- Volume 67, Issue 12, 2017
Volume 67, Issue 12, 2017
- Notification List
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- New Taxa
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- Actinobacteria
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Streptomyces kalpinensis sp. nov., an actinomycete isolated from a salt water beach
More LessA novel actinobacterium designated TRM 46509T was isolated from a salt water beach at Kalpin, Xinjiang, north-west China. The strain was aerobic and Gram-stain-positive, with an optimum NaCl concentration for growth of 1 % (w/v). The isolate formed sparse aerial mycelium and produced spiral spores at the end of the aerial mycelium on Gauze’s No. 1 medium. The isolate contained ll-diaminopimelic acid as the diagnostic diamino acid and ribose as the major whole-cell sugar. The polar lipids included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol, phosphatidylinositol mannosides and an unidentified phospholipid. The predominant menaquinones were MK-9(H2), MK-9(H6) and MK-9(H8). The major fatty acids were C16:0, iso-C16 : 0, anteiso-C15 : 0, iso-C15 : 0 and iso-C14 : 0. The G+C content of the DNA was 69.3 mol%. Phylogenetic analysis showed that strain TRM 46509T shared 16S rRNA gene sequence similarity of 97.6 % with the closest described species Streptomyces tacrolimicus ATCC 55098T. On the basis of evidence from this polyphasic study, strain TRM 46509T should be designated as representing a novel species of the genus Streptomyces , for which the name Streptomyces kalpinensis sp. nov. is proposed. The type strain is TRM 46509T (=CCTCC AA 2015028T=KCTC 39667T).
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Frankia asymbiotica sp. nov., a non-infective actinobacterium isolated from Morella californica root nodule
The taxonomic status of strain M16386T, a nitrogen-fixing but non-nodulating isolate from Morella californica, was established on the basis of a polyphasic approach. The strain grows as branched hyphae, with vesicles and non-motile productive multilocular sporangia. It metabolizes short fatty acids, TCA cycle intermediates and carbohydrates as carbon sources, and fixes nitrogen in the absence of combined nitrogen source in the growth media. Chemotaxonomic traits of strain M16386T are consistent with its affiliation to the genus Frankia . The characteristic diamino acid in the cell wall is meso-diaminopimelic acid. Strain M16386T contains phosphatidylinositol, phosphatidylglycerol, diphosphatidylglycerol, glycophospholipid and phospholipid as polar lipids; MK-9(H4) and MK-9(H6) as the predominant menaquinones; iso-C16 : 0 and C17 : 1ω8c as major fatty acids; and galactose, glucose, mannose, rhamnose and ribose as whole-cell sugars. Strain M16386T showed 98.2 % 16S rRNA gene sequence similarity with its closest phylogenetic neighbour, Frankia inefficax DSM 45817T. Based on these results, strain M16386T (=DSM 100626T=CECT 9040T) is designated the type strain of a novel species of the genus Frankia , for which the name Frankia asymbiotica sp. nov. is proposed.
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Two novel species of rapidly growing mycobacteria: Mycobacterium lehmannii sp. nov. and Mycobacterium neumannii sp. nov.
Two rapidly growing mycobacteria with identical 16S rRNA gene sequences were the subject of a polyphasic taxonomic study. The strains formed a well-supported subclade in the mycobacterial 16S rRNA gene tree and were most closely associated with the type strain of Mycobacterium novocastrense . Single and multilocus sequence analyses based on hsp65, rpoB and 16S rRNA gene sequences showed that strains SN 1900T and SN 1904T are phylogenetically distinct but share several chemotaxonomic and phenotypic features that are are consistent with their classification in the genus Mycobacterium . The two strains were distinguished by their different fatty acid and mycolic acid profiles, and by a combination of phenotypic features. The digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values for strains SN 1900T and SN 1904T were 61.0 % and 94.7 %, respectively; in turn, the corresponding dDDH and ANI values with M. novocastrense DSM 44203T were 41.4 % and 42.8 % and 89.3 % and 89.5 %, respectively. These results show that strains SN1900T and SN 1904T form new centres of taxonomic variation within the genus Mycobacterium . Consequently, strains SN 1900T (40T=CECT 8763T=DSM 43219T) and SN 1904T (2409T=CECT 8766T=DSM 43532T) are considered to represent novel species, for which the names Mycobacterium lehmannii sp. nov. and Mycobacterium neumannii sp. nov. are proposed. A strain designated as ‘ Mycobacterium acapulsensis’ was shown to be a bona fide member of the putative novel species, M. lehmannii.
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Streptomyces amphotericinicus sp. nov., an amphotericin-producing actinomycete isolated from the head of an ant (Camponotus japonicus Mayr)
More LessA novel actinomycete, designated strain 1H-SSA8T, was isolated from the head of an ant (Camponotus japonicus Mayr) and was found to produce amphotericin. A polyphasic approach was employed to determine the status of strain 1H-SSA8T. Morphological and chemotaxonomic characteristics were consistent with those of members of the genus Streptomyces . The menaquinones detected were MK-9(H6), MK-9(H8) and MK-9(H4). The phospholipid profile consisted of diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine and phosphatidylinositol mannoside. The major fatty acids were identified as iso-C16 : 0, C16 : 0, C15 : 0 and anteiso-C15 : 0. Analysis of the 16S rRNA gene sequence showed that strain 1H-SSA8T belongs to the genus Streptomyces with high sequence similarity to Streptomyces ramulosus NRRL B-2714T (99.2 %). Two tree-making algorithms based on 16S rRNA gene sequences showed that the isolate formed a phyletic line with Streptomyces himastatinicus ATCC 53653T (98.7 %). The MLSA utilizing partial sequences of the housekeeping genes (atpD, gyrB, recA, rpoB and trpB) also supported the position. However, evolutionary distances were higher than the 0.007 MLSA evolutionary distance threshold proposed for species-level relatedness. Moreover, the low level of DNA–DNA relatedness and phenotypic differences allowed the novel isolate to be differentiated from its most closely related strain S. ramulosus NRRL B-2714T and strain S. himastatinicus ATCC 53653T. It is concluded that the organism can be classified as representing a novel species of the genus Streptomyces , for which the name Streptomyces amphotericinicus sp. nov. is proposed. The type strain is 1H-SSA8T (=CGMCC 4.7350T=DSM 103128T).
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Kocuria salina sp. nov., an actinobacterium isolated from the rhizosphere of the halophyte Arthrocnemum macrostachyum and emended description of Kocuria turfanensis
A novel, non-motile coccoid, Gram-positive and non-endospore forming bacterium, designated Hv14bT, was isolated from the rhizosphere of the halophyte Arthrocnemum macrostachyum. It was observed to be catalase positive and oxidase negative and able to hydrolyse starch. MK-8(H2) was identified as the dominant menaquinone and the major cellular fatty acids were anteiso-C15 : 0 and iso-C15 : 0. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid. The 16S rRNA genes showed the highest 16S rRNA sequence identity with K. polaris DSM 14382T, K. rosea DSM 20447T and K. turfanensis DSM 22143T. Based on the phenotypic and molecular features and DNA–DNA hybridization data, it is concluded that strain Hv14bT is proposed to represent a novel species in the genus Kocuria , Kocuria salina sp. nov., with the type strain Hv14bT=DSM 28714T=CECT 9229T.
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Nonomuraea glycinis sp. nov., a novel actinomycete isolated from the root of black soya bean [Glycine max (L.) Merr]
More LessA novel actinomycete, designated strain NEAU-BB2C19T, was isolated from the root of black soya bean [Glycine max (L.) Merr] collected from Harbin, Heilongjiang Province, China, and characterized using a polyphasic approach. The strain was an aerobic, Gram-stain-positive actinomycete that formed extensively branched substrate mycelium and aerial hyphae. The predominant menaquinones were MK-9(H2) and MK-9(H0). The major cellular fatty acid profile consisted of iso-C16 : 0, 10-methyl C17 : 0 and 10-methyl C18 : 0. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside, phosphatidylglycerol and glycolipid. The DNA G+C content was 68.2±0.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NEAU-BB2C19T should be assigned to the genus Nonomuraea and formed a distinct branch with its closest neighbour Nonomuraea guangzhouensis NEAU-ZJ3T (98.75 % 16S rRNA gene sequence similarity). The morphological and chemotaxonomic properties of the strain were also consistent with those of members of the genus Nonomuraea . A combination of DNA–DNA hybridization results and some phenotypic characteristics indicated that strain NEAU-BB2C19T could be clearly differentiated from its closest phylogenetic relative. Thus, the strain is concluded to represent a novel species of the genus Nonomuraea , for which the name Nonomuraea glycinis sp. nov. is proposed. The type strain is NEAU-BB2C19T (=CGMCC 4.7430T=DSM 104838T).
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Verrucosispora endophytica sp. nov., isolated from the root of wild orchid (Grosourdya appendiculata (Blume) Rchb.f.)
More LessA novel endophytic filamentous bacterium strain A-T 7972T, was isolated from wild orchid Grosourdya appendiculata (Blume) Rchb.f. collected in Thailand. The bacterium developed single non-motile spores with warty surface on substrate mycelia. The taxonomic position was described using a polyphasic approach. The 16S rRNA gene sequence and phylogenetic analysis indicated that strain A-T 7972T belonged to the genus Verrucosispora and shared the highest sequence similarity with V. lutea YIM 013T (98.71 %) and V. gifhornensis DSM 44337T (98.53 %). The values of DNA–DNA relatedness that distinguished this novel strain from its closest species were below 70 %. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The whole-cell sugars were mannose, ribose, glucose and xylose. The predominant menaquinone was MK-9(H4). The predominant fatty acids were branched fatty acids iso-C15 : 0 and iso-C16 : 0. The diagnostic phospholipids profile consisted of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. The G+C content of the genomic DNA was 70.5 mol%. Based on its phenotypic, chemotaxonomic and genotypic characteristics, the new isolate A-T 7972T (=BCC 50981T=TBRC 6031T=NBRC 112512T) is proposed to be the type strain of novel species, Verrucosispora endophytica sp. nov.
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Gordonia phthalatica sp. nov., a di-n-butyl phthalate-degrading bacterium isolated from activated sludge
A phthalate esters-degrading bacterial strain, designated QH-11T, was isolated from an activated sludge wastewater treatment plant in Beijing, PR China. The cells were aerobic, Gram-stain-positive, non-motile, catalase-positive, oxidase-negative, short rods and formed white colonies on trypticase soy agar. This isolate contained meso-diaminopimelic acid as the diagnostic diamino acid and whole-cell hydrolysates contained arabinose and ribose. Diphosphatidylglycerol and phosphatidylethanolamine were the predominant polar lipids. According to the results of full-length of 16S rRNA gene sequence analysis, QH-11T represented a member of the genus Gordonia and showed the highest sequence similarity to Gordonia hydrophobica DSM 44015T (99.2 %), but was distinguishable by a low level of DNA–DNA relatedness (37.8 %). Genome-based comparisons indicated a clear distinction from the top ten most similar type strains (16S rRNA gene sequence) with pairwise average nucleotide identities (ANI) between 74.6 and 83.4 %. The predominant respiratory quinone was MK-9(H2), the mycolic acids present had 56 to 62 carbon atoms, and the major fatty acids were C16 : 0 (33.3 %), C17 : 1ω8c (23.4 %) and C18 : 1ω9c (17.9 %). The DNA G+C content was 68.0 mol%. On the basis of the results of DNA–DNA hybridization, ANI and physiological and biochemical tests, it is proposed that QH-11T represents a novel species of the genus Gordonia , for which the name Gordonia phthalatica sp. nov. is proposed. The type strain is QH-11T (CICC 24107T =KCTC 39933T).
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Streptomyces odonnellii sp. nov., a proteolytic streptomycete isolated from soil under cerrado (savanna) vegetation cover
A novel streptomycete, strain 594T, isolated from Brazilian soil collected under cerrado (savanna) vegetation cover is described. Strain 594T produced thermophilic chitinolytic proteases in assays containing feather meal and corn steep liquor as sole sources of carbon and nitrogen. The strain produced white to grey aerial mycelium and spiral chains of spiny-surfaced spores on the aerial mycelium and did not produce diffusible pigments. The ll-isomer of diaminopimelic acid was present in the cell wall and menaquinones were predominantly MK-9(H6) (52 %) and MK-9(H8) (30 %) with 6 % MK-9(H4) and slightly less than 1 % MK-9(H2). Polar lipids present were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and an unknown phospholipid. The major fatty acids were anteiso-C15 : 0, anteiso-C16 : 0, anteiso-C14 : 0 and anteiso-C17 : 0. The G+C content of the genomic DNA was 70.4 mol%. Phylogenetic analysis of the nearly complete 16S rRNA gene sequence indicated that it differed from described Streptomyces species. Multilocus sequence analysis (MLSA) using five housekeeping genes (atpD, gyrB, rpoB, recA and trpB) comparing Streptomyces type strains showed that the MLSA distance of strain 594T to the most closely related species was greater than the 0.007 threshold. The in silico DNA–DNA relatedness between the genome sequence of strain 594T and that of the phylogenetically nearest species was well below the species level recommendation. There was thus multiple evidence justifying the description of this strain as representing a novel species, for which the name Streptomyces odonnellii sp. nov. is proposed. The type strain is 594T (=IMPPG 594T=DSM 41949T=NRRL B-24891T).
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Nocardioides immobilis sp. nov., isolated from iron mine soil
More LessA Gram-positive, non-motile, rod-shaped aerobic bacterial strain FLL521T was isolated from iron mine soil. Phylogenetic trees based on 16S rRNA gene sequences showed that strain FLL521T belonged to genus Nocardioides in family Nocardioidaceae , with the highest sequence identity to Nocardioides panacisoli GSoil 346T (96.3 %). The DNA G+C content of strain FLL521T was 70.3 mol%. The cell-wall peptidoglycan type was ll-2,6-diaminopimelic acid. The major respiratory quinone was MK-8(H4), and the predominant fatty acids (>5 %) were iso-C16 : 0, C18 : 1ω9c and C17 : 1ω8c. The polar lipids of strain FLL521T were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and three unidentified phospholipids. Strain FLL521T showed physiological and biochemical differences with the related strains in the Voges-Proskauer test, hydrolysis of l-arginine, utilization of d-mannose, inositol, phenylalanine and acid production from l-arabinose. Based on the phenotypic, genotypic and phylogenetic analyses, strain FLL521T represents a novel species of Nocardioides , for which the name Nocardioides immobilis sp. nov. is proposed. The type strain is FLL521T (=KCTC 39931T=CCTCC AB 2017083T).
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Leucobacter weissii sp. nov., an isolate from activated sludge once described as first representative of the peptidoglycan variation B2δ, and emended description of the genus Leucobacter
More LessStrain S27T is a Gram-stain-positive, regular rod-shaped, non-motile, non-spore-forming, yellow pigmented actinobacterium which was isolated from an aerated laboratory scale fermenter fed with wastes of a yeast factory. The strain was classified as Microbacterium sp. after the analysis of its peptidoglycan revealed a novel B-type structure established as variation B2δ by Hensel in 1984. As the combination of the peptidoglycan amino acids 2,4-diaminobutyric acid (Dab), threonine (Thr), glycine (Gly), alanine (Ala) and glutamic acid (Glu) is in disagreement with the current genus definition of Microbacterium but is typical of several Leucobacter species, the taxonomic status of strain S27T was re-examined by a polyphasic study. Comparative analyses of 16S rRNA gene sequences and the occurrence of l-Dab, d-Ala, l-Ala, Gly, l-Thr, d-Glu and lower amounts of l-Glu in the peptidoglycan in combination with the predominating menaquinones MK-11, MK-10 and MK-9, phosphatidylglycerol, and one unknown glycolipid as the major polar lipids (and trace amounts of diphosphatidylglycerol and an unknown phospholipid), a profile with anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0, anteiso-C17 : 0 and iso-C17 : 0 as major fatty acids and the G+C value of 70.1 mol% confirmed the affiliation to the genus Leucobacter and revealed that S27T (=DSM 20621T =CCM 8762T) is the type strain of a new species for which the name Leucobacter weissii sp. nov. is proposed. The availability of new data allows for an emended description of the genus Leucobacter .
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- Archaea
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Nitrosopumilus maritimus gen. nov., sp. nov., Nitrosopumilus cobalaminigenes sp. nov., Nitrosopumilus oxyclinae sp. nov., and Nitrosopumilus ureiphilus sp. nov., four marine ammonia-oxidizing archaea of the phylum Thaumarchaeota
Four mesophilic, neutrophilic, and aerobic marine ammonia-oxidizing archaea, designated strains SCM1T, HCA1T, HCE1T and PS0T, were isolated from a tropical marine fish tank, dimly lit deep coastal waters, the lower euphotic zone of coastal waters, and near-surface sediment in the Puget Sound estuary, respectively. Cells are straight or slightly curved small rods, 0.15–0.26 µm in diameter and 0.50–1.59 µm in length. Motility was not observed, although strain PS0T possesses genes associated with archaeal flagella and chemotaxis, suggesting it may be motile under some conditions. Cell membranes consist of glycerol dibiphytanyl glycerol tetraether (GDGT) lipids, with crenarchaeol as the major component. Strain SCM1T displays a single surface layer (S-layer) with p6 symmetry, distinct from the p3-S-layer reported for the soil ammonia-oxidizing archaeon Nitrososphaera viennensis EN76T. Respiratory quinones consist of fully saturated and monounsaturated menaquinones with 6 isoprenoid units in the side chain. Cells obtain energy from ammonia oxidation and use carbon dioxide as carbon source; addition of an α-keto acid (α-ketoglutaric acid) was necessary to sustain growth of strains HCA1T, HCE1T, and PS0T. Strain PS0T uses urea as a source of ammonia for energy production and growth. All strains synthesize vitamin B1 (thiamine), B2 (riboflavin), B6 (pyridoxine), and B12 (cobalamin). Optimal growth occurs between 25 and 32 °C, between pH 6.8 and 7.3, and between 25 and 37 ‰ salinity. All strains have a low mol% G+C content of 33.0–34.2. Strains are related by 98 % or greater 16S rRNA gene sequence identity, sharing ~85 % 16S rRNA gene sequence identity with Nitrososphaera viennensis EN76T. All four isolates are well separated by phenotypic and genotypic characteristics and are here assigned to distinct species within the genus Nitrosopumilus gen. nov. Isolates SCM1T (=ATCC TSD-97T =NCIMB 15022T), HCA1T (=ATCC TSD-96T), HCE1T (=ATCC TSD-98T), and PS0T (=ATCC TSD-99T) are type strains of the species Nitrosopumilus maritimus sp. nov., Nitrosopumilus cobalaminigenes sp. nov., Nitrosopumilus oxyclinae sp. nov., and Nitrosopumilus ureiphilus sp. nov., respectively. In addition, we propose the family Nitrosopumilaceae fam. nov. and the order Nitrosopumilales ord. nov. within the class Nitrososphaeria .
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- Bacteroidetes
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Winogradskyella haliclonae sp. nov., isolated from a marine sponge of the genus Haliclona
A yellow-pigmented, Gram-stain-negative, motile and rod-shaped bacterium, strain M1A16T, was isolated from the internal tissue of a sponge of the genus Haliclona, which was long-term cultured in the CEMarin aquaria system at Justus Liebig University of Giessen. The strain grew well at 20–32 °C (optimum 25 °C), in the presence of 0–6 % NaCl (optimum 3 %), and at pH 5.5–9.0 (optimum pH 7.0–8.0). Phylogenetic analysis based on its 16S rRNA gene sequence placed the strain within the monophyletic cluster of the genus Winogradskyella with highest sequence similarity to Winogradskyella jejuensis CP32T (98.3 % 16S rRNA gene sequence similarity). Sequence similarities to all other type strains were 98.0 % or less. DNA–DNA hybridization of strain M1A16T with W. jejuensis CP32T resulted in hybridization values of 44.1 % (reciprocal 68.1 %). Major cellular fatty acids of strain M1A16T were iso-C15 : 1 G (18.1 %), iso-C15 : 0 (13.7 %), C16 : 1ω7c (12.9 %), iso-C17 : 0 3-OH (10.6 %) and iso-C16 : 0 3-OH (10.2 %). The overall polyamine content was very low with major components being cadaverine, spermidine and sym-homospermidine. The major quinone was menaquinone MK-6. The polar lipid profile contained predominantly phosphatidylethanolamine, two unidentified aminolipids and two unidentified lipids devoid of a detectable functional group. The genomic DNA G+C content was 32.7 mol%. Based on the phylogenetic, chemotaxonomic and phenotypic analyses, strain M1A16T represents a novel species of the genus Winogradskyella , for which the name Winogradskyella haliclonae sp. nov. is proposed. The type strain is M1A16T (=DSM 103138T=CCM 8681T=LMG 29588T=CIP 111091T).
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Spirosoma flavum sp. nov., isolated from Arctic tundra soil
More LessA yellow-pigmented strain, designated Y4AR-5T, was characterized by using a polyphasic approach. The strain was isolated from a tundra soil from near Longyearbyen, Svalbard Islands, Norway. The cells were Gram-stain-negative, aerobic, rod-shaped and non-motile. Growth occurred at 4–28 °C (optimum 20 °C) and pH 6.0–9.0 (optimum pH 8.0) and with 0–0.5 % (w/v) NaCl (optimum 0 %). The major respiratory quinone was MK-7. The polar lipids were phosphatidylethanolamine (PE), an aminophospholipid (APL), a phospholipid (PL), an unidentified aminolipid (AL) and two unidentified lipids. The results of analysis of the 16S rRNA gene indicated that the novel strain was most closely related to members of the genus Spirosoma (96.2 % sequence similarity with Spirosoma endophyticum ). The genomic DNA G+C content was 45.9 mol%. The major cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 1ω5c, iso-C17 : 0 3-OH and iso-C15 : 0. On the basis of its phenotypic and genotypic properties, strain Y4AR-5T should be classified as representing a novel species of the genus Spirosoma , for which the name Spirosoma flavum sp. nov. is proposed. The type strain is Y4AR-5T (=CCTCC AB 2015352T=KCTC 52490T).
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Massilia neuiana sp. nov., isolated from wet soil
More LessA novel aerobic, Gram-stain-negative, rod-shaped, motile bacterium, strain PTW21T, was isolated from wet soil. 16S rRNA gene sequence phylogenetic analysis of strain PTW21T revealed an affiliation to the genus Massilia and it shared 98.5 and 98.1 % similarity with Massilia niastensis 5516 S-1T and Massilia tieshanensis TS3T, respectively. Growth occurred at 10–45 °C, pH 4.5–12.5 and NaCl concentrations up to 2 % (w/v). The major fatty acids were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C16 : 0. The predominant respiratory quinone was Q-8. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content of strain PTW21T was 64.6 mol%. The results of DNA–DNA hybridization revealed that strain PTW21T showed 37.4 % relatedness with Massilia niastensis 5516 S-1T and 40.0 % with M. tieshanensis TS3T. Based on phenotypic, chemotaxonomic and phylogenetic differences, strain PTW21T (=CICC 24113T=BCRC 81061T) is proposed as the type strain of novel species of the genus Massilia with the names Massilia neuiana sp. nov.
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Spirosoma litoris sp. nov., a bacterium isolated from beach soil
A Gram-stain-negative, non-motile, non-spore-forming, rod-shaped, aerobic bacterium, designated 15J16-2T3AT, was isolated from beach soil on Jeju Island, South Korea. Strain 15J16-2T3AT grew at 10–37 °C (optimum growth at 25 °C) and pH 6.5–8.5 (optimum growth at pH 7). Based on 16S rRNA gene phylogenetic analysis, the novel strain was closely related to members of the genus Spirosoma (94.8–89.9 % similarities) and formed a separate branch within the genus together with Spirosoma luteolum 16F6ET in neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees. The G+C content of the genomic DNA of strain 15J16-2T3AT was 47.6 mol%. The detection of menaquinone MK-7 as the predominant respiratory quinone, a fatty acid profile with summed feature 3 (C16 : 1ω7c/C16 : 1ω6c; 35.5 %), C16 : 1ω5c (26.6 %), and iso C15 : 0 (10.1 %) as the major components, phosphatidylethanolamine and unidentified aminophospholipid as the major polar lipids also support the affiliation of strain 15J16-2T3AT with the genus Spirosoma . The results of physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain 15J16-2T3AT from members the genus Spirosoma . On the basis of its phenotypic properties and phylogenetic distinctiveness, strain 15J16-2T3AT represents a novel species of the genus Spirosoma , for which the name Spirosoma litoris sp. nov. is proposed. The type strain is 15J16-2T3AT (=KCTC 52029T=JCM 31999T)
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Frondibacter mangrovi sp. nov., a member of the family Flavobacteriaceae isolated from seawater by in situ cultivation, and emended description of Frondibacter aureus
More LessA Gram-stain-negative, rod-shaped, non-motile, strictly aerobic, chemoheterotrophic, light-yellow-pigmented bacterium, designated strain 02OK1/10-76T, was isolated from a mangrove estuary in Japan by use of an in situ cultivation technique. Preliminary analysis based on the 16S rRNA gene sequence revealed that the novel isolate was affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes and that it showed highest sequence similarity (96.9 %) to Frondibacter aureus A5Q-67T. The DNA G+C content of strain 02OK1/10-76T was 35 mol%; MK-6 was the only menaquinone; and iso-C15 : 0, iso-C17 : 0 3-OH and iso-C16 : 0 3-OH were the major (>10 %) cellular fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, three unidentified aminolipids, an unidentified aminophospholipid and an unidentified lipid. From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain represents a novel species of the genus Frondibacter , for which the name Frondibacter mangrovi sp. nov. is proposed. The type strain is 02OK1/10-76T (= KCTC 52666T = NBRC 112695T). An emended description of F. aureus is also provided.
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Pedobacter kyonggii sp. nov., a psychrotolerant bacterium isolated from forest soil
More LessStrain K-4-11-1T, a psychrotolerant, light salmon-coloured, Gram-stain-negative, non-motile and rod-shaped bacterium, was isolated from forest soil of Kyonggi University, Suwon, South Korea. It was able to grow at 0–32 °C, at pH 5.0–10.0 and with 0–1.5 % (w/v) NaCl. This strain was taxonomically characterized by a polyphasic approach. Based on 16S rRNA gene sequence analysis, strain K-4-11-1T belongs to the genus Pedobacter and is closely related to Pedobacter ginsenosidimutans THG-45T (98.75 % sequence similarity), Pedobacter borealis G-1T (98.48 %), Pedobacter terrae DS-57T (98.20 %), Pedobacter agri PB92T (97.92 %) and Pedobacter suwonensis 15-52T (97.84 %). The only respiratory quinone was menaquinone-7. The major polar lipids were phosphatidylethanolamine and unidentified glycolipids. The predominant fatty acids of strain K-4-11-1T were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C15 : 0, iso-C17 : 0 3-OH, anteiso-C17 : 0 and summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl). The genomic DNA G+C content of this novel strain was 38.3 mol%. The DNA–DNA relatedness values between strain K-4-11-1T and P. ginsenosidimutans KACC 14530T, P. borealis KACC 14287T, P. terrae KACC 13766T, P. agri KACC 13768T and P. suwonensis KACC 11317T were 40.0, 36.3, 37.0, 32.3 and 29.7 %, respectively. The morphological, physiological, chemotaxonomic and phylogenetic analyses clearly distinguished this novel strain from its closest phylogenetic neighbours. Thus, strain K-4-11-1T represents a novel species of the genus Pedobacter , for which the name Pedobacter kyonggii sp. nov. is proposed. The type strain is K-4-11-1T (=KEMB 9005-574T=KACC 19174T=JCM 31916T).
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Larkinella soli sp. nov., isolated from biological soil crusts
More LessA novel bacterial strain, designated MIMbqt9T, was isolated from biological soil crusts collected in Erdos Plateau in Inner Mongolia. Cells were light pink, rod-shaped, aerobic, Gram-reaction-negative, motile by gliding, oxidase- and catalase-positive. Cell growth could be observed at 5–40 °C (optimum at 30 °C), at pH 4.0–6.0 (optimum at 6.0) and with 1 % (w/v) NaCl. Phylogenetic analysis of 16S rRNA gene sequence showed that strain MIMbqt9T was most closely related to the members of genus Larkinella , including L. bovis M2T2B15T (92.06 %), L. arboricola Z0532T (92.00 %) and L. insperata LMG 22510T (91.94 %). The major cellular fatty acids of strain MIMbqt9T were C16 : 1ω5c, iso-C15 : 0 and iso-C17 : 0 3-OH. Polar lipids of the strain MIMbqt9T were mainly composed of phosphatidylethanolamine (PE), phosphatidylserine (PS), two unidentified aminolipids (AL1 and AL2) and two unidentified phospholipids (PL1 and PL2). Menaquinone 7 (MK-7) was the major respiratory quinone. The G+C content of the chromosomal DNA was 57.63 mol%. On the basis of morphology, physiology, fatty acid composition, phylogeny and 16S rRNA gene sequence analysis, the isolates are assigned to a novel species of the genus Larkinella , for which the name Larkinella soli sp. nov. is proposed. The type strain is MIMbqt9T (=MCCC 1K01309T=KCTC 42800T).
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Tenacibaculum agarivorans sp. nov., an agar-degrading bacterium isolated from marine alga Porphyra yezoensis Ueda
More LessA novel Gram-stain-negative, aerobic, rod-shaped, non-flagellated and agar-digesting marine bacterium, designated as HZ1T, was isolated from the marine alga Porphyra yezoensis Ueda (AST58-103) collected from the coastal area of Weihai, PR China. Phylogenetic analysis based on 16S rRNA gene sequences placed HZ1T in the genus Tenacibaculum , and it formed a distinct clade in the phylogenetic tree with the type strains of Tenacibaculum amylolyticum and Tenacibaculum skagerrakense , with 97.0 % and 96.7 % 16S rRNA gene sequence similarities, respectively. The DNA G+C content of the isolate was 31.8 mol%. HZ1T contained MK-6 as the predominant menaquinone and iso-C15 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C17 : 0 3-OH and iso-C15 : 1G as the major fatty acids. The major polar lipids were phosphatidylethanolamine, four unidentified lipids and five unidentified aminolipids. On the basis of the results of the phylogenetic analysis and phenotypic properties, it is concluded that HZ1T represents a novel species of the genus Tenacibaculum , for which the name Tenacibaculum agarivorans sp. nov. is proposed. The type strain is HZ1T (=MCCC 1H00174T=KCTC 52476T).
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Flavobacterium amniphilum sp. nov., isolated from a stream
More LessStrain KYPY10T, isolated from a water sample taken from the Funglin Stream in Taiwan, was characterized using a polyphasic taxonomic approach. Cells of strain KYPY10T were Gram-stain-negative, strictly aerobic, motile by gliding, rod-shaped surrounded by a thick capsule, and formed light-yellow colonies. Growth occurred at 20–30 °C (optimum, 25 °C), at pH 6–7 (optimum, pH 6) and with 0–0.2 % NaCl (optimum, 0 % w/v). Phylogenetic analyses, based on 16S rRNA gene sequences, showed that strain KYPY10T belonged to the genus Flavobacterium and was most closely related to Flavobacterium brevivitae TTM-43T (98.4 % sequence similarity) and Flavobacterium vireti THG-SM1T (98.0 %). Strain KYPY10T contained iso-C15 : 0, iso-C15 : 1 G, summed feature 9 (iso-C17 : 1ω9c and/or 10-methyl C16 : 0), iso-C17 : 0 3-OH, iso-C15 : 0 3-OH and iso-C16 : 0 as the predominant fatty acids. The major isoprenoid quinone was MK-6. The polar lipid profile consisted of phosphatidylethanolamine, four uncharacterized aminophospholipids, five uncharacterized phospholipids and one uncharacterized lipid. The major polyamines were homospermidine and putrescine. The genomic DNA G+C content of strain KYPY10T was 41.0 mol%. The DNA–DNA relatedness of strain KYPY10T with respect to recognized species of the genus Flavobacterium was less than 70 %. On the basis of the phylogenetic inference and phenotypic data, strain KYPY10T was recognized as a representative of a novel species within the genus Flavobacterium . The name Flavobacterium amniphilum sp. nov. is proposed, with strain KYPY10T (=BCRC 81006T=LMG 29727T=KCTC 52443T) as the type strain.
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Changchengzhania lutea gen. nov., sp. nov., a new member of the family Flavobacteriaceae isolated from Antarctic intertidal sediment
A Gram-negative, aerobic, yellow pigmented, non-flagellated, non-gliding, rod-shaped bacterial strain, designated SM1355T, was isolated from Antarctic intertidal sediment collected near the Chinese Antarctic Great Wall Station. The strain grew at 4–35 °C and with 0.5–7.0 % (w/v) NaCl. It hydrolysed aesculin but didn’t reduce nitrate to nitrite. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SM1355T formed a distinct phylogenetic lineage within the family Flavobacteriaceae , sharing the highest 16S rRNA gene sequence similarity with Flaviramulus ichthyoenteri (96.3 %) and fairly high sequence similarities (95.0–96.0 %) with over 20 recognized species in eight genera of the family Flavobacteriaceae . The predominant fatty acids were anteiso-C15 : 0, iso-C15 : 0 and iso-C15 : 1 G. The major polar lipids were phosphatidylethanolamine and one unidentified lipid. The genomic DNA G+C content of strain SM1355T was 36.2 mol%. Based on the results of the polyphasic characterization for strain SM1355T, it is identified as the representative of a novel species in a new genus of the family Flavobacteriaceae , for which the name Changchengzhania lutea gen. nov., sp. nov. is proposed. The type strain of Changchengzhania lutea is SM1355T (=JCM 30336T=CCTCC AB 2014246T).
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Soonwooa purpurea sp. nov., isolated from a fresh water river
More LessA pale-brown-coloured, rod-shaped, non-motile, and Gram-reaction-negative bacterium, strain I54T, was isolated from a water sample of a freshwater river in Iksan, Republic of Korea. The phylogenetic affiliation based on 16S rRNA gene sequence analysis showed that strain I54T belonged to the genus Soonwooa of the family Flavobacteriaceae with a sequence similarity of 97.5 % to Soonwooa buanensis HM0024T. The major fatty acids (>5 %) of strain I54T were iso-C15 : 0, anteiso-C15 : 0, summed feature 3 (C16 : 1 ω7c/C16 : 1ω6c) and iso-C17 : 0 3-OH. Phosphatidylethanolamine, one aminolipid and two unknown lipids were the major polar lipids. The G+C content of the genomic DNA was 34.2 (±0.3)mol% and MK6 was the sole respiratory quinone. On the basis of its molecular and phenotypic characteristics, strain I54T represents a novel species in the genus Soonwooa , for which the name Soonwooa purpurea sp. nov. is proposed. The type strain is I54T (=KCTC 52722T=JCM 31880T).
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Spirosoma koreense sp. nov., a species of the family Cytophagaceae isolated from beach soil
A Gram-stain-negative, non-motile, non-spore-forming, rod-shaped, aerobic bacterium, designated 15J8-5T, was isolated from beach soil on Jeju Island, Republic of Korea. The isolate grew at 10–37 °C (optimal 25 °C), pH 6–8 (optimal pH 7) and in the presence of 0–1 % (w/v) NaCl. The results of comparative 16S rRNA gene sequence analysis indicated that strain 15J8-5T represented a member of the family Cytophagaceae , phylum Bacteroidetes and was most closely related to Spirosoma knui 15J8-12T (93.1 % similarity), Spirosoma spitsbergense SPM-9T (93.1 %) and Spirosoma endophyticum EX36T (93.1 %). The G+C content of the genomic DNA of the novel strain was 48.0 mol%. The isolate contained menaquinone MK-7 as the predominant respiratory quinone, phosphatidylethanolamine as the major polar lipid, and summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c; 32.8 %), C16 : 1 ω5c (24.8 %) and C16 : 0 (11.7 %) as the major fatty acids, which supported the affiliation of strain 15J8-5T to the genus Spirosoma . The results of physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain 15J8-5T from members of the genus Spirosoma . Based on its phenotypic properties and phylogenetic distinctiveness, strain 15J8-5T represents a novel species of the genus Spirosoma , for which the name Spirosoma koreense sp. nov. is proposed. The type strain is 15J8-5T (=KCTC 52027T=JCM 31992T).
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Rurimicrobium arvi gen. nov., sp. nov., a member of the family Chitinophagaceae isolated from farmland soil
More LessTwo strains of bacteria, designated J107-1T and J107-2, were isolated from farmland soil. Cells were aerobic, Gram-stain-negative, catalase- and oxidase-positive, non-motile, non-spore-forming, coccoid rod-shaped and yellow-pigmented. Flexirubin-type pigments were absent. Both strains hydrolysed casein and tyrosine. Strains could grow at pH 9.0 and at 42 °C. A phylogenetic analysis based on its 16S rRNA gene sequence revealed that strains J107-1T and J107-2 formed a lineage within the phylum Bacteroidetes that was distinct from various members of the family Chitinophagaceae , including Ferruginibacter paludis HME8881T (89.71 % sequence similarity), Ferruginibacter yonginensis HME8442T, Niastella yeongjuensis GR20-13T (89.70 %), Chitinophaga niabensis DSM 24787T (89.57 %), Lacibacter cauensis CGMCC 1.7271T (89.56 %) and Taibaiella koreensis THG-DT86T (89.52 %). The 16S rRNA gene similarities of other members of the family Chitinophagaceae are less than 89.51 %. The predominant respiratory quinone was MK-7. The major polar lipids were phosphatidylethanolamine, an unidentified aminolipid and an unidentified polar lipid. Major cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH and iso-C17 : 0. The DNA G+C content of strains ranged from 47.8 to 48.0 mol%. On the basis of phenotypic, genotypic, chemotaxonomic and phylogenetic analysis, strains J107-1T and J107-2 represent a novel genus in the family Chitinophagaceae, for which the name Rurimicrobium arvi gen. nov., sp. nov. is proposed. The type strain of Rurimicrobium arvi is J107-1T (=KEMB 9005-549T=KACC 19167T=JCM 31921T).
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Ravibacter arvi gen. nov., sp. nov., isolated from farmland soil during development of new culture techniques
More LessTwo novel strains, J77-1T and J76-1, were isolated from farmland soil and were taxonomically characterized by a polyphasic approach. Both strains were yellow, Gram-stain-negative, strictly aerobic, non-motile and rod-shaped bacteria. These strains were non-sporulating, catalase-positive and oxidase-negative. J77-1T and J76-1 were able to grow at 15–40 °C, pH 5.0–10.0, and 0–1.0 % (w/v) NaCl concentration. Phylogenetic analyses revealed that both strains formed a distinct separate lineage within the family Cytophagaceae of the phylum Bacteroidetes . J77-1T and J76-1 showed low 16S rRNA gene sequence similarity to the most closely related type strain Dyadobacter koreensis WPCB159T (85.09 %) and exhibited less than 85.0 % sequence similarity with other members of the family Cytophagaceae. The pairwise sequence similarity between strains J77-1T and J76-1 was observed to be 99.86 %. In both strains, the only respiratory quinone was menaquinone-7 (MK-7); the major polar lipid was phosphatidylethanolamine; and the major fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0, iso-C15 : 0, iso-C17 : 0 3-OH C16 : 1ω5c, and C16 : 0 3-OH. The genomic DNA G+C content values of J77-1T and J76-1 were 50.1 and 50.9 mol%, respectively. On the basis of the results of phenotypic, genotypic and phylogenetic analysis, J77-1T represents a novel species of a novel genus, for which the name Ravibacter arvi gen. nov., sp. nov. is proposed, within the family Cytophagaceae. The type strain of Ravibacter arvi is J77-1T (=KEMB 9005-548T=KACC 19172T=JCM 31920T), and J76-1 is an additional strain.
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Maribacter cobaltidurans sp. nov., a heavy-metal-tolerant bacterium isolated from deep-sea sediment
More LessA Gram-stain-negative, aerobic, non-motile and rod-shaped bacterium, designated B1T, was isolated from deep-sea sediment collected from the South Atlantic Ocean. Cells of strain B1T grew in medium containing 0.5–6.0 % (w/v) NaCl (optimum 1.0–2.0 %), at pH 5.5–7.5 (optimum pH 7.0) and at 15–37 °C (optimum 30 °C). Aesculin, starch and Tweens 20, 40 and 60 were hydrolysed. The strain was able to grow in medium containing a high concentration of Co2+ (10 mM). The 16S rRNA gene sequence of strain B1T shared high similarity with respect to Maribacter orientalis DSM 16471T (97.7 %), and exhibited less than 97.0 % sequence similarity with the type strains of other species with validly published names. Phylogenetic analyses revealed that strain B1T fell within the cluster comprising Maribacter species and formed an independent lineage. The average nucleotide identity and in silico DNA–DNA hybridization values between strain B1T and M. orientalis DSM 16471T were 72.0 % and 17.6 %, respectively. Strain B1T contained menaquinone 6 (MK-6) as the sole isoprenoid quinone and iso-C17 : 0 3-OH, iso-C15 : 0 and iso-C15 : 1 G as the predominant cellular fatty acids. The major polar lipids were phosphatidylethanolamine, one unidentified aminolipid and two unidentified lipids. The DNA G+C content was 39.7 mol%. According to the phylogenetic, chemotaxonomic and phenotypic data, B1T represents a novel species of the genus Maribacter , for which the name Maribacter cobaltidurans sp. nov. is proposed. The type strain is B1T (=CGMCC 1.15508T=KCTC 52882T=MCCC 1K03318T).
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Shewanella carassii sp. nov., isolated from surface swabs of crucian carp and faeces of a diarrhoea patient
More LessTwo strains, 08MAS2251T and LZ2016-166, were isolated from diverse samples in China collected from the surface of crucian carp and the faeces of a diarrhoea patient, respectively. Both strains were pink-orange coloured, Gram-negative, oxidase- and catalase-positive, facultative anaerobic and motile bacteria, produced H2S and reduced nitrates to nitrites. Growth occurred in the presence of 0–9 % (w/v) NaCl and at 10–42 °C. The optimum conditions were with 1 % (w/v) NaCl and at 35 °C. The phylogenetic tree of 16S rRNA gene demonstrated that strains 08MAS2251T and LZ2016-166 clustered in a distinctive clade next to the species Shewanella chilikensis JC5T within the genus Shewanella . Meanwhile, gyrB gene sequence analysis indicated that the two strains formed an independent branch that was clearly separate from all the other Shewanella species with sequence similarities from 68.49 to 95.74 %. The DNA G+C content of strain 08MAS2251T was 52.68 mol%. Genomic relatedness of in silico DNA–DNA hybridization between strain 08MAS2251T and phylogenetic neighbours ranged from 50.5–51.8 %, below the cutoff of 70 %. In addition, corresponding average nucleotide identity values were between 93.01 to 93.49%, which were lower than 95 % threshold. The major fatty acids of strain 08MAS2251T were C17 : 1ω8c (27.2 %), iso-C15 : 0 (22.5 %), summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c; 8.7 %), C16 : 0 (6.2 %), iso-C13 : 0 (5.6 %) and C17 : 0 (4.5 %). Based on phenotypic and genetic analysis, strains 08MAS2251T and LZ2016-166 are identified as a novel species of the genus Shewanella , for which the name Shewanella carassii sp. nov. is proposed. The type strain is 08MAS2251T (=DSM 104682T=CGMCC 1.16033T).
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- Firmicutes and Related Organisms
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Paenibacillus azotifigens sp. nov., a novel nitrogen-fixing bacterium isolated from paddy soil
More LessA nitrogen-fixing bacterium, designated NF2-4-5T, was isolated from a paddy soil in Anseong City, Korea. Cells of strain NF2-4-5T were Gram-staining-positive, motile rods and aerobic. Phylogenetic analysis based on 16S rRNA gene sequence comparison revealed that the strain formed a distinct lineage within the genus Paenibacillus and was closely related to Paenibacillus graminis RSA19T (98.7 %), Paenibacillus jilunlii Be17T (98.6 %), Paenibacillus salinicaeni LAM0A28T (98.6 %) and Paenibacillus riograndensis SBR5T (98.6 %). Growth of strain NF2-4-5T occurs at temperatures of 18–37 °C, at pH 6.0–8.5 and between 0.5% and 2 % NaCl (w/v). The only respiratory quinone was MK-7. The cell wall peptidoglycan of strain NF2-4-5T contained meso-diaminopimelic acid. The main cellular fatty acids were C16 : 0 and anteiso-C15 : 0. The major polar lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and phosphatidylethanolamine (PE). The DNA G+C content was 56.36 mol%. The DNA–DNA hybridization relatedness between strain NF2-4-5T and four reference strains, Paenibacillus graminis RSA19T, Paenibacillus jilunlii Be17T, Paenibacillus sonchi X19-5T and Paenibacillus riograndensis SBR5T, was 22.0±0.3, 20.1±0.7, 18.3±0.3 and 12.6±0.5 %, respectively. The phenotypic, phylogenetic and chemotaxonomic results indicate that the strain NF2-4-5T represents a novel species of the genus Paenibacillus , for which the name Paenibacillus azotifigens sp. nov. is proposed. The type strain is NF2-4-5T (=KACC 18967T=LMG 29963T).
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Lactobacillus allii sp. nov. isolated from scallion kimchi
More LessA novel strain of lactic acid bacteria, WiKim39T, was isolated from a scallion kimchi sample consisting of fermented chili peppers and vegetables. The isolate was a Gram-positive, rod-shaped, non-motile, catalase-negative and facultatively anaerobic lactic acid bacterium. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain WiKim39T belonged to the genus Lactobacillus , and shared 97.1–98.2 % pair-wise sequence similarities with related type strains, Lactobacillus nodensis , Lactobacillus insicii , Lactobacillus versmoldensis , Lactobacillus tucceti and Lactobacillus furfuricola . The G+C content of the strain based on its genome sequence was 35.3 mol%. The ANI values between WiKim39T and the closest relatives were lower than 80 %. Based on the phenotypic, biochemical, and phylogenetic analyses, strain WiKim39T represents a novel species of the genus Lactobacillus , for which the name Lactobacillus allii sp. nov. is proposed. The type strain is WiKim39T (=KCTC 21077T=JCM 31938T).
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Paenibacillus nebraskensis sp. nov., isolated from the root surface of field-grown maize
A Gram-positive-staining, aerobic, non-endospore-forming bacterial strain (JJ-59T), isolated from a field-grown maize plant in Dunbar, Nebraska in 2014 was studied by a polyphasic approach. Based on 16S rRNA gene sequence similarity comparisons, strain JJ-59T was shown to be a member of the genus Paenibacillus , most closely related to the type strains of Paenibacillus aceris (98.6 % 16S rRNA gene sequence similarity) and Paenibacillus chondroitinus (97.8 %). For all other type strains of species of the genus Paenibacillus lower 16S rRNA gene sequence similarities were obtained. DNA–DNA hybridization values of strain JJ-59T to the type strains of P. aceris and P. chondroitinus were 26 % (reciprocal, 59 %) and 52 % (reciprocal, 59 %), respectively. Chemotaxonomic characteristics such as the presence of meso-diaminopimelic acid in the peptidoglycan, the major quinone MK-7 and spermidine as the major polyamine were in agreement with the characteristics of the genus Paenibacillus . Strain JJ-59T shared with its next related species P. aceris the major lipids diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified aminophospholipid, but the presence/absence of certain lipids was clearly distinguishable. Major fatty acids of strain JJ-59T were anteiso-C15 : 0, iso-C15 : 0 and iso-C16 : 0, and the genomic G+C content is 47.2 mol%. Physiological and biochemical characteristics of strain JJ-59T were clearly different from the most closely related species of the genus Paenibacillus . Thus, strain JJ-59T represents a novel species of the genus Paenibacillus , for which the name Paenibacillus nebraskensis sp. nov. is proposed, with JJ-59T (=DSM 103623T=CIP 111179T=LMG 29764T) as the type strain.
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Clostridium pabulibutyricum sp. nov., a butyric-acid-producing organism isolated from high-moisture grass silage
A Gram-stain-variable, strictly anaerobic, rod-shaped, catalase-negative and endospore-forming bacterial strain, designated MJC39T, was isolated from grass silage preserved in Hokkaido, Japan. Growth occurred at 20–42 °C, pH 5.0–7.0 and NaCl concentrations up to 2 % (w/v). The isolated strain MJC39T produced butyric acid in peptone yeast extract medium with glucose. The DNA G+C content of strain MJC39T was 34.4±0.2 mol%. The major cellular fatty acids (>10 %) were C14 : 0, C16 : 0 and summed feature 3 (including C16 : 1ω7c/C16 : 1ω6c). No respiratory quinones were detected. The polar lipids of strain MJC39T were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, one unidentified lipid, one unidentified aminolipid, two unidentified glycolipids, one unidentified phospholipid, one unidentified aminoglycolipid and one unidentified phosphoaminoglycolipid. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MJC39T was a member of the genus Clostridium and is closely related to Clostridium tyrobutyricum JCM 11008T (95.8 % similarity) and Clostridium algifaecis MB9-7T (95.5 % similarity). Based on the genotypic, phenotypic and chemotaxonomic characteristics, strain MJC39T represents a novel species of the genus Clostridium , for which the name Clostridium pabulibutyricum sp. nov. is proposed. The type strain is MJC39T (=JCM 31506T=DSM 103944T).
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Floricoccus tropicus gen. nov., sp. nov. and Floricoccus penangensis sp. nov. isolated from fresh flowers of durian tree and hibiscus
Three strains of Gram-staining-positive, coccus-shaped, lactic acid bacteria, designated as HibF3T, HibF2 and HibF5 were isolated from fresh flowers of hibiscus, and a fourth, DF1T, was isolated from fresh flowers of durian tree, in Penang, Malaysia. Taxonomic characterisation was performed by polyphasic analysis. Sequence similarities of the 16S rRNA gene and the housekeeping rpoA and pheS genes of these strains with their closely-related lactococcal and streptococcal relatives were 92–94, 78 and 81 %, respectively. The results of phylogenetic analysis indicated that strains DF1T, HibF2, HibF5 and HibF3T were clustered together but were clearly separated from species of the genera Streptococcus and Lactococcus , indicating that they represent members of a novel genus of the family Streptococcaceae . Calculation of average nucleotide identity (ANI) values between the genomes of DF1T and HibF3T yielded values of 92.50–92.93 %. ANI values below the cut-off value and distinctive chemotaxonomic characteristics supported the hypothesis that these strains represented two novel species. Major cellular fatty acids in DF1T, HibF2 and HibF5 were C18 : 1ω7c and C16 : 0, while C12 : 0 and C14 : 0 were also dominant, in addition to C18 : 1ω7c and C16 : 0, in HibF3T. A novel genus is proposed with the name Floricoccus gen. nov. which consists of two species, Floricoccus tropicus sp. nov as the type species, and Floricoccus penangensis sp. nov. The respective type strains are DF1T (=LMG 29833T=JCM 31733T) and HibF3T (=LMG 29831T=DSM 31735T).
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Monoglobus pectinilyticus gen. nov., sp. nov., a pectinolytic bacterium isolated from human faeces
A novel anaerobic pectinolytic bacterium (strain 14T) was isolated from human faeces. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 14T belonged to the family Ruminococcaceae , but was located separately from known clostridial clusters within the taxon. The closest cultured relative of strain 14T was Acetivibrio cellulolyticus (89.7 % sequence similarity). Strain 14T shared ~99 % sequence similarity with cloned 16S rRNA gene sequences from uncultured bacteria derived from the human gut. Cells were Gram-stain-positive, non-motile cocci approximately 0.6 µm in diameter. Strain 14T fermented pectins from citrus peel, apple, and kiwifruit as well as carbohydrates that are constituents of pectins and hemicellulose, such as galacturonic acid, xylose, and arabinose. TEM images of strain 14T, cultured in association with plant tissues, suggested extracellular fibrolytic activity associated with the bacterial cells, forming zones of degradation in the pectin-rich regions of middle lamella. Phylogenetic and phenotypic analysis supported the differentiation of strain 14T as a novel genus in the family Ruminococcaceae . The name Monoglobus pectinilyticus gen. nov., sp. nov. is proposed; the type strain is 14T (JCM 31914T=DSM 104782T).
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Streptococcus azizii sp. nov., isolated from naïve weanling mice
More LessThree isolates of a previously reported novel catalase-negative, Gram-stain-positive, coccoid, alpha-haemolytic, Streptococcus species that were associated with meningoencephalitis in naïve weanling mice were further evaluated to confirm their taxonomic status and to determine additional phenotypic and molecular characteristics. Comparative 16S rRNA gene sequence analysis showed nearly identical intra-species sequence similarity (≥99.9 %), and revealed the closest phylogenetically related species, Streptococcus acidominimus and Streptococcuscuniculi, with 97.0 and 97.5 % sequence similarity, respectively. The rpoB, sodA and recN genes were identical for the three isolates and were 87.6, 85.7 and 82.5 % similar to S. acidominimus and 89.7, 86.2 and 80.7 % similar to S. cuniculi , respectively. In silico DNA–DNA hybridization analyses of mouse isolate 12-5202T against S. acidominimus CCUG 27296T and S. cuniculi CCUG 65085T produced estimated values of 26.4 and 25.7 % relatedness, and the calculated average nucleotide identity values were 81.9 and 81.7, respectively. These data confirm the taxonomic status of 12-5202T as a distinct Streptococcus species, and we formally propose the type strain, Streptococcus azizii 12-5202T (=CCUG 69378T=DSM 103678T). The genome of Streptococcus azizii sp. nov. 12-5202T contains 2062 total genes with a size of 2.34 Mbp, and an average G+C content of 42.76 mol%.
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Paenibacillus solanacearum sp. nov., isolated from rhizosphere soil of a tomato plant
More LessThe taxonomic position of a bacterial strain designated T16R-228T, isolated from a rhizosphere soil sample of a tomato plant collected from a farm in Buyeo, Chungcheongnam-do, Republic of Korea, was determined using a polyphasic approach. On the basis of morphological, genetic and chemotaxonomic characteristics, it was determined to belong to the genus Paenibacillus . It was an aerobic, Gram-stain-positive, non-motile, catalase-negative, oxidase-negative rod with peritrichous flagella. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, hydroxyl- phosphatidylethanolamine and one unidentified polar lipid. Menaquiones were MK-7. Predominant cellular fatty acids were anteiso-C15 : 0, C16 : 0 and iso-C16 : 0. DNA G+C content was 56.8 mol%. The phylogenetic tree constructed based on the 16S rRNA gene sequences showed the strain formed a clade with P. mucilaginosus VKPM B-7519T, P. edaphicus T7T, P. ehimensis KCTC 3748T, P. koreensis YC300T, P. tianmuensis B27T and P. elgii SD17T, showing the highest sequence similarity with P. mucilaginosus VKPM B-7519T (96.5 %). The polyphasic data supported that strain T16R-228T was clearly distinguished from its closely related species and represents a novel species of the genus Paenibacillus for which the name Paenibacillus solanacearum is proposed. The type strain is T16R-228T (=KACC 18654T=NBRC 111896T).
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Lactobacillus musae sp. nov., a novel lactic acid bacterium isolated from banana fruits
Two Gram-stain-positive, catalase-negative, rod-shaped, bacterial strains (313T and 311) were isolated from banana fruits in Taiwan. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the highest similarity to both strains corresponded to the type strain of Lactobacillus nantensis (99.19 %), followed by Lactobacillus crustorum (98.99 %), Lactobacillus heilongjiangensis (98.59 %) and Lactobacillus farciminis (98.52 %). Phylogenetic analysis based on the sequences of two housekeeping genes, pheS and rpoA, revealed that these two strains were well separated from the Lactobacillus reference strains. DNA–DNA relatedness values revealed genotype separation of the two strains from the above four species. The DNA G+C content of strain 313T was 35.5 mol%. The strains were homofermentative and mainly produced l-lactic acid from glucose. The major cellular fatty acids of strain 313T were 18 : 1ω6c and/or 18 : 1ω7c, 16 : 0, and 19 : 1ω6c and/or 19 : 0 cyclo ω10c. Based on their physiological and genotypic characteristics, the isolates represent a novel species of the genus Lactobacillus , for which the name Lactobacillus musae sp. nov. is proposed. The type strain is 313T=NBRC 112868T=BCRC 81020T).
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Enterococcus wangshanyuanii sp. nov., isolated from faeces of yaks (Bos grunniens)
More LessThe taxonomic position of four phenotypically closely related strains isolated from faecal samples of yaks (Bos grunniens) collected from the Qinghai-Tibetan plateau, China, was determined by a polyphasic approach. The strains were non-spore-forming, non-motile Gram-stain-positive, ovoid cocci, occurring predominantly in pairs and short chains or in irregular clusters. The 16S rRNA gene of strain MN05T was related phylogenetically to those of Enterococcus haemoperoxidus , Enterococcus rotai , Enterococcus quebecensis , Enterococcus plantarum , Enterococcus crotali , Enterococcus moraviensis , Enterococcus silesiacus , Enterococcus caccae , Enterococcus termitis , Enterococcus ureasiticus and Enterococcus ureilyticus , all belonging to the Enterococcus faecalis species group. The sequence similarities of three selected genes of MN05T to those of the type strains of phylogenetically related species were measured, with values within the range of 99.2–99.5 % (16S rRNA gene), 90.0–97.3 % (rpoA) and 80.0–85.3 % (pheS), respectively. The genome of MN05T (3 842 361 bp) contained 4299 genes with a DNA G+C content of 37.5 mol%. A whole-genome phylogenetic tree based on 808 core genes confirmed that MN05T belongs to a distinct lineage, well separated from all recognized species of the Enterococcus faecalis species group. DNA–DNA hybridization in silico showed that MN05T displayed less than 70 % DNA–DNA relatedness with the other 13 species of the Enterococcus faecalis species group. Moreover, their phenotypic features distinguished the four strains from the other species of the Enterococcus faecalis species group. Based upon these data obtained from the polyphasic characterization performed in the present study, a novel species of the genus Enterococcus , Enterococcus wangshanyuanii sp. nov., is proposed, with the type strain MN05T (=DSM 104047T=CGMCC 1.15942T).
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- Other Bacteria
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Tuwongella immobilis gen. nov., sp. nov., a novel non-motile bacterium within the phylum Planctomycetes
A gram-negative, budding, catalase negative, oxidase positive and non-motile bacterium (MBLW1T) with a complex endomembrane system has been isolated from a freshwater lake in southeast Queensland, Australia. Phylogeny based on 16S rRNA gene sequence analysis places the strain within the family Planctomycetaceae , related to Zavarzinella formosa (93.3 %), Telmatocola sphagniphila (93.3 %) and Gemmata obscuriglobus (91.9 %). Phenotypic and chemotaxonomic analysis demonstrates considerable differences to the type strains of the related genera. MBLW1T displays modest salt tolerance and grows optimally at pH values of 7.5–8.0 and at temperatures of 32–36 °C. Transmission electron microscopy analysis demonstrates the presence of a complex endomembrane system, however, without the typically condensed nucleoid structure found in related genera. The major fatty acids are 16 : 1 ω5c, 16 : 0 and 18 : 0. Based on discriminatory results from 16S rRNA gene sequence analysis, phenotypic, biochemical and chemotaxonomic analysis, MBLW1T should be considered as a new genus and species, for which the name Tuwongella immobilis gen. nov., sp. nov. is proposed. The type strain is MBLW1T (=CCUG 69661T=DSM 105045T).
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- Proteobacteria
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Bradyrhizobium namibiense sp. nov., a symbiotic nitrogen-fixing bacterium from root nodules of Lablab purpureus, hyacinth bean, in Namibia
More LessFour strains of symbiotic bacteria from root nodules of hyacinth bean (Lablab purpureus (L.) Sweet) from Namibia were previously identified as a novel group within the genus Bradyrhizobium . To confirm their taxonomic status, these strains were further characterized by taking a polyphasic approach. The type strain possessed 16S rRNA gene sequences identical to Bradyrhizobium paxllaeri LMTR 21T and Bradyrhizobium icense LMTR 13T, the full-length sequences were identical to those retrieved from SAMN05230119 and SAMN05230120, respectively. However, the intergenic spacer sequences of the novel group showed identities of less than 93.1 % to described Bradyrhizobium species and were placed in a well-supported separate lineage in the phylogenetic tree. Phylogenetic analyses of six concatenated housekeeping genes, recA, glnII, gyrB, dnaK, atpD and rpoB, corroborated that the novel strains belonged to a lineage distinct from named species of the genus Bradyrhizobium , with highest sequence identities to Bradyrhizobium jicamae and B. paxllaeri (below 93 %). The species status was validated by results of DNA–DNA hybridization and average nucleotide identity values of genome sequences. The combination of phenotypic characteristics from several tests, including carbon source utilization and antibiotic resistance, could be used to differentiate representative strains from recognized species of the genus Bradyrhizobium . Phylogenetic analysis of nodC and nifH genes placed the novel strains in a group with B. paxllaeri and B. lablabi . Novel strain 5-10T induces effective nodules on Lablab purpureus, Vigna subterranea, Vigna unguiculata and Arachis hypogaea. Based on our results, we conclude that our strains represent a novel species for which the name Bradyrhizobium namibiense sp. nov. is proposed, with type strain 5-10T[LMG 28789, DSM 100300, NTCCM0017 (Windhoek)].
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Oceaniglobus indicus gen. nov., sp. nov., a member of the family Rhodobacteraceae isolated from surface seawater
More LessA Gram-stain-negative, non-motile, aerobic and heterotrophic strain, designated 1-19bT, was isolated from surface seawater in the Indian Ocean. The cells were ovoid or coccus (0.8–1.0 µm in diameter) with no flagellum. Activities of catalase and oxidase were positive. Growth was observed at salinity of 0.5–10 (%NaCl, w/v) with an optimum of 3–4, at pH 5–10 with an optimum of 7–8, and at 5–37 °C with an optimum of 28-35 °C. It accumulated poly-β-hydroxybutyrate granules inside the cell. Bacteriochlorophyll a was absent. The respiratory quinone was Q-10 and the dominant fatty acid was summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The major polar lipids comprised phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, an unidentified phospholipid and two unidentified polar lipids. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 1-19bT belonged to the family Rhodobacteraceae and formed a distinct monophyletic clade with 'Oceaniovalibus guishaninsula' JLT2003 and Pontibaca methylaminivorans GRP21T, exhibiting similarities of 94.7 and 92.2 %, respectively. The genomic DNA G+C content was 64.2 mol%. Based on the phenotypic, chemotaxonomic and genotypic data, strain 1-19bT represents a novel species in a new genus of the family Rhodobacteraceae , for which the name Oceaniglobus indicus gen. nov., sp. nov. is proposed, with the type strain 1-19bT (=MCCC 1A11863T=KCTC 52709T).
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Franconibacter daqui sp. nov., a facultatively alkaliphilic species isolated from a Daqu sample
More LessA novel bacterium, designated strain DL503T, was isolated from a Daqu sample and its taxonomic position determined using a polyphasic taxonomy. Strain DL503T was a Gram-stain-negative, facultatively anaerobic, non-sporulating, motile and coccoid-rod-shaped bacterium. Optimum growth occurred at 20–45 °C, pH 5.0–10.0 and 1.5 % (w/v) NaCl. Comparative analysis of the 16S rRNA gene sequence showed that the isolate belongs to the genus Franconibacter , showing highest levels of similarity with respect to Franconibacter pulveris JCM 16471T (98.94 %) and Franconibacter helveticus DSM 18396T (98.39 %). Cells contained the quinones Q-8 and MK-8, and the polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, three unidentified polar lipids and three unidentified amino lipids. The DNA G+C content was 53.3 mol% and the major fatty acids were C16 : 0, C17 : 0 cyclo, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), summed feature 4 (C17 : 1 iso I and/or C17 : 1 anteiso B) and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The DNA–DNA relatedness values between strain DL503T and its close relatives, including F. pulveris JCM 16471T and F. helveticus DSM 18396T, were 51.5±0.5 % and 45.2±1.1 %, respectively. Based on phylogenetic analysis, phenotypic and genotypic data, it is concluded that the isolate represents a novel species of the genus Franconibacter , for which the name Franconibacter daqui sp. nov. is proposed. The type strain is DL503T (=LMG 29914T=CGMCC 1.15944T).
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Desulfonatronum parangueonense sp. nov., a sulfate-reducing bacterium isolated from sediment of an alkaline crater lake
Novel Gram-stain-negative, non-spore-forming, vibrio-shaped, anaerobic, alkaliphilic, sulfate-reducing bacteria, designated strains PAR180T and PAR190, were isolated from sediments collected at an alkaline crater lake in Guanajuato (Mexico). Strain PAR180T grew at temperatures between 15 and 40 °C (optimum 35 °C), and at pH between 8.3 and 10.4 (optimum 9). It was halotolerant, growing with up to 8 % (w/v) NaCl. Lactate, formate, pyruvate and ethanol were used as electron donors in the presence of sulfate and were incompletely oxidized to acetate and CO2. The isolate was able to grow with hydrogen and with CO2 as a carbon source. Beside sulfate, sulfite and thiosulfate were used as terminal electron acceptors. The isolate was able to grow by disproportionation of sulfite and thiosulfate, but not elemental sulfur, using acetate as a carbon source. The predominant fatty acids were C16 : 0, C16 : 1ω7c and summed feature 10 (C18 : 1ω7c and/or C18 : 1ω9t and/or C18 : 1ω12t). The DNA G+C content was 56.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that it belongs to the genus Desulfonatronum , class Deltaproteobacteria . Its closest relative is Desulfonatronum thiosulfatophilum (98.7 % 16S rRNA gene sequence similarity). The DNA–DNA relatedness value between strain PAR180T and the type strain of D. thiosulfatophilum was 37.1±2.5 %. On the basis of phylogenetic, phenotypic and chemotaxonomic characteristics, the isolates is considered to represent a novel species of the genus Desulfonatronum , for which the name Desulfonatronum parangueonense sp. nov. is proposed. The type strain is PAR180T (=DSM 103602T=JCM 31598T).
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Gemmobacter straminiformis sp. nov., isolated from an artificial fountain
More LessA Gram-stain-negative, non-motile and facultative anaerobic bacterium, designated CAM-8T, was isolated from an artificial fountain at Chonbuk National University, South Korea. The novel strain grew at 20–37 °C (optimum 25 °C), pH 5.5–7.0 (optimum 6.0) and with 0–2 % NaCl (optimum 0 %). Oxidase and catalase activities were positive. The cell morphology of strain CAM-8T was atypical rods 0.6–0.8 µm in width and 4.5–6.5 µm in length, with a peaked tip and sometimes a bulb shape. CAM-8T existed as single cells, and as pairs or chains of cells. The phylogenetic analysis of 16S rRNA gene sequences indicated that strain CAM-8T clustered with Gemmobacter nectariphilus JCM 11959T and Gemmobacter megaterium JCM 18498T within the genus Gemmobacter . The DNA G+C content of strain CAM-8T was 65.9 mol%. The respiratory quinone was ubiquinone Q-10. The major fatty acids were C18 : 1 ω7c and/or C18 : 1 ω6c. The polar lipids of strain CAM-8T consisted of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, two uncharacterized phospholipids, an uncharacterized aminolipid, an uncharacterized glycolipid, an uncharacterized aminophospholipid and four uncharacterized lipids. On the basis of phenotypic, phylogenetic and chemotaxonomic data, strain CAM-8T (=KACC 19224T=JCM 31905T) is considered to represent a novel species of the genus Gemmobacter , for which the name Gemmobacter straminiformis sp. nov. is proposed.
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Characterization of thermotolerant phototrophic bacteria, Rhodoplanes tepidicaeni sp. nov. and Rhodoplanes azumiensis sp. nov., isolated from a geothermal spring
More LessTwo strains of thermotolerant phototrophic alphaproteobacteria, designated strains TUT3542T and TUT3581T, were isolated from sediment mud and cyanobacterial mats in a geothermal spring in Japan, respectively, and taxonomically characterized. Both the strains were budding motile rods and were able to grow at 45 °C. Phototrophically grown cells of strains TUT3542T and TUT3581T produced pink and brownish red cultures, respectively, and showed in vivo absorption maxima at 800, 858–859 and 892–895 nm in the near infrared region, indicating the presence of a core reaction centre and peripheral pigment complexes with bacteriochlorophyll a. The intracytoplasmic membrane system was of the lamellar type parallel to the cytoplasmic membrane. 16S rRNA gene sequence comparisons showed that strains TUT3542T and TUT3581T had the highest similarity level to Rhodoplanes oryazae NBRC 109406T (99.6 %) and Rhodoplanes elegans AS130T (99.3 %), respectively. Genomic DNA–DNA reassociation studies revealed that strains TUT3542T and TUT3581T had hybridization levels of less than 62 and 56 % to the type strains of all established species of the genus Rhodoplanes , respectively. The G+C contents of genomic DNA were 67.7 mol% for strain TUT3542T and 70.4 mol% for strain TUT3581T. Results of phenotypic studies showed that the two novel strains could be differentiated from any of the previously described Rhodoplanes species. Thus, the author proposes the names Rhodoplanes tepidicaeni sp. nov. for strain TUT3542T and Rhodoplanes azumiensis sp. nov. for strain TUT3581T. The type strain of Rhodoplanes tepidicaeni is TUT3542T (=KCTC 15602T=NBRC 112815T) and the type strain of Rhodoplanes azumiensis is TUT3581T (=KCTC 15603T=NBRC 112816T).
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Aurantimonas aggregata sp. nov., isolated from deep-sea sediment
More LessA novel bacterium, designated R14M6T, was isolated from deep-sea sediment collected from the Ross Sea, Antarctica. Cells are Gram-stain-negative, aerobic, pale yellow, short-rod-shaped, polar-flagellated and aggregate-forming. Growth occurs at 4–36 °C, pH 6.0–8.3, and in 1–15 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain R14M6T clustered together with Aurantimonas endophytica EGI6500337T and fell within the genus Aurantimonas . The 16S rRNA gene sequence of strain R14M6T shared similarity with A. endophytica EGI6500337T (99.15 %), A. manganoxydans DSM 21871T (97.73 %), A. coralicida DSM 14790T (97.58 %) and ‘ A. litoralis ’ KCTC 12094 (97.51 %). The DNA–DNA relatedness values between strain R14M6T and A. endophytica EGI6500337T, A. coralicida DSM 14790T, A. manganoxydans DSM 21871T and ‘ A. litoralis ’ KCTC 12094 were 36.9±4.5, 27.6±2.8, 29.6±1.2 and 25.2±2.4 % respectively. The major fatty acid of strain R14M6T was C18 : 1 ω7c. The major polar lipids were phosphatidylcholine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified aminolipid. Strain R14M6T contained Q-10 as the dominant isoprenoid quinone. The DNA G+C content of strain R14M6T was 67.4 mol%. Based on the phylogenetic, physiological and chemotaxonomic analyses, strain R14M6T represents a novel species of the genus Aurantimonas , for which the name Aurantimonas aggregata sp. nov. is proposed. The type strain is R14M6T (=GDMCC 1.1202T=KCTC 52919T).
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Paraferrimonas haliotis sp. nov., isolated from the intestine of abalone, Haliotis discus hannai and emendation of description of the genus Paraferrimonas
More LessTwo strains, AFRC7-2-1T and CFD7-4-2, were isolated from the intestine of abalone, Haliotis discus hannai. The bacterial cells were Gram-stain-negative, stick-shaped and non-flagellated. They were facultative anaerobic bacteria and could reduce Fe(III) to Fe(II). The 16S rRNA genes of two strains shared 99.7 % sequence similarity, and had the highest similarity of 97.3–97.5 % with Paraferrimonas sedimenticola NBRC 101628T, and of <94.0 % with other species. Phylogenetic relationship showed that the two strains formed a tight clade with an isolate Paraferrimonas sp. CGB11 obtained from the intestine of small abalone, H. diversicolor, and P. sedimenticola NBRC 101628T. The resulted DNA–DNA hybridization (DDH) values of strains AFRC7-2-1T and CFD7-4-2 compared with P. sedimenticola NBRC 101628T was 18.8–18.9 %. The resultant average nucleotide identity (ANI) values of AFRC7-2-1T and CFD7-4-2 compared with P. sedimenticola NBRC 101628T was 71.3–71.5 %. The predominant fatty acids (>5 %) of strains AFRC7-2-1T and CFD7-4-2 were iso-C15 : 0, iso-C13 : 0, C14 : 0, C16 : 0, C17 : 1 ω8c and summed feature 3 (C16 : 1ω7c/C16 : 1ω6c). The quinone system of strains AFRC7-2-1T and CFD7-4-2 were quinone-8, menaquinone-6, menaquinone-7, and quinone-7. The predominant polar lipids of strain AFRC7-2-1T were identified as phosphatidylethanolamine (PE), phosphatidylglycerol (PG), one unidentified phospholipid (PL), and three minor unidentified lipids (Ls). The genomic DNA G+C contents of two strains were 47.2 mol%. In summary, the two strains represented a novel species of the genus Paraferrimonas , for which the name Paraferrimonas haliotis sp. nov. was proposed, with type strain AFRC7-2-1T (=MCCC 1A11748T=KCTC 52632T=NBRC 112785T) and strain CFD7-4-2 (=MCCC 1A11749=KCTC 52631=NBRC 112786).
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Actibacterium pelagium sp. nov., a novel alphaproteobacterium, and emended description of the genus Actibacterium
A Gram-stain-negative, non-motile, rod-shaped bacterium, designated JN33T, was isolated from seawater collected from the western Pacific Ocean. Strain JN33T was positive for hydrolysis of aesculin and gelatin. On the basis of 16S rRNA gene sequence analysis, strain JN33T showed high 16S rRNA gene sequence similarity to Actibacterium atlanticum 22II-S11-z10T (97.3 %), A. mucosum KCTC 23349T (96.6 %) and A. ureilyticum LS-811T (95.7 %) and exhibited less than 97.0 % 16S rRNA gene sequence similarity with respect to the other type strains within the family Rhodobacteraceae. Phylogenetic analysis revealed that strain JN33T fell within the cluster of the genus Actibacterium. The average nucleotide identity and in silico DNA–DNA hybridization values between strain JN33T and the type strains of Actibacterium species were 73.1–73.8 % and 19.8–20.1 %, respectively. The sole respiratory quinone was ubiquinone 10 (Q-10). The principal fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The major polar lipids were phosphatidylglycerol, one unidentified phospholipid and two unidentified aminolipids. The DNA G+C content was 57.8 mol%. Distinctly different phylogenetic characteristics, chemotaxonomic differences, as well as phenotypic properties, revealed that strain JN33T could be differentiated from the Actibacterium species with validly published names. Therefore, it is proposed that strain JN33T represents a novel species of the genus Actibacterium, for which the name Actibacterium pelagium sp. nov. (type strain, JN33T=CGMCC 1.16012T=KCTC 52653T) is proposed.
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Reclassification of a Polynucleobacter cosmopolitanus strain isolated from tropical Lake Victoria as Polynucleobacter victoriensis sp. nov.
The genus Polynucleobacter (family Burkholderiaceae ) is phylogenetically subdivided into at least four subclusters. One of those, subcluster PnecC, was recognized as a cryptic species complex. Here we test by comparative genome analyses whether subcluster PnecD, currently solely represented by the species Polynucleobacter cosmopolitanus , also represents such a cryptic species complex. The genome sequences of the two P. cosmopolitanus strains, MWH-MoIso2T and MWH-VicM1, were determined. The latter strain was also characterized in the previous description of P. cosmopolitanus . These two strains originate from a temperate lake located in Austria and from the large tropical Lake Victoria located in East Africa, respectively. Strains MWH-MoIso2T and MWH-VicM1 possess quite small genomes of 1.78 and 1.63 Mbp, respectively, and share similar G+C values of 44.1 and 43.1 mol%, respectively. Both strains encode only a single copy of the ribosomal operon, and their 16S rRNA genes differ only in four positions, equalling a sequence similarity of 99.74 %. Both genomes possess characteristics indicating evolutionary genome streamlining, such as high coding densities of 93.9 and 94.6 % of bases, respectively. Average nucleotide identity (ANI) comparisons of the genomes of the two strains resulted in a value of 78.4 %, suggesting that each of the strains represents a separate species. Our investigation suggests that PnecD represents an additional cryptic species complex within the genus Polynucleobacter that was not resolved by 16S rRNA gene sequence analyses. We propose reclassification of strain MWH-VicM1 as Polynucleobacter victoriensis sp. nov., with type strain MWH-VicM1T(=DSM 21486T=JCM 32005T).
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