phylogenetic analysis of nucleotide sequence of three genes, the internal transcribed spacer region 1 and 2 plus 5.8S ribosomal RNA gene (ITS), D1/D2 domain of the large subunit ribosomal RNA gene (LSU D1/D2) and the small subunit of the ribosomal RNA gene (SSU), revealed that these two strains were related to but distinguished from Heterocephalacriaarrabidensis. Several distinct physiological characteristics of these two strains were detected, namely inability to assimilate glycerol, dl-lactic acid, succinic acid, citric acid, d-gluconic acid, and ability to grow well at 25 °C, which were different from those of H. arrabidensis. Accordingly, the name Heterocephalacria mucosa sp. nov., is proposed to accommodate this novel species. The MycoBank number is MB 828624.
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Spencerozyma acididurans sp. nov., an acid-tolerant basidiomycetous yeast species isolated from acid mine drainage
More LessStrain SYSU-17, representing a novel acid-tolerant yeast species which can grow at pH 2.0 weakly, was isolated from acid mine drainage collected in a tailing impoundment of the Fankou Lead/Zinc Mine, Guangdong Province, PR China. Phylogenetic analysis of strain SYSU-17 based on the internal transcribed spacer (ITS) region and the D1/D2 domains of the large subunit ribosomal RNA (LSU rRNA) gene suggested that strain SYSU-17 was a novel species belonging to the genus Spencerozyma (class Microbotryomycetes, subphylum Pucciniomycotina). It differed from the type strain of the closest related species, Spencerozyma crocea CBS 2029T, by 0.7 % sequence divergence (three gaps and one nucleotide substitution out of 594 bp) in the D1/D2 domains of the LSU rRNA gene and 7.6 % sequence divergence (32 gaps and 22 nucleotide substitutions out of 714 bp) in the ITS region. In contrast to the physiological properties of S. crocea, the novel yeast species was unable to assimilate galactose, d-ribose, xylitol, succinate, d-xylose, ethanol, nitrate and nitrite. The name Spencerozyma acididurans sp. nov. is proposed and SYSU-17 is designated as the holotype.
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Aspergillus olivimuriae sp. nov., a halotolerant species isolated from olive brine
A facultative halo-tolerant Aspergillus strain was isolated from olive brine waste, the effluent from the debittering process of table olives. Phenotypic and molecular characteristics showed clearly that the isolate represents a novel species. Based on the source of isolation, the new species has been named Aspergillus olivimuriae. It was found tolerant to high concentrations of NaCl (15 %) or sucrose (60 %) and it exhibits substantial growth under these conditions. Although the new species grew profusely at 37 °C, no growth was observed at 40 °C, conidia en masse were avellaneous on all media. The description of the new species Aspergillus olivimuriae brings the total species of Aspergillus sect. Flavipedes to 15. The type strain of A. olivimuriae sp. nov. is NRRL 66783 (CCF 6208), its whole genome has been deposited as PRJNA498048.
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- Evolution, Phylogeny and Biodiversity
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Lysinibacillus mangiferihumi, Lysinibacillus tabacifolii and Lysinibacillus varians are later heterotypic synonyms of Lysinibacillus sphaericus
More LessThe current study evaluates the taxonomic positions of Lysinibacillus mangiferihumi , Lysinibacillus sphaericus , Lysinibacillus tabacifolii and Lysinibacillus varians . Phylogenomic and genomic comparisons show the four strains are conspecific based on standard species thresholds for this genus (monophyletic and pairwise average nucleotide identities >96 %). Analysis of the 16S rRNA gene sequences provided in original descriptions with genome-derived 16S rRNA gene sequences from the current study showed significant differences in three of the four strains. Variant analysis of the 16S rRNA gene sequences using the genomic data showed that the 16S rRNA gene copies are polyallelic for these species. Previously reported distinguishing phenotypes were re-examined and the strains show phenotype congruence, with the exception of a few variable traits. Based on the rules of priority, L. mangiferihumi , L. tabacifolii and L. varians are later heterotypic synonyms of L. sphaericus .
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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)