- Volume 59, Issue 4, 2009
Volume 59, Issue 4, 2009
- Editorial
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- Notification List
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Notification that new names and new combinations have appeared in volume 59, part 1, of the IJSEM
This listing of names published in a previous issue of the IJSEM is provided as a service to bacteriology to assist in the recognition of new names and new combinations. This procedure was proposed by the Judicial Commission [Minute 11(ii), Int J Syst Bacteriol 41 (1991), p. 185]. The names given herein are listed according to the Rules of priority (i.e. page number and order of valid publication of names in the original articles). Taxonomic opinions included in this List (i.e. the creation of synonyms or the emendation of circumscriptions) cannot be considered as validly published nor, in any other way, approved by the International Committee on Systematics of Prokaryotes and its Judicial Commission.
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- New Taxa
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- Actinobacteria
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Demequina lutea sp. nov., isolated from a high Arctic permafrost soil
Two Gram-stain-positive, pigmented, non-motile, non-spore-forming, pleomorphic, rod-shaped bacteria (strains SV45T and SV47), isolated from a permafrost soil collected from the Adventdalen valley, Spitsbergen, northern Norway, have been characterized taxonomically using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the two permafrost isolates formed a distinct phyletic line within the suborder Micrococcineae of the order Actinomycetales. DNA–DNA hybridization analyses indicate that strains SV45T and SV47 are closely related (60–69 % relatedness) and belong to the same species, although they show slightly different colony pigmentation. The closest phylogenetic neighbour was Demequina aestuarii JC2054T, with 96 % 16S rRNA gene sequence similarity. Optimum growth of SV45T and SV47 occurred aerobically in the absence of NaCl, but both isolates tolerated up to 2 % NaCl (w/v) in the growth medium. Growth under anaerobic conditions was slow and weak. The peptidoglycan of both isolates was of the A4β type with l-ornithine as the diamino acid and serine as a component of the interpeptide bridge with either d-aspartate (SV45T) or d-glutamate (SV47) as the N-terminal amino acid. The major fatty acids present in both isolates were C15 : 0 (3.2–8.6 %), iso-C16 : 0 (5.0–8.9 %), anteiso-C15 : 0 (59.4–61.5 %), anteiso-C17 : 0 (4.1–8.8 %) and anteiso-C15 : 1 (4.4–6.4 %). Isoprenoid quinones were present at exceptionally low levels in both isolates, and only demethylmenaquinone DMK-9(H4) could be identified with any degree of confidence. Phylogenetic analysis and differences in physiological and biochemical characteristics between the strains and Demequina aestuarii JC2054T indicate that these isolates belong to a novel species within the genus Demequina, for which the name Demequina lutea sp. nov. is proposed. The type strain is SV45T (=LMG 24795T =DSM 19970T).
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Leucobacter chironomi sp. nov., a chromate-resistant bacterium isolated from a chironomid egg mass
More LessA Gram-positive, rod-shaped, aerobic, non-motile, yellow-pigmented bacterial strain, designated MM2LBT, was isolated from a chironomid egg mass that was sampled in a waste stabilization pond in northern Israel. 16S rRNA gene sequence analysis indicated that the isolate should be placed in the genus Leucobacter (family Microbacteriaceae). Levels of 16S rRNA gene sequence similarity between strain MM2LBT and the type strains of recognized Leucobacter species were 97.1 % or lower. The dominant cellular fatty acids of strain MM2LBT were anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0, which are typical of members of the genus Leucobacter. Strain MM2LBT grew at 17–37 °C, in the presence of 0–7.0 % NaCl and at pH 4.0–9.5. Cell-wall amino acids were alanine, glycine, threonine, 2,4-diaminobutyric acid, glutamic acid and γ-aminobutyric acid in a B-type cross-linked peptidoglycan. The quinone system consisted of menaquinones MK-11, MK-10 and MK-12. The novel isolate was able to grow in medium containing 18 mM Cr(VI). On the basis of phenotypic properties and phylogenetic distinctiveness, strain MM2LBT is considered to represent a novel species of the genus Leucobacter, for which the name Leucobacter chironomi sp. nov. is proposed. The type strain is MM2LBT (=LMG 24399T=DSM 19883T).
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Streptomyces nanshensis sp. nov., isolated from the Nansha Islands in the South China Sea
More LessA novel actinomycete strain, designated SCSIO 01066T, was isolated from a marine sediment sample collected from the Nansha Islands in the South China Sea and was subjected to a polyphasic taxonomic study. A phylogenetic tree based on 16S rRNA gene sequences showed that strain SCSIO 01066T had the highest similarity (96.5 %) to members of the genus Streptomyces and was loosely associated with Streptomyces armeniacus JCM 3070T, Streptomyces cacaoi subsp. cacaoi NBRC 12748T and Streptomyces sodiiphilus YIM 80305T. Predominant menaquinones, major fatty acids and morphological properties were also consistent with typical characteristics of the genus Streptomyces; however, the presence of phosphatidylglycerol in the phospholipid pattern differs greatly from those of members of the genus Streptomyces. Additionally, strain SCSIO 01066T showed some physiological differences from its most closely related neighbours. Based on the polyphasic data, a novel species, Streptomyces nanshensis sp. nov., is proposed, with the type strain SCSIO 01066T (=KCTC 19400T=CCTCC AA 208005T).
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Actinomadura keratinilytica sp. nov., a keratin-degrading actinobacterium isolated from bovine manure compost
More LessA novel keratinolytic actinobacterium, strain WCC-2265T, was isolated from bovine hoof keratin ‘baited’ into composting bovine manure from southern Alberta, Canada, and subjected to phenotypic and genotypic characterization. Strain WCC-2265T produced well-developed, non-fragmenting and extensively branched hyphae within substrates and aerial hyphae, from which spherical spores possessing spiny cell sheaths were produced in primarily flexuous or straight chains. The cell wall contained meso-diaminopimelic acid, whole-cell sugars were galactose, glucose, madurose and ribose, and the major menaquinones were MK-9(H6), MK-9(H8), MK-9(H4) and MK-9(H2). These characteristics suggested that the organism belonged to the genus Actinomadura and a comparative analysis of 16S rRNA gene sequences indicated that it formed a distinct clade within the genus. Strain WCC-2265T could be differentiated from other species of the genus Actinomadura by DNA–DNA hybridization, morphological and physiological characteristics and the predominance of iso-C16 : 0, iso-C17 : 0 and 10-methyl C17 : 0 fatty acids. The broad range of phenotypic and genetic characters supported the suggestion that this organism represents a novel species of the genus Actinomadura, for which the name Actinomadura keratinilytica sp. nov. is proposed; the type strain is strain WCC-2265T (=DSM 45195T=CCUG 56181T).
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Pseudoclavibacter soli sp. nov., a β-glucosidase-producing bacterium
More LessA Gram-positive, aerobic, rod-shaped and non-motile bacterium, designated strain KP02T, was isolated from soil from a ginseng field in Daejeon, South Korea. On the basis of 16S rRNA gene sequence similarity, this strain was shown to be related to ‘Pseudoclavibacter alba’ NBRC 15616 (95.5 %), ‘Pseudoclavibacter faecalis’ NBRC 15706 (93.9 %), Pseudoclavibacter helvolus DSM 20419T (93.7 %) and ‘Pseudoclavibacter bifida’ IAM 14848 (93.0 %). Chemotaxonomic data revealed that strain KP02T possessed MK-9 and MK-8 as major menaquinones and anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and C16 : 0 as predominant fatty acids. The genomic DNA G+C content of strain KP02T was 64.4 mol%. The physiological and biochemical tests suggested that strain KP02T represents a novel species. Based on these data, strain KP02T (=KCTC 19255T=JCM 15058T) should be classified as the type strain of a novel Pseudoclavibacter species, for which the name Pseudoclavibacter soli sp. nov. is proposed.
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Mycobacterium noviomagense sp. nov.; clinical relevance evaluated in 17 patients
Eighteen isolates of a nonchromogenic, slowly growing, non-tuberculous species of the genus Mycobacterium were cultured from respiratory specimens obtained over the last eight years from 17 patients in the Netherlands. These isolates were grouped because they revealed a unique 16S rRNA gene sequence and were related to Mycobacterium xenopi. None of the 17 patients met the American Thoracic Society diagnostic criteria for non-tuberculous mycobacterial disease, which distinguishes the novel isolates from the related species, M. xenopi. A polyphasic taxonomic approach, including identification by biochemical and phenotypical analysis, hsp65 gene sequencing and PCR restriction enzyme pattern analysis, and sequence analyses of the rpoB gene and 16S–23S internal transcribed spacer supported the separate species status of the novel isolates. The name Mycobacterium noviomagense sp. nov. is proposed for the novel strains. The type strain is NLA000500338T (=DSM 45145T=CIP 109766T). A more distinctive taxonomy of NTM is a prerequisite for the assessment of their clinical relevance.
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Four novel Arthrobacter species isolated from filtration substrate
More LessFour Gram-positive, non-motile, non-spore-forming bacterial strains, LC4T, LC6T, LC10T and LC13T, were isolated from a filtration substrate made from trass, a volcanic rock, and their taxonomic positions were investigated by a polyphasic taxonomic approach. The novel strains grew over a temperature range of 5–40 °C, at pH values of 6–11 and in the presence of 3–7 % (w/v) NaCl. A phylogenetic tree based on 16S rRNA gene sequences showed the novel strains formed a distinct evolutionary lineage within the genus Arthrobacter. Chemotaxonomic analyses demonstrated that the major menaquinone was MK-9(H2), a menaquinone typical of the Arthrobacter globiformis group. The major fatty acid was anteiso-C15 : 0 and the major amino acid present in the cell-wall peptidoglycan was l-lysine. These observations supported the affiliation of the novel strains to the genus Arthrobacter. On the basis of their morphological, physiological and genotypic characteristics, the new isolates are considered to represent four novel species of the genus Arthrobacter, for which the names Arthrobacter niigatensis sp. nov. (type strain LC4T=IAM 15382T=CCTCC AB 206012T), Arthrobacter alkaliphilus sp. nov. (type strain LC6T=IAM 15383T=CCTCC AB 206013T), Arthrobacter echigonensis sp. nov. (type strain LC10T=IAM 15385T=CCTCC AB 206017T) and Arthrobacter albidus sp. nov. (type strain LC13T=IAM 15386T=CCTCC AB 206018T) are proposed.
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Nesterenkonia alba sp. nov., an alkaliphilic actinobacterium isolated from the black liquor treatment system of a cotton pulp mill
An alkaliphilic actinobacterium, designated strain CAAS 252T, was isolated from the black liquor treatment system of a cotton pulp mill in Wuhan, China. Cells of strain CAAS 252T were Gram-positive, non-motile, non-endospore-forming, short rod-shaped, and grew optimally at 42 °C and pH 9–10 in the presence of 3 % (w/v) NaCl. Strain CAAS 252T contained MK-7, MK-8 and MK-9 as the major menaquinones and anteiso-C17 : 0, anteiso-C15 : 0 and C16 : 0 as the predominant cellular fatty acids and had a peptidoglycan type of A4α, Lys–Gly-d-Asp. The DNA G+C content was 60.2 mol%. Based on analysis of 16S rRNA gene sequences (94.7–96.8 % similarity), DNA–DNA hybridization (<70 % relatedness) and chemotaxonomic characteristics, strain CAAS 252T belonged to the genus Nesterenkonia, but differed from all recognized species. Therefore, it is proposed that strain CAAS 252T represents a novel species of the genus Nesterenkonia, for which the name Nesterenkonia alba sp. nov. is proposed. The type strain is CAAS 252T (=CCTCC AB 207011T=DSM 19423T).
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Iamia majanohamensis gen. nov., sp. nov., an actinobacterium isolated from sea cucumber Holothuria edulis, and proposal of Iamiaceae fam. nov.
More LessA novel, Gram-positive bacterial strain, F12T, was isolated from the abdominal epidermis of a sea cucumber, Holothuria edulis, collected from seawater off the coast of Japan. According to 16S rRNA gene sequence analysis, this strain represents a novel, deep-rooting lineage within the class Actinobacteria and clusters with uncultured bacteria and Acidimicrobium ferrooxidans. Compared to species with validly published names, the highest 16S rRNA gene sequence similarity (89.8 %) was to Acidimicrobium ferrooxidans DSM 10331T. Phylogenetic analyses showed that strain F12T represents a distinct phylogenetic lineage related closely to the genus Acidimicrobium. Strain F12T contained MK-9(H6) as the major menaquinone, whilst 17 : 0, 17 : 1ω8c, 15 : 0 and 16 : 0 were the major cellular fatty acids. The cell-wall peptidoglycan of strain F12T was composed of meso-diaminopimelic acid as the diagnostic diamino acid, alanine and glutamic acid (1 : 2 : 1). The cell-wall sugars detected were rhamnose, mannose, arabinose, galactose and xylose. The G+C content of the DNA was 74.4 mol%. From the taxonomic data obtained in this study, the name Iamia majanohamensis gen. nov., sp. nov. is proposed for the isolate, with type strain F12T (=NBRC 102561T=DSM 19957T). The name Iamiaceae fam. nov. is also proposed for the distinct phyletic line represented by the genus Iamia.
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- Archaea
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Methanolobus profundi sp. nov., a methylotrophic methanogen isolated from deep subsurface sediments in a natural gas field
A mesophilic, methylotrophic methanogen, strain MobMT, was isolated from a natural gas field in Japan. Strain MobMT grew on methanol and methylamines, but not on H2/CO2, formate, acetate or dimethyl sulfide. The cells were motile, irregular cocci (diameter, 0.9–1.2 μm) and occurred singly, in pairs, as tetracocci or (occasionally) as aggregates. Strain MobMT grew at 9–37 °C (optimally at 30 °C) and at pH 6.1–7.8 (optimally at pH 6.5). Sodium and magnesium were required for growth, at 0.1–1.0 M Na+ (optimally at 0.35 M) and 10–400 mM Mg2+ (optimally at 15–25 mM). The G+C content of the genomic DNA was 42.4 mol%. 16S rRNA gene sequencing revealed that the isolate is a member of the genus Methanolobus, but distinct from its closest neighbours, Methanolobus tindarius DSM 2278T (sequence similarity, 98.0 %) and Methanolobus vulcani DSM 3029T (98.1 %). On the basis of phenotypic and phylogenetic features of MobMT, it is clear that this strain represents a novel species of the genus Methanolobus, for which the name Methanolobus profundi sp. nov. is proposed. The type strain is MobMT (=DSM 21213T=NBRC 104158T).
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Methanofollis ethanolicus sp. nov., an ethanol-utilizing methanogen isolated from a lotus field
More LessA novel methane-producing archaeon, designated strain HASUT, was isolated from a lotus field. Cells were Gram-negative, non-motile, irregular cocci, 2–3 μm in diameter, and occurred singly. Growth was observed at 15–40 °C (optimum, 37 °C) and pH 6.5–7.5 (optimum, pH 7.0). The G+C content of the genomic DNA was 60.9 mol%. Strain HASUT utilized ethanol, 1-propanol, 1-butanol, hydrogen and formate for growth and methane production. It converted ethanol to methane and acetate. Based on comparative 16S rRNA gene sequence analysis, strain HASUT was shown to be affiliated with the genus Methanofollis. It was related most closely to the type strain of Methanofollis liminatans (96.1 % 16S rRNA gene sequence similarity). Based on phylogenetic analysis and phenotypic characteristics, strain HASUT is considered to represent a novel species of the genus Methanofollis, for which the name Methanofollis ethanolicus sp. nov. is proposed. The type strain is HASUT (=NBRC 104120T=JCM 15103T=DSM 21041T).
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- Bacteroidetes
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Cellulophaga tyrosinoxydans sp. nov., a tyrosinase-producing bacterium isolated from seawater
More LessAn aerobic, gliding, yellow-pigmented bacterium lacking flagella and showing strong tyrosinase activity, designated strain EM41T, was isolated from seawater on the eastern coast of Jeju Island in Korea. Growth was observed at 15–35 °C (optimum, 25–30 °C) and at pH 6.5–9.0 (optimum, pH 7.0–8.5). Cells were Gram-negative, negative for flexirubin pigments and catalase- and oxidase-positive. The G+C content of the genomic DNA was 33.5 mol% and the major respiratory quinone was menaquinone-6 (MK-6). Comparative 16S rRNA gene sequence analysis showed that strain EM41T formed a distinct phyletic line within the genus Cellulophaga with a 100 % bootstrap value and was most closely related to Cellulophaga pacifica KMM 3664T (97.0 % sequence similarity). The level of DNA–DNA relatedness between strain EM41T and C. pacifica KMM 3664T was about 17.8 %. On the basis of phenotypic and genotypic data, strain EM41T is considered to represent a novel species of the genus Cellulophaga, for which the name Cellulophaga tyrosinoxydans sp. nov. is proposed. The type strain is EM41T (=KCTC 22297T=DSM 21164T).
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Chryseobacterium arothri Campbell et al. 2008 is a later heterotypic synonym of Chryseobacterium hominis Vaneechoutte et al. 2007
More LessThe type strains of the species Chryseobacterium arothri (DSM 19326T) and Chryseobacterium hominis (NF802T) were compared in order to clarify the taxonomic relationship of the two species. The 16S rRNA gene sequences of the two strains shared 99.9 % identity. DNA–DNA pairing studies between the two strains showed 100 % (reciprocal, 76.0 %) relatedness. Phenotypic data, including fatty acid patterns and substrate utilization profiles, showed no pronounced differences between the type strains of the two species. On the basis of these results, we propose the reclassification of Chryseobacterium arothri Campbell et al. 2008 as a later heterotypic synonym of Chryseobacterium hominis Vaneechoutte et al. 2007 .
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Aequorivita capsosiphonis sp. nov., isolated from the green alga Capsosiphon fulvescens, and emended description of the genus Aequorivita
A marine bacterial strain, designated A71T, was isolated from marine algae collected from the South Sea, Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain A71T belonged to the family Flavobacteriaceae and was closely related to Aequorivita antarctica SW49T (96.5 % sequence similarity). Cells of strain A71T were Gram-negative, aerobic, oxidase-negative, catalase-positive, yellow/orange-pigmented and non-motile. The major fatty acids were iso-C15 : 0 (20.6 %), iso-C17 : 1 ω9c (13.3 %), anteiso-C15 : 0 (13.1 %), iso-C17 : 0 3-OH (12.7 %) and summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1 ω7c; 6.6 %). The DNA G+C content was 36.9 mol%. Several phenotypic characteristics served to differentiate the isolate from recognized members of the genus Aequorivita. Data from this polyphasic study clearly demonstrated that strain A71T represents a novel species of the genus Aequorivita. The name Aequorivita capsosiphonis sp. nov. is proposed, with strain A71T (=KCTC 22183T =JCM 15070T) as the type strain. In addition, an emended description of the genus Aequorivita is presented.
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Prevotella micans sp. nov., isolated from the human oral cavity
More LessFour strains of anaerobic Gram-negative bacilli isolated from the human mouth were characterized using a variety of phenotypic and genotypic tests. The strains were found to comprise a homogeneous group and 16S rRNA gene sequence analysis revealed them to be distinct from but related to a loose cluster of Prevotella species including Prevotella buccalis, Prevotella nanceiensis and Prevotella marshii. A novel species, Prevotella micans sp. nov., is proposed to accommodate these strains. Prevotella micans is saccharolytic and produces acetic, isovaleric and succinic acids and minor amounts of isobutyric acid as end products of fermentation. The G+C content of the DNA of the type strain is 46 mol%. The type strain of Prevotella micans is E7.56T (=DSM 21469T =CCUG 56105T).
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Pseudozobellia thermophila gen. nov., sp. nov., a bacterium of the family Flavobacteriaceae, isolated from the green alga Ulva fenestrata
Two novel aerobic, dark-orange-pigmented, Gram-negative bacterial strains, designated KMM 3531T and KMM 3953, were isolated from the green alga Ulva fenestrata. Analysis of the 16S rRNA gene sequences showed that the strains represented a novel lineage within the family Flavobacteriaceae. The most closely related genera with validly published names were Costertonia, Flagellimonas, Kriegella, Maribacter, Muricauda and Zobellia, with 16S rRNA gene sequence similarities of 93.3–91.8 %. Cells of strains KMM 3531T and KMM 3953 were rod-shaped, motile by gliding and grew at temperatures up to 49 °C. They produced acid from carbohydrates and possessed oxidase, catalase, β-galactosidase and agarase activities. The predominant cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 1 G, summed feature 3 (comprising C16 : 1 ω7c and/or iso-С15 : 0 2-OH), iso-C17 : 1 ω9c and iso-C15 : 0 3-OH. The DNA G+C content was 47–49 mol%. On the basis of phenotypic and genotypic characteristics, strains KMM 3531T and KMM 3953 represent a novel genus and species, for which the name Pseudozobellia thermophila gen. nov., sp. nov. is proposed. The type strain is KMM 3531T (=DSM 19858T=JCM 11733T=KCTC 22016T).
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Reclassification of Donghaeana dokdonensis Yoon et al. 2006 as Persicivirga dokdonensis comb. nov. and emended descriptions of the genus Persicivirga and of Persicivirga xylanidelens O'Sullivan et al. 2006
More LessThe accurate taxonomic position of Donghaeana dokdonensis DSW-6T was investigated. Phylogenetic analysis revealed that the 16S rRNA gene sequences of the strain studied and of Persicivirga xylanidelens SW256T shared 98.2 % similarity. On the basis of phylogenetic evidence, phenotypic data and DNA–DNA reassociation values, it is proposed that strain DSW-6T be reclassified as Persicivirga dokdonensis comb. nov. Emended descriptions of the genus Persicivirga and of P. xylanidelens are also proposed.
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Spirosoma spitsbergense sp. nov. and Spirosoma luteum sp. nov., isolated from a high Arctic permafrost soil, and emended description of the genus Spirosoma
More LessTwo pigmented, Gram-negative, non-motile, pleomorphic rod-shaped bacteria (strains SPM-9T and SPM-10T) were isolated from a permafrost soil collected from the Adventdalen valley, Spitsbergen, northern Norway. A third isolate (strain M5-H2) was recovered from the same soil sample after the sample had been exposed to simulated Martian environmental conditions. The three strains were characterized taxonomically by using a polyphasic approach. Phylogenetic, chemotaxonomic, physiological and morphological analyses demonstrated that the three isolates were most closely related to members of the genus Spirosoma. 16S rRNA gene sequence data indicated that the three isolates could be divided into two clusters: (i) strain SPM-9T and (ii) strains SPM-10T and M5-H2. This grouping was confirmed by DNA–DNA hybridization experiments. Strains SPM-9T and SPM-10T exhibited 92 % 16S rRNA gene sequence similarity to both Spirosoma linguale LMG 10896T and Spirosoma rigui WPCB 118T. The major fatty acids present in all three isolates were summed feature 3 (comprising iso-C15:0 2-OH and/or C16 : 1 ω7c; 43.0–48.2 % of the total), C16 : 1 ω5c (19.1–21.3 %), C16 : 0 (6.7–7.3 %), iso-C17 : 0 3-OH (4.7–6.0 %) and iso-C15 : 0 (2.6–5.7 %). On the basis of their phenotypic and genotypic characteristics, the new strains are assigned to two novel species of the genus Spirosoma, for which the names Spirosoma spitsbergense sp. nov. and Spirosoma luteum sp. nov. are proposed. The type strain of Spirosoma spitsbergense is SPM-9T (=NCIMB 14407T=DSM 19989T) and the type strain of Spirosoma luteum is SPM-10T (=NCIMB 14406T=DSM 19990T). An emended description of the genus Spirosoma is also proposed.
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- Firmicutes And Related Organisms
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Bacillus beijingensis sp. nov. and Bacillus ginsengi sp. nov., isolated from ginseng root
More LessFour alkaligenous, moderately halotolerant strains, designated ge09, ge10T, ge14T and ge15, were isolated from the internal tissue of ginseng root and their taxonomic positions were investigated by using a polyphasic approach. Cells of the four strains were Gram-positive-staining, non-motile, short rods. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains ge09 and ge10T formed one cluster and strains ge14T and ge15 formed another separate cluster within the genus Bacillus. 16S rRNA gene sequence similarities with type strains of other Bacillus species were less than 97 %. Levels of DNA–DNA relatedness among the four strains showed that strains ge09 and ge10T and strains ge14T and ge15 belonged to two separate species; the mean level of DNA–DNA relatedness between ge10T and ge14T was only 28.7 %. Their phenotypic and physiological properties supported the view that the two strains represent two different novel species of the genus Bacillus. The DNA G+C contents of strains ge10T and ge14T were 49.9 and 49.6 mol%, respectively. Strains ge10T and ge14T showed the peptidoglycan type A4α l-Lys–d-Glu. The lipids present in strains ge10T and ge14T were diphosphatidylglycerol, phosphatidylglycerol, a minor amount of phosphatidylcholine and two unknown phospholipids. Their predominant respiratory quinone was MK-7. The fatty acid profiles of the four novel strains contained large quantities of branched and saturated fatty acids. The predominant cellular fatty acids were iso-C15 : 0 (42.5 %), anteiso-C15 : 0 (22.2 %), anteiso-C17 : 0 (7.3 %) and C16 : 1 ω7c alcohol (5.7 %) in ge10T and iso-C15 : 0 (50.7 %) and anteiso-C15 : 0 (20.1 %) in ge14T. On the basis of their phenotypic properties and phylogenetic distinctiveness, two novel species of the genus Bacillus are proposed, Bacillus beijingensis sp. nov. (type strain ge10T =DSM 19037T =CGMCC 1.6762T) and Bacillus ginsengi sp. nov. (type strain ge14T =DSM 19038T =CGMCC 1.6763T).
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Lactobacillus kisonensis sp. nov., Lactobacillus otakiensis sp. nov., Lactobacillus rapi sp. nov. and Lactobacillus sunkii sp. nov., heterofermentative species isolated from sunki, a traditional Japanese pickle
Thirty six Gram-positive, rod-shaped, non-spore-forming, non-motile bacterial strains were isolated from the non-salted pickle solution used in producing sunki products, a traditional Japanese pickle. The novel strains were discriminated and separated into four groups by amplified fragment length polymorphism profiling, and by analysis based on recA gene sequences. The strains were classified into four species groups belonging to the Lactobacillus buchneri species group, which consists of L. buchneri, Lactobacillus diolivorans, Lactobacillus hilgardii, Lactobacillus kefiri, Lactobacillus parabuchneri and Lactobacillus parakefiri. The phenotypic and genotypic features of the four groups demonstrated that they represented four novel species, for which the names Lactobacillus kisonensis sp. nov. (type strain YIT 11168T=NRIC 0741T=JCM 15041T=DSM 19906T), Lactobacillus otakiensis sp. nov. (type strain YIT 11163T=NRIC 0742T=JCM 15040T=DSM 19908T), Lactobacillus rapi sp. nov. (type strain YIT 11204T=NRIC 0743T=JCM 15042T=DSM 19907T) and Lactobacillus sunkii sp. nov. (type strain YIT 11161T=NRIC 0744T=JCM 15039T=DSM 19904T) are proposed.
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Streptococcus merionis sp. nov., isolated from Mongolian jirds (Meriones unguiculatus)
Gram-positive, catalase-negative, chain-forming, coccus-shaped organisms were isolated both from intraperitoneally grown vesicles of the fox tapeworm Echinococcus multilocularis and the oropharynges of laboratory-kept Mongolian jirds (Meriones unguiculatus). The strains displayed no haemolytic activity on Columbia sheep blood agar, pyrrolidonyl arylamidase activity was negative and the organisms reacted weakly with Lancefield group D antiserum. On the basis of phenotypic characteristics, the strains were tentatively identified as members of the genus Streptococcus. Comparative 16S rRNA gene sequencing studies confirmed their assignment to the genus Streptococcus and revealed that Streptococcus hyointestinalis DSM 20770T was their closest phylogenetic neighbour (96.5 % sequence similarity). The levels of 16S rRNA gene sequence similarity between the isolates and representatives of species of the genus Streptococcus were only 95.7–96.2 %. On the basis of the phenotypic and molecular data presented, the isolates from Mongolian jirds represent a novel species of the genus Streptococcus, for which the name Streptococcus merionis sp. nov. is proposed. The type strain is WUE3771T (=DSM 19192T=CCUG 54871T).
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Lacticigenium naphtae gen. nov., sp. nov., a halotolerant and motile lactic acid bacterium isolated from crude oil
More LessA novel lactic acid bacterium, strain MIC1-18T, was isolated from crude oil collected at an oil–water well in Akita, Japan. Cells of strain MIC1-18T were found to be facultatively anaerobic, mesophilic, neutrophilic, Gram-negative, non-sporulating, motile by means of peritrichous flagella and oval rods, 1.8–2.5 μm long. Optimum growth was observed at 30 °C, pH 7.0 and 3 % (w/v) NaCl. Strain MIC1-18T produced acid from l-arabinose, ribose, glucose, fructose, mannose, N-acetylglucosamine, amygdalin, arbutin, salicin, cellobiose, maltose, sucrose, trehalose, gentiobiose and 5-ketogluconate. l-Lactic acid was the major end product from glucose. The major cellular fatty acid was C16 : 1 ω7c. The cell-wall murein type was A4α containing Lys–Glu. The G+C content of the genomic DNA was 37.8 mol%. Phylogenetic analysis based on the 16S rRNA gene revealed that strain MIC1-18T was accommodated as a member of the lactic acid bacteria of the low-G+C content Gram-positive bacteria; the closest neighbour of this organism was Atopococcus tabaci CCUG 48253T, with only 90.0 % sequence similarity. On the basis of the phenotypic features and phylogenetic position, a novel genus and species, Lacticigenium naphtae gen. nov., sp. nov., are proposed for strain MIC1-18T (=NBRC 101988T=DSM 19658T).
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Salinicoccus albus sp. nov., a halophilic bacterium from a salt mine
A novel Gram-positive-staining, catalase- and oxidase-positive, non-motile, non-spore-forming coccus, designated YIM-Y21T, was isolated from a salt mine in Yunnan, south-west China. The strain was moderately halophilic, facultatively alkaliphilic and obligately aerobic. Colonies were white. Growth occurred with 1.0–30.0 % NaCl (optimum, 10.0 % NaCl), at pH 6.0–10.0 (optimum, pH 8.5) and at 5–40 °C (optimum, 25 °C). The major amino acid constituents of the cell wall were glycine and lysine. The major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C15 : 0. MK-6 was the predominant respiratory quinone, with MK-7 present in minor amounts. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol and an unidentified phospholipid. The DNA G+C content was 46.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain YIM-Y21T was most closely related to the type strains of the nine recognized species of the genus Salinicoccus. The sequence similarities between the isolate and the type strains of members of this genus were in the range of 90.6–93.8 %, which indicated that strain YIM-Y21T is a representative of a novel species within the genus Salinicoccus. Together with the phenotypic characteristics and chemotaxonomic differences, these results support the proposal of a novel species of the genus Salinicoccus, Salinicoccus albus sp. nov., with YIM-Y21T (=CCTCC AA 207024T =DSM 19776T =KCTC 13192T) as the type strain.
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- Other Bacteria
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Leptospira kmetyi sp. nov., isolated from an environmental source in Malaysia
A single Leptospira strain (designated Bejo-Iso9T) was isolated from a soil sample taken in Johor, Malaysia. The isolate showed motility and morphology typical of the genus Leptospira under dark-field microscopy. Cells were found to be 10–13 μm in length and 0.2 μm in diameter, with a wavelength of 0.5 μm and an amplitude of approximately 0.2 μm. Phenotypically, strain Bejo-Iso9T grew in Ellinghausen–McCullough–Johnson–Harris medium at 13, 30 and 37 °C, and also in the presence of 8-azaguanine. Serologically, strain Bejo-Iso9T produced titres towards several members of the Tarassovi serogroup, but was found to be serologically unique by cross-agglutinin absorption test and thus represented a novel serovar. The proposed name for this serovar is Malaysia. Phylogenetic analysis of 16S rRNA gene sequences placed this novel strain within the radiation of the genus Leptospira, with sequence similarities within the range 90.4–99.5% with respect to recognized Leptospira species. DNA–DNA hybridization against the three most closely related Leptospira species was used to confirm the results of the 16S rRNA gene sequence analysis. The G+C content of the genome of strain Bejo-Iso9T was 36.2 mol%. On the basis of phenotypic, serological and phylogenetic data, strain Bejo-Iso9T represents a novel species of the genus Leptospira, for which the name Leptospira kmetyi sp. nov. is proposed. The type strain is Bejo-Iso9T (=WHO LT1101T=KIT Bejo-Iso9T).
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Deinococcus xinjiangensis sp. nov., isolated from desert soil
More LessA Gram-positive-staining, spherical-shaped and faintly pink-pigmented bacterial strain, X-82T, was isolated from soil samples collected from a desert in Xinjiang, China. The organism was found to be resistant to UV radiation but sensitive to gamma radiation and desiccation. The optimum growth pH, NaCl concentration and temperature were pH 7.0, 0–1 % NaCl and 30 °C. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain X-82T is member of a novel species belonging to the genus Deinococcus, with Deinococcus hopiensis KR-140T as its closest relative (93.5 % similarity). The DNA G+C content (60 mol%), quinone type (MK-8), major cellular fatty acids (16 : 1ω7c, 16 : 0 and 17 : 1 iso ω9c), the presence of peptidoglycan with l-ornithine and the dominant polar lipid (phosphoglycolipids and glycolipids) support the affiliation of strain X-82T with the genus Deinococcus. A novel species is proposed, for which the name Deinococcus xinjiangensis sp. nov. is proposed, with the type strain X-82T (=CCTCC AB 207226T =NRRL B-51287T).
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- Proteobacteria
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Ectothiorhodospira variabilis sp. nov., an alkaliphilic and halophilic purple sulfur bacterium from soda lakes
During studies of moderately halophilic strains of Ectothiorhodospira from steppe soda lakes, we found a novel group of bacteria related to Ectothiorhodospira haloalkaliphila with salt optima at 50–80 g NaCl l−1. Phylogenetic analysis using 16S rRNA gene sequences of strains from soda lakes in Mongolia, Egypt and Siberia revealed separation of the group of new isolates from other Ectothiorhodospira species, including the closely related Ect. haloalkaliphila. DNA–DNA hybridization studies demonstrated that the new isolates form a homogeneous group at the species level, but at the same time are distinct from related species such as Ect. haloalkaliphila, Ect. vacuolata, Ect. shaposhnikovii and Ect. marina. The new isolates are considered to be strains of a novel species, for which the name Ectothiorhodospira variabilis sp. nov. is proposed, with the type strain WN22T (=VKM B-2479T =DSM 21381T). Photosynthetic pigments of the novel species are bacteriochlorophyll a and carotenoids of the spirilloxanthin series with spirilloxanthin and derivatives thereof, together with small amounts of lycopene and rhodopin. Gas vesicles are formed by most of the strains, particularly in media containing yeast extract (0.5 g l−1) and acetate (0.5–2.0 g l−1). Sequence analysis of nifH (nitrogenase) and cbbL (RuBisCO) confirmed the assignment of the strains to the genus Ectothiorhodospira and in particular the close relationship to Ect. haloalkaliphila. The novel species Ect. variabilis is found in soda lakes separated by great geographical distances and is an alkaliphilic and halophilic bacterium that tolerates salt concentrations up to 150–200 g NaCl l−1.
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Moraxella pluranimalium sp. nov., isolated from animal specimens
Four unusual Gram-negative, catalase-positive, oxidase-positive, coccus-shaped bacteria isolated from one sheep and three pigs were characterized using phenotypic and molecular genetic methods. On the basis of cellular morphology and biochemical criteria, the isolates were tentatively assigned to the genus Moraxella, although the organisms did not appear to correspond to any recognized species. Comparative 16S rRNA gene sequencing studies demonstrated that the isolates represent a novel subline within the genus Moraxella. The most closely related species in phylogenetic terms was Moraxella cuniculi, with 16S rRNA gene sequence similarity of 97.9 % to the type strain CCUG 2154T, although the DNA–DNA relatedness value was only 29 %. The novel isolates were readily distinguished from all recognized Moraxella species by means of physiological and biochemical tests. On the basis of molecular genetic and phenotypic evidence, therefore, the four isolates represent a novel species of the genus Moraxella, for which the name Moraxella pluranimalium sp. nov. is proposed. The type strain is 248-01T (=CECT 7295T =CCUG 54913T).
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Lysobacter oryzae sp. nov., isolated from the rhizosphere of rice (Oryza sativa L.)
More LessThe taxonomic position of a novel bacterial strain, YC6269T, isolated from the rhizosphere of rice (Oryza sativa L.) managed under no-tillage practice in Jinju, South Korea, was studied using polyphasic approach. Cells of the strain were Gram-negative, rod-shaped and facultatively anaerobic. The novel strain grew at a temperature of 15–42 °C (optimum at 28 °C). Growth of the strain occurred between pH 5.5 and 11.0, with an optimum at pH 7.0–8.0. The G+C content of the total DNA was 67.4 mol%. The 16S rRNA gene sequence of the strain was most closely related to species of the genus Lysobacter, Lysobacter yangpyeongensis DSM 17635T (98.6 %), Lysobacter niabensis GH34-4T (97.2 %), Lysobacter enzymogenes DSM 2043T (96.9 %), Lysobacter daejeonensis DSM 17634T (96.3 %) and Lysobacter niastensis GH41-7T (96.2 %). The novel strain showed <96.0 % similarity with other species of the genus Lysobacter. Chemotaxonomic data (major quinone, Q-8; major polar lipids, phosphatidylethanolamine, phosphatidylglycerol and phosphatidyl-N-methylethanolamine, and major fatty acids, C15 : 0 iso, C16 : 0 iso, C17 : 0 iso and C17 : 1 iso ω9c) supported the affiliation of strain YC6269T to the genus Lysobacter. Phylogenetic analysis based on the 16S rRNA gene sequences, DNA–DNA hybridization data and biochemical and physiological characteristics strongly supported the genotypic and phenotypic differentiation of strain YC6269T from recognized species of the genus Lysobacter. Strain YC6269T, therefore, represents a novel member of the genus Lysobacter, for which the name Lysobacter oryzae sp. nov. is proposed. The type strain is YC6269T (=KCTC 22249T=DSM 21044T).
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Aquabacterium fontiphilum sp. nov., isolated from spring water
More LessA short-rod-shaped, Gram-negative, motile bacterial strain, designated CS-6T, was isolated from a water sample collected from a spring located inside Nature Valley, Hsinchu County, Taiwan, and was characterized using a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain formed a monophyletic branch at the periphery of the evolutionary radiation occupied by the genus Aquabacterium in the class Betaproteobacteria. The closest neighbours were Aquabacterium parvum B6T (96.7 % sequence similarity), Aquabacterium commune B8T (96.6 %) and Aquabacterium citratiphilum B4T (95.9 %). The predominant fatty acids were 18 : 1ω7c (30.5 %), 16 : 0 (27.9 %) and summed feature 3 (16 : 1ω7c and/or iso-15 : 0 2-OH) (22.7 %). The DNA–DNA relatedness of the strain with respect to recognized species of the genus Aquabacterium was less than 70 %. The isolate was also distinguishable from members of the genus Aquabacterium on the basis of phenotypic and biochemical characteristics. It is evident from the genotypic, chemotaxonomic and phenotypic data, therefore, that strain CS-6T represents a novel species of the genus Aquabacterium, for which the name Aquabacterium fontiphilum sp. nov. is proposed. The type strain is CS-6T (=LMG 24215T=BCRC 17729T).
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Thalassomonas actiniarum sp. nov. and Thalassomonas haliotis sp. nov., isolated from marine animals
More LessTwo marine heterotrophic bacteria, A5K-61T and A5K-106T, were isolated from marine animals. 16S rRNA gene sequence analysis data showed that the isolates were affiliated with the genus Thalassomonas; highest 16S rRNA gene sequence similarity values were found with Thalassomonas viridans DSM 13754T (97.5 and 98.1 %, respectively). DNA–DNA hybridization values of strains A5K-61T and A5K-106T with T. viridans DSM 13754T (22.2–49.1 %) were clearly below 70 %, the generally accepted limit for species delineation. The isolates produced a brown diffusible pigment. The major respiratory quinone was Q-8 and the predominant cellular fatty acids were C16 : 1 ω7c and C16 : 0. Based on DNA–DNA hybridization data, some biochemical characteristics and 16S rRNA gene sequence comparison, the isolates represent two novel species of the genus Thalassomonas, for which the names Thalassomonas actiniarum sp. nov. (type strain A5K-106T =MBIC08328T =NCIMB 14418T =NBRC 104231T) and Thalassomonas haliotis sp. nov. (type strain A5K-61T =MBIC08329T =NCIMB 14417T =NBRC 104232T) are proposed.
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Rhodanobacter ginsenosidimutans sp. nov., isolated from soil of a ginseng field in South Korea
More LessA novel gammaproteobacterium, designated Gsoil 3054T, was isolated from soil of a ginseng field in Pocheon province, South Korea, and was characterized using a polyphasic approach to determine its taxonomic position. The strain was Gram-negative, aerobic, non-motile, non-spore-forming and rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain belonged to the genus Rhodanobacter; it was most closely related to Rhodanobacter fulvus Jip2T and Rhodanobacter thiooxydans LCS2T (97.9 and 97.2 % 16S rRNA gene sequence similarity, respectively). Chemotaxonomic data, i.e. Q-8 as the predominant ubiquinone and iso-C15 : 0, 10-methyl C16 : 0 and iso-C17 : 0 as major fatty acids, also supported classification of strain Gsoil 3054T in the genus Rhodanobacter. However, DNA–DNA hybridization values of Gsoil 3054T with R. fulvus Jip2T and R. thiooxydans LCS2T were 45 and 31 %, respectively. Moreover, physiological and biochemical tests enabled strain Gsoil 3054T to be differentiated phenotypically from other established species of Rhodanobacter. Therefore, the isolate represents a novel species, for which the name Rhodanobacter ginsenosidimutans sp. nov. is proposed; the type strain is Gsoil 3054T (=KACC 12822T =DSM 21013T =KCTC 22231T =LMG 24457T).
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Description of Enterovibrio nigricans sp. nov., reclassification of Vibrio calviensis as Enterovibrio calviensis comb. nov. and emended description of the genus Enterovibrio Thompson et al. 2002
More LessEleven strains of halophilic, facultative anaerobes isolated from healthy and diseased Dentex dentex and Sparus aurata (bony fishes) cultured in Spanish Mediterranean fisheries have been studied by a polyphasic approach that included a wide phenotypic characterization, DNA–DNA hybridization and phylogenetic analysis using 16S rRNA, recA and rpoD gene sequences. All strains were phylogenetically related to Enterovibrio species and Vibrio calviensis. On the basis of sequence analysis and DNA–DNA hybridization data, eight of the strains were identified as Enterovibrio coralii. The remaining three strains formed a tight, independent clade in all sequence analyses and showed less than 70 % DNA–DNA hybridization with strains of the closest Enterovibrio species, from which they could be differentiated by several phenotypic traits. We conclude that these three strains represent a novel species in the genus Enterovibrio and we thus propose the name Enterovibrio nigricans sp. nov., with strain DAl 1-1-5T (=CECT 7320T =CAIM 661T) as the type strain. In addition, we propose the reclassification of Vibrio calviensis Denner et al. 2002 as Enterovibrio calviensis comb. nov. (type strain RE35/F12T =CIP 107077T =DSM 14347T =CECT 7414T) and we provide an emended description of the genus Enterovibrio.
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Sphingomonas sanxanigenens sp. nov., isolated from soil
More LessStrain NX02T, a Gram-negative, non-spore-forming, rod-shaped bacterium, was isolated from soil, and its taxonomic position was investigated using a polyphasic approach. Chemotaxonomic analysis revealed that strain NX02T possessed Q-10 as the predominant ubiquinone, sym-homospermidine as the major polyamine and C18 : 1 ω7c, C16 : 0 and C14 : 0 2-OH as the major fatty acids. The main polar lipids were sphingoglycolipid, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine and an unidentified glycolipid. The DNA G+C content was 66.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain NX02T belongs to the α-4 subgroup of the Proteobacteria, exhibiting the highest sequence similarity with respect to Sphingomonas azotifigens NBRC 15497T (95.9 %), Sphingomonas pituitosa DSM 13101T (95.8 %) and Sphingomonas dokdonensis KCTC 12541T (95.8 %). On the basis of these results, strain NX02T represents a novel species of the genus Sphingomonas sensu stricto, for which the name Sphingomonas sanxanigenens sp. nov. is proposed. The type strain is NX02T (=DSM 19645T =CGMCC 1.6417T).
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Classification of the taxon 2 and taxon 3 complex of Bisgaard within Gallibacterium and description of Gallibacterium melopsittaci sp. nov., Gallibacterium trehalosifermentans sp. nov. and Gallibacterium salpingitidis sp. nov.
This investigation was based on 23 isolates from several European countries collected over the past 30 years, and included characterization of all isolates. Published data on amplified fragment length polymorphism typing of isolates representing all biovars as well as protein profiles were used to select strains that were then further characterized by polyamine profiling and sequencing of 16S rRNA, infB, rpoB and recN genes. Comparison of 16S rRNA gene sequences revealed a monophyletic group within the avian 16S rRNA group of the Pasteurellaceae, which currently includes the genera Avibacterium, Gallibacterium and Volucribacter. Five monophyletic subgroups related to Gallibacterium anatis were recognized by 16S rRNA, rpoB, infB and recN gene sequence comparisons. Whole-genome similarity between strains of the five subgroups and the type strain of G. anatis calculated from recN sequences allowed us to classify them within the genus Gallibacterium. In addition, phenotypic data including biochemical traits, protein profiling and polyamine patterns clearly indicated that these taxa are related. Major phenotypic diversity was observed for 16S rRNA gene sequence groups. Furthermore, comparison of whole-genome similarities, phenotypic data and published data on amplified fragment length polymorphism and protein profiling revealed that each of the five groups present unique properties that allow the proposal of three novel species of Gallibacterium, for which we propose the names Gallibacterium melopsittaci sp. nov. (type strain F450T =CCUG 36331T =CCM 7538T), Gallibacterium trehalosifermentans sp. nov. (type strain 52/S3/90T =CCUG 55631T =CCM 7539T) and Gallibacterium salpingitidis sp. nov. (type strain F150T =CCUG 15564T =CCUG 36325T =NCTC 11414T), a novel genomospecies 3 of Gallibacterium and an unnamed taxon (group V). An emended description of the genus Gallibacterium is also presented.
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Allochromatium phaeobacterium sp. nov.
More LessA rod-shaped, phototrophic, purple sulfur bacterium was isolated in pure culture from brackish water near Bheemli, Visakhapatnam, India, in a medium that contained 2 % NaCl (w/v). Strain JA144T was Gram-negative and motile. It did not require salt, but tolerated up to 3 % NaCl (w/v). Intracellular photosynthetic membranes were of the vesicular type. Bacteriochlorophyll a and carotenoids that probably belonged to the rhodopinal series were present as photosynthetic pigments. Strain JA144T was able to grow photolithoautotrophically, photolithoheterotrophically and photoorganoheterotrophically. It did not require vitamins. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that strain JA144T clustered with species of the genus Allochromatium belonging to the class Gammaproteobacteria. Highest sequence similarities of strain JA144T were found with the type strains of Allochromatium vinosum (96.7 % similarity), Allochromatium renukae (96.3 %), Allochromatium minutissimum (95.6 %) and Allochromatium warmingii (89.2 %). Based on 16S rRNA gene sequence analysis and morphological and physiological characteristics, strain JA144T is sufficiently different from other Allochromatium species to represent a novel species, Allochromatium phaeobacterium sp. nov.; the type strain is JA144T (=JCM 14796T=DSM 19781T).
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Azospirillum picis sp. nov., isolated from discarded tar
A polyphasic taxonomic study was performed on a pink-coloured unknown bacterium isolated from discarded road tar. Comparative analysis of the 16S rRNA gene sequence demonstrated that the isolate belongs phylogenetically to the genus Azospirillum with Azospirillum lipoferum, A. melinis and A. rugosum as its closest phylogenetic relatives (96.7, 96.6 and 96.6 % similarity to the respective type strains). The generic assignment was confirmed on the basis of chemotaxonomic data, which revealed a fatty acid profile characteristic for the genus Azospirillum, consisting of straight-chain saturated and unsaturated fatty acids, with C18 : 1 ω7c as the major unsaturated non-hydroxylated fatty acid, and C16 : 0 3-OH as the major hydroxylated fatty acid, and a ubiquinone with ten isoprene units (Q-10) as the predominant respiratory quinone. On the basis of both the phenotypic and molecular genetic evidence, it is proposed that the unknown isolate should be classified within a novel species of the genus Azospirillum, for which the name Azospirillum picis sp. nov. is proposed. The type strain is IMMIB TAR-3T (=CCUG 55431T =DSM 19922T).
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Geoalkalibacter subterraneus sp. nov., an anaerobic Fe(III)- and Mn(IV)-reducing bacterium from a petroleum reservoir, and emended descriptions of the family Desulfuromonadaceae and the genus Geoalkalibacter
More LessA strictly anaerobic Fe(III)-reducing bacterium, designated strain Red1T, was isolated from the production water of the Redwash oilfield, USA. The cells were motile rods (1–5×0.5–0.6 μm) that stained Gram-negative and possessed polar flagella. Strain Red1T obtained energy from the reduction of Fe(III), Mn(IV), nitrate, elemental sulfur and trimethylamine N-oxide in the presence of a wide range of electron donors, including a variety of organic acids, alcohols, biological extracts and hydrogen. Strain Red1T was incapable of fermentative growth. The novel isolate grew optimally at 40 °C (temperature range for growth, 30–50 °C) and at pH 7 (pH range, 6–9) with 2 % (w/v) NaCl (NaCl range, 0.1–10 %, w/v). The DNA G+C content was 52.5 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain Red1T was a member of the order Desulfuromonadales within the class Deltaproteobacteria and most closely related to Geoalkalibacter ferrihydriticus Z-0531T (95.8 %), Desulfuromonas palmitatis SDBY1T (92.5 %) and ‘Desulfuromonas michiganensis’ BB1 (92.4 %). On the basis of phenotypic and phylogenetic differences, the novel strain is proposed to represent a novel species, Geoalkalibacter subterraneus sp. nov. (type strain Red1T=JCM 15104T=KCTC 5626T).
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Lysobacter ximonensis sp. nov., isolated from soil
A bacterial isolate, strain XM415T, obtained from soil of Tibet in China was characterized using a polyphasic taxonomic approach. Strain XM415T was aerobic, Gram-negative, gliding, rod-shaped, oxidase-negative and catalase-positive. Strain XM415T showed the highest 16S rRNA gene sequence similarity with Lysobacter niastensis GH41-7T (96.0 %). Ubiquinone Q-8 and branched fatty acids, such as iso-C16 : 0 (24.0 %), iso-C15 : 0 (22.6 %), iso-C17 : 1 ω9c (6.7 %), iso-C14 : 0 (6.1 %) and iso-C11 : 0 3-OH (5.2 %), were predominant in strain XM415T as well as in all type strains of recognized Lysobacter species. The DNA G+C content of XM415T was 63.5 mol%. The genotypic and phenotypic data show that strain XM415T represents a novel species of the genus Lysobacter, for which the name Lysobacter ximonensis sp. nov. is proposed. The type strain is XM415T (=CCTCC AB 207091T =NRRL B-51263T).
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Paracoccus aestuarii sp. nov., isolated from tidal flat sediment
A Gram-negative micro-organism, designated strain B7T, was isolated from tidal flat sediment and subjected to a polyphasic taxonomic study involving morphological, physiological, biochemical and 16S rRNA gene sequence analyses. A phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain B7T belonged to the genus Paracoccus and was closely related phylogenetically to Paracoccus marcusii MH1T (97.5 % sequence similarity), Paracoccus marinus KKL-A5T (97.5 %), Paracoccus haeundaensis BC74171T (97.3 %), Paracoccus carotinifaciens E-396T (97.3 %), Paracoccus homiensis DD-R11T (97.2 %), Paracoccus seriniphilus MBT-A4T (96.9 %) and other type strains of the genus Paracoccus (95.2–96.7 %). The G+C content of the genomic DNA and the major isoprenoid quinone of the type strain were 62.0 mol% and ubiquinone-10, respectively. The major fatty acid components were C18 : 1 ω7c (68.9 %) and C18 : 0 (18.1 %); this profile, with C18 : 1 ω7c as the predominant fatty acid, was characteristic of members of the genus Paracoccus. The 16S rRNA gene sequence analysis, DNA–DNA hybridization studies and physiological and biochemical tests identified genotypic and phenotypic differences between strain B7T and recognized Paracoccus species. On the basis of these data, therefore, strain B7T represents a novel species of the genus Paracoccus, for which the name Paracoccus aestuarii sp. nov. is proposed. The type strain is B7T (=KCTC 22049T=DSM 19484T=JCM 15119T).
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Devosia albogilva sp. nov. and Devosia crocina sp. nov., isolated from a hexachlorocyclohexane dump site
More LessTwo bacterial strains, IPL15T and IPL20T, isolated from a hexachlorocyclohexane dump site in India, were characterized by using a polyphasic approach. Based on 16S rRNA gene sequence analysis, both strains belonged to the genus Devosia; highest sequence similarities of strain IPL15T were observed with Devosia neptuniae J1T and Devosia geojensis BD-c194T (96.2 % in each case) and the highest sequence similarity of strain IPL20T was observed with Devosia soli GH2-10T (98.6 %). Phylogenetic analysis showed the distinct lineages of strains IPL15T and IPL20T among members of the genus Devosia. The presence of C18 : 0 3-OH and C10 : 0 3-OH fatty acids supported their respective positions within the genus Devosia. On the basis of phenotypic characteristics, phylogenetic analysis and DNA–DNA hybridization results, it is concluded that strains IPL15T and IPL20T represent two distinct species of the genus Devosia for which the names Devosia albogilva sp. nov. and Devosia crocina sp. nov., respectively, are proposed. The type strains are Devosia albogilva IPL15T (=CCM 7427T=MTCC 8594T) and Devosia crocina IPL20T (=CCM 7425T=MTCC 8590T).
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Nautella italica gen. nov., sp. nov., isolated from a marine electroactive biofilm
Five isolates obtained from a marine electroactive biofilm grown on a stainless steel cathode were investigated by using a polyphasic taxonomic approach. Analyses of whole-cell fatty acid methyl esters and 16S rRNA gene sequences showed that the isolates belonged to the Roseobacter lineage of the class Alphaproteobacteria. Both phenotypic and genotypic analyses demonstrated that the five new isolates constituted a single species that did not represent a recognized member of the Roseobacter lineage. Therefore the five isolates represent a novel genus and species, for which the name Nautella italica gen. nov., sp. nov. is proposed. The type strain is LMG 24365T (=CCUG 55857T). The DNA G+C content of the type strain is 61 mol%.
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Pelagibius litoralis gen. nov., sp. nov., a marine bacterium in the family Rhodospirillaceae isolated from coastal seawater
More LessA Gram-negative, strictly aerobic, slightly curved rod-shaped bacterial strain, designated CL-UU02T, was isolated from coastal seawater off the east coast of Korea. 16S rRNA gene sequence analysis revealed a clear affiliation of this novel strain with the family Rhodospirillaceae. Strain CL-UU02T formed a robust cluster with the type strains of species of the genus Rhodovibrio at 16S rRNA gene sequence similarity levels of 89.9–90.4 %. Strain CL-UU02T shared no more than 89 % 16S rRNA gene sequence similarity with the type strains of other species in the family Rhodospirillaceae. Strain CL-UU02T was able to grow in the presence of 2–6 % sea salts, and grew optimally at 28–30 °C and pH 7–8. The DNA G+C content of strain CL-UU02T was 66.3 mol%. On the basis of phylogenetic analyses and chemotaxonomic and physiological data, strain CL-UU02T is considered to represent a novel species of a new genus in the family Rhodospirillaceae, for which the name Pelagibius litoralis gen. nov., sp. nov. is proposed. The type strain of Pelagibius litoralis is CL-UU02T (=KCCM 42323T=JCM 15426T).
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Mesorhizobium metallidurans sp. nov., a metal-resistant symbiont of Anthyllis vulneraria growing on metallicolous soil in Languedoc, France
A polyphasic taxonomic approach was used to characterize 31 rhizobial isolates obtained from Anthyllis vulneraria, a metallicolous legume species, growing close to a zinc mine in the south of France (Saint Laurent le Minier). Comparative analysis of nearly full-length 16S rRNA gene sequences showed that these Gram-negative bacteria belonged to the genus Mesorhizobium and that they were related most closely to Mesorhizobium tianshanense ORS 2640T. The phylogenetic relationships of these isolates with other Mesorhizobium species were confirmed by sequencing and analysis of the recA and atpD genes, which were used as alternative chromosomal markers. These novel mesorhizobial strains tolerated high concentrations of heavy metals: 16–32 mM Zn and 0.3–0.5 mM Cd. DNA–DNA hybridizations revealed >73 % relatedness between the strains isolated from A. vulneraria, but only 19–33 % relatedness between these and the type strains of M. tianshanense and Mesorhizobium mediterraneum. These results, together with other phenotypic characteristics, support the conclusion that these isolates represent a single, novel species of the genus Mesorhizobium, for which the name Mesorhizobium metallidurans sp. nov. is proposed. The type strain is STM 2683T (=CFBP 7147T=LMG 24485T).
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Salinivibrio siamensis sp. nov., from fermented fish (pla-ra) in Thailand
A Gram-negative, facultatively anaerobic, moderately halophilic bacterium, strain ND1-1T, was isolated from fermented fish (pla-ra) in Thailand. The cells were curved rods, motile and non-endospore-forming. The novel strain grew optimally at 37 °C, at pH 8 and in the presence of 9−10 % (w/v) NaCl. The predominant respiratory lipoquinone was Q-8. The major cellular fatty acids were C16 : 0 and C12 : 0. Polar lipid analysis revealed the presence of phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C content was 49.0 mol%. Comparative 16S rRNA gene sequence analyses indicated that strain ND1-1T was closely related to Salinivibrio costicola, which comprises three subspecies, and Salinivibrio proteolyticus with gene sequence similarities of 98.3–98.6 %. Strain ND1-1T showed low levels of DNA–DNA relatedness with S. costicola subsp. costicola JCM 15095T (33.2 %), S. costicola subsp. alcaliphilus DSM 16359T (38.4 %), S. costicola subsp. vallismortis JCM 15096T (59.7 %), and S. proteolyticus AF-2004T (42.1 %). On the basis of the physiological and biochemical characteristics and the molecular data presented, strain ND1-1T should be classified as a novel species of the genus Salinivibrio for which the name Salinivibrio siamensis sp. nov. is proposed. The type strain is ND1-1T (=JCM 14472T=PCU 301T=TISTR 1810T).
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Marinobacter santoriniensis sp. nov., an arsenate-respiring and arsenite-oxidizing bacterium isolated from hydrothermal sediment
More LessA Gram-negative, arsenate-respiring and arsenite-oxidizing marine bacterium, NKSG1T, was isolated from hydrothermal sediment at Santorini, Greece. Strain NKSG1T was a facultatively anaerobic, motile, non-spore-forming, rod-shaped bacterium. Growth occurred optimally at 35–40 °C, between pH 5.5 and 9.0 and with 0.5–16 % NaCl. Energy was conserved by the aerobic oxidation of a range of complex substrates, carbohydrates and organic acids, or anaerobically by arsenate reduction, nitrate reduction coupled to the oxidation of organic carbon or lactate fermentation. Oxidation of arsenite and anaerobic nitrate-dependent oxidation of Fe(II) were facilitated by the presence of an organic carbon source. The DNA G+C content was 58.1 mol%. The major respiratory quinone was Q-9. The significant fatty acids were 16 : 1ω9c, summed feature 3 (iso-15 : 0 2-OH/16 : 1ω7c), 16 : 0 and 18 : 1ω9c. Analysis of 16S rRNA gene sequences showed that strain NKSG1T fits within the phylogenetic cluster of the genus Marinobacter and is most closely related to Marinobacter koreensis DD-M3T (99.3 % similarity). The degree of relatedness with M. koreensis DSM 17924T based on DNA–DNA hybridization was 56 %. The results of a polyphasic study indicated that strain NKSG1T is a representative of a novel species within the genus Marinobacter, for which the name Marinobacter santoriniensis sp. nov. is proposed. The type strain is NKSG1T (=DSM 21262T =NCIMB 14441T=ATCC BAA-1649T). The capacity for arsenic reduction or oxidation has not been demonstrated previously for this genus.
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- Eukaryotic Micro-Organisms
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Selective recovery of the cultivation-prone components from mixed trypanosomatid infections: a case of several novel species isolated from Neotropical Heteroptera
More LessMixed trypanosomatid infections (a simultaneous presence of two or more parasites in the same host) have long been suspected to represent an obstacle for recovering cultures that would faithfully represent original species descriptions. However, without the means to directly compare the parasites in the host and in culture, this would remain just a possibility. Here we have used PCR-based genotyping of spliced leader RNA gene repeats to analyse several novel species of insect trypanosomatids isolated from heteropteran hosts and to compare them with the parasites that had been detected in the gut smears of the same hosts. We have found that, whereas the original infections were dominated by some blastocrithidia-like parasites, most of the respective axenic cultures contained novel species of Crithidia and Leptomonas. Therefore, we concluded that, in each case, this replacement was caused by differences in cultivation properties between the original predominant blastocrithidia and the less fastidious parasite that was later recovered in culture. The properties of the new organisms, including their morphology and ultrastructure, as well as their phylogenetic affinities within the family, were investigated and used to describe five novel species.
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Cryptococcus bromeliarum sp. nov., an orange-coloured basidiomycetous yeast isolated from bromeliads in Brazil
More LessDuring a survey of yeasts associated with the phylloplane of several bromeliad species in Itapuã Park in southern Brazil, we isolated four orange-coloured strains which were found to represent a novel anamorphic tremellaceous (Tremellales, Agaricomycotina, Basidiomycota) yeast species, Cryptococcus bromeliarum sp. nov. (type strain BI20T =CBS 10424T =NRRL Y-48112T). PCR-fingerprinting profiles of the four strains with primers M13 and (GTG)5 were almost identical, which suggested conspecificity among the isolates. On the basis of D1/D2 26S rDNA sequence analysis, C. bromeliarum is phylogenetically closely related to other orange-coloured Cryptococcus species, namely Cryptococcus armeniacus, C. amylolyticus, C. tibetensis and C. cistialbidi, but differed from these species by at least six nucleotide substitutions and was thus considered a separate species. Physiological differences from C. armeniacus, C. amylolyticus and C. cistialbidi included the inability of C. bromeliarum to assimilate citrate and to form starch-like compounds. Differentiation from C. tibetensis can be achieved by the ability of the latter to assimilate ethylamine.
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Jaminaea angkorensis gen. nov., sp. nov., a novel anamorphic fungus containing an S943 nuclear small-subunit rRNA group IB intron represents a basal branch of Microstromatales
More LessIn the course of molecular characterization of yeasts isolated from decaying leaves collected in Cambodia, anamorphic yeast strains were detected that clustered with the Microstromatales in molecular phylogenetic analyses of the chromosomal regions coding for the D1/D2 domain of the large-subunit 26S rRNA gene, the small-subunit 18S rRNA gene and the internal transcribed spacer ITS1-5.8S rRNA gene-ITS2. In the trees obtained, the isolates formed a distinct, basal branch of Microstromatales supported with high bootstrap values. As the isolates could not be identified with any known genus, we have described them as Jaminaea angkorensis gen. et sp. nov. (type strain C5bT=CBS 10918T=CCY 88-1-1T). In the chromosomal region coding for the 18S rRNA gene, the type strain of the novel species contained a group IB intron that was similar in location and sequence to introns found in certain species of Exobasidiales and Entylomatales. As no similar introns have been detected in Microstromatales, the new genus might represent a phylogenetic link connecting these three orders.
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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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