- Volume 64, Issue Pt_9, 2014
Volume 64, Issue Pt_9, 2014
- New Taxa
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- Bacteroidetes
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Parafilimonas terrae gen. nov., sp. nov., isolated from greenhouse soil
A Gram-stain-negative, short rod-shaped, non-flagellated, yellow bacterium, designated strain 5GHs7-2T, was isolated from a greenhouse soil sample in South Korea. 16S rRNA gene sequence analysis of strain 5GHs7-2T indicated that the isolate belonged to the family Chitinophagaceae , and exhibited the highest sequence similarities with members of the genera Terrimonas (89.2–92.6 %), Sediminibacterium (90.8–91.4 %) and Chitinophaga (89.2–91.7 %), Filimonas lacunae YT21T (91.7 %), members of the genus Segetibacter (90.2–91.6 %), Parasegetibacter luojiensis RHYL-37T (90.9 %) and Flavihumibacter petaseus T41T (91.2 %). Flexirubin-type pigments were present. The major cellular fatty acids of the novel strain were iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G. The polar lipid profile consisted of a large amount of phosphatidylethanolamine, and moderate and small amounts of several unknown aminolipids and lipids. The only respiratory quinone of strain 5GHs7-2T was MK-7, and the DNA G+C content was 47.6 mol%. On the basis of the evidence presented, it is concluded that strain 5GHs7-2T represents a novel species of a new genus in the family Chitinophagaceae , for which the name Parafilimonas terrae gen. nov., sp. nov. is proposed. The type strain of the type species is 5GHs7-2T ( = KACC 17343T = DSM 28286T).
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Chryseobacterium artocarpi sp. nov., isolated from the rhizosphere soil of Artocarpus integer
More LessA bacterial strain, designated UTM-3T, isolated from the rhizosphere soil of Artocarpus integer (cempedak) in Malaysia was studied to determine its taxonomic position. Cells were Gram-stain-negative, non-spore-forming rods, devoid of flagella and gliding motility, that formed yellow-pigmented colonies on nutrient agar and contained MK-6 as the predominant menaquinone. Comparative analysis of the 16S rRNA gene sequence of strain UTM-3T with those of the most closely related species showed that the strain constituted a distinct phyletic line within the genus Chryseobacterium with the highest sequence similarities to Chryseobacterium lactis NCTC 11390T, Chryseobacterium viscerum 687B-08T, Chryseobacterium tructae 1084-08T, Chryseobacterium arthrosphaerae CC-VM-7T, Chryseobacterium oncorhynchi 701B-08T, Chryseobacterium vietnamense GIMN1.005T, Chryseobacterium bernardetii NCTC 13530T, Chryseobacterium nakagawai NCTC 13529T, Chryseobacterium gallinarum LMG 27808T, Chryseobacterium culicis R4-1AT, Chryseobacterium flavum CW-E2T, Chryseobacterium aquifrigidense CW9T, Chryseobacterium ureilyticum CCUG 52546T, Chryseobacterium indologenes NBRC 14944T, Chryseobacterium gleum CCUG 14555T, Chryseobacterium jejuense JS17-8T, Chryseobacterium oranimense H8T and Chryseobacterium joostei LMG 18212T. The major whole-cell fatty acids were iso-C15 : 0 and iso-C17 : 1ω9c, followed by summed feature 4 (iso-C15 : 0 2-OH and/or C16 : 1ω7t) and iso-C17 : 0 3-OH, and the polar lipid profile consisted of phosphatidylethanolamine and several unknown lipids. The DNA G+C content strain UTM-3T was 34.8 mol%. On the basis of the phenotypic and phylogenetic evidence, it is concluded that the isolate represents a novel species of the genus Chryseobacterium , for which the name Chryseobacterium artocarpi sp. nov. is proposed. The type strain is UTM-3T ( = CECT 8497T = KCTC 32509T).
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Lacihabitans soyangensis gen. nov., sp. nov., a new member of the family Cytophagaceae, isolated from a freshwater reservoir
More LessA Gram-staining-negative, non-motile and orange-pigmented bacterium, designated strain HME6675T, was isolated from freshwater of a reservoir in Korea. The major fatty acids of strain HME6675T were iso-C15 : 0 (33.4 %) and summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c; 31.3 %). The major respiratory quinone was MK-7. The polar lipids were phosphatidylethanolamine, one unidentified aminolipid, one unidentified aminophospholipid and three unidentified polar lipids. The DNA G+C content of strain HME6675T was 37.7 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain HME6675T formed a lineage within the family Cytophagaceae and was related to Leadbetterella byssophila 4M15T (93.0 % sequence similarity), Fluviimonas pallidilutea TQQ6T (90.6 %) and Emticicia oligotrophica GPTSA100-15T (89.1 %). On the basis of the evidence presented in this study, strain HME6675T represents a novel genus and species of the family Cytophagaceae , for which the name Lacihabitans soyangensis gen. nov., sp. nov. is proposed. The type strain of Lacihabitans soyangensis is HME6675T ( = KCTC 23259T = CECT 7826T).
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Spirosoma oryzae sp. nov., isolated from rice soil and emended description of the genus Spirosoma
More LessA bacterial strain, designated RHs22T, was isolated from a soil sample cultivated with rice in the Suwon region of South Korea. The cells were aerobic, Gram-stain-negative, non-spore-forming, non-flagellated rods or occasionally filaments. The strain grew at 10–37 °C (optimum, 28–30 °C), at pH 5.0–10.0 (optimum, 7.0) and in the presence of 0–1 % (w/v) NaCl (optimum, 0 %). Phylogenetically, the strain was closely related to members of the genus Spirosoma , as its 16S rRNA gene sequence had similarity of 90.3–92.1 % with respect to those of members of the genus Spirosoma , showing the highest sequence similarity with Spirosoma panaciterrae DSM 21099T. Strain RHs22T revealed relatively low sequence similarities of less than 90 % with all the other species with validly published names. It contained MK-7 as the predominant menaquinone and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), C16 : 1ω5c, iso-C15 : 0 and iso-C17 : 0 3-OH as the main fatty acids. The polar lipids of strain RHs22T were phosphatidylethanolamine, one unknown aminolipid, two unknown aminophospholipids, one unknown phospholipid and five unknown lipids. The DNA G+C content was 57.0 mol%. Phylogenetic, phenotypic and chemotaxonomic data obtained in this study indicate that strain RHs22T represents a novel species of the genus Spirosoma , for which the name Spirosoma oryzae sp. nov. is proposed. The type strain is RHs22T ( = KACC 17324T = DSM 28354T). An emended description of the genus Spirosoma is also proposed.
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Flavihumibacter cheonanensis sp. nov., isolated from sediment of a shallow stream
More LessA Gram-reaction-positive, rod-shaped, strictly aerobic and non-motile bacterial strain, designated WS16T, was isolated from the sediment of a shallow stream located in Cheonan, Korea. The strain grew optimally at 28 °C, at pH 7.0 and in the absence of NaCl. Phylogenetic trees based on 16S rRNA gene sequences suggested that the isolate belonged to the genus Flavihumibacter of the phylum Bacteroidetes . Comparative 16S rRNA gene sequence analysis showed that strain WS16T was related most closely to Flavihumibacter petaseus T41T (96.8 % similarity). The isolate contained MK-7 as the predominant menaquinone and iso-C15 : 0, iso-C15 : 1 and iso-C17 : 0 3-OH as the major fatty acids. The genomic DNA G+C content of the isolate was 45.9 mol%. The results of a polyphasic taxonomic approach indicated that strain WS16T represents a novel species of the genus Flavihumibacter , for which the name Flavihumibacter cheonanensis sp. nov. is proposed. The type strain is WS16T ( = KACC 17467T = JCM 19322T).
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- Other Bacteria
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Streptobacillus hongkongensis sp. nov., isolated from patients with quinsy and septic arthritis, and emended descriptions of the genus Streptobacillus and Streptobacillus moniliformis
Two bacterial strains, HKU33T and HKU34, were isolated in Hong Kong from the pus aspirated from the right peritonsillar abscess of a patient with quinsy and the left elbow joint fluid of another patient with tophaceous gout and left elbow septic arthritis, respectively. The bacteria were Gram-stain-negative, non-motile, non-spore-forming, non-haemolytic pleomorphic bacilli. They grew best on Columbia agar with 5 % defibrinated sheep blood in an anaerobic environment or aerobic environment with 5 % CO2. They also grew on chocolate agar but not on MacConkey agar. They were catalase- and cytochrome oxidase-negative. They showed a unique profile of enzyme activities distinguishable from their closely related species. Phylogenetic analysis of the complete 16S rRNA gene, and partial groEL, gyrB and recA gene sequences showed the two isolates formed a distinct branch within the family Leptotrichiaceae , being related most closely to Streptobacillus moniliformis . Hierarchical cluster analysis of mass spectra of whole-cell protein contents showed that strains HKU33T and HKU34 were closely related to each other, but were distinct from Streptobacillus moniliformis , Sneathia sanguinegens and ‘Leptotrichia amnionii’. The DNA G+C content of strain HKU33T was 26.0±2.1 mol% (mean±sd; n = 3). DNA–DNA hybridization demonstrated ≤45.02 % DNA relatedness between the two isolates and Streptobacillus moniliformis CCUG 13453T. A novel species, Streptobacillus hongkongensis sp. nov., is proposed to accommodate strains HKU33T and HKU34, with HKU33T ( = JCM 18691T = NCTC 13659T = DSM 26322T) designated the type strain. Emended descriptions of the genus Streptobacillus and Streptobacillus moniliformis are also given.
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Thermosipho activus sp. nov., a thermophilic, anaerobic, hydrolytic bacterium isolated from a deep-sea sample
A novel obligately anaerobic, extremely thermophilic, organotrophic bacterium, strain Rift-s3T, was isolated from a deep-sea sample containing Riftia pachyptila sheath from Guaymas Basin, Gulf of California. Cells of the novel isolate were rods, 0.3–0.8 µm in width and 1.5–10 µm in length, surrounded by a sheath-like structure (toga). Strain Rift-s3T grew at temperatures ranging from 44 to 75 °C, at pH 5.5 to 8.0, and with NaCl concentrations of 3 to 60 g l−1. Under optimum conditions (65 °C, pH 6.0, NaCl 25 g l−1), the doubling time was 30 min. The isolate was able to ferment mono-, oligo- and polysaccharides including cellulose, chitin, xylan and pectin, and proteins including β-keratins, casein and gelatin. Acetate, hydrogen and carbon dioxide were the main products of glucose fermentation. The G+C content of the DNA was 30 mol%. Phylogenetic analysis of 16S rRNA gene sequences showed the affiliation of strain Rift-s3T with the genus Thermosipho , with Thermosipho atlanticus Ob7T as the closest relative (96.5 % 16S rRNA gene sequence similarity). Based on the phylogenetic analysis and physiological properties of the novel isolate we propose a novel species of the genus Thermosipho , Thermosipho activus sp. nov., with Rift-s3T ( = DSM 26467T = VKM B-2803T) as the type strain.
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- Eukaryotic Micro-organisms
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Morphology and phylogenetic analysis of two oxytrichid soil ciliates from China, Oxytricha paragranulifera n. sp. and Oxytricha granulifera Foissner and Adam, 1983 (Protista, Ciliophora, Hypotrichia)
More LessThe morphology and infraciliature of two hypotrichous ciliates, Oxytricha paragranulifera n. sp. and Oxytricha granulifera Foissner and Adam, 1983, collected respectively from the surface of a sandy soil in the Huguang mangrove forest, Zhanjiang, China, and the surface of soil in a forest beside Ziwu Road, Xian, north-west China, were examined. O. paragranulifera n. sp. is characterized by an elongate body with slightly tapered anterior end, two macronuclear nodules and two micronuclei, paroral and endoral in Stylonychia-pattern, colourless cortical granules distributed in clusters or irregular short rows, adoral zone occupying 37 % of the body length, marginal rows almost confluent posteriorly, six dorsal kineties and three caudal cirri, caudal cirri and dorsal bristles almost indistinguishable when viewed in vivo. The well-known O. granulifera Foissner and Adam, 1983 was also redescribed and can be separated from the novel species by having cortical granules arranged along dorsal kineties and marginal rows on both sides (vs grouped in clusters as well as in short irregular rows), paroral and endoral in Oxytricha-pattern (vs in Stylonychia-pattern), macronuclear nodules obviously detached (vs adjacent) and a non-saline terrestrial habitat (vs saline terrestrial). The separation of these two taxa is also firmly supported by the molecular data, which show a significant difference between the two in their SSU rRNA gene sequences (similarity 97.1 %). Phylogenetic analyses based on SSU rRNA gene sequence data suggest a close relationship within the Oxytrichidae assemblage between O. paragranulifera n. sp. and O. granulifera.
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Basidioascus persicus sp. nov., a yeast-like species of the order Geminibasidiales isolated from soil
A novel species of basidiomycetes was isolated from kitchen garden soil in Shahryar city, Tehran province, Iran. Molecular and conventional methods were employed to identify and classify this single isolate. Morphologically, the isolate was considered yeast-like with hyaline and oval cells reproducing by monopolar budding, forming ballistoconidia, hyphae, arthroconidia and didymospores. Basidia and basidiospores resembling those produced by Basidioascus species were observed. Sequencing and Bayesian phylogenetic analysis of rRNA genes and the internal transcribed spacer region revealed its sister relationship to described species of the genus Basidioascus. Assimilation and fermentation tests, cell-wall carbohydrate analysis and enzyme activity tests were performed to provide insight into the metabolism of the isolate. Based on morphology, physiology and phylogeny of rRNA gene sequences, the isolate was shown to represent a novel species of the genus Basidioascus, described as Basidioascus persicus sp. nov. (holotype IBRC P1010180T = ex-type IBRC M30078T = isotype CBS 12808T). The MycoBank number of the novel species is MB 804703. An emended description of the genus Basidioascus is also provided.
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Barnettozyma siamensis f.a., sp. nov., a lipid-accumulating ascomycete yeast species
More LessTwo strains, DMKU-UbN24(1)T and DMKU-CPN24(1), of a novel yeast species were obtained from soil and palm oil fruit, respectively, collected in Thailand by an enrichment isolation technique using a nitrogen-limited medium containing glycerol as the sole source of carbon. On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics and sequence analysis of the D1/D2 region of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region, the two strains were found to represent a novel species of the genus Barnettozyma although the formation of ascospores was not observed. The novel species was related most closely to the type strain of Candida montana but differed by 5.4 % nucleotide substitutions in the D1/D2 region of the LSU rRNA gene and by 10.3–10.5 % nucleotide substitutions in the ITS region. The name Barnettozyma siamensis f.a., sp. nov. is proposed. The type strain is DMKU-UbN24(1)T ( = BCC 61189T = NBRC 109701T = CBS 13392T).
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Papiliotrema siamense f.a., sp. nov., a yeast species isolated from plant leaves
More LessTwo strains representing a novel species were isolated from the external surface of a sugar cane leaf (DMKU-SP85T) and tissue of a rice leaf (DMKU-RE97) collected in Thailand. On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics, and sequence analysis of the D1/D2 region of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region, the two strains were determined to represent a novel species of the genus Papiliotrema although sexual reproduction was not observed. The sequences of the D1/D2 region of the LSU rRNA gene and ITS region of the two strains were identical, but differed from those of the type strain of Cryptococcus nemorosus by 0.6 % nucleotide substitutions (four nucleotide substitutions out of 597 nucleotides) in the D1/D2 region of the LSU rRNA gene and 1.8 % nucleotide substitutions (nine nucleotide substitutions out of 499 nucleotides) in the ITS region. The name Papiliotrema siamense f.a., sp. nov. is proposed. The type strain is DMKU-SP85T( = BCC 69499T = CBS 13330T).
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- Errata
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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)