- Volume 65, Issue Pt_9, 2015
Volume 65, Issue Pt_9, 2015
- NEW TAXA
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- Proteobacteria
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Rhizobium ecuadorense sp. nov., an indigenous N2-fixing symbiont of the Ecuadorian common bean (Phaseolus vulgaris L.) genetic pool
There are two major centres of genetic diversification of common bean (Phaseolus vilgaris L.), the Mesoamerican and the Andean, and the legume is capable of establishing nitrogen-fixing symbioses with several rhizobia; Rhizobium etli seems to be the dominant species in both centres. Another genetic pool of common bean, in Peru and Ecuador, is receiving increasing attention, and studies of microsymbionts from the region can help to increase our knowledge about coevolution of this symbiosis. We have previously reported several putative new lineages from this region and here present data indicating that strains belonging to one of them, PEL4, represent a novel species. Based on 16S rRNA gene sequence phylogeny, PEL4 strains are positioned in the Rhizobium phaseoli/R. etli/Rhizobium leguminosarum clade, but show unique properties in several morphological, physiological and biochemical analyses, as well as in BOX-PCR profiles ( < 75 % similarity with related species). PEL4 strains also differed from related species based on multilocus sequence analysis of three housekeeping genes (glnII, gyrB and recA). Nucleotide identities of the three concatenated genes between PEL4 strains and related species ranged from 91.8 to 94.2 %, being highest with Rhizobium fabae. DNA–DNA hybridization ( < 47 % DNA relatedness) and average nucleotide identity values of the whole genomes ( < 90.2 %) also supported the novel species status. The PEL4 strains were effective in nodulating and fixing N2 with common beans. The data supported the view that PEL4 strains represent a novel species, Rhizobium ecuadorense sp. nov. The type strain is CNPSo 671T ( = UMR 1450T = PIMAMPIRS I 5T = LMG 27578T).
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Pseudoxanthomonas sangjuensis sp. nov., isolated from greenhouse soil
More LessOne bacterial strain, designated 5GH38-5T, which was characterized as aerobic, Gram-staining-negative, non-flagellated rods, was isolated from a soil sample from a greenhouse in Sangju region, Republic of Korea. It grew at temperatures of 15–45 °C, pH 5.0–9.0 and NaCl concentrations (w/v) of 0–3.0 %. 16S rRNA gene sequence analysis showed the strain was closely related to Pseudoxanthomonas kaohsiungensis J36T (97.3 %), Pseudoxanthomonas suwonensis 4M1T (96.8 %), Pseudoxanthomonas daejeonensis TR6-08T (96.7 %) and Pseudoxanthomonas kalamensis JA40T (96.7 %). Its major fatty acids were iso-C16 : 0, anteiso-C15 : 0 and iso-C15 : 0. The predominant ubiquinone was Q-8. The major polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C content was 71.1 mol%. The DNA–DNA hybridization value between strain 5GH38-5T and P. kaohsiungensis J36T was less than 70 %. The combined phenotypic, chemotaxonomic and phylogenetic data showed that strain 5GH38-5T could be clearly distinguished from closely related members of the genus Pseudoxanthomonas. Therefore, the results of this study indicated the existence of a novel species of the genus Pseudoxanthomonas, for which we propose the name Pseudoxanthomonas sangjuensis sp. nov., with strain 5GH38-5T ( = KACC 16961T = DSM 28345T = JCM 19948T) as the type strain.
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- Bacteroidetes
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Winogradskyella eckloniae sp. nov., a marine bacterium isolated from the brown alga Ecklonia cava
More LessA novel bacterial strain, designated EC29T, was isolated from the brown alga Ecklonia cava collected on Jeju Island, Republic of Korea. Cells of strain EC29T were Gram-stain-negative, aerobic, rod-shaped and motile by gliding. Growth was observed at 10–30 °C (optimum, 20–25 °C), at pH 6.0–9.5 (optimum, pH 7.5) and in the presence of 1–5 % (w/v) NaCl. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that the strain belonged to the genus Winogradskyella. Strain EC29T exhibited the highest 16S rRNA gene sequence similarities, of 96.5–97.8 %, to the type strains of Winogradskyella pulchriflava EM106T, Winogradskyella echinorum KMM 6211T and Winogradskyella ulvae KMM 6390T. Strain EC29T exhibited < 27 % DNA–DNA relatedness with Winogradskyella pulchriflava EM106T and Winogradskyella echinorum KMM 6211T. The predominant fatty acids of strain EC29T were iso-C15 : 0, iso-C15 : 1 G, C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 0 3-OH and anteiso-C15 : 0. The DNA G+C content was 31.1 mol% and the major respiratory quinone was menaquinone-6 (MK-6). Based on a polyphasic study, strain EC29T is considered to represent a novel species of the genus Winogradskyella, for which the name Winogradskyella eckloniae sp. nov. is proposed. The type strain is EC29T ( = KCTC 32172T = JCM 18703T).
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Flavobacterium nitrogenifigens sp. nov., isolated from switchgrass (Panicum virgatum)
More LessA yellow, nitrogen-fixing bacterial strain, NXU-44T, isolated from the rhizosphere of switchgrass (Panicum virgatum) in Auburn, Alabama, USA, was studied to determine its taxonomic position. Cells of the isolate were rod-shaped and Gram-stain-negative. A comparison of the 16S rRNA gene sequence with the sequences of the type strains of the most closely related species showed that the strain belongs to the genus Flavobacterium with highest sequence similarities to the type strains of Flavobacterium ginsenosidimutans (97.9 %), Flavobacterium phragmitis (97.6 %) and Flavobacterium anhuiense (97.5 %). The 16S rRNA gene sequence similarities to all other species of the genus Flavobacterium were below 97.5 %. The fatty acid profile of strain NXU-44T consisted of the major fatty acids iso-C15 : 0, iso-C15 : 0 2-OH/C16 : 1ω7c and iso-C17 : 0 3-OH. The major compounds in the polar lipid profile were phosphatidylethanolamine, phosphatidylserine, one aminolipid and two polar lipids. The quinone system was composed exclusively of menaquinone MK-6. The polyamine pattern contained the major compound sym-homospermidine and only minor amounts of other polyamines. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid. These data and the differential biochemical and chemotaxonomic properties show that strain NXU-44T represents a novel species of the genus Flavobacterium for which the name Flavobacterium nitrogenifigens sp. nov. is proposed. The type strain is NXU-44T ( = LMG 28694T = CIP 110894T).
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Prolixibacter denitrificans sp. nov., an iron-corroding, facultatively aerobic, nitrate-reducing bacterium isolated from crude oil, and emended descriptions of the genus Prolixibacter and Prolixibacter bellariivorans
More LessThe facultatively aerobic, non-hydrogenotrophic, iron (Fe0)-corroding, nitrate-reducing Prolixibacter sp. strain MIC1-1T was characterized for representation of a novel species of the genus Prolixibacter. Strain MIC1-1T grew optimally at 35–37 °C, at pH 6.5 and with 2 % (w/v) NaCl. Strain MIC1-1T also grew fermentatively on some pentoses, hexoses, disaccharides and soluble starch. Succinic acid was the major end-product from d-glucose fermentation. Strain MIC1-1T was differentiated from the type strain of Prolixibacter bellariivorans by cell size, optimum growth temperature, range of temperature and NaCl for growth, and nitrate reduction. On the basis of phenotypic features and the phylogenetic position, a novel species of the genus Prolixibacter is proposed for strain MIC1-1T, to be named Prolixibacter denitrificans sp. nov. The type strain is MIC1-1T ( = JCM 18694T = NBRC 102688T = DSM 27267T). Emended descriptions of the genus Prolixibacter and Prolixibacter bellariivorans are also provided.
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Winogradskyella crassostreae sp. nov., isolated from an oyster (Crassostrea gigas)
More LessA Gram-stain-negative, non-flagellated, non-gliding, aerobic and rod-shaped bacterium, designated TYO-19T, was isolated from an oyster collected from the South Sea in South Korea, and was subjected to a taxonomic study using a polyphasic approach. Strain TYO-19T grew optimally at 30 °C, at pH 7.0–8.0 and in the presence of 1.0–2.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences showed that strain TYO-19T belonged to the genus Winogradskyella, clustering coherently with the type strain of Winogradskyella epiphytica. Strain TYO-19T exhibited a 16S rRNA gene sequence similarity value of 99.7 % to W. epiphytica KMM 3906T and 94.2–96.9 % to the type strains of other species of the genus Winogradskyella. Strain TYO-19T contained MK-6 as the predominant menaquinone and iso-C15[hairsp] :[hairsp] 1 G, iso-C17[hairsp] :[hairsp] 0 3-OH, iso-C15[hairsp] :[hairsp] 0 and anteiso-C15[hairsp] :[hairsp] 0 as the major fatty acids. The major polar lipids detected in strain TYO-19T were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content was 39.0 mol% and the mean DNA–DNA relatedness value with the type strain of W. epiphytica was 59 ± 4.3 %. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, revealed that strain TYO-19T is separated from recognized species of the genus Winogradskyella. On the basis of the data presented, strain TYO-19T is considered to represent a novel species of the genus Winogradskyella, for which the name Winogradskyella crassostreae sp. nov. is proposed. The type strain is TYO-19T ( = KCTC 42462T = NBRC 110924T).
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Mariniphaga sediminis sp. nov., isolated from coastal sediment
More LessA Gram-stain-negative and facultatively anaerobic bacterium, SY21T, was isolated from marine sediments of the coastal area in Weihai, China (122° 0′ 37″ E 37° 31′ 33″ N). Cells of strain SY21T were 0.3–0.5 μm wide and 1.5–2.5 μm long, catalase- and oxidase-positive. Colonies on 2216E agar were transparent, beige- to pale-brown-pigmented, and approximately 0.5 mm in diameter. Growth occurred optimally at 33–37 °C, pH 7.0–7.5 and in the presence of 2–3 % (w/v) NaCl. Phylogenetic analysis of the 16S rRNA gene indicated that strain SY21T was a member of the genus Mariniphaga within the family Prolixibacteraceae. The closest described neighbour in terms of 16S rRNA gene sequences identity was Mariniphaga anaerophila Fu11-5T (94.7 %). The major respiratory quinone of strain SY21T was MK-7, and the dominant fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and anteiso-C15 : 0. The major polar lipids were phosphatidylethanolamine, aminolipid and an unidentified lipid, and the DNA G+C content was 37.9 mol%. The distinct phylogenetic position and phenotypic traits distinguished the novel isolate from M. anaerophila Fu11-5T. Phenotypic and genotypic analysis indicated that strain SY21T could be assigned to the genus Mariniphaga. The name Mariniphaga sediminis sp. nov. is proposed, with the type strain SY21T ( = KCTC 42260T = MCCC 1H00107T).
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Bizionia arctica sp. nov., isolated from Arctic fjord seawater, and emended description of the genus Bizionia
A Gram-stain-negative, yellow-pigmented, aerobic, non-flagellated, non-gliding bacterial strain, designated SM1203T, was isolated from surface seawater of Kongsfjorden, Svalbard. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SM1203T was affiliated with the genus Bizionia in the family Flavobacteriaceae. The strain shared the highest 16S rRNA gene sequence similarity (>96 %) with the type strains of Formosa spongicola (96.8 %), Bizionia paragorgiae (96.3 %), B. saleffrena (96.3 %) and B. echini (96.1 %) and 95.4–95.7 % sequence similarity with the type strains of other known species of the genus Bizionia. The strain grew at 4–30 °C and in the presence of 1.0–5.0 % (w/v) NaCl. The major fatty acids of strain SM1203T were iso-C15 : 0, iso-C15 : 1, anteiso-C15 : 0 and C15 : 0 and the main polar lipids were phosphatidylethanolamine and an unidentified lipid. The major respiratory quinone of strain SM1203T was menaquinone 6 (MK-6). The genomic DNA G+C content of strain SM1203T was 34.8 mol%. Based on the polyphasic characterization of strain SM1203T in this study, the strain represents a novel species in the genus Bizionia, for which the name Bizionia arctica sp. nov. is proposed. The type strain is SM1203T ( = CGMCC 1.12751T = JCM 30333T). An emended description of the genus Bizionia is also given.
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Sphingobacterium mucilaginosum sp. nov., isolated from rhizosphere soil of a rose
More LessA Gram-stain-negative, strictly aerobic, motile, short-rod-shaped bacterium, designated strain THG-SQA8T, was isolated from rhizosphere soil of rose in PR China. Strain THG-SQA8T was closely related to members of the genus Sphingobacterium, showed the highest sequence similarities with Sphingobacterium multivorum KACC 14105T (98.0 %) and Sphingobacterium ginsenosidimutans KACC 14526T (97.4 %). DNA–DNA hybridization showed values of 35.2 ± 0.9 % and 8.8 ± 0.3 % DNA reassociation with S. multivorum KACC 14105T and S. ginsenosidimutans KACC 14526T, respectively. Chemotaxonomic data revealed that strain THG-SQA8T possesses menaquinone-7 as the only respiratory quinone, and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C15 : 0 and C16 : 0 as the major fatty acids. The major polar lipid was phosphatidylethanolamine. The DNA G+C content was 40.7 mol%. These data corroborated the affiliation of strain THG-SQA8T to the genus Sphingobacterium. Thus, the isolate represents a novel species, for which the name Sphingobacterium mucilaginosum sp. nov. is proposed, with THG-SQA8T as the type strain ( = CCTCC AB 2014317T = KCTC 42503T).
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Bizionia fulviae sp. nov., isolated from the gut of an egg cockle, Fulvia mutica
A novel Gram-staining-negative, non-spore-forming, non-flagellated, non-motile, aerobic, saffron-coloured, rod-shaped bacterium that did not produce flexirubin-type pigments was designated strain EM7T and was distinct from other members of the genus Bizionia by produce carotenoid-type pigments and being able to grow independently of NaCl. Strain EM7T was isolated from the intestinal tract of an egg cockle, Fulvia mutica, which had been collected from the West Sea in Korea. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain EM7T belonged to the genus Bizionia, and showed sequence similarity to Bizionia paragorgiae KMM 6029T (97.9 %) and Bizionia saleffrena HFDT (97.73 %). Growth occurred on marine agar 2216 at 0–25 °C (optimum, 20 °C) and at pH 6–9 (optimum, pH 7). Growth occurred in the presence of 0–10 % (w/v) NaCl (optimum, 2 %, w/v, NaCl). The major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, iso-C15 : 1 G, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C17 : 0 3-OH and iso-C16 : 0 3-OH. The major respiratory quinone was menaquinone MK-6. The polar lipids of strain EM7T comprised phosphatidylethanolamine, three unidentified aminolipids, an unidentified aminophospholipid and two unidentified lipids. The genomic DNA G+C content was 34.8 mol%. Bizionia paragorgiae KMM 6029T and Bizionia saleffrena HFDT to Bizionia paragorgiae KCTC 12304T and Bizionia saleffrena CIP 108534T, respectively. Thus, it is proposed that the isolate represents a novel species, Bizionia fulviae sp. nov., with strain EM7T ( = KACC 18255T = JCM 30417T) as the type strain.
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Maribacter confluentis sp. nov., isolated from the junction between the ocean and a freshwater spring
More LessA Gram-stain-negative, aerobic, non-spore-forming, non-flagellated, non-gliding and rod-shaped bacterial strain, SSK2-2T, was isolated from the place where the ocean and a freshwater spring meet at Jeju island, South Korea. Strain SSK2-2T grew optimally at 30 °C, at pH 7.0–8.0 and in the presence of 2.0–3.0 % (w/v) NaCl. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain SSK2-2T fell within the clade comprising the type strains of species of the genus Maribacter, joining the type strain of Maribacter sedimenticola with which it shared 99.4 % similarity. Sequence similarities to the type strains of other Maribacter species were 94.6–98.2 %. Strain SSK2-2T contained MK-6 as the predominant menaquinone and iso-C17 : 0 3-OH, iso-C15 : 0, iso-C15 : 1 G, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 9 (iso-C17 : 1ω9c and/or 10-methyl C16 : 0) as the major fatty acids. The major polar lipids of strain SSK2-2T were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content of strain SSK2-2T was 38.2 mol% and mean levels of DNA–DNA relatedness with the type strains of four phylogenetically related species of the genus Maribacter were 11–24 %. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, revealed that strain SSK2-2T is separate from other Maribacter species. On the basis of the data presented, strain SSK2-2T is considered to represent a novel species of the genus Maribacter, for which the name Maribacter confluentis sp. nov. is proposed. The type strain is SSK2-2T ( = KCTC 42604T = CECT 8869T).
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Niastella gongjuensis sp. nov., isolated from greenhouse soil
An aerobic, Gram-stain-negative, non-flagellated, long rod or rod-shaped bacterial strain, 5GH22-11T, was isolated from a soil sample of a greenhouse in Gongju, Republic of Korea. According to 16S rRNA gene sequence analysis, strain 5GH22-11T showed the highest sequence similarities with Niastella populi THYL-44T (97.1 %), Niastella koreensis GR20-10T (95.7 %) and Niastella yeongjuensis GR20-13T (95.6 %), and < 93 % sequence similarity with all other species with validly published names. The phylogenetic tree also showed strain 5GH22-11T formed a compact cluster with members of the genus Niastella. DNA–DNA hybridization revealed strain 5GH22-11T is a novel species, showing far less than 70 % DNA–DNA relatedness with Niastella populi THYL-44T. Strain 5GH22-11T contained iso-C15 : 0 (34.3 %), iso-C17 : 0 3-OH (24.8 %) and iso-C15 : 1 G (18.2 %) as the major fatty acids; phosphatidylethanolamine, six unknown aminolipids, two unknown lipids and one unknown phospholipid as the polar lipids; and MK-7 as the predominant isoprenoid quinone. The DNA G+C content was 41.4 mol%. Based on these phylogenetic, physiological and chemotaxonomic data, it was demonstrated that strain 5GH22-11T represents a novel species of the genus Niastella, for which the name Niastella gongjuensis sp. nov. is proposed. The type strain is 5GH22-11T ( = KACC 17399T = JCM 19941T).
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- Other bacteria
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Cephalothrix gen. nov. (Cyanobacteria): towards an intraspecific phylogenetic evaluation by multilocus analyses
For more than a decade, the taxonomy of the Phormidiaceae has been problematic, since morphologically similar organisms represent phylogenetically distinct entities. Based on 16S rRNA gene sequence analyses, the polyphyletic genus Phormidium and other gas-vacuolated oscillatorioids appear scattered throughout the cyanobacterial tree of life. Recently, several studies have focused on understanding the oscillatorioid taxa at the generic level. At the specific level, few studies have characterized cyanobacterial strains using combined datasets (morphology, ultrastructure and molecular multilocus analyses). Using a multifaceted approach, we propose a new, well-defined genus, Cephalothrix gen. nov., by analysing seven filamentous strains that are morphologically ‘intermediate’ between gas-vacuolated taxa and Phormidium. Furthermore, we characterize two novel species: Cephalothrix komarekiana sp. nov. (strains CCIBt 3277, CCIBt 3279, CCIBt 3523, CCALA 155, SAG 75.79 and UTEX 1580) and Cephalothrix lacustris sp. nov. (strain CCIBt 3261). The generic name and specific epithets are proposed under the provisions of the International Code of Nomenclature for Algae, Fungi, and Plants.
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Deinococcus metallilatus sp. nov. and Deinococcus carri sp. nov., isolated from a car air-conditioning system
Two bacterial strains, designated MA1002T and MA1003T, were isolated from the air-conditioning system of a car. Cells of both strains were Gram-reaction-positive, non-motile, non-spore-forming coccoids, catalase- and oxidase-positive and UV-radiation resistant. The major fatty acids of strain MA1002T were iso-C17 : 0 and iso-C15 : 0 and those of strain MA1003T were iso-C16 : 0 and iso-C16 : 1 H. The polar lipid profile of MA1002T contained phosphatidylethanolamine, two unidentified phosphoglycolipids, an unidentified phospholipid, an unidentified aminophospholipid, an unidentified aminolipid and an unidentified lipid. MA1003T had three unidentified phosphoglycolipids, six unidentified phospholipids, two unidentified glycolipids and two unidentified polar lipids as the polar lipids. The G+C contents of the genomic DNA of MA1002T and MA1003T were 70.5 and 76.0 mol%, respectively. MK-8 was the predominant respiratory quinone for both strains. 16S rRNA gene sequence analysis showed that strain MA1002T was phylogenetically related to Deinococcus apachensis DSM 19763T, D. geothermalis DSM 11300T, D. aerius TR0125T and D. aetherius ST0316T (92.9, 92.6, 92.0 and 91.9 % sequence similarity, respectively), and MA1003T showed the highest sequence similarity to Deinococcus hopiensis KR-140T (92.9 %) and D. xinjiangensis X-82T (91.4 %). The results of genotypic and phenotypic characterizations showed that both strains could be distinguished from phylogenetically related species, and that the strains represented novel species within the genus Deinococcus, for which we propose the names Deinococcus metallilatus sp. nov. (type strain MA1002T = KACC 17964T = NBRC 110141T) and Deinococcus carri sp. nov. (type strain is MA1003T = KACC 17965T = NBRC 110142T).
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- Eukaryotic micro-organisms
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Pichia dushanensis sp. nov. and Hyphopichia paragotoi sp. nov., two sexual yeast species associated with insects and rotten wood
More LessSeven yeast strains were isolated from the gut of insect larvae and decayed wood, which were collected from three localities near Nanyang, Henan Province, China. These strains were identified as two novel species through comparison of sequences in the D1/D2 domains of the large subunit (LSU) rRNA gene and other taxonomic characteristics. Pichia dushanensis sp. nov. was closely related to species in the Pichia clade and produced one to four spheroid ascospores in a deliquescent ascus. The D1/D2 sequence of P. dushanensis sp. nov. differed from its closest relative, Issatchenkia (Pichia) sp. NRRL Y-12824, by 3.6 % sequence divergence (16 substitutions and 4 gaps). The species also differed from its four closest known species, Candida rugopelliculosa, Pichia occidentalis, Pichia exigua and Candida phayaonensis, by 4.1–4.4 % sequence divergence (22–24 substitutions and 0–2 gaps) in the D1/D2 sequences. Hyphopichia paragotoi sp. nov. belonged to the Hyphopichia clade, and its nearest phylogenetic neighbours were Candida gotoi, Candida pseudorhagii, Candida rhagii and Hyphopichia heimii with 3.2–4.2 % sequence divergence (16–21substitutions and 1 gap) in the D1/D2 sequences. In comparison with previously established species, H. paragotoi sp. nov. formed one hat-shaped ascospore in a persistent ascus. The type strain of P. dushanensis sp. nov. is NYNU 14658T ( = CICC 33049T = CBS 13912T), and the type strain of H. paragotoi sp. nov. is NYNU 14666T ( = CICC 33048T = CBS 13913T).
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Cyberlindnera xylosilytica sp. nov., a xylitol-producing yeast species isolated from lignocellulosic materials
Independent surveys of yeasts associated with lignocellulosic-related materials led to the discovery of a novel yeast species belonging to the Cyberlindnera clade (Saccharomycotina, Ascomycota). Analysis of the sequences of the internal transcribed spacer (ITS) region and the D1/D2 domains of the large subunit rRNA gene showed that this species is related to C. japonica, C. maesa and C. easanensis. Six isolates were obtained from different sources, including rotting wood, tree bark and sugar cane filter cake in Brazil, frass from white oak in the USA and decayed leaf in Taiwan. A novel species is suggested to accommodate these isolates, for which the name C. xylosilytica sp. nov. is proposed. The type strain of C. xylosilytica sp. nov. is NRRL YB-2097T ( = CBS 13984T = UFMG-CM-Y347T) and the allotype is UFMG-CM-Y409 ( = CBS 14083). The novel species is heterothallic and complementary mating types are represented by the type and allotype strains. The MycoBank number is MB 811428.
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- Evolution, Phylogeny and Biodiversity
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Genome-based taxonomic framework for the class Negativicutes: division of the class Negativicutes into the orders Selenomonadales emend., Acidaminococcales ord. nov. and Veillonellales ord. nov.
More LessThe class Negativicutes is currently divided into one order and two families on the basis of 16S rRNA gene sequence phylogenies. We report here comprehensive comparative genomic analyses of the sequenced members of the class Negativicutes to demarcate its different evolutionary groups in molecular terms, independently of phylogenetic trees. Our comparative genomic analyses have identified 14 conserved signature indels (CSIs) and 48 conserved signature proteins (CSPs) that either are specific for the entire class or differentiate four main groups within the class. Two CSIs and nine CSPs are shared uniquely by all or most members of the class Negativicutes, distinguishing this class from all other sequenced members of the phylum Firmicutes. Four other CSIs and six CSPs were specific characteristics of the family Acidaminococcaceae, two CSIs and four CSPs were uniquely present in the family Veillonellaceae, six CSIs and eight CSPs were found only in Selenomonas and related genera, and 17 CSPs were identified uniquely in Sporomusa and related genera. Four additional CSPs support a pairing of the groups containing the genera Selenomonas and Sporomusa. We also report detailed phylogenetic analyses for the Negativicutes based on core protein sequences and 16S rRNA gene sequences, which strongly support the four main groups identified by CSIs and by CSPs. Based on the results from different lines of investigation, we propose a division of the class Negativicutes into an emended order Selenomonadales containing the new families Selenomonadaceae fam. nov. and Sporomusaceae fam. nov. and two new orders, Acidaminococcales ord. nov. and Veillonellales ord. nov., respectively containing the families Acidaminococcaceae and Veillonellaceae.
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Reconsideration of the ‘well-known’ hypotrichous ciliate Pleurotricha curdsi (Shi et al., 2002) Gupta et al., 2003 (Ciliophora, Sporadotrichida), with notes on its morphology, morphogenesis and molecular phylogeny
More LessThe oxytrichid species Pleurotricha curdsi ( Shi et al., 2002 ) Gupta et al., 2003 , isolated from a tributary of the Yangtze River in the Mudong district of Chongqing, southern China, was reinvestigated with emphasis on its morphology, morphogenesis and small-subunit (SSU) rDNA-based phylogeny. Compared with three previously described populations, the Mudong population of P. curdsi is characterized by its large body size, 170–295 × 65–110 μm in vivo, and by having a variable number of right marginal rows, either two or three. Likewise, the number of right marginal rows anlagen (RMA) is also variable, i.e. usually two, but sometimes several small extra anlagen that give rise to the formation of the third row, are present to the left of the RMAs. We posit that the Mudong population is an intermediate form between the three previously described populations. Phylogenetic analyses based on the SSU rDNA sequence data show that all populations of P. curdsi cluster with the type species of the genus, Pleurotricha lanceolata, in a clade nested within the Oxytrichidae.
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- TAXONOMIC NOTE
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On the valid publication of names and combinations
More LessThe valid publication of names and combinations in a single journal was one of the innovations in the 1975 revision of the International Code of Nomenclature of Bacteria. A number of assumptions are often made with regards the way names or combinations are evaluated as being validly published. A re-examination of the process of valid publication is appropriate.
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- ICSP MATTERS
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Identification of strains Bacillus aerophilus MTCC 7304T as Bacillus altitudinis and Bacillus stratosphericus MTCC 7305T as a Proteus sp. and the status of the species Bacillus aerius Shivaji et al. 2006. Request for an Opinion
On the basis of 16S rRNA, rpoB, gyrB and pycA gene sequence analyses, characterization of biochemical features and other phenotypic traits and pulsed-field gel electrophoresis (PFGE) fingerprinting, it was ascertained that strains Bacillus aerius MTCC 7303T, Bacillus aerophilus MTCC 7304T and Bacillus stratosphericus MTCC 7305T do not conform to the descriptions of the type strains of the respective species. Strains MTCC 7303T and MTCC 7304T were indistinguishable from Bacillus altitudinis DSM 21631T, while strain MTCC 7305T should be classified as a representative of a Proteus sp. Our attempts to find other deposits of the type strains of these species were unsuccessful. Therefore, the results support the Request for an Opinion on the status of the species Bacillus aerophilus and Bacillus stratosphericus by Branquinho et al. [Branquinho, R., Klein, G., Kämpfer, P. & Peixe, L. V. (2015). Int J Syst Evol Microbiol 65, 1101]. It is also proposed that the Judicial Commission should place the name Bacillus aerius on the list of rejected names if a suitable replacement type strain cannot be found or a neotype is not proposed within two years following the publication of this Request (Rule 18c).
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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)