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Volume 56,
Issue 1,
2006
Volume 56, Issue 1, 2006
- New Taxa
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- Other Gram-Positive Bacteria
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Pilibacter termitis gen. nov., sp. nov., a lactic acid bacterium from the hindgut of the Formosan subterranean termite (Coptotermes formosanus)
More LessA previously undescribed anaerobic, heterofermentative, non-spore-forming, Gram-positive rod was isolated from the hindgut of the Formosan subterranean termite Coptotermes formosanus Shiraki. The DNA G+C content of this bacterium was 37·8 mol%. Sequence analysis of the 16S rRNA gene revealed that this organism is related to, but distinct from, several genera of lactic acid bacteria, principally several species of the genus Enterococcus. Phenotypic traits that serve to separate this organism from related genera include high levels of the cellular fatty acid C18 : 1ω9c and the production of ethanol along with lactic acid as fermentation products. Based on the collected phylogenetic and phenotypic evidence, it is proposed that the unknown organism represents a novel species in a new genus, Pilibacter termitis gen. nov., sp. nov. The type strain is TI-1T (=ATCC BAA-1030T=CCUG 49613T).
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Lactobacillus sobrius sp. nov., abundant in the intestine of weaning piglets
To obtain porcine isolates related to Lactobacillus amylovorus, we screened strains from piglet intestine grown on Lactobacillus-specific MRS agar for hybridization to a fluorescent 16S rRNA-targeted DNA probe. Six strains were isolated and further characterized by phenotypic and molecular taxonomic methods. The isolates were Gram-positive, catalase-negative, facultatively anaerobic rods. They had similar phenotypic characteristics and displayed genomic DNA–DNA relatedness values of >78 % to each other, indicating that they belong to a single species. Comparative 16S rRNA gene sequence analysis demonstrated that the novel isolates were members of Lactobacillus rRNA group I, which includes Lactobacillus delbrueckii, the type species of the genus. Based on 16S rRNA gene sequence similarity, Lactobacillus kitasatonis (99 %), Lactobacillus crispatus (98 %) and Lactobacillus amylovorus (97 %) were the nearest relatives of the novel isolates, but their DNA–DNA relatedness was found to be lower than 49 %. One of the isolates, strain OTU171-001T, was further characterized using physiological and biochemical tests. Together, the results enabled genotypic and phenotypic differentiation of strain OTU171-001T from the other species that showed 16S rRNA gene sequence similarity values greater than 97 %. Strain OTU171-001T merits species status and the name Lactobacillus sobrius sp. nov. is proposed. The type strain is OTU171-001T (=DSM 16698T=NCCB 100067T).
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Bacillus koreensis sp. nov., a spore-forming bacterium, isolated from the rhizosphere of willow roots in Korea
More LessAn endospore-forming, rod-shaped bacterium was isolated from the rhizosphere of willow roots in Korea. The bacterium, designated strain BR030T, was a strictly aerobic, motile rod. The cell wall contained type A1γ peptidoglycan with meso-diaminopimelic acid as the diagnostic diamino acid. The major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, iso-C14 : 0 and iso-C16 : 0. The major cellular phospholipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and unknown phospholipids (PL1, PL2). The genomic DNA G+C content was 36 mol%. Comparative 16S rRNA gene sequence analyses showed that strain BR030T formed a distinct phyletic line within the genus Bacillus and was most closely related to Bacillus flexus DSM 1320T, with 16S rRNA gene sequence similarity of 96·8 %. Sequence similarities to other type strains were lower than 96·2 %. On the basis of physiological and molecular properties, the isolate represents a novel species within the genus Bacillus, for which the name Bacillus koreensis sp. nov. is proposed. The type strain is BR030T (=KCTC 3914T=DSM 16467T).
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Reclassification of Leuconostoc argentinum as a later synonym of Leuconostoc lactis
Leuconostoc argentinum, Leuconostoc lactis and ten related strains from Romanian dairy products formed a single cluster, clearly separated from other Leuconostoc species, after numerical analysis of repetitive extragenic palindromic-PCR patterns, whole-cell protein profiles (SDS-PAGE) and fluorescent amplified fragment length polymorphism (FAFLP) band patterns. 16S rRNA gene sequence analysis confirmed a very high similarity between both type strains and representative dairy isolates (>99·6 %). DNA–DNA hybridization experiments revealed high relatedness values between the type strains of L. argentinum and L. lactis and between these strains and representative Romanian strains. These data and the lack of phenotypic distinctive characteristics demonstrate that L. argentinum and L. lactis are synonymous.
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Virgibacillus koreensis sp. nov., a novel bacterium from a salt field, and transfer of Virgibacillus picturae to the genus Oceanobacillus as Oceanobacillus picturae comb. nov. with emended descriptions
More LessA novel Virgibacillus strain, BH30097T, was isolated from a salt field near Taean-Gun on the Yellow Sea in Korea. Cells were Gram-positive rods and bore ellipsoidal endospores in terminal positions. The optimum pH and temperature for growth of this organism were pH 7 and 25 °C, respectively. The main respiratory quinone was MK-7 and the major cellular fatty acids were anteiso-C15 : 0 and iso-C16 : 0. Analysis based on 16S rRNA gene sequence data revealed that the isolate formed an evolutionary lineage distinct from other Virgibacillus species. Levels of sequence similarity between the isolate and other Virgibacillus species ranged from 93·8 to 96·7 %. DNA–DNA relatedness values between strain BH30097T and a phylogenetically closely related strain, Virgibacillus halodenitrificans KCTC 3790T, were less than 24 %. On the basis of morphological, physiological and chemotaxonomic characteristics, 16S rRNA gene sequence comparison and DNA–DNA hybridization, a novel species, Virgibacillus koreensis sp. nov., is proposed, with the type strain BH30097T (=KCTC 3823T=JCM 12387T). It is also proposed that Virgibacillus picturae be transferred to the genus Oceanobacillus as Oceanobacillus picturae comb. nov. based on its 16S rRNA gene sequences and other taxonomic characteristics.
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‘Candidatus Phytoplasma fragariae’, a novel phytoplasma taxon discovered in yellows diseased strawberry, Fragaria×ananassa
More LessSymptoms of general stunting and yellowing of leaves were observed in diseased cultivated strawberry (Fragaria×ananassa Duchesne) in Lithuania. Analysis of 16S rRNA gene sequences amplified by PCR indicated that the symptoms were associated with infection by a phytoplasma, designated strawberry yellows (StrawY) phytoplasma. Phylogenetic analysis of 16S rRNA gene sequences indicated that StrawY phytoplasma, ‘Candidatus Phytoplasma australiense’, ‘Candidatus Phytoplasma asteris’, stolbur phytoplasma and ‘Candidatus Phytoplasma japonicum’ shared a common ancestor, but were mutually distinct. Nucleotide sequence alignments of a 1·3 kb 16S rRNA gene sequence fragment revealed that StrawY phytoplasma shared 97·4 % or less similarity with previously described ‘Candidatus Phytoplasma’ species. These results, in addition to natural host and geographical occurrence, support the recognition of StrawY phytoplasma as a representative of a novel taxon, ‘Candidatus Phytoplasma fragariae’.
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- Evolution, Phylogeny And Biodiversity
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Molecular evolution of the nif gene cluster carrying nifI 1 and nifI 2 genes in the Gram-positive phototrophic bacterium Heliobacterium chlorum
More LessA major nif cluster was detected in the strictly anaerobic, Gram-positive phototrophic bacterium Heliobacterium chlorum. The cluster consisted of 11 genes arranged within a 10 kb region in the order nifI 1, nifI 2, nifH, nifD, nifK, nifE, nifN, nifX, fdx, nifB and nifV. The phylogenetic position of Hbt. chlorum was the same in the NifH, NifD, NifK, NifE and NifN trees; Hbt. chlorum formed a cluster with Desulfitobacterium hafniense, the closest neighbour of heliobacteria based on the 16S rRNA phylogeny, and two species of the genus Geobacter belonging to the Deltaproteobacteria. Two nifI genes, known to occur in the nif clusters of methanogenic archaea between nifH and nifD, were found upstream of the nifH gene of Hbt. chlorum. The organization of the nif operon and the phylogeny of individual and concatenated gene products showed that the Hbt. chlorum nif operon carrying nifI genes upstream of the nifH gene was an intermediate between the nif operon with nifI downstream of nifH (group II and III of the nitrogenase classification) and the nif operon lacking nifI (group I). Thus, the phylogenetic position of Hbt. chlorum nitrogenase may reflect an evolutionary stage of a divergence of the two nitrogenase groups, with group I consisting of the aerobic diazotrophs and group II consisting of strictly anaerobic prokaryotes.
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Molecular signatures in protein sequences that are characteristics of the phylum Aquificae
More LessSpecies of the phylum Aquificae are of great interest due to their strict extreme thermophilic growth characteristics. Presently, there is no known molecular characteristic which is unique to this group of bacteria. This work describes six conserved inserts and deletions (indels or signature sequences) in four widely distributed proteins that are distinctive features of species from the phylum Aquificae. These include three signatures consisting of a 2 aa insert, a 5–6 aa insert and a 6 aa deletion in DNA polymerase I (PolA), a 6–7 aa insert in glucose-inhibited protein A (GidA), a 52 aa insert in the RNA polymerase β′-subunit (RpoC) and a 4 aa insert in elongation factor Tu (EF-Tu). Fragments of these genes were amplified in most cases from Hydrogenobacter hydrogenophilus, Hydrogenothermus marinus and Thermocrinis ruber and combined with available sequence data from ‘Aquifex aeolicus’ and Sulfurihydrogenibium azorense. The presence of the PolA, GidA and RpoC indels in all of the species sequenced provides evidence that they are probably distinctive characteristics of the entire phylum. The indel in EF-Tu, which is shared by Aquifex species and Hydrogenobacter but not Hydrogenothermus and Sulfurihydrogenibium, may provide a molecular marker for the family Aquificaceae. We have also identified a 51 aa insert in SecA preprotein translocase that is commonly shared by various species of the Aquificae as well as two Thermotoga species (Thermotoga maritima and Thermotoga neapolitana) which may be due to lateral gene transfer between these groups. In phylogenetic trees based on a concatenated dataset of fragments from eight different proteins as well as 16S rRNA, the observed branching pattern of these species was very similar and it was consistent with the relationships inferred from various indels. The identified indels provide a novel means for distinguishing species of the Aquificae from all other bacteria in molecular terms and may prove useful for functional studies aimed at understanding the unique biochemical and physiological characteristics of the Aquificae.
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RFLP analysis of the rRNA operon of a Brazilian collection of bradyrhizobial strains from 33 legume species
More LessGenetic diversity in tropical rhizobial species is still poorly known. With the aim of increasing this knowledge, three ribosomal regions of 119 strains belonging to the official Brazilian culture collection of rhizobia and classified as Bradyrhizobium based on morphological and physiological characteristics in vitro were analysed by RFLP-PCR. The strains were isolated from 33 legume species, representing nine tribes and all three subfamilies; they all form very effective N2-fixing nodules and 43 of them are recommended for use in Brazilian commercial inoculants as the most effective for their hosts. For the 16S rRNA gene, type and reference strains of Bradyrhizobium japonicum fell into two major clusters, joined at a level of similarity of 50 %, which included 52 strains, 90 % of which were isolated from soybean. Two other clusters, joined at a similarity of 53 %, included reference strains of Bradyrhizobium elkanii, but not USDA 76T; furthermore, two other major clusters were identified and all strains were clustered at a final level of similarity of only 28 %. For the intergenic spacer (IGS) between genes coding for the 16S and 23S rRNA, strains were clustered at a final level of similarity of 27 %. Reference strains of B. japonicum fell into a major group with 51 strains, 84 % isolated from soybean, with a similarity of 59 %, while strains of B. elkanii fell into another major group, with a similarity of 55 %, clustering 44 strains, 59 % of which were isolated from hosts other than soybean. New clusters were also observed for the IGS region. The largest number of differences was detected in the analysis of the 23S rRNA gene, and 16 groups and isolated strains were joined at a very low level of similarity (16 %). In a combined analysis with the three ribosomal regions, the majority of strains isolated from soybean clustered with a similarity of 54 % with type and reference strains of B. japonicum, while most strains isolated from Brazilian indigenous legume species grouped with B. elkanii at a level of similarity of 46 %. All strains were clustered at a very low level of similarity (27 %), and at least two new clusters were clearly defined. These new clusters might be related to intraspecific differences or to novel subspecies, or even to novel species; indeed, strains from one of these clusters show higher 16S rRNA gene sequence similarity to members of the genus Burkholderia. The results obtained in this study emphasize the high level of diversity of symbiotic diazotrophic bacteria in the tropics that still remains to be determined.
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- Letters To The Editor
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Volumes and issues
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Volume 75 (2025)
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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)
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