-
Volume 57,
Issue 8,
2007
Volume 57, Issue 8, 2007
- New Taxa
-
- Other Gram-Positive Bacteria
-
-
Oscillibacter valericigenes gen. nov., sp. nov., a valerate-producing anaerobic bacterium isolated from the alimentary canal of a Japanese corbicula clam
More LessA mesophilic, strictly anaerobic bacterium, strain Sjm18-20T, was isolated from the alimentary canal of a Japanese corbicula clam. Cells of strain Sjm18-20T were Gram-negative, non-sporulating, straight to slightly curved rods, 2.5–6.0 μm long, and were motile with oscillatory movements by means of peritrichous flagella. Cells elongated to 30 μm after prolonged cultivation. Optimum growth was observed at 30 °C and pH 6.0–6.5. Growth occurred below 4.0 % (w/v) NaCl. Strain Sjm18-20T produced acid from d-glucose and a few pentoses such as l-arabinose, d-ribose and d-xylose. n-Valeric acid was the major end product from glucose. The genomic DNA G+C content of strain Sjm18-20T was 52.9 mol%. Phylogenetic analysis based on the 16S rRNA gene revealed that strain Sjm18-20T could be accommodated in clostridial cluster IV of the low-G+C-content Gram-positive bacteria and that the closest neighbour of this organism (92.6–92.9 % similarity) was the cloned 16S rRNA gene sequence of a not-yet cultured bacterium, thought to represent Oscillospira guilliermondii. The nearest cultivated neighbours of strain Sjm18-20T were Clostridium orbiscindens DSM 6740T and Clostridium viride T2-7T, with sequence similarities of 91.3 and 89.1 %, respectively. On the basis of phenotypic features and phylogenetic position, it is proposed that this isolate represents a novel species in a new genus, Oscillibacter valericigenes gen. nov., sp. nov. The type strain of Oscillibacter valericigenes is Sjm18-20T (=NBRC 101213T =DSM 18026T).
-
-
-
Planifilum yunnanense sp. nov., a thermophilic thermoactinomycete isolated from a hot spring
More LessA thermophilic actinomycete, strain LA5T, was isolated from a hot spring in Yunnan province, People's Republic of China. The isolate grew aerobically at temperatures of 50–75 °C. Aerobic mycelia were not observed. Single spores were produced along the substrate hypha. Strain LA5T was characterized chemotaxonomically by having MK-7 as the predominant menaquinone and iso-C17 : 0 (27.7 %) and C16 : 0 (22.4 %) as the major fatty acids. The cell wall contained meso-diaminopimelic acid. The DNA G+C content was 56.8 mol%. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain LA5T belongs to the genus Planifilum. Levels of DNA–DNA relatedness between strain LA5T and Planifilum fimeticola H0165T and Planifilum fulgidum 500275T were 43.6 and 52.7 %, respectively. On the basis of phenotypic properties and phylogeny, strain LA5T represents a novel species of the genus Planifilum, for which we propose the name Planifilum yunnanense sp. nov., with the type strain LA5T (=CCTCC AA206002T=KCTC 13052T).
-
-
-
Sporosarcina saromensis sp. nov., an aerobic endospore-forming bacterium
More LessTwo Gram-positive, endospore-forming, rod-shaped bacterial strains, HG645T and HG711, were respectively isolated from surface water of a brackish lake and sediment of a fishery harbour in Japan and were subsequently characterized taxonomically using a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains HG645T and HG711 are affiliated phylogenetically to the genus Sporosarcina, and they exhibit sequence similarities of 95.7–97.3 % to the type strains of Sporosarcina species. DNA–DNA relatedness between strain HG645T and the type strain of the phylogenetically related species Sporosarcina aquimarina was less than 10 %. The DNA G+C content of strains HG645T and HG711 were respectively 46.0 and 45.2 mol%. Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The cell-wall peptidoglycan type (Lys–Glu), major cellular fatty acids (iso-C15 : 0 and anteiso-C15 : 0) and quinone type (MK-7) of the isolates support their affiliation to the genus Sporosarcina. On the basis of phylogenetic analysis and physiological and chemotaxonomic data, the isolates represent a novel species of the genus Sporosarcina, for which the name Sporosarcina saromensis sp. nov. is proposed. The type strain is strain HG645T (=MBIC08270T=IAM 15429T =KCTC 13119T).
-
-
-
Clostridium nitrophenolicum sp. nov., a novel anaerobic p-nitrophenol-degrading bacterium, isolated from a subsurface soil sample
More LessAn obligate anaerobic, mesophilic, motile and endospore-forming bacterium, designated 1DT, was isolated from a subsurface soil sample. The young culture of strain 1DT was Gram-positive and formed oval spores that were central in position. Based on the biochemical, chemotaxonomic and physiological data, strain 1DT appears to be a member of the genus Clostridium. Strain 1DT was found to be capable of degrading p-nitrophenol (pNP) at a concentration of 0.5 mM under anaerobic conditions as revealed by HPLC analysis. The major fatty acids were C16 : 0 (28.02 %), iso-C17 : 1 I/anteiso B (23.05 %) and C14 : 0 (10.02 %). The major polar lipid content was diphosphatidylglycerol. Strain 1DT showed highest 16S rRNA gene sequence similarity to Clostridium aciditolerans JW/YJL-B3T (98.2 %) and similarity was less for Clostridium scatologenes ATCC 25775T (95.1 %), Clostridium drakei SL1T (95.0 %) and Clostridium carboxidivorans P7T (95.0 %). Phylogenetic analysis showed that it formed a coherent cluster with the species belonging to cluster I of the genus Clostridium. The DNA G+C content was 35.5 mol%. DNA–DNA hybridization analysis indicated a mean value of 36.4 % between strain 1DT and its closest relative C. aciditolerans. Several phenotypic differences from the closely related species were also revealed. On the basis of the polyphasic characteristics, strain 1DT represents a novel species of the genus Clostridium, for which the name Clostridium nitrophenolicum sp. nov. is proposed. The type strain is 1DT (=MTCC 7832T=JCM 14030T).
-
-
-
Salinicoccus luteus sp. nov., isolated from a desert soil
More LessA moderately halophilic bacterium, strain YIM 70202T, was isolated from a desert soil sample collected from Egypt and was subjected to a taxonomic investigation. In a phylogenetic dendrogram based on 16S rRNA gene sequence analysis, strain YIM 70202T was affiliated to the Salinicoccus clade, showing 94.5–96.8 % 16S rRNA gene sequence similarity to the recognized species of the genus Salinicoccus, in which Salinicoccus roseus CCM 3516T was the nearest neighbour. The DNA–DNA relatedness value of the novel isolate with S. roseus CCM 3516T was 12.7 %. The novel isolate grew at temperatures between 4 and 45 °C and at pH values ranging from 7.0 to 11.0, with an optimum of 30 °C and pH 8.0–9.0, respectively. Strain YIM 70202T grew optimally in the presence of 10 % NaCl (w/v) and growth was observed at NaCl concentrations in the range 1–25 % (w/v). Chemotaxonomic data revealed that strain YIM 70202T contained MK-6 as the predominant respiratory quinone, possessed l-Lys–Gly5 as the cell-wall peptidoglycan, had phosphatidylglycerol, diphosphatidylglycerol and an unknown glycolipid as the polar lipids and contained i-C15 : 0 and ai-C15 : 0 as the predominant fatty acids. The DNA G+C content was 49.7 mol%. The biochemical and chemotaxonomic properties demonstrate that strain YIM 70202T represents a novel species of the genus Salinicoccus. The name Salinicoccus luteus sp. nov. is proposed with strain YIM 70202T (=CGMCC 1.6511T=KCTC 3941T) as the type strain.
-
-
-
Bacillus niabensis sp. nov., isolated from cotton-waste composts for mushroom cultivation
A group of five bacilli, designated strains 4T12, 4T19T, 5M45, 5M53 and 5T52, isolated from cotton-waste composts for mushroom cultivation, were examined. These strains were Gram-positive, aerobic, motile, spore-forming rods. 16S rRNA gene sequence analyses revealed that the isolates belonged to the genus Bacillus, showing the highest levels of similarity (approx. 96.6–96.9 %) with respect to Bacillus herbersteinensis DSM 16534T. The values for DNA–DNA hybridization (approx. 85–96 %) among these five strains revealed that they belong to the same species. The major menaquinone present was MK-7 and the predominant cellular fatty acids were anteiso-C15 : 0 (approx. 24.5–33.9 %) and C16 : 0 (approx. 15.1–34.1 %). The DNA G+C contents were 37.7–40.9 mol%. On the basis of physiological, biochemical, chemotaxonomic and comparative genomic analyses, the five isolates represent a novel species of the genus Bacillus, for which the name Bacillus niabensis sp. nov. is proposed. The type strain is 4T19T (=KACC 11279T =DSM 17723T).
-
-
-
Aminiphilus circumscriptus gen. nov., sp. nov., an anaerobic amino-acid-degrading bacterium from an upflow anaerobic sludge reactor
More LessStrain ILE-2T was isolated from an upflow anaerobic sludge bed reactor treating brewery wastewater. The motile, non-sporulating, slightly curved cells (2–4×0.1 μm) stained Gram-negative and grew optimally at 42 °C and pH 7.1 with 0.5 % NaCl. The strain required yeast extract for growth and fermented Casamino acids, peptone, isoleucine, arginine, lysine, alanine, valine, glutamate, histidine, glutamine, methionine, malate, fumarate, glycerol and pyruvate to acetate, propionate and minor amounts of branched-chain fatty acids. Carbohydrates, formate, acetate, propionate, butyrate, isovalerate, methanol, ethanol, 1-propanol, butanol, lactate, succinate, starch, casein, gelatin, xylan and a number of other amino acids were not utilized. The DNA G+C content of strain ILE-2T was 52.7 mol%. 16S rRNA gene sequence analysis revealed that ILE-2T was distantly related to members of the genera Aminobacterium (83 % similarity) and Aminomonas (85 % similarity) in the family Syntrophomonadaceae, order Clostridiales, phylum Firmicutes. On the basis of the results of our polyphasic analysis, strain ILE-2T represents a novel species and genus within the family Syntrophomonadaceae, for which the name Aminiphilus circumscriptus gen. nov., sp. nov. is proposed. The type strain of Aminiphilus circumscriptus is ILE-2T (=DSM 16581T =JCM 14039T).
-
- Evolution, Phylogeny And Biodiversity
-
-
-
Comparison of gyrB gene sequences, 16S rRNA gene sequences and DNA–DNA hybridization in the Bacillus subtilis group
More LessThe Bacillus subtilis group comprises eight closely related species that are indistinguishable from one another by 16S rRNA gene sequence analysis. Therefore, the gyrB gene, which encodes the subunit B protein of DNA gyrase, was selected as an alternative phylogenetic marker. To determine whether gyrB gene sequence analysis could be used for phylogenetic analysis and species identification of members of the B. subtilis group, the congruence of gyrB grouping with both 16S rRNA gene sequencing and DNA–DNA hybridization data was evaluated. Ranges of gyrB nucleotide and translated amino acid sequence similarities among the eight type strains were 75.4–95.0 % and 88.5–99.2 %, respectively, whereas 16S rRNA gene sequence similarities were 98.1–99.8 %. Results showed that gyrB gene sequences provide higher resolution than 16S rRNA gene sequences. The classification achieved by gyrB sequence analysis was in agreement with results obtained with DNA–DNA hybridization. It is concluded that the gyrB gene may be an efficient alternative target for identification and taxonomic analysis of members of the B. subtilis group.
-
-
-
-
Computer-simulated RFLP analysis of 16S rRNA genes: identification of ten new phytoplasma groups
More LessPhytoplasmas are cell wall-less bacteria that cause numerous plant diseases. As no phytoplasma has been cultured in cell-free medium, phytoplasmas cannot be differentiated and classified by the traditional methods which are applied to culturable prokaryotes. Over the past decade, the establishment of a phytoplasma classification scheme based on 16S rRNA restriction fragment length polymorphism (RFLP) patterns has enabled the accurate and reliable identification and classification of a wide range of phytoplasmas. In the present study, we expanded this classification scheme through the use of computer-simulated RFLP analysis, achieving rapid differentiation and classification of phytoplasmas. Over 800 publicly available phytoplasma 16S rRNA gene sequences were aligned using the clustal_x program and the aligned 1.25 kb fragments were exported to pDRAW32 software for in silico restriction digestion and virtual gel plotting. Based on distinctive virtual RFLP patterns and calculated similarity coefficients, phytoplasma strains were classified into 28 groups. The results included the classification of hundreds of previously unclassified phytoplasmas and the delineation of 10 new phytoplasma groups representing three recently described and seven novel putative ‘Candidatus Phytoplasma’ taxa.
-
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
