-
Volume 63,
Issue Pt_7,
2013
Volume 63, Issue Pt_7, 2013
- New Taxa
-
- Proteobacteria
-
-
Caulobacter daechungensis sp. nov., a stalked bacterium isolated from a eutrophic reservoir
More LessA Gram-stain-negative, aerobic, non-spore-forming, curved, rod-shaped bacterium, H-E3-2T, was isolated from a water sample taken from Daechung Reservoir, Republic of Korea, during the late-blooming period of cyanobacteria. Strain H-E3-2T was motile with a single polar flagellum or non-motile (stalked cell). Comparative 16S rRNA gene sequence studies showed the isolate had a clear affiliation with the class Alphaproteobacteria and was most closely related to Caulobacter fusiformis ATCC 15257T and Caulobacter mirabilis LMG 24261T, showing 97.6 and 97.3 % 16S rRNA gene sequence similarity, respectively, and 95.3–96.3 % similarity to all other species of the genus Caulobacter . The predominant ubiquinone was Q-10. The major fatty acids were summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c) and C16 : 0. The G+C content of the genomic DNA of strain H-E3-2T was 64.7 mol%. DNA–DNA hybridization values of strain H-E3-2T with C. fusiformis ATCC 15257T and C. mirabilis LMG 24261T were 21.2 and 19.7 %, respectively. Thus, based on the results of polyphasic analysis, it is proposed that strain H-E3-2T represents a novel species of the genus Caulobacter , for which the name Caulobacter daechungensis sp. nov. is proposed. The type strain is H-E3-2T ( = KCTC 32211T = JCM 18689T).
-
-
-
Sphingopyxis italica sp. nov., isolated from Roman catacombs
More LessA Gram-stain-negative, aerobic, motile, rod-shaped bacterium, strain SC13E-S71T, was isolated from tuff, volcanic rock, where the Roman catacombs of Saint Callixtus in Rome, Italy, was excavated. Analysis of 16S rRNA gene sequences revealed that strain SC13E-S71T belongs to the genus Sphingopyxis , and that it shows the greatest sequence similarity with Sphingopyxis chilensis DSM 14889T (98.72 %), Sphingopyxis taejonensis DSM 15583T (98.65 %), Sphingopyxis ginsengisoli LMG 23390T (98.16 %), Sphingopyxis panaciterrae KCTC 12580T (98.09 %), Sphingopyxis alaskensis DSM 13593T (98.09 %), Sphingopyxis witflariensis DSM 14551T (98.09 %), Sphingopyxis bauzanensis DSM 22271T (98.02 %), Sphingopyxis granuli KCTC 12209T (97.73 %), Sphingopyxis macrogoltabida KACC 10927T (97.49 %), Sphingopyxis ummariensis DSM 24316T (97.37 %) and Sphingopyxis panaciterrulae KCTC 22112T (97.09 %). The predominant fatty acids were C18 : 1ω7c, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), C14 : 0 2-OH and C16 : 0. The predominant menaquinone was MK-10. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and sphingoglycolipid. These chemotaxonomic data are common to members of the genus Sphingopyxis . However, a polyphasic approach using physiological tests, DNA base ratios, DNA–DNA hybridization and 16S rRNA gene sequence comparisons showed that the isolate SC13E-S71T belongs to a novel species within the genus Sphingopyxis , for which the name Sphingopyxis italica sp. nov. is proposed. The type strain is SC13E-S71T ( = DSM 25229T = CECT 8016T).
-
-
-
Enterobacter sacchari sp. nov., a nitrogen-fixing bacterium associated with sugar cane (Saccharum officinarum L.)
More LessFive nitrogen-fixing bacterial strains (SP1T, NN143, NN144, NN208 and HX148) were isolated from stem, root or rhizosphere soil of sugar cane (Saccharum officinarum L.) plants. Cells were Gram-negative, motile, rods with peritrichous flagella. DNA G+C content was 55.0±0.5 mol%. Sequence determinations and phylogenetic analysis of 16S rRNA gene and rpoB indicated that the strains were affiliated with the genus Enterobacter and most closely related to E. radicincitans DSM 16656T and E. oryzae LMG 24251T. Fluorimetric determination of thermal denaturation temperatures after DNA–DNA hybridization, enterobacterial repetitive intergenic consensus PCR and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry differentiated the whole-genome, genotype and protein profiles from those of E. radicincitans and E. oryzae . The strains’ cell fatty acid composition differentiated them from E. radicincitans and E. oryzae by containing a higher level of summed feature 2 (C16 : 1ω7c and/or C16 : 1ω6c) and a lower level of C17 : 0 cyclo. Their physiological and biochemical profiles differentiated them from E. radicincitans by being positive for methyl red test, ornithine decarboxylase and utilization of putrescine, d-arabitol, l-fucose and methyl α-d-glucoside and being negative for arginine dihydrolase, and differentiated them from E. oryzae by being positive for aesculin hydrolysis and utilization of putrescine, d-arabitol and l-rhamnose and being negative for arginine dihydrolase, lysine decarboxylase and utilization of mucate. The five strains therefore represent a novel species, for which the name Enterobacter sacchari sp. nov. is proposed, with the type strain SP1T ( = CGMCC 1.12102T = LMG 26783T).
-
-
-
Gibbsiella papilionis sp. nov., isolated from the intestinal tract of the butterfly Mycalesis gotama, and emended description of the genus Gibbsiella
More LessA novel Gram-negative, non-motile, facultative anaerobic and rod-shaped bacterium, designated strain LEN33T, was isolated from the intestinal tract of a butterfly (Mycalesis gotama). Strain LEN33T grew optimally at 37 °C in the presence of 1 % (w/v) NaCl and at pH 9. The novel strain was oxidase-negative and catalase-positive. The major cellular fatty acids were C14 : 0, C16 : 0 and cyclo-C17 : 0. Strain LEN33T contained two unidentified lipids, three unidentified amino-phospholipids, phosphatidylethanolamine (PE) and phosphatidylglycerol (PG). The major isoprenoid quinone was ubiquinone-8 (Q-8). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain LEN33T was most closely related to Gibbsiella quercinecans FRB 97T and Gibbsiella dentisursi NUM 1720T, with 98.7 % similarities. DNA–DNA hybridization experiments indicated less than 40.7±2 % relatedness to the closest phylogenetic species, G. quercinecans FRB 97T. The G+C content of genomic DNA was 58.7 mol%. Phenotypic, phylogenetic and genotypic analysis indicated that strain LEN33T represents a novel species within the genus Gibbsiella , for which the name Gibbsiella papilionis is proposed. The type strain is referred to as LEN33T ( = KACC 16707T = JCM 18389T). An emended description of the genus Gibbsiella is also proposed.
-
-
-
Azospirillum humicireducens sp. nov., a nitrogen-fixing bacterium isolated from a microbial fuel cell
More LessA Gram-negative, facultative anaerobic, motile, spiral, straight-to-slightly curved rod-shaped and nitrogen-fixing strain, designated SgZ-5T, was isolated from a microbial fuel cell (MFC) and was characterized by means of a polyphasic approach. Growth occurred with 0–1 % (w/v) NaCl (optimum 1 %) and at pH 5.5–8.5 (optimum pH 7.2) and at 25–37 °C (optimum 30 °C) in nutrient broth (NB). The strain had the ability to grow under anaerobic conditions via the oxidation of various organic compounds coupled to the reduction of anthraquione-2,6-disulfonate (AQDS). Chemotaxonomic characteristics (main ubiquinone Q-10, major fatty acid C18 : 1ω7c/C18 : 1ω6c and DNA G+C content 67.7 mol%) were similar to those of members of the genus Azospirillum . According to the results of phylogenetic analyses, strain SgZ-5T belonged to the genus Azospirillum within the family Rhodospirillaceae of the class Alphaproteobacteria , and was related most closely to the type strains of Azospirillum lipoferum , Azospirillum thiophilum and Azospirillum oryzae (98.0, 97.6 and 97.1 % 16S rRNA gene sequence similarity, respectively). DNA–DNA pairing studies showed that the unidentified organism displayed reassociation values of 36.7±3.7, 24.1±2.2 and 22.3±2.4 % to the type strains of A. lipoferum , A. thiophilum and A. oryzae , respectively. Similarities between nifH gene sequences of strain SgZ-5T and members of the genus Azospirillum ranged from 94.0 to 97.0 %. A combination of phenotypic, chemotaxonomic, phylogenetic and genotypic data clearly indicated that strain SgZ-5T represents a novel species, for which the name Azospirillum humicireducens sp. nov. is proposed. The type strain is SgZ-5T ( = CCTCC AB 2012021T = KACC 16605T).
-
-
-
Novosphingobium aquaticum sp. nov., isolated from the humic-matter-rich bog lake Grosse Fuchskuhle
A yellow‐pigmented, Gram-negative rod, designated FNE08-86T, was isolated from subsurface water of the humic-matter-rich and almost-neutral north-east basin of the experimentally divided bog lake Grosse Fuchskuhle (Brandenburg, Germany). Analysis of the nearly full-length 16S rRNA gene sequence showed the highest 16S rRNA gene sequence similarity with Novosphingobium rosa IAM 14222T (96.3 %). Sequence similarities with all other members of the genus Novosphingobium species were <96 %, but phylogenetic tree construction clearly showed the placement of strain FNE08-86T within the genus Novosphingobium . The predominant fatty acids were C18 : 1ω7c and C16 : 0, and only a single 2-hydroxy fatty acid, C14 : 0 2-OH, was detected. The polar lipid profile revealed phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine as major compounds, with smaller amounts of sphingoglycolipid, phosphatidylmonomethylethanolamine, diphosphatidylglycerol and several unidentified lipids. In the quinone system ubiquinone Q-10 was predominant and in the polyamine pattern spermidine was predominant. Characterization by genotypic, chemotaxonomic and phenotypic analysis indicated that strain FNE08-86T represents a novel species of the genus Novosphingobium , for which we propose the name Novosphingobium aquaticum sp. nov. (type strain FNE08-86T = DSM 25088T = CCM 7983T).
-
-
-
Rhodomicrobium udaipurense sp. nov., a psychrotolerant, phototrophic alphaproteobacterium isolated from a freshwater stream
More LessTwo strains (JA643T and JA755) of Gram-stain-negative, facultatively anaerobic phototrophic, bacteria capable of growth at low temperatures (10–15 °C) were isolated from freshwater streams from different geographical regions of India. Both strains contain bacteriochlorophyll a and carotenoids of the spirilloxanthin series. Phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified phospholipid (PL), unidentified amino lipids (AL1–AL6, AL9) and an unidentified lipid (L1) were the polar lipids present in both strains. The major cellular fatty acid was C18 : 1ω7c (76–79 % of the total). Bacteriohopane derivatives (BHD1,2), unidentified hopanoids (UH1–5), diplopterol (DPL) and diploptene (DPE) were the major hopanoids of both strains. The DNA G+C content was 64.2–64.5 mol%. 16S rRNA gene sequence-based phylogenetic analysis showed that both strains are closely related to the genus Rhodomicrobium and clustered with Rhodomicrobium vannielii DSM 162T (99 % sequence similarity). However, both strains exhibited only 46.1 % DNA–DNA hybridization with R. vannielii DSM 162T. Strains JA643T and JA755 shared >99 % 16S rRNA gene sequence similarity and were >85 % related on the basis of DNA–DNA hybridization; they are therefore considered to represent a novel species in the genus Rhodomicrobium , for which the name Rhodomicrobium udaipurense sp. nov. is proposed. The type strain is JA643T ( = KCTC 15219T = NBRC 109057T).
-
-
-
Methylobacterium trifolii sp. nov. and Methylobacterium thuringiense sp. nov., methanol-utilizing, pink-pigmented bacteria isolated from leaf surfaces
More LessThree pink-pigmented, aerobic, Gram-stain-negative, rod-shaped and facultatively methylotrophic strains were isolated from the phyllosphere of Trifolium repens and Cerastium holosteoides. 16S rRNA gene sequence analysis support the affiliation of all strains to the genus Methylobacterium . The closest relatives of strains C34T and T5 were Methylobacterium gnaphalii 23eT (98.0 and 98.5 % sequence similarity, respectively) and Methylobacterium organophilum JCM 2833T (97.0 and 97.2 %, respectively). Strain TA73T showed the highest sequence similarities to Methylobacterium marchantiae JT1T and Methylobacterium bullatum F3.2T (both 97.9 %), followed by Methylobacterium phyllosphaerae CBMB27T and Methylobacterium brachiatum DSM 19569T (both 97.8 %), Methylobacterium cerastii C15T and Methylobacterium radiotolerans JCM 2831T (both 97.7 %). The major components in the fatty acid profiles were C18 : 1ω7c, C16 : 0 and one unknown fatty acid for strain TA73T and C18 : 1ω7c, C16 : 1ω7c/iso-C15 : 0 2-OH, C18 : 0 and C16 : 0 for strains C34T and T5. Physiological and biochemical analysis, including DNA–DNA hybridization, revealed clear differences between the investigated strains and their closest phylogenetic neighbours. DNA–DNA hybridization studies also showed high similarities between strains C34T and T5 (59.6–100 %). Therefore, the isolates represent two novel species within the genus Methylobacterium , for which the names Methylobacterium trifolii sp. nov. (type strain TA73T = LMG 25778T = CCM 7786T) and Methylobacterium thuringiense sp. nov. (type strain C34T = LMG 25777T = CCM 7787T) are proposed.
-
-
-
Pleionea mediterranea gen. nov., sp. nov., a gammaproteobacterium isolated from coastal seawater
A Gram-negative, aerobic, cream-pigmented, non-motile, non-spore-forming straight rod, strain MOLA115T, was isolated from a coastal water sample from the Mediterranean Sea. On the basis of phylogenetic analysis of the 16S rRNA gene sequences, strain MOLA115T was shown to belong to the Gammaproteobacteria , adjacent to members of the genera Marinicella , Arenicella and Kangiella , sharing less than 89 % 16S rRNA gene sequence similarity with strains of all recognized species within the Gammaproteobacteria . The only isoprenoid quinone was ubiquinone-8. Polar lipids in strain MOLA115T included phosphatidylethanolamine, an aminolipid, phosphatidylglycerol and an aminophospholipid. Fatty acid analysis revealed iso-C15 : 0 and iso-C17 : 1ω9c to be the dominant components. The DNA G+C content was 44.5 mol%. Based upon the phenotypic and phylogenetic data, we propose that strain MOLA115T should be considered to represent a novel species in a new genus, for which the name Pleionea mediterranea gen. nov., sp. nov. is proposed. The type strain of Pleionea mediterranea is MOLA115T ( = CIP 110343T = DSM 25350T).
-
- Bacteroidetes
-
-
Flavobacterium nitratireducens sp. nov., an amylolytic bacterium of the family Flavobacteriaceae isolated from coastal surface seawater
More LessA novel Gram-negative, rod-shaped, non-motile bacterium, designated strain N1T, was isolated from a marine water sample collected from the sea shore, Bay of Bengal, Visakhapatnam, India. The strain was positive for starch hydrolysis, nitrate reduction and ornithine decarboxylase activities and negative for citrate utilization, urease, oxidase, catalase and DNase activities. The predominant fatty acids were C16 : 0 3-OH, iso-C15 : 0, iso-C15 : 0 3-OH, iso-C17 : 0 3-OH, anteiso-C15 : 0, C16 : 0, C15 : 0 3-OH, and C16 : 1ω7c and/or iso-C15 : 0 2-OH (summed feature 3). Strain N1T contained menaquinone 6 (MK-6) as the sole respiratory quinone. The only polyamine was homospermidine and the major polar lipids were phosphatidylethanolamine (PE), three unidentified aminolipids (AL1–AL3) and two unidentified lipids (L1, L2). The DNA G+C content of the strain was 36.3 mol%. 16S rRNA gene sequence analysis indicated that strain N1T was a member of the genus Flavobacterium and closely related to Flavobacterium resistens with pairwise sequence similarity of 96.5 %. Phylogenetic analysis showed that strain N1T clustered with Flavobacterium glycines and Flavobacterium daejeonense with a distance of 4.8 and 6.0 % (95.2 and 94.0 % similarity), respectively. Based on the phenotypic characteristics and on phylogenetic inference, strain N1T represents a novel species of the genus Flavobacterium , for which the name Flavobacterium nitratireducens sp. nov. is proposed. The type strain is N1T ( = MTCC 11155T = JCM 17678T).
-
-
-
Maribacter chungangensis sp. nov., isolated from a green seaweed, and emended descriptions of the genus Maribacter and Maribacter arcticus
More LessA Gram-stain-negative, non-spore-forming, strictly aerobic, orange-pigmented bacterial strain, motile by gliding, designated CAU 1044T, was isolated from a green seaweed and its taxonomic position was investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CAU 1044T formed a distinct lineage within the genus Maribacter and was most closely related to Maribacter antarcticus JCM 15445T and Maribacter arcticus KOPRI 20941T (96.3 and 95.7 % similarity, respectively). Strain CAU 1044T contained menaquinone 6 as the only isoprenoid quinone and iso-C15 : 0, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c and/or iso-C15 : 0 2-OH), iso-C17 : 0 3-OH and iso-C15 : 1 G as the major fatty acids. The cell wall peptidoglycan of strain CAU 1044T contained meso-diaminopimelic acid and the major whole-cell sugars were glucose and ribose. The polar lipids were composed of phosphatidylethanolamine, one unidentified phospholipid, six unidentified aminolipids and four unidentified lipids. The DNA G+C content was 40.2 mol%. On the basis of phenotypic data and phylogenetic inference, strain CAU 1044T should be classified as a representative of a novel species in the genus Maribacter for which the name Maribacter chungangensis sp. nov. is proposed. The type strain is CAU 1044T ( = KCTC 23735T = CCUG 61948T). Emended descriptions of the genus Maribacter and the species M. arcticus KCTC 22053T are also proposed.
-
-
-
Chryseobacterium frigidisoli sp. nov., a psychrotolerant species of the family Flavobacteriaceae isolated from sandy permafrost from a glacier forefield
More LessDuring diversity studies of the glacier forefields of the Larsemann Hills, East Antarctica, a novel psychrotolerant, non-motile Gram-negative, shiny yellow, rod-shaped, aerobic bacterium, designated strain PB4T was isolated from a soil sample. Strain PB4T produces indole from tryptophan and hydrolyses casein. It grows between 0 and 25 °C with an optimum growth temperature of 20 °C. A wide range of substrates are used as sole carbon sources and acid is produced from numerous carbohydrates. The major menaquinone is MK-6. Identified polar lipids are ethanolamines and ornithine lipids. Major fatty acids (>10 %) are iso-C15 : 0 (13.0 %) and iso-2OH-C15 : 0 (51.2 %). G+C content is 33.7 mol%. The polyamine pattern is composed of sym-homospermidine (25.1 µmol g−1 dry weight), minor amounts of cadaverine (0.2 µmol g−1 dry weight) and spermidine (0.4 µmol g−1 dry weight) and traces of putrescine and spermine (<0.1 µmol g−1 dry weight). Strain PB4T had highest 16S rRNA gene similarities with the type strains of Chryseobacterium humi (97.0 %) and Chryseobacterium marinum (96.5 %). Considering phenotypic and genotypic characterization, strain PB4T represents a novel species in the genus Chryseobacterium (family Flavobacteriaceae ), for which the name Chryseobacterium frigidisoli sp. nov. is proposed. The type strain is PB4T ( = DSM 26000T = LMG 27025T).
-
-
-
Muricauda taeanensis sp. nov., isolated from a marine tidal flat
More LessA novel Gram-stain-negative, heterotrophic, moderate halophilic and strictly aerobic bacterium, strain 105T, was isolated from a tidal flat of Taean in Korea. Cells were catalase- and oxidase-positive long rods that showed gliding motility. Optimum temperature, pH and salinity for the growth of strain 105T were observed at 30–37 °C, at pH 7.0–7.5, and in the presence of 2–4 % (w/v) NaCl, respectively. The major cellular fatty acids were iso-C15 : 1 G, iso-C15 : 0 and iso-C17 : 0 3-OH. Phosphatidylethanolamine and five unidentified lipids were identified as the major polar lipids. The genomic DNA G+C content of strain 105T was 42.4 mol% and MK-6 was detected as the predominant isoprenoid quinone. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 105T formed a phyletic lineage with members of the genus Muricauda . Strain 105T was most closely related to Muricauda aquimarina SW-63T (97.6 %), Muricauda beolgyonensis BB-My12T (97.5 %), Muricauda lutimaris SMK-108T (97.5 %), Muricauda ruestringensis B1T (97.3 %), Muricauda flavescens CL-SS4T (97.2 %) and Muricauda olearia (96.2 %). The DNA–DNA relatedness values of strain 105T with M. aquimarina JCM 11811T, M. beolgyonensis KCTC 23501T, M. lutimaris KCTC 22173T, M. ruestringensis DSM 13258T and M. flavescens JCM 11812T were 17.2±6.0, 8.7±2.2, 3.7±0.5, 11.0±1.9 and 7.1±1.3 %, respectively. On the basis of phenotypic and molecular features, strain 105T represents a novel species of the genus Muricauda , for which the name Muricauda taeanensis sp. nov. is proposed. The type strain is 105T ( = KACC 16195T = JCM 17757T).
-
-
-
Lutibacter agarilyticus sp. nov., a marine bacterium isolated from shallow coastal seawater
More LessA Gram-staining-negative, non-spore-forming, non-gliding and rod-shaped bacterial strain KYW566T, was isolated from seawater of the Suncheon Bay, Korea, and its taxonomic position was investigated by using a polyphasic study. The cells contained MK-6 as the only respiratory quinone and contained iso-C15 : 0 (13.8 %), iso-C16 : 0 3-OH (13.1 %), anteiso-C15 : 0 (9.3 %), iso-C15 : 0 3-OH (8.7 %), iso-C15 : 1 G (6.3 %) and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) (6.0 %) as the major fatty acids. The DNA G+C content of strain KYW566T was 41.6±0.8 mol% (mean±sd of three determinations). A phylogenetic tree based on 16S rRNA gene sequences showed that strain KYW566T forms an evolutionary lineage within the radiation enclosing the members of the genus Lutibacter with Lutibacter flavus IMCC1507T as its nearest neighbour (96.7 % sequence similarity). A number of phenotypic characteristics distinguished strain KYW566T from described members of the genus Lutibacter . On the basis of the evidences presented in this study, strain KYW566T represents a novel species, for which the name Lutibacter agarilyticus sp. nov. is proposed. The type strain is KYW566T ( = KCTC 23842T = JCM 18281T).
-
- Other Bacteria
-
-
Leptospira idonii sp. nov., isolated from environmental water
Strain Eri-1T was isolated from a water sample on the campus of Kyushu University, Fukuoka, Japan. The motility and morphology of the isolate were similar to those of members of the genus Leptospira , but the spiral structure of the isolate was sharper under dark-field microscopy. Cells were 10.6±1.3 µm long and 0.2 µm in diameter, with a wavelength of 0.9 µm and an amplitude of 0.4 µm. Strain Eri-1T grew in Korthof’s medium at both 13 and 30 °C, and also in the presence of 8-azaguanine. 16S rRNA gene-based phylogenetic analysis placed strain Eri-1T within the radiation of the genus Leptospira where it formed a unique lineage within the clade of the known saprophytic species of the genus Leptospira . The strain was not pathogenic to hamsters. Strain Eri-1T exhibited low levels (11.2–12.6 %) of similarity by DNA–DNA hybridization to the three most closely related species of the genus Leptospira . The DNA G+C content of the genome of strain Eri-1T was 42.5±0.1 mol%. These results suggest that strain Eri-1T represents a novel species of the genus Leptospira , for which the name Leptospira idonii sp. nov. is proposed. The type strain is Eri-1T ( = DSM 26084T = JCM 18486T).
-
- Eukaryotic Micro-organisms
-
-
Two novel ascomycetous yeast species, Wickerhamomyces scolytoplatypi sp. nov. and Cyberlindnera xylebori sp. nov., isolated from ambrosia beetle galleries
More LessThirteen strains of yeasts were isolated from ambrosia beetle galleries at several sites in Japan. Based on the morphological and biochemical characteristics and phylogenetic analysis of the D1/D2 domain of the large subunit (LSU) rRNA gene of the yeasts, 10 strains were shown to represent a novel species of the genus Wickerhamomyces, described as Wickerhamomyces scolytoplatypi sp. nov. (type strain NBRC 11029T = CBS 12186T), and were closely related to Wickerhamomyces hampshirensis. The three other strains represented a novel species of the genus Cyberlindnera, described as Cyberlindnera xylebori sp. nov. (type strain NBRC 11048T = CBS 12187T), and were closely related to Cyberlindnera euphorbiiphila. It is suggested that these species are associated with ambrosia beetles and we consider ambrosia beetle galleries as good sources of novel yeasts.
-
- Evolution, Phylogeny and Biodiversity
-
-
-
Molecular signatures for Bacillus species: demarcation of the Bacillus subtilis and Bacillus cereus clades in molecular terms and proposal to limit the placement of new species into the genus Bacillus
More LessThe genus Bacillus is a phylogenetically incoherent taxon with members of the group lacking a common evolutionary history. Comprising aerobic and anaerobic spore-forming bacteria, no characteristics are known that can distinguish species of this genus from other similar endospore-forming genera. With the availability of complete genomic data from over 30 different species from this group, we have constructed detailed phylogenetic trees to determine the relationships among Bacillus and other closely related taxa. Additionally, we have performed comparative genomic analysis for the determination of molecular markers, in the form of conserved signature indels (CSIs), to assist in the understanding of relationships among species of the genus Bacillus in molecular terms. Based on the analysis, we report here the identification of 11 and 6 CSIs that clearly differentiate a ‘ Bacillus subtilis clade’ and a ‘ Bacillus cereus clade’, respectively, from all other species of the genus Bacillus . No molecular markers were identified that supported a larger clade within this genus. The subtilis and the cereus clades were also the largest observed monophyletic groupings among species from the genus Bacillus in the phylogenetic trees based on 16S rRNA gene sequences and those based upon concatenated sequences for 20 conserved proteins. Thus, the relationships observed among these groups of species through CSIs are independently well supported by phylogenetic analysis. The molecular markers identified in this study provide a reliable means for the reorganization of the currently polyphyletic genus Bacillus into a more evolutionarily consistent set of groups. It is recommended that the genus Bacillus sensu stricto should comprise only the monophyletic subtilis clade that is demarcated by the identified CSIs, with B. subtilis as its type species. Members of the adjoining cereus clade (referred to as the Cereus clade of bacilli), although they are distinct from the subtilis clade, will also retain the Bacillus genus name as they contain several clinically important species, and their transfer into a new genus could have serious consequences. However, all other species that are currently part of the genus Bacillus and not part of these two clades should be eventually transferred to other genera. We also propose that all novel species of the genus Bacillus must meet minimal requirements, foremost among which is that the branching of the prospective species with the Bacillus sensu stricto clade or the Cereus clade of bacilli should be strongly supported by 16S rRNA gene sequence trees or trees based upon concatenated protein sequences. Additionally, the presence of one or more of the CSIs that are specific for these clades may be used to confirm molecularly the placement of the species into these clades. The identified CSIs, in addition to their usefulness for taxonomic and diagnostic purposes, also provide novel probes for genetic and biochemical studies of these bacteria.
-
-
-
-
Genomes of the class Erysipelotrichia clarify the firmicute origin of the class Mollicutes
More LessThe tree of life is paramount for achieving an integrated understanding of microbial evolution and the relationships between physiology, genealogy and genomics. It provides the framework for interpreting environmental sequence data, whether applied to microbial ecology or to human health. However, there remain many instances where there is ambiguity in our understanding of the phylogeny of major lineages, and/or confounding nomenclature. Here we apply recent genomic sequence data to examine the evolutionary history of members of the classes Mollicutes (phylum Tenericutes ) and Erysipelotrichia (phylum Firmicutes ). Consistent with previous analyses, we find evidence of a specific relationship between them in molecular phylogenies and signatures of the 16S rRNA, 23S rRNA, ribosomal proteins and aminoacyl-tRNA synthetase proteins. Furthermore, by mapping functions over the phylogenetic tree we find that the erysipelotrichia lineages are involved in various stages of genomic reduction, having lost (often repeatedly) a variety of metabolic functions and the ability to form endospores. Although molecular phylogeny has driven numerous taxonomic revisions, we find it puzzling that the most recent taxonomic revision of the phyla Firmicutes and Tenericutes has further separated them into distinct phyla, rather than reflecting their common roots.
-
-
-
Taxonomic revision of Harveyi clade bacteria (family Vibrionaceae) based on analysis of whole genome sequences
More LessUse of inadequate methods for classification of bacteria in the so-called Harveyi clade (family Vibrionaceae, Gammaproteobacteria) has led to incorrect assignment of strains and proliferation of synonymous species. In order to resolve taxonomic ambiguities within the Harveyi clade and to test usefulness of whole genome sequence data for classification of Vibrionaceae, draft genome sequences of 12 strains were determined and analysed. The sequencing included type strains of seven species: Vibrio sagamiensis NBRC 104589T, Vibrio azureus NBRC 104587T, Vibrio harveyi NBRC 15634T, Vibrio rotiferianus LMG 21460T, Vibrio campbellii NBRC 15631T, Vibrio jasicida LMG 25398T, and Vibrio owensii LMG 25443T. Draft genome sequences of strain LMG 25430, previously designated the type strain of [Vibrio communis], and two strains (MWB 21 and 090810c) from the ‘beijerinckii’ lineage were also determined. Whole genomes of two additional strains (ATCC 25919 and 200612B) that previously could not be assigned to any Harveyi clade species were also sequenced. Analysis of the genome sequence data revealed a clear case of synonymy between V. owensii and [V. communis], confirming an earlier proposal to synonymize both species. Both strains from the ‘beijerinckii’ lineage were classified as V. jasicida, while the strains ATCC 25919 and 200612B were classified as V. owensii and V. campbellii, respectively. We also found that two strains, AND4 and Ex25, are closely related to Harveyi clade bacteria, but could not be assigned to any species of the family Vibrionaceae. The use of whole genome sequence data for the taxonomic classification of the Harveyi clade bacteria and other members of the family Vibrionaceae is also discussed.
-
- International Committee on Systematics of Prokaryotes
-
- Minutes
Volumes and issues
-
Volume 75 (2025)
-
Volume 74 (2024)
-
Volume 73 (2023)
-
Volume 72 (2022 - 2023)
-
Volume 71 (2020 - 2021)
-
Volume 70 (2020)
-
Volume 69 (2019)
-
Volume 68 (2018)
-
Volume 67 (2017)
-
Volume 66 (2016)
-
Volume 65 (2015)
-
Volume 64 (2014)
-
Volume 63 (2013)
-
Volume 62 (2012)
-
Volume 61 (2011)
-
Volume 60 (2010)
-
Volume 59 (2009)
-
Volume 58 (2008)
-
Volume 57 (2007)
-
Volume 56 (2006)
-
Volume 55 (2005)
-
Volume 54 (2004)
-
Volume 53 (2003)
-
Volume 52 (2002)
-
Volume 51 (2001)
-
Volume 50 (2000)
-
Volume 49 (1999)
-
Volume 48 (1998)
-
Volume 47 (1997)
-
Volume 46 (1996)
-
Volume 45 (1995)
-
Volume 44 (1994)
-
Volume 43 (1993)
-
Volume 42 (1992)
-
Volume 41 (1991)
-
Volume 40 (1990)
-
Volume 39 (1989)
-
Volume 38 (1988)
-
Volume 37 (1987)
-
Volume 36 (1986)
-
Volume 35 (1985)
-
Volume 34 (1984)
-
Volume 33 (1983)
-
Volume 32 (1982)
-
Volume 31 (1981)
-
Volume 30 (1980)
-
Volume 29 (1979)
-
Volume 28 (1978)
-
Volume 27 (1977)
-
Volume 26 (1976)
-
Volume 25 (1975)
-
Volume 24 (1974)
-
Volume 23 (1973)
-
Volume 22 (1972)
-
Volume 21 (1971)
-
Volume 20 (1970)
-
Volume 19 (1969)
-
Volume 18 (1968)
-
Volume 17 (1967)
-
Volume 16 (1966)
-
Volume 15 (1965)
-
Volume 14 (1964)
-
Volume 13 (1963)
-
Volume 12 (1962)
-
Volume 11 (1961)
-
Volume 10 (1960)
-
Volume 9 (1959)
-
Volume 8 (1958)
-
Volume 7 (1957)
-
Volume 6 (1956)
-
Volume 5 (1955)
-
Volume 4 (1954)
-
Volume 3 (1953)
-
Volume 2 (1952)
-
Volume 1 (1951)
Most Read This Month
