- Volume 59, Issue 7, 2009
Volume 59, Issue 7, 2009
- New Taxa
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- Proteobacteria
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Marinobacter lacisalsi sp. nov., a moderately halophilic bacterium isolated from the saline-wetland wildfowl reserve Fuente de Piedra in southern Spain
A Gram-negative, non-spore-forming, motile, moderately halophilic, aerobic, rod-shaped bacterium, designated strain FP2.5T, was isolated from the inland hypersaline lake Fuente de Piedra, a saline-wetland wildfowl reserve located in the province of Málaga in southern Spain. Strain FP2.5T was subjected to a polyphasic taxonomic study. It produced colonies with a light-yellow pigment. Strain FP2.5T grew at salinities of 3–15 % (w/v) and at temperatures of 20–40 °C. The pH range for growth was 5–9. Strain FP2.5T was able to utilize various organic acids as sole carbon and energy source. Its major fatty acids were C16 : 0, C18 : 1 ω9c and C16 : 1 ω9c. The DNA G+C content was 58.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain FP2.5T appeared to be a member of the genus Marinobacter and clustered closely with the type strains of Marinobacter segnicrescens, Marinobacter bryozoorum and Marinobacter gudaonensis (levels of 16S rRNA gene sequence similarity of 98.1, 97.4 and 97.2 %, respectively). However, DNA–DNA relatedness between the new isolate and the type strains of its closest related Marinobacter species was low; levels of DNA–DNA relatedness between strain FP2.5T and M. segnicrescens LMG 23928T, M. bryozoorum DSM 15401T and M. gudaonensis DSM 18066T were 36.3, 32.1 and 24.9 %, respectively. On the basis of phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness data, strain FP2.5T is considered to represent a novel species of the genus Marinobacter, for which the name Marinobacter lacisalsi sp. nov. is proposed. The type strain is FP2.5T (=CECT 7297T=LMG 24237T).
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Microbulbifer variabilis sp. nov. and Microbulbifer epialgicus sp. nov., isolated from Pacific marine algae, possess a rod–coccus cell cycle in association with the growth phase
Phylogenetic and taxonomic characterization was performed for 14 strains of bacteria that produce anticancer antibiotics (pelagiomicins) (represented by strain Ni-2088T) and one strain that produces UV-absorbing substances (strain F-104T), isolated from marine algae and seagrass collected from coastal areas of tropical Pacific islands and a subtropical island of Japan. All 15 isolates were Gram-negative, strictly aerobic, non-motile and non-spore-forming. Sequence analysis of the 16S rRNA gene showed that the isolates occupied positions in the phylogenetic radiation of the genus Microbulbifer, with similarities of 93.6–97.6 %. The cells possessed a clearly discernible rod–coccus cell cycle in association with the growth phase; cells were rods during the growth phase and all converted to coccoid–ovoid cells when proliferation ceased. The coccoid–ovoid cells were optically denser than the rod cells and were viable for extended periods. They were considered to constitute a resting form. The type strains of described species of Microbulbifer were also found to possess identical rod–coccus cell cycles. The G+C content of the DNA was 48.1–49.7 mol%. The major respiratory quinone system was ubiquinone-8. The major fatty acids were C18 : 1 ω7c and C16 : 0, and the hydroxy acids comprised C10 : 0 3-OH, C12 : 0 3-OH and iso-C11 : 0 3-OH. The polar lipids comprised phosphatidylethanolamine, phosphatidylglycerol and phosphatidylserine. The group of 14 pelagiomicin-producing strains and strain F-104T each constituted a single genomic species. Based on phylogenetic affiliation, phenotypic characteristics and genomic distinctness, the isolates represent two novel species in the genus Microbulbifer, for which the names Microbulbifer variabilis sp. nov. (type strain Ni-2088T =MBIC01082T =ATCC 700307T) and Microbulbifer epialgicus sp. nov. (type strain F-104T =MBIC03330T =DSM 18651T) are proposed.
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Oceanibaculum indicum gen. nov., sp. nov., isolated from deep seawater of the Indian Ocean
More LessA taxonomic study was carried out on strain P24T, which was isolated from a polycyclic aromatic hydrocarbon-degrading consortium, enriched from a deep-seawater sample collected from the Indian Ocean. The isolate was Gram-negative, rod-shaped, motile by means of a polar flagellum, moderately halophilic and capable of reducing nitrate to nitrite. Growth was observed at salinities of 0–9 % and at temperatures of 10–42 °C. The strain was unable to degrade Tween 80 or gelatin. The dominant fatty acids were C16 : 0 (15.2 % of the total), C18 : 0 (10.3 %), C18 : 1 ω7c (52.0 %), C18 : 1 2-OH (4.7 %) and C19 : 0 ω8c cyclo (4.7 %). The G+C content of the chromosomal DNA was 64.8 mol%. 16S rRNA gene sequence comparisons showed that strain P24T was related most closely to Thalassobaculum litoreum CL-GR58T (92.7 % similarity); levels of similarity between strain P24T and type strains of recognized species in the family Rhodospirillaceae were all less than 90.8 %. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain P24T formed a distinct evolutionary lineage within the family Rhodospirillaceae. Strain P24T could be distinguished from phylogenetically related genera based on differences in several phenotypic properties. On the basis of the phenotypic and phylogenetic data presented, strain P24T is considered to represent a novel species of a new genus, for which the name Oceanibaculum indicum gen. nov., sp. nov. is proposed. The type strain is P24T (=CCTCC AB 208226T=LMG 24626T=MCCC 1A02083T).
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Parasutterella excrementihominis gen. nov., sp. nov., a member of the family Alcaligenaceae isolated from human faeces
More LessA novel, strictly anaerobic, non-spore-forming, Gram-negative coccobacillus (strain YIT 11859T) was isolated from human faeces. Biochemically, this strain was largely unreactive and was asaccharolytic. Growth of strain YIT 11859T in peptone-yeast extract broth produced no visible turbidity, and a trace amount of propionate was detected as an end product of metabolism. 16S rRNA gene sequence analysis showed that strain YIT 11859T was related most closely to the type strains of Sutterella species, with 90.8–88.0 % sequence similarity. Phylogenetic analysis of these and other related sequences confirmed that strain YIT 11859T was phylogenetically most closely associated with Sutterella species, but formed a separate cluster, indicating that strain YIT 11859T represents a novel member of the family Alcaligenaceae. Fatty acid analysis demonstrated the presence of a high concentration of C18 : 1 ω9c (75 % of the total). The main respiratory quinones were menaquinone (MK–6) and methylated menaquinone (MMK-6). The G+C content of the DNA was 49.8 mol%. These results suggest that strain YIT 11859T represents a novel species of a new genus, for which the name Parasutterella excrementihominis gen. nov., sp. nov. is proposed. The type strain of Parasutterella excrementihominis is YIT 11859T (=DSM 21040T =JCM 15078T).
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- Eukaryotic Micro-Organisms
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Pseudozyma pruni sp. nov., a novel ustilaginomycetous anamorphic fungus from flowers in Taiwan
More LessTwo ustilaginomycetous anamorphic strains were isolated from flowers in Taiwan. Phylogenetic analysis based on the combined rRNA gene sequence of internal transcribed spacer 1 (ITS1)–5.8S–ITS2 and large-subunit D1/D2 domains indicated that the closest recognized species was Pseudozyma fusiformata. The results of DNA–DNA hybridization and physiological characteristics showed that the two strains represent a novel species within the genus Pseudozyma. The name Pseudozyma pruni sp. nov. is proposed, with FIRDI 005T (=BCRC 34227T =CBS 10937T) as the type strain.
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Lachancea dasiensis sp. nov., an ascosporogenous yeast isolated from soil and leaves in Taiwan
More LessA novel yeast species, Lachancea dasiensis sp. nov., is proposed in this paper based on two strains isolated from leaves and one strain from soil in Taiwan. The strains produce one or two spherical ascospores in each ascus, preceded by conjugation of individual cells. Genus assignment and distinction of the species from other recognized species of Lachancea are based on morphological and physiological characteristics and on phylogenetic analysis of nucleotide sequences of the D1/D2 domains of the large subunit (LSU) rRNA gene. Sequence analysis of the D1/D2 domains of the LSU rRNA gene reveals that the phylogenetically closest relatives of L. dasiensis sp. nov. are Lachancea thermotolerans and Lachancea waltii. The novel species could be differentiated from the latter two species based on electrophoretic karyotypes. The type strain of Lachancea dasiensis sp. nov. is SC5L02T (=CBS 10888T =BCRC 23139T), which was isolated from a leaf of Angiopteris lygodiifolia Rosenst. in Dasi, Taoyuan, Taiwan.
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- Methods
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Differentiation of species of the family Acetobacteraceae by AFLP DNA fingerprinting: Gluconacetobacter kombuchae is a later heterotypic synonym of Gluconacetobacter hansenii
More LessAmplified fragment length polymorphism (AFLP) DNA fingerprinting was investigated as a tool for fast and accurate identification of acetic acid bacteria (AAB) to the species level. One hundred and thirty five reference strains and 15 additional strains, representing 50 recognized species of the family Acetobacteraceae, were subjected to AFLP analysis using the restriction enzyme combination ApaI/TaqI and the primer combination A03/T03. The reference strains had been previously subjected to either DNA–DNA hybridization or 16S–23S rRNA spacer region gene sequence analysis and were regarded as being accurately classified at the species level. The present study revealed that six of these strains should be reclassified, namely Gluconacetobacter europaeus LMG 1518 and Gluconacetobacter xylinus LMG 1510 as Gluconacetobacter xylinus and Gluconacetobacter europaeus, respectively; Gluconacetobacter kombuchae LMG 23726T as Gluconacetobacter hansenii; and Acetobacter orleanensis strains LMG 1545, LMG 1592 and LMG 1608 as Acetobacter cerevisiae. Cluster analysis of the AFLP DNA fingerprints of the reference strains revealed one cluster for each species, showing a linkage level below 50 % with other clusters, except for Acetobacter pasteurianus, Acetobacter indonesiensis and Acetobacter cerevisiae. These three species were separated into two, two, and three clusters, respectively. At present, confusion exists regarding the taxonomic status of Gluconacetobacter oboediens and Gluconacetobacter intermedius; the AFLP data from this study supported their classification as separate taxa. The 15 additional strains could all be identified at the species level. AFLP analysis further revealed that some species harboured genetically diverse strains, whereas other species consisted of strains showing similar banding patterns, indicating a more limited genetic diversity. It can be concluded that AFLP DNA fingerprinting is suitable for accurate identification and classification of a broad range of AAB, as well as for the determination of intraspecific genetic diversity.
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- International Committee On Systematics Of Prokaryotes
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Proposed minimal standards for describing new genera and species of the suborder Micrococcineae
The Subcommittee on the Taxonomy of the Suborder Micrococcineae of the International Committee on Systematics of Prokaryotes has agreed on minimal standards for describing new genera and species of the suborder Micrococcineae. The minimal standards are intended to provide bacteriologists involved in the taxonomy of members of the suborder Micrococcineae with a set of essential requirements for the description of new taxa. In addition to sequence data comparisons of 16S rRNA genes or other appropriate conservative genes, phenotypic and genotypic criteria are compiled which are considered essential for the comprehensive characterization of new members of the suborder Micrococcineae. Additional features are recommended for the characterization and differentiation of genera and species with validly published names.
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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 46 (1996)
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Volume 25 (1975)
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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 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)