- Volume 58, Issue 10, 2008
Volume 58, Issue 10, 2008
- Notification List
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Notification that new names and new combinations have appeared in volume 58, 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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Nocardioides koreensis sp. nov., Nocardioides bigeumensis sp. nov. and Nocardioides agariphilus sp. nov., isolated from soil from Bigeum Island, Korea
More LessThree Gram-positive, coccoid to rod-shaped actinobacteria, designated strains MSL-09T, MSL-19T and MSL-28T, were isolated from a soil sample collected from Bigeum Island in Korea, and were subjected to a polyphasic taxonomic analysis. All three isolates grew optimally at pH 7.5–9.0 and 28–30 °C. 16S rRNA gene analysis revealed that all three strains belonged to the genus Nocardioides, with strains MSL-09T, MSL-19T and MSL-28T respectively showing the highest sequence similarity to Nocardioides aquaticus DSM 11439T (96.25 %), Nocardioides aquiterrae GW-9T (95.75 %) and Nocardioides terrigena DS-17T (95.61 %). Chemotaxonomically, they contain ll-2,6-diaminopimelic acid in the cell-wall peptidoglycan, MK-8(H4) as the predominant menaquinone and diphosphatidylglycerol, phosphatidylglycerol and some unknown lipids as the polar lipids found in the cell wall. iso-C16 : 0 is a major fatty acid. The G+C content of the DNA was respectively 69.9, 69.3 and 69.4 mol% for strains MSL-09T, MSL-19T and MSL-28T. Based on morphological, physiological, biochemical and chemotaxonomic characters presented in this study, the three strains represent novel species of the genus Nocardioides. The names Nocardioides koreensis sp. nov. (type strain MSL-09T =KCTC 19272T =DSM 19266T), Nocardioides bigeumensis sp. nov. (type strain MSL-19T =KCTC 19290T =DSM 19320T) and Nocardioides agariphilus sp. nov. (type strain MSL-28T =KCTC 19276T =DSM 19323T) are proposed.
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Agrococcus jejuensis sp. nov., isolated from dried seaweed
More LessA novel marine actinomycete, designated strain SSW1-48T, was isolated from a dried seaweed sample collected from a beach in Jeju, Republic of Korea. Cells of the organism were non-motile, non-endospore-forming, Gram-positive and rod-shaped. Colonies were circular, smooth, translucent and yellow-coloured. The diagnostic diamino acid in the peptidoglycan was 2,4-diaminobutyric acid and the murein was of the acetyl type. Mycolic acids were absent. The predominant menaquinones were MK-10 and MK-9. The major fatty acids were anteiso-C15 : 0 and iso-C16 : 0. The G+C content of the DNA was 73.0 mol%. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that the isolate formed a distinct branch between Agrococcus lahaulensis and Agrococcus casei in the family Microbacteriaceae. The values for 16S rRNA gene sequence similarity between strain SSW1-48T and type strains of recognized Agrococcus species were in the range 95.5–97.5 % and those between this bacterium and other representatives of the family Microbacteriaceae were in the range 93.7–96.4 %. On the basis of the combined data from the phenotypic and phylogenetic analyses, strain SSW1-48T represents a novel species of the genus Agrococcus, for which the name Agrococcus jejuensis sp. nov. is proposed. The type strain is SSW1-48T (=KCTC 19198T=JCM 14256T).
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Reclassification of Streptomyces flavidofuscus as a synonym of Nocardiopsis dassonvillei subsp. dassonvillei
More LessDuring the course of quality control studies of the collection of the NITE Biological Resource Center (NBRC), phylogenetic analysis based on 16S rRNA gene sequences of actinomycetes revealed that Streptomyces flavidofuscus NBRC 15404T formed a cluster with Nocardiopsis dassonvillei and Nocardiopsis synnemataformans. Strain NBRC 15404T contained meso-diaminopimelic acid as a cell-wall diamino acid and DNA–DNA hybridization studies also showed that S. flavidofuscus NBRC 15404T was a close relative of N. dassonvillei subsp. dassonvillei NBRC 14626T. Based on chemotaxonomic, phenotypic and genetic analysis of the type strain, Streptomyces flavidofuscus should be reclassified as a later heterotypic synonym of Nocardiopsis dassonvillei subsp. dassonvillei.
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Phycicoccus aerophilus sp. nov., isolated from air
A Gram-positive, short rod-shaped, non-spore-forming bacterium, designated 5516T-20T, was isolated from an air sample. The results of 16S rRNA gene sequence analyses showed that strain 5516T-20T belonged to the family Intrasporangiaceae, having the highest sequence similarities (97.5 and 96.1 %, respectively) with respect to the type strains of Phycicoccus dokdonensis and Phycicoccus jejuensis. The value for DNA–DNA hybridization between 5516T-20T and P. dokdonensis DS-8T was 41 %. Strain 5516T-20T contained menaquinone MK-8(H4) as the major isoprenoid quinone, possessed phosphatidylethanolamine, phosphatidylinositol and diphosphatidylglycerol as the polar lipids and contained glucose and ribose as whole-cell sugars. The major fatty acids were C17 : 1 ω8c, iso-C16 : 0, iso-C15 : 0, C17 : 0 and iso-C14 : 0. The G+C content of the DNA from strain 5516T-20T was 70.5 mol%. On the basis of the data from the polyphasic taxonomic study, strain 5516T-20T represents a novel species within the genus Phycicoccus, for which the name Phycicoccus aerophilus sp. nov. is proposed. The type strain is 5516T-20T (=KACC 20658T =DSM 18548T).
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Curtobacterium ginsengisoli sp. nov., isolated from soil of a ginseng field
More LessA Gram-positive, non-motile, pale-yellow, short rod-shaped bacterium, strain DCY26T, was isolated from soil of a ginseng field in South Korea and was investigated to determine its taxonomic position. The organism grew optimally at 30–37 °C. The G+C content of its DNA was 65.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain DCY26T was related most closely to species of the genus Curtobacterium, in the family Microbacteriaceae. Strain DCY26T showed highest 16S rRNA gene sequence similarity to Curtobacterium pusillum DSM 20527T (96.3 %), Curtobacterium luteum DSM 20542T (96.2 %), Curtobacterium flaccumfaciens LMG 3645T (96.2 %), Curtobacterium citreum DSM 20528T (96.1 %), Curtobacterium albidum DSM 20512T (96.1 %) and Curtobacterium herbarum DSM 14013T (95.3 %). The predominant menaquinone of strain DCY26T was MK-9. Other chemotaxonomic data also supported the affiliation of strain DCY26T to the genus Curtobacterium. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain DCY26T is considered to represent a novel species of the genus Curtobacterium, for which the name Curtobacterium ginsengisoli sp. nov. is proposed. The type strain is DCY26T (=KCTC 13163T =JCM 14773T).
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Mycobacterium arosiense sp. nov., a slowly growing, scotochromogenic species causing osteomyelitis in an immunocompromised child
A yellow-pigmented, scotochromogenic, slowly growing mycobacterial strain, designated T1921T, was isolated from the disseminated osteomyelitic lesions of a 7-year-old child with an underlying partial gamma interferon receptor alpha-1 deficiency. Hybridization by the line probe assay indicated the presence of a Mycobacterium species. Sequencing of the 16S rRNA gene, the internally transcribed spacer (ITS) region and the hsp65 and rpoB genes revealed that strain T1921T could be differentiated from all recognized species of the genus Mycobacterium. Phylogenetic analysis based on the 16S rRNA gene indicated that strain T1921T was related most closely to Mycobacterium intracellulare, whereas analysis based on the ITS and hsp65 and rpoB genes indicated that it was most closely related to Mycobacterium avium. Phenotypic tests were not able to differentiate strain T1921T from similar slowly growing mycobacteria. Strain T1921T is considered to represent a novel species of the genus Mycobacterium, for which the name Mycobacterium arosiense sp. nov. is proposed. The type strain is T1921T (=DSM 45069T =ATCC BAA-1401T).
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Phycicoccus bigeumensis sp. nov., a mesophilic actinobacterium isolated from Bigeum Island, Korea
More LessAn actinomycete strain, designated MSL-03T, was isolated from a soil sample collected from Bigeum Island in the Republic of Korea. The coccoid cells of the organism were Gram-positive and non-motile and did not form endospores. The colonies were yellow, small, circular with entire margins and contained meso-diaminopimelic acid as the diagnostic diamino acid in the peptidoglycan. The major menaquinone was MK-8(H4). The polar lipids detected were diphosphatidylglycerol and phosphatidylglycerol. The major fatty acids were iso-C15 : 0, iso-C16 : 0, C17 : 0, anteiso-C15 : 0, 10-methyl C17 : 0, iso-C14 : 0 and C17 : 1 ω8c. The DNA G+C content was 73.4 mol%. Phylogenetic analyses based on the 16S rRNA gene sequence positioned strain MSL-03T in a clade comprising Phycicoccus jejuensis KSW2-15T and Phycicoccus dokdonensis DS-8T. The organism showed the highest level of sequence similarity with respect to P. dokdonensis DS-8T (99.58 % over 1424 nt), with differences in 64 positions out of 1488. The levels of DNA–DNA relatedness with its closest neighbours (<70 %) showed that the isolate represents a distinct genomic species. On the basis of the phenotypic and genotypic results, strain MSL-03T represents a novel species of the genus Phycicoccus, for which the name Phycicoccus bigeumensis sp. nov. is proposed. The type strain is strain MSL-03T (=KCTC 19266T =DSM 19264T).
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Marihabitans asiaticum gen. nov., sp. nov., a meso-diaminopimelic acid-containing member of the family Intrasporangiaceae
More LessStrain HG667T, isolated from surface seawater collected at the Kesennuma ferry port in Miyagi Prefecture, Japan, was found to be a Gram-positive, catalase-positive bacterium comprising irregular short rods and cocci. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The major menaquinone was MK-8(H4). Mycolic acids were not detected. The G+C content of the DNA was 70 mol%. Analysis of the 16S rRNA gene sequence revealed that the strain represents a novel lineage within the family Intrasporangiaceae, order Actinomycetales, being associated with the genus Kribbia. On the basis of morphological, biochemical and chemotaxonomic properties of the strain, together with phylogenetic data relating to the 16S rRNA gene sequence, HG667T represents a novel genus and species in the family Intrasporangiaceae, for which the name Marihabitans asiaticum gen. nov., sp. nov. is proposed. The type strain of Marihabitans asiaticum is HG667T (=MBIC07497T =DSM 18935T).
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Kineococcus gynurae sp. nov., isolated from a Thai medicinal plant
More LessA novel, Gram-positive, motile, coccus-shaped, orange-pigmented organism, designated strain KKD096T, was isolated from the roots of a Thai medicinal plant, Gynura pseudochina DC. var. hispida Thwaites. Growth of strain KKD096T occurred at temperatures of 14–34 °C, at pH 5.0–9.0 and at NaCl concentrations up to 7 % (w/v). Whole-cell hydrolysates contained arabinose and galactose as the characteristic sugars. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid. The glycan moiety of the murein contained acetyl residues. The predominant menaquinone was MK-9(H2); mycolic acids were not detected. The genomic DNA G+C content was 73.3 mol%. The major cellular fatty acid was anteiso-C15 : 0 (81.42 % of the total). Strain KKD096T was assigned to the genus Kineococcus on the basis of 16S rRNA gene sequence analysis; it was most closely related to Kineococcus radiotolerans DSM 14245T (97.1 % similarity). DNA–DNA hybridization revealed 39.4 % relatedness between these two taxa. On the basis of the genotypic and phenotypic data presented, strain KKD096T is considered to represent a novel species of the genus Kineococcus, for which the name Kineococcus gynurae sp. nov. is proposed. The type strain is KKD096T (=TISTR 1856T=NRRL B-24568T=BCC 26245T=NBRC 103943T).
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Actinopolymorpha rutila sp. nov., isolated from a forest soil
More LessA Gram-positive, aerobic actinomycete, designated strain YIM 45725T, was isolated from a forest soil sample in Yunnan Province, China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate was a member of the family Nocardioidaceae and was related most closely to Actinopolymorpha singaporensis IM 7744T (99.4 % 16S rRNA gene sequence similarity). Chemotaxonomic data, including cell-wall components, menaquinones and polar lipids, supported the affiliation of strain YIM 45725T to the genus Actinopolymorpha. The results of physiological and biochemical investigations and DNA–DNA hybridization experiments demonstrated that strain YIM 45725T differed from the single recognized species of the genus Actinopolymorpha. Strain YIM 45725T is therefore considered to represent a novel species of the genus Actinopolymorpha, for which the name Actinopolymorpha rutila sp. nov. is proposed. The type strain is YIM 45725T (=CCTCC AA 206004T=DSM 18448T).
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- Archaea
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Halomicrobium katesii sp. nov., an extremely halophilic archaeon
Two extremely halophilic archaea, strains Al-5T and K-1, were isolated from Lake Tebenquiche (Atacama Saltern, Chile) and Ezzemoul sabkha (Algeria), respectively. Cells of the two strains were short-rod-shaped and Gram-negative; colonies were orange-pigmented. They grew optimally at 37–40 °C and pH 7.0–7.5 in the presence of 25 % (w/v) NaCl. Magnesium was not required. Polar lipid analysis revealed the presence of phosphatidylglycerol and phosphatidylglycerophosphate methyl ester, the absence of phosphatidylglycerosulfate, and the presence of sulfated diglycosyl diether and diether diglycosyl as the sole glycolipids. DNA G+C contents of strains Al-5T and K-1 were 52.4 and 52.9 mol% (T m method), respectively. 16S rRNA gene sequence comparison with database sequences showed that strains Al-5T and K-1 were most closely related to Halomicrobium mukohataei DSM 12286T (similarities of 97.5 and 96.9 %, respectively). DNA–DNA hybridization indicated that strains Al-5T and K-1 were members of a single species. However, DNA–DNA relatedness to Halomicrobium mukohataei was 55.7±2.5 %. A comparative analysis of phenotypic characteristics and DNA–DNA hybridization between the isolates and Halomicrobium mukohataei DSM 12286T supported the conclusion that Al-5T and K-1 represent a novel species within the genus Halomicrobium, for which the name Halomicrobium katesii sp. nov. is proposed. The type strain is Al-5T (=CECT 7257T=DSM 19301T).
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Natrinema gari sp. nov., a halophilic archaeon isolated from fish sauce in Thailand
Two Gram-negative, rod-shaped, halophilic archaea, designated strains HIS40-3T and HDS3-1, were isolated from anchovy fish sauce (nam-pla) collected from two different locations in Thailand. The two strains were able to grow at 20–60 °C (optimum 37–40 °C), at 1.7–5.1 M NaCl (optimum 2.6–3.4 M NaCl) and at pH 5.5–8.5 (optimum pH 6.0–6.5). Hypotonic treatment with less than 1.7 M NaCl caused cell lysis. The major polar lipids of the isolates were C20C20 and C20C25 derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate, two glycolipids and one unidentified lipid. The DNA G+C contents were 64.0–65.4 mol%. In addition to phenotypic and chemotaxonomic characteristics, phylogenetic analysis based on 16S rRNA gene sequence similarities showed that strains HIS40-3T and HDS3-1 were related most closely to species of the genus Natrinema. Levels of 16S rRNA gene sequence similarity between strains HIS40-3T and HDS3-1 and the type strains of recognized Natrinema species were 99.1–96.6 %. The two novel strains could be distinguished from recognized Natrinema species on the basis of low levels of DNA–DNA relatedness and differences in whole-cell protein patterns and phenotypic properties. Levels of 16S rRNA gene sequence similarity and DNA–DNA relatedness between the two strains were 99.7 and 77.7 %, respectively, suggesting that they should be classified as representing a single species. Based on these taxonomic data, strains HIS40-3T and HDS3-1 are considered to represent a novel species of the genus Natrinema, for which the name Natrinema gari sp. nov. is proposed. The type strain is HIS40-3T (=BCC 24370T =JCM 14663T =PCU 303T).
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- Bacteroidetes
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Flavobacterium resistens sp. nov., isolated from stream sediment
More LessAn aerobic, yellow-pigmented, Gram-negative bacterium, designated strain BD-b365T, was isolated from sediment of the Hakjang stream in Busan, South Korea. Growth was observed at 15–40 °C (optimum 20–30 °C) and at pH 6.0–9.5 (optimum pH 7.0–8.0). Cells were non-spore-forming rods that showed gliding motility and contained branched and hydroxy fatty acids. The G+C content of the genomic DNA was 35.4 mol%. The major respiratory quinone was menaquinone-6 (MK-6). The major polar lipid of strain BD-b365T was phosphatidylethanolamine. Comparative 16S rRNA gene sequence analysis showed that strain BD-b365T formed a distinct phyletic line within the genus Flavobacterium. Based on levels of 16S rRNA gene sequence similarity, the novel strain was related most closely to Flavobacterium aquidurense WB 1.1-56T, but the level of DNA–DNA relatedness between these two strains was only 9.6 %. On the basis of phenotypic and genotypic data, it is clear that strain BD-b365T represents a novel species of the genus Flavobacterium, for which the name Flavobacterium resistens sp. nov. is proposed. The type strain is BD-b365T (=KCTC 22078T =DSM 19382T).
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Eudoraea adriatica gen. nov., sp. nov., a novel marine bacterium of the family Flavobacteriaceae
More LessA novel aerobic, non-motile, Gram-negative bacterium, designated AS06/20aT, was isolated from coastal waters of the Adriatic Sea and subjected to polyphasic taxonomic analysis. Cells were rod-shaped and formed non-pigmented punctiform colonies on agar plates. The novel isolate grew heterotrophically on a variety of carbon compounds, including organic acids, carbohydrates, polyols, amino acids and complex organic substrates. Cells grew at 15–33 °C (optimum 30 °C), pH 6.5–8.5 (optimum pH 7.5–8.0) and between 2 and 6 % (w/v) NaCl (optimum 2 %). The dominant fatty acids (>5 %) detected in strain AS06/20aT were iso-C15 : 1 G, iso-C15 : 0, iso-C15 : 0 3-OH, iso-C17 : 1 ω9c and iso-C17 : 0 3-OH. The major respiratory quinone was MK-6. The G+C content of the genomic DNA was 38.9 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain AS06/20aT fell within the family Flavobacteriaceae in the phylum Bacteroidetes. Comparative 16S rRNA gene sequence analysis indicated that strain AS06/20aT was most closely related to members of the genera Zeaxanthinibacter and Robiginitalea, sharing 92–93 % 16S rRNA gene sequence similarity with representatives of these genera. It is proposed, from the results of the polyphasic taxonomic analysis, that the strain should be placed in a new genus, Eudoraea gen. nov., with Eudoraea adriatica sp. nov. as the type species. The type strain is AS06/20aT (=DSM 19308T=CIP 109577T=OOB 358T).
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Bizionia argentinensis sp. nov., isolated from surface marine water in Antarctica
A marine bacterial strain, designated strain JUB59T, was isolated from surface seawater in Antarctica and subsequently characterized. Cells were found to be Gram-negative, non-motile rods forming butyrous, shiny, yellowish orange colonies on marine agar. Growth occurred at 2–28 °C (optimally at 22–25 °C) but not at 30 °C; Na+ ions were required, but 9 % NaCl (w/v) was not tolerated. Phylogenetic analysis, based on comparisons of the complete 16S rRNA gene sequence of the novel isolate with the sequences of closely related strains, showed that strain JUB59T belonged to the family Flavobacteriaceae, representing a novel species of the genus Bizionia. The highest levels of sequence similarity were found with respect to Bizionia myxarmorum ADA-4T (97.4 %) and Bizionia algoritergicola APA-1T (97.1 %). However, the DNA–DNA relatedness of strain JUB59T with respect to these two strains was low (15.9–17.3 and 19.3–22.1 %, respectively). The predominant fatty acids of strain JUB59T were iso-15 : 1ω10c (18.1 %), iso-15 : 0 (17.3 %), anteiso-15 : 0 (13.9 %), iso-17 : 0 3-OH (9.2 %), 15 : 0 (6.0 %) and iso-16 : 0 3-OH (5.3 %). The main polar lipids were phosphatidylethanolamine, an aminolipid, an amino-positive phospholipid and two unidentified lipids. MK-6 was the major respiratory quinone (>90 %) and the DNA G+C content was 34 mol%. On the basis of the data obtained, strain JUB59T represents a novel species of the genus Bizionia, for which the name Bizionia argentinensis sp. nov. is proposed. The type strain is JUB59T (=DSM 19628T=CCM-A-29 1259T).
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- Other Bacteria
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Leptospira weilii serovar Topaz, a new member of the Tarassovi serogroup isolated from a bovine source in Queensland, Australia
This paper reports on a Leptospira isolate of bovine origin and its identification as belonging to a previously unknown serovar, for which the name Topaz is proposed. The isolate (94-79970/3) was cultured from bovine urine from a north Queensland dairy farm in Australia. Strain 94-79970/3 grew at 30 °C in Ellinghausen McCullough Johnson Harris (EMJH) medium but failed to grow at 13 °C in EMJH medium or in the presence of 8-azaguanine. Serologically, strain 94-79970/3 produced titres against the Leptospira borgpetersenii serovar Tarassovi, the reference strain for the Tarassovi serogroup; however, no significant titres to any other serovars within the serogroup were obtained. Using 16S rRNA and DNA gyrase subunit B gene analysis, strain 94-79970/3 was identified as a member of the species Leptospira weilii. We propose that the serovar be named Topaz, after the location where the original isolate was obtained. The reference strain for this serovar is 94-79970/3 (=KIT 94-79970/3=LT722).
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Exilispira thermophila gen. nov., sp. nov., an anaerobic, thermophilic spirochaete isolated from a deep-sea hydrothermal vent chimney
A novel thermophilic, anaerobic bacterium, strain RASENT, was isolated from a deep-sea hydrothermal vent chimney sample collected in the Iheya North field, Okinawa Trough, Japan, at a water depth of 982 m. The cells were motile, Gram-negative and helical with hooked ends, 0.23–0.28×15–27 μm in size with an approximate wavelength of 1.1–1.5 μm. Growth of the strain was observed at 37–60 °C (optimum 50 °C), in 2.5–3.5 % (w/v) NaCl (optimum 2.5–3 % NaCl) and at pH 6.0–7.5 (optimum pH 7.0). The strain grew on yeast extract only of the substrates examined in this study. The G+C content of the genomic DNA was 27.1 mol%. Major fatty acids for the strain were C16 : 0, C18 : 1(Δ9) trans, C18 : 0 and C18 : 1(Δ9) cis. Based on comparative 16S rRNA gene sequence analysis, strain RASENT formed a deeply branching lineage within the phylum Spirochaetes and had only low levels of sequence similarity with other species of the phylum (range of similarity 72.1–80.6 %). Hence, we propose the name Exilispira thermophila gen. nov., sp. nov. The type strain of Exilispira thermophila is strain RASENT (=JCM 14728T =NBRC 103205T =KCTC 5595T).
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Leptospira wolffii sp. nov., isolated from a human with suspected leptospirosis in Thailand
A single Leptospira strain (designated Khorat-H2T) was isolated from the urine of an adult male patient with suspected leptospirosis from the province of Nakornrachasima, Thailand. The isolate showed typical Leptospira motility and morphology under dark-field microscopy. Cells were 10–13 μm long and 0.2 μm in diameter, with a wavelength of 0.5 μm and an amplitude of approximately 0.3 μm. Phenotypically, strain Khorat-H2T did not grow at 13 °C but grew at 30 and 37 °C and in the presence of 8-azaguanine. Serological identification using the microscopic agglutination test revealed that strain Khorat-H2T had no cross-reaction with any recognized Leptospira serogroups. Phylogenetic analysis of the 16S rRNA gene sequence placed the novel strain within the radiation of the genus Leptospira, with sequence similarities of 88.1–97.7 % to recognized Leptospira species. DNA–DNA hybridization against the type strains of the three most closely related Leptospira species was used to confirm the results of the 16S rRNA sequence analysis. The G+C content of strain Khorat-H2T was 41.8 mol%. On the basis of phenotypic, serological and phylogenetic data, strain Khorat-H2T represents a novel species of the genus Leptospira, for which the name Leptospira wolffii sp. nov. is proposed. The type strain is Khorat-H2T (=WHO LT1686T =KIT Khorat-H2T).
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Deinococcus aquaticus sp. nov., isolated from fresh water, and Deinococcus caeni sp. nov., isolated from activated sludge
The taxonomic positions of two environmental isolates from South Korea were established using a combination of genotypic and phenotypic data. The organisms, designated PB314T and Ho-08T, were Gram-negative, rod-shaped and non-spore-forming and had chemotaxonomic properties consistent with their classification in the genus Deinococcus 16S rRNA gene tree, the highest sequence similarities being shown to the type strains of Deinococcus grandis (96.3–96.7 %) and Deinococcus indicus (96.3–96.4 %). The isolates shared relatively high 16S rRNA gene sequence similarity (98.1 %) but had a DNA–DNA relatedness value of only 22 %. Chemotaxonomic data revealed that both strains possess quinone system MK-8 as the predominant compound, C16 : 1 ω7c and C16 : 0 as major fatty acids and ornithine as a diamino acid in the peptidoglycan structure, corroborating our assignment of the strains to the genus Deinococcus. The results of phylogenetic analyses based on 16S rRNA gene sequences, DNA–DNA relatedness values and physiological and biochemical tests clearly demonstrated that the two strains represent distinct species. On the basis of these data, two novel species, Deinococcus aquaticus sp. nov. (type strain PB314T =KCTC 12552T =NBRC 101311T) and Deinococcus caeni sp. nov. (type strain Ho-08T =KCTC 12553T =NBRC 101312T), are proposed.
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- Proteobacteria
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Psychromonas heitensis sp. nov., a psychrotolerant bacterium isolated from seawater in Japan
More LessFour bacterial strains, 04HE-4-40, A4I-9, A4I-21 and AK15-027T, were isolated from Heita Bay off Kamaishi in Japan. Based on 16S rRNA gene sequence analysis, the isolates were placed as a new lineage within the genus Psychromonas. The 16S rRNA gene sequence similarity values between the isolates and type strains of recognized Psychromonas species were less than 97 %. The DNA G+C contents of the isolates were about 38 mol%. The major respiratory quinone was Q-8, and the predominant cellular fatty acids were 16 : 1ω7c and 16 : 0. The isolates were able to grow at 30 °C, unlike other Psychromonas species. Based on the results of the phylogenetic analysis and phenotypic characteristics and DNA–DNA hybridization data, the isolates represent a novel species, for which the name Psychromonas heitensis sp. nov. is proposed. The type strain is AK15-027T (=MBIC 06898T=NCIMB 14416T).
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Rheinheimera soli sp. nov., a gammaproteobacterium isolated from soil in Korea
More LessA Gram-negative, non-spore-forming bacterium, designated strain BD-d46T, was isolated from a playground soil sample in Jinju, South Korea. Cells were straight or curved rods and showed catalase- and oxidase-positive reactions. Growth of strain BD-d46T was observed between 15 and 35 °C (optimum 25–30 °C) and between pH 6.5 and 8.0 (optimum pH 7.0–7.5). The predominant fatty acids were summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH), C12 : 0 3-OH and C16 : 0. Strain BD-d46T contained phosphatidylethanolamine and phosphatidylglycerol as major polar lipids. Isoprenoid quinones were Q-8 (75 %) and MK-7 (25 %). The G+C content of the genomic DNA was 49.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BD-d46T formed a distinct lineage with Rheinheimera chironomi K19414T within the genus Rheinheimera. Levels of 16S rRNA gene sequence similarity between strain BD-d46T and the type strains of recognized Rheinheimera species ranged from 94.4 to 96.9 %. On the basis of chemotaxonomic data and molecular properties, strain BD-d46T is considered to represent a novel species of the genus Rheinheimera, for which the name Rheinheimera soli sp. nov. is proposed. The type strain is BD-d46T (=KCTC 22077T =DSM 19413T).
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Phenylobacterium composti sp. nov., isolated from cotton waste compost in Korea
More LessA light-yellow-coloured bacterium, designated strain 4T-6T, was isolated from cotton waste compost in Korea. Cells of the strain were strictly aerobic, Gram-negative, motile (by means of single polar flagella) and rod-shaped. Optimal growth occurred at 30 °C and at pH 7.0–8.0. The major fatty acids were 11-methyl C18 : 1 ω7c (23.8 %), C18 : 1 ω7c (23.2 %), C16 : 0 (19.8 %) and C17 : 0 (14.8 %). The DNA G+C content was 67.5 mol%. A phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 4T-6T was a member of the genus Phenylobacterium, showing the highest sequence similarities with those of ‘Phenylobacterium zucineum’ HLK1 (98.8 %) and Phenylobacterium lituiforme DSM 14363T (98.4 %). However, the values for DNA–DNA relatedness between strain 4T-6T and ‘P. zucineum’ HLK1 and P. lituiforme DSM 14363T were 45 and 43 %, respectively. Phylogenetic characteristics, physiological properties and DNA–DNA hybridization data indicate that strain 4T-6T represents a novel species of the genus Phenylobacterium, for which the name Phenylobacterium composti sp. nov. is proposed. The type strain is 4T-6T (=KACC 12597T=DSM 19425T).
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Alkanibacter difficilis gen. nov., sp. nov. and Singularimonas variicoloris gen. nov., sp. nov., hexane-degrading bacteria isolated from a hexane-treated biofilter
More LessTwo Gram-negative, rod-shaped, non-spore-forming bacterial strains were isolated from a hexane-treated, full-scale biofilter from an oil mill. The strains were cultivated with hexane as the sole carbon source. One strain, MN154.3T, showed a fatty acid profile that contained 16 : 0, 18 : 1cis11 and 19 : 0 cyclo11–12 as major compounds, while the second strain, isolate MN28T, contained 14 : 0 3-OH, 16 : 0 and 18 : 1cis11 as the predominant fatty acids. On the basis of almost-complete 16S rRNA gene sequences, both strains could be allocated to the Nevskia branch of the class Gammaproteobacteria. The sequence similarities for strains MN154.3T and MN28T with respect to the most closely related type strains of this branch were 90.5 and 94.1 %, respectively. The sequence similarity between strains MN154.3T and MN28T was 90.6 %. The DNA G+C content of strain MN154.3T was 62.8 mol% and that for strain MN28T was 64.9 mol%. Both strains possessed ubiquinone-8 as the major quinone. On the basis of the 16S rRNA gene sequences of these two new isolates and several phenotypic differences exhibited with respect to known species of the Nevskia branch, strains MN154.3T and MN28T represent two novel genera and species, for which the names Alkanibacter difficilis gen. nov., sp. nov. and Singularimonas variicoloris gen. nov., sp. nov. are proposed. The type strain of Alkanibacter difficilis gen. nov., sp. nov. is MN154.3T (=DSM 14804T=LMG 22842T) and that of Singularimonas variicoloris gen. nov., sp. nov. is MN28T (=DSM 15731T=LMG 22844T).
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Nisaea denitrificans gen. nov., sp. nov. and Nisaea nitritireducens sp. nov., two novel members of the class Alphaproteobacteria from the Mediterranean Sea
More LessTwo novel Gram-negative bacteria, designated strains DR41_21T and DR41_18T, were isolated from coastal, surface waters of the north-western Mediterranean Sea. The cells were motile, pleomorphic rods, 2.9 μm long and 0.9 μm wide and formed cream colonies on marine agar medium. The G+C content of the genomic DNA was 60 mol%. Phylogenetic analysis of 16S rRNA gene sequences positioned the isolates in the class Alphaproteobacteria within the family Rhodospirillaceae. The 16S rRNA gene sequence similarity of the two strains was 98.8 % but DNA–DNA hybridization indicated only 55 % relatedness. Strain DR41_21T was able to denitrify and possessed nirK and nosZ genes, unlike strain DR41_18T, which possessed only nirK. These isolates represent two novel species of a new genus, Nisaea gen. nov., for which the names Nisaea denitrificans sp. nov. and Nisaea nitritireducens sp. nov. are proposed. The type strain of Nisaea denitrificans is DR41_21T (=DSM 18348T=CIP 109265T=OOB 129T) and the type strain of Nisaea nitritireducens is DR41_18T (=DSM 19540T=CIP 109601T=OOB 128T).
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Sphingopyxis ginsengisoli sp. nov., isolated from soil of a ginseng field in South Korea
More LessA Gram-negative, aerobic, motile, rod-shaped bacterium (strain Gsoil 250T) was isolated from soil of a ginseng field in Pocheon province (South Korea) and was characterized using a polyphasic approach in order to determine its taxonomic position. Comparative analysis of 16S rRNA gene sequences showed that strain Gsoil 250T belonged to the family Sphingomonadaceae of the class Alphaproteobacteria, and was related to Sphingopyxis macrogoltabida (98.7 %), Sphingopyxis chilensis (98.2 %), Sphingopyxis alaskensis (97.9 %), Sphingopyxis taejonensis (97.9 %) and Sphingopyxis witflariensis (97.8 %). The phylogenetic distance from any other species with validly published names within the genus Sphingopyxis was greater than 3.8 %. The G+C content of the genomic DNA of strain Gsoil 250T was 69.2 mol%. Strain Gsoil 250T contained Q-10 as the predominant respiratory lipoquinone and C18 : 1 ω7c and summed feature 4 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH; 34.6 %) as the major fatty acids. No 3-hydroxy fatty acids were detected. Major polar lipids consisted of sphingoglycolipid, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, diphosphatidylglycerol and two unknown glycolipids. Phenotypic and chemotaxonomic data supported the affiliation of strain Gsoil 250T to the genus Sphingopyxis. The results of DNA–DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain Gsoil 250T from the eight recognized Sphingopyxis species. Strain Gsoil 250T therefore represents a novel species, for which the name Sphingopyxis ginsengisoli sp. nov. is proposed, with the type strain Gsoil 250T (=KCTC 12582T=LMG 23390T).
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Pseudogulbenkiania subflava gen. nov., sp. nov., isolated from a cold spring
More LessA yellow-coloured bacterial strain, designated BP-5T, was isolated from a water sample of a cold spring located in the Hsinchu area of northern Taiwan. Cells of the strain were Gram-negative, non-spore-forming rods with a polar flagellum. The isolate was able to grow at 15–42 °C, 0–1 % NaCl and pH 6–8. The predominant fatty acids were summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH), C16 : 0 and C18 : 1 ω7c. The major respiratory quinone was ubiquinone 8. The DNA G+C content was 63.2 mol%. 16S rRNA gene sequence analysis indicated that strain BP-5T belonged to the class Betaproteobacteria and was a member of the family Neisseriaceae. Its closest phylogenetic neighbours were Gulbenkiania mobilis E4FC31T (95.0 % 16S rRNA gene sequence similarity), Chromobacterium subtsugae PRAA4-1T (95.0 %), Chromobacterium violaceum ATCC 12472T (94.3 %), Vogesella indigofera ATCC 19706T (93.8 %) and Aquitalea magnusonii TRO-001DR8T (93.7 %). On the basis of the evidence from this polyphasic study, strain BP-5T is considered to represent a novel species of a new genus, for which the name Pseudogulbenkiania subflava gen. nov., sp. nov. is proposed. The type strain of Pseudogulbenkiania subflava is BP-5T (=BCRC 17727T =LMG 24211T).
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Sphingopyxis marina sp. nov. and Sphingopyxis litoris sp. nov., isolated from seawater
More LessTwo yellow-pigmented, Gram-negative, aerobic bacterial strains, designated FR1087T and FR1093T, were isolated from surface seawater off Jeju Island, Republic of Korea. Both strains required sea salts for growth. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the two isolates belong to the genus Sphingopyxis, showing the highest level of sequence similarity with respect to Sphingopyxis flavimaris SW-151T (97.9 %). The two isolates shared 98.5 % sequence similarity. DNA–DNA hybridization between the isolates and the type strain of Sphingopyxis flavimaris clearly suggested that strains FR1087T and FR1093T represent two separate novel species in the genus Sphingopyxis. Several phenotypic characteristics served to differentiate these two isolates from recognized members of the genus Sphingopyxis. The data from the polyphasic study presented here indicated that strains FR1087T and FR1093T should be classified as representing novel species in the genus Sphingopyxis, for which the names Sphingopyxis marina sp. nov. and Sphingopyxis litoris sp. nov., respectively, are proposed. The type strain of Sphingopyxis marina sp. nov. is FR1087T (=IMSNU 14132T=KCTC 12763T=JCM 14161T) and the type strain of Sphingopyxis litoris sp. nov. is FR1093T (=IMSNU 14133T=KCTC 12764T=JCM 14162T).
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Rheinheimera tangshanensis sp. nov., a rice root-associated bacterium
More LessA Gram-negative, aerobic, rod-shaped bacterium, designated strain JA3-B52T, was isolated from the roots of fresh rice plants (Oryza sativa). The cells were motile by means of polar single or lateral flagella. The colonies were non-pigmented. On the basis of 16S rRNA gene sequence comparisons, the strain was phylogenetically related to species of the genus Rheinheimera, having the greatest level of sequence similarity with respect to Rheinheimera texasensis A62-14BT (97.16 %). The bacterium grew at temperatures from 10 to 37 °C, with an optimum at 30 °C. The strain exhibited growth with 0–3.0 % (w/v) NaCl and at pH 6.0–8.5. The main cellular fatty acids were C16 : 1 ω7c, C17 : 1 ω8c, C 16 : 0, C18 : 1 ω7c and C12 : 0 3-OH. The DNA G+C content was 47.0 mol%. The levels of similarity between the 16S rRNA gene sequence of strain JA3-B52T and those of the type strains of Rheinheimera species ranged from 95.38 to 97.16 %. The mean level of DNA–DNA relatedness between strain JA3-B52T and R. texasensis A62-14BT, the strain most closely related to the isolate, was 20.4 %. On the basis of physiological and biochemical characteristics and genotypic data obtained in this work, strain JA3-B52T represents a novel species of the genus Rheinheimera, for which the name Rheinheimera tangshanensis sp. nov. is proposed. The type strain is JA3-B52T (=CGMCC 1.6362T =DSM 19460T).
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Desulfovibrio marinisediminis sp. nov., a novel sulfate-reducing bacterium isolated from coastal marine sediment via enrichment with Casamino acids
To obtain amino acid-utilizing sulfate reducers, enrichment culture was carried out with a medium containing Casamino acids and sulfate and inoculated with coastal marine sediment from the eutrophic Tokyo Bay, Japan. A sulfate reducer, designated strain C/L2T, was isolated from the sulfide-producing enrichment culture after further enrichment with lactate and sulfate by means of the agar shake dilution method. Cells of strain C/L2T were vibrio-shaped, Gram-negative, motile rods (0.7–1.0 μm wide and 1.0–3.5 μm long) with single polar flagella. The optimum temperature for its growth was 37 °C, the optimum pH was around 7.5 and the optimum NaCl concentration was 20–25 g l−1. Hydrogen, formate, lactate, pyruvate, fumarate, malate, succinate, ethanol, propanol, glycerol, glycine, alanine, serine, aspartate, Casamino acids, peptone and yeast extract were used as electron donors. Sulfate, sulfite and thiosulfate each served as an electron acceptor, but elemental sulfur, nitrate, fumarate, acrylate and 2,4,6-tribromophenol did not. Disproportionation of thiosulfate was not observed. Desulfoviridin, c-type cytochromes and catalase were present. The major respiratory quinone was MK-6(H2). The G+C content of the genomic DNA was 46.2 mol%. Comparisons based on 16S rRNA gene sequences and on dissimilatory sulfite reductase gene sequences clearly showed that strain C/L2T belonged to the genus Desulfovibrio: its closest relatives were the uncharacterized Desulfovibrio sp. strain TBP-1 (16S rRNA gene sequence similarity of 99.4 %) and Desulfovibrio acrylicus DSM 10141T (16S rRNA gene sequence similarity of 98.7 %). The level of DNA–DNA hybridization with Desulfovibrio acrylicus DSM 10141T was 10.3 %. On the basis of the data from this study and the physiological and phylogenetic differences that exist between the isolate and Desulfovibrio acrylicus, strain C/L2T represents a novel species of the genus Desulfovibrio, for which the name Desulfovibrio marinisediminis sp. nov. is proposed. The type strain is C/L2T (=NMRC 101113T=JCM 14577T=DSM 17456T).
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Pseudochrobactrum glaciei sp. nov., isolated from sea ice collected from Peter the Great Bay of the Sea of Japan
More LessAn aerobic, Gram-negative, non-pigmented, non-motile bacterium, KMM 3858T, was isolated from a sea-ice sample collected from Peter the Great Bay of the Sea of Japan, Russia, and subjected to a phenotypic and phylogenetic study. Comparative analyses based on the 16S rRNA and recA gene sequences placed strain KMM 3858T within the genus Pseudochrobactrum. The major chemotaxonomic characteristics were found to be the presence of phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unknown aminolipid and phosphatidylcholine, major fatty acids C18 : 1 ω7c and C19 : 0 cyclo, and ubiquinone Q-10, confirming the affiliation of strain KMM 3858T to the genus Pseudochrobactrum. On the basis of the phylogenetic analysis and the physiological and biochemical characterization, strain KMM 3858T should be classified as representing a novel species of the genus Pseudochrobactrum, for which the name Pseudochrobactrum glaciei sp. nov. is proposed. The type strain is strain Pi26T (=KMM 3858T=NRIC 0733T=JCM 15115T).
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- Other Gram-Positive Bacteria
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Gracilibacillus lacisalsi sp. nov., a halophilic Gram-positive bacterium from a salt lake in China
More LessTwo Gram-positive, motile, rod-shaped, halophilic bacteria showing optimum growth at 5–7 % (w/v) NaCl were isolated from a salt lake, Xin-Jiang Province, China. The strains, designated BH312T and BH314, grew in the presence of 1–18 % (w/v) NaCl and at temperatures of 15–50 °C (optimum: 40 °C) and pH values of 5.5–10.0 (optimum: pH 7.5–8.0). The major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0. The DNA G+C content was 38.8–39.0 mol% and the predominant lipoquinone was MK-7. The major cellular phospholipids were phosphatidylglycerol, diphosphatidylglycerol and two unidentified phospholipids. Phylogenetic analyses based on 16S rRNA gene sequences showed that the isolates formed a cluster with Gracilibacillus orientalis XH-63T within the genus Gracilibacillus. The levels of 16S rRNA gene sequence similarity with closely related type strains were lower than 96.2 %. On the basis of phylogenetic, phenotypic and chemotaxonomic properties, the isolates represent a novel species of the genus Gracilibacillus for which the name Gracilibacillus lacisalsi sp. nov. is proposed. The type strain is BH312T (=KCTC 13129T=DSM 19029T).
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Proposal for transfer of Pelagibacillus goriensis Kim et al. 2007 to the genus Terribacillus as Terribacillus goriensis comb. nov.
More LessThe phenotypic, chemotaxonomic and genotypic characteristics of two recently described genera were compared. Terribacillus saccharophilus and Pelagibacillus goriensis (both type species of their respective genera) are similar in many phenotypic characteristics and in their fatty acid profiles, both have MK-7 as the major menaquinone and they have similar G+C contents. Comparison of the 16S rRNA gene sequence of P. goriensis CL-GR16T with those of T. saccharophilus 002-048T and Terribacillus halophilus 002-051T showed high degrees of sequence similarity, respectively 99.8 and 98.9 %. Phylogenetically, these three taxa are closely related and form a coherent cluster in the phylogenetic tree. The genomic relatedness of P. goriensis DSM 18252T with T. saccharophilus JCM 21759T and T. halophilus JCM 21760T is 51.7 and 35.6 %, respectively, which is well below the value of 70 % recommended for delineation of species. P. goriensis differs from T. saccharophilus in motility, the Voges–Proskauer test and acid production from and utilization of some carbohydrates. Based on these analyses, we conclude that Pelagibacillus should not be considered a separate genus and hence Pelagibacillus goriensis should be transferred to the genus Terribacillus as Terribacillus goriensis comb. nov., with the type strain CL-GR16T (=KCCM 42329T =DSM 18252T).
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Sporolactobacillus vineae sp. nov., a spore-forming lactic acid bacterium isolated from vineyard soil
More LessTwo spore-forming, facultatively anaerobic, lactic acid bacteria, strains SL153T and SL1153, were isolated from vineyard soil in Korea. Cells of both strains were slightly curved, Gram-positive, motile rods that measured between 1 and 4 μm in length and were approximately 0.5 μm in diameter. Strains SL153T and SL1153 fermented glucose, fructose, mannose and sorbitol, but were negative for nitrate reduction, catalase and oxidase. The predominant cellular fatty acids of the two isolates were iso-C15 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. meso-Diaminopimelic acid, glucose, mannose and galactose were determined in their whole-cell hydrolysates. 16S rRNA gene sequences from the two strains were almost identical (99.9 %) and they could be placed in the genus Sporolactobacillus according to phylogenetic analysis. The species most closely related to SL153T were Sporolactobacillus inulinus and Sporolactobacillus terrae with 16S rRNA gene similarities of 95.7 and 95.5 %, respectively, with the type strains. Levels of DNA–DNA relatedness between strain SL153T and the type strains of S. inulinus, S. terrae and Sporolactobacillus kofuensis were 18.5, 18.0 and 17.0 %, respectively. On the basis of the phylogenetic (16S rRNA gene), chemotaxonomic and phenotypic evidence given in this study, it is proposed that strains SL153T and SL1153 should be assigned to the genus Sporolactobacillus as representatives of the novel species Sporolactobacillus vineae sp. nov. The type strain is SL153T (=KCTC 5376T=JCM 14637T).
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Bacillus cecembensis sp. nov., isolated from the Pindari glacier of the Indian Himalayas
More LessStrain PN5T is a Gram-positive, aerobic, motile, rod-shaped, peritrichously flagellated bacterium that was isolated from the Pindari glacier using nutrient agar medium. Cells of PN5T are catalase-positive and oxidase-negative and contain lysine, glutamic acid and alanine in the peptidoglycan (peptidoglycan type A4α). Further, the cells are characterized by the presence of iso-C15 : 0 and iso-C16 : 1 as the predominant fatty acids and MK-7 as the isoprenoid quinone. Based on the above characteristics, strain PN5T was assigned to the genus Bacillus. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain PN5T clustered with the type strain of Bacillus silvestris with a sequence similarity of 97.2 %. DNA–DNA hybridization between PN5T and B. silvestris DSM 12223T resulted in a relatedness of only 15 %, clearly indicating that strain PN5T represents a novel species. Further, PN5T was different from B. silvestris with respect to various phenotypic and chemotaxonomic characteristics. Therefore, strain PN5T is identified as a representative of a novel species of the genus Bacillus, for which the name Bacillus cecembensis sp. nov. is proposed. Bacillus cecembensis is unique among psychrotolerant Bacillus species in containing l-Lys–d-Glu in the cell-wall peptidoglycan. The type strain is PN5T (=LMG 23935T =MTCC9127T =JCM 15113T).
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Anoxybacillus bogrovensis sp. nov., a novel thermophilic bacterium isolated from a hot spring in Dolni Bogrov, Bulgaria
More LessA novel moderately thermophilic bacterium, designated strain BT 13T, was isolated from a geothermal water source in Dolni Bogrov, near Sofia, Bulgaria. The isolate was spore-forming, Gram-positive, facultatively anaerobic, alkalitolerant and heterotrophic, and was able to ferment a wide variety of carbon sources including d-glucose, sucrose, l-arabinose, l-rhamnose, starch, sorbitol and glycogen. Strain BT 13T grew optimally at pH 8.0 and 65 °C. Intracellular amylolytic activity was registered with glucose as the main product of starch hydrolysis. Phylogenetic analysis based on the 16S rRNA gene revealed that the strain belonged to the genus Anoxybacillus, the closest relatives being Anoxybacillus flavithermus and Anoxybacillus kamchatkensis. The DNA G+C content was 44.1 mol%. The fatty acid profile with a content of iso-branched fatty acids of around 80 % of the total fatty acids is similar to that of recognized Anoxybacillus species. On the basis of genotypic differentiation and significant differences in phenotypic characteristics, it was concluded that strain BT 13T represents a novel species of the genus Anoxybacillus, for which the name Anoxybacillus bogrovensis sp. nov. is proposed. The type strain is BT 13T (=DSM 17956T=NBIMCC 8427T).
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Gracilibacillus halophilus sp. nov., a moderately halophilic bacterium isolated from saline soil
A Gram-positive, moderately halophilic, moderately thermophilic, endospore-forming, catalase- and oxidase-positive, obligately aerobic bacterium, strain YIM-C55.5T, was isolated from saline soil in the Qaidam Basin, north-west China. Cells were slender rods, motile by means of peritrichous flagella. Filamentous forms were present throughout the growth cycle. Strain YIM-C55.5T was able to grow in the presence of 7–30 % (w/v) NaCl and at pH 6.0–9.0, with optimum growth at 15 % (w/v) NaCl and pH 7.0. It was able to grow at 28–60 °C, with optimum growth at 45–50 °C. meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. The major cellular fatty acids were iso-C15 : 0, C16 : 0, anteiso-C15 : 0, anteiso-C17 : 0 and C18 : 0. Strain YIM-C55.5T possessed menaquinone 7 (MK-7) as the predominant respiratory quinone and diphosphatidylglycerol and phosphatidylglycerol as polar lipids. The genomic DNA G+C content was 42.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YIM-C55.5T belonged to the family Bacillaceae and was related most closely to members of the genus Gracilibacillus, but with low levels of similarity to the type strains of recognized species of the genus (Gracilibacillus orientalis XH-63T, 95.1 %; Gracilibacillus boraciitolerans T-16XT, 94.0 %; Gracilibacillus dipsosauri DD1T, 93.7 %; Gracilibacillus halotolerans NNT, 93.5 %). Together with phenotypic data, these results suggest that strain YIM-C55.5T represents a novel species of the genus Gracilibacillus, for which the name Gracilibacillus halophilus sp. nov. is proposed. The type strain is YIM-C55.5T (=DSM 17856T =CGMCC 1.6303T).
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Virgibacillus salarius sp. nov., a halophilic bacterium isolated from a Saharan salt lake
More LessA Gram-positive, endospore-forming, rod-shaped and moderately halophilic bacterium was isolated from a salt-crust sample collected from Gharsa salt lake (Chott el Gharsa), Tunisia. The newly isolated bacterium, designated SA-Vb1T, was identified based on polyphasic taxonomy including genotypic, phenotypic and chemotaxonomic characterization. Strain SA-Vb1T was closely related to the type strains of Virgibacillus marismortui and Virgibacillus olivae, with 16S rRNA gene sequence similarities of 99.7 and 99.4 %, respectively. However, strain SA-Vb1T was distinguished from these two type strains on the basis of phenotypic characteristics and DNA–DNA relatedness (29.4 and 5.1 %, respectively). The genetic relationship between strain SA-Vb1T and Virgibacillus pantothenticus IAM 11061T (the type strain of the type species) and other type strains of the genus was 96–98 % based on 16S rRNA gene sequence similarity and 18.3–22.3 % based on DNA–DNA hybridization. Biochemical analysis resulted in determination of major fatty acids iso-C15 : 0, anteiso-C15 : 0 and anteiso-C17 : 0 (33.3, 29.2 and 9.8 %, respectively); phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine were the main polar lipids and MK-7 was the predominant menaquinone (∼100 %). The distinct characteristics demonstrated by strain SA-Vb1T represent properties of a novel species of the genus Virgibacillus, for which the name Virgibacillus salarius sp. nov. is proposed. The type strain is SA-Vb1T (=JCM 12946T =DSM 18441T).
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Exiguobacterium soli sp. nov., a psychrophilic bacterium from the McMurdo Dry Valleys, Antarctica
A novel psychrophilic bacterium, designated strain DVS 3YT, was isolated from a moraine sample from the McMurdo Dry Valleys, Antarctica. Phenotypic and chemotaxonomic characteristics and data from a phylogenetic analysis based on 16S rRNA gene sequences indicated that strain DVS 3YT was related to the genus Exiguobacterium. Strain DVS 3YT exhibited >97 % gene sequence similarity with respect to Exiguobacterium acetylicum DSM 20416T (97.4 %), Exiguobacterium oxidotolerans DSM 17272T (97.4 %), Exiguobacterium indicum IAM 15368T (97.6 %), Exiguobacterium undae DSM 14481T (98.2 %), Exiguobacterium sibiricum DSM 17290T (98.6 %) and Exiguobacterium antarcticum DSM 14480T (99.6 %). However, the levels of DNA–DNA relatedness between strain DVS 3YT and E. acetylicum DSM 20416T, E. oxidotolerans JCM 12280T, E. indicum IAM 15368T, E. undae DSM 14481T, E. sibiricum DSM 17290T and E. antarcticum DSM 14480T were less than 70 % (52, 25, 16, 33, 16 and 38 %, respectively). Strain DVS 3YT also differed from these six closely related species in a number of phenotypic traits. Phenotypic, chemotaxonomic and phylogenetic data suggest that strain DVS 3YT represents a novel species of the genus Exiguobacterium, for which the name Exiguobacterium soli sp. nov. is proposed. The type strain is DVS 3YT (=MTCC 4816T=JCM 14376T).
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Bacillus alkalidiazotrophicus sp. nov., a diazotrophic, low salt-tolerant alkaliphile isolated from Mongolian soda soil
Strain MS 6T was obtained from a microoxic enrichment with a soda soil sample from north-eastern Mongolia in nitrogen-free alkaline medium at pH 10. The isolate had clostridia-like motile cells and formed ellipsoid endospores. It was able to fix dinitrogen gas growing on nitrogen-free alkaline medium. Strain MS 6T was a strictly fermentative bacterium without a respiratory chain, although it had a high catalase activity and tolerated aerobic conditions. It was an obligate alkaliphile with a pH range for growth between 7.5 and 10.6 (optimum at 9.0–9.5). Growth and nitrogen fixation at pH 10 were possible at a total salt content of up to 1.2 M Na+ (optimum at 0.2–0.3 M). The dominant cellular fatty acids included C16 : 0, C16 : 1 ω7, anteiso-C15 : 0 and C14 : 0. The dominant isoprenoid quinone was MK-7. The cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. 16S rRNA gene sequencing identified strain MS 6T as a member of the genus Bacillus. Its closest relative was Bacillus arseniciselenatis E1HT. The key functional nitrogenase gene nifH was detected in both strain MS 6T and its close relative and these strains formed a novel lineage in the nifH gene family. On the basis of these phenotypic and genetic comparisons, strain MS 6T is proposed to represent a novel species of the genus Bacillus, Bacillus alkalidiazotrophicus sp. nov. with the type strain MS 6T (=NCCB 100213T=UNIQEM U377T).
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- Evolution, Phylogeny And Biodiversity
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Automated RFLP pattern comparison and similarity coefficient calculation for rapid delineation of new and distinct phytoplasma 16Sr subgroup lineages
More LessPhytoplasmas are cell wall-less bacteria that cause numerous diseases in several hundred plant species. During adaptation to transkingdom parasitism in diverse plant and insect hosts, phytoplasma evolution has given rise to widely divergent lineages. Since phytoplasmas cannot be cultured in a cell-free medium, measurable phenotypic characters suitable for conventional microbial classification are mostly inaccessible. Currently, phytoplasma differentiation and classification are mainly dependent on restriction fragment length polymorphism (RFLP) analysis of 16S rRNA gene sequences. Extending our recent efforts in the exploitation of computer-simulated 16S rRNA gene RFLP analysis and virtual gel plotting for rapid classification of phytoplasmas, we have developed a Perl program for automated RFLP pattern comparison and similarity coefficient calculation. This program streamlines virtual RFLP pattern analysis and has led to the establishment of a criterion for phytoplasma 16Sr subgroup classification and to the delineation of new and distinct subgroup lineages in the clover proliferation phytoplasma group (16SrVI).
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- Methods
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Phylogenetic analysis and siderotyping as useful tools in the taxonomy of Pseudomonas stutzeri: description of a novel genomovar
An examination of the results of phylogenetic analyses based on the sequences of fragments of the 16S rRNA, gyrB and rpoD genes, and the discrimination of genomovars based on siderophore diversity within the genus Pseudomonas, has added important taxonomic tools in the characterization of Pseudomonas stutzeri. Eighteen reference strains, nine newly identified hydrocarbon-degrading strains and three strains showing relevant physiological characteristics of P. stutzeri, together with the type strains of four related species, were included in the study. A novel genomovar within the species is described. A summary of the methodology used in these studies and the results of our attempts to define a solid internal subdivision of this important species within the genus Pseudomonas are presented and discussed.
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- International Committee On Systematics Of Prokaryotes
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- Minutes
- Taxonomic Note
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Proposed revision of Rule 33c to perpetuate the citation of revived names
More LessAll names published prior to 1980 that were not included in the Approved Lists are available for reuse without reference to their past application. However, the International Code of Nomenclature of Bacteria endorses the revival of disused names in the sense in which they were previously used and provides Rules (28a, 33c and 33d) as guidance. Nevertheless, the Code is obscure as to how citations are to be reported for this use to be perpetuated in subsequent nomenclatural revisions. A revision of Rule 33c is proposed.
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Volumes and issues
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Volume 74 (2024)
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Volume 73 (2023)
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Volume 72 (2022 - 2023)
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Volume 71 (2020 - 2021)
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Volume 70 (2020)
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Volume 69 (2019)
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Volume 68 (2018)
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Volume 67 (2017)
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Volume 66 (2016)
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Volume 65 (2015)
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Volume 64 (2014)
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Volume 63 (2013)
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Volume 62 (2012)
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Volume 61 (2011)
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Volume 60 (2010)
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Volume 59 (2009)
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Volume 58 (2008)
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Volume 57 (2007)
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Volume 56 (2006)
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Volume 55 (2005)
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Volume 54 (2004)
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Volume 53 (2003)
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Volume 52 (2002)
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Volume 51 (2001)
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Volume 50 (2000)
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Volume 49 (1999)
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Volume 48 (1998)
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Volume 47 (1997)
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Volume 46 (1996)
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Volume 45 (1995)
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Volume 44 (1994)
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Volume 43 (1993)
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Volume 42 (1992)
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Volume 41 (1991)
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Volume 40 (1990)
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Volume 39 (1989)
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Volume 38 (1988)
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Volume 37 (1987)
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Volume 36 (1986)
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Volume 35 (1985)
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Volume 34 (1984)
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Volume 33 (1983)
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Volume 32 (1982)
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Volume 31 (1981)
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Volume 30 (1980)
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Volume 29 (1979)
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Volume 28 (1978)
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Volume 27 (1977)
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Volume 26 (1976)
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Volume 25 (1975)
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Volume 24 (1974)
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Volume 23 (1973)
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Volume 22 (1972)
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Volume 21 (1971)
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Volume 20 (1970)
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Volume 19 (1969)
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Volume 18 (1968)
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Volume 17 (1967)
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Volume 16 (1966)
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Volume 15 (1965)
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Volume 14 (1964)
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Volume 13 (1963)
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Volume 12 (1962)
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Volume 11 (1961)
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Volume 10 (1960)
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Volume 9 (1959)
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Volume 8 (1958)
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Volume 7 (1957)
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Volume 6 (1956)
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Volume 5 (1955)
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Volume 4 (1954)
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Volume 3 (1953)
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Volume 2 (1952)
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Volume 1 (1951)