- Volume 57, Issue 10, 2007
Volume 57, Issue 10, 2007
- Notification List
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Notification that new names and new combinations have appeared in volume 57, part 7, 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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Catenulispora rubra sp. nov., an acidophilic actinomycete isolated from forest soil
More LessIn the course of screening novel secondary metabolites, an acidophilic actinomycete strain, designated Aac-30T, was isolated from forest soil and subjected to a polyphasic taxonomic characterization study. It grew well on media in which the pH ranged from 4 to 6, but not on medium with pH adjusted to 7. It possessed ll-diaminopimelic acid and glycine in the cell-wall peptidoglycan, MK-9(H6) and MK-9(H8) as major isoprenoid quinones, iso-C16 : 0 and anteiso-C17 : 0 as major cellular fatty acids, and phosphatidylglycerol and phosphatidylinositol as polar lipids. The G+C content of the genomic DNA was 69.1 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that the organism belonged to the family Catenulisporaceae and consistently formed a monophyletic cluster with members of the genus Catenulispora. Physiological, biochemical and chemotaxonomic data revealed that this novel organism could be readily differentiated from recognized members of the genus Catenulispora and that it merits separate species status. Based on the phenotypic and genetic evidence presented, strain Aac-30T is considered to represent a novel species of the genus Catenulispora, for which the name Catenulispora rubra sp. nov. is proposed. The type strain is Aac-30T (=NBRC 101179T=DSM 44948T).
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Microbacterium sediminicola sp. nov. and Microbacterium marinilacus sp. nov., isolated from marine environments
Two novel Microbacterium species are described on the basis of phenotypic, chemotaxonomic and genotypic studies. The two strains, designated YM10-847T and YM11-607T, were isolated from river sediment and unidentified hydroid, respectively, of a marine lake. The strains were Gram-positive, catalase-positive bacteria with l-ornithine as the diagnostic diamino acid of the peptidoglycan. The acyl type of the peptidoglycan was N-glycolyl. The major menaquinones were MK-10 and MK-11 for YM10-847T, and MK-11 and MK-12 for YM11-607T. Mycolic acids were not detected. The DNA G+C content of strains YM10-847T and YM11-607T was 67.8 and 71.6 mol%, respectively. Comparative 16S rRNA gene sequence analysis revealed that the two strains belong to the genus Microbacterium. DNA–DNA relatedness data showed that YM10-847T and YM11-607T are two novel species of this genus. On the basis of these results, strains YM10-847T and YM11-607T represent two novel species of the genus Microbacterium, for which the names Microbacterium sediminicola sp. nov. and Microbacterium marinilacus sp. nov. are proposed. The type strains are YM10-847T (=MBIC08264T=DSM 18905T) and YM11-607T (=MBIC07778T=DSM 18904T), respectively.
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- Archaea
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Halococcus thailandensis sp. nov., from fish sauce in Thailand
More LessFifteen strains of red-pigmented, strictly aerobic, coccoid, extremely halophilic archaea were isolated from fish sauce (nam-pla) produced in Thailand. They grew optimally at 37 °C, pH 6–8 and in the presence of 20–30 % (w/v) NaCl. The DNA G+C contents of the isolates were 60.0–61.8 mol%. They had MK-8(H2) as a major menaquinone component and C20C20 and C20C25 derivatives of phosphatidylglycerol, phosphatidylglycerol methylphosphate and a sulfated glycolipid, S-DGA-1, as major polar lipid components. 16S rRNA gene sequence comparisons revealed that a representative strain, HDB5-2T, was affiliated with Halococcus dombrowskii JCM 12289T, Halococcus qingdaonensis JCM 13587T and Halococcus morrhuae JCM 8876T (levels of similarity of 98.2–98.7 %). Based on data from DNA–DNA hybridization experiments, the 15 strains represented a single species, showing hybridization values of >78.9 % to representative strain HDB5-2T, but were unrelated to either Halococcus dombrowskii JCM 12289T or Halococcus morrhuae JCM 8876T, with levels of relatedness of <50 %. Moreover, a comparison of phenotypic properties discriminated these new isolates from recognized species of the genus Halococcus. The 15 strains are thus considered to represent a novel species of the genus Halococcus, for which the name Halococcus thailandensis sp. nov. is proposed. The type strain is HDB5-2T (=BCC 20213T =JCM 13552T =PCU 278T).
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Halorubrum litoreum sp. nov., an extremely halophilic archaeon from a solar saltern
More LessAn extremely halophilic archaeon, strain Fa-1T, was isolated from a marine solar saltern in Fujian, China. Strain Fa-1T required Mg2+ and at least 2.0 M NaCl for growth. It was able to grow at pH 6.5–9.0 (optimally at pH 7.0–7.5) and at 20–55 °C (optimally at 37–42 °C). The major polar lipids of strain Fa-1T were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and a sulfated diglycosyl diether. On the basis of a 16S rRNA gene sequence analysis, strain Fa-1T was closely related to nine species of the genus Halorubrum, showing sequence similarities of 97.4–98.4 %. The G+C content of the DNA of strain Fa-1T is 64.9 mol% (T m). DNA–DNA hybridization values between strain Fa-1T and the most closely related members of the genus Halorubrum were below 51 %. On the basis of the data from this study, strain Fa-1T represents a novel species of the genus Halorubrum, for which the name Halorubrum litoreum sp. nov. is proposed. The type strain is Fa-1T (=CGMCC 1.5336T =JCM 13561T).
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Halalkalicoccus jeotgali sp. nov., a halophilic archaeon from shrimp jeotgal, a traditional Korean fermented seafood
A novel, extremely halophilic archaeon B3T was isolated from shrimp-salted seafood. Its morphology, physiology, biochemical features and 16S rRNA gene sequence were characterized. Strain B3T is non-motile, Gram-variable, requires at least 10 % (w/v) NaCl for growth and grows in the ranges of 21–50 °C and pH 6.5–9.0. The DNA G+C content of strain B3T was 63.2 mol%. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain B3T belonged to the genus Halalkalicoccus and was phylogenetically closely related to the type strain Halalkalicoccus tibetensis (98.64 %). However, DNA–DNA hybridization experiments showed 7.0 % relatedness between strain B3T and a strain of a reference species of the genus Halalkalicoccus. Combined analysis of 16S rRNA gene sequences, DNA–DNA relatedness data, physiological and biochemical tests indicated that the genotypic and phenotypic characteristics differentiate strain B3T from other Halalkalicoccus species. On the basis of the evidence presented in this report, strain B3T represents a novel species of the genus Halalkalicoccus, for which the name Halalkalicoccus jeotgali. sp. nov. is proposed. The type strain is B3T (=KCTC 4019T=DSM 18796T=JCM 14584T=CECT 7217T).
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- Bacteroidetes
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Prevotella nanceiensis sp. nov., isolated from human clinical samples
More LessThree strains of anaerobic, non-pigmented, Gram-negative bacilli isolated from various human clinical samples were characterized in terms of phenotypic and genotypic tests, including sequence analysis of 16S rRNA and rpoB genes. The strains were most closely related to the type strains of Prevotella marshii and Prevotella shahii on the basis of both 16S rRNA (89.8 and 89.0 % identity, respectively) and rpoB gene sequences (83.1 and 82.8 % identity, respectively). Phylogenetic analysis showed that the isolates constituted a robust homogeneous group distinct from known species in the genus Prevotella. The rrn skeleton (as determined by PFGE) and the DNA G+C content, determined to be 39.4 mol% for strain LBN 293T, distinguished the novel isolates from the type strains of P. marshii and P. shahii. The three strains were saccharolytic and produced acetic, lactic and succinic acids as major metabolic end products. Polyphasic investigations supported the proposal of a novel species, Prevotella nanceiensis sp. nov., with LBN 293T (=AIP 261.03T =CIP 108993T =CCUG 54409T) as the type strain.
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Pedobacter duraquae sp. nov., Pedobacter westerhofensis sp. nov., Pedobacter metabolipauper sp. nov., Pedobacter hartonius sp. nov. and Pedobacter steynii sp. nov., isolated from a hard-water rivulet
More LessFive isolates that were related phylogenetically to members of the genus Pedobacter were isolated from freshwater of the hard-water creek Westerhöfer Bach, North Germany. The five strains (WB 2.1-25T, WB 2.3-71T, WB 3.3-3T, WB 3.3-22T and WB 2.3-45T) were Gram-negative and chemoheterotrophic, with rod-shaped cells. Most of their metabolic properties matched those given in the description of the genus Pedobacter. Consistent with the genus description, their fatty acids included mainly iso-C15 : 0 and summed feature 3 (C16 : 1 ω7c, iso-C15 : 0 2-OH or both); C16 : 1 ω5c, C16 : 0, iso-C15 : 0 3-OH, C16 : 0 3-OH and iso-C17 : 0 3-OH were present in smaller amounts. The major isoprenoid quinone was menaquinone 7. With one exception, binary similarity values of the almost complete 16S rRNA gene sequences determined among the isolates as well as between the isolates and type strains of Pedobacter species were lower than 98.5 %. The only exception was the close relationship between Pedobacter caeni DSM 16990T and strain WB 2.3-45T (99.2 % similarity). DNA–DNA reassociation values determined for this pair of strains was 29.8 %, indicating that strain WB 2.3-45T represents a unique genospecies. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains WB 2.1-25T and WB 2.3-71T form a group that is moderately related to P. caeni and strain WB 2.3-45T (98.5 % similarity). Strains WB 3.3-3T and WB 3.3-22T (98.5 % similarity) branched separately from these four organisms. The five phylogenetically isolated strains differed from each other as well as from the type strain of the type species (Pedobacter heparinus DSM 2366T) and some related representatives of the genus in several metabolic reactions and cultural parameters. On the basis of phenotypic and phylogenetic distinctiveness, five novel species are proposed: Pedobacter duraquae sp. nov., with WB 2.1-25T (=DSM 19034T=CIP 109481T) as the type strain; Pedobacter westerhofensis sp. nov., with WB 3.3-22T (=DSM 19036T=CIP 109479T) as the type strain; Pedobacter metabolipauper sp. nov., with WB 2.3-71T (=DSM 19035T=CIP 109480T) as the type strain; Pedobacter hartonius sp. nov., with WB 3.3-3T (=DSM 19033T=CIP 109468T) as the type strain; and Pedobacter steynii sp. nov., with WB 2.3-45T (=DSM 19110T=CIP 109507T) as the type strain.
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Rapidithrix thailandica gen. nov., sp. nov., a marine gliding bacterium isolated from samples collected from the Andaman sea, along the southern coastline of Thailand
The taxonomic positions of three strains of marine gliding bacteria, TISTR 1736, TISTR 1741 and TISTR 1750T, isolated from the southern coastline of Thailand were evaluated by using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the three isolates formed a distinct lineage within the family ‘Flammeovirgaceae’, phylum Bacteroidetes, and were related to the genus Flexithrix. The DNA G+C contents of the isolates were in the range 40–43 mol%. The major respiratory quinone was MK-7. The major cellular fatty acids were 16 : 1ω5c (cis-5-hexadecenoic acid) and 15 : 0 (pentadecanoic acid). The major hydroxyl fatty acids were 3-OH 17 : 0 (3-hydroxyheptadecanoic acid), 3-OH 15 : 0 (3-hydroxypentadecanoic acid) and 3-OH 16 : 0 (3-hydroxyhexadecanoic acid). On the basis of phenotypic, chemotaxonomic, genotypic and phylogenetic data, these marine bacteria are considered to represent a novel species of a new genus, for which the name Rapidithrix thailandica gen. nov., sp. nov. is proposed. The type strain of Rapidithrix thailandica is TISTR 1750T (=IAM 15448T).
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Chryseobacterium haifense sp. nov., a psychrotolerant bacterium isolated from raw milk
More LessStrain H38T was isolated during a study on the diversity of culturable psychrotolerant bacteria in raw milk. Comparative 16S rRNA gene sequence analysis showed that strain H38T belongs to the genus Chryseobacterium (family Flavobacteriaceae, phylum Bacteroidetes), with the highest similarity (96.7 %) to Chryseobacterium hispanicum VP48T. Strain H38T grows aerobically, at 4–41 °C, with 0–2.5 % NaCl and at pH 6.5–10.5. Light induces the formation of yellow carotenoid pigments. The dominant cellular fatty acids are 15 : 0 iso (41.6 %), 15 : 0 anteiso (16.6 %) and 17 : 0 iso 3-OH (10.3 %). The G+C content of the DNA is 37.8 mol%. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain H38T (=LMG 24029T =DSM 19056T) is classified in the genus Chryseobacterium as the type strain of a novel species, for which the name Chryseobacterium haifense sp. nov. is proposed.
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Mucilaginibacter paludis gen. nov., sp. nov. and Mucilaginibacter gracilis sp. nov., pectin-, xylan- and laminarin-degrading members of the family Sphingobacteriaceae from acidic Sphagnum peat bog
More LessTwo facultatively aerobic, heterotrophic bacteria capable of degrading pectin, xylan, laminarin and some other polysaccharides were obtained from the acidic Sphagnum peat bog Bakchar, in western Siberia, Russia, and were designated strains TPT18T and TPT56T. Cells of these isolates are Gram-negative, non-motile, long rods that are covered by large capsules. On ageing, they transform into spherical L-forms. Strains TPT18T and TPT56T are acido- and psychrotolerant organisms capable of growth at pH 4.2–8.2 (with an optimum at pH 6.0–6.5) and at 2–33 °C (with an optimum at 20 °C). The major fatty acids are iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c); the quinones are MK-7 and MK-6. Comparative 16S rRNA gene sequence analysis revealed that the novel strains share 97 % sequence similarity and belong to the family Sphingobacteriaceae; however, they are related only distantly to members of the genera Pedobacter (91.8–93.3 % similarity) and Sphingobacterium (89.6–91.2 % similarity). The DNA G+C content of strains TPT18T and TPT56T is 42.4 and 46.1 mol%, respectively. The low DNA–DNA hybridization value (42 %) and a number of phenotypic differences between strains TPT18T and TPT56T indicated that they represent two separate species. Since the two isolates are clearly distinct from all currently described members of the family Sphingobacteriaceae, we propose a novel genus, Mucilaginibacter gen. nov., containing two novel species, Mucilaginibacter gracilis sp. nov. and Mucilaginibacter paludis sp. nov. The type strains of Mucilaginibacter gracilis and Mucilaginibacter paludis are respectively TPT18T (=ATCC BAA-1391T =VKM B-2447T) and TPT56T (=ATCC BAA-1394T =VKM B-2446T).
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- Other Bacteria
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Bellilinea caldifistulae gen. nov., sp. nov. and Longilinea arvoryzae gen. nov., sp. nov., strictly anaerobic, filamentous bacteria of the phylum Chloroflexi isolated from methanogenic propionate-degrading consortia
Thermophilic (strain GOMI-1T) and mesophilic (strain KOME-1T) strains were isolated from two different cultures of propionate-degrading consortia obtained from thermophilic digester sludge and rice paddy soil, respectively. The two strains were non-spore-forming, non-motile and Gram-negative. Both strains were obligately anaerobic micro-organisms, showing multicellular filamentous morphotypes more than 100 μm in length. The cell width for strain GOMI-1T was 0.2–0.4 μm and that of strain KOME-1T was 0.4–0.6 μm. Strain GOMI-1T could grow at 45–65 °C with a pH range of 6.0–7.5 (optimum growth at 55 °C, pH 7.0). The temperature range for growth of strain KOME-1T was 30–40 °C and the pH range was pH 5.0–8.5 (optimum growth around 37 °C, pH 7.0). Yeast extract was required for growth of both strains. Strain GOMI-1T was able to grow with a number of carbohydrates in the presence of yeast extract. In yeast extract-containing medium, strain KOME-1T could utilize proteins and a limited range of sugars for growth. The G+C contents of the DNA of strains GOMI-1T and KOME-1T were respectively 54.7 and 57.6 mol%. Major fatty acids of strain GOMI-1T were C16 : 0, C14 : 0 and iso-C15 : 0, whereas those of strain KOME-1T were iso-C15 : 0, anteiso-C15 : 0 and C14 : 0. Based on comparative analysis of 16S rRNA gene sequences of strains GOMI-1T and KOME-1T, the strains were placed in different phylogenetic positions in the class Anaerolineae of the bacterial phylum Chloroflexi. Their phenotypic and genetic traits strongly supported the conclusion that the strains should be described as two independent taxa in the class Anaerolineae. Hence, we propose the names Bellilinea caldifistulae gen. nov., sp. nov., and Longilinea arvoryzae gen. nov., sp. nov., for strains GOMI-1T and KOME-1T. The type strains of Bellilinea caldifistulae and Longilinea arvoryzae are respectively GOMI-1T (=JCM 13669T =DSM 17877T) and KOME-1T (=JCM 13670T =KTCC 5380T).
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Fervidobacterium changbaicum sp. nov., a novel thermophilic anaerobic bacterium isolated from a hot spring of the Changbai Mountains, China
More LessA thermophilic, obligately anaerobic, rod-shaped bacterium (strain CBS-1T) was isolated from a hot spring mixture of water and mud of the Changbai Mountains, China. Strain CBS-1T was found to be non-sporulating, Gram-negative, with optimal growth at 75–80 °C. It grew on a wide range of carbon sources, including glucose, lactose, maltose, starch, sorbitol and pyruvate amongst others. The DNA G+C content of strain CBS-1T was 31.9 mol%. The 16S rRNA gene sequence analysis indicated that the strain was a member of the genus Fervidobacterium. The high concentration of C16 : 0 (52.2 %) in the fatty acid profile of the cell envelope supported its inclusion as a member of the genus Fervidobacterium. On the basis of the low values of DNA–DNA hybridization (25.8 and 20.5 %) and phenotypic features, strain CBS-1T represents a novel species of the genus Fervidobacterium, for which the name Fervidobacterium changbaicum sp. nov. is proposed. The type strain is CBS-1T (=DSM 17883T=JCM 13353T).
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Rubritalea spongiae sp. nov. and Rubritalea tangerina sp. nov., two carotenoid- and squalene-producing marine bacteria of the family Verrucomicrobiaceae within the phylum ‘Verrucomicrobia’, isolated from marine animals
More LessTwo Gram-negative, non-motile, coccoid or rod-shaped, chemoheterotrophic bacteria designated strains YM21-132T and YM27-005T were isolated from marine animals, and were subjected to a polyphasic taxonomic examination. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the two isolates belong to the genus Rubritalea of the phylum ‘Verrucomicrobia’ (subdivision 1). The novel isolates shared approximately 97–98 % sequence similarity with each other and showed 93–97 % similarity with Rubritalea species of the family Verrucomicrobiaceae. The level of DNA–DNA relatedness between strains YM21-132T and YM27-005T was less than 70 %, which is accepted as the phylogenetic definition of a species. Both strains produced reddish carotenoid pigments and squalene. The cell wall peptidoglycan of both strains contained muramic acid and meso-diaminopimelic acid. The G+C contents of the genomic DNA were 48.0 mol% (strain YM21-132T) and 50.3 mol% (strain YM27-005T). The presence of MK-8 and MK-9 as the major isoprenoid quinones, and iso-C14 : 0, iso-C16 : 0 and C16 : 1 ω7c as the major cellular fatty acids supported the identification of the two novel strains as members of the genus Rubritalea. On the basis of polyphasic taxonomic studies, it was concluded that these strains should be classified as representing two novel, separate species in the genus Rubritalea within the phylum ‘Verrucomicrobia’, for which the names Rubritalea spongiae sp. nov. (type strain YM21-132T=MBIC08281T=KCTC 12906T) and Rubritalea tangerina sp. nov. (type strain YM27-005T=MBIC08282T=KCTC 12907T) are proposed.
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- Proteobacteria
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Halomonas kribbensis sp. nov., a novel moderately halophilic bacterium isolated from a solar saltern in Korea
A moderately halophilic, Gram-negative bacterium, designated strain BH843T, was isolated from a solar saltern in Korea and subjected to a taxonomic analysis. Strain BH843T grew at salinities of 1–14 % (w/v) NaCl and at temperatures of 10–40 °C. The cells were motile cocci or short rods with single flagella and contained C16 : 0, C19 : 0 cyclo ω8c and C17 : 0 cyclo as the major fatty acids. The G+C content of the genomic DNA was 66 mol% and the predominant ubiquinone was Q-9. Comparative 16S rRNA gene sequence analyses showed that strain BH843T formed a distinct phyletic line within the genus Halomonas, and the levels of 16S rRNA gene sequence similarity with respect to recognized Halomonas species were below 95.1 %. The levels of DNA–DNA relatedness between strain BH843T and the type strains of phylogenetically closely related Halomonas species were below 25 %. On the basis of phenotypic, chemotaxonomic and molecular data, strain BH843T represents a novel species within the genus Halomonas, for which the name Halomonas kribbensis is proposed. The type strain is BH843T (=KCTC 12584T=DSM 17892T).
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Altererythrobacter epoxidivorans gen. nov., sp. nov., an epoxide hydrolase-active, mesophilic marine bacterium isolated from cold-seep sediment, and reclassification of Erythrobacter luteolus Yoon et al. 2005 as Altererythrobacter luteolus comb. nov.
A novel marine bacterium, strain JCS350T, was isolated from marine sediment samples collected from a cold-seep area. The 16S rRNA gene sequence of the isolate showed high similarity to that of Erythrobacter luteolus SW-109T (95.9 % sequence similarity). Lower 16S rRNA gene sequence similarities were shown to other members of the genus Erythrobacter (94.6–95.4 %) and members of the genus Porphyrobacter (94.5–95.2 %). Phylogenetic analysis with all members of the family Erythrobacteraceae and several members of the family Sphingomonadaceae revealed that the isolate formed a phyletic line with [Erythrobacter] luteolus that was distinct from other members of the family Erythrobacteraceae. The dominant fatty acids of strain JCS350T were 18 : 1ω7c, 16 : 1ω7c and cyclopropane 17 : 0. The major respiratory quinone was ubiquinone 10. The DNA G+C content was 54.5 mol%. The isolate did not contain bacteriochlorophyll a. Optimal growth required the presence of 2 % (w/v) NaCl with either 0.18 % CaCl2 or 0.59 % MgCl2, at pH 6.5 and at 35 °C. On the basis of the evidence of this polyphasic taxonomic study, strain JCS350T should be classified in a novel genus and species in the family Erythrobacteraceae, for which the name Altererythrobacter epoxidivorans gen. nov., sp. nov. is proposed. The misclassified species [Erythrobacter] luteolus is transferred to the new genus as Altererythrobacter luteolus comb. nov. The type strain of Altererythrobacter epoxidivorans is JCS350T (=KCCM 42314T =JCM 13815T) and the type strain of Altererythrobacter luteolus is SW-109T (=KCTC 12311T =JCM 12599T).
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Devosia subaequoris sp. nov., isolated from beach sediment
More LessA novel marine bacterium was isolated from a sediment sample from Hwasun Beach in Jeju, Republic of Korea. The cells were found to be Gram-negative, aerobic, oxidase-positive, catalase-positive, motile rods. The organism required natural seawater or artificial sea salts for growth. The temperature and pH ranges for growth were 20–42 °C and pH 5.1–12.1, respectively. Phylogenetic analyses based on 16S rRNA gene sequences showed that the organism belonged to the order Rhizobiales and formed a robust cluster with members of the genus Devosia. Its phylogenetic neighbours were the type strains of Devosia riboflavina (96.8 % 16S rRNA gene sequence similarity), Devosia neptuniae (96.7 %), Devosia soli (96.5 %) and Devosia limi (96.2 %), ‘Devosia terrae’ DCY11 (96.2 %) and ‘Candidatus Devosia euplotis’ (96.2 %). The predominant ubiquinone was Q-10, the major fatty acids were C18 : 1, C18 : 0 and C16 : 0 and the G+C content of the DNA was 59.1 mol%. On the basis of phenotypic data and the results of phylogenetic analyses, strain HST3-14T represents a novel species of the genus Devosia, for which the name Devosia subaequoris sp. nov. is proposed. The type strain is strain HST3-14T (=KCTC 12772T =JCM 14206T).
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Burkholderia bryophila sp. nov. and Burkholderia megapolitana sp. nov., moss-associated species with antifungal and plant-growth-promoting properties
A polyphasic taxonomic study including DNA–DNA reassociation experiments and an extensive biochemical characterization was performed on 14 Burkholderia isolates from moss gametophytes of nutrient-poor plant communities on the southern Baltic Sea coast in northern Germany. The strains were classified within two novel species, for which the names Burkholderia bryophila sp. nov. and Burkholderia megapolitana sp. nov. are proposed. The former species also includes isolates from grassland and agricultural soil collected in previous studies. Strains Burkholderia bryophila 1S18T (=LMG 23644T =CCUG 52993T) and Burkholderia megapolitana A3T (=LMG 23650T =CCUG 53006T) are the proposed type strains. They were isolated from Sphagnum rubellum and Aulacomnium palustre, respectively, growing in the ‘Ribnitzer Großes Moor’ nature reserve (Mecklenburg-Pommern, Germany). All moss isolates of both novel species showed antifungal activity against phytopathogens as well as plant-growth-promoting properties.
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Brevundimonas lenta sp. nov., isolated from soil
More LessA Gram-negative, rod-shaped, Brevundimonas-like bacterial strain, DS-18T, was isolated from soil in Dokdo, Korea, and its exact taxonomic position was investigated by using a polyphasic approach. Strain DS-18T grew optimally at pH 6.5–7.0 and 25 °C without NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DS-18T belonged to the genus Brevundimonas. Strain DS-18T contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c and C16 : 0 as the major fatty acids. The DNA G+C content was 68.7 mol%. Strain DS-18T exhibited levels of 16S rRNA gene sequence similarity of 96.3–98.7 % to the type strains of Brevundimonas species and Mycoplana bullata. Mean DNA–DNA relatedness values between strain DS-18T and the type strains of phylogenetically related Brevundimonas species and M. bullata were in the range 15–32 %. Strain DS-18T differed from Brevundimonas species and M. bullata in several phenotypic characteristics. On the basis of phenotypic, phylogenetic and genetic data, strain DS-18T represents a novel species of the genus Brevundimonas, for which the name Brevundimonas lenta sp. nov. is proposed. The type strain is DS-18T (=KCTC 12871T =JCM 14602T).
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Vibrio rhizosphaerae sp. nov., a red-pigmented bacterium that antagonizes phytopathogenic bacteria
More LessTwo novel red-pigmented Vibrio strains, MSSRF3T and MSSRF10, with antibacterial activity against phytopathogens were isolated from the rhizosphere region of mangrove-associated wild rice (Porteresia coarctata Tateoka), in Pichavaram, India. The cells were Gram-negative, facultatively anaerobic and rod-shaped and were motile by means of single polar flagella. The two strains were catalase-positive and oxidase-negative, and were able to grow in 0.1–10 % NaCl (with optimum growth in 2 % NaCl) and at temperatures of 20–42 °C (optimum growth at 25–30 °C). Both strains produced acid and gas from d-glucose under anaerobic conditions and utilized a wide range of compounds as sole carbon and energy sources. The DNA G+C contents determined were 51.3 mol% for strain MSSRF3T and 51.0 mol% for strain MSSRF10. Phylogenetic analysis based on 16S rRNA, rpoA, recA and pyrH gene sequences showed that strains MSSRF3T and MSSRF10 belong to the genus Vibrio and are very closely related to Vibrio ruber JCM 11486T, with which they share 98.3–98.5 % (16S rRNA), 98.3–99.7 % (rpoA), 90.2–99.8 % (recA) and 91.3–99.4 % (pyrH) gene sequence similarities, respectively. Levels of DNA–DNA relatedness were 44 % between strains MSSRF3T and MSSRF10, 80 % between strain MSSRF10 and V. ruber JCM 11486T and 45 % between strain MSSRF3T and V. ruber JCM 11486T. Strain MSSRF3T was phenotypically similar to V. ruber JCM 11486T. However, the inability to reduce nitrate to nitrite, the ability to grow in 0.1 % NaCl and the presence of caseinase were characteristics that allowed differentiation between V. ruber JCM 11486T and strain MSSRF3T. In addition, strain MSSRF3T could be differentiated from strain MSSRF10 and its closest relative V. ruber JCM 11486T with respect to its genomic fingerprinting analysis (random amplified polymorphic DNA, GTG5, BOX, PCR-restriction fragment length polymorphism and ribotyping). Therefore, based on phenotypic, genotypic, phylogenetic and DNA–DNA hybridization analyses, strain MSSRF3T (=LMG 23790T=DSM 18581T) should be classified as representing the type strain of a novel species of the genus Vibrio, for which the name Vibrio rhizosphaerae sp. nov. is proposed.
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Chromohalobacter japonicus sp. nov., a moderately halophilic bacterium isolated from a Japanese salty food
More LessA Gram-negative, non-spore-forming, rod-shaped, motile bacterium, designated strain 43T, was isolated from a Japanese salty food and then subjected to a polyphasic taxonomic study. Strain 43T is moderately halophilic, growing at NaCl concentrations in the range 5–25 % (w/v), with optimum growth between 7.5 and 12.5 % (w/v) NaCl. Growth occurs at temperatures from 15 to 42 °C (optimally at 28–37 °C) and at pH 5.5–9.0 (optimally at pH 7.0–8.0). A phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain 43T belongs to the genus Chromohalobacter. The closest relatives were Chromohalobacter canadensis ATCC 43984T (99.3 % 16S rRNA gene sequence similarity), Chromohalobacter beijerinckii ATCC 19372T (99.1 %), Chromohalobacter sarecensis LV4T (98.3 %), Chromohalobacter nigrandesensis LTS-4NT (97.9 %) and Chromohalobacter marismortui ATCC 17056T (97.9 %). The DNA G+C content was 62.9 mol%, which is within the range described for the genus Chromohalobacter. DNA–DNA hybridization studies between strain 43T and C. canadensis CECT 5385T and C. beijerinckii DSM 7218T showed 38 and 49 % relatedness, respectively; lower DNA–DNA hybridization percentages were obtained with respect to other related Chromohalobacter species. The major fatty acids of strain 43T were C16 : 0, C19 : 0 cyclo ω8c and C12 : 0 3-OH. Overall, the phenotypic, genotypic and phylogenetic results demonstrated that strain 43T represents a novel species within the genus Chromohalobacter. The name Chromohalobacter japonicus sp. nov. is proposed, with strain 43T (=CECT 7219T =CCM 7416T) as the type strain.
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Kaistia granuli sp. nov., isolated from anaerobic granules in an upflow anaerobic sludge blanket reactor
A Gram-negative, chemo-organotrophic, non-motile, non-spore-forming, rod-shaped bacterium (designated strain Ko04T) was isolated from anaerobic granules in an upflow anaerobic sludge blanket reactor, and was investigated using a polyphasic taxonomic approach. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Ko04T belongs to the order Rhizobiales in the Alphaproteobacteria. Comparative 16S rRNA gene sequence analysis showed that strain Ko04T was most closely related to Kaistia adipata (97.5 %) and that sequence similarities with other species of Rhizobiales with validly published names were less than 92.5 %. The predominant ubiquinone was Q-10 and the major fatty acids were C18 : 1 ω7c/ω9t/ω12t, C19 : 0 cyclo ω8c and C18 : 0. The G+C content of the genomic DNA of strain Ko04T was 67.8 mol%. The level of DNA–DNA relatedness with K. adipata Chj404T was 15 %. The results of the genotypic analyses in combination with chemotaxonomic and physiological data demonstrated that strain Ko04T represents a novel species within the genus Kaistia, for which the name Kaistia granuli sp. nov. is proposed. The type strain is Ko04T (=KCTC 12575T=LMG 23410T).
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Herbaspirillum rhizosphaerae sp. nov., isolated from rhizosphere soil of Allium victorialis var. platyphyllum
More LessTwo Gram-negative, milky-white-pigmented, motile, slightly curved rod-shaped bacterial isolates, UMS-37T and UMS-40, were isolated from rhizosphere soil of wild edible greens cultivated on Ulleung island, Korea, and their taxonomic positions were investigated by a polyphasic approach. They grew optimally at 25–30 °C and contained Q-8 as the predominant ubiquinone. The major cellular fatty acids (>10 % of total fatty acids) were C16 : 0, cyclo C17 : 0 and C16 : 1 ω7c and/oriso-C15 : 0 2-OH. The DNA G+C contents of the two isolates were 59.8 and 60.0 mol%. Isolates UMS-37T and UMS-40 exhibited no difference in their 16S rRNA gene sequences and possessed a mean DNA–DNA relatedness level of 94 %; they exhibited 16S rRNA gene sequence similarity levels of 96.8–98.2 % to the type strains of recognized Herbaspirillum species. Phylogenetic analyses based on 16S rRNA gene sequences showed that isolates UMS-37T and UMS-40 formed a distinct phylogenetic lineage within the genus Herbaspirillum. DNA–DNA relatedness levels between isolates UMS-37T and UMS-40 and the type strains of some phylogenetically related Herbaspirillum species were in the range 3–56 %. On the basis of differences in phenotypic properties and phylogenetic distinctiveness and genomic data, isolates UMS-37T and UMS-40 were classified in the genus Herbaspirillum within a novel species, for which the name Herbaspirillum rhizosphaerae sp. nov. is proposed, with the type strain UMS-37T (=KCTC 12558T =CIP 108917T).
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Modicisalibacter tunisiensis gen. nov., sp. nov., an aerobic, moderately halophilic bacterium isolated from an oilfield-water injection sample, and emended description of the family Halomonadaceae Franzmann et al. 1989 emend Dobson and Franzmann 1996 emend. Ntougias et al. 2007
An aerobic, moderately halophilic, Gram-negative, motile, non-sporulating bacterium, strain LIT2T, was isolated from an oilfield-water injection after enrichment on crude oil. Strain LIT2T grew between 15 and 45 °C and optimally at 37 °C. It grew in the presence of 1–25 % (w/v) NaCl, with an optimum at 10 % (w/v) NaCl. Predominant fatty acids were C16 : 0 (26.9 %), C18 : 1 ω7c (22.6 %), C16 : 1 ω7c (20.4 %) C19 : 0 cyclo ω8c (10.9 %) and C17 : 0 (8 %). Interestingly, the relative percentages of these last two fatty acids were intermediate compared with most species among the family Halomonadaceae for which fatty acid composition has been determined. The DNA G+C content was 53.7 mol%, which is very low among the family Halomonadaceae. Strain LIT2T exhibited 16S rRNA gene sequence similarity values of 94.06–95.15 % to members of the genus Chromohalobacter, 94.21–94.65 % to members of the genus Halomonas and 93.57 % with the single species representative of the genus Cobetia. Based on the phylogenetic and phenotypic evidence presented in this paper, we propose the name Modicisalibacter tunisiensis gen. nov., sp. nov. to accommodate strain LIT2T. The type strain of Modicisalibacter tunisiensis is LIT2T (=CCUG 52917T =CIP 109206T). A reassignment of the descriptive 16S rRNA signature characteristics of the family Halomonadaceae permitted placement of the new genus Modicisalibacter into the family.
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Desulfothermus okinawensis sp. nov., a thermophilic and heterotrophic sulfate-reducing bacterium isolated from a deep-sea hydrothermal field
More LessA novel thermophilic and heterotrophic sulfate-reducing bacterium, strain TFISO9T, was isolated from a deep-sea hydrothermal field at the Yonaguni Knoll IV in the Southern Okinawa Trough. The cells were motile rods 2.5–5.0 μm in length and 0.6–0.9 μm in width. Strain TFISO9T was an obligate heterotroph and reduced sulfate. It grew between 35 and 60 °C (optimum 50 °C), at pH 5.4–7.9 (optimum pH 5.9–6.4) and with 1.5–4.5 % NaCl (optimum 2.5 %). The fatty acid composition was C16 : 0 (61.5 %) and 12Me16 : 0 (38.5 %). The DNA G+C content was 34.9 mol%. The 16S rRNA gene sequence analysis indicated that strain TFISO9T belonged to the genus Desulfothermus. Based on physiological and phylogenetic characteristics, strain TFISO9T represents a novel species for which the name Desulfothermus okinawensis sp. nov. is proposed. The type strain is TFISO9T (=JCM 13304T=DSM 17375T).
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Microbulbifer celer sp. nov., isolated from a marine solar saltern of the Yellow Sea in Korea
More LessA Gram-negative, non-motile, rod-shaped, Microbulbifer-like bacterial strain, ISL-39T, was isolated from a marine solar saltern of the Yellow Sea in Korea and was subjected to a polyphasic taxonomic investigation. Strain ISL-39T grew optimally at pH 7.0–8.0 and 37 °C. It contained Q-8 as the predominant ubiquinone and iso-C15 : 0, C16 : 0 and iso-C17 : 0 as the major fatty acids. The DNA G+C content was 57.7 mol%. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain ISL-39T belonged to the genus Microbulbifer. Strain ISL-39T exhibited 16S rRNA gene sequence similarity values of 94.7–97.5 % with respect to the type strains of four recognized Microbulbifer species. DNA–DNA relatedness data and the differential phenotypic properties and phylogenetic distinctiveness of ISL-39T make this strain distinguishable from the recognized Microbulbifer species. On the basis of the phenotypic, phylogenetic and genetic data, strain ISL-39T represents a novel species of the genus Microbulbifer, for which the name Microbulbifer celer sp. nov. is proposed. The type strain is ISL-39T (=KCTC 12973T=CCUG 54356T).
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Reinekea blandensis sp. nov., a marine, genome-sequenced gammaproteobacterium
A novel heterotrophic, moderately halophilic, strictly aerobic, motile bacterium was isolated from a seawater sample collected at the Blanes Bay Microbial Observatory in the north-western Mediterranean Sea. Analysis of its 16S rRNA gene sequence, retrieved from the whole-genome sequence, showed that this bacterium was most closely related to the single-species genera Reinekea and Saccharospirillum (95 and 94 % sequence similarity, respectively) within the class Gammaproteobacteria. The data from phenotypic, genotypic, chemotaxonomic and phylogenetic analyses supported the creation of a novel species of the genus Reinekea to accommodate this bacterium, for which the name Reinekea blandensis sp. nov. is proposed. The type strain is MED297T (=CECT 7120T =CCUG 52066T).
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Rheinheimera texasensis sp. nov., a halointolerant freshwater oligotroph
More LessA Gram-negative, rod-shaped, motile, non-spore-forming bacterium, designated strain A62-14BT, was isolated from a constant-temperature, spring-fed, freshwater lake. On the basis of the complete 16S rRNA gene sequence, strain A62-14BT was shown to belong to the class Gammaproteobacteria, being most closely related to Rheinheimera sp. HTB082 (96.2 % sequence similarity), Rheinheimera baltica (95.01 %), Rheinheimera pacifica (96.35 %), Rheinheimera perlucida and Alishewanella fetalis (95.9 %). The major fatty acids (C16 : 1 ω7c, 38.56 %; C16 : 0, 19.04 %; C12 : 0 3-OH, 12.83 %; C18 : 1 ω7c, 7.70 %) and the motility of strain A62-14BT support its affiliation to the genus Rheinheimera. The salt intolerance of strain A62-14BT, together with the results of other physiological and biochemical tests, allowed the differentiation of this strain from the three species of the genus Rheinheimera with validly published names. Therefore strain A62-14BT represents a novel species of the genus Rheinheimera, for which the name Rheinheimera texasensis sp. nov. is proposed. The type strain is A62-14BT (=ATCC BAA-1235T=DSM 17496T). The description of the genus Rheinheimera is emended to reflect the halointolerance and freshwater origin of strain A62-14BT.
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Anderseniella baltica gen. nov., sp. nov., a novel marine bacterium of the Alphaproteobacteria isolated from sediment in the central Baltic Sea
More LessA bacterial isolate from the Baltic Sea, designated strain BA141T, was characterized for its physiological and biochemical features, fatty acid profile, pigment spectrum, DNA G+C content and phylogenetic position based on comparative 16S rRNA gene sequence analysis. The strain was isolated from the surface of sediment in a deep basin of the central Baltic Sea. Phylogenetic analysis of the 16S rRNA gene sequence revealed a clear affiliation with the Alphaproteobacteria, and showed that the closest phylogenetic relationship was with the genus Rhodobium. The G+C content of the DNA was 61.2 mol%. Cells of strain BA141T were red-pigmented, Gram-negative, pleomorphic to rod-shaped, non-motile and catalase- and oxidase-positive. Growth was observed at salinities of 0.8–6 %, with optimum growth at 1.5–3 %. The temperature range for growth was 10–37 °C, with optimum growth at 25–30 °C. The fatty acids were dominated by unsaturated fatty acids (>86 %); the number of fatty acids detected was very low, with 18 : 1ω7c (73 %) as the predominant fatty acid; other major fatty acids were 19 : 0 cyclo 8c (10 %) and 16 : 0 (8 %). The pigment spectrum indicated the presence of carotenoids and unknown pigment(s) with an absorption maximum at 430 nm, but not bacteriochlorophyll a. According to phylogenetic analysis based on the 16S rRNA gene sequence and the phenotypic features, strain BA141T represents a new genus and species. The name Anderseniella baltica gen. nov., sp. nov. is proposed, with strain BA141T (=CIP 109499T=LMG 24028T) as the type strain.
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- Eukaryotic Micro-Organisms
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Polyphasic re-examination of Yarrowia lipolytica strains and the description of three novel Candida species: Candida oslonensis sp. nov., Candida alimentaria sp. nov. and Candida hollandica sp. nov.
The type strain of Yarrowia lipolytica and 38 strains identified as Yarrowia lipolytica, four strains of Candida deformans, including the type and two subcultures of the type, two strains of Candida galli and six unidentified strains that resembled Y. lipolytica were examined by PCR fingerprints using primers M13 and (GAC)5. The same strains, together with four strains of the recently introduced Candida yakushimensis nom. inval., were sequenced for the D1/D2 domain of the 26S rRNA gene and parts of the ITS domain and also studied for their physiological properties. Of the strains identified previously as Y. lipolytica, CBS 2076 had the same fingerprint as the type of C. deformans and strain CBS 4855 was distinct from all other strains. The six strains that resembled Y. lipolytica were separated into two groups distinct from any of the other clades. A total of six groups obtained by fingerprint and sequence data were evaluated by performing DNA reassociation reactions. Mating experiments among the 35 strains of Y. lipolytica sensu stricto showed that 15 strains represented one mating type and 16 strains represented the opposite mating type, while four strains were self-sporulating. Teleomorph states were not produced by C. deformans, C. galli or any of the unidentified isolates. However, positive mating reactions were rarely observed in crosses among C. galli and some strains of Y. lipolytica and C. deformans. Consequently, sharing the same mating type system, C. deformans and C. galli could be considered anamorphs of unnamed Yarrowia species. Results from PCR fingerprints, sequencing and mating studies support the grouping of the studied strains into Y. lipolytica, C. galli, C. deformans, C. yakushimensis nom. inval. and three novel species in the Yarrowia clade: Candida oslonensis sp. nov. (type strain CBS 10146T =NRRL Y-48252T; Mycobank number MB 510769), Candida alimentaria sp. nov. (type strain CBS 10151T =NRRL Y-48253T; Mycobank number MB 510770) and Candida hollandica sp. nov. (type strain CBS 4855T =NRRL Y-48254T; Mycobank number MB 510771).
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- Other Gram-Positive Bacteria
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Thermoanaerobacter pseudethanolicus sp. nov., a thermophilic heterotrophic anaerobe from Yellowstone National Park
More LessStrain 39ET, originally characterized as Clostridium thermohydrosulfuricum strain 39E and later renamed as Thermoanaerobacter ethanolicus strain 39E, shows less than 97 % 16S rRNA gene sequence similarity with the type strain of the type species of the genus Thermoanaerobacter, T. ethanolicus strain JW 200T. On the basis of a polyphasic analysis that included DNA–DNA hybridization studies with the subspecies of Thermoanaerobacter brockii, its closest phylogenetic relatives, strain 39ET represents a novel species of the genus Thermoanaerobacter, for which the name Thermoanaerobacter pseudethanolicus sp. nov. is proposed. The type strain is 39ET (=DSM 2355T=ATCC 33223T).
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Paenibacillus humicus sp. nov., isolated from poultry litter compost
Two bacterial strains, PC-142 and PC-147T, isolated from poultry litter compost, were characterized with respect to their phenetic and phylogenetic characteristics. The isolates were endospore-forming rods that were reddish in colour after Gram staining. They were catalase- and oxidase-positive, were able to degrade starch and gelatin and grew at 15–40 °C and pH 5.5–10.0. The predominant fatty acids were anteiso-C15 : 0, iso-C15 : 0 and iso-C16 : 0, the major respiratory quinone was menaquinone MK-7, the cell-wall peptidoglycan was of the A1γ type and the G+C content of the DNA was 58 mol%. The 16S rRNA gene sequence analysis and phenetic characterization indicated that these organisms belong to the genus Paenibacillus, with Paenibacillus pasadenensis SAFN-007T as the closest phylogenetic neighbour (97.5 %). Strains PC-142, PC-147T and P. pasadenensis SAFN-007T represent a novel lineage within the genus Paenibacillus, characterized by a high DNA G+C content (58–63 mol%). The low levels of 16S rRNA gene sequence similarity with respect to other taxa with validly published names and the identification of distinctive phenetic features in the two isolates indicate that strains PC-142 and PC-147T represent a novel species of the genus Paenibacillus, for which the name Paenibacillus humicus sp. nov. is proposed. The type strain is PC-147T (=DSM 18784T =NBRC 102415T =LMG 23886T).
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Acidaminococcus intestini sp. nov., isolated from human clinical samples
Eleven strains of a hitherto unknown, Gram-negative, anaerobic coccus were recovered from various human clinical samples of patients hospitalized in two geographically distant French hospitals. These strains displayed the morphology and growth characteristics of those related to the genus Acidaminococcus. The clinical isolates shared at least 99.9 and 99.7 % of their nucleotide positions in the 16S and 23S rRNA gene sequences, respectively. They displayed 95.6 and 88.9 % 16S and 23S rRNA gene sequence similarities, respectively, with Acidaminococcus fermentans. The 16S rRNA-based phylogeny revealed that all the clinical isolates grouped in a statistically well supported cluster separate from A. fermentans. Enzymic activity profiles as well as metabolic end product patterns, including propionic acid production, differentiated the novel bacteria from A. fermentans. Finally, phenotypic, genotypic and phylogenetic data, including large-scale chromosome structure and DNA G+C content, supported the proposal of a novel species of the genus Acidaminococcus, for which the name Acidaminococcus intestini sp. nov. is proposed. The type strain is ADV 255.99T (=AIP 283.01T=CIP 108586T=CCUG 50930T).
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Dethiosulfatibacter aminovorans gen. nov., sp. nov., a novel thiosulfate-reducing bacterium isolated from coastal marine sediment via sulfate-reducing enrichment with Casamino acids
A sulfate-reducing enrichment culture originating from coastal marine sediment of the eutrophic Tokyo Bay, Japan, was successfully established with Casamino acids as a substrate. A thiosulfate reducer, strain C/G2T, was isolated from the enrichment culture after further enrichment with glutamate. Cells of strain C/G2T were non-motile rods (0.6–0.8 μm×2.2–4.8 μm) and were found singly or in pairs and sometimes in short chains. Spores were not formed. Cells of strain C/G2T stained Gram-negatively, despite possessing Gram-positive cell walls. The optimum temperature for growth was 28–30 °C, the optimum pH was around 7.8 and the optimum salt concentration was 20–30 g l−1. Lactate, pyruvate, serine, cysteine, threonine, glutamate, histidine, lysine, arginine, Casamino acids, peptone and yeast extract were fermented as single substrates and no sugar was used as a fermentative substrate. A Stickland reaction was observed with some pairs of amino acids. Fumarate, alanine, proline, phenylalanine, tryptophan, glutamine and aspartate were utilized only in the presence of thiosulfate. Strain C/G2T fermented glutamate to H2, CO2, acetate and propionate. Thiosulfate and elemental sulfur were reduced to sulfide. Sulfate, sulfite and nitrate were not utilized as electron acceptors. The growth of strain C/G2T on Casamino acids or glutamate was enhanced by co-culturing with Desulfovibrio sp. isolated from the original mixed culture enriched with Casamino acids. The DNA G+C content of strain C/G2T was 41.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain C/G2T formed a distinct cluster with species of the genus Sedimentibacter. The closest relative was Sedimentibacter hydroxybenzoicus (with a gene sequence similarity of 91 %). On the basis of its phylogenetic and phenotypic properties, strain C/G2T (=JCM 13356T=NBRC 101112T=DSM 17477T) is proposed as representing a new genus and novel species, Dethiosulfatibacter aminovorans gen. nov., sp. nov.
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Salinicoccus kunmingensis sp. nov., a moderately halophilic bacterium isolated from a salt mine in Yunnan, south-west China
A novel yellow-pigmented, non-motile, non-sporulating, catalase- and oxidase-positive, obligately aerobic, moderately halophilic, facultatively alkaliphilic Gram-positive coccus, strain YIM Y15T, was isolated from a brine sample from a salt mine in Yunnan, south-west China. Strain YIM Y15T grew in the presence of 0.5–25 % (w/v) NaCl and at pH 6.0–10.0, with optimum growth at 8–10 % (w/v) NaCl and pH 8.0. It grew at 4–45 °C, with optimum growth at 37.0 °C. The major cellular fatty acids were anteiso-C15 : 0 and iso-C15 : 0. Menaquinone 6 (MK-6) was the major respiratory quinone. The cell wall contained Lys and Gly. The DNA G+C content was 46.2 mol%. Phylogenetic analyses based on 16S rRNA gene sequence comparisons revealed that strain YIM Y15T was a member of the genus Salinicoccus, with low 16S rRNA gene sequence similarity to the type strains of the five described species of the genus, Salinicoccus alkaliphilus JCM 11311T (sequence similarity 96.0 %), Salinicoccus roseus DSM 5351T (94.9 %), Salinicoccus jeotgali KCTC 13030T (94.8 %), Salinicoccus salsiraiae LMG 22840T (94.8 %) and Salinicoccus hispanicus DSM 5352T (94.7 %). Together with the phenotypic differences, these results supported the proposal of a novel species of the genus Salinicoccus, Salinicoccus kunmingensis sp. nov., with YIM Y15T (=DSM 17847T =CGMCC 1.6302T) as the type strain.
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Salsuginibacillus kocurii gen. nov., sp. nov., a moderately halophilic bacterium from soda-lake sediment
More LessA Gram-positive, endospore-forming, alkali-tolerant, moderately halophilic bacterium, designated strain CH9dT, was isolated from the sediment of Lake Chagannor in the Inner Mongolia Autonomous Region, China. The cells were rod-shaped and motile. Isolate CH9dT grew at pH 5.8–10.0 (optimally at pH 8.5), at salinities of 3–20 % (w/v) marine salts (optimally at 10.0 %, w/v) and between 20 and 50 °C (optimally at 37 °C). The cell wall contained meso-diaminopimelic acid and the major respiratory isoprenoid quinone was MK-7. The predominant cellular fatty acids of strain CH9dT were anteiso-C15 : 0, anteiso-C17 : 0, iso-C17 : 0 and iso-C15 : 0 and its polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and two unknown phospholipids. The G+C content of the DNA was 44.7 mol%. Strain CH9dT exhibited a 16S rRNA gene sequence similarity value of only 91 % with respect to Thalassobacillus devorans DSM 16966T and showed values below 91 % with respect to members of the genera Bacillus, Halobacillus and Marinococcus. Strain CH9dT could be clearly differentiated from its closest phylogenetic neighbours on the basis of several phenotypic, genotypic and chemotaxonomic features. Therefore, data from the polyphasic study support the placement of strain CH9dT in a novel genus and species, for which the name Salsuginibacillus kocurii gen. nov., sp. nov. is proposed. The type strain is CH9dT (=CCM 7365T=CECT 7154T=CGMCC 1.6287T=DSM 18087T).
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Reclassification of Marinococcus albus Hao et al. 1985 as Salimicrobium album gen. nov., comb. nov. and Bacillus halophilus Ventosa et al. 1990 as Salimicrobium halophilum comb. nov., and description of Salimicrobium luteum sp. nov.
More LessA Gram-positive, non-motile, coccoid-shaped, non-spore-forming halophilic bacterial strain, BY-5T, was isolated from a marine solar saltern in Korea and its taxonomic position was investigated by using a polyphasic approach. The novel strain grew optimally at 37 °C and in the presence of 10 % (w/v) NaCl. Strain BY-5T had meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan, MK-7 as the predominant menaquinone and anteiso-C15 : 0, iso-C15 : 0, anteiso-C17 : 0 and iso-C17 : 0 as the major fatty acids. The DNA G+C content was 47.9 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain BY-5T formed a coherent cluster with Bacillus halophilus and Marinococcus albus. Strain BY-5T exhibited 16S rRNA gene sequence similarity values of 98.7 and 97.4 % to the type strains of B. halophilus and M. albus, respectively. Strain BY-5T was distinguished from B. halophilus and M. albus by several phenotypic properties and DNA–DNA relatedness data. On the basis of the combined chemotaxonomic and phylogenetic data, it is proposed that M. albus, B. halophilus and strain BY-5T should be placed in a new genus as three separate species. Marinococcus albus and Bacillus halophilus are reclassified in a new genus, Salimicrobium gen. nov., as Salimicrobium album comb. nov. and Salimicrobium halophilum comb. nov., respectively. The type species of the new genus is Salimicrobium album. Strain BY-5T (=KCTC 3989T=CIP 108918T) is placed in the genus Salimicrobium as a novel species Salimicrobium luteum sp. nov.
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- Evolution, Phylogeny And Biodiversity
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Phylogeny of the Mycoplasma mycoides cluster based on analysis of five conserved protein-coding sequences and possible implications for the taxonomy of the group
More LessA phylogenetic tree of the Mycoplasma mycoides cluster was inferred from a set of concatenated sequences from five housekeeping genes (fusA, glpQ, gyrB, lepA and rpoB). The relevance of this phylogeny was reinforced by detailed analysis of the congruence of the phylogenies derived from each of the five individual gene sequences. Two subclusters were distinguished. The M. mycoides subcluster comprised M. mycoides subsp. mycoides biotypes Small Colony (SC) and Large Colony (LC) and M. mycoides subsp. capri. The latter two groups could not be clearly separated, which supports previous proposals that they be united into a single taxonomic entity. The Mycoplasma capricolum subcluster included M. capricolum subsp. capricolum, M. capricolum subsp. capripneumoniae and Mycoplasma sp. bovine group 7 of Leach, a group of strains that remains unassigned. This group constituted a distinct branch within this cluster, supporting its classification as a subspecies of M. capricolum. Mycoplasma cottewii and Mycoplasma yeatsii clustered in a group that was distinct from Mycoplasma putrefaciens and they were all clearly separated from the M. mycoides cluster. In conclusion, this approach has allowed us to assign phylogenetic positions to all members of the M. mycoides cluster and related species and has proved the need to adjust the existing taxonomy. Furthermore, this method may be used as a reference technique to assign an unequivocal position to any particular strain related to this cluster and may lead to the development of new techniques for rapid species identification.
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Phylogenetic relationships within the family Halobacteriaceae inferred from rpoB′ gene and protein sequences
More LessIn order to clarify the current phylogeny of the haloarchaea, particularly the closely related genera that have been difficult to sort out using 16S rRNA gene sequences, the DNA-dependent RNA polymerase subunit B′ gene (rpoB′) was used as a complementary molecular marker. Partial sequences of the gene were determined from 16 strains of the family Halobacteriaceae. Comparisons of phylogenetic trees inferred from the gene and protein sequences as well as from corresponding 16S rRNA gene sequences suggested that species of the genera Natrialba, Natronococcus, Halobiforma, Natronobacterium, Natronorubrum, Natrinema/Haloterrigena and Natronolimnobius formed a monophyletic group in all trees. In the RpoB′ protein tree, the alkaliphilic species Natrialba chahannaoensis, Natrialba hulunbeirensis and Natrialba magadii formed a tight group, while the neutrophilic species Natrialba asiatica formed a separate group with species of the genera Natronorubrum and Natronolimnobius. Species of the genus Natronorubrum were split into two groups in both the rpoB′ gene and protein trees. The most important advantage of the use of the rpoB′ gene over the 16S rRNA gene is that sequences of the former are highly conserved amongst species of the family Halobacteriaceae. All sequences determined so far can be aligned unambiguously without any gaps. On the other hand, gaps are necessary at 49 positions in the inner part of the alignment of 16S rRNA gene sequences. The rpoB′ gene and protein sequences can be used as an excellent alternative molecular marker in phylogenetic analysis of the Halobacteriaceae.
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Phylogeny and evolution of the family Ectothiorhodospiraceae based on comparison of 16S rRNA, cbbL and nifH gene sequences
The occurrence of genes encoding nitrogenase and ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) was investigated in the members of the family Ectothiorhodospiraceae. This family forms a separate phylogenetic lineage within the Gammaproteobacteria according to 16S rRNA gene sequence analysis and mostly includes photo- and chemoautotrophic halophilic and haloalkaliphilic bacteria. The cbbL gene encoding the large subunit of ‘green-like’ form I RubisCO was found in all strains, except the type strains of Alkalispirillum mobile and Arhodomonas aquaeolei. The nifH gene encoding nitrogenase reductase was present in all investigated species of the phototrophic genera Ectothiorhodospira, Halorhodospira and Thiorhodospira, but not of the genus Ectothiorhodosinus. Unexpectedly, nifH fragments were also obtained for the chemotrophic species Thioalkalispira microaerophila and Alkalilimnicola halodurans, for which diazotrophic potential has not previously been assumed. The cbbL-, nifH- and 16S rRNA gene-based trees were not highly congruent in their branching patterns since, in the ‘RubisCO’ and ‘nitrogenase’ trees, representatives of the Ectothiorhodospiraceae are divided in a number of broadly distributed clusters and branches. However, the data obtained may be regarded as evidence of the monophyletic origin of the cbbL and nifH genes in most species within the family Ectothiorhodospiraceae and mainly corresponded to the current taxonomic structure of this family. The cbbL phylogeny of the chemolithoautotrophic sulfur-oxidizers Thioalkalivibrio nitratireducens and Thioalkalivibrio paradoxus and the nitrifier Nitrococcus mobilis deviated significantly from the 16S-rRNA gene-based phylogeny. These species clustered with one of the duplicated cbbL genes of the purple sulfur bacterium Allochromatium vinosum, a member of the family Chromatiaceae.
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Barcoding ciliates: a comprehensive study of 75 isolates of the genus Tetrahymena
The mitochondrial cytochrome-c oxidase subunit 1 (cox1) gene has been proposed as a DNA barcode to identify animal species. To test the applicability of the cox1 gene in identifying ciliates, 75 isolates of the genus Tetrahymena and three non-Tetrahymena ciliates that are close relatives of Tetrahymena, Colpidium campylum, Colpidium colpoda and Glaucoma chattoni, were selected. All tetrahymenines of unproblematic species could be identified to the species level using 689 bp of the cox1 sequence, with about 11 % interspecific sequence divergence. Intraspecific isolates of Tetrahymena borealis, Tetrahymena lwoffi, Tetrahymena patula and Tetrahymena thermophila could be identified by their cox1 sequences, showing <0.65 % intraspecific sequence divergence. In addition, isolates of these species were clustered together on a cox1 neighbour-joining (NJ) tree. However, strains identified as Tetrahymena pyriformis and Tetrahymena tropicalis showed high intraspecific sequence divergence values of 5.01 and 9.07 %, respectively, and did not cluster together on a cox1 NJ tree. This may indicate the presence of cryptic species. The mean interspecific sequence divergence of Tetrahymena was about 11 times greater than the mean intraspecific sequence divergence, and this increased to 58 times when all isolates of species with high intraspecific sequence divergence were excluded. This result is similar to DNA barcoding studies on animals, indicating that congeneric sequence divergences are an order of magnitude greater than conspecific sequence divergences. Our analysis also demonstrated low sequence divergences of <1.0 % between some isolates of T. pyriformis and Tetrahymena setosa on the one hand and some isolates of Tetrahymena furgasoni and T. lwoffi on the other, suggesting that the latter species in each pair is a junior synonym of the former. Overall, our study demonstrates the feasibility of using the mitochondrial cox1 gene as a taxonomic marker for ‘barcoding’ and identifying Tetrahymena species and some other ciliated protists.
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- Methods
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EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences
16S rRNA gene sequences have been widely used for the identification of prokaryotes. However, the flood of sequences of non-type strains and the lack of a peer-reviewed database for 16S rRNA gene sequences of type strains have made routine identification of isolates difficult and labour-intensive. In the present study, we generated a database containing 16S rRNA gene sequences of all prokaryotic type strains. In addition, a web-based tool, named EzTaxon, for analysis of 16S rRNA gene sequences was constructed to achieve identification of isolates based on pairwise nucleotide similarity values and phylogenetic inference methods. The system developed provides users with a similarity-based search, multiple sequence alignment and various phylogenetic analyses. All of these functions together with the 16S rRNA gene sequence database of type strains can be successfully used for automated and reliable identification of prokaryotic isolates. The EzTaxon server is freely accessible over the Internet at http://www.eztaxon.org/
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- International Committee On Systematics Of Prokaryotes
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Recommended minimal standards for describing new taxa of the family Halomonadaceae
Following Recommendation 30b of the Bacteriological Code (1990 Revision), a proposal of minimal standards for describing new taxa within the family Halomonadaceae is presented. An effort has been made to evaluate as many different approaches as possible, not only the most conventional ones, to ensure that a rich polyphasic characterization is given. Comments are given on the advantages of each particular technique. The minimal standards are considered as guidelines for authors to prepare descriptions of novel taxa. The proposals presented here have been endorsed by the International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Halomonadaceae.
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- Request For An Opinion
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Recommendation for the conservation of the name Streptomyces scabies. Request for an Opinion
More LessThe primary streptomycete inciting common scab of potato was first legitimately described by Thaxter in 1892 as ‘Oospora scabies’, preserving the spelling of an epithet in use since 1846. The name Streptomyces scabies, dating to 1948, was revived in 1989, but changed to Streptomyces scabiei in 1997 to follow grammatical convention. Considering the long-established use and general recognition of ‘scabies’, it is proposed that the original epithet be conserved.
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Volumes and issues
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