- Volume 59, Issue 3, 2009
Volume 59, Issue 3, 2009
- Validation List
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List of new names and new combinations previously effectively, but not validly, published
The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper, to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries (i.e. documents certifying deposition and availability of type strains). It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors' names will be included in the author index of the present issue. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.
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- Notification List
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Notification that new names and new combinations have appeared in volume 58, part 12, 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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Desmospora activa gen. nov., sp. nov., a thermoactinomycete isolated from sputum of a patient with suspected pulmonary tuberculosis, and emended description of the family Thermoactinomycetaceae Matsuo et al. 2006
More LessA novel Gram-positive, aerobic, catalase-positive, filamentous micro-organism, designated strain IMMIB L-1269T, originating from sputum was characterized using phenotypic and molecular taxonomic methods. It showed cell-wall chemotype III, phospholipid type PII (with phosphatidylethanolamine as the diagnostic phospholipid) and contained an unsaturated menaquinone with seven isoprene units (MK-7) as the predominant isoprenoid quinone. It synthesized long-chain cellular fatty acids of the straight-chain saturated, monounsaturated and iso- and anteiso-branched types (with iso-C15 : 0, C16 : 0 and iso-C17 : 0 predominating) and possessed a DNA G+C content of 49.3 mol%. On the basis of its morphological, biochemical and chemical characteristics, strain IMMIB L-1269T did not conform to any presently recognized taxon. Comparative analyses based on 16S rRNA gene sequences confirmed the distinctiveness of the isolate, as it displayed sequence-divergence values greater than 7.7 % with respect to recognized Gram-positive taxa. Phylogenetic treeing analysis served to reinforce the view that strain IMMIB L-1269T was distinct from recognized taxa, as it formed a relatively long subline branching within a 16S rRNA gene sequence cluster that encompassed the genera Thermoactinomyces, Laceyella, Mechercharimyces, Thermoflavimicrobium, Planifilum, Seinonella and Shimazuella of the family Thermoactinomycetaceae. On the basis of phenotypic and molecular phylogenetic evidence, strain IMMIB L-1269T represents a novel genus and species, for which the name Desmospora activa gen. nov., sp. nov. is proposed. The type strain of Desmospora activa is strain IMMIB L-1269T (=DSM 45169T =CCUG 55916T). An emended description of the family Thermoactinomycetaceae is also given.
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Streptomyces xiamenensis sp. nov., isolated from mangrove sediment
More LessActinomycete strain MCCC 1A01550T, isolated from the national mangrove reserve in Fujian Province, China, was determined to belong to the genus Streptomyces based on a polyphasic approach. The cell wall of the novel strain contained ll-diaminopimelic acid and galactose. The predominant menaquinones were MK-9(H4) and MK-9(H6) and the major fatty acids were iso-C16 : 0, cis9-C16 : 1 and C16 : 0. The diagnostic phospholipid was phosphatidylethanolamine. The DNA G+C content of the novel strain was 71.6 mol%. Phylogenetic analysis of 16S rRNA gene sequences confirmed the separation of the novel strain from recognized members of the genus Streptomyces available in public databases. DNA–DNA relatedness values between strain MCCC 1A01550T and the type strains of three related species ranged from 21.29 % to 43.38 %. Based on its phenotypic and genotypic characteristics, strain MCCC 1A01550T (=DSM 41903T=CGMCC 4.3534T) represents the type strain of a novel species, for which the name Streptomyces xiamenensis sp. nov. is proposed.
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Amycolatopsis marina sp. nov., an actinomycete isolated from an ocean sediment
A Gram-positive, aerobic, non-motile actinobacterium, designated strain Ms392AT, was isolated from an ocean-sediment sample collected from the South China Sea. The isolate contained chemical markers that supported chemotaxonomic assignment to the genus Amycolatopsis. On the basis of an analysis of 16S rRNA gene sequence similarities, strain Ms392AT represents a novel subclade within the genus Amycolatopsis, with Amycolatopsis palatopharyngis 1BDZT as its closest phylogenetic neighbour (99.4 % similarity). However, DNA–DNA hybridization demonstrated that strain Ms392AT was distinct from A. palatopharyngis AS 4.1729T (48.6 % relatedness). The polyphasic analysis demonstrated that the ocean isolate can be clearly distinguished from recognized species of the genus Amycolatopsis. Therefore, strain Ms392AT represents a novel species of the genus Amycolatopsis, for which the name Amycolatopsis marina sp. nov. is proposed. The type strain is Ms392AT (=CGMCC 4.3568T =NBRC 104263T).
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Glaciibacter superstes gen. nov., sp. nov., a novel member of the family Microbacteriaceae isolated from a permafrost ice wedge
Gram-positive, aerobic, non-spore-forming, irregular rod-shaped bacteria, designated strains AHU1791T and AHU1810, were isolated from a permafrost ice wedge in Alaska. Cells were motile by means of a polar flagellum. The strains were psychrophilic, growing at −5 to 25 °C. Phylogenetic analysis of 16S rRNA gene sequences indicated that the ice-wedge isolates formed a clade distinct from other genera affiliated with the family Microbacteriaceae. The novel strains showed highest levels of 16S rRNA gene sequence similarity with members of the genera Agreia and Subtercola (95.6–95.9 %). The level of 16S rRNA gene sequence similarity between strains AHU1791T and AHU1810 was 99.8 %. The cell-wall peptidoglycan type of the two strains was B2γ, containing 2,4-diaminobutyric acid as the diagnostic amino acid. The predominant menaquinones were MK-12 and MK-13 (strain AHU1791T) and MK-11 and MK-12 (strain AHU1810). The major fatty acids of the two strains were 12-methyl tetradecanoic acid (anteiso-C15 : 0), 14-methyl hexadecanoic acid (anteiso-C17 : 0), 14-methyl pentadecanoic acid (iso-C16 : 0) and 13-methyl tetradecanoic acid (iso-C15 : 0). The DNA G+C contents of strains AHU1791T and AHU1810 were approximately 65 mol%. These phenotypic characteristics differentiated the ice-wedge strains from their closest phylogenetic neighbours, namely Subtercola boreus and the two recognized species of the genus Agreia. The sequences of the housekeeping genes coding for DNA gyrase subunit B (gyrB), RNA polymerase subunit B (rpoB) and recombinase A (recA) were almost identical between strains AHU1791T and AHU1810. Although the predominant menaquinones found in strains AHU1791T and AHU1810 were different, no other distinct differences were found with regard to other phenotypic and genotypic characteristics, indicating that the two strains were members of the same species. Accordingly, strains AHU1791T and AHU1810 are considered to represent a single novel species of a new genus, for which the name Glaciibacter superstes gen. nov., sp. nov. is proposed. The type strain of Glaciibacter superstes is AHU1791T (=DSM 21135T =NBRC 104264T).
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Emended description of Actinomyces naeslundii and descriptions of Actinomyces oris sp. nov. and Actinomyces johnsonii sp. nov., previously identified as Actinomyces naeslundii genospecies 1, 2 and WVA 963
More LessActinomyces naeslundii is an important early colonizer in the oral biofilm and consists of three genospecies (1, 2 and WVA 963) which cannot be readily differentiated using conventional phenotypic testing or on the basis of 16S rRNA gene sequencing. We have investigated a representative collection of type and reference strains and clinical and oral isolates (n=115) and determined the partial gene sequences of six housekeeping genes (atpA, rpoB, pgi, metG, gltA and gyrA). These sequences identified the three genospecies and differentiated them from Actinomyces viscosus isolated from rodents. The partial sequences of atpA and metG gave best separation of the three genospecies. A. naeslundii genospecies 1 and 2 formed two distinct clusters, well separated from both genospecies WVA 963 and A. viscosus. Analysis of the same genes in other oral Actinomyces species (Actinomyces gerencseriae, A. israelii, A. meyeri, A. odontolyticus and A. georgiae) indicated that, when sequence data were obtained, these species each exhibited <90 % similarity with the A. naeslundii genospecies. Based on these data, we propose the name Actinomyces oris sp. nov. (type strain ATCC 27044T =CCUG 34288T) for A. naeslundii genospecies 2 and Actinomyces johnsonii sp. nov. (type strain ATCC 49338T =CCUG 34287T) for A. naeslundii genospecies WVA 963. A. naeslundii genospecies 1 should remain as A. naeslundii sensu stricto, with the type strain ATCC 12104T =NCTC 10301T =CCUG 2238T.
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Actinomadura miaoliensis sp. nov., a thermotolerant polyester-degrading actinomycete
More LessAn actinomycete, strain BC 44T-5T, with the ability to degrade poly(d-3-hydroxybutyrate) was isolated from a soil sample collected from Miaoli County, Taiwan. The isolate displayed substrate mycelia and short spore chains were borne on the aerial mycelia. Spores were non-motile, round, 1 μm in diameter and spiny. The aerial spore mass was blue. Strain BC 44T-5T had meso-diaminopimelic acid as the diagnostic diamino acid of the cell-wall peptidoglycan. Whole-cell sugars of the novel strain were identified as glucose, galactose and madurose. Diphosphatidylglycerol and phosphatidylinositol were detected. The predominant menaquinones were MK-9(H4) and MK-9(H2). Mycolic acids were not detected. Major cellular fatty acids were iso-C16 : 0 (14.82 %), C16 : 0 (14.63 %), C17 : 0 (13.79 %) and 10-methyl-C17 : 0 (23.77 %.) The DNA G+C content of strain BC 44T-5T was 70.6 mol%. On the basis of phenotypic and genotypic data, it is proposed that strain BC 44T-5T (=FIRDI 002T=BCRC 16873T=LMG 24335T) should be classified as the type strain of a novel species of the genus Actinomadura, Actinomadura miaoliensis sp. nov.
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Actinomyces massiliensis sp. nov., isolated from a patient blood culture
More LessGram-positive, non-spore-forming rods (strain 4401292T) were isolated from a human blood sample. Based on cellular morphology and the results of biochemical tests, this strain was tentatively identified as belonging to an undescribed species of the genus Actinomyces. Phylogenetic analysis based on 16S rRNA gene sequence comparison showed that the bacterium was related closely to Actinomyces gerencseriae (95.1 % 16S rRNA gene sequence similarity), Actinomyces israelii (95.2 %), Actinomyces oricola (95.2 %), Actinomyces ruminicola (93.3 %) and Actinomyces dentalis (91.4 %). The predominant fatty acids were C18 : 1ω9c and C16 : 0. On the basis of phenotypic data and phylogenetic inference, the novel species Actinomyces massiliensis sp. nov. is proposed; the type strain is 4401292T (=CSUR P18T=CCUG 53522T).
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Kineosporia babensis sp. nov., isolated from plant litter in Vietnam
More LessThree actinomycetes, designated strains VN05A0342, VN05A0351 and VN05A0415T, were isolated from plant-litter samples collected in the north of Vietnam and examined in a polyphasic taxonomic study. Phylogenetic analysis based on the 16S rRNA gene sequences showed that these isolates were most closely related to the type strain of Kineosporia mikuniensis (98.5 % sequence similarity). Morphological properties (the formation of spore domes and motile spores) and chemotaxonomic data supported the assignment of the three isolates to the genus Kineosporia. The isolates all contained the following: meso-diaminopimelic acid in the peptidoglycan (with small amounts of the ll isomer); ribose, mannose, galactose and glucose as the whole-cell sugars; MK-9(H4) as the predominant isoprenoid quinone; C18 : 1 and C16 : 0 as the major cellular fatty acids; and phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol and phosphatidylinositol as the phospholipids. The high DNA–DNA relatedness (>71 %) among the three isolates showed that they represented a single species. On the other hand, the DNA–DNA relatedness between the novel isolates and all type strains of Kineosporia species was less than 46 %. The physiological properties of our isolates were distinct from those of all of the Kineosporia species with validly published names, e.g. decomposition of l-tyrosine and aesculin and the utilization of raffinose and d-arabitol. Therefore, strains VN05A0342, VN05A0351 and VN05A0415T represent a novel species of the genus Kineosporia, for which the name Kineosporia babensis sp. nov. is proposed. The type strain is VN05A0415T (=VTCC-A-0961T =NBRC 104154T).
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Saccharopolyspora halophila sp. nov., a novel halophilic actinomycete isolated from a saline lake in China
More LessA halophilic actinomycete strain, designated YIM 90500T, was isolated from a saline lake in Xinjiang province, north-west China and subjected to a polyphasic taxonomic study. Good growth of the novel isolate occurred at 28–37 °C, pH 7–8 and with 10–15 % (w/v) NaCl; no growth occurred without any salts. Strain YIM 90500T contained meso-diaminopimelic acid with glucose, arabinose and ribose as the whole-cell sugars. The major phospholipids were phosphatidylcholine and diphosphatidylglycerol. MK-9(H4) was the predominant menaquinone. The major fatty acids were iso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The chemotaxonomic data together with the morphological properties of strain YIM 90500T consistently assigned the strain as belonging to the genus Saccharopolyspora. Phylogenetic analysis based on 16S rRNA gene sequences further revealed that strain YIM 90500T formed a distinct phyletic lineage in the genus Saccharopolyspora and showed low 16S rRNA gene similarities (<96.4 %) with other species of the genus. On the basis of the evidence from the polyphasic study, a novel species, Saccharopolyspora halophila sp. nov., is proposed. The type strain is YIM 90500T (=DSM 45007T=KCTC 19162T).
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Pseudonocardia endophytica sp. nov., isolated from the pharmaceutical plant Lobelia clavata
An endophytic actinomycete strain, designated YIM 56035T, was isolated from the inner tissue of the traditional Chinese medicinal plant Lobelia clavata. The strain stained Gram-positive, was aerobic and exhibited branching, white aerial mycelium and yellowish-brown substrate mycelium. The strain formed spore chains on aerial hyphae. The G+C content of the genomic DNA was 70.3 mol%. On the basis of morphological, physiological, chemotaxonomic and phylogenetic characteristics, strain YIM 56035T was assigned to the genus Pseudonocardia. Analysis of 16S rRNA gene sequences showed 98.5, 97.3, 97.3 and 97.1 % similarity to the closely related type strains Pseudonocardia kongjuensis LM 157T, Pseudonocardia autotrophica IMSNU 20050T, Pseudonocardia ammonioxydans H9T and Pseudonocardia compacta IMSNU 20111T, respectively. The results of DNA–DNA hybridizations and comparison of some phenotypic characteristics revealed that the strain represents a novel species of the genus Pseudonocardia. The name Pseudonocardia endophytica sp. nov. is proposed, with the type strain YIM 56035T (=DSM 44969T =CCTCC AA 206026T =KCTC 19150T).
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Stackebrandtia albiflava sp. nov. and emended description of the genus Stackebrandtia
More LessA novel actinomycete, designated YIM 45751T, was isolated from a soil sample collected from the Xishuang Banna tropical rainforest, Yunnan province, south-west China, and was subjected to a polyphasic taxonomic study. The cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. Whole-cell hydrolysates contained ribose, xylose and glucose. The predominant menaquinones were MK-10(H4), MK-10(H6), MK-11(H4) and MK-11(H6). The polar lipids were diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and three unknown phospholipids. 16S rRNA gene sequence analysis showed that Stackebrandtia nassauensis DSM 44728T was the closest phylogenetic neighbour (95.8 % 16S rRNA gene sequence similarity). On the basis of phylogenetic and some common chemotaxonomic data, the isolate should belong to the genus Stackebrandtia. However, phylogenetic analysis and comparison of physiological and chemotaxonomic characteristics demonstrated that the isolate is distinct from S. nassauensis DSM 44728T. Strain YIM 45751T represents a separate species of the genus Stackebrandtia, for which the name Stackebrandtia albiflava sp. nov. is proposed. The type strain is YIM 45751T (=DSM 45044T=CCTCC AA 206003T). Furthermore, the description of the genus Stackebrandtia is also required to be emended.
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An update of the structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the proposal of two new suborders and four new families and emended descriptions of the existing higher taxa
More LessThe higher ranks of the class Actinobacteria were proposed and described in 1997. At each rank, the taxa were delineated from each other solely on the basis of 16S rRNA gene sequence phylogenetic clustering and taxon-specific 16S rRNA signature nucleotides. In the past 10 years, many novel members have been assigned to this class while, at the same time, some members have been reclassified. The new 16S rRNA gene sequence information and the changes in phylogenetic positions of some taxa influence decisions about which 16S rRNA nucleotides to define as taxon-specific. As a consequence, the phylogenetic relationships of Actinobacteria at higher levels may need to be reconstructed. Here, we present new 16S rRNA signature nucleotide patterns of taxa above the family level and indicate the affiliation of genera to families. These sets replace the signatures published in 1997. In addition, Actinopolysporineae subord. nov. and Actinopolysporaceae fam. nov. are proposed to accommodate the genus Actinopolyspora, Kineosporiineae subord. nov. and Kineosporiaceae fam. nov. are proposed to accommodate the genera Kineococcus, Kineosporia and Quadrisphaera, Beutenbergiaceae fam. nov. is proposed to accommodate the genera Beutenbergia, Georgenia and Salana and Cryptosporangiaceae fam. nov. is proposed to accommodate the genus Cryptosporangium. The families Nocardiaceae and Gordoniaceae are proposed to be combined in an emended family Nocardiaceae. Emended descriptions are also proposed for most of the other higher taxa.
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- Bacteroidetes
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Psychroflexus sediminis sp. nov., a mesophilic bacterium isolated from salt lake sediment in China
A novel Gram-negative, mesophilic, slightly halophilic, catalase- and oxidase-positive, obligately aerobic bacterium, designated strain YIM-C238T, was isolated from a sediment sample from a salt lake in the Qaidam Basin, north-west China. Cells were non-sporulating, non-motile, straight to slightly curved rods. Coccoid bodies and filaments of varying length developed in older cultures. Growth occurred with 0.5–6 % (w/v) NaCl [optimum, 2–3 % (w/v) NaCl], at pH 6.0–10.0 (optimum, pH 7.0–8.0) and at 10–40 °C (optimum, 25–30 °C). The major cellular fatty acids were anteiso-C15 : 0, 3-OH iso-C16 : 0 and anteiso-C15 : 1 ω10c, and menaquinone 6 was the sole respiratory quinone. Non-diffusible carotenoid pigments were produced. Flexirubin pigments were absent. The genomic DNA G+C content was 35.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YIM-C238T should be assigned to the genus Psychroflexus. The sequence similarities between the isolate and the type strains of members of the genus Psychroflexus were in the range 95.5–97.0 %. The combination of phylogenetic analysis, DNA–DNA hybridization data, phenotypic characteristics and chemotaxonomic differences supported the view that strain YIM-C238T represents a novel species of the genus Psychroflexus, for which the name Psychroflexus sediminis sp. nov. is proposed. The type strain is YIM-C238T (=CCTCC AA 207030T=KCTC 22166T).
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- Firmicutes And Related Organisms
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Clostridium lavalense sp. nov., a glycopeptide-resistant species isolated from human faeces
Two vancomycin-resistant, strictly anaerobic, Gram-positive, rod-shaped, spore-forming organisms (strains CCRI-9842T and CCRI-9929) isolated from human faecal specimens in Québec, Canada, and Australia were characterized using phenotypic, biochemical and molecular taxonomic methods. Pairwise analysis of the 16S rRNA gene sequences showed that both strains were closely related to each other genetically (displaying 99.2 % sequence similarity) and represented a previously unknown subline within the Clostridium coccoides rRNA group of organisms (rRNA cluster XIVa of the genus Clostridium). Strains CCRI-9842T and CCRI-9929 used carbohydrates as fermentable substrates, producing acetic acid as the major product of glucose metabolism. The novel strains were most closely related to Clostridium asparagiforme, Clostridium bolteae and Clostridium clostridioforme, but morphological, biochemical and phylogenetic studies demonstrated that they represent a previously unidentified species of the genus Clostridium. This was confirmed by the unique cellular fatty acid composition of strains CCRI-9842T and CCRI-9929. Therefore, on the basis of data from the polyphasic taxonomic analysis, it is proposed that strains CCRI-9842T and CCRI-9929 represent a novel species of the genus Clostridium, for which the name Clostridium lavalense sp. nov. is proposed. The type strain is CCRI-9842T (=CCUG 54291T=JCM 14986T=NML 03-A-015T).
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Streptococcus plurextorum sp. nov., isolated from pigs
More LessBiochemical and molecular genetic studies were performed on an unknown Gram-positive, catalase-negative, coccus-shaped organism isolated from clinical samples from pigs. On the basis of the results of cellular morphological and biochemical tests, the organism was identified as a streptococcal species. 16S rRNA gene sequence comparisons confirmed its identification as a member of the genus Streptococcus, but the organism was distinct from any recognized species of this genus. The closest phylogenetic relative of the unknown organism corresponded to Streptococcus suis NCTC 10234T (97.2 % 16S rRNA gene sequence similarity) and this phylogenetic position was confirmed by analysis of rpoB and sodA sequences. DNA–DNA hybridization studies showed that the unidentified organism produced a DNA reassociation value of 36.6 % with respect to S. suis NCTC 10234T. The novel bacterium was distinguished from S. suis and other Streptococcus species using biochemical tests. On the basis of phenotypic and phylogenetic data, the unidentified organism represents a novel species of the genus Streptococcus, for which the name Streptococcus plurextorum sp. nov. is proposed. The type strain is 1956-02T (=CECT 7308T=CCUG 52972T).
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Paenibacillus thailandensis sp. nov. and Paenibacillus nanensis sp. nov., xylanase-producing bacteria isolated from soil
More LessTwo strains of xylanase-producing bacteria, S3-4AT and MX2-3T, isolated from soils in Thailand, were characterized on the basis of their phenotypic and chemotaxonomic characteristics, DNA–DNA relatedness and 16S rRNA gene sequences. The novel strains were Gram-positive, facultatively anaerobic, spore-forming, rod-shaped bacteria. They contained meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. The DNA G+C contents of strains S3-4AT and MX2-3T were 52.7 and 52.9 mol%, respectively. The major isoprenoid quinone was MK-7. The dominant cellular fatty acids were anteiso-C15 : 0 and iso-C16 : 0. Phylogenetic analyses using 16S rRNA gene sequences showed that both novel strains were affiliated to the genus Paenibacillus. Strains S3-4AT and MX2-3T were closely related to Paenibacillus agaridevorans DSM 1355T with 97 % and 97.3 % gene sequence similarities, respectively. The DNA–DNA relatedness between strains S3-4AT, MX2-3T and P. agaridevorans DSM 1355T was low (6.0–30.3 %). The novel strains could be clearly distinguished from P. agaridevorans DSM 1355T by physiological and biochemical characteristics. Therefore, these two strains represent novel species of the genus Paenibacillus, for which the names Paenibacillus thailandensis sp. nov. (type strain S3-4AT=KCTC 13043T=PCU 275T=TISTR 1827T) and Paenibacillus nanensis sp. nov. (type strain MX2-3T=KCTC 13044T=PCU 276T=TISTR 1828T) are proposed.
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Reclassification of Pediococcus dextrinicus (Coster and White 1964) Back 1978 (Approved Lists 1980) as Lactobacillus dextrinicus comb. nov., and emended description of the genus Lactobacillus
More LessThe taxonomic status of Pediococcus dextrinicus is described and transfer of the species to the genus Lactobacillus, with the name Lactobacillus dextrinicus comb. nov., is proposed. This reclassification is supported by multilocus sequence analysis of the 16S rRNA gene and Cpn60, PheS, RecA and RpoA proteins. The mode of cell division and existing phenotypic information also show that P. dextrinicus does not belong to the genus Pediococcus, but rather to the genus Lactobacillus. As such, we propose that Pediococcus dextrinicus is reclassified as Lactobacillus dextrinicus comb. nov. (type strain ATCC 33087T=DSM 20335T=JCM 5887T=LMG 11485T=NCDO 1561T).
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- Other Bacteria
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Psychrilyobacter atlanticus gen. nov., sp. nov., a marine member of the phylum Fusobacteria that produces H2 and degrades nitramine explosives under low temperature conditions
More LessA Gram-negative and obligately anaerobic marine bacterium, strain HAW-EB21T, was isolated in a previous study from marine sediment from the Atlantic Ocean, near Halifax Harbor, Canada, and found to have the potential to degrade both hexahydro-1,3,5-trinitro-1,3,5-triazine and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine. In the present study, phylogenetic analyses showed that strain HAW-EB21T was only distantly related to the genera Propionigenium and Ilyobacter with 6.6–7.5 % and 8.2–10.5 % dissimilarity as measured by 16S rRNA and 23S rRNA gene sequence analyses, respectively. Strain HAW-EB21T displayed unique properties in being psychrotrophic (18.5 °C optimum) and unable to utilize any of the carbon substrates (succinate, l-tartrate, 3-hydroxybutyrate, quinate or shikimate) used for isolating members of the genera Propionigenium and Ilyobacter. Strain HAW-EB21T utilized glucose, fructose, maltose, N-acetyl-d-glucosamine, citrate, pyruvate, fumarate and Casitone as carbon sources and produced H2 and acetate as the major fermentation products. Cells grown at 10 °C produced C15 : 1 (30 %), C16 : 1 ω7 (15 %) and C16 : 0 (16 %) as major membrane fatty acids. The novel strain had a genomic DNA G+C content of 28.1 mol%, lower than the values of the genera Ilyobacter and Propionigenium. Based on the present results, the novel isolate is suggested to be a member of a new genus for which the name Psychrilyobacter atlanticus gen. nov., sp. nov. is proposed. The type strain of the type species is HAW-EB21T (=DSM 19335T=JCM 14977T).
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- Proteobacteria
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Dyella ginsengisoli sp. nov., isolated from soil of a ginseng field in South Korea
More LessA Gram-negative, aerobic, yellow-pigmented, non-spore-forming, motile, rod-shaped bacterium, designated strain Gsoil 3046T, was isolated from soil from a ginseng field in Pocheon Province, South Korea, and was characterized taxonomically by using a polyphasic approach. A comparative analysis of 16S rRNA gene sequences revealed that strain Gsoil 3046T belongs to the family Xanthomonadaceae in the Gammaproteobacteria. The greatest sequence similarity was found with respect to Dyella koreensis KCTC 12359T (97.7 %), Dyella japonica IAM 15069T (97.4 %), Frateuria aurantia DSM 6220T (96.7 %), Fulvimonas soli LMG 19981T (96.2 %) and Luteibacter rhizovicinus DSM 16549T (96.0 %). The phylogenetic distances from other recognized species within the family Xanthomonadaceae, including Dyella yeojuensis KACC 11405T, were greater than 4.0 % (i.e. the sequence similarities were less than 96.0 %). DNA–DNA hybridization experiments showed that the levels of DNA–DNA relatedness between strain Gsoil 3046T and its phylogenetically closest neighbours were below 25 %. The G+C content of the genomic DNA was 66.6 mol%. In addition, the presence of ubiquinone Q-8 as the predominant respiratory quinone, iso-C17 : 1 ω9c, iso-C16 : 0, iso-C15 : 0 and iso-C17 : 0 as the major cellular fatty acids and iso-C13 : 0 3-OH and iso-C11 : 0 3-OH as the major hydroxy fatty acids supported the affiliation of strain Gsoil 3046T to the genus Dyella. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil 3046T represents a novel species in the genus Dyella, for which the name Dyella ginsengisoli sp. nov. is proposed. The type strain is Gsoil 3046T (=KCTC 12599T=DSM 18387T).
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Gluconobacter japonicus sp. nov., an acetic acid bacterium in the Alphaproteobacteria
Five strains, NBRC 3271T, NBRC 3272, NBRC 3263, NBRC 3260 and NBRC 3269 were examined genetically, phylogenetically, phenotypically and chemotaxonomically. The DNA G+C contents of the five strains were 55.1–56.4 mol%. The five strains had low levels of DNA–DNA hybridization of 13–51 % to the type strains of Gluconobacter frateurii, Gluconobacter thailandicus, Gluconobacter oxydans, Gluconobacter cerinus, Gluconobacter albidus and Gluconobacter kondonii and formed a cluster that was separate from the type strains of the six Gluconobacter species given above in phylogenetic trees based on 16S rRNA gene and 16S–23S rRNA gene internal transcribed spacer sequences. The five strains weakly produced dihydroxyacetone from glycerol, but not 2,5-diketo-d-gluconate or a water-soluble brown pigment from d-glucose and contained ubiquinone-10. The five strains were assigned as representing a novel species of the genus Gluconobacter, for which the name Gluconobacter japonicus sp. nov. is proposed. The type strain is NBRC 3271T (=BCC 14458T=strain 7T, K. Kondo). Cells of the type strain are motile by means of polar flagella and the DNA G+C content is 56.4 mol%.
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Thalassobacter arenae sp. nov., isolated from sea sand in Korea
A Gram-negative, short rod-shaped bacterium, strain GA2-M15T, was isolated from a sea-sand sample at Homi Cape, Pohang city, Republic of Korea. 16S rRNA gene sequence analysis demonstrated that this isolate was unique, showing 95.9 % sequence similarity to the type strain of Thalassobacter stenotrophicus and similarities of 94.0–95.2 % to the type strains of species of the genera Octadecabacter (94.4–95.2 %), Jannaschia (94.0–94.4 %) and Thalassobius (94.0–94.7 %). Chemotaxonomic characteristics (diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine as the major polar lipids and C18 : 1 ω7c as the predominant fatty acid) and DNA G+C content (56 mol%) were also similar to those of Thalassobacter stenotrophicus. 16S rRNA gene sequence similarity, physiological properties and some fatty acid components showed that strain GA2-M15T could be differentiated from Thalassobacter stenotrophicus. On the basis of these results, strain GA2-M15T is considered to represent a novel species of the genus Thalassobacter, for which the name Thalassobacter arenae sp. nov. is proposed. The type strain is GA2-M15T (=KACC 12675T =DSM 19593T).
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Pigmentiphaga litoralis sp. nov., a facultatively anaerobic bacterium isolated from a tidal flat sediment
A novel Gram-negative, facultatively anaerobic, non-sporulating, non-motile, catalase- and oxidase-positive, rod-shaped bacterium (strain JSM 061001T) was isolated from a tidal flat in the South China Sea, China. Growth occurred with 0–5 % (w/v) NaCl [optimum, 0.5–1 % (w/v) NaCl], at pH 5.0–10.0 (optimum, pH 7.0) and at 4–35 °C (optimum, 25–30 °C). The major cellular fatty acids were C16 : 0, cyclo C17 : 0, C18 : 1 ω7c and C16 : 1. Strain JSM 061001T contained ubiquinone Q-8 as the predominant respiratory quinone, and phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid as the polar lipids. The genomic DNA G+C content was 65.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain JSM 061001T belongs to the family Alcaligenaceae and was related most closely to the type strains of the two recognized species of the genus Pigmentiphaga. The three strains formed a robust cluster in the neighbour-joining, maximum-parsimony and maximum-likelihood phylogenetic trees. Levels of DNA–DNA relatedness between strain JSM 061001T and the type strains of Pigmentiphaga daeguensis and Pigmentiphaga kullae were 15.8 and 10.5 %, respectively. The combination of phylogenetic analysis, DNA–DNA hybridization data, phenotypic characteristics and chemotaxonomic differences supported the view that strain JSM 061001T represents a novel species of the genus Pigmentiphaga, for which the name Pigmentiphaga litoralis sp. nov. is proposed. The type strain is JSM 061001T (=CCTCC AA207034T=KCTC 22165T).
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Zoogloea caeni sp. nov., a floc-forming bacterium isolated from activated sludge
More LessTwo floc-forming, nitrogen-fixing bacteria, strains EMB43T and EMB61, obtained from activated sludge of a domestic wastewater treatment plant in Korea, were characterized. The two strains were very closely related, sharing 99.7 % 16S rRNA gene sequence similarity and showing a level of DNA–DNA relatedness of 93 %, which suggests that they represent members of a single species. Phylogenetic analysis based on 16S rRNA gene sequences showed that the two novel isolates formed a distinct phyletic lineage within the genus Zoogloea and were related most closely to Zoogloea resiniphila DhA-35T and Zoogloea oryzae A-7T, with sequence similarities of 97.2 %. Levels of DNA–DNA relatedness between strain EMB43T and Z. resiniphila DhA-35T and Z. oryzae A-7T were 12.8 and 7.4 %, respectively. Cells of strains EMB43T and EMB61 were facultatively aerobic, rod-shaped, Gram-negative and motile by means of a polar flagellum. The strains grew at temperatures of 15–40 °C (optimum: 25–30 °C) and at pH 6.0–9.0 (optimum: pH 6.5–7.5). The predominant fatty acids were C16 : 0, C10 : 0 3-OH and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH), and the predominant polar lipid was phosphatidylethanolamine. The genomic DNA G+C content was 64.9–65.0 mol% and the major isoprenoid quinone was ubiquinone-8 (Q-8). On the basis of phenotypic, chemotaxonomic and molecular data, the isolates are considered to represent a novel species of the genus Zoogloea, for which the name Zoogloea caeni sp. nov. is proposed. The type strain is EMB43T (=KCTC 22084T=DSM 19389T).
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Rhodoplanes serenus sp. nov., a purple non-sulfur bacterium isolated from pond water
More LessA bright pink to red-coloured, phototropic, purple non-sulfur bacterium, designated strain TUT3530T, was isolated from pond water. Cells of the novel isolate were found to be Gram-negative, motile, budding rods. Cell extracts from phototrophically grown cultures had absorption maxima at 378, 482, 512, 550, 590, 800 and 850 nm, indicating the presence of bacteriochlorophyll a and carotenoids of the spirilloxanthin series. The intracytoplasmic membrane system was of the lamellar type. Anaerobic photo-organotrophy with simple organic acids such as pyruvate was the preferred mode of growth. Aerobic growth at full atmospheric oxygen tension and anaerobic denitrifying growth in darkness were also possible. Photolithotrophic growth occurred with thiosulfate, but not with sulfide or hydrogen, as the electron donor. No growth factors were required. The major whole-cell fatty acid was C18 : 1 ω7c. The major quinones were ubiquinone-10 and rhodoquinone-10. A phylogenetic analysis based on 16S rRNA gene sequences and studies involving DNA–DNA hybridization demonstrated that strain TUT3530T occupies a distinct taxonomic position within the genus Rhodoplanes. On the basis of these data, strain TUT3530T represents a novel species of the genus Rhodoplanes, for which the name Rhodoplanes serenus sp. nov. is proposed. The type strain is TUT3530T (=DSM 18633T=NBRC 102049T).
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Shinella yambaruensis sp. nov., a 3-methyl-sulfolane-assimilating bacterium isolated from soil
More LessA bacterial strain, designated MS4T, was isolated from soil in the Ryukyu Archipelago, Japan. The bacterium grew with 3-methyl sulfolane as sole sulfur source. Phylogenetic analysis based on 16S rRNA gene sequences suggested that strain MS4T belonged to the genus Shinella; it was closely related to the type strains of Shinella granuli and Shinella zoogloeoides (16S rRNA gene sequence similarities of 98.2 and 96.7 %, respectively). Strain MS4T was a Gram-negative, non-motile, rod-shaped, aerobic bacterium. The major respiratory quinone was ubiquinone-10 and the predominant cellular fatty acid was C18 : 1 ω7c. The DNA G+C content was 66.4 mol%. Based on phylogenetic and phenotypic traits, it was concluded that the organism represents a novel species in the genus Shinella for which the name Shinella yambaruensis sp. nov. is proposed; the type strain is MS4T (=NBRC 102122T=DSM 18801T).
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Microbulbifer donghaiensis sp. nov., isolated from marine sediment of the East China Sea
More LessA Gram-negative, aerobic, neutrophilic, rod-shaped bacterium, designated strain CN85T, was isolated from a sediment sample collected from the East China Sea and was subjected to a polyphasic taxonomic characterization. This isolate grew in the presence of 0.5–6.0 % (w/v) NaCl and at 20–40 °C; optimum growth was observed with 3 % (w/v) NaCl and at 35 °C. Chemotaxonomic analysis showed that Q-8 was the predominant respiratory quinone and that iso-C15 : 0, iso-C11 : 0 3-OH, iso-C17 : 1 ω9c, iso-C17 : 0, iso-C11 : 0 and C16 : 0 were the major fatty acids. The G+C content of the genomic DNA was 57.8 mol%. On the basis of 16S rRNA gene sequence analysis, the isolate was affiliated to the genus Microbulbifer. Strain CN85T exhibited most phylogenetic affinity with respect to the type strain of Microbulbifer maritimus (97.0 % sequence similarity) and showed less than 97 % sequence similarity with respect to other described Microbulbifer species with known 16S rRNA gene sequences. The DNA–DNA hybridization between strain CN85T and M. maritimus JCM 12187T was 44 %. On the basis of phenotypic and genotypic data, strain CN85T represents a novel species of the genus Microbulbifer, for which the name Microbulbifer donghaiensis sp. nov. is proposed. The type strain is CN85T (=CGMCC 1.7063T =JCM 15145T).
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Halomonas ilicicola sp. nov., a moderately halophilic bacterium isolated from a saltern
A Gram-negative, heterotrophic, aerobic, pale orange-pigmented, non-endospore-forming and motile bacterial strain, designated strain SP8T, was isolated from a salty water sample from the solar salterns of Santa Pola, located on the Mediterranean coast of Spain. The strain grew optimally at 37 °C, pH 6.5 and in the presence of 10 % NaCl. A polyphasic taxonomic study was conducted in order to characterize the strain in detail. Phylogenetic analyses based on 16S rRNA gene sequence comparisons indicated that strain SP8T clustered within the branch constituted by species of the genus Halomonas. The closest phylogenetic neighbours of strain SP8T were Halomonas muralis LMG 20969T (96.0 % sequence similarity), Halomonas pantelleriensis AAPT (95.9 %) and Halomonas campaniensis 5AGT (95.8 %). Phenotypic features, the fatty acid profile and the DNA G+C content of the novel strain further supported its placement in the genus Halomonas. On the basis of phenotypic, chemotaxonomic and phylogenetic distinctiveness, it is suggested that strain SP8T represents a novel species for which the name Halomonas ilicicola sp. nov. is proposed. The type strain is SP8T (=CECT 7331T=CCM 7522T=DSM 19980T).
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Thiobacillus thiophilus sp. nov., a chemolithoautotrophic, thiosulfate-oxidizing bacterium isolated from contaminated aquifer sediments
More LessStrain D24TNT was enriched and isolated from sediment collected from a tar oil-contaminated aquifer at a former gasworks site located in Duesseldorf-Flingern, Germany. Cells of strain D24TNT were rod-shaped, non-spore-forming and stained Gram-negative. Thiosulfate was used as an electron donor. The organism was obligately chemolithoautotrophic and facultatively anaerobic, and grew with either oxygen or nitrate as electron acceptor. Growth was observed at pH values between 6.3 and 8.7 and at temperatures of −2 to 30 °C; optimum growth occurred at pH 7.5–8.3 and 25–30 °C. The DNA G+C content was 61.5 mol%. On the basis of the 16S rRNA gene sequence analysis, strain D24TNT clustered in the Betaproteobacteria and was most closely related to Thiobacillus denitrificans (97.6 %) and Thiobacillus thioparus (97.5 %). Based on the phenotypic, chemotaxonomic and phylogenetic data, strain D24TNT represents a novel species of the genus Thiobacillus, for which the name Thiobacillus thiophilus sp. nov. is proposed. The type strain is D24TNT (=DSM 19892T=JCM 15047T).
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Maritalea myrionectae gen. nov., sp. nov., isolated from a culture of the marine ciliate Myrionecta rubra
More LessA Gram-negative, rod-shaped, strictly aerobic bacterium, designated strain CL-SK30T, was isolated from a culture of the marine ciliate Myrionecta rubra. 16S rRNA gene sequence analysis revealed that strain CL-SK30T was most closely related to Cucumibacter marinus (92.0 % similarity) and next to the type strains of species of the genus Devosia (89.8–91.3 % similarities) in the family Hyphomicrobiaceae. Phylogenetic analyses of the 16S rRNA gene sequences showed that strain CL-SK30T formed a robust clade together with C. marinus, but the sequence divergence value of 8 % between them indicated that the novel bacterium represented a distinct lineage. Strain CL-SK30T grew optimally in the presence of 2–5 % sea salts at 30–35 °C and pH 7.2–8.0. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, two unidentified glycolipids, an unidentified phospholipid and an unidentified lipid. Ubiquinone 10 was the major quinone. The DNA G+C content was 52.7 mol%. Based on its phenotypic, chemotaxonomic and phylogenetic characteristics, strain CL-SK30T represents a novel genus and species of the family Hyphomicrobiaceae, for which the name Maritalea myrionectae gen. nov., sp. nov. is proposed. The type strain is CL-SK30T (=KCCM 90060T=DSM 19524T).
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- Eukaryotic Micro-Organisms
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Cystofilobasidium lacus-mascardii sp. nov., a basidiomycetous yeast species isolated from aquatic environments of the Patagonian Andes, and Cystofilobasidium macerans sp. nov., the sexual stage of Cryptococcus macerans
More LessHere, we report on two novel sexual basidiomycetous red yeast species of the genus Cystofilobasidium. Cystofilobasidium lacus-mascardii sp. nov. is based on sexually compatible strains isolated from Lake Mascardi, an ultraoligotrophic lake in north-western Patagonia, Argentina. Following the discovery of the first isolate of this species, additional (sexually compatible) strains were isolated using a selective medium containing erythritol as the sole source of carbon. The second novel species corresponds to the sexual state of Cryptococcus macerans. In spite of accounts over the last 20 years of sexually compatible strains of this species, the complete life has never been observed. We provide evidence of a Cystofilobasidium-like basidial stage with teliospores and slender holobasidia, based on the study of self-fertile (homothallic) and self-sterile (heterothallic) isolates of Cryptococcus macerans. A revised molecular phylogeny of the genus Cystofilobasidium is presented and the most salient features of Cystofilobasidium lacus-mascardii sp. nov. (type strain CBS 10642T =PYCC 5819T =CRUB 1046T) and Cystofilobasidium macerans sp. nov. (type strain CBS 10757T) are discussed and compared with those of the remaining species in the genus. Information on additional Patagonian isolates belonging to the Cystofilobasidiales is also included in this report.
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Cryptococcus terrestris sp. nov., a tremellaceous, anamorphic yeast phylogenetically related to Cryptococcus flavescens
Cryptococcus terrestris sp. nov. (Basidiomycota, Agaricomycotina, Tremellomycetes, Tremellales) is typified by CJDX4 Y23T (=CBS 10810T =NRRL Y-48451T), isolated from forest soil in Oklahoma, USA. This species is most readily identified by the sequence of the D1/D2 domain region of the 26S rDNA and ITS (internal transcribed spacer) region. Additional strains from Oklahoma (C107DX4 Y11 =CBS 10813 =NRRL Y-48452) and Brazil (Ep11c =CBS 10812 =NRRL Y-48454; 56e =CBS 10811 =NRRL Y-48453) either had identical sequences or differed minimally. C. terrestris differs physiologically from the most closely related species, Cryptococcus flavescens, by the weak or delayed assimilation of ribose and salicin, and differs from Cryptococcus aureus by the utilization of nitrate and nitrite and growth in vitamin-free medium.
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- International Committee On Systematics Of Prokaryotes
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- Minutes
- Taxonomic Note
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Emended descriptions of genera of the family Halobacteriaceae
More LessThe family Halobacteriaceae currently contains 96 species whose names have been validly published, classified in 27 genera (as of September 2008). In recent years, many novel species have been added to the established genera but, in many cases, one or more properties of the novel species do not agree with the published descriptions of the genera. Authors have often failed to provide emended genus descriptions when necessary. Following discussions of the International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Halobacteriaceae, we here propose emended descriptions of the genera Halobacterium, Haloarcula, Halococcus, Haloferax, Halorubrum, Haloterrigena, Natrialba, Halobiforma and Natronorubrum.
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Volumes and issues
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