- Volume 66, Issue 7, 2016
Volume 66, Issue 7, 2016
- Validation List no. 170
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List of new names and new combinations previously effectively, but not validly, published
More LessThe 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. 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. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in the nomenclature of prokaryotes. 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 of prokaryotes, new combinations and new taxonomic opinions have appeared in volume 66, part 4, of the IJSEM
More LessThis listing of names of prokaryotes 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).
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- List of Changes in taxonomic opinion no. 24
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- New taxa
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- Archaea
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Halostella salina gen. nov., sp. nov., an extremely halophilic archaeon isolated from solar salt
A novel halophilic archaeon designated strain CBA1114T was isolated from solar salt in the Republic of Korea. Strain CBA1114T, cells of which were coccoid and Gram-stain-negative, grew in the presence of 15–30 % (w/v) NaCl (optimum, 20 %) and at 20–50 °C (optimum, 40 °C) and pH 7.0–9.0 (optimum, pH 8.0). Strain CBA1114T required Mg2+ for growth. Strain CBA1114T had three 16S rRNA genes, rrnA, rrnB and rrnC; levels of similarity between the sequences were 99.7–99.9 %. The 16S rRNA gene sequence of strain CBA1114T showed 91.7 % similarity to that of Haloterrigena thermotolerans PR5T. In multilocus sequence analysis (MLSA), five housekeeping genes, atpB, EF-2, radA, rpoB′ and secY, were found to be closely related to those of the members of the genera Halorientalis (89.7 % similarity of the atpB gene sequence), Halomicroarcula (91.9 %, EF-2), Haloterrigena (85.4 %, radA), Natronoarchaeum (89.2 %, rpoB′) and Natrinema (75.7 %, secY). A phylogenetic tree generated from the results of MLSA of the five housekeeping genes showed that strain CBA1114T was closely related to species of the genus Halorientalis in the family Halobacteriaceae . The major polar lipids were identified as phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and unidentified lipids. The G+C content of the genomic DNA of strain CBA1114T was 68.1 mol%. According to the results of phylogenetic, phenotypic and chemotaxonomic analyses, we designate strain CBA1114T (=JCM 30111T=KCTC 4206T) as the type strain of Halostella salina gen. nov., sp. nov., a novel species of a new genus within the family Halobacteriaceae .
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- Actinobacteria
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Corynebacterium faecale sp. nov., isolated from the faeces of Assamese macaque
A Gram-stain-positive, facultatively anaerobic, short rod-shaped, oxidase-negative and non-motile novel strain, designated YIM 101505T, was isolated from the faeces of a primate, Assamese macaque, and was studied to determine its taxonomic position. The cell wall contained meso-diaminopimelic acid and short-chain mycolic acids. Whole cell sugars were mannose, galactose and arabinose as major components. The major fatty acids (>10 %) were C18 : 1 ω9c, C16 : 0 and C17 : 1 ω8c and the major menaquinone was MK-9(H2). The polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, glycolipid and six unidentified lipids. The new isolate shared most of the typical chemotaxonomic characteristics of members of the genus Corynebacterium . The closest related species was Corynebacterium efficiens based on 16S rRNA gene (98.1 % similarity) and partial rpoB gene (91.4 % similarity) sequences. Similarities with other species of this genus were below 97 % based on the 16S rRNA gene. The DNA–DNA hybridization value between YIM 101505T and C. efficiens DSM 44549T was 47.7±3.6 %. Moreover, the physiological and biochemical characteristics of YIM 101505T and C. efficiens DSM 44549T were different. Thus, strain YIM 101505T is considered to represent a novel member of the genus Corynebacterium , for which the name Corynebacterium faecale sp. nov. is proposed. The type strain is YIM 101505T (=DSM 45971T=CCTCC AB 2013226T).
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Streptosporangium becharense sp. nov., an actinobacterium isolated from desert soil
The taxonomic position of a novel actinobacterium, strain SG1T, isolated from a Saharan soil sample collected from Béni-Abbès, Béchar (south-west Algeria), was established by using a polyphasic approach. The micro-organism had morphological and chemical features that were consistent with its classification in the genus Streptosporangium . The cell-wall peptidoglycan contained meso-diaminopimelic acid. The whole-cell sugars contained ribose and glucose, but not madurose. The predominant menaquinones were MK-9(H2) and MK-9(H4). The polar lipid profile contained diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylhydroxymethylethanolamine, phosphatidylhydroxyethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. The predominant cellular fatty acids were C17 : 1 ω8c, iso-C16 : 0, 10-methyl C17 : 0, C18 : 1 ω9c and C17 : 0. 16S rRNA gene sequence similarity analysis supported the classification of the isolate in the genus Streptosporangium and indicated that it was related most closely to ‘ Streptosporangium subfuscum ’ DSM 46724 (99.7 % similarity), Streptosporangium pseudovulgare DSM 43181T (98.7 %), Streptosporangium fragile DSM 43847T (98.6 %) and Streptosporangium sandarakinum DSM 45763T (98.5 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain SG1T formed a cluster with its closest relative ‘ S. subfuscum ’ DSM 46724. However, DNA–DNA relatedness as well as physiological and chemotaxonomical analyses showed that strain SG1T could be differentiated from its closest phylogenetic relatives. Therefore, it is proposed that strain SG1T should be classified as representing a novel species in the genus Streptosporangium , for which the name Streptosporangium becharense sp. nov. is proposed. The type strain is SG1T (=DSM 46887T=CECT 8961T).
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Humibacter soli sp. nov., isolated from soil
More LessA novel actinobacterial strain, designated R1-20T, was isolated during a study of the bacterial diversity of the soil at a white heron nesting site. The isolate was non-motile, Gram-stain-positive and short rod-shaped. Colonies were dull white and convex with entire margin during the early stages of growth, and gradually became yellow. 16S rRNA gene sequence analysis indicated that the isolate belongs to the genus Humibacter of the family Microbacteriaceae , as sequence similarity with its nearest neighbours was 97.16 % with Humibacter antriD7-27Tand 96.44 % with Humibacter albusDSM 18994T. However, the combination of cultural and physiological as well as chemotaxonomic properties clearly distinguished strain R1-20T from other Humibacter species. The DNA G+C content of strain R1-20T was 65.5 mol%, and the major respiratory isoprenoid quinone was menaquinone MK-11. The acyl group of the peptidoglycan was of acetyl type, and the diagnostic diamino acid was 2,4-diaminobutyric acid. Glutamic acid, alanine and glycine were also present in the cell wall. The major fatty acids of strain R1-20T were anteiso-C17 : 0, iso-C16 : 0 and anteiso-C15 : 0. On the basis of phylogenetic, phenotypic and chemotaxonomic analysis, strain R1-20T merits recognition as a representative of a novel species of the genus Humibacter , for which the name Humibacter soli sp. nov. is proposed. The type strain is R1-20T (=KCTC 39614T=JCM 31015T).
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Description of Salilacibacter albus gen. nov., sp. nov., isolated from a dried salt lake, and reclassification of Paraglycomyces xinjiangensis Luo et al. 2015 as a later heterotypic synonym of Salininema proteolyticum Nikou et al. 2015 with emended descriptions of the genus Salininema and Salininema proteolyticum
A novel halophilic actinomycete, designated strain J11Y309T, was isolated from a soil sample collected from a dried salt lake in China. This isolate grew optimally at 28‒37 °C, with 3‒5 % (w/v) NaCl and at pH 7.0‒7.5. It contained meso-diaminopimelic acid as the diagnostic diamino acid and glucose, ribose and xylose were present in the whole-cell hydrolysates. MK-10(H4) was detected as the predominant menaquinone. The major fatty acids were anteiso-C17 : 0, iso-C16 : 0, iso-C17 : 0 and iso-C15 : 0. Polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, phosphoglycolipids, glycolipids, an unidentified phospholipid and additional unidentified lipids. The G+C content of the genomic DNA was 63.0 mol%. The novel strain shared highest 16S rRNA gene sequence similarity with Salininema proteolyticum Miq-4T (95.80 %), Paraglycomyces xinjiangensis TRM 49201T (95.77 %) and Haloglycomyces albus YIM 92370T (94.84 %). Phylogenetic trees showed that it could not be clearly assigned to any known genus within the family Glycomycetaceae and formed a distinct phylogenetic line in the clade comprising members of the genera Salininema , Paraglycomyces and Haloglycomyces . Based on data from the present polyphasic taxonomic study, strain J11Y309T represents a novel species of a new genus in the family Glycomycetaceae , for which the name Salilacibacter albus gen. nov., sp. nov. is proposed with Salilacibacter albus sp. nov. as the type species. The type strain of Salilacibacter albus is J11Y309T (=DSM 46875T=CGMCC 4.7242T=LMG 29297T). Reclassification of Paraglycomyces xinjiangensis Luo et al. 2015 as a later heterotypic synonym of Salininema roteolyticum Nikou et al. 2015 is also discussed in this study.
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Dermabacter jinjuensis sp. nov., a novel species of the genus Dermabacter isolated from a clinical specimen
A Gram-stain-positive, catalase-positive, facultatively anaerobic, non-motile, coryneform bacterium, designated strain 32T, was isolated from a closed pus sample from a patient having finger necrosis in Korea. Strain 32T was considered as representing a novel species according to its initial identification by matrix-assisted laser desorption/ionization-time-of-flight MS. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 32T belonged to the genus Dermabacter and was closely related to Dermabacter hominis DSM 7083T (=ATCC 49369T) (98.34 % similarity). Optimal growth was observed at 30–40 °C and pH 7. Growth occurred in the presence of 0–6 % (w/v) NaCl. Menaquinones MK-8, MK-7 and MK-9 were the major respiratory quinones. The major polar lipids were phosphatidylethanolamine, phosphatidylcholine, glycolipid and two unknown lipids. The major cellular fatty acids were anteiso-C17 : 0, anteiso-C15 : 0, iso-C16 : 0 and iso-C15 : 0. The DNA G+C content of strain 32T was 62.58 mol%, and the mean level of DNA–DNA relatedness between strain 32T and D. hominis ATCC 49369T was 49±1.6 %. Based on the phenotypic and genotypic characteristics, strain 32T is confirmed to represent a novel species of the genus Dermabacter , for which the name Dermabacter jinjuensis sp. nov. is proposed. The type strain is 32T (=NCCP 16133T=DSM 101003T).
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Plantactinospora soyae sp. nov., an endophytic actinomycete isolated from soybean root [Glycine max (L.) Merr]
A novel actinomycete, designated strain NEAU-gxj3T, was isolated from soybean root [Glycine max (L.) Merr.] collected from Harbin, Heilongjiang Province, China, and characterized using a polyphasic approach. The 16S rRNA gene sequence of strain NEAU-gxj3T showed highest similarity to those of Micromonospora equina Y22T (98.2 %) and Plantactinospora endophytica YIM 68255T (98.0 %). Phylogenetic analysis based on the 16S rRNA gene and gyrB gene demonstrated that the isolate clustered with the members of the genus Plantactinospora . The chemotaxonomic properties of strain NEAU-gxj3Twere also consistent with those of members of the genus Plantactinospora . The cell wall contained meso-diaminopimelic acid and whole-cell sugars were xylose, glucose and galactose. The predominant menaquinones were MK-10(H6), MK-9(H8), MK-10(H2) and MK-10(H4). The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The major fatty acids were identified as anteiso-C17 : 0, iso-C16 : 0, iso-C15 : 0 and C15 : 0. A combination of DNA–DNA hybridization result and some phenotypic characteristics indicated that strain NEAU-gxj3Tcould be differentiated clearly from its closest phylogenetic relatives. Therefore, the strain is concluded to represent a novel species of the genus Plantactinospora , for which the name Plantactinospora soyae sp. nov. is proposed. The type strain is NEAU-gxj3T (=CGMCC 4.7221T=DSM 46832T).
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Actinomadura adrarensis sp. nov., an actinobacterium isolated from Saharan soil
A novel actinobacterial strain, designated ACD12T, was isolated from a Saharan soil sample collected from Adrar province, southern Algeria. A polyphasic study was carried out to establish the taxonomic position of this strain. Strain ACD12T was observed to form extensively branched substrate mycelia. Aerial mycelium was absent or was weakly produced on all media tested, while spore chains were short with a hooked and irregular spiral form (2–3 turns). The dominant diaminopimelic acid isomer in the cell wall was meso-diaminopimelic acid. Glucose, ribose, galactose, mannose and madurose occured in whole-cell hydrolysates. The major phospholipid was diphosphatidylglycerol and phosphatidylinositol. The predominant menaquinone was MK-9(H6). The fatty acid profile was characterized by the presence of C16 : 0, C17 : 0, C15 : 0, C18 : 0, C18 : 1 cis9 and iso-C16 : 0. Results of 16S rRNA gene sequence comparisons revealed that strain ACD12T shared the highest degree of 16S rRNA gene sequence similarity with Actinomadura sputi DSM 45233T (98.3 %) and Actinomadura hallensis DSM 45043T (97.8 %). All tree-making algorithms used also supported strain ACD12T forming a distinct clade with its most closely related species. In addition, DNA–DNA hybridization indicated only 39.8 % relatedness with A. sputi DSM 45233T and 18.7 % relatedness with A. hallensis DSM 45043T. The combined phenotypic and genotypic data show that the novel isolate represents a novel species of the genus Actinomadura , for which the name Actinomadura adrarensis sp. nov., is proposed, with the type strain ACD12T (=DSM 46745T =CECT 8842T).
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Actinophytocola algeriensis sp. nov., an actinobacterium isolated from Saharan soil
During our investigations of new actinobacterial taxa, a novel actinobacterial strain, designated MB20T, was isolated from a Saharan soil sample, collected in the Mzab region (Ghardaïa province, southern Algeria). In order to reveal its taxonomic position, the novel strain was characterized following a polyphasic taxonomic approach. It was noticed that strain MB20T produced white, branched and fragmented substrate mycelium with no aerial mycelium on most of the media tested. Chemotaxonomic and phylogenetic studies clearly demonstrated that strain MB20T belonged to the family Pseudonocardiaceae and was closely related to the genus Actinophytocola . Cell-wall hydrolysates contained meso-diaminopimelic acid but not glycine, and whole-cell hydrolysates contained galactose, glucose and ribose. The diagnostic phospholipid was phosphatidylethanolamine. Mycolic acids were not detected while the predominant fatty acid was found to be iso-branched hexadecanoate (iso-C16 : 0). The major menaquinone was MK-9(H4). Results of the 16S rRNA gene sequence comparison revealed that strain MB20T shared the highest degree of similarity with Actinophytocola gilvus DSM 45828T (98.5 %), Actinophytocola corallina DSM 45659T (98.0 %) and Actinophytocola timorensis DSM 45660T (97.5 %). However, DNA–DNA hybridization studies showed only 32.9 % similarity with A. timorensis , 23.7 % similarity with A. gilvus and 17.9 % similarity with A. corallina . On the basis of phenotypic characteristics, 16S rRNA gene sequence comparisons and DNA–DNA hybridization, strain MB20T was revealed to be a representative of a novel species of the genus Actinophytocola , for which the name Actinophytocola algeriensis sp. nov. (type strain MB20T =DSM 46746T =CECT 8960T) is proposed.
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- Firmicutes and related organisms
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Domibacillus antri sp. nov., isolated from the soil of a cave
More LessA Gram-reaction-positive, strictly aerobic, capsule-forming, motile and rod-shaped bacterium, designated strain XD80T, was isolated from the soil of a native cave in Lichuan, Hubei province, China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain XD80T was most closely related to Domibacillus iocasae CCTCC AB 2015183T (98.66 % sequence similarity), followed by Domibacillus robiginosus DSM 25058T(97.83 %), Domibacillus tundrae KCTC 33549T (97.70 %), Domibacillus enclensis CCTCC AB 2011121T (97.21 %) and Domibacillus indicus DSM 28032T (96.96 %). Levels of DNA–DNA relatedness between strain XD80T and D. iocasae CCTCC AB 2015183T, D. robiginosusDSM 25058T, D. tundrae KCTC 33549T and D. enclensis CCTCC AB 2011121T were 37.4 %, 53.8 %, 53.6 % and 52.7 %, respectively. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, aminophospholipid and two unknown phospholipids. The predominant fatty acids (>5 %) were iso-C15 : 0 (37.3 %), anteiso-C15 : 0 (10.8 %), C16 : 0 (10.4 %), iso-C17 : 0 (10.3 %), C16 : 1ω11c (9.6 %) and anteiso-C17 : 0 (7.4 %). MK-6 (86.4 %) was the major respiratory quinone. The DNA G+C content was 46.4 mol%. The cell-wall peptidoglycan contained meso-diaminopimelic acid (type A1γ). Ribose and glucose were the major whole-cell sugars. In addition, strain XD80T showed differential physiological characteristics from most members of the genus Domibacillus , encompassing hydrolysis of starch, acid production from inositol and raffinose, and production of valine arylamidase. The results of this polyphasic study indicated that strain XD80T represents a novel species of the genus Domibacillus , for which the name Domibacillus antri sp. nov. is proposed. The type strain is XD80T (=CCTCC AB 2015053T=KCTC 33636T).
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Paenibacillus cucumis sp. nov., isolated from a cucumber plant
A Gram-positive-staining, aerobic, endospore-forming bacterial strain, isolated from the stem of a cucumber plant, was studied in detail for its taxonomic position. Based on 16S rRNA gene sequence similarity comparisons, strain AP-115T was grouped into the genus Paenibacillus , most closely related to Paenibacillus amylolyticus (98.8 %), Paenibacillus tundrae and Paenibacillus barcinonensis (both 98.4 %). The 16S rRNA gene sequence similarity to other species of the genus Paenibacillus was ≤98.4 %. Chemotaxonomic characterization supported allocation of the strain to the genus Paenibacillus . The quinone system contained exclusively menaquinone MK-7, and in the polar lipid profile diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylserine were predominating. The major component in the polyamine pattern was spermidine, and the diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid. The major fatty acids were iso- and anteiso-branched fatty acids. The results of physiological and biochemical tests allowed phenotypic differentiation of strain AP-115T from closely related species. Thus, AP-115T represents a novel species of the genus Paenibacillus , for which the name Paenibacillus cucumis sp. nov. is proposed, with AP-115T (=LMG 29222T=CCM 8653T) as the type strain.
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Bacillus loiseleuriae sp. nov., isolated from rhizosphere soil from a loiseleuria plant
More LessA Gram-stain-positive, rod-shaped, endospore-forming, aerobic bacterium, designated strain FJAT-27997T, was isolated from the rhizosphere soil of a Loiseleuria plant collected from Sichuan province in China. Growth was observed aerobically between 20 and 35 °C (optimum 30 °C), between 0 and 3.0 % (w/v) NaCl (optimum at 0 %) concentration and pH in the range 6.0–9.0 (optimum at pH 7.0). The cell-wall peptidoglycan contained meso-diaminopimelic acid and the major isoprenoid quinone was menaquinone MK-7. The main fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C14 : 0, C16 : 0 and C14 : 0. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Phylogenetic analyses based on 16S rRNA gene sequences showed that isolate FJAT-27997T was a member of the genus Bacillus and was related most closely to Bacillus simplex DSM 1321T (97.95 % similarity), followed by Bacillus huizhouensis GSS03T (97.9 %). The average nucleotide identity value between strain FJAT-27997T and the most closely related species, B . simplex DSM 1321T, was 71.60 % (JSpecies), less than the previously proposed cut-off value of 96 % for differentiating species within the genus. The in silico DNA–DNA hybridization values between strain FJAT-27997T and its most closely related species were <70 %, again indicating they belong to different taxa. The main fatty acids were iso-C15 : 0 and anteiso-C15 : 0. The novel strain could be differentiated from other known Bacillus species on the basis of several phenotypic characters and fatty acid profiles. This taxononomic/genomic study revealed that strain FJAT-27997T represents a novel Bacillus species, for which the name Bacillus loiseleuriae sp. nov. (type strain FJAT-27997T =CCTCC AB 2015285T=DSM 101776T) is proposed.
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Caenibacillus caldisaponilyticus gen. nov., sp. nov., a thermophilic, spore-forming and phospholipid-degrading bacterium isolated from acidulocompost
A thermophilic and phospholipid-degrading bacterium, designated strain B157T, was isolated from acidulocompost, a garbage compost processed under acidic conditions at moderately high temperature. The organism was Gram-stain-positive, aerobic, spore-forming and rod-shaped. Growth was observed to occur at 40–65 °C and pH 4.8–8.1 (optimum growth: 50–60 °C, pH 6.2). The strain was catalase- and oxidase-positive. The cell wall contained meso-diaminopimelic acid, alanine, glutamic acid and galactose. The predominant respiratory quinone was menaquinone-7 (MK-7) and the major fatty acids were anteiso-C17 : 0 and iso-C17 : 0. Comparative 16S rRNA gene sequence analysis showed that strain B157T was related most closely to Tuberibacillus calidus 607T (94.8 % identity), and the phylogenetic analysis revealed that it belonged to the family Sporolactobacillaceae . The DNA G+C content was determined as 51.8 mol%. In spite of many similarities with the type strains of members of the family Sporolactobacillaceae, genotypic analyses suggest that strain B157T represents a novel species of a new genus, Caenibacillus caldisaponilyticus gen. nov., sp. nov. The type strain of Caenibacillus caldisaponilyticus is B157T (=NBRC 111400T=DSM 101100T).
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Salipaludibacillus aurantiacus gen. nov., sp. nov. a novel alkali tolerant bacterium, reclassification of Bacillus agaradhaerens as Salipaludibacillus agaradhaerens comb. nov. and Bacillus neizhouensis as Salipaludibacillus neizhouensis comb. nov.
More LessTwo novel (S9T and S12) Gram-stain-positive, rod shaped, non-motile and endospore forming bacteria were isolated from Narayan Sarovar lake, in India. The high 16S rRNA gene sequence similarity (99.9 %) and DNA–DNA relatedness (86±2 %) indicated that strains S9T and S12 were members of a single species. Based on the 16S rRNA gene sequence analysis, these strains were identified as belonging to the class Firmibacteria and were most closely related to Bacillus agaradhaerens PN-105T (96.8 % sequence similarity), Bacillus neizhouensis JSM 071004T (96.5 %) and Bacillus luteus JC167T (96.1 %). However, these strains shared only 90.3 % 16S rRNA gene sequence similarity with Bacillus subtilis subsp. subtilis DSM 10T, indicating that they might not be members of the genus Bacillus . The cell-wall peptidoglycan contained meso-diaminopimelic acid. Polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, one unknown phospholipid and an unknown lipid. The predominant isoprenoid quinone was MK-7. Major fatty acids (>5 %) included anteiso-C15 : 0, C16 : 0, iso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and summed feature 3. The results of phylogenetic, chemotaxonomic and biochemical tests allowed a clear differentiation of strains S9T and S12 from all other members of the family Bacillaceae .The strains therefore represent a novel member of a new genus from the family Bacillaceae , for which the name Salipaludibacillus aurantiacus gen. nov., sp. nov. is proposed. The type strain is S9T (=KCTC 33633T=LMG 28644T). Based on the present study, it is also proposed to transfer Bacillus agaradhaerens and Bacillus neizhouensis to this new genus as Salipaludibacillus agaradhaerens comb. nov. and Salipaludibacillus neizhouensis comb. nov.
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- Proteobacteria
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Altererythrobacter rigui sp. nov., isolated from wetland freshwater
More LessA non-motile and yellow-pigmented bacterium, designated strain WW3T, was isolated from freshwater of Woopo wetland, Republic of Korea. Cells were Gram-reaction-negative, aerobic, catalase-positive and oxidase-negative. A maximum-likelihood phylogenetic tree based on 16S rRNA gene sequences showed that strain WW3T forms an independent lineage within the genus Altererythrobacter . Strain WW3T was related distantly to Altererythrobacter dongtanensisJM27T and Altererythrobacter troitsensisKMM 6042T (97.1% 16S rRNA gene sequence similarity). DNA–DNA relatedness between strain WW3T and the reference strains was low (30–41 %). The major fatty acids of strain WW3T were C17 : 1ω6c, C17 : 1ω8c, C15 : 0 2-OH and summed feature 8 comprising C18 : 1ω6c and/or C18 : 1ω7c. The predominant isoprenoid quinone of the isolate was ubiquinone-10. The DNA G+C content of strain WW3T was 63 mol%. Phenotypic characteristics distinguished strain WW3T from related species of the genus Altererythrobacter . On the basis of the evidence presented in this study,strain WW3T represents a novel species of the genus Altererythrobacter, for which the name Altererythrobacter rigui sp. nov. is proposed. The type strain is WW3T (=KCTC 42620T =JCM 30975T).
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Polaromonas eurypsychrophila sp. nov., isolated from an ice core
A Gram-stain-negative, aerobic, rod-shaped, beige bacterium, strain B717-2T, was isolated from an ice core drilled from Muztagh Glacier on the Tibetan Plateau, China. According to phylogenetic analyses based on 16S rRNA gene sequences, the novel strain was related most closely to Polaromonas vacuolataand shared 97.7 % similarity with the type strain of this species. It grew optimally at pH 7, at 15 °C and with 2 % (w/v) NaCl. Major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The major fatty acids were summed feature 3 (C16 : 1 ω 7 c and/or iso-C15 : 0 2-OH), summed feature 8 (C18 : 1 ω 7 c, C18 : 1 ω 6 c) and C16 : 0. The sole respiratory quinone was Q-8. The DNA G+C content was 63.4 mol %. In DNA–DNA hybridization tests, strain B717-2T shared 37.0±1.9, 30.0±1.7, 26.0±0.9, 23.4±0.5 and 18.4±1.9 % DNA–DNA relatedness with Polaromonas jejuensisJS12-13T, P. vacuolata 34-PT, Polaromonas aquatica CCUG 39402T, Polaromonas glacialisCr4-12T and Polaromonas cryoconitiCr4-35T, respectively. Based on the phenotypic, phylogenetic and genetic characteristics, strain B717-2T represents a novel species of the genus Polaromonas , for which the name Polaromonas eurypsychrophila sp. nov. is proposed. The type strain is B717-2T (=CGMCC 1.15322T=JCM 31171T).
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Dissulfurirhabdus thermomarina gen. nov., sp. nov., a thermophilic, autotrophic, sulfite-reducing and disproportionating deltaproteobacterium isolated from a shallow-sea hydrothermal vent
A thermophilic, anaerobic, chemolithoautotrophic bacterium, strain SH388T, was isolated from a shallow, submarine hydrothermal vent (Kuril Islands, Russia). Cells of strain SH388T were Gram-stain-negative short rods, 0.2–0.4 µm in diameter and 1.0–2.5 µm in length, and motile with flagella. The temperature range for growth was 25–58 °C (optimum 50 °C), and the pH range for growth was pH 5.0–7.0 (optimum pH 6.0–6.5). Growth of strain SH388T was observed in the presence of NaCl concentrations ranging from 0.5 to 4.0 % (w/v) (optimum 2.0–2.5 %). The strain grew chemolithoautotrophically with molecular hydrogen as electron donor, sodium sulfite as electron acceptor and bicarbonate/CO2 as a carbon source. It was also able to grow by disproportionation of sulfite and elemental sulfur but not thiosulfate. Sulfate, Fe(III) and nitrate were not used as electron acceptors either with H2 or organic electron donors. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belonged to the class Deltaproteobacteria and was most closely related to Dissulfuribacter thermophilus and Dissulfurimicrobium hydrothermale (91.6 % and 90.4 % sequence similarity). On the basis of its physiological properties and results of phylogenetic analyses, strain SH388T is considered to represent a novel species of a new genus, for which the name Dissulfurirhabdus thermomarina gen. nov., sp. nov. is proposed. The type strain of the species is SH388T (=DSM 100025T=VKM B-2960T). It is the first thermophilic disproportionator of sulfur compounds isolated from a shallow-sea environment.
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Description of Variovorax humicola sp. nov., isolated from a forest topsoil
More LessEmploying a modified cultivation method, we studied two bacterial strains, UC10 and UC38T, found on the Kyonggi University campus, Suwon in Gyeonggi-Do province, South Korea. These strains were non-spore-forming, Gram-stain-negative, motile and rod-shaped. Growth occurred in the presence of 0–2 % (w/v) NaCl, at pH 4–9 and a temperature range of 4–35 °C. On an R2A agar plate incubated for 5 days at 28 °C, irregular, raised and pale-yellowish colonies were observed. Comparative analysis of nearly full-length 16S rRNA gene sequences indicated that these strains were closely related to Variovorax guangxiensis GXGD002T, with 98.6 % similarity. Strains UC10 and UC38T were 98.0 % similar to V.ariovorax soli GH9-3T; 97.8 % to V.ariovorax dokdonensis DS-43T; 97.3–97.7 % to V.ariovorax ginsengisoli Gsoil 3165T; 97.7–98.0 % to V.ariovorax paradoxus IAM 12373T; 97.4–97.6 % to V.ariovorax defluvii 2C1-bT; and 97.3–97.4 % to V.ariovorax boronicumulans BAM-48T. The predominant ubiquinone was Q-8. The primary polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major fatty acids were C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C17 : 0 cyclo. DNA–DNA hybridization assays indicated 89.2–91.4 % genomic DNA similarity between strains UC10 and UC38T. Moreover, genomic DNA similarity between these novel strains and reference strains of the genus Variovoraxwas less than the 70 %. Based on these results, strain UC38T was designated a representative of a novel species of the genus Variovorax , with the proposed name Variovorax humicola sp. nov. The type strain is UC38T (=KACC 18501T=NBRC 111520T).
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Loktanella marina sp. nov., isolated from seawater
More LessA Gram-stain-negative, coccoid- or short-rod-shaped and non-motile bacterial strain, designated MDM-7T, was isolated from seawater of the Yellow Sea, South Korea, and was subjected to a polyphasic taxonomic study. Strain MDM-7T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 2–3 % (w/v) NaCl. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain MDM-7T fell within the clade comprising species of the genus Loktanella , clustering with the type strains of Loktanella vestfoldensisand Loktanella agnita , with which it exhibited 96.1 and 95.6 % similarity, respectively. 16S rRNA gene sequence similarity values between strain MDM-7T and the type strains of other Loktanella species were 93.1–95.0 %. The DNA G+C content of strain MDM-7T was 62.6 mol%. Strain MDM-7T contained Q-10 as the predominant ubiquinone and summed feature 8 (C18 : 1 ω7c and/ or C18 : 1 ω6c) as the major fatty acid. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol and an unidentified aminolipid. Differential phenotypic properties, together with phylogenetic distinctiveness, demonstrated that strain MDM-7T is distinguishable from recognized Loktanella species. On the basis of the data presented, strain MDM-7T is considered to represent a novel species of the genus Loktanella , for which the name Loktanella marina sp. nov. is proposed. The type strain is MDM-7T (=KCTC 42722T=CECT 8899T).
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Corticibacterium populi gen. nov., sp. nov., a member of the family Phyllobacteriaceae, isolated from bark of Populus×euramericana
More LessTwo Gram-staining-negative, aerobic, motile, slimy, glossy bacterial strains were isolated from bark tissue of Populus×euramericana. The bacteria grew at 10–37 °C, pH 5–10, with optimal growth at 28–30 °C, pH 6.0–8.0. Both strains grew with 0–3 % (w/v) NaCl. In the maximum-likelihood phylogenetic tree, the two isolates formed a distinct branch within the family Phyllobacteriaceae , and they were not closely related to any of the genera within the family Phyllobacteriaceae . The two novel isolates werepositive for oxidase andcatalase activity. The polar lipids profile revealed diphosphatidylglycerol, phosphatidylcholine, phospholipid, phosphatidylethanolamine, phosphatidylglycerol and five unknown lipids. The major fatty acids were C18 : 1ω7c and C16 : 0. The DNA G+C content was 56.4 mol%. On the basis of phylogenetic, chemotaxonomic and phenotypic data, the two strains represent a novel species belonging to a novel genus of the family Phyllobacteriaceae , for which the name Corticibacterium populi gen. nov., sp. nov. is proposed. The type strain of the type species is 16B10-2-7T (=CFCC 12884T=KCTC 42249T).
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Phenylobacterium panacis sp. nov., isolated from the rhizosphere of rusty mountain ginseng
More LessA novel, Gram-stain-negative, rod-shaped bacterial strain, designated as DCY109T, was isolated from the rhizosphere of rusty mountain ginseng root located on Hwacheon mountain of Gangwon province, South Korea. 16S rRNA gene sequence analysis revealed that strain DCY109T belonged to the genus Phenylobacterium and was related closely to Phenylobacterium muchangponense KACC 15042T (98.2 % similarity), Phenylobacterium immobile DSM 1986T (96.9 %) and Phenylobacterium koreense KCTC 12206T (96.7 %). The predominant isoprenoid quinone was ubiquinone (Q-10) and the DNA G+C content was 66.9 mol%. The major polar lipids were phosphatidylglycerol, an unidentified glycolipid and an unidentified lipid. The major fatty acids (>10 %) were C16 : 0, summed feature 3 (which comprised C16 : 1 ω7c and/or C16 : 1 ω6c) and summed feature 8 (which comprised C18 : 1 ω7c and/or C18 : 1 ω6c). Mean DNA–DNA relatedness between strain DCY109T and its closest relative, P. muchangponense KACC 15042T, was 15.1±3.9 %. Based on the physiological, biochemical, chemotaxonomic and genetic analyses, strain DCY109T is considered to represent a novel species of the genus Phenylobacterium , for which the name Phenylobacterium panacis sp. nov. is proposed. The type strain is DCY109T (=KCTC 42749T=JCM 31045T).
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Sulfurovum riftiae sp. nov., a mesophilic, thiosulfate-oxidizing, nitrate-reducing chemolithoautotrophic epsilonproteobacterium isolated from the tube of the deep-sea hydrothermal vent polychaete Riftia pachyptila
An anaerobic, nitrate-reducing, sulfur- and thiosulfate-oxidizing bacterium, designated strain 1812ET, was isolated from the vent polychaete Riftia pachyptila, which was collected from a deep-sea hydrothermal vent on the East Pacific Rise. Cells were Gram-stain-negative rods, measuring approximately 1.05±0.11 µm by 0.40±0.05 µm. Strain 1812ET grew at 25 – –45 °C (optimum 35 °C), with 1.5–4.0 % (w/v) NaCl (optimum 3.0 %) and at pH 5.0–8.0 (optimum pH 6.0). The generation time under optimal conditions was 3 h. Strain 1812ET was an anaerobic chemolithotroph that grew with either sulfur or thiosulfate as the energy source and carbon dioxide as the sole carbon source. Nitrate was used as a sole terminal electron acceptor. The predominant fatty acids were C16 : 1 ω7c, C18 : 1 ω7c and C16 : 0. The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The major respiratory quinone was menaquinone MK-6 and the G+C content of the genomic DNA was 47.4 mol%. Phylogenetic analysis of the 16S rRNA gene of strain 1812ET showed that the isolate belonged to the Epsilonproteobacteria , and its closest relatives were Sulfurovum lithotrophicum 42BKTT and Sulfurovum aggregans Monchim 33T (98.3 and 95.7 % sequence similarity, respectively). DNA–DNA relatedness between strain 1812ET and the type strain of S. lithotrophicum was 29.7 %, demonstrating that the two strains are not members of the same species. Based on the phylogenetic, molecular, chemotaxonomic and physiological evidence, strain 1812ET represents a novel species within the genus Sulfurovum , for which the name Sulfurovum riftiae sp. nov. is proposed. The type strain is 1812ET (=DSM 101780T=JCM 30810T).
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Paludibacterium purpuratum sp. nov., isolated from wetland soil
More LessA novel bacterium, designated KJ031T, was isolated from a wetland soil sample taken from Jeju island, Republic of Korea. Cells were Gram-stain-negative, curved rod shaped, oxidase- and catalase- positive, motile and facultatively anaerobic. Growth was observed at pH 6.0–8.0 and at 20–37 °C on R2A agar. Comparative analysis of 16S rRNA gene sequences revealed that strain KJ031T is a member of the genus Paludibacterium , sharing highest sequence similarities with Paludibacterium paludis KBP-21T (96.2 %) and Paludibacterium. yongneupense 5YN8-15T (96.0 %). The major fatty acids were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0 and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The predominant respiratory quinone was Q-8. The major polar lipids of strain KJ031T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminophospholipid, two unidentified phospholipids and one unidentified polar lipid. The DNA G+C content was 59.2 mol%. On the basis of the evidence presented in this study, strain KJ031T represents a novel species of the genus Paludibacterium , for which the name Paludibacterium purpuratum sp. nov. is proposed. The type strain is KJ031T (=KCTC 42852T =CECT 8976T).
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Description of Comamonas sediminis sp. nov., isolated from lagoon sediments
More LessStrain S3T was isolated from lagoon sediments, and appeared as transparent colonies on agar plates, with cells staining Gram-negative. Catalase and oxidase were positive. S3T hydrolyzed starch, casein and tween-20, while urea, chitin, gelatin and tween-80 were not hydrolysed. C18 : 1ω6c/C18 : 1ω7c, C16 : 1ω6c/C16 : 1ω7c,C17 : 0 cyclo and C16 : 0 were the predominant fatty acids with minor amounts of C10 : 0 3-OH, C12 : 0, C14 : 0 and C16 : 0 2-OH. S3T contained diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), and phosphatidylethanolamine (PE) as major polar lipids with minor amounts of unidentified phospholipid (PL) and unidentified lipids (L1–2). Genomic DNA G+C content was 68.3 mol%. 16S rRNA gene sequence comparisons indicated that S3T represents a member of the genus Comamonas in family Comamonadaceae of the class Betaproteobacteria . S3T has a sequence similarity of 98.96 % with Comamonas koreensis YH12T, 97.93 % with Comamonas guangdongensis CY01T and <96.97 % with other members of the genus Comamonas . DNA–DNA hybridization values between S3T and the type strains of the most closely related species were clearly below the 70 % threshold. On the basis of phenotypic, genotypic and phylogenetic analysis, it is proposed that S3T represents a novel species of the genus Comamonas , for which the name Comamonas sediminis sp. nov. is proposed. The type strain is S3T (=KEMB 563–466T =JCM 31169T).
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Pseudoalteromonas fenneropenaei sp. nov., a marine bacterium isolated from sediment of a Fenneropenaeus chinensis pond
More LessA novel Gram-stain-negative, motile, oxidase- and catalase-positive, non-spore-forming, non-pigmented, aerobic bacterium, designated rzy34T, was isolated from the sediment of a pond containing farmed Fenneropenaeus chinensis Rizhao, China. The strain was able to grow at pH 6–10 (optimum pH 7), 20–40 °C (optimum 30 °C) and in the presence of 1.0–6.0 % NaCl (optimum 1.0–2.0 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that the nearest relative of strain rzy34T was Pseudoalteromonas xiamenensis Y2T, with the highest sequence similarity of 96.09 %. Within the genus Pseudoalteromonas , it showed the lowest similarity of 92.7 % to Pseudoalteromonas donghaensis . The G+C content of the chromosomal DNA of strain rzy34T was 45.3 mol%. The predominant cellular fatty acids were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0, C17 : 1ω8c and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c). The major respiratory quinone was Q-8. Polar lipid analysis indicated the presence of phosphatidylethanolamine and phosphatidylcholine. On the basis of the phenotypic and phylogenetic characteristics, strain rzy34T represents a novel species of the genus Pseudoalteromonas , for which the name Pseudoalteromonas fenneropenaei sp. nov. is proposed. The type strain is rzy34T (=CGMCC 1.15325T=KCTC 42730T).
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- Bacteroidetes
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Moheibacter stercoris sp. nov., isolated from an input sample of a biogas plant
More LessA Gram-stain-negative, rod-shaped bacterium, strain 784B1_12E-CasoT, was isolated from a mixed manure sample used as input material of a German biogas plant. Phylogenetic identification based on the nearly full-length 16S rRNA gene sequence placed the strain within the family Flavobacteriaceae (Bacteroidetes) with highest sequence similarity to the type strain of Moheibacter sediminis (93.7 %) followed by Empedobacter brevis (90.7 %). Major cellular fatty acids of strain 784B1_12E-CasoT were iso-C15 : 0 and iso-C17 : 0 3-OH. The polyamine pattern contained predominantly sym-homospermidine and the quinone system consisted exclusively of menaquinone MK-6. Major polar lipids were phosphatidylethanolamine and an unidentified polar lipid only detectable after staining for total lipids. The DNA G+C content was 34.5 mol%. Based on phylogenetic, chemotaxonomic and physiological analyses, a novel species of the genus Moheibacter is proposed, Moheibacter stercoris sp. nov. (type strain 784B1_12E-CasoT=CIP 110830T=LMG 28502T).
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Fulvivirga lutimaris sp. nov., isolated from a tidal flat sediment
More LessA Gram-stain-negative, non-flagellated, non-gliding and rod-shaped bacterial strain, designated TM-6T, was isolated from a tidal flat sediment in the Korean peninsula. Strain TM-6T was found to grow optimally at pH 7.0–8.0, at 30 °C and in the presence of 2–3% (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain TM-6T joined the clade comprising recognized species of the genus Fulvivirga , with which it exhibited 94.7– 95.2 % sequence similarity. Strain TM-6T was found to contain iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH as major fatty acids. The only isoprenoid quinone was menaquinone-7 (MK-7). The major polar lipids were identified as phosphatidylethanolamine and three unidentified lipids. The DNA G+C content of strain TM-6T was 50.9 mol%. Differential phenotypic properties, together with the phylogenetic distinctiveness, revealed that strain TM-6T is distinguishable from recognized Fulvivirgaspecies. On the basis of the data presented, strain TM-6T is proposed to represent a novel species of the genus Fulvivirga , for which the name Fulvivirga lutimaris sp. nov. is proposed. The type strain is TM-6T (=KCTC 42720T=CECT 9024T).
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Tenacibaculum sediminilitoris sp. nov., isolated from a tidal flat
More LessA Gram-stain-negative, non-flagellated, non-gliding, non-spore-forming bacterial strain, designated YKTF-3T, was isolated from a tidal flat on the Yellow Sea, South Korea. Strain YKTF-3T grew optimally at 30 °C and in the presence of 2.0–4.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences showed that strain YKTF-3T fell within the clade comprising the type strains of Tenacibaculumspecies. The novel strain exhibited 16S rRNA gene sequence similarity values of 97.22–98.34 % to the type strains of Tenacibaculum gallaicum, Tenacibaculum ascidiaceicola , Tenacibaculum litoreum, Tenacibaculum discolor , Tenacibaculum aestuarii and Tenacibaculum lutimaris, and of 95.08–96.95 % to the type strains of the other Tenacibaculum species. Strain YKTF-3T contained MK-6 as the predominant menaquinone and iso-C15 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and iso-C17 : 0 3-OH as the major fatty acids. The major polar lipids of strain YKTF-3T were phosphatidylethanolamine, one unidentified lipid, one unidentified aminophospholipid, one unidentified glycolipid and one unidentified aminolipid. The DNA G+C content was 32.3 mol% and its mean DNA–DNA relatedness values with the type strains of the six phylogenetically closely relatedTenacibaculum species were 10–27 %. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, revealed that strain YKTF-3T is separate from other recognized species of the genus Tenacibaculum . On the basis of the data presented, strain YKTF-3T is considered to represent a novel species of the genus Tenacibaculum , for which the name Tenacibaculum sediminilitoris sp. nov. is proposed. The type strain is YKTF-3T (=KCTC 52210T=NBRC 111991T).
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Kordia ulvae sp. nov., a bacterium isolated from the surface of green marine algae Ulva sp.
More LessA novel bacterial strain, SC2T, was isolated from Ulva sp., a green marine algae, which was collected from Dadeng island, Xiamen, China. Strain SC2T was Gram-stain-negative, aerobic, rod-shaped and had no flagellum. Oxidase and catalase were positive. Strain SC2Twas able to degrade skimmed milk, agar, soluble starch, Tween 20 and Tween 80 but not colloidal chitin. Growth was observed at salinities of 1–6 % and temperatures of 15–37 °C, with optimal salinity and temperature of 2 % and 30 °C, respectively. Phylogenetic analysis based on the 16S rRNA gene indicated that strain SC2T was affiliated to the genus Kordia , with highest sequence similarity to Kordia algicida OT-1T (97.23 %), Kordia antarctica IMCC 3317T (97.23 %) and Kordia jejudonensis SSK3-3T (97.02 %); the type strains of other species of the genus Kordia shared 93.98–95.78 % gene sequence similarity with strain SC2T. The average nucleotide identity value and estimated DNA–DNA hybridization value between strain SC2T and the above three type strains ( K. algicida OT-1T, K. antarctica IMCC 3317T and K. jejudonensis SSK3-3T) were found to be 79.4–82.4 % and 24.2–27.0 %, respectively. The predominant fatty acids (>5.0 %) were C16 : 0, iso-C15 : 0, iso-C15 : 0 3-OH, iso-C17 : 0 3-OH, summed feature 3 (comprising C16 : 1 ω7c/C16 : 1 ω6c), summed feature 8 (comprising C18 : 1 ω7c/C18 : 1 ω6c) and summed feature 9 (comprising iso-C17 : 1 ω9c/C16 : 0 10-methyl). The respiratory quinone was determined to be solely menaquinone-6 (MK-6). The polar lipid profile of strain SC2T consisted of four unknown lipids, three unidentified phospholipids, one unidentified aminolipid and phosphatidylethanolamine. The G+C content of the genomic DNA was 34.5 mol%. The combined genotypic and phenotypic data showed that strain SC2T represents a novel species within the genus Kordia , for which the name Kordia ulvae sp. nov. is proposed. The type strain is SC2T (= KCTC 42872T=MCCC 1A01772T=LMG 29123T).
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Flavobacterium tyrosinilyticum sp. nov., isolated from the rhizosphere of wild strawberry
Juan Du and Tae-Hoo YiA Gram-stain-negative, facultatively anaerobic, motile and rod-shaped bacterial strain, designated THG-DN8.8T, was isolated from the rhizosphere of a wild strawberry plant, located on Gyeryong Mountain, Daejeon, Republic of Korea. According to 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Flavobacterium and was related most closely to Flavobacterium banpakuense 15F3T (97.7 % sequence similarity), Flavobacterium ginsenosidimutans THG-01T(97.3 %), Flavobacterium ginsengiterrae DCY55T (96.9 %) and Flavobacterium chungbukense CS100T (96.7 %). Catalase and oxidase tests were positive. Levels of DNA–DNA relatedness with its phylogenetically closest neighbours were below 40.0 %. The DNA G+C content was determined to be 39.1 mol%. Strain THG-DN8.8T also was found to be able to grow at 4–33 °C, with 0–2 % (w/v) NaCl and at pH 5.5–9.5. The major fatty acids were iso-C15 : 0, summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c) and C16 : 0. Menaquinone-6 (MK-6) was the dominant respiratory quinone, and phosphatidylethanolamine and phosphatidyldiethanolamine were the main polar lipids. On the basis of the data presented, strain THG-DN8.8T represents a novel species, for which the name Flavobacterium tyrosinilyticum sp. nov. is proposed. The type strain is THG-DN8.8T (=KCTC 42726T=CCTCC AB 2015295T).
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Lentimicrobium saccharophilum gen. nov., sp. nov., a strictly anaerobic bacterium representing a new family in the phylum Bacteroidetes, and proposal of Lentimicrobiaceae fam. nov.
A novel, strictly anaerobic, short rod-shaped bacterium, designated strain TBC1T, was isolated from methanogenic granular sludge in a full-scale mesophilic upflow anaerobic sludge blanket reactor treating high-strength starch-based organic wastewater. Cells of this strain were 2–4 µm long and 0.4–0.6 µm wide. They were non-motile and Gram-stain-negative. The optimum growth temperature was 30–37 °C, with a range of 20–40 °C. The optimum pH for growth was around pH 7.0, while growth occurred in a range of pH 6.5–9.0. Strain TBC1T grew chemo-organotrophically on a narrow range of carbohydrates under anaerobic conditions. Yeast extract was required for its growth. The major fermentative end products from glucose, supplemented with yeast extract, were acetate, malate, propionate, formate and hydrogen. Doubling time under optimal growth conditions was estimated to be 1 day. The DNA G+C content of strain TBC1T was 49.2 mol% as determined by HPLC. Major cellular fatty acids were C16 : 0, C18 : 0, C16 : 1 ω9c and C18 : 1 ω9c. Based on its 16S rRNA gene sequence, strain TBC1T was shown to represent a distinct lineage at the family level in the phylum Bacteroidetes . Among previously described species of this phylum, Mucilaginibacter boryungensis BDR-9T ( Sphingobacteriaceae ) displayed the highest sequence similarity (85.9 %) with strain TBC1T. Phylogenomic analyses using 38–83 single copy marker genes also supported the novelty of strain TBC1T at the family level. Based on its characteristics, strain TBC1T (=JCM 30898T=DSM 100618T) is considered to be the type strain of a novel species of a new genus, Lentimicrobium saccharophilum gen. nov., sp. nov. A new family, Lentimicrobiaceae fam. nov., is also proposed encompassing the strain and related environmental 16S rRNA gene clone sequences.
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Sphingobacterium zeae sp. nov., an endophyte of maize
More LessA yellow-pigmented strain (JM-1081T) isolated from healthy stem tissue of Zea mays was taxonomically characterized. Cells of the strain were rod-shaped and Gram-stain-negative. Comparative 16S rRNA gene sequence analysis revealed closest relationship to the type strains of Sphingobacterium multivorum (98.1 % similarity), Sphingobacterium mucilaginosum (97.9 %) and Sphingobacterium siyangense (97.8 %). 16S rRNA gene sequence similarities to the type strains of all other Sphingobacterium species were below 97.8 %. Fatty acid analysis of whole-cell hydrolysates of the strain resulted in a pattern typical of the genus Sphingobacterium with iso-C15 : 0 2-OH and/or C16 : 1 ω7c, iso-C15 : 0, iso-C17 : 0 3-OH and C16 : 0 and as major compounds. The polyamine pattern contained predominantly sym-homospermidine. The major quinone was menaquinone MK-7 and the only identified lipids in the polar lipid profile were phosphatidylethanolamine and phosphatidylserine. In addition, 15 unidentified lipids were detected in moderate to major amounts. Sphingolipid was detected. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid. DNA–DNA hybridizations with two of the closely related type strains, those of S. multivorum and S. siyangense , as well as Sphingobacterium canadense resulted in values below 70 %. In addition to the genotypic differences, differential biochemical and chemotaxonomic properties confirmed that the isolate JM-1081T represents a novel species, for which the name Sphingobacterium zeae sp. nov. is proposed. The type strain is JM-1081T (=LMG 29191T=CCM 8652T).
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Niabella pedocola sp. nov., isolated from soil
More LessAn aerobic, Gram-stain-negative, oxidase-positive and catalase-negative, non-motile, non-spore-forming, rod-shaped, orange-pigmented bacterium designated strain R384T was isolated from soil. Flexirubin-type pigments were present. Phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain R384T formed a lineage within the family Chitinophagaceae of the phylum Bacteroidetes that was distinct from various species of the genus Niabella , including ‘ Niabella thaonhiensis ’ NHI-24 (98.47 % sequence similarity), Niabellaaurantiaca DSM 17617T (96.89 %), Niabelladrilacis E90T (96.63 %), Niabellahirudinis E96T (96.61 %), Niabellatibetensis 15-4T (95.53 %), Niabellasoli DSM 19437T (94.81 %), Niabellaginsengisoli GR10-1T (94.19 %) and Niabellayanshanensis CCBAU 05354T (93.67 %). The major isoprenoid quinone was menaquinone-7 (MK-7) and the major polar lipid was phosphatidylethanolamine. The major cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G, summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c) and iso-C17 : 0 3-OH. The DNA G+C content of strain R384Twas 44.7 mol %. DNA–DNA hybridization values between strain R384T and other members of the genus Niabella ranged from 26 to 55 %. On the basis of phenotypic, genotypic and phylogenetic analysis, strain R384T represents a novel species of the genus Niabella , for which the name Niabellapedocola sp. nov. is proposed. The type strain is R384T (=KEMB 9005-329T=KACC 18454T=JCM 31011T).
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Aquaticitalea lipolytica gen. nov., sp. nov., isolated from Antarctic seawater
A Gram-stain-negative, rod-shaped bacterium, designated Ar-125T, was isolated from Antarctic seawater. It produced carotenoid-like pigments and did not produce Bchl a. Ar-125T was positive for hydrolysis of DNA, aesculin, gelatin, starch, Tween 40 and Tween 60. The sole respiratory quinone was MK-6. The major polar lipids were phosphatidylethanolamine, one unidentified aminolipid, one unidentified glycolipid and two unidentified lipids. The principal fatty acids were branched-chain fatty acids, including iso-C15 : 0, iso-C15 : 1 G, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C16 : 0, iso-C17 : 0 3-OH, iso-C16 : 0 3-OH and iso-C15 : 0 3-OH, as well as C15 : 0. The genomic DNA G+C content was 31.8 mol%. On the basis of 16S rRNA gene sequence analysis, Ar-125T is closely related to the species of the genera Bizionia (with 16S rRNA gene pairwise sequence similarity of 93.7–96.5 %), Formosa (94.3–95.8 %), Gaetbulibacter (94.2–95.7 %), Geojedonia (95.5 %), Gelidibacter (93.3–95.4 %), Meridianimaribacter (95.3 %) and Psychroserpens (94.8–95.3 %), of the family Flavobacteriaceae . Phylogenetic analysis indicated that it represented an independent lineage and that the closest relatives were members of the genus Gelidibacter . Differential phenotypic properties and chemotaxonomic differences, together with phylogenetic distinctiveness, revealed that Ar-125T could be differentiated from members of closely related genera. Therefore, it is proposed that Ar-125T represents a novel species in a new genus, for which the name Aquaticitalea lipolytica gen. nov., sp. nov. (type strain Ar-125T =CGMCC 1.15295T =JCM 30876T) is proposed.
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Roseivirga maritima sp. nov., isolated from seawater
More LessA Gram-stain-negative, non-flagellated, non-gliding and rod-shaped bacterial strain, designated GM-5T, was isolated from seawater from near the Korean peninsula. Strain GM-5T was found to grow optimally at pH 7.0–8.0, at 25 °C and in the presence of 2 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain GM-5T falls within the clade comprising the genus Roseivirga , with which it exhibits 94.8–96.8 % sequence similarity. Strain GM-5T was found to contain MK-7 as the predominant menaquinone and iso-C15 : 1 G, iso-C15 : 0, and iso-C17 : 0 3-OH as the major fatty acids. The major polar lipids were identified as phosphatidylethanolamine, an unidentified phospholipid and two unidentified lipids. The DNA G+C content of strain GM-5T was determined to be 42.3 mol%. Differential phenotypic properties, together with the phylogenetic distinctiveness, revealed that strain GM-5T is distinguishable from species of the genus Roseivirga with validly published names. On the basis of the data presented, strain GM-5T is proposed to represent a novel species of the genus Roseivirga , for which the name Roseivirga maritima sp. nov. is proposed. The type strain is GM-5T (=KCTC 42718T =NBRC 111589T).
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Lutibacter profundi sp. nov., isolated from a deep-sea hydrothermal system on the Arctic Mid-Ocean Ridge and emended description of the genus Lutibacter
More LessA bacterial strain designated LP1T was isolated from a microbial mat growing on the surface of a black smoker chimney at the Loki’s Castle hydrothermal system, which is located on the Arctic Mid-Ocean Ridge. Phylogenetic analyses based on 16S rRNA gene sequences positioned strain LP1T within the family Flavobacteriaceae with Lutibacter holmesii as the closest relative (97.5 % 16S rRNA gene sequence similarity). Strain LP1T was rod-shaped, Gram-reaction-negative and non-motile. It grew in a modified artificial seawater medium supplemented with tryptone and vitamins at pH 5.5–7.5 (optimum pH 6.0–6.5), within a temperature range of 13–34 °C (optimum 23 °C), and under microaerobic conditions. The most abundant fatty acids (>10 %) were iso-C15 : 0 (25.2 %) and iso-C15 : 0 3-OH (14.5 %). The genome of strain LP1T has a DNA G+C content of 29.8 mol%. Based on the results of the polyphasic characterization presented here, strain LP1T is considered to represent a novel species of the genus Lutibacter , for which the name Lutibacter profundi sp. nov. is proposed. The type strain is LP1T (=DSM 100437T =JCM 30585T). An emended description of the genus Lutibacter is also provided to fit the description of strain LP1T.
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Gramella sediminilitoris sp. nov., isolated from a tidal flat
More LessA Gram-stain-negative, aerobic, non-spore-forming, motile by gliding and coccoid, ovoid or rod-shaped bacterial strain, designated GHTF-27T, was isolated from a tidal flat at Goheung, South Korea, and subjected to a taxonomic study using a polyphasic approach. The novel strain grew optimally at 30 °C, at pH 7.0–8.0 and in the presence of 2.0–5.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain GHTF-27T belongs to the genus Gramella . It exhibited 16S rRNA gene sequence similarity values of 97.6–98.3 % to the type strains of Gramella aestuariivivens , Gramella echinicola , Gramella gaetbulicola , Gramella aquimixticola , Gramella aestuarii and Gramella portivictoriae , respectively, and of 93.8–96.7 % to the type strains of the other species of the genus Gramellawith validly published names. Strain GHTF-27T contained MK-6 as the predominant menaquinone and iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. The major polar lipids of strain GHTF-27T were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content of strain GHTF-27T was 39.7 mol% and DNA–DNA relatedness values with the type strains of the six phylogenetically closely related species of the genus Gramellawere 12–28 %. The differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain GHTF-27T is separated from other species of the genus Gramella . On the basis of the data presented, strain GHTF-27T is considered to represent a novel species of the genus Gramella , for which the name Gramella sediminilitorissp. nov. is proposed. The type strain is GHTF-27T (=KCTC 52208T =NBRC 111992T).
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Filimonas zeae sp. nov., an endophytic bacterium isolated from maize root
A novel Gram-stain-negative, aerobic, motile by gliding and filamentous strain, designated 772T,was isolated from surface-sterilized root tissue of maize planted in the Fangshan District of Beijing, China. 16S rRNA gene sequence analysis indicated that strain 772T was closely related to Filimonas endophytica SR2-06T and Filimonas lacunae YT21T of the family Chitinophagaceae with sequence similarities of 99.0 and 96.9 %, respectively. However, the new isolate exhibited relatively low levels of DNA–DNA relatedness with respect to Filimonas. endophytica KCTC 42060T (18.7±1.8 %) and Filimonas. lacunae DSM 21054T (17.9±2.0%). The DNA G+C content of strain 772T was 44.9 mol%. The respiratory quinone was menaquinone-7 and the polar lipid profile consisted of phosphatidylethanolamine, two unidentified aminophospholipids, two unidentified phospholipids and one unidentified lipid. The major fatty acids were iso-C15 : 0 and iso-C15 : 1 G. The results of the physiological and biochemical tests and minor differences in the fatty acid profiles allowed the clear phenotypic differentiation of strain 772T from the closely related species Filimonas. endophytica andF. lacunae. Strain 772T thus represents a novel species within the genus Filimonas , for which the name Filimonas zeae sp. nov. is proposed. The type strain is 772T (=CGMCC 1.15290T=DSM 100760T).
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- Eukaryotic micro-organisms
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Wickerhamomyces orientalis f.a., sp. nov.: an ascomycetous yeast species belonging to the Wickerhamomyces clade
Five closely related yeast strains were isolated from soil in Kharg Island, Persian Gulf, Iran, and from fallen fruits in Galle, Sri Lanka, during separate projects. Morphologically, the strains produced white-coloured yeast colonies, with cells that were ovoid to ellipsoidal, making branched, true hyphae and pseudohyphae. Ascospore formation was not observed. Biochemically, the strains were able to ferment d-glucose and weakly ferment d-galactose. The strains could use a wide variety of carbon sources except methanol and hexadecane. Phylogenetic analyses using combined sequences of the small ribosomal subunit and the D1/D2 domains of the LSU, as well as the internal transcribed spacer regions, suggested that these strains belong to the Wickerhamomyces clade and that together they form one strongly supported phylogenetic clade. Differences in their sequences, biochemistry and morphology suggest they are representatives of distinct species of the genus Wickerhamomyces. Therefore, the name Wickerhamomyces orientalis f.a., sp. nov. is proposed to accommodate these novel strains; the type strain is IBRC-M 30103T (=CBS 13306T). The MycoBank number is MB 807323.
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Disentangling identity of species of the genus Taphrina parasitizing herbaceous Rosaceae, with proposal of Taphrina gei-montani sp. nov.
Five strains (CCY 058-007-001T, CCY 058-007-002, CCY 058-007-003, CCY 058-007-004 and CCY 058-007-005) of a novel parasitic yeast belonging to the genus Taphrina were isolated from leaf tissues of Geum montanum L. (Rosaceae), collected from the Vysoké Tatry Mountains, Slovakia. Genetic analyses revealed that these isolates differ by 15 unique substitutions in the ITS region and by six substitutions in the rns gene from all other species of the genus Taphrina analysed hitherto. The novel strains are also distinguished from all other species of the genus Taphrina by their morphology, biochemical properties and ecology. These strains represent a novel species, for which the name Taphrina gei-montani sp. nov. is proposed. The type strain is CCY 058-007-001T (=CBS 14159=BU001). The MycoBank number is MB815677. The present study also demonstrates that two distinct species of the genus Taphrina parasitize the herbaceous Rosaceae: Taphrina gei-montani sp. nov. on Geum montanum and Taphrina tormentillae on Potentilla species.
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Metahyphopichia laotica gen. nov., sp. nov., a polymorphic yeast related to Hyphopichia
More LessFour strains alternating between yeast and filamentous growth morphologies were isolated from flowers in two regions of Laos. In liquid environment the isolates propagated by budding and developed irregularly shaped pseudohyphae. On solid media, their yeast cells switched to hyphal growth which could return to the yeast phase by developing lateral blastoconidia. The sequences of the D1/D2 domains of the large subunit (LSU) 26S rRNA genes, the internal transcribed spacer (ITS) regions and the small subunit (SSU) 18S rRNA genes were identical in the four strains and differed from the corresponding sequences of other yeast species available in databases by at least 11 % (D1/D2), 13 % (ITS) and 7 % (SSU). In an independent project, two strains with D1/D2 and ITS sequences very similar to those of the Laotian strains were found in bark samples collected in Brazil. The six strains also differed from the closest yeast species in physiological properties, indicating that they represented a hitherto undescribed species. Phylogenetic analysis of the D1/D2 sequences, and the concatenated sequences of the SSU rRNA genes, D1/D2 domains of LSU rRNA genes as well as the protein-encoding genes ACT1 and TEF1 placed thestrains close to Hyphopichia. To reflect this position, the novel genus name Metahyphopichia gen. nov. and the novel species name Metahyphopichia laotica gen. nov., sp. nov. are proposed for them. The type strain of the type species is 11-1006T(=CBS 13022T=CCY 092-001-001T=NCAIM Y.02126T) and was isolated in Luang Prabang (Laos). MycoBank registration numbers are MB 808253 (Metahyphopichia) and MB 808254 (Metahyphopichia laotica).
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Aspergillus asper sp. nov. and Aspergillus collinsii sp. nov., from Aspergillus section Usti
More LessIn sampling fungi from the built environment, two isolates that could not confidently be placed in described species were encountered. Phenotypic analysis suggested that they belonged in Aspergillus sect. Usti. In order to verify the sectional placement and to assure that they were undescribed rather than phenotypically aberrant isolates, DNA was isolated and sequenced at the beta-tubulin, calmodulin, internal transcribed spacer and RNA polymerase II loci and sequences compared with those from other species in the genus Aspergillus. At each locus, each new isolate was distant from existing species. Phylogenetic trees calculated from these data and GenBank data for species of the section Usti excluded the placement of these isolates in existing species, with statistical support. Because they were excluded from existing taxa, the distinct species Aspergillus asper (type strain NRRL 35910T) and Aspergillus collinsii (type strain NRRL 66196T) in sect. Usti are proposed to accommodate these strains.
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Myrmecridium hiemale sp. nov. from snow-covered alpine soil is the first eurypsychrophile in this genus of anamorphic fungi
More LessMyrmecridium hiemale sp. nov. was isolated from snow-covered alpine bare soil and is described as the first eurypsychrophilic species of this genus of filamentous fungi. Colony growth temperature experiments were carried out in the range 4–37 °C. Morphological characteristics and colony appearance were in accordance with characteristics typical for Myrmecridium, but M. hiemale does not grow at temperatures of 25 °C and above. Sequence analyses of the internal transcribed spacer and LSU rRNA D1/D2 regions indicated that the strain in question represents a distinct taxon within the genus Myrmecridium (Myrmecridiaceae, Sordariomycetes, Ascomycota). The type strain of M. hiemale is CBS 141017T(=JMRC 12083T). A morphological description is provided, and a key is presented for the currently known taxa of Myrmecridium, a group of interesting fungi that are either saprobes or plant endophytes.
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Yamadazyma endophytica f.a. sp. nov., an ascomycetous yeast species isolated from leaf tissue
More LessStrain DMKU-CE23T representing a novel yeast species was isolated from tissue of a corn leaf (Zea may L.) collected in Thailand. A phylogenetic analysis based on the combined sequences of the internal transcribed spacer (ITS) region and the D1/D2 region of the LSU rRNA gene indicated that strain DMKU-CE23T belongs to the Yamadazyma clade and is clearly distinct from other related species. It therefore represents a novel species of the genus Yamadazyma although the formation of ascospores was not observed. The strain of novel species was most closely related to the type strain of Yamadazyma epiphylla but with 5.1 % nucleotide substitutions in the ITS region and 3.7 % nucleotide substitutions in the D1/D2 region of the LSU rRNA gene. The name Yamadazyma endophytica f.a., sp. nov. is proposed. The type strain is DMKU-CE23T (=CBS 14163T=TBRC 5174T).
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- Evolution, Phylogeny and Biodiversity
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Recombination and phenotype evolution dynamics of Helicobacter pylori in colonized hosts
More LessThe ample genetic diversity and variability of Helicobater pylori, and therefore its phenotypic evolution, relate not only to frequent mutation and selection but also to intra-specific recombination. Webb and Blaser applied a mathematical model to distinguish the role of selection and mutation for Lewis antigen phenotype evolution during long-term gastric colonization in infected animal hosts (mice and gerbils). To investigate the role of recombination in Lewis antigen phenotype evolution, we have developed a prior population dynamic by adding recombination term to the model. We simulate and interpret the new model simulation's results with a comparative analysis of biological aspects. The main conclusions are as follows: (i) the models and consequently the hosts with higher recombination rate require a longer time for stabilization; and (ii) recombination and mutation have opposite effects on the size of H. pylori populations with phenotypes in the range of the most-fit ones (i.e. those that have a selective advantage) due to natural selection, although both can increase phenotypic diversity.
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- Taxonomic Note
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Description of strain FC3T as the neotype strain of Actinobaculum massiliense
More LessActinobaculum massiliense (Euzéby, 2006) was isolated from the urine of an elderly woman in 2001. Unfortunately, the strain deposited as the type strain was, by error, an Actinobaculum schaalii strain ( Yassin et al., 2015 ). In 2015, we isolated a new strain of A. massiliense , FC3, from the urine of a 12-year-old patient with acute cystitis. We herein present the characteristics of strain FC3 (=CSUR P1982=DSM 100580) and formally propose it as the neotype strain of A. massiliense.
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Volumes and issues
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Volume 74 (2024)
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Volume 73 (2023)
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Volume 72 (2022 - 2023)
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Volume 71 (2020 - 2021)
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Volume 70 (2020)
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Volume 69 (2019)
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Volume 68 (2018)
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Volume 67 (2017)
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Volume 26 (1976)
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Volume 25 (1975)
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Volume 23 (1973)
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Volume 22 (1972)
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Volume 21 (1971)
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Volume 20 (1970)
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Volume 19 (1969)
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Volume 6 (1956)
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Volume 5 (1955)
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Volume 4 (1954)
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Volume 3 (1953)
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Volume 2 (1952)
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Volume 1 (1951)