- Volume 57, Issue 6, 2007
Volume 57, Issue 6, 2007
- New Taxa
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- Proteobacteria
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Reclassification of Pseudomonas aurantiaca as a synonym of Pseudomonas chlororaphis and proposal of three subspecies, P. chlororaphis subsp. chlororaphis subsp. nov., P. chlororaphis subsp. aureofaciens subsp. nov., comb. nov. and P. chlororaphis subsp. aurantiaca subsp. nov., comb. nov.
Pseudomonas chlororaphis, Pseudomonas aureofaciens and Pseudomonas aurantiaca were considered as separate species until 1989, when P. aureofaciens was proposed as a later heterotypic synonym of P. chlororaphis with P. aurantiaca remaining as a separate species. Nevertheless, analysis of the almost complete 16S rRNA gene sequences revealed that the type strain of P. aurantiaca, NCIMB 10068T, shows gene sequence similarities close to 99.5 % with respect to P. chlororaphis DSM 50083T and P. aureofaciens DSM 6698T. DNA–DNA hybridization experiments among strains of P. aurantiaca, P. chlororaphis and P. aureofaciens showed values higher than 70 %, confirming that they represent members of the same species. The results of fatty acid analysis and phenotypic traits showed that these strains are closely related, although there are some differences among the strains belonging to P. aurantiaca, those from P. chlororaphis and those from P. aureofaciens. All these results confirm the previous reclassification of P. aureofaciens into P. chlororaphis and support the reclassification of P. aurantiaca as a synonym of P. chlororaphis. Phenotypic and molecular data permit the description of three novel subspecies within this last species, for which the following names are proposed: P. chlororaphis subsp. chlororaphis subsp. nov. [with the type strain DSM 50083T (=ATCC 9446T=NCIMB 9392T)], P. chlororaphis subsp. aureofaciens subsp. nov., comb. nov. [with the type strain DSM 6698T (=ATCC 13985T=NCIMB 9030T)] and P. chlororaphis subsp. aurantiaca subsp. nov., comb. nov. [with the type strain NCIMB 10068T (=ATCC 33663T=CIP 106718T)].
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Aquincola tertiaricarbonis gen. nov., sp. nov., a tertiary butyl moiety-degrading bacterium
Strains L10T, L108 and CIP I-2052 were originally obtained from methyl tert-butyl ether (MTBE)-contaminated groundwater and from a wastewater treatment plant, respectively. All share the ability to grow on tert-butanol, an intermediate of MTBE degradation. Cells are strictly aerobic, motile by a polar flagellum and exhibit strong pili formation. Poly β-hydroxybutyrate (PHB) granules are formed. The DNA G+C content is 69–70.5 mol% and the main ubiquinone is Q-8. The major cellular fatty acids are 16 : 1 cis-9 and 16 : 0 and the only hydroxy fatty acid is 10 : 0 3-OH. The major phospholipids are phosphatidylethanolamine (PE) 16 : 1/16 : 1 and phosphatidylglycerol 16 : 0/16 : 1. A significant amount of PE 17 : 0/16 : 1 is present. The 16S rRNA gene sequences of these strains are almost identical and form a separate line of descent in the Rubrivivax–Roseateles–Leptothrix–Ideonella–Aquabacterium branch of the Betaproteobacteria with 97 % similarity to 16S rRNA genes of the type strains of Rubrivivax gelatinosus, Leptothrix mobilis and Ideonella dechloratans. However, physiological properties, DNA–DNA relatedness values and the phospholipid and cellular fatty acid profiles distinguish the novel isolates from the three closely related genera. Therefore, it is concluded that strains L10T, L108 and CIP I-2052 represent a new genus and novel species for which the name Aquincola tertiaricarbonis gen. nov., sp. nov., is proposed. The type strain is strain L10T (=DSM 18512T=CIP 109243T).
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Ruegeria mobilis sp. nov., a member of the Alphaproteobacteria isolated in Japan and Palau
More LessThe taxonomic positions of two bacterial strains, MBIC01146T and MBIC01099, isolated from marine environments of Japan and Palau, respectively, were determined by using a polyphasic approach. The bacteria were aerobic, motile, Gram-negative rods and formed star-shaped aggregations. The G+C content of the genomic DNA ranged from 58.5 to 58.7 mol%. The major respiratory quinone was ubiquinone-10 and the predominant cellular fatty acids were C16 : 0, C18 : 1 ω6c and C18 : 1 ω7c. 16S rRNA gene sequence analyses based on both neighbour-joining and maximum-parsimony methods revealed that strains MBIC01146T and MBIC01099 were positioned within the cluster comprising Ruegeria atlantica and Silicibacter lacuscaerulensis within subgroup α-3 of the Proteobacteria. The phenotypic and chemotaxonomic characteristics of the novel strains were similar to those of Ruegeria atlantica; however, DNA–DNA hybridization tests showed that the isolates represented an independent species. The isolates could be differentiated from Ruegeria atlantica based on several characteristics. Therefore, strains MBIC01146T and MBIC01099 are considered to represent a novel species of the genus Ruegeria, for which the name Ruegeria mobilis sp. nov. is proposed. The type strain is MBIC01146T (=NBRC 101030T=CIP 109181T). An emended description of Ruegeria atlantica Uchino et al. 1999 is also given.
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Devosia insulae sp. nov., isolated from soil, and emended description of the genus Devosia
More LessA Gram-negative, motile, aerobic and oval- or rod-shaped bacterial strain, DS-56T, which is phylogenetically closely related to the genus Devosia, was isolated from soil from Dokdo, Korea. Strain DS-56T grew optimally at pH 6.5–7.5 and 25 °C in the presence of 0.5 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain DS-56T joins the cluster comprising Devosia species, at a bootstrap resampling value of 100 %. The levels of 16S rRNA gene sequence similarity between strain DS-56T and the type strains of recognized Devosia species ranged from 95.4 to 96.4 %. Strain DS-56T contained Q-11 as the predominant ubiquinone, unlike Devosia species, which contain Q-10 as the predominant ubiquinone. The novel strain also contained some fatty acids, including branched and hydroxy fatty acids, that are not detected in Devosia species. The DNA G+C content of strain DS-56T was 66.2 mol%. On the basis of the phenotypic, chemotaxonomic and phylogenetic data, strain DS-56T represents a novel species of the genus Devosia, for which the name Devosia insulae sp. nov. is proposed. The type strain is DS-56T (=KCTC 12821T=DSM 17955T).
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‘Candidatus Magnetoglobus multicellularis’, a multicellular, magnetotactic prokaryote from a hypersaline environment
Phylogenetic analysis and phenotypic characterization were used to assign a multicellular magnetotactic prokaryote the name ‘Candidatus Magnetoglobus multicellularis’. ‘Candidatus Magnetoglobus multicellularis' lives in a large hypersaline coastal lagoon from Brazil and has properties that are unique among prokaryotes. It consists of a compact assembly or aggregate of flagellated bacterial cells, highly organized in a sphere, that swim in either helical or straight trajectories. The life cycle of ‘Candidatus Magnetoglobus multicellularis' is completely multicellular, in which one aggregate grows by enlarging the size of its cells and approximately doubling the volume of the whole organism. Cells then divide synchronously, maintaining the spherical arrangement; finally the cells separate into two identical aggregates. Phylogenetic 16S rRNA gene sequence analysis showed that ‘Candidatus Magnetoglobus multicellularis' is related to the dissimilatory sulfate-reducing bacteria within the Deltaproteobacteria and to other previously described, but not yet well characterized, multicellular magnetotactic prokaryotes.
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Alcanivorax balearicus sp. nov., isolated from Lake Martel
A bacterial strain designated MACL04T was isolated from Lake Martel, a subterraneous saline lake in Mallorca (Spain). The complete 16S rRNA gene sequence of this strain showed nearly 100 % similarity to that of Alcanivorax dieselolei B-5T. Despite this high similarity, strain MACL04T showed phenotypic, chemotaxonomic and molecular differences with respect to A. dieselolei, indicating that strain MACL04T represents a separate species. Cells of strain MACL04T were motile by means of a single polar or subpolar flagellum and colonies formed on media containing 1 % (v/v) Tween 20 were opaque and mucoid, with blue–green iridescence. The generation time of strain MACL04T in this medium was approximately half that of A. dieselolei B-5T and strain MACL04T did not produce lipases after incubation for 5 days. Strain MACL04T did not require NaCl for growth and grew in the presence of up to 15 % (w/v) NaCl. The strain was able to use alkanes as a sole carbon source; however, glucose could also be used, albeit weakly, as a carbon source. Several amino acids and organic acids were used as carbon sources. Strain MACL04T produced acid in media containing pyruvate as the sole carbon source. The major fatty acids were C19 : 0 cyclo ω8c and C16 : 0. The fatty acid C16 : 1 ω8c, present in strain MACL04T, was not detected in the recognized Alcanivorax species. The sequences of the large and short 16S–23S intergenic spacer regions showed similarities of 97.2 and 98.8 % (ungapped) with respect to A. dieselolei B-5T. Partial sequences of gyrB and alkb genes showed 94.0 % similarity between strain MACL04T and A. dieselolei B-5T. The G+C content of strain MACL04T was 62.8 mol%. The data from this polyphasic study indicate that strain MACL04T represents a novel species of the genus Alcanivorax, for which the name Alcanivorax balearicus sp. nov. is proposed. The type strain is MACL04T (=LMG 22508T=CECT 5683T).
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Sphingomonas pseudosanguinis sp. nov., isolated from the water reservoir of an air humidifier
More LessA yellow-pigmented bacterial isolate, strain G1-2T, obtained from the surface of an air humidifier, was characterized taxonomically. 16S rRNA gene sequence analysis, physiological characterization and estimation of the ubiquinone and polar lipid patterns and fatty acid composition revealed that strain G1-2T was similar to Sphingomonas yabuuchiae and Sphingomonas sanguinis, but also showed pronounced differences. On the basis of these results, a novel species of the genus Sphingomonas is described, for which the name Sphingomonas pseudosanguinis sp. nov. is proposed. The type strain is G1-2T (=CCUG 54232T=CIP 109431T).
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Psychromonas hadalis sp. nov., a novel piezophilic bacterium isolated from the bottom of the Japan Trench
More LessAn obligately piezophilic bacterium was isolated from sediment collected from the bottom of the Japan Trench at a depth of 7542 m. The isolated strain, designated K41GT, was closely affiliated with members of the genus Psychromonas on the basis of 16S rRNA gene sequence analysis. Levels of DNA–DNA relatedness between strain K41GT and Psychromonas reference strains were significantly lower than that accepted as the phylogenetic definition of a species. The optimal temperature and pressure for growth of strain K41GT were 6 °C and 60 MPa, respectively. The DNA G+C content was 39.1 mol%. Whole-cell fatty acids consisted of significant amounts of unsaturated fatty acids C16 : 1 (37 %) and C14 : 1 (17 %), saturated fatty acid C16 : 0 (31 %) and polyunsaturated fatty acid C22 : 6 (8 %). Based on the taxonomic differences observed, strain K41GT is considered to represent a novel obligately piezophilic Psychromonas species. The name Psychromonas hadalis (type strain, K41GT=JCM 11830T=ATCC BAA-638T) is proposed. This is the second species of obligately piezophilic bacteria to be proposed in the genus Psychromonas.
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- Other Gram-Positive Bacteria
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Halobacillus profundi sp. nov. and Halobacillus kuroshimensis sp. nov., moderately halophilic bacteria isolated from a deep-sea methane cold seep
More LessTwo Gram-positive, rod-shaped, moderately halophilic bacteria were isolated from a deep-sea carbonate rock at a methane cold seep in Kuroshima Knoll, Japan. These bacteria, strains IS-Hb4T and IS-Hb7T, were spore-forming and non-motile. They were able to grow at temperatures as low as 9 °C and hydrostatic pressures up to 30 MPa. Based on high sequence similarity of their 16S rRNA genes to those of type strains of the genus Halobacillus, from 96.4 % (strain IS-Hb7T to Halobacillus halophilus NCIMB 9251T) to 99.4 % (strain IS-Hb4T to Halobacillus dabanensis D-8T), the strains were shown to belong to this genus. DNA–DNA relatedness values of 49.5 % and 1.0–33.0 %, respectively, were determined between strains IS-Hb4T and IS-Hb7T and between these strains and other Halobacillus type strains. Both strains showed the major menaquinone MK7 and l-orn–d-Asp cell-wall peptidoglycan type. Straight-chain C16 : 0, unsaturated C16 : 1 ω7c alcohol and C18 : 1 ω7c and cyclopropane C19 : 0 cyc fatty acids were predominant in both strains. The DNA G+C contents of IS-Hb4T and IS-Hb7T were respectively 43.3 and 42.1 mol%. Physiological and biochemical analyses combined with DNA–DNA hybridization results allowed us to place strains IS-Hb4T (=JCM 14154T=DSM 18394T) and IS-Hb7T (=JCM 14155T=DSM 18393T) in the genus Halobacillus as the respective type strains of the novel species Halobacillus profundi sp. nov. and Halobacillus kuroshimensis sp. nov.
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Planococcus columbae sp. nov., isolated from pigeon faeces
More LessAn orange-pigmented, Gram-positive bacterial strain, designated PgEx11T, was isolated from pigeon faeces. Analysis of the 16S rRNA gene sequence of the isolate indicated that it had 94.2–98.2 % sequence identity with respect to those of seven recognized species of the genus Planococcus. The strain PgEx11T contained anteiso-C15 : 0 as a major cellular fatty acid and MK-7 and MK-8 as the major menaquinones. The DNA G+C content of strain PgEx11T was 50.5 mol%. Furthermore, analysis of the 16S rRNA gene sequence indicated high levels of similarity with Planococcus rifietoensis (98.2 %), Planococcus maitriensis (97.6 %), Planococcus citreus (97.5 %) and Planococcus maritimus (97.1 %). However, the mean value for DNA–DNA relatedness between PgEx11T and these four closely related species was in the range 45.4–16.8 %, respectively. Moreover, strain PgEx11T also differs from its close relatives with regard to biochemical and chemotaxonomic characteristics. On the basis of phenotypic, chemotaxonomic and genotypic differences, strain PgEx11T represents a novel species of the genus Planococcus, for which the name Planococcus columbae sp. nov. is proposed. The type strain is PgEx11T (=MTCC 7251T=DSM 17517T).
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Streptococcus orisuis sp. nov., isolated from the pig oral cavity
More LessFive bacterial strains, designated as NUM 1001T, NUM 1002, NUM 1003, NUM 1004 and NUM 1005, were isolated from the oral cavities of pigs. Colonies grown on mitis salivarius agar were similar in morphology to those of mutans streptococci. The novel isolates were analysed biochemically using the Rapid ID 32 Strep microsystem, subjected to DNA–DNA hybridization with oral streptococci and had their 16S rRNA genes sequenced. On the basis of the phylogenetic and phenotypic evidence obtained, the strains represent a novel species of the genus Streptococcus, for which the name Streptococcus orisuis sp. nov. is proposed. The type strain is NUM 1001T (=JCM 14035T=DSM 18307T).
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Proposal of six species of moderately thermophilic, acidophilic, endospore-forming bacteria: Alicyclobacillus contaminans sp. nov., Alicyclobacillus fastidiosus sp. nov., Alicyclobacillus kakegawensis sp. nov., Alicyclobacillus macrosporangiidus sp. nov., Alicyclobacillus sacchari sp. nov. and Alicyclobacillus shizuokensis sp. nov.
Moderately thermophilic, acidophilic, spore-forming bacteria (146 strains) were isolated from various beverages and environments. Based on the results of sequence analysis of the hypervariable region of the 16S rRNA gene, eight of the strains represent novel species of the genus Alicyclobacillus. These strains were designated 3-A191T, 4-A336T, 5-A83JT, 5-A167N, 5-A239-2O-AT, E-8, RB718T and S-TABT. Phylogenetic analyses of 16S rRNA and DNA gyrase B subunit (gyrB) nucleotide sequences confirmed that the eight strains belonged to the Alicyclobacillus clade. Cells of the eight strains were Gram-positive or Gram-variable, strictly aerobic and rod-shaped. The strains grew well under acidic and moderately thermal conditions, produced acid from various sugars, contained menaquinone 7 as the major isoprenoid quinone and did not produce guaiacol. ω-Alicyclic fatty acids were the predominant lipid component of strains 4-A336T, 5-A83JT, 5-A167N, RB718T and S-TABT. No ω-alicyclic fatty acids were detected in strains 3-A191T, 5-A239-2O-AT or E-8, but iso- and anteiso-branched fatty acids and small amounts of straight-chain saturated fatty acids were detected instead. According to the DNA–DNA hybridization data and distinct morphological, physiological, chemotaxonomical and genetic traits, the eight strains represent six novel species within the genus Alicyclobacillus, for which the following names are proposed: Alicyclobacillus contaminans sp. nov. (type strain 3-A191T=DSM 17975T=IAM 15224T), Alicyclobacillus fastidiosus sp. nov. (type strain S-TABT=DSM 17978T=IAM 15229T), Alicyclobacillus kakegawensis sp. nov. (type strain 5-A83JT=DSM 17979T=IAM 15227T), Alicyclobacillus macrosporangiidus sp. nov. (type strain 5-A239-2O-AT=DSM 17980T=IAM 15370T), Alicyclobacillus sacchari sp. nov. (type strain RB718T=DSM 17974T=IAM 15230T) and Alicyclobacillus shizuokensis sp. nov. (type strain 4-A336T=DSM 17981T=IAM 15226T).
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Aerococcus suis sp. nov., isolated from clinical specimens from swine
Biochemical and molecular genetic studies were performed for five isolates of unknown Gram-positive, catalase-negative, cocci-shaped micro-organisms obtained from clinical samples from pigs. The micro-organisms were tentatively identified as Aerococcus species on the basis of the results from cellular morphological and biochemical tests. 16S rRNA gene sequencing studies confirmed the provisional identification of the isolates as members of the genus Aerococcus, but the micro-organism did not correspond to any recognized species of this genus. The nearest phylogenetic relatives of these unknown cocci isolated from pigs were Aerococcus viridans (95.9 % 16S rRNA gene sequence similarity) and Aerococcus urinaeequi (95.8 %). The unknown bacterium, however, was distinguishable from these two species and from other animal aerococci by using biochemical tests. On the basis of both phenotypic and phylogenetic findings, the isolates represent a novel species of the genus Aerococcus, for which the name Aerococcus suis sp. nov. is proposed. The type strain is 1821/02T (=CECT 7139T=CCUG 52530T).
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Clostridium aestuarii sp. nov., from tidal flat sediment
More LessA strictly anaerobic, halophilic, motile, endospore-forming, rod-shaped bacterium, designated strain HY-45-18T, was isolated from a sediment sample of a tidal flat in Korea. The isolate produced butyric acid, propionic acid, glycerol and H2 as fermentation end products from glucose. Strain HY-45-18T is halophilic as it was unable to grow in the absence of sea salts. A 16S rRNA gene sequence analysis clearly indicated that the tidal flat isolate is a member of cluster I of the order Clostridiales, which contains the type species of Clostridium, Clostridium butyricum. The closest phylogenetic neighbour of strain HY-45-18T was Clostridium ganghwense KCTC 5146T (96.5 % 16S rRNA gene sequence similarity). Several phenotypic characteristics can be readily used to differentiate the isolate from phylogenetically related clostridia. Therefore, strain HY-45-18T represents a novel species of the genus Clostridium, for which the name Clostridium aestuarii sp. nov. is proposed. The type strain is HY-45-18T (=IMSNU 40129T=KCTC 5147T=JCM 13194T).
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Paenibacillus fonticola sp. nov., isolated from a warm spring
A novel bacterial strain, designated ZLT, isolated from a warm spring in Jhonglun, Taiwan, was characterized by using a polyphasic taxonomic approach. The novel strain had chemotaxonomic and morphological properties consistent with its classification in the genus Paenibacillus. Cells were Gram-variable, aerobic, sporulating, motile rods. 16S rRNA gene sequence analysis demonstrated that this novel isolate was unique, showing 94.3 % sequence similarity to Paenibacillus assamensis GPTSA 11T and lower levels to Paenibacillus timonensis 2301032T (94.0 %), Paenibacillus macerans ATCC 8244T (93.3 %), Paenibacillus barengoltzii SAFN-016T (93.3 %) and Paenibacillus sanguinis 2301083T (93.2 %). The novel isolate could be distinguished from the type strains of all of these species based on a range of phenotypic data. The major cellular phospholipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and one unknown phosphoglycolipid. The predominant isoprenologue was an unsaturated menaquinone with seven isoprene units (MK-7). The major fatty acids of strain ZLT were C16 : 0 (33.5 %), anteiso-C15 : 0 (32.5 %) and iso-C16 : 0 (9.3 %). The G+C content of the genomic DNA was 49.2 mol%. It is evident from the genotypic and phenotypic data that strain ZLT should be classified as representing a novel species of the genus Paenibacillus, for which the name Paenibacillus fonticola sp. nov. is proposed. The type strain is ZLT (=BCRC 17579T=LMG 23577T).
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Paenibacillus taiwanensis sp. nov., isolated from soil in Taiwan
More LessAmong a large collection of Taiwanese soil isolates, a novel Gram-variable, rod-shaped, motile and endospore-forming bacterial strain, designated G-soil-2-3T, was isolated from farmland soil in Wu-Feng, Taiwan. The isolate was subjected to a polyphasic study including 16S rRNA gene sequence analysis, DNA–DNA hybridization experiments, fatty acid analysis and comparative phenotypic characterization. 16S rRNA gene sequence analysis indicated that the organism belongs within the genus Paenibacillus. It contained menaquinone MK-7 as the predominant isoprenoid quinone and anteiso-C15 : 0 (40.5 %), iso-C15 : 0 (13.1 %), iso-C16 : 0 (10.8 %) and anteiso-C17 : 0 (7.3 %) as the major fatty acids. Phylogenetically, the closest relatives of strain G-soil-2-3T were the type strains of Paenibacillus assamensis, Paenibacillus alvei and Paenibacillus apiarius, with 16S rRNA gene sequence similarity of 95.7, 95 and 95.2 %, respectively. DNA–DNA hybridization experiments showed levels of relatedness of 2.8–9.0 % of strain G-soil-2-3T with these strains. The G+C content of the DNA was 44.6 mol%. Strain G-soil-2-3T was clearly distinguishable from P. assamensis, P. alvei and P. apiarius and thus represents a novel species of the genus Paenibacillus, for which the name Paenibacillus taiwanensis sp. nov. is proposed. The type strain is G-soil-2-3T (=BCRC 17411T=IAM 15414T=LMG 23799T=DSM 18679T).
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- Evolution, Phylogeny And Biodiversity
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Use of the novel phylogenetic marker dnaJ and DNA–DNA hybridization to clarify interrelationships within the genus Aeromonas
The interrelationships of 27 Aeromonas strains were investigated using dnaJ sequences and DNA–DNA hybridization. dnaJ sequence similarities showed a stronger relationship with DNA–DNA relatedness values than did 16S rRNA gene sequence similarities. Additionally, dnaJ sequence analysis, with interspecies divergence over 5.2 % in most cases, gave better resolution than 16S rRNA gene sequences for the differentiation of strains at the species level. Relationships among Aeromonas species were therefore elucidated on the basis of dnaJ sequences and DNA–DNA reassociation. Strains of Aeromonas encheleia and Aeromonas sp. HG11 were unquestionably grouped in the same genetic species, since they shared 98.7 % dnaJ sequence similarity and 82–85 % genomic relatedness. The phylogenetically close relationships obtained from dnaJ sequence analysis (1.7–3.3 % genetic distance) were corroborated by high DNA–DNA relatedness (73–97 %) to support the previous suggestion that Aeromonas culicicola and Aeromonas allosaccharophila are later heterotypic synonyms of Aeromonas veronii. Our findings will contribute to the clarification of controversial relationships in the genus Aeromonas and also demonstrate that analysis of dnaJ sequences can be a powerful tool for interspecies study of the genus.
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- Letters To The Editor
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- International Committee On Systematics Of Prokaryotes
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- Minutes
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 68 (2018)
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