- Volume 63, Issue Pt_4, 2013
Volume 63, Issue Pt_4, 2013
- New Taxa
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- Bacteroidetes
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Pedobacter ginsengiterrae sp. nov., isolated from soil of a ginseng field
More LessA Gram-stain-negative, oxidase- and catalase-positive bacterial strain that was motile by gliding and produced a pink pigment, designated DCY49T, was isolated from soil of a ginseng field in a mountainous region of Chungbuk province, South Korea. 16S rRNA gene sequence analysis revealed that strain DCY49T belonged to the genus Pedobacter (93.0–96.3 % similarity). Strain DCY49T contained MK-7 as the predominant menaquinone. The major fatty acids were summed feature 3 (containing C16 : 1ω7c, C16 : 1ω6c and/or iso-C15 : 0 2-OH), iso-C15 : 0, iso-C17 : 0 3-OH and C16 : 0, and the main polar lipid was phosphatidylethanolamine. The G+C content of the genomic DNA of strain DCY49T was 40.5 mol%. Strain DCY49T differed from related Pedobacter species by a number of phenotypic characteristics. On the basis of data from the present polyphasic study, strain DCY49T is described as representing a novel species of the genus Pedobacter , for which the name Pedobacter ginsengiterrae sp. nov. is proposed. The type strain is DCY49T ( = KCTC 23317T = JCM 17338T).
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Pedobacter luteus sp. nov., isolated from soil
Two strains of Gram-staining-negative, rod-shaped bacteria that were motile by gliding, N7d-4T and B4a-b5, were isolated during a study of culturable bacteria in soil cultivated with potatoes. These isolates grew at 15–37 °C and at pH 6.5–7.0. The major cellular fatty acids were summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), anteiso-C15 : 0, iso-C15 : 0, iso-C17 : 0 3-OH and iso-C17 : 1ω9c. The major polar lipids were phosphatidyl-N-methylethanolamine and phosphatidylethanolamine. The strains contained d-18 : 0 and d-19 : 0 sphingosines. The DNA G+C contents of strains N7d-4T and B4a-b5 were 48.5 and 46.9 mol% (HPLC), respectively. A phylogenetic analysis based on 16S rRNA gene sequences showed that strains N7d-4T and B4a-b5 were affiliated with Pedobacter species in the family Sphingobacteriaceae . Strains N7d-4T and B4a-b5 shared 99.9 % sequence similarity, and the most closely related Pedobacter type strains were Pedobacter composti TR6-06T (96.5 and 96.7 % sequence similarity, respectively), P. oryzae N7T (95.4 and 95.6 %) and P. caeni LMG 22862T (94.0 and 94.4 %). Phenotypic data and phylogenetic inference clearly distinguished the two isolates from other Pedobacter species. Based on these data, the isolates are considered to represent a novel species of the genus Pedobacter , for which the name Pedobacter luteus sp. nov. is proposed. The type strain is N7d-4T ( = KCTC 22699T = DSM 22385T).
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Description of Alloprevotella rava gen. nov., sp. nov., isolated from the human oral cavity, and reclassification of Prevotella tannerae Moore et al. 1994 as Alloprevotella tannerae gen. nov., comb. nov.
More LessFive strains of anaerobic, Gram-negative bacilli isolated from the human oral cavity were subjected to a comprehensive range of phenotypic and genotypic tests and were found to comprise a homogeneous group. Phylogenetic analysis of full-length 16S rRNA gene sequences showed that these strains represented a novel group within the family Prevotellaceae , and the most closely related species was Prevotella tannerae . P. tannerae and the novel taxon are deeply branched from the genus Prevotella , with sequence identities to the type strain of the type species of Prevotella , Prevotella melaninogenica , of 82.2 and 85.6 %, respectively. The novel genus Alloprevotella gen. nov. is proposed to accommodate the novel species Alloprevotella rava gen. nov., sp. nov. and the previously named Prevotella tannerae Moore et al. 1994 as Alloprevotella tannerae gen. nov., comb. nov. The type species is Alloprevotella tannerae. The type strain of Alloprevotella rava is 81/4-12T ( = DSM 22548T = CCUG 58091T) and the type strain of Alloprevotella tannerae is ATCC 51259T = CCUG 34292T = CIP 104476T = NCTC 13073T. Alloprevotella rava is weakly to moderately saccharolytic and produces moderate amounts of acetic acid and major amounts of succinic acid as end products of fermentation. Strains are sensitive to 20 % bile and hydrolyse gelatin. The principal cellular long-chain fatty acids are anteiso-C15 : 0, iso-C15 : 0, C16 : 0, iso-C17 : 0 and iso-C17 : 0 3-OH. The G+C content of the DNA of the type strain is 47 mol%.
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- Other Bacteria
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Dehalogenimonas alkenigignens sp. nov., a chlorinated-alkane-dehalogenating bacterium isolated from groundwater
More LessTwo strictly anaerobic bacterial strains, designated IP3-3T and SBP-1, were isolated from groundwater contaminated by chlorinated alkanes and alkenes at a Superfund Site located near Baton Rouge, Louisiana (USA). Both strains reductively dehalogenate a variety of polychlorinated aliphatic alkanes, including 1,2-dichloroethane, 1,2-dichloropropane, 1,1,2,2-tetrachloroethane, 1,1,2-trichloroethane and 1,2,3-trichloropropane, when provided with hydrogen as the electron donor. To clarify their taxonomic position, strains IP3-3T and SBP-1 were characterized using a polyphasic approach. Both IP3-3T and SBP-1 are mesophilic, non-spore-forming, non-motile and Gram-stain-negative. Cells of both strains are irregular cocci with diameters of 0.4–1.1 µm. Both are resistant to ampicillin and vancomycin. The genomic DNA G+C contents of strains IP3-3T and SBP-1 are 55.5±0.4 and 56.2±0.2 mol% (HPLC), respectively. Major cellular fatty acids include C18 : 1ω9c, C16 : 0, C14 : 0 and C16 : 1ω9c. 16S rRNA gene sequence based phylogenetic analyses indicated that the strains cluster within the phylum Chloroflexi most closely related to but distinct from the species Dehalogenimonas lykanthroporepellens (96.2 % pairwise similarity) and Dehalococcoides mccartyi (90.6 % pairwise similarity). Physiological and chemotaxonomic traits as well as phylogenetic analysis support the conclusion that these strains represent a novel species within the genus Dehalogenimonas for which the name Dehalogenimonas alkenigignens sp. nov. is proposed. The type strain is IP3-3T ( = JCM 17062T = NRRL B-59545T).
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Lentisphaera marina sp. nov., and emended description of the genus Lentisphaera
More LessTwo Gram-stain-negative, non-motile, non-pigmented cocci, designated IMCC11369T and IMCC11389, were isolated from surface seawater of the East Sea of Korea by high-throughput cultivation based on dilution to extinction. Strains IMCC11369T and IMCC11389 shared 99.9 % 16S rRNA gene sequence similarity and >86.3 % DNA–DNA relatedness, which suggested that they belong to the same genomic species. The isolates were most closely related to Lentisphaera araneosa HTCC2155T (99.0 % 16S rRNA gene sequence similarity). Phylogenetic analysis revealed that the isolates formed a robust cluster with L. araneosa HTCC2155T. DNA–DNA relatedness values, however, showed that the isolates were distantly related to L. araneosa HTCC2155T (2.0–18.6 %), which suggested that they represent a separate genomic species in the genus Lentisphaera . The two isolates were phenotypically differentiated from their closest relative by several characteristics, including degradation of macromolecules and carbon source utilization. The DNA G+C content was 44.5–45.2 mol% and the predominant cellular fatty acids were C14 : 0, C16 : 1ω9c and C16 : 0. Strain IMCC11369T contained MK-7 as the respiratory quinone and phosphatidylethanolamine and an unknown lipid as the major polar lipids. On the basis of data obtained in this study, a novel species is proposed to accommodate the isolates, Lentisphaera marina sp. nov. The type strain is IMCC11369T ( = KCTC 23780T = NBRC 108776T).
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Phylogenetic analysis identifies a ‘Candidatus Phytoplasma oryzae ’-related strain associated with yellow leaf disease of areca palm (Areca catechu L.) in India
More LessYellow leaf disease (YLD) with phytoplasmal aetiology is a serious disease of arecanut palm in India. The present study was undertaken to characterize the 16S rRNA and secA gene sequences of the Indian arecanut YLD phytoplasma for ‘Candidatus Phytoplasma ’ species assignment and 16Sr group/subgroup classification. Phytoplasma 16S rRNA genes were amplified using three sets of semi-nested/nested primers, 1F7/7R3–1F7/7R2, 4Fwd/3Rev–4Fwd/5Rev and P1/P7–R16F2n/R16R2, producing amplicons of 491, 1150 and 1250 bp, respectively, from diseased samples. The amplicons were cloned and sequenced. A blast search showed that the sequences had 99 % similarity with sugar cane white leaf phytoplasma (16SrXI) and Napier grass stunt phytoplasma (16SrXI). Phylogenetic analysis based on the 16S rRNA gene revealed the clustering of YLD phytoplasma with the rice yellow dwarf and Bermuda grass white leaf groups. The YLD phytoplasma F2nR2 sequence shared 97.5 % identity with that of ‘Candidatus Phytoplasma oryzae ’ and 97.8 % identity with that of ‘Candidatus Phytoplasma cynodontis ’. Hence, for finer differentiation, we examined the secA gene-based phylogeny, where the YLD phytoplasma clustered with Napier grass stunt and sugar cane grassy shoot phytoplasmas, both belonging to the rice yellow dwarf group. Hence, we are assigning the Indian arecanut YLD phytoplasma as a ‘Candidatus Phytoplasma oryzae ’-related strain. Virtual RFLP analysis of a 1.2 kb fragment of the 16S rRNA gene (F2nR2 region) identified the Indian arecanut YLD phytoplasma as a member of 16SrXI-B subgroup. We name the phytoplasma Indian yellow leaf disease phytoplasma, to differentiate it from the Hainan YLD phytoplasma, which belongs to group 16SrI.
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- Eukaryotic Micro-organisms
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Wickerhamomyces siamensis sp. nov., a novel yeast species isolated from the phylloplane in Thailand
More LessStrain DMKU-RK359T, representing a novel yeast species, was isolated from the external surface of a sugar-cane leaf collected in Thailand. On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics, sequence analysis of the D1/D2 region of the large-subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region, strain DMKU-RK359T was assigned to a novel Wickerhamomyces species. The novel species was closest to Wickerhamomyces ciferrii, but differed from it by 0.7 % nucleotide substitutions in the D1/D2 region of the LSU rRNA gene and 6 % nucleotide substitutions in the ITS region. The name Wickerhamomyces siamensis sp. nov. is proposed (type strain DMKU-RK359T = BCC 50732T = NBRC 108900T = CBS 12570T).
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- ICSP
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Volumes and issues
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Volume 74 (2024)
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Volume 71 (2020 - 2021)
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Volume 69 (2019)
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Volume 1 (1951)