- Volume 59, Issue 8, 2009
Volume 59, Issue 8, 2009
- Notification List
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Notification that new names and new combinations have appeared in volume 59, part 5, 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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Transfer of Actinomadura spadix Nonomura and Ohara 1971 to Actinoallomurus spadix gen. nov., comb. nov., and description of Actinoallomurus amamiensis sp. nov., Actinoallomurus caesius sp. nov., Actinoallomurus coprocola sp. nov., Actinoallomurus fulvus sp. nov., Actinoallomurus iriomotensis sp. nov., Actinoallomurus luridus sp. nov., Actinoallomurus purpureus sp. nov. and Actinoallomurus yoronensis sp. nov.
More LessTen actinomycete strains that form chains of spiral or looped spores were isolated from soil and dung samples in Japan. They contained d- and l-lysine, meso-diaminopimelic acid (A2pm), d-glutamic acid and d- and l-alanine in the cell-wall peptidoglycan, madurose as a characteristic whole-cell sugar, MK-9(H6) and MK-9(H8) as the major isoprenoid quinones and iso-C16 : 0 as the major cellular fatty acid and showed genomic DNA G+C contents of 69–74 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that the isolated actinomycete strains consistently formed a monophyletic cluster with Actinomadura spadix NBRC 14099T and a separate line of descent in the phylogenetic cluster of the family Thermomonosporaceae. Actinomadura spadix NBRC 14099T also contained d- and l-lysine in addition to meso-A2pm. This genetic and phenotypic evidence revealed that the actinomycete strains could be clearly differentiated from the other members of the family Thermomonosporaceae and that they warranted separate genus status. We conclude that Actinomadura spadix should be assigned the status of the type species of a new genus as Actinoallomurus spadix gen. nov., comb. nov. (type strain NBRC 14099T =ATCC 27298T =BCRC 13386T =CBS 261.72T =CIP 105479T =DSM 43459T =JCM 3146T =KCTC 9252T =NCIMB 11118T =NRRL B-16128T). Further, we conclude that the ten new isolates should be assigned to the novel species Actinoallomurus amamiensis sp. nov. (type strain TT00-28T =NBRC 103682T =KCTC 19537T), Actinoallomurus caesius sp. nov. (type strain A3015T =NBRC 103678T =KCTC 19535T), Actinoallomurus coprocola sp. nov. (type strain TT04-09T =NBRC 103688T =KCTC 19542T), Actinoallomurus fulvus sp. nov. (type strain TT99-66T =NBRC 103680T =KCTC 19536T), Actinoallomurus iriomotensis sp. nov. (type strain TT02-47T =NBRC 103685T =KCTC 19539T), Actinoallomurus luridus sp. nov. (type strain TT02-15T =NBRC 103683T =KCTC 19538T), Actinoallomurus purpureus sp. nov. (type strain TTN02-30T =NBRC 103687T =KCTC 19541T) and Actinoallomurus yoronensis sp. nov. (type strain TTN02-22T =NBRC 103686T =KCTC 19540T).
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Georgenia thermotolerans sp. nov., an actinobacterium isolated from forest soil
More LessA Gram-positive bacterium strain, designated TT02-04T, was isolated from a forest soil sample in Iriomote Island, Japan, and its taxonomic position was investigated by using a polyphasic approach. The peptidoglycan type of this organism was found to be A4α and lysine was the diagnostic cell-wall diamino acid of the peptidoglycan. The only menaquinone was MK-8(H4), and the major fatty acid was anteiso-C15 : 0. Galactose was detected as the cell-wall sugar. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol mannosides. The DNA G+C content was 73.0 mol%. 16S rRNA gene sequencing studies indicated that strain TT02-04T was closely related to the type strains of Georgenia ruanii (99.0 %) and Georgenia muralis (97.7 %). However, DNA–DNA hybridization results and phenotypic characteristics revealed that the strain differed from the currently recognized species of the genus Georgenia. Therefore, strain TT02-04T represents a novel species of the genus Georgenia, for which the name Georgenia thermotolerans sp. nov. is proposed. The type strain is TT02-04T (=NBRC 104148T=DSM 21501T).
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Corynebacterium timonense sp. nov. and Corynebacterium massiliense sp. nov., isolated from human blood and human articular hip fluid
More LessGram-positive, facultatively anaerobic, rod-shaped bacteria were isolated from the blood of a patient with endocarditis (strain 5401744T) and from the hip joint fluid of a patient with an infected orthopaedic prosthesis (strain 5402485T). These strains were characterized by using a polyphasic taxonomic approach. Based on cellular morphology and biochemical criteria the two isolates were tentatively assigned to the genus Corynebacterium, although they did not correspond to any recognized species. The predominant fatty acids were a mix of C18 : 2 ω6,9c and anteiso-C18 : 0 (32.1 % of the total), C16 : 0 (26.3 %) and C18 : 1 ω9c (22.5 %) for strain 5402485T and C18 : 1 ω9c (36.4 %), C17 : 1 ω9c (27.1 %) and C16 : 0 (10.9 %) for strain 5401744T. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that strain 5401744T was closely related to the type strains of Corynebacterium auris, Corynebacterium capitovis, Corynebacterium lipophiloflavum and Corynebacterium mycetoides (97.0, 96.6, 96.5 and 96.3 % similarity, respectively) and strain 5402485T was closely related to the type strains of Corynebacterium macginleyi, Corynebacterium accolens, Corynebacterium tuberculostearicum, Corynebacterium confusum, Corynebacterium mastitidis and Corynebacterium renale (95.6, 95.3, 95.3, 94.5, 94.0 and 93.5 %, respectively). On the basis of phenotypic data and phylogenetic inference, these isolates are considered to represent two novel species of the genus Corynebacterium, for which the names Corynebacterium timonense sp. nov. (type strain, 5401744T=CSUR P20T=CIP 109424T=CCUG 53856T) and Corynebacterium massiliense sp. nov. (type strain, 5402485T=CSUR P19T=CIP 109423T=CCUG 53857T) are proposed.
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Brevibacterium massiliense sp. nov., isolated from a human ankle discharge
More LessGram-positive, non-spore-forming rods, strain 5401308T, were isolated from a human ankle discharge. Based on cellular morphology and the results of biochemical testing, this strain was tentatively identified as an undescribed member of the genus Brevibacterium. The major fatty acids were anteiso-C15 : 0 (45.3 %), anteiso-C17 : 0 (19.2 %) and iso-C15 : 0 (18.3 %). Phylogenetic analysis based on 16S rRNA gene sequence comparison showed that the bacterium was closely related to the type strains of Brevibacterium mcbrellneri (96.3 % similarity) and Brevibacterium paucivorans (95.8 %). On the basis of phenotypic data and phylogenetic inference, it is proposed that this strain represents a novel species, designated Brevibacterium massiliense sp. nov.; the type strain is 5401308T (=CSUR P26T=CIP 109422T=CCUG 53855T).
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Gordonia kroppenstedtii sp. nov., a phenol-degrading actinomycete isolated from a polluted stream
More LessA phenol-degrading actinomycete, strain NP8-5T, was isolated from a polluted stream in Gumi, Korea. The strain was aerobic, Gram-positive-staining, non-motile and non-spore-forming, displayed a rod–coccus growth cycle, exhibited white opaque colonies on complex media and showed chemotaxonomic markers that were consistent with its classification in the genus Gordonia. Phylogenetic analysis, based on 16S rRNA gene sequencing, also showed that strain NP8-5T belonged to the genus Gordonia, sharing the highest levels of sequence similarity with Gordonia araii IFM 10211T, G. hydrophobica DSM 44015T and G. sinesedis NCIMB 13802T (96.4, 96.0 and 95.9 %, respectively) and forming a separate lineage within this genus. Combined phylogenetic and phenotypic data supported the conclusion that strain NP8-5T represents a novel species of the genus Gordonia, for which the name Gordonia kroppenstedtii sp. nov. is proposed. The type strain is NP8-5T (=KCTC 19360T =DSM 45133T).
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Bifidobacterium bombi sp. nov., from the bumblebee digestive tract
More LessGram-positive-staining, anaerobic, non-spore-forming, lactate- and acetate-producing bacterial strains were isolated from the digestive tracts of different bumblebee species (Bombus lucorum, Bombus pascuorum and Bombus lapidarius). All of the isolates produced fructose-6-phosphate phosphoketolase activity. A representative strain, BluCI/TPT, was characterized further. Cells of strain BluCI/TPT showed occasional bifurcation and irregular constrictions. The bacterium utilized a wide range of carbohydrates. Glucose was fermented to acetate and lactate. The DNA base composition was 47.2 mol% G+C. Complete 16S rRNA and partial hsp60 gene sequences were obtained and phylogenetic relationships were determined. Strain BluCI/TPT and related isolates were located in the actinobacterial cluster and were closely related to the genera Bifidobacterium, Scardovia, Aeriscardovia and Parascardovia. The results presented support the proposal of a novel species to accommodate strain BluCI/TPT, with the name Bifidobacterium bombi sp. nov.; the type strain is BluCI/TPT (=DSM 19703T =ATCC BAA-1567T).
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Zhihengliuella alba sp. nov., and emended description of the genus Zhihengliuella
More LessA Gram-positive, non-motile, white-pigmented, short rod actinobacterium, designated YIM 90734T, was isolated from a saline soil sample collected from Ganjiahu Suosuo Forest National Nature Reserve in Xinjiang province, north-west China, and its taxonomic position was investigated by using a polyphasic approach. Strain YIM 90734T grew optimally at 28–37 °C and pH 6.0–8.0 and in 5 % (w/v) NaCl. The peptidoglycan type was A4α, l-Lys–l-Ala–l-Glu and tyvelose and mannose were the major cell-wall sugars. The predominant menaquinones were MK-10 and MK-9. Major cellular fatty acids (>10 % of total) were anteiso-C15 : 0 and anteiso-C17 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, one unknown phospholipid and two unknown glycolipids. The DNA G+C content was 70.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM 90734T belonged to the genus Zhihengliuella. The 16S rRNA gene sequence similarity between strain YIM 90734T and the type strain of the only recognized Zhihengliuella species, Zhihengliuella halotolerans, was 97.7 %. However, the level of DNA–DNA relatedness of the two strains was 41.4 %. The DNA–DNA relatedness data and differential phenotypic properties, together with the phylogenetic distinctiveness, demonstrated that strain YIM 90734T could be differentiated from Z. halotolerans. On the basis of the data presented, strain YIM 90734T is considered to represent a novel species of the genus Zhihengliuella, for which the name Zhihengliuella alba sp. nov. is proposed. The type strain is YIM 90734T (=KCTC 19375T=DSM 21143T). The description of the genus Zhihengliuella has also been emended.
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Streptomyces hypolithicus sp. nov., isolated from an Antarctic hypolith community
More LessAs part of an enzyme-screening programme, an actinobacterium, strain HSM#10T, was isolated from a sample collected from the base of a translucent quartz rock in Miers Valley, eastern Antarctica. The isolate produced branching vegetative mycelium that was characteristic of filamentous actinobacteria. The chemotaxonomic characteristics of the strain suggested that HSM#10T should be classified as a member of the genus Streptomyces. Furthermore, phylogenetic analysis based on 16S rRNA gene sequences showed that the strain was closely related to members of the genus Streptomyces, which supports the classification of this strain within the family Streptomycetaceae. Phenotypic and phylogenetic results allowed strain HSM#10T to be differentiated from known streptomycetes. DNA–DNA hybridization data also showed that strain HSM#10T could be differentiated from its nearest phylogenetic neighbours Streptomyces chryseus DSM 40420T (53.55±3.15 % DNA relatedness), Streptomyces helvaticus DSM 40431T (38.75±2.75 %), Streptomyces flavidovirens DSM 40150T (30.7±2.90 %) and Streptomyces albidochromogenes DSM 41800T (33.9±0.10 %). Therefore, the name Streptomyces hypolithicus sp. nov. is proposed, with HSM#10T (=DSM 41950T =NRRL B-24669T) as the type strain.
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Microbacterium invictum sp. nov., isolated from homemade compost
Strain DC-200T was isolated from homemade compost produced from kitchen refuse and characterized using a polyphasic approach. The isolate was a Gram-positive motile short rod, facultatively aerobic, catalase-positive and oxidase-negative, and was able to grow at 10–37 °C, pH 6.0–9.5 and with up to 5 % of NaCl. The peptidoglycan was of the type B1 alpha and the muramic acid residues were glycolylated. The major fatty acids were anteiso-C15 : 0 and anteiso-C17 : 0. The predominant respiratory menaquinones were MK-11 and MK-12. The G+C content of the genomic DNA was 70 mol%. Based on the analysis of the 16S rRNA gene sequence, the closest phylogenetic neighbours of strain DC-200T were Microbacterium lacus A5E-52T (98.7 %) and Microbacterium aoyamense KV-492T (98.2 %). The phenetic characterization of the isolate supports its inclusion within the genus Microbacterium; however, its distinctive phenotypic features and the results from the 16S rRNA gene sequence analysis and the DNA–DNA hybridization study suggest that the isolate represents a novel species. The name Microbacterium invictum sp. nov. is proposed. The type strain is DC-200T (=DSM 19600T=LMG 24557T).
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Corynebacterium freiburgense sp. nov., isolated from a wound obtained from a dog bite
More LessA non-lipophilic, coryneform bacterium, isolated from a patient's wound obtained from a dog bite, was characterized by phenotypic, chemotaxonomic and molecular genetic methods. Chemotaxonomic features suggested assignment of the unknown bacterium to the genus Corynebacterium. The isolate exhibited the following peculiar features which made it possible to differentiate it phenotypically from all other medically relevant corynebacteria: older colonies exhibited a ‘spoke-wheel’ macroscopic morphology, colonies were strongly adherent to blood agar and the strain did not have pyrazinamidase activity, but was positive for β-galactosidase. 16S rRNA gene sequencing showed that the closest phylogenetic relative exhibited more than 3.9 % divergence from the unknown isolate. Based on phenotypic and molecular genetic data, it is proposed that the isolate should be classified as a representative of a novel species, Corynebacterium freiburgense sp. nov., with strain 1045T (=CCUG 56874T =DSM 45254T) as the type strain.
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Paraoerskovia marina gen. nov., sp. nov., an actinobacterium isolated from marine sediment
A Gram-positive-staining, facultatively anaerobic bacterial strain, CTT-37T, was isolated from a marine sediment sample collected from Tottori city, located on the shore of the Sea of Japan. A 16S rRNA gene sequence comparison indicated that the isolate represents a novel clade that clusters with members of the families Cellulomonadaceae and Sanguibacteraceae. Strain CTT-37T shared maximum 16S rRNA gene sequence similarity of 96.4 % with Oerskovia paurometabola DSM 14281T and 96.2 % with Oerskovia enterophila DSM 43852T. The DNA–DNA hybridization value between strain CTT-37T and O. enterophila JCM 7350T was 10–12 %. The following chemotaxonomic characteristics of strain CTT-37T were markedly different from those of strains in the genus Oerskovia. The cell wall contained l-serine in the peptidoglycan interpeptide bridge. The predominant menaquinone was MK-9 (H4); other quinones detected were MK-9 and MK-9(H2). The only polar lipid was phosphatidylglycerol and the G+C content of the DNA was 70 mol%. Differences in phenotypic characteristics and large phylogenetic distances between strain CTT-37T and all members of the genus Oerskovia supported the classification of CTT-37T within a new genus and species, for which the name Paraoerskovia marina gen. nov., sp. nov. is proposed. The type strain of Paraoerskovia marina is CTT-37T (=NBRC 104352T =DSM 21750T).
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- Archaea
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Halorubrum chaoviator sp. nov., a haloarchaeon isolated from sea salt in Baja California, Mexico, Western Australia and Naxos, Greece
Three halophilic isolates, strains Halo-G*T, AUS-1 and Naxos II, were compared. Halo-G* was isolated from an evaporitic salt crystal from Baja California, Mexico, whereas AUS-1 and Naxos II were isolated from salt pools in Western Australia and the Greek island of Naxos, respectively. Halo-G*T had been exposed previously to conditions of outer space and survived 2 weeks on the Biopan facility. Chemotaxonomic and molecular comparisons suggested high similarity between the three strains. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that the strains clustered with Halorubrum species, showing sequence similarities of 99.2–97.1 %. The DNA–DNA hybridization values of strain Halo-G*T and strains AUS-1 and Naxos II are 73 and 75 %, respectively, indicating that they constitute a single species. The DNA relatedness between strain Halo-G*T and the type strains of 13 closely related species of the genus Halorubrum ranged from 39 to 2 %, suggesting that the three isolates constitute a different genospecies. The G+C content of the DNA of the three strains was 65.5–66.5 mol%. All three strains contained C20C20 derivatives of diethers of phosphatidylglycerol, phosphatidylglyceromethylphosphate and phosphatidylglycerolsulfate, together with a sulfated glycolipid. On the basis of these results, a novel species that includes the three strains is proposed, with the name Halorubrum chaoviator sp. nov. The type strain is strain Halo-G*T (=DSM 19316T =NCIMB 14426T =ATCC BAA-1602T).
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- Bacteroidetes
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Muricauda olearia sp. nov., isolated from crude-oil-contaminated seawater, and emended description of the genus Muricauda
More LessA Gram-staining-negative, rod-shaped and non-motile bacterium, designated CL-SS4T, was isolated from crude-oil-contaminated seawater from the west coast of Korea and was investigated by means of a polyphasic taxonomic approach. Strain CL-SS4T grew optimally at 25–30 °C, at pH 6.8–7.7 and in the presence of 2–3 % sea salts. The major fatty acids were iso-C17 : 0 3-OH, iso-C15 : 0 and iso-C15 : 1 G. The major isoprenoid quinone was MK-6. The DNA G+C content was 50.7 mol%. Analysis of the 16S rRNA gene sequence of strain CL-SS4T revealed that it was a member of the genus Muricauda, sharing 95.7–96.9 % sequence similarity with the type strains of Muricauda species and being most closely related to Muricauda aquimarina SW-63T. Phylogenetic analyses based on 16S rRNA gene sequences confirmed that strain CL-SS4T formed a deep lineage related to the genus Muricauda. Strain CL-SS4T was distinguishable from recognized Muricauda species on the basis of differential phenotypic characteristics and DNA G+C content. Based on these results, it is proposed that strain CL-SS4T represents a novel species of the genus Muricauda, for which the name Muricauda olearia sp. nov. is proposed. An emended description of the genus Muricauda is also proposed. The type strain is CL-SS4T (=KCCM 90075T=JCM 15563T).
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Paraprevotella clara gen. nov., sp. nov. and Paraprevotella xylaniphila sp. nov., members of the family ‘Prevotellaceae’ isolated from human faeces
More LessTwo anaerobic, non-spore-forming, pleomorphic, Gram-negative rods, designated YIT 11840T and YIT 11841T, were isolated from human faeces. The organisms were catalase-negative, produced succinic and acetic acids as end products of glucose metabolism and had DNA G+C contents of approximately 48–49 mol%. Although the phenotypic characteristics of these two strains were very similar, analysis of their 16S rRNA gene sequences showed that they are only distantly related (93.8 %), indicating that they represent two different species. A comparative sequence analysis revealed that these two species are members of the family ‘Prevotellaceae’ but are phylogenetically distant (<88 % sequence similarity) from the known genera belonging to this family, including Prevotella, Hallela and Xylanibacter. On the basis of the phylogenetic analysis and physiological tests, strains YIT 11840T and YIT 11841T represent two novel species of a new genus, for which the names Paraprevotella clara gen. nov., sp. nov. (type strain YIT 11840T =JCM 14859T =DSM 19731T), the type species, and Paraprevotella xylaniphila sp. nov. (type strain YIT 11841T =JCM 14860T =DSM 19681T) are proposed.
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Bacteroides graminisolvens sp. nov., a xylanolytic anaerobe isolated from a methanogenic reactor treating cattle waste
More LessA strictly anaerobic bacterial strain, designated XDT-1T, was isolated from plant residue from a methanogenic reactor treating waste from cattle farms. Cells of the strain were Gram-negative, non-motile, non-spore-forming rods. Haemin was required for growth. The strain utilized xylan as well as various sugars including arabinose, xylose, glucose, mannose, cellobiose, raffinose, starch and pectin. The strain produced acetate, propionate and succinate from saccharides in the presence of haemin. The optimum pH for growth was approximately 7.2 and the optimum growth temperature was 30–35 °C. The strain was sensitive to bile. The major cellular fatty acids of the strain were anteiso-C15 : 0 and iso-C17 : 0 3-OH, MK-10(H0) was the major respiratory quinone and the genomic DNA G+C content was 38.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences placed the strain in the phylum Bacteroidetes. The closest phylogenetic neighbour of strain XDT-1T was Bacteroides ovatus NCTC 11153T, with a 16S rRNA gene sequence similarity of 94.2 %. On the basis of data from the phylogenetic, physiological and chemotaxonomic analyses, strain XDT-1T represents a novel species of the genus Bacteroides, for which the name Bacteroides graminisolvens sp. nov. is proposed. The type strain is XDT-1T (=JCM 15093T =DSM 19988T).
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Solitalea koreensis gen. nov., sp. nov. and the reclassification of [Flexibacter] canadensis as Solitalea canadensis comb. nov.
A Gram-negative, rod-shaped, non-spore-forming bacterium, designated strain R2A36-4T, was isolated from greenhouse soil and subjected to a polyphasic taxonomic analysis. 16S rRNA gene sequence analysis revealed that the strain represented a novel member of the family Sphingobacteriaceae. Its nearest phylogenetic neighbour was the type strain of [Flexibacter] canadensis CIP 104802T (93.2 % 16S rRNA gene sequence similarity). Strain R2A36-4T and [F.] canadensis CIP 104802T fell in a distinct cluster within the family Sphingobacteriaceae. Strain R2A36-4T contained MK-7 as the predominant quinone. Strain R2A36-4T and [F.] canadensis CIP 104802T had iso-C15 : 0, iso-C17 : 0 3-OH, summed feature 3 and C15 : 1 ω6c as the major fatty acids. Strain R2A36-4T could be distinguished from [F.] canadensis on the basis of several physiological properties and fatty acid compositions. Based on phenotypic characterization and 16S rRNA gene sequence analysis, strain R2A36-4T represents a novel species within a new genus, for which the name Solitalea koreensis gen. nov., sp. nov. is proposed. The type strain of Solitalea koreensis is strain R2A36-4T (=KACC 12953T=DSM 21342T). It is also proposed that [F.] canadensis be transferred to this genus as Solitalea canadensis comb. nov. (type strain UASM 9DT=ATCC 29591T=CIP 104802T=DSM 3403T=NBRC 15130T=JCM 21819T=KACC 13276T=LMG 8368T).
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Lutaonella thermophila gen. nov., sp. nov., a moderately thermophilic member of the family Flavobacteriaceae isolated from a coastal hot spring
A yellow-pigmented, Gram-staining-negative, aerobic, non-motile, moderately thermophilic, rod-shaped bacterium, CC-MHSW-2T, was isolated from a coastal hot spring of Green Island (Lutao), located off Taituang, Taiwan. The 16S rRNA gene sequence analysis demonstrated that it shared <93.2 % sequence similarity with Aquimarina species. The organism was unable to produce acid from carbohydrates, but it could utilize a number of organic acids and amino acids. Menaquinone 6 (MK-6) was the major respiratory quinone and iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c) were the predominant fatty acids. This fatty acid profile distinguished the isolate from members of the genera Aquimarina, Tamlana, Zhouia, Leeuwenhoekiella and Cellulophaga. The DNA G+C content of strain CC-MHSW-2T was 39.7±1 mol%. On the basis of the 16S rRNA gene sequence analysis and the chemotaxonomic and physiological data, strain CC-MHSW-2T represents a novel genus and species in the family Flavobacteriaceae, for which the name Lutaonella thermophila gen. nov., sp. nov. is proposed. The type strain is CC-MHSW-2T (=KCTC 22538T =JCM 15069T).
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- Firmicutes And Related Organisms
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Lactobacillus oeni sp. nov., from wine
More LessTen Lactobacillus strains, previously isolated from different Bobal grape wines from the Utiel-Requena Origin Denomination of Spain, were characterized phylogenetically, genotypically and phenotypically. The 16S rRNA genes were sequenced and phylogenetic analysis showed that they form a tight phylogenetic clade that is closely related to reference strains Lactobacillus satsumensis NRIC 0604T, ‘Lactobacillus uvarum’ 8 and Lactobacillus mali DSM 20444T. DNA–DNA hybridization results confirmed the separation of the strains from other Lactobacillus species. Genotypically, the strains could be differentiated from their closest neighbours by 16S amplified rDNA restriction analysis and random amplified polymorphic DNA patterns. The strains were Gram-staining-positive, facultatively anaerobic rods that did not exhibit catalase activity. Phenotypically, they could be distinguished from their closest relatives by several traits such as their inabilities to grow at pH 3.3, to ferment sucrose, amygdalin and arbutin or to hydrolyse aesculin. The characteristics of the ten wine isolates suggest that they represent a novel species, for which the name Lactobacillus oeni sp. nov. is proposed. The type strain is 59bT (=CECT 7334T =DSM 19972T).
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Bacillus canaveralius sp. nov., an alkali-tolerant bacterium isolated from a spacecraft assembly facility
More LessTwo Gram-positive, rod-shaped, alkali-tolerant (pH 10.5), endospore-forming bacteria (strains KSC SF8bT and KSC SF10a) were isolated from surfaces within the Payload Hazardous Servicing Facility, where robotic spacecraft are assembled and tested before launch, at the Kennedy Space Center at Cape Canaveral. Based on 16S rRNA gene sequence similarities, these strains were shown to belong to the family Bacillaceae and the genus Bacillus. The highest 16S rRNA gene sequence similarity was ∼97.5 %, observed between the novel strains and Bacillus selenatarsenatis SF-1T. Several phenotypic characteristics, such as growth with 10 % NaCl and assimilation of melibiose and lactose, were useful in the discrimination of this novel species from the closely related alkali-tolerant species Bacillus firmus and B. selenatarsenatis. DNA–DNA hybridization studies revealed reassociation values of less than 45 % between strain KSC SF8bT and its closest genotypic neighbours. The combination of unique phenotypic and genotypic characteristics allowed the differentiation of these alkali- and halotolerant spore-forming strains from related Bacillus species, and a novel species, Bacillus canaveralius sp. nov., is proposed. The type strain is KSC SF8bT (=ATCC BAA-1493T=MTCC 8908T).
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Natronovirga wadinatrunensis gen. nov., sp. nov. and Natranaerobius trueperi sp. nov., halophilic, alkalithermophilic micro-organisms from soda lakes of the Wadi An Natrun, Egypt
More LessNovel strains of anaerobic, halophilic, alkalithermophilic bacteria were isolated from sediments of the alkaline, hypersaline lakes of the Wadi An Natrun, Egypt. Strains JW/NM-WN-LUT (and related strains) and JW/NM-WN-LH1T were non-spore-forming, non-motile bacteria with a Gram-type positive cell wall. Optimal growth of strain JW/NM-WN-LUT occurred at pH55 °C 9.5, 52 °C and with 3.7 M Na+ (2.2 M added NaCl). Optimal growth of strain JW/NM-WN-LH1T occurred at pH55 °C 9.9, 51 °C and with 3.9 M Na+ (2.3 M added NaCl). Both strains were obligately anaerobic and chemoorganotrophic; producing lactate and acetate as organic acids from pyruvate in different ratios. The DNA G+C contents of strains JW/NM-WN-LUT and JW/NM-WN-LH1T were 41.0 and 42.0 mol%, respectively. The main cellular fatty acids in both strains were anteiso-branched 15 : 0 and iso-branched 15 : 0. Phylogenetic analysis showed that both novel isolates belonged to the family Natranaerobiaceae within the order Natranaerobiales. Based on genotypic and phenotypic data, strain JW/NM-WN-LUT (=DSM 18760T=ATCC BAA-1443T) represents the type strain of a novel species, Natranaerobius trueperi sp. nov. Strain JW/NM-WN-LH1T represents a novel genus and species within the family Natranaerobiaceae, Natronovirga wadinatrunensis gen. nov., sp. nov. The type strain of the type species is JW/NM-WN-LH1T (=DSM 18770T=ATCC BAA-1444T).
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Virgibacillus sediminis sp. nov., a moderately halophilic bacterium isolated from a salt lake in China
A Gram-positive, moderately halophilic, alkalitolerant, strictly aerobic, oxidase- and catalase-positive, rod-shaped bacterium, strain YIM kkny3T, was isolated from a sediment sample collected from a salt lake in the Qaidam Basin of north-west China. Cells were motile by means of peritrichous flagella and formed ellipsoidal endospores lying in subterminal swollen sporangia. Growth occurred with 1–20 % (w/v) total salts (optimum, 5–10 %) and at pH 6.0–10.5 (optimum, pH 7.5–8.0) and 10–55 °C (optimum, 35–40 °C). It was unable to grow with NaCl as the only salt. meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. The strain contained menaquinone 7 (MK-7) as the predominant respiratory quinone and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid as polar lipids. The major cellular fatty acids were anteiso-C15 : 0 and anteiso-C17 : 0. The DNA G+C content was 40.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YIM kkny3T belonged to the genus Virgibacillus, and was most closely related to the type strains of Virgibacillus olivae (97.1 % similarity), Virgibacillus marismortui (97.0 %) and Virgibacillus kekensis (96.8 %). Levels of DNA–DNA relatedness between strain YIM kkny3T and the type strains of V. olivae, V. marismortui and V. kekensis were 12.4, 10.6 and 15.7 %, respectively. The combination of phylogenetic analysis, genotypic data, phenotypic characteristics and chemotaxonomic differences indicated that strain YIM kkny3T represents a novel species of the genus Virgibacillus, for which the name Virgibacillus sediminis sp. nov. is proposed. The type strain is YIM kkny3T (=CCTCC AA 207023T=DSM 19797T=KCTC 13193T).
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Lactobacillus taiwanensis sp. nov., isolated from silage
More LessStrain FIRDI 006T, isolated from silage cattle feed, was characterized by using phenotypic and molecular taxonomic methods. The strain was a homofermentative lactic acid bacterium; the cells stained Gram-positive and were catalase-negative, non-motile, facultatively anaerobic rods. 16S rRNA gene sequence analysis revealed that the strain belongs phylogenetically to the genus Lactobacillus and can be placed within the Lactobacillus acidophilus–delbrueckii group. Lactobacillus gasseri and Lactobacillus johnsonii were the most closely related species, with 16S rRNA gene sequence similarities of 99.53 and 99.46 % to the respective type strains. Low gyrB gene sequence similarities (<90 %) and low DNA–DNA reassociation values (<45 %) were obtained between the strain and the phylogenetically closest neighbours. Based on phenotypic and genetic evidence, the strain is considered to represent a novel species, for which the name Lactobacillus taiwanensis sp. nov. is proposed. The type strain is FIRDI 006T (=BCRC 17755T =DSM 21401T).
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Paenibacillus macquariensis subsp. defensor subsp. nov., isolated from boreal soil
Two Gram-variable, aerobic, motile, rod-shaped, endospore-forming bacterial strains, M4-2T and M4-1, were isolated from soil samples collected from Oblast Magadan, Russian Far East, as micro-organisms antagonistic to the psychrophilic phytopathogenic fungus Typhula ishikariensis. Strains M4-2T and M4-1 were identified as members of the genus Paenibacillus by phenotypic and phylogenetic analyses based on 16S rRNA gene sequences. The strains contained anteiso-C15 : 0 as the major fatty acid (63.0–64.7 %) and MK-7 as the major isoprenoid quinone. The DNA G+C contents were 42.8 and 41.7 mol%, respectively. 16S rRNA gene sequence analysis showed that strains M4-2T and M4-1 exhibited high similarities with Paenibacillus macquariensis DSM 2T (99.5 and 99.7 %, respectively) and Paenibacillus antarcticus LMG 22078T (99.4 and 99.5 %, respectively). There were no clear differences in the phenotypic characteristics and chemotaxonomic and phylogenetic data between the novel isolates and P. macquariensis DSM 2T. DNA–DNA hybridization experiments between strain M4-2T and P. macquariensis DSM 2T and P. antarcticus LMG 22078T revealed reassociation values of 56 and 49 %, respectively. Multilocus sequence analysis confirmed the differences between the new isolates and reference strains that were observed with the DNA–DNA hybridization studies. On the basis of the results described above, it is proposed that the isolates represent a novel subspecies of P. macquariensis, Paenibacillus macquariensis subsp. defensor subsp. nov. The type strain is M4-2T (=JCM 14954T=NCIMB 14397T).
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Selenomonas bovis sp. nov., isolated from yak rumen contents
More LessTwo strictly anaerobic, crescent-shaped bacterial strains, designated WGT and Ycb08, were isolated from a cellulose-degrading mixed culture enriched from yak rumen contents. The strains were Gram-negative, non-spore-forming and motile, with four to six flagella situated at the centre of the concave side of the cell. The cells were 0.9–1.1×4–6 μm. Growth was observed at 27–46 °C (optimum 39 °C) and pH 4.2–8.3 (optimum pH 7.0–7.2). Arabinose, glucose, mannose, cellobiose, lactose, sucrose, trehalose, melibiose, raffinose, salicin and aesculin were fermented. The end products of glucose fermentation were acetate, propionate and CO2. The G+C contents of strains WGT and Ycb08 were respectively 63.9±0.2 and 62.5±0.2 mol% (T m). Phylogenetic analysis based on 16S rRNA gene sequences revealed that the two strains were related to the genera Mitsuokella and Selenomonas at similarity levels below 97 %; however, they differed from members of the genus Mitsuokella in their flagellar arrangement. On the basis of phenotypic, genotypic and physiological evidence, strains WGT and Ycb08 are identified as members of a novel species of the genus Selenomonas, for which the name Selenomonas bovis sp. nov. is proposed. The type strain is WGT (=CGMCC 1.5073T =JCM 15470T).
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- Other Bacteria
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Deinococcus aerius sp. nov., isolated from the high atmosphere
An orange-pigmented, non-motile, coccoid bacterial strain, designated TR0125T, was isolated from dust samples collected in the high atmosphere above Japan. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain was within the radiation of Deinococcus species. The major peptidoglycan amino acids were d-glutamic acid, glycine, d-alanine, l-alanine and ornithine. The predominant fatty acids were iso-C17 : 0, iso-C17 : 1 ω9c and iso-C15 : 0. Strong resistance to desiccation, UV-C and gamma radiation and high DNA G+C content also supported the affiliation of strain TR0125T to the genus Deinococcus. Strain TR0125T showed the highest 16S rRNA gene sequence similarity value (95.7 %) to the type strain of Deinococcus apachensis, and phylogenetic analysis showed that it was further separated from D. apachensis than from Deinococcus geothermalis, indicating that strain TR0125T was not a member of these two Deinococcus species. In addition, phenotypic differences were found between strain TR0125T and the type strains of these two Deinococcus species. Therefore, a novel species of the genus Deinococcus, Deinococcus aerius sp. nov. (type strain, TR0125T=JCM 11750T=DSM 21212T), is proposed to accommodate this isolate.
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- Proteobacteria
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Aliagarivorans marinus gen. nov., sp. nov. and Aliagarivorans taiwanensis sp. nov., facultatively anaerobic marine bacteria capable of agar degradation
More LessTwo agarolytic strains of Gram-negative, heterotrophic, facultatively anaerobic, marine bacteria, designated AAM1T and AAT1T, were isolated from seawater samples collected in the shallow coastal region of An-Ping Harbour, Tainan, Taiwan. Cells grown in broth cultures were straight rods that were motile by means of a single polar flagellum. The two isolates required NaCl for growth and grew optimally at about 25–30 °C, in 2–4 % NaCl and at pH 8. They grew aerobically and could achieve anaerobic growth by fermenting d-glucose or other sugars. The major isoprenoid quinone was Q-8 (79.8–92.0 %) and the major cellular fatty acids were summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH; 26.4–35.6 %), C18 : 1 ω7c (27.1–31.4 %) and C16 : 0 (14.8–16.3 %) in the two strains. Strains AAM1T and AAT1T had DNA G+C contents of 52.9 and 52.4 mol%, respectively. The two strains had a 16S rRNA gene sequence similarity of 98.6 % and shared 84.9–92.4 % sequence similarity with the type strains of Agarivorans albus (91.2–92.4 %), eight Alteromonas species (84.9–87.1 %), two Aestuariibacter species (86.0–87.0 %), Bowmanella denitrificans (86.1–86.7 %), eight Glaciecola species (85.0–87.9 %) and Salinimonas chungwhensis (85.9–86.1 %). Despite their high sequence similarity, strains AAM1T and AAT1T had a DNA–DNA relatedness value of only 4.5 %. The data obtained from these polyphasic taxonomic studies revealed that the two agarolytic isolates could be classified as representatives of two novel species in a new genus, Aliagarivorans gen. nov., with Aliagarivorans marinus sp. nov. [type strain is AAM1T (=BCRC 17888T=JCM 15522T)] as the type species and Aliagarivorans taiwanensis sp. nov. [type strain is AAT1T (=BCRC 17889T=JCM 15537T)] as a second species.
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Shewanella marina sp. nov., isolated from seawater
More LessA motile, rod-shaped, pale-brown-pigmented bacterium, designated strain C4T, was isolated from seawater collected from the South Sea (Republic of Korea). Cells were Gram-negative, facultatively anaerobic, and catalase- and oxidase-positive. The major fatty acids were summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH; 19.4 %), C16 : 0 (16.3 %), C17 : 1 ω8c (9.5 %) and iso-C15 : 0 (7.7 %). The DNA G+C content was 40.8 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain C4T formed a lineage within the genus Shewanella (92.7–96.1 % sequence similarity to representative strains of the genus Shewanella) and was part of a distinct branch with the clade comprising Shewanella haliotis DW01T and Shewanella algae ATCC 51192T. Phenotypic characteristics enabled strain C4T to be distinguished from S. haliotis and S. algae. On the basis of the data presented in this study, strain C4T represents a novel species, for which the name Shewanella marina sp. nov. is proposed. The type strain is C4T (=KCTC 22185T=JCM 15074T).
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Reclassification of the members of the genus Tetrathiobacter Ghosh et al. 2005 to the genus Advenella Coenye et al. 2005
More LessThe taxonomic position of the genera Advenella and Tetrathiobacter was examined. 16S rRNA gene sequence analysis revealed that the two genera are closely related, representing a monophyletic cluster with high sequence similarity (98.1–99.7 %) within the family Alcaligenaceae. The phenotypic characteristics of the type strains of Advenella incenata, Tetrathiobacter kashmirensis and Tetrathiobacter mimigardefordensis were re-examined using the API 20NE, API ZYM and API 50CH systems. Phylogenetic data together with similarities in phenotypic characteristics, G+C content and cellular acid composition suggest that they should be classified in the same genus. On the basis of the data presented, the two species of the genus Tetrathiobacter should be transferred to the genus Advenella, since this genus has nomenclatural priority. Therefore, Tetrathiobacter kashmirensis and Tetrathiobacter mimigardefordensis should be transferred to the genus Advenella as Advenella kashmirensis comb. nov. (type strain WT001T =LMG 22695T =MTCC7002T) and Advenella mimigardefordensis comb. nov. (type strain DPN7T =DSM 17166T =LMG 22922T). Emended descriptions of Advenella incenata and the genus Advenella are also presented.
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Rhizobium mesosinicum sp. nov., isolated from root nodules of three different legumes
More LessThirteen novel strains were isolated from root nodules of three different leguminous plants of the genera Albizia, Kummerowia and Dalbergia grown in China. Cells of these strains were Gram-negative, strictly aerobic, non-spore-forming, motile rods. Phylogenetic analysis of 16S rRNA gene sequences revealed that they belong to the genus Rhizobium. A representative strain, CCBAU 25010T, showed 98.8 % 16S rRNA gene sequence similarity to its closest phylogenetic relative, Rhizobium sullae IS123T. The 16S–23S intergenic spacer (ITS) sequence of CCBAU 25010T shared 91.5 and 87.2 % sequence similarity, respectively, with those of Rhizobium etli CFN 42T and Rhizobium leguminosarum LMG 14904T. Analysis of the sequences of the housekeeping genes atpD and recA was in agreement with the results of ITS sequence analysis. The nodC gene sequence of CCBAU 25010T was identical to that of Rhizobium tropici CFN 299. DNA–DNA hybridization values for strain CCBAU 25010T ranged from 20.7 % (with Rhizobium mongolense USDA 1844T) to 34.4 % (with R. leguminosarum USDA 2370T). Cell protein SDS-PAGE, BOX-PCR and several phenotypic characteristics, such as use of sole carbon sources and antibiotic resistance, could differentiate the novel strains from defined Rhizobium species. We therefore propose that the novel strains reported in this study form a novel species, Rhizobium mesosinicum sp. nov., with the type strain CCBAU 25010T (=LMG 24135T =JCM 14777T).
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Paracoccus saliphilus sp. nov., a halophilic bacterium isolated from a saline soil
More LessA Gram-negative, coccoid to short rod-shaped, non-spore-forming, moderately halophilic bacterium, designated strain YIM 90738T, was isolated from a salt lake in Xinjiang province, north-west China, and was subjected to a polyphasic taxonomic study. The strain was non-motile and grew at pH 6.0–8.0 (optimal growth at pH 7.0), 10–55 °C (optimal growth at 37 °C) and salinities of 1–15 % NaCl (w/v, optimal growth at 8 % NaCl). Ubiquinone 10 was detected as the major respiratory quinone. The cellular fatty acid profile had C18 : 1 ω7c (80.4 % of the total) as the major component, similar to those of members of the genus Paracoccus. The nearest phylogenetic neighbour of strain YIM 90738T was the type strain of Paracoccus homiensis, as determined by 16S rRNA gene sequence analysis (97.5 % similarity). The level of DNA–DNA relatedness between P. homiensis DSM 17862T and strain YIM 90738T was 51.5 %. The G+C content of the genomic DNA of strain YIM 90738T was 60.3 mol%. On the basis of phenotypic and phylogenetic data and its genotypic distinctiveness, strain YIM 90738T (=CCTCC AB 206074T =KCTC 22163T) is proposed as the type strain of a novel species of the genus Paracoccus, Paracoccus saliphilus sp. nov.
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Bradyrhizobium pachyrhizi sp. nov. and Bradyrhizobium jicamae sp. nov., isolated from effective nodules of Pachyrhizus erosus
Several strains isolated from the legume Pachyrhizus erosus were characterized on the basis of diverse genetic, phenotypic and symbiotic approaches. These novel strains formed two groups closely related to Bradyrhizobium elkanii according to their 16S rRNA gene sequences. Strains PAC48T and PAC68T, designated as the type strains of these two groups, presented 99.8 and 99.1 % similarity, respectively, in their 16S rRNA gene sequences with respect to B. elkanii USDA 76T. In spite of these high similarity values, the analysis of additional phylogenetic markers such as atpD and glnII genes and the 16S–23S intergenic spacer (ITS) showed that strains PAC48T and PAC68T represented two separate novel species of the genus Bradyrhizobium with B. elkanii as their closest relative. Phenotypic differences among the novel strains isolated from Pachyrhizus and B. elkanii were found regarding the assimilation of carbon sources and antibiotic resistance. All these differences were congruent with DNA–DNA hybridization analysis which revealed 21 % genetic relatedness between strains PAC48T and PAC68T and 46 % and 25 %, respectively, between these strains and B. elkanii LMG 6134T. The nodD and nifH genes of strains PAC48T and PAC68T were phylogenetically divergent from those of bradyrhizobia species that nodulate soybean. Soybean was not nodulated by the novel Pachyrhizus isolates. Based on the genotypic and phenotypic data obtained in this study, the new strains represent two novel species for which the names Bradyrhizobium pachyrhizi sp. nov. (type strain PAC48T=LMG 24246T=CECT 7396T) and Bradyrhizobium jicamae sp. nov. (type strain PAC68T=LMG 24556T=CECT 7395T) are proposed.
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Roseibaca ekhonensis gen. nov., sp. nov., an alkalitolerant and aerobic bacteriochlorophyll a-producing alphaproteobacterium from hypersaline Ekho Lake
More LessA Gram-negative, aerobic rod was isolated from the hypersaline, heliothermal and meromictic Ekho Lake (East Antarctica) at a depth of 6 m. The novel strain (designated EL-50T) was oxidase-positive and weakly catalase-positive and metabolized a variety of carboxylic acids, alcohols, sugars and lipids. Cells of strain EL-50T had an absolute requirement for artificial seawater or NaCl. Optimum growth occurred at 16 °C and at pH values ranging from 7.0 to 9.5. A large in vivo absorption band at 865–866 nm indicated the production of bacteriochlorophyll (bchl) a. The predominant cellular fatty acid of strain EL-50T was 18 : 1ω7c, with 3-OH 14 : 1, 16 : 1ω9c, 16 : 0 and 18 : 1ω9c present in lower amounts. Fatty acids 16 : 0 and 18 : 1ω9c were probably amide-linked. The main polar lipids were diphosphatidylglycerol, phospatidylethanolamine, phosphatidylglycerol and phosphatidylcholine. Ubiquinone 10 was produced. The cell-wall diamino acid was meso-diaminopimelic acid. The DNA G+C content of strain EL-50T was 61 mol%. 16S rRNA gene sequence comparisons indicated that the novel isolate was phylogenetically most closely related to alkaliphilic Rhodobaca and Roseinatronobacter species (approximately 96 % 16S rRNA gene similarity). The organism had no particular relationship to any other cultivated members within the Alphaproteobacteria. The distinct morphological, physiological and genotypic differences from the previously described taxa studied supported the description of a new genus and novel species, for which the name Roseibaca ekhonensis gen. nov., sp. nov. is proposed. The type strain is EL-50T (=DSM 11469T=CECT 7235T).
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Ideonella azotifigens sp. nov., an aerobic diazotroph of the Betaproteobacteria isolated from grass rhizosphere soil, and emended description of the genus Ideonella
More LessStrain 1a22T, a nitrogen-fixing bacterium, was isolated from soil associated with the rhizosphere of a perennial grass growing in a fallow agricultural field in Ithaca, New York, USA. Analysis of the 16S rRNA gene sequence placed the strain in the Rubrivivax–Roseateles–Leptothrix–Azohydromonas–Aquincola–Ideonella branch of the Betaproteobacteria and the closest characterized relative was the type strain of Ideonella dechloratans (97.7 % 16S rRNA sequence similarity). Cells of strain 1a22T were Gram-negative, motile, straight rods, which formed polyhydroxybutyrate-like granules and were positive for oxidase and weakly positive for catalase. Cells were chemo-organotrophic, unable to grow by reduction of chlorate or nitrate and grew exclusively through aerobic respiration. Growth with mannitol on N-free solid media caused the strain to produce copious amounts of slime. The G+C content of the genomic DNA was 67.4 mol%. The major cellular fatty acids were C16 : 1 cis-9 and C16 : 0 and cells contained significant amounts of the hydroxy fatty acids C10 : 0 3-OH, C12 : 0 2-OH and C12 : 0 3-OH. Based on DNA–DNA hybridization studies, 16S rRNA gene sequence analysis, fatty acid analysis, and morphological and physiological characteristics, strain 1a22T represents a novel species in the genus Ideonella, for which the name Ideonella azotifigens sp. nov. is proposed. The type strain of Ideonella azotifigens is 1a22T (=JCM 15503T=DSM 21438T).
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Dokdonella ginsengisoli sp. nov., isolated from soil from a ginseng field, and emended description of the genus Dokdonella
A Gram-negative, aerobic, rod-shaped, non-motile, non-spore-forming bacterial strain, designated Gsoil 191T, was isolated from a soil sample from a ginseng field in Pocheon Province, South Korea, and was characterized taxonomically by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain Gsoil 191T belongs to the family Xanthomonadaceae and is related to Dokdonella fugitiva LMG 23001T (97.8 % sequence similarity) and Dokdonella koreensis KCTC 12396T (96.9 %). The G+C content of the genomic DNA was 68.7 mol%. The major respiratory quinone was Q-8 and the major fatty acids were iso-C17 : 1 ω9c (30.6 %), iso-C17 : 0 (21.6 %) and iso-C15 : 0 (13.0 %), supporting the affiliation of strain Gsoil 191T to the genus Dokdonella. DNA–DNA hybridization experiments showed that the DNA–DNA relatedness values between strain Gsoil 191T and its closest phylogenetic neighbours were below 40 %. The results of physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain Gsoil 191T from recognized species of the genus Dokdonella. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil 191T represents a novel species of the genus Dokdonella, for which the name Dokdonella ginsengisoli sp. nov. is proposed. The type strain is Gsoil 191T (=KCTC 12564T=DSM 17954T=CCUG 52462T).
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Dokdonella soli sp. nov., a gammaproteobacterium isolated from soil
An aerobic, Gram-negative, yellow-coloured, rod-shaped bacterial strain, designated KIS28-6T, was isolated from soil from Ulleung, an island located in the East Sea of Korea. A phylogenetic analysis revealed that strain KIS28-6T was a member of the genus Dokdonella, having 16S rRNA gene sequence similarities of 98.1 and 96.9 % with respect to Dokdonella fugitiva CIP 108692T and Dokdonella koreensis DSM 17203T, respectively. Strain KIS28-6T showed DNA–DNA hybridization values of 38 and 32 % with respect to D. fugitiva CIP 108692T and D. koreensis DSM 17203T, respectively. The major fatty acids (>10 %) were iso-C17 : 1 ω9c (35.7 %), iso-C17 : 0 (26.9 %) and iso-C15 : 0 (11.7 %), the major respiratory quinone was Q-8 and the DNA G+C content was 73.0 mol%. On the basis of the results obtained in this polyphasic taxonomic analysis, strain KIS28-6T represents a novel species of the genus Dokdonella, for which the name Dokdonella soli sp. nov. is proposed. The type strain is KIS28-6T (=KACC 12741T =JCM 15421T).
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Microvirga guangxiensis sp. nov., a novel alphaproteobacterium from soil, and emended description of the genus Microvirga
More LessA Gram-negative-staining bacterium, designated strain 25BT, was isolated from a soil sample from a rice field in Guangxi Province, China, and its taxonomic position was investigated by using a polyphasic approach. Cells were rod-shaped, non-spore-forming, non-motile and strictly aerobic. Strain 25BT grew optimally at 37 °C and pH 7.0. The predominant fatty acids of this soil isolate were C18 : 1 ω7c, C19 : 0 cyclo ω8c and C16 : 0. Phylogenetic analysis based on the almost-complete 16S rRNA gene sequence showed that strain 25BT formed a monophyletic clade with the type strain of Microvirga subterranea; the two organisms shared 97.2 % 16S rRNA gene sequence similarity. However, the two strains shared low DNA–DNA relatedness. Strain 25BT was also readily distinguishable from Microvirga subterranea DSM 14364T by various phenotypic characteristics. The combination of genotypic and phenotypic data suggests that the isolate represents a novel species of the genus Microvirga, for which the name Microvirga guangxiensis sp. nov. is proposed. The type strain is 25BT (=CGMCC 1.7666T=JCM 15710T).
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Emended description of the genus Polynucleobacter and the species Polynucleobacter necessarius and proposal of two subspecies, P. necessarius subsp. necessarius subsp. nov. and P. necessarius subsp. asymbioticus subsp. nov.
More LessHeckmann and Schmidt described the genus Polynucleobacter for bacterial endosymbionts of freshwater ciliates affiliated with the genus Euplotes, and the species Polynucleobacter necessarius for obligate endosymbionts living in the cytoplasm of Euplotes aediculatus. Pure cultures of the type strain could not be established due to the obligate nature of the symbiotic relationship between the endosymbionts and their hosts. Therefore, Polynucleobacter necessarius is one of a few bacterial species with validly published names that lack a deposited pure culture. Meanwhile, it was demonstrated that the endosymbionts used for the description of the type of Polynucleobacter necessarius are closely related to obligately free-living strains. Similarity values of the 16S rRNA gene sequences obtained from the endosymbionts in the ciliate culture and free-living isolates in the range 99.1–99.4 % indicate that these organisms belong to the same species. Here, we have emended the description of Polynucleobacter necessarius by characterization of free-living strains maintained as pure cultures. The species Polynucleobacter necessarius was characterized as having low G+C contents of the DNA (44–46 mol%), small genome sizes (1.5–2.5 Mbp) and a lack of motility. Because of distinct differences in lifestyle and the genome size of Polynucleobacter necessarius strains, we propose that two novel subspecies should be established, Polynucleobacter necessarius subsp. necessarius subsp. nov. [with a type, which is a description based on endosymbionts in the culture ‘stock 15’ of the ciliate E. aediculatus (ATCC 30859)] and Polynucleobacter necessarius subsp. asymbioticus subsp. nov. [with the type strain QLW-P1DMWA-1T (=DSM 18221T=CIP 109841T)], for the obligate endosymbionts of E. aediculatus and Euplotes harpa and obligately free-living strains, respectively.
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Psychrobacter lutiphocae sp. nov., isolated from the faeces of a seal
More LessThe taxonomic status of a Gram-negative-staining bacterium, isolated from the faeces of a seal, was investigated using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that the novel isolate formed a distinct phyletic line within the genus Psychrobacter, displaying >3.3 % sequence divergence with other known Psychrobacter species. The generic assignment was confirmed by chemotaxonomic data, which revealed a fatty acid profile that included straight-chain saturated, unsaturated and 3-hydroxylated fatty acids, with C18 : 1 ω9c as the major fatty acid. A ubiquinone with eight isoprene units (Q-8) was the predominant respiratory quinone and spermidine was the predominant polyamine. The novel isolate was distinguished from other members of the genus Psychrobacter by using a set of phenotypic properties. On the basis of phenotypic and phylogenetic considerations, it is proposed that the new isolate represents a novel species, for which the name Psychrobacter lutiphocae sp. nov. is proposed. Strain IMMIB L-1110T (=DSM 21542T=CCUG 56590T) is the type strain.
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Novosphingobium indicum sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from a deep-sea environment
More LessA novel polycyclic aromatic hydrocarbon (PAH)-degrading bacterium, strain H25T, which was isolated from deep-sea water of the Indian Ocean, was studied phenotypically, genotypically and phylogenetically. Strain H25T can utilize several PAHs including phenanthrene and fluoranthene as sole carbon sources. The 16S rRNA gene sequence of strain H25T showed the highest similarity with that of Novosphingobium naphthalenivorans TUT562T (96.3 %), and showed lower similarities (92.1–96.0 %) with other members of the genus Novosphingobium. The major fatty acids of strain H25T were C14 : 0 2-OH (3.2 %), C16 : 0 (13.6 %), C16 : 1 ω7c (5.2 %), C18 : 0 (13.4 %) and C18 : 1 ω7c (57.0 %), which accounted for 92.3 % of the total fatty acids. It had ubiquinone 10 as the major respiratory quinone and spermidine as the major polyamine. All these characteristics were consistent with those of recognized Novosphingobium species. Results of DNA–DNA hybridization experiments and BOX-PCR fingerprint comparisons also indicate that strain H25T represents a novel Novosphingobium species, for which the name Novosphingobium indicum sp. nov. is proposed. The type strain is H25T (=MCCC 1A01080T =CGMCC 1.6784T =LMG 24713T).
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Phaeospirillum chandramohanii sp. nov., a phototrophic alphaproteobacterium with carotenoid glycosides
More LessA Gram-negative, spiral-shaped, phototrophic, purple non-sulfur bacterial strain, designated JA145T, was isolated from a freshwater habitat. Cells of strain JA145T were motile by means of a monopolar flagellum. Intracellular photosynthetic membranes were of the stacked type. Bacteriochlorophyll a and the carotenoid lycopene and its glucosides were present as photosynthetic pigments. There was no vitamin requirement for strain JA145T. The predominant cellular fatty acids were C16 : 1 ω7c/C16 : 1 ω6c (22.24 %), C16 : 0 (22.97 %) and C18 : 1 ω7c (43.24 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain JA145T clustered with species of the genus Phaeospirillum, in the class Alphaproteobacteria. The highest sequence similarities of strain JA145T were found with the type strains of Phaeospirillum fulvum (96.12 %) and Phaeospirillum molischianum (96.19 %). Based on the 16S rRNA gene sequence analysis and the morphological and physiological characteristics, strain JA145T is considered to represent a novel species, for which the name Phaeospirillum chandramohanii sp. nov. is proposed. The type strain is JA145T (=JCM 14933T=KCTC 5703T=NBRC 104961T).
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Vibrio hangzhouensis sp. nov., isolated from sediment of the East China Sea
More LessStrain CN83T, a Gram-negative, aerobic, rod-shaped bacterium, was isolated from sediment of the East China Sea. The isolate was catalase- and oxidase-positive and cells were motile by means of polar flagella. The DNA G+C content was 44.9 mol%. The major fatty acids were C16 : 1 ω7c and/or iso-C15 : 0 2-OH, C16 : 0, C18 : 1 ω7c, C14 : 0 and C12 : 0. 16S rRNA gene sequence analysis showed that strain CN83T belonged to the genus Vibrio and had the highest sequence similarity to Vibrio agarivorans (98.4 %) and Vibrio campbellii (97.8 %). Phylogenetic analysis revealed that strain CN83T formed a monophyletic clade adjacent to the type strain of V. agarivorans. The DNA–DNA hybridization values of strain CN83T with V. agarivorans DSM 13756T and V. campbellii DSM 19270T were 44.6 and 25.5 %, respectively. On the basis of the phenotypic and genotypic data, strain CN83T represents a novel species of the genus Vibrio, for which the name Vibrio hangzhouensis sp. nov. is proposed. The type strain is CN83T (=CGMCC 1.7062T=JCM 15146T).
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- Eukaryotic Micro-Organisms
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Candida materiae sp. nov., a yeast species isolated from rotting wood in the Atlantic Rain Forest
More LessThree strains of a novel yeast species, Candida materiae sp. nov., were isolated from rotting wood in an Atlantic rain forest site in Brazil. Analysis of the sequences of the D1/D2 domains of the large-subunit rDNA showed that this species belonged to the Spathaspora clade and was related to Candida jeffriesii and Spathaspora passalidarum. Unlike C. jeffriesii and S. passalidarum, C. materiae sp. nov. did not ferment xylose. The type strain of C. materiae sp. nov. is UFMG-07-C15.1BT (=CBS 10975T=CBMAI 956T).
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- Evolution, Phylogeny And Biodiversity
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Phylogenetic analysis and identification of Aeromonas species based on sequencing of the cpn60 universal target
More LessAn analysis of the universal target (UT) sequence from the cpn60 gene was performed in order to evaluate its usefulness in phylogenetic and taxonomic studies and as an identification marker for the genus Aeromonas. Sequences of 555 bp, corresponding to the UT region, were obtained from a collection of 35 strains representing all of the species and subspecies of Aeromonas. From the analysis of these sequences, a range of divergence of 0–23.3 % was obtained, with a mean of 11.2±0.9 %. Comparative analyses between cpn60 and gyrB, rpoD and 16S rRNA gene sequences were carried out from the same Aeromonas strain collection. Sequences of the cpn60 UT region showed similar discriminatory power to gyrB and rpoD sequences. The phylogenetic relationships inferred from cpn60 sequence distances indicated an excellent correlation with the present affiliation of Aeromonas species with the exception of Aeromonas hydrophila subsp. dhakensis, which appeared in a separate phylogenetic line, and Aeromonas sharmana, which exhibited a very loose phylogenetic relationship to the genus Aeromonas. Sequencing of cpn60 from 33 additional Aeromonas strains also allowed us to establish intra- and interspecific threshold values. Intraspecific divergence rates were ≤3.5 %, while interspecific divergence rates fell between 3.7 and 16.9 %, excluding A. sharmana. In this study, cpn60 UT sequencing was shown to be a universal, useful, simple and rapid method for the identification and phylogenetic affiliation of Aeromonas strains.
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rRNA operons and genome size of ‘Candidatus Liberibacter americanus’, a bacterium associated with citrus huanglongbing in Brazil
More LessHuanglongbing is one of the most severe diseases of citrus worldwide and is associated with ‘Candidatus (Ca.) Liberibacter africanus’ in Africa, ‘Ca. Liberibacter asiaticus’ in Asia and the Americas (Brazil, USA and Cuba) and ‘Ca. Liberibacter americanus’ (Lam) in Brazil. In the absence of axenic cultures, genetic information on liberibacters is scarce. The sequences of the entire 23S rRNA and 5S rRNA genes from Lam have now been obtained, using a consensus primer designed on known tRNAMet sequences of rhizobia. The size of the Lam genome was determined by PFGE, using Lam-infected periwinkle plants for bacterial enrichment, and was found to be close to 1.31 Mbp. In order to determine the number of ribosomal operons on the Lam genome, probes designed to detect the 16S rRNA gene and the 3′ end of the 23S rRNA gene were developed and used for Southern hybridization with I-CeuI-treated genomic DNA. Our results suggest that there are three ribosomal operons in a circular genome. Lam is the first liberibacter species for which such data are available.
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- International Committee On Systematics Of Prokaryotes
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Proposed minimal standards for describing new taxa of aerobic, endospore-forming bacteria
Minimal standards for describing new taxa within the aerobic endospore-forming bacteria are proposed, following Recommendation 30b of the Bacteriological Code (1990 Revision). These minimal standards are recommended as guidelines to assist authors in the preparation of descriptions for novel taxa. They encourage broad polyphasic characterization and the construction of descriptions that are practically useful in routine diagnostic laboratories. The proposals have been endorsed by the Subcommittee on the Taxonomy of the Genus Bacillus and Related Organisms of the International Committee on Systematics of Prokaryotes.
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- Request For An Opinion
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Emended descriptions of the genera Myxococcus and Corallococcus, typification of the species Myxococcus stipitatus and Myxococcus macrosporus and a proposal that they be represented by neotype strains. Request for an Opinion
More LessThe genus Corallococcus was separated from the genus Myxococcus mainly on the basis of differences in morphology and consistency of swarms and fruiting bodies of the respective members. Phylogenetic, chemotaxonomic and physiological evidence is presented here that underpins the separate status of these phylogenetically neighbouring genera. Emended descriptions of the two genera are presented. The data also suggest that the species Corallococcus macrosporus belongs to the genus Myxococcus. To the best of our knowledge, the type strains of the species Myxococcus macrosporus and Myxococcus stipitatus are not available from any established culture collection or any other source. A Request for an Opinion is made regarding the proposal that strain Cc m8 (=DSM 14697 =CIP 109128) be formally recognized as the neotype strain for the species Myxococcus macrosporus, replacing the designated type strain Windsor M271T, and that strain Mx s8 (=DSM 14675 =JCM 12634) be formally recognized as the neotype strain for the species Myxococcus stipitatus, replacing the designated type strain Windsor M78T.
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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 1 (1951)