- Volume 68, Issue 6, 2018
Volume 68, Issue 6, 2018
- Notification List
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- Mini Review
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LPSN – List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on
More LessThe List of Prokaryotic Names with Standing in Nomenclature (LPSN) was established in 1997 as the List of Bacterial Names with Standing in Nomenclature (LBSN); it quickly became a key online resource for anyone interested in bacterial and archaeal nomenclature and classification. This review looks at numbers of prokaryotic names published since the Approved Lists of Bacterial Names, current usage of LPSN and future developments.
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- New Taxa
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- Actinobacteria
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Streptomyces manganisoli sp. nov., a novel actinomycete isolated from manganese-contaminated soil
More LessA novel actinomycete isolate, designated strain MK44T, was isolated from a Manganese-polluted soil sample collected near Xiangtan Manganese Mine, South Central China and subjected to a polyphasic taxonomic characterization. Comparison of 16S rRNA gene sequences showed that strain MK44T was a member of the genus Streptomyces and most closely related to Streptomyces specialis JCM 16611T (97.9 %) and Streptomyces mayteni JCM 16957T (97.4 %). The DNA–DNA relatedness between strain MK44T and the above two related type species were 30.9±0.3 and 29.9±3.5 %, respectively, values which are far lower than the 70 % threshold for the delineation of a novel prokaryotic species. Furthermore, the results of physiological, biochemical and chemotaxonomic tests allowed further phenotypic differentiation. Therefore, it is concluded that strain MK44T represents a novel species of the genus Streptomyces , for which the name Streptomyces manganisoli sp. nov. is proposed. The type strain is MK44T (=GDMCC 4.137T=KCTC 39920T).
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Propionicimonas ferrireducens sp. nov., isolated from dissimilatory iron(III)-reducing microbial enrichment obtained from paddy soil
A novel strain, designated Y1A-10 4-9-1T, with Gram-stain-positive and rod-shaped cells, was isolated from paddy soil in Yingtan, Jiangxi, China. Cells were 0.15–0.2 µm wide and 1.5–3.3 µm long. The optimal growth temperature was 30 °C and the optimal pH was 7.0. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the novel strain is closely related to Propionicimonas paludicola JCM 11933T (98.57 %). The genomic DNA G+C content was 63.9 mol%. The predominant menaquinone was MK-9(H4) and meso-diaminopimelic acid was present in the cell-wall peptidoglycan layer. The major polar lipids were diphosphatidylglycerol, one unidentified phospholipid and two unidentified lipids. The dominant cellular fatty acids detected were anteiso-C15 : 0 and iso-C16 : 0. The phylogenetic and phenotypic results supported that strain Y1A-10 4-9-1T is a novel species of the genus Propionicimonas , for which the name Propionicimonas ferrireducens sp. nov. is proposed. The type strain is Y1A-10 4-9-1T (=CCTCC AB 2016249T=KCTC 15566T=LMG 29810T).
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Nocardioides pelophilus sp. nov., isolated from freshwater mud
More LessA Gram-stain-positive, aerobic, motile, rod- or cocci-shaped bacterium with flagella bacterium (THG-T63T) was isolated from freshwater mud. Growth occurred at 10–40 °C (optimum, 28–35 °C), at pH 6–8 (optimum, 7) and at 0–6 % NaCl (optimum, 2 %). Based on 16S rRNA sequence analysis, the nearest phylogenetic neighbours of strain THG-T63T were identified as Nocardioides panacisoli KCTC 19470T (97.5 %), Nocardioides caeni KCTC 19600T (96.4 %), Nocardioides humi KCTC 19265T (96.3 %), Nocardioides kongjuensis KCTC 19054T (96.1 %) and Nocardioides nitrophenolicus KCTC 457BPT (96.1 %). 16S rRNA sequence similarities among strain THG-T63T and other species were lower than 96.0 %. The polar lipids were phosphatidylglycerol, phosphatidylinositol and one unidentified phospholipid. The quinone system was composed of MK-8 (H4). The major fatty acids were C16 : 0, C17 : 1 ω6c, C17 : 1 ω8c, C18 : 0 10-methyl, C18 : 1 ω9c and iso-C16 : 0. The cell-wall peptidoglycan contained ll-2,6-diaminopimelic acid. The DNA G+C content of strain THG-T63T was 74.6 mol%. Strain THG-T63T exhibited levels of DNA–DNA relatedness of 20–44 % to the type strains of phylogenetically related Nocardioides species and could be differentiated from these species based on differences in phenotypic characteristics. On the basis of the data presented here, strain THG-T63T represents a novel species of the genus Nocardioides , for which the name Nocardioides pelophilus sp. nov. is proposed. The type strain is THG-T63T(=KACC 19192T=CGMCC 4.7388T).
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Pseudonocardia lutea sp. nov., a novel actinobacterium isolated from soil in Chad
A novel actinomycete, designated strain NEAU-G57T was isolated from a soil sample collected from the bottom of a river in Chad. A polyphasic approach was employed to determine the status of strain NEAU-G57T. Phylogenetic analysis based on its 16S rRNA gene sequence indicated that the organism should be assigned to the genus Pseudonocardia and formed a monophyletic clade with its closest relatives Pseudonocardia yuanmoensis YIM 75926T (98.8 %), Pseudonocardia halophobica DSM 43089T (98.2 %) and Pseudonocardia kujensis A 4038T (97.6 %). Moreover, morphological and chemotaxonomic properties of strain NEAU-G57T also confirmed the affiliation of the isolate to the genus Pseudonocardia . The cell wall contained meso-diaminopimelic acid and whole-cell sugars were glucose, xylose, arabinose and galactose. The predominant menaquinone was MK-8(H4). The phospholipid profile consisted of diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, hydroxyphosphatidylmethylethanolamine, hydroxyphosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol mannosides, one unidentified glycolipid and one unidentified lipid. The major fatty acids were C16 : 0 and C16 : 1ω7c. The DNA G+C content was 73.3 mol%. However, the low level of DNA–DNA relatedness and some phenotypic characteristics allowed the isolate to be differentiated from its closely related species. Therefore, it is concluded that strain NEAU-G57T can be classified as representing a novel species of the genus Pseudonocardia , for which the name Pseudonocardia lutea sp. nov. is proposed. The type strain is NEAU-G57T (=JCM 32387T=CGMCC 4.7397T).
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Whole-genome sequence analysis of the Mycobacterium avium complex and proposal of the transfer of Mycobacterium yongonense to Mycobacterium intracellulare subsp. yongonense subsp. nov.
More LessBacterial whole-genome sequences contain informative features of their evolutionary pathways. Comparison of whole-genome sequences have become the method of choice for classification of prokaryotes, thus allowing the identification of bacteria from an evolutionary perspective, and providing data to resolve some current controversies. Currently, controversy exists about the assignment of members of the Mycobacterium avium complex, as is for the cases of Mycobacterium yongonense and ‘Mycobacterium indicus pranii’. These two mycobacteria, closely related to Mycobacterium intracellulare on the basis of standard phenotypic and single gene-sequences comparisons, were not considered a member of such species on the basis on some particular differences displayed by a single strain. Whole-genome sequence comparison procedures, namely the average nucleotide identity and the genome distance, showed that those two mycobacteria should be considered members of the species M. intracellulare . The results were confirmed with other whole-genome comparison supplementary methods. According to the data provided, Mycobacterium yongonense and ‘Mycobacterium indicus pranii’ should be considered and renamed and included as members of M. intracellulare . This study highlights the problems caused when a novel species is accepted on the basis of a single strain, as was the case for M. yongonense . Based mainly on whole-genome sequence analysis, we conclude that M. yongonense should be reclassified as a subspecies of Mycobacterium intracellulare as Mycobacterium intracellulare subsp. yongonense and ‘Mycobacterium indicus pranii’ classified in the same subspecies as the type strain of Mycobacterium intracellulare and classified as Mycobacterium intracellulare subsp. intracellulare.
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- Archaea
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Salinirubellus salinus gen. nov., sp. nov., isolated from a marine solar saltern
More LessA halophilic archaeal strain, designated ZS-35-S2T, was isolated from Zhoushan marine solar saltern in Zhejiang Province, China. Cells were pleomorphic, Gram-stain-negative and formed red-pigmented colonies on agar plates. The cells lysed in distilled water and the minimal NaCl concentration to prevent cell lysis was 8 % (w/v). Strain ZS-35-S2T was able to grow at 25–50 °C (optimum, 37 °C), with 1.4–4.8 M NaCl (optimum, 2.1 M), with 0–1.0 M MgCl2 (optimum, 0.1 M) and at pH 5.0–9.5 (optimum, pH 7.5). Phylogenetic tree reconstructions based on 16S rRNA genes and rpoB′ genes revealed that strain ZS-35-S2T was distinct from the related genera Halomarina , Natronomonas , Halorientalis , Salinirubrum and Halobaculum of the order Halobacteriales . The major polar lipids of the strain were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and three unidentified glycolipids. The two major glycolipids were chromatographically identical to S-DGD-1 and DGD-1, respectively. The DNA G+C content of strain ZS-35-S2T is 67.0 mol%. The phenotypic, chemotaxonomic and phylogenetic properties suggested that strain ZS-35-S2T (=CGMCC 1.12551T=JCM 30036T) represents a novel species of a new genus within the order Halobacteriales , for which the name Salinirubellus salinus gen. nov., sp. nov. is proposed.
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Sulfurisphaera javensis sp. nov., a hyperthermophilic and acidophilic archaeon isolated from Indonesian hot spring, and reclassification of Sulfolobus tokodaii Suzuki et al. 2002 as Sulfurisphaera tokodaii comb. nov.
A novel hyperthermophilic, acidophilic and facultatively anaerobic archaeon, strain KD-1T, was isolated from an acidic hot spring in Indonesia and characterized with the phylogenetically related species Sulfurisphaera ohwakuensis Kurosawa et al. 1998, Sulfolobus tokodaii Suzuki et al., 2002 and Sulfolobus yangmingensis Jan et al. 1999. Cells of KD-1T were irregular cocci with diameters of 0.9–1.3 µm. The strain grew at 60–90 °C (optimum 80–85 °C), pH 2.5–6.0 (optimum pH 3.5–4.0) and 0–1.0 % (w/v) NaCl concentration. KD-1T grew anaerobically in the presence of S0 (headspace: H2/CO2) and FeCl3 (headspace: N2). Under aerobic conditions, chemolithoautotrophic growth occurred on S0, pyrite, K2S4O6, Na2S2O3 and H2. This strain utilized various complex substrates, such as yeast extract, but did not grow on sugars and amino acids as the sole carbon source. The main core lipids were calditoglycerocaldarchaeol and caldarchaeol. The DNA G+C content was 30.6 mol%. Analyses of phylogenetic trees based on 16S rRNA and 23S rRNA genes indicated that KD-1T formed an independent lineage near Sulfurisphaera ohwakuensis TA-1T, Sulfolobus tokodaii 7T and Sulfolobus yangmingensis YM1T. On the basis of the results of morphological, physiological, chemotaxonomic and phylogenetic analyses, KD-1T represents a novel species of the genus Sulfurisphaera Kurosawa et al. 1998, for which the name Sulfurisphaera javensis sp. nov. is proposed. The type strain is KD-1T (=JCM 32117T=InaCC Ar81T). Based on the data, we also propose the reclassification of Sulfolobus tokodaii Suzuki et al., 2002 as Sulfurisphaera tokodaii comb. nov. (type strain 7T=JCM 10545T=DSM 16993T).
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- Bacteroidetes
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Flavobacterium aurantiibacter sp. nov., an orange-pigmented bacterium isolated from cyanobacterial aggregates in a eutrophic lake
More LessA bacterial strain, designated TH167T, was isolated from cyanobacterial aggregates in eutrophic Lake Taihu in China. Cells were observed to be slightly curved rod-shaped, motile by gliding, aerobic, Gram-stain-negative, proteorhodopsin-containing. Optimal growth was obtained at pH 7.0 (range: 6.0–9.0), 28 °C (range: 4–32 °C) and 0 % (w/v) NaCl (range: 0–2.0 %) in Reasoner’s 2A broth. No growth was observed at 37 °C. The cells were found to be positive for catalase and oxidase activities. The major fatty acids (>10 %) were identified as iso-C15 : 0, iso-C15 : 1 G and anteiso-C15 : 0. The major polar lipids of the isolate comprised phosphatidylethanolamine, one unidentified phospholipid and two unidentified aminolipids. The major respiratory quinone was menaquinone-6. The genomic G+C content of strain TH167T was 40.4 mol% based on total genome calculations. Based on similarities of 16S rRNA gene sequences, strain TH167T was affiliated with the genus Flavobacterium , exhibiting the highest sequence similarities to Flavobacterium eburneum SA31T (94.16 %), Flavobacterium yanchengense hgT (94.09 %) and Flavobacterium lacus NP180T (93.95 %). The phenotypic, chemotaxonomic and phylogenetic properties, and genome analysis suggested that strain TH167T represented a novel species within the genus Flavobacterium , for which the name Flavobacterium aurantiibacter sp. nov. is proposed. The type strain is TH167T (=CGMCC 1.15805T=LMG 29719T).
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Fluviicola kyonggii sp. nov., a bacterium isolated from forest soil and emended description of the genus Fluviicola
More LessA novel bacterium, designated strain CA-1T, was isolated from forest soil in Kyonggi University. Cells were strictly aerobic, Gram-stain-negative, catalase-positive, oxidase-negative, non-motile, non-spore-forming, rod-shaped and red-orange-pigmented. Strain CA-1T hydrolysed casein and DNA. It was able to grow at 15–37 °C, pH 5.5–9.0 and at 0–2 % (w/v) NaCl concentration. Flexirubin-type pigments were present. Phylogenetic analysis based on its 16S rRNA gene sequence indicated that strain CA-1T formed a lineage within the family Crocinitomicaceae of the phylum Bacteroidetes that was distinct from Fluviicola hefeinensis MYL-8T (96.8 % sequence similarity) and Fluviicola taffensis DSM 16823T (96.1 %). Strain CA-1T contained menaquinone-6 as a sole respiratory quinone. The major polar lipids were phosphatidylethanolamine, unidentified aminolipids, an unidentified aminophospholipid and an unidentified lipid. The major cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, C15 : 0 2-OH, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and iso-C15 : 1 G. The DNA G+C content of strain CA-1T was 44.1 mol%. The polyphasic characterization revealed that strain CA-1T represents a novel species in the genus Fluviicola , for which the name Fluviicola kyonggii sp. nov. is proposed. The type strain is CA-1T (=KEMB 9005-526T=KACC 19148T=NBRC 112684T).
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Carboxylicivirga sediminis sp. nov., isolated from coastal sediment
More LessA yellow-pigmented bacterial strain (JR1T) isolated from a sediment sample was subjected to a taxonomic study, based on phenotypic, genetic and physiological characterization. Here, we describe the cultivation and characteristics of strain JR1T, a novel member of the genus Carboxylicivirga in the family Marinilabiliaceae . Cells of strain JR1T were rod-shaped, Gram-stain-negative, non-motile and facultatively anaerobic. The temperature range for growth was 15–42 °C (optimum, 33 °C) and the pH range for growth was pH 6.0–8.5 (optimum, pH 7.0–7.5). Growth occurred in the presence of 0.0–10.0 % (w/v) NaCl (optimum 2.0–3.0 %). 16S rRNA gene sequence analysis produced results with 97.4 % similarity to Carboxylicivirga taeanensis MEBiC 08903T, 96.8 % similarity to Carboxylicivirga mesophila MEBiC 07026T, 94.9 % similarity to Carboxylicivirga linearis FB218T and 94.6 % similarity to Carboxylicivirga flava Q15T. The DNA G+C content was 42.3 mol% and the major fatty acids were iso-C15 : 0, C15 : 0, anteiso-C15 : 0, C17 : 1ω6c and iso-C17 : 0-3OH. The major polar lipids detected were phosphatidylethanolamine and two unidentified lipids; the major respiratory quinone detected was MK-7. The results of the phenotypical, phylogenetic and biochemical analyses between the study strain and some related type strains indicated that this strain represent a novel species of the genus Carboxylicivirga within the family Marinilabiliaceae , for which the name Carboxylicivirga sediminis sp. nov. is proposed. The type strain is JR1T (=MCCC 1K03323T=KCTC 52869T).
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Flavobacterium alvei sp. nov., isolated from a freshwater river
Yunho Lee and Che Ok JeonA yellow-pigmented, Gram-stain-negative, strictly aerobic, catalase-negative and oxidase-positive bacterium, designated strain HR-AYT, was isolated from a water sample of the Han River. Cells were non-motile rods without flagella. Growth was observed at 5–30 °C (optimum, 20 °C), pH 5–9 (optimum, pH 7) and 0 % NaCl. The major respiratory quinone was menaquinone-6. Strain HR-AYT did not produce flexirubin-type pigments. The major fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), anteiso-C15 : 0, iso-C15 : 0 and C16 : 0. The polar lipids comprised phosphatidylethanolamine and an unidentified phosphoamino lipid as major polar lipids, and four unidentified lipids were also detected as minor lipids. The DNA G+C content of strain HR-AYT was 34.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain HR-AYT belonged to the family Flavobacteriaceae in the phylum Bacteroidetes , and formed a phylogenic lineage with members of the genus Flavobacterium . The 16S rRNA gene sequence similarity showed that strain HR-AYT was most closely related to Flavobacterium chungbukense CS100T (97.91 %) and Flavobacterium glaciei 0499T (97.74 %). Based on these results, strain HR-AYT represents a novel species of the genus Flavobacterium , for which the name Flavobacterium alvei sp. nov. is proposed. The type strain is HR-AYT (=KACC 19407T=JCM 32264T).
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Siphonobacter curvatus sp. nov., isolated from a freshwater river
Yunho Lee and Che Ok JeonA novel orange-pigmented, Gram-stain-negative and strictly aerobic bacterium, designated strain HR-UT, was isolated from a water sample of the Han River located in the Republic of Korea. Cells were catalase-positive and oxidase-positive, and non-motile curved rods without flagella. The strain grew at 5–35 °C (optimum 25 °C), pH 6–10 (optimum of 7–8) and 0–3 % (w/v) NaCl (optimum 0 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain HR-UT formed a tight phylogenic lineage with Siphonobacter aquaeclarae DSM 21668T and ‘ Siphonobacter intestinalis’ 63MJ-2. The 16S rRNA gene sequence comparison of strain HR-UT and other reported type strains showed that it shared the highest sequence similarity to S. aquaeclarae DSM 21668T (96.9 %) and ‘S. intestinalis’ 63MJ-2 (96.6 %), and had lower similarities than 87.0 % to other bacteria with validly published names. Average nucleotide identity and in silico DNA–DNA hybridization values between strain HR-UT and the most closely related strain S. aquaeclarae were 71.7 and 18.4 %, respectively. The major respiratory quinone was menaquinone-7, and the dominant fatty acids (>5 %) consisted of C16 : 1 ω5c, summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH) and iso-C15 : 0. The polar lipids comprised phosphatidylethanolamine, four unidentified aminolipids and three unidentified lipids. The DNA G+C content was 47.9 mol%. Based on the genotypic, chemotaxonomic and phenotypic analyses, strain HR-UT represents a novel species of the genus Siphonobacter , for which the name Siphonobacter curvatus sp. nov. is proposed. The type strain is HR-UT (=KACC 19409T=JCM 32267T).
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Rhodohalobacter barkolensis sp. nov., isolated from a saline lake and emended description of the genus Rhodohalobacter
A Gram-stain-negative, non-motile, aerobic, rod-shaped bacterium, designated 15182T, was isolated from a saline lake in China. The novel strain 15182T was able to grow at 10–40 °C (optimum, 37 °C), pH 7.0–8.0 (optimum, 7.5) and with 0.5–4 % NaCl (optimum, 2–3 %, w/v). The phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 15182T was most closely related to the genus Rhodohalobacter by sharing the highest sequence similarity of 97.0 % with Rhodohalobacter halophilus JZ3C29T. Chemotaxonomic analysis showed that the sole respiratory quinone was menaquinone 7, the major fatty acids included C16 : 0 N alcohol and C16 : 1 ω11c. The major polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, four uncharacterized glycolipids, one uncharacterized phospholipid and two uncharacterized lipids. The genomic DNA G+C content of the strain 15182T was 42.4 mol%. The average nucleotide identity value between 15182T and R. halophilus JZ3C29T was 75.4 %, and the in silico DNA–DNA hybridization value of the two strains was 19.1 %. On the basis of its phenotypic, chemotaxonomic, genotypic and genomic characteristics presented in this study, strain 15182T is suggested to represent a novel species in the genus Rhodohalobacter, for which the name Rhodohalobacter barkolensis sp. nov. is proposed. The type strain is 15182T (=KCTC 62172T=MCCC 1K03442T). An emended description of the genus Rhodohalobacter is also presented.
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Hymenobacter aquatilis sp. nov., isolated from a mesotrophic artificial lake
More LessA novel strain, designated HMF3095T, isolated from freshwater of a mesotrophic artificial lake in the Republic of Korea, was characterized by polyphasic taxonomy. The cells were Gram-stain-negative, aerobic, non-motile, straight rods and formed reddish colonies. Phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain HMF3095T fell within the cluster of the genus Hymenobacter and was most closely related to Hymenobacter seoulensis 16F7GT and Hymenobacter tenuis POB6T (96.7 % sequence similarity). Sequence similarities to all other type strains were 96.3 % or less. The major fatty acids were iso-C15 : 0, C16 : 1ω5c, summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and anteiso-C15 : 0. The major isoprenoid quinone was menaquinone 7. The major polar lipids were phosphatidylethanolamine, three unidentified aminophospholipids and one unidentified phospholipid. The DNA G+C content was 58.9 mol%. On the basis of the evidence presented in this study, strain HMF3095T represents a novel species of the genus Hymenobacter , for which the name Hymenobacter aquatilis sp. nov. is proposed. The type strain is HMF3095T (=KCTC 52398T=NBRC 112669T).
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- Firmicutes and Related Organisms
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Camelliibacillus cellulosilyticus gen. nov., sp. nov., a cellulose-degrading bacterium isolated from tea
More LessA Gram-stain-positive, oxidase- and catalase-positive, endospore-forming, aerobic, non-motile and rod-shaped bacterium (THG-YT1T) was isolated from green tea. Growth occurred at 10–40 °C (optimum, 25–30 °C), at pH 6–8 (optimum, 7) and at 0–2 % NaCl (optimum, 0 %). Based on 16S rRNA gene sequences, phylogenetic analyses showed that strain THG-YT1T formed a distinct lineage with respect to closely related genera in the family Bacillaceae . Strain THG-YT1T was most closely related to the genera within the families Pullulanibacillus , Scopulibacillus , Tuberibacillus and Caenibacillu, with levels of 16S rRNA gene sequence similarity to the type species of members of these genera of less than 95.0 %. The menaquinone was MK-7. The polar lipids were phosphatidylethanolamine, two unidentified aminophospholipids, two unidentified aminolipids and two unidentified glycolipids. The major fatty acids of strain THG-YT1T were C18 : 3 ω7c and anteiso-C17 : 0. The cell-wall peptidoglycan type was A1γ with meso-diaminopimelic acid as the diagnostic diamino acid plus alanine and glutamic acid. The cell-wall sugar was glucose. The DNA G+C content of strain THG-YT1T was determined to be 53.5 mol%. Based on the data presented here, strain THG-YT1T represents a novel species of a new genus of the family Bacillaceae , for which the name Camelliibacillus cellulosilyticus gen. nov., sp. nov. is proposed. The type strain is Camelliibacillus cellulosilyticus THG-YT1T(=KACC 19471T=CGMCC 1.16306T).
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Lactobacillus micheneri sp. nov., Lactobacillus timberlakei sp. nov. and Lactobacillus quenuiae sp. nov., lactic acid bacteria isolated from wild bees and flowers
More LessGram-stain-positive, rod-shaped, non-spore forming bacteria have been isolated from flowers and the guts of adult wild bees in the families Megachilidae and Halictidae. Phylogenetic analysis of the 16S rRNA gene indicated that these bacteria belong to the genus Lactobacillus , and are most closely related to the honey-bee associated bacteria Lactobacillus kunkeei (97.0 % sequence similarity) and Lactobacillus apinorum (97.0 % sequence similarity). Phylogenetic analyses of 16S rRNA genes and six single-copy protein coding genes, in situ and in silico DNA–DNA hybridization, and fatty-acid profiling differentiates the newly isolated bacteria as three novel Lactobacillus species: Lactobacillus micheneri sp. nov. with the type strain Hlig3T (=DSM 104126T,=NRRL B-65473T), Lactobacillus timberlakei with the type strain HV_12T (=DSM 104128T,=NRRL B-65472T), and Lactobacillus quenuiae sp. nov. with the type strain HV_6T (=DSM 104127T,=NRRL B-65474T).
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Paenibacillus yanchengensis sp. nov., isolated from farmland soil
More LessA Gram-variable, short-rod-shaped, motile, spore-forming, strictly aerobic and alkaliresistant bacterium, designed strain J-3T, was isolated from farmland soil sampled in Yancheng city, Jiangsu province, China. Optimal growth occurred at 30 °C, pH 7.0–8.0 and 0.5 % (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain J-3T was most closely related to Paenibacillusripae HZ1T (96.8 %), followed by Paenibacillussputi KIT00200-70066-1T (94.7 %). The major cellular fatty acids were anteiso-C15 : 0 and C16 : 0. The dominant respiratory quinone was menaquinone-7 and the DNA G+C content was 41.2 mol%. The major polar lipids of strain J-3T were aminolipid, phospholipid, diphosphatidylglycerol, phosphatidylglycerol, phosphoaminolipid and phosphatidylethanolamine. The diagnostic diamino acid of the cell-wall peptidoglycan was meso-diaminopimelic acid. On the basis of genotypic and phenotypic data, strain J-3T represents a novel species of the genus Paenibacillus , for which the name Paenibacillus yanchengensis sp. nov. is proposed. The type strain is J-3T (=KCTC 33926T=CGMCC 1.16455T).
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Virgibacillus indicus sp. nov. and Virgibacillus profundi sp. nov, two moderately halophilic bacteria isolated from marine sediment by using microfluidic streak plates
More LessThree Gram-variable, moderately halophilic, motile, endospore-forming rods, designated P2-C2T, P3-H5T and P3-B8, were isolated from marine sediment of the Southwest Indian Ocean by using the microfluidic streak plate method. Phylogeny based on 16S rRNA gene sequences showed that strains P2-C2T and P3-H5T formed a robust cluster within the genus Virgibacillus and exhibited 16S rRNA gene similarity levels of 95.3–96.8 and 94.9–96.3 % to the type strains of Virgibacillus species, respectively. The 16S rRNA gene similarity between P2-C2T and P3-H5T was 97.6 %. Strain P3-B8 has an identical 16S rRNA gene sequence to strain P3-H5T. For all the novel strains, the predominant cellular fatty acids were anteiso-C15 : 0 and anteiso-C17 : 0, the main menaquinone was MK-7, and the polar lipid profiles contained diphosphatidylglycerol and phosphatidylglycerol. The genomic DNA G+C contents of strains P2-C2T, P3-H5T and P3-B8 were 38.3, 37.3 and 37.5 mol%, respectively. Combined data from phenotypic and genotypic studies demonstrated that strains P2-C2T and P3-H5T/P3-B8 are representatives of two different novel species of the genus Virgibacillus , for which the name Virgibacillus indicus sp. nov. and Virgibacillus profundi are proposed. The type strains are P2-C2T (=CGMCC 1.16138T=NBRC 113014T) and P3-H5T (=CGMCC 1.16139T=NBRC 113015T).
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Lawsonibacter asaccharolyticus gen. nov., sp. nov., a butyrate-producing bacterium isolated from human faeces
More LessAn obligately anaerobic, Gram-positive, non-spore-forming, straight rod-shaped bacterium, designated strain 3BBH22T, was isolated from a faecal sample of a healthy Japanese woman. The 16S rRNA gene sequence analysis showed that strain 3BBH22T formed a monophyletic cluster with species in the genera Pseudoflavonifractor and Flavonifractor within the family Ruminococcaceae and had highest similarity to Pseudoflavonifractor capillosus ATCC 29799T (96.7 % sequence similarity), followed by Flavonifractor plautii ATCC 29863T (96.4 %). Acetate and butyrate were produced by strain 3BBH22T as metabolic end-products. The major cellular fatty acids were C14 : 0, C16 : 0, C18 : 1ω9c, C16 : 0 dimethyl acetal, C18 : 0 and C18 : 2ω6,9c. No respiratory quinones were detected. In contrast to F. plautii JCM 32125T, strain 3BBH22T did not degrade quercetin, one of the flavonoids. P. capillosus JCM 32126T also did not. Strain 3BBH22T was differentiated from P. capillosus JCM 32126T by its inability to hydrolyse aesculin. The G+C content of the genomic DNA was 61.2±1.0 mol%. On the basis of these data and the phylogenetic tree based on 89 proteins, strain 3BBH22T represents a novel species in a novel genus of the family Ruminococcaceae , for which the name Lawsonibacter asaccharolyticus gen. nov., sp. nov. is proposed. The type strain of L. asaccharolyticus is 3BBH22T (=JCM 32166T=DSM 106493T).
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Isolation and characterization of Streptococcus respiraculi sp. nov. from Marmota himalayana (Himalayan marmot) respiratory tract
More LessTwo bacterial strains were individually isolated from Marmota himalayana respiratory tracts; the animals were from the Tibet–Qinghai Plateau, PR China. The isolates were Gram-stain-positive, catalase-negative, coccus-shaped, chain-forming organisms. Analysis of 16S rRNA gene sequences indicated that the type strain HTS25T shared 98.0, 97.4, 97.2 and 97.1 % similarity with Streptococcus cuniculi , Streptococcus acidominimus , Streptococcus marmotae and Streptococcus himalayensis respectively. Sequence analysis of the sodA and rpoB genes indicated that HTS25T was closely related to S. marmotae (similarities of 94.7 and 91.4 % respectively). Analysis of groEL sequences showed interspecies similarity of 84.8 % between HTS25T and S. himalayensis . A whole-genome phylogenetic tree reconstructed from 81 core genes from the genomes of 17 members of the genus Streptococcus was used to validate that HTS25T forms a distinct subline from other recognized species of the genus Streptococcus . DNA–DNA hybridization of HTS25T showed a maximum estimated DNA reassociation value of 32.1 % to Streptococcus cuniculi CCUG 65085T. On the basis of the results of phenotypic and phylogenetic analyses, we propose that the two isolates be classified as representing a novel species of the genus Streptococcus , named Streptococcus respiraculi sp. nov. The type strain is HTS25T (=DSM 101998T=CGMCC 1.15531T). The genome of Streptococcus respiraculi sp. nov. strain HTS25T (2 067 971 bp) contains 2001 genes with an average DNA G+C content of 42.7 mol%.
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- Proteobacteria
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Stenotrophomonas lactitubi sp. nov. and Stenotrophomonas indicatrix sp. nov., isolated from surfaces with food contact
More LessFive Gram-stain-negative, rod-shaped, none-spore-forming isolates were obtained from biofilms on different sites of a milking machine in Germany. Another strain with similar morphological characteristics was isolated from dirty dishes. Based on phylogenetic analysis of the 16S rRNA and gyrB genes, all isolates were assigned to the genus Stenotrophomonas , but were divided into three different groups. Chemotaxonomic characterization of the isolates led to the detection of iso-C15 : 0 and anteiso-C15 : 0 as the predominant cellular fatty acids, as well as small amounts of the hydroxyl fatty acids iso-C11 : 0 3-OH, C12 : 0 3-OH and iso-C13 : 0 3-OH. One group could be assigned to the species Stenotrophomonas maltophilia , while the genome sequences of two groups displayed average nucleotide identity values of less than 94 % between each other and the genome sequences of the next related type strains Stenotrophomonas maltophilia ATCC 13637T and Stenotrophomonas rhizophila DSM 14405T. Further phylogenetic, phenotypic and chemotaxonomic analyses enabled the differentiation of these strains from these closely related species. They are therefore considered to represent two novel species, for which the names Stenotrophomonas lactitubi and Stenotrophomonas indicatrix are proposed, with strains M15T (=DSM 104152T=LMG29943T) and WS40T (=DSM28278T=LMG29942T) as type strains.
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Pseudaeromonas paramecii sp. nov., isolated from the ciliate Paramecium caudatum and emendation of the genus Pseudaeromonas
More LessA Gram-stain-negative, oxidase-negative and catalase-negative, motile, rod-shaped bacterial strain, designated PCS8T, hosted by the ciliate Paramecium caudatum was investigated by using a polyphasic approach. Strain PCS8T was observed to be able to grow at 12–44 °C (optimum, 36–37 °C), at pH 6.0–10.0 (optimum, 7.0) and in the presence of 0–3 % NaCl (optimum, 1–2 %). It could hydrolyse starch and aesculin and produce acid from d-sorbitol, myo-inositol, glycerol and l-rhamnose. The sequence similarity of the new isolate was 96.9 % with respect to Pseudaeromonas pectinilytica and 96.3 % with respect to Pseudaeromonas sharmana . Phylogenetically, strain PCS8T falls within the cluster comprising the Pseudaeromonas species. The predominant cellular fatty acids of strain PCS8T were C16 : 0 (35.8 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 35.1 %) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 10.8 %). This novel strain also contained various fatty acids that are not detected in other members of the genus Pseudaeromonas , such as C16 : 0 3-OH, C18 : 1ω9c and summed feature 5 (C18 : 2ω6,9c and/or C18 : 0 ante). Strain PCS8T contained ubiquinone-8 as the sole respiratory quinone and phosphatidylethanolamine and phosphatidylglycerol as major polar lipids. The G+C content of the genomic DNA of the type strain was 66.5 mol%. Based on the distinct phenotypic, phylogenetic, chemotaxonomic and G+C content results, strain PCS8T represents a currently undescribed species within the genus Pseudaeromonas in the family Aeromonadaceae , for which we suggest the name Pseudaeromonas paramecii sp. nov. with the type strain PCS8T (=KCTC 62038T=JCM 32226T). An emended description of the genus Pseudaeromonas is also provided.
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Roseovarius ramblicola sp. nov., a moderately halophilic bacterium isolated from saline soil in Spain
More LessStrain D15T was isolated from a soil sample taken from Rambla Salada (Murcia), south-eastern Spain, by using the dilution-to-extinction method. The strain, a Gram-stain-negative aerobic bacteria, is non-motile, ovoid- or rod-shaped, catalase- and oxidase-positive, and grows at NaCl concentrations within the range 0.5–10 % (w/v) [optimum 3 % (w/v)], at 5–30 °C (optimum 28 °C) and at pH 6–9 (optimum pH 7.0). The 16S rRNA gene sequence indicates that it belongs to the genus Roseovarius in the class Alphaproteobacteria . Its closest relatives are Roseovarius tolerans EL-172T and Roseovarius azorensis SSW084T, to which the strain shows 16S rRNA gene-sequence similarity values of 96.1 and 95.3 %, respectively. The DNA G+C content is 63 mol%. The major fatty acids (>5 % of the total fatty acids) of strain D15T are C18 : 1ω7c, C16 : 0 and C12 : 0. The only detected isoprenoid quinone of strain D15T is ubiquinone 10 (Q-10). The polar lipid profile contains phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, aminolipid and three polar lipids. Based on the phylogenetic, genotypic, phenotypic and chemotaxonomic data, the strain represents a novel species of the genus Roseovarius , for which the name Roseovarius ramblicola sp. nov. is proposed. Strain D15T (=CECT 9424=LMG 30322) is the type strain.
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Xanthomonas prunicola sp. nov., a novel pathogen that affects nectarine (Prunus persica var. nectarina) trees
Three isolates obtained from symptomatic nectarine trees (Prunus persica var. nectarina) cultivated in Murcia, Spain, which showed yellow and mucoid colonies similar to Xanthomonas arboricola pv. pruni, were negative after serological and real-time PCR analyses for this pathogen. For that reason, these isolates were characterized following a polyphasic approach that included both phenotypic and genomic methods. By sequence analysis of the 16S rRNA gene, these novel strains were identified as members of the genus Xanthomonas , and by multilocus sequence analysis (MLSA) they were clustered together in a distinct group that showed similarity values below 95 % with the rest of the species of this genus. Whole-genome comparisons of the average nucleotide identity (ANI) of genomes of the strains showed less than 91 % average nucleotide identity with all other species of the genus Xanthomonas . Additionally, phenotypic characterization based on API 20 NE, API 50 CH and BIOLOG tests differentiated the strains from the species of the genus Xanthomonas described previously. Moreover, the three strains were confirmed to be pathogenic on peach (Prunus persica), causing necrotic lesions on leaves. On the basis of these results, the novel strains represent a novel species of the genus Xanthomonas , for which the name Xanthomonas prunicola is proposed. The type strain is CFBP 8353 (=CECT 9404=IVIA 3287.1).
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Mesorhizobium wenxiniae sp. nov., isolated from chickpea (Cicer arietinum L.) in China
Three chickpea rhizobial strains (WYCCWR 10195T=S1-3-7, WYCCWR 10198=S1-4-3 and WYCCWR 10200=S1-5-1) isolated from Northwest China formed a group affiliated to Mesorhizobium based on 16S rRNA gene sequence comparison. To clarify their species status, multilocus sequence analysis and average nucleotide identity (ANI) values of whole genome sequences between the novel group and the type strains of the related species were further performed. Similarities of 95.7–96.6 % in the concatenated sequences of atpD-recA-glnII and 91.9–93.1 % of ANI values to the closest-related species Mesorhizobium muleiense , Mesorhizobium mediterraneum and Mesorhizobium temperatum demonstrated the novel group a unique genospecies. The most abundant fatty acid in cells of WYCCWR 10195T were C19 : 0 cyclo ω8c (51.4 %), followed by C18 : 1 ω7c 11-methyl (9.5 %) and C16 : 0 (9.3 %). Its genome size was 6.37 Mbp, comprising 6633 predicted genes with a DNA G+C content of 61.9 mol%. The similarities of 99.0–99.8 % for the nodC gene and 98.3–99.44 % for the nifH gene to those of the chickpea rhizobial species and nodulation with Cicer arietinum L. confirmed the strains of the new genospecies as symbiovar ciceri. The weak utilization of most of the tested sugars/organic acids and non-utilization of l(+)-rhamnose, l-cysteine and l-glycine as sole carbon source, tolerance to 1 % (w/v) NaCl, resistance to 5 µg ml−1 chloromycetin and non-hydrolysis of l-tyrosine distinguished the novel group from the related species and supported this group as a novel species, for which the name Mesorhizobium wenxiniae sp. nov. is proposed, with WYCCWR 10195T (=S1-3-7=HAMBI 3692T=LMG 30254T) as the type strain.
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Pinisolibacter ravus gen. nov., sp. nov., isolated from pine forest soil and allocation of the genera Ancalomicrobium and Pinisolibacter to the family Ancalomicrobiaceae fam. nov., and emendation of the genus Ancalomicrobium Staley 1968
More LessA novel bacterium, designated strain E9T, was isolated from pine forest soil of Kyonggi University (Suwon, Republic of Korea). Cells were facultatively anaerobic, Gram-staining-negative, catalase-negative, oxidase-positive, non-motile, non-spore-forming, rod-shaped and straw coloured. Prosthecae were absent. Glucose was fermented. The strain grew in the pH range of 5.0–10.0 (optimum, 6.5–8.5) and at 45 °C (optimum, 28–32 °C). E9T was sensitive to NaCl at low concentration and tolerated only 0.2 % NaCl (w/v). A phylogenetic analysis based on 16S rRNA gene sequences revealed that E9T formed a lineage within the phylum Proteobacteria that was distinct from various members of the order Rhizobiales , including Ancalomicrobium adetum DSM 4722T (94.76 % sequence similarity), ‘ Nitratireductor lucknowense ’ IITR-21 (92.72 %), Prosthecomicrobium hirschii 16T (92.66 %) and Kaistia soli DSM 19436T (92.53 %). The predominant isoprenoid quinone was Q-10. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and phosphatidyl-N-methylethanolamine. Major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), and C16 : 0. The DNA G+C content of the type strain was 68.4 mol%. Polyphasic characterization indicated that strain E9T represented a novel species in a novel genus within a novel family, for which the name Pinisolibacter ravus gen. nov., sp. nov. is proposed. The type strain of Pinisolibacter ravus is E9T (=KEMB 9005-534T=KACC 19120T=NBRC 112686T). A formal allocation of the genus Ancalomicrobium to the family Ancalomicrobiaceae fam. nov. is also proposed.
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Paraburkholderia caseinilytica sp. nov., isolated from the pine and broad-leaf mixed forest soil
More LessA novel Gram-stain-negative, aerobic, non-spore-forming, motile and rod-shaped bacterial strain, designated HM451T, was isolated from forest soil sampled at the Dinghushan Biosphere Reserve, Guangdong Province, PR China (112° 31′ E 23° 10′ N). It grew optimally at 28 °C, pH 5.0–6.0 and in the presence of 0–2.5 % (w/v) NaCl on R2A medium. Strain HM451T was closely related to Paraburkholderia mimosarum NBRC 106338T (98.6 % 16S rRNA gene sequence similarity), Paraburkholderia heleia NBRC 101817T (98.4 %) and Paraburkholderia silvatlantica SRMrh-20T (98.0 %). The 16S rRNA gene sequence analysis showed that strain HM451T and the three closely related strains formed a clade within the genus Paraburkholderia , but was clearly separated from the established species. The DNA–DNA relatedness value between strain HM451T and its phylogenetically closest relative, P. mimosarum NBRC 106338T, was much lower than 70 %. Strain HM451T contained ubiquinone 8 as the major respiratory quinone. Major fatty acids were C16 : 0, C17 : 0cyclo and summed feature 8 (C18 : 1ω7c and/or C18 : 1 ω6c). The DNA G+C content of strain HM451T was 65.4 mol%. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, two unidentified aminophospholipids, one unidentified aminolipid and a polar lipid. The phenotypic, chemotaxonomic and phylogenetic data showed that strain HM451T represents a novel species of the genus Paraburkholderia , for which the name Paraburkholderia caseinilytica sp. nov. is proposed. The type strain is HM451T (=GDMCC 1.1190T=LMG 30092T).
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Vibrio gangliei sp. nov., a novel member of Vibrionaceae isolated from sawdust in a pigpen
More LessA Gram-stain-negative, rod-shaped, catalase- and oxidase-positive, facultatively anaerobic, and motile bacterium, designated strain SZDIS-1T, was isolated from pigpen sawdust bedding in Xiamen, Fujian Province, China. Cells grew at 10–50 °C, pH 6.0–9.0, up to 12 % (w/v) NaCl, resisted vibriostatic agent O/129 and were negative for gelatin and alginate hydrolysis. No growth on thiosulfate citrate bile salts sucrose agar medium. Based on 16S rRNA gene sequences and multilocus sequence analysis, this strain should be assigned to the genus Vibrio , with the closest relatives being Vibrio aphrogenes CA-1004T (97.7 % 16S rRNA gene sequence pairwise similarity), Vibrio algivorus SA2T (96.6 %), Vibrio casei WS 4539T (96.3 %), Vibrio rumoiensis S-1T (96.1 %) and Vibrio litoralis MANO22DT (95.5 %), but separate from them by large distances in different phylogenetic trees. Based on whole genome analysis, the orthologous average nucleotide identity and in silico DNA–DNA hybridization values against the five relatives were 76.1–78.7 and 20.1–28.7 %. The major fatty acids were summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c), C16 : 0, summed feature 2 (one or more of C12 : 0 aldehyde, C14 : 0 3OH and/or iso-C16 : 1) and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c). The DNA G+C content was 43.0 mol% from whole genomic sequence analysis. Therefore, phylogenetic, genotypic, phenotypic and chemotaxonomic characteristics showed that the isolate represented a novel species of the genus Vibrio , for which the name Vibrio gangliei sp. nov. is proposed. The type strain is SZDIS-1T (=DSM 104291T=CGMCC 1.15236T).
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Polynucleobacter meluiroseus sp. nov., a bacterium isolated from a lake located in the mountains of the Mediterranean island of Corsica
More LessStrain AP-Melu-1000-B4 was isolated from a lake located in the mountains of the Mediterranean island of Corsica (France). Phenotypic, chemotaxonomic and genomic traits were investigated. Phylogenetic analyses based on 16S rRNA gene sequencing referred the strain to the cryptic species complex PnecC within the genus Polynucleobacter . The strain encoded genes for biosynthesis of proteorhodopsin and retinal. When pelleted by centrifugation the strain showed an intense rose colouring. Major fatty acids were C16 : 1ω7c, C16 : 0, C18 : 1ω7c and summed feature 2 (C16 : 1 isoI and C14 : 0-3OH). The sequence of the 16S rRNA gene contained an indel which was not present in any previously described Polynucleobacter species. Genome sequencing revealed a genome size of 1.89 Mbp and a G+C content of 46.6 mol%. In order to resolve the phylogenetic position of the new strain within subcluster PnecC, its phylogeny was reconstructed from sequences of 319 shared genes. To represent all currently described Polynucleobacter species by whole genome sequences, three type strains were additionally sequenced. Our phylogenetic analysis revealed that strain AP-Melu-100-B4 occupied a basal position compared with previously described PnecC strains. Pairwise determined whole genome average nucleotide identity (gANI) values suggested that strain AP-Melu-1000-B4 represents a new species, for which we propose the name Polynucleobacter meluiroseus sp. nov. with the type strain AP-Melu-1000-B4T (=DSM 103591T=CIP 111329T)
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Roseovarius salinarum sp. nov., isolated from a marine solar saltern
More LessA Gram-stain-negative, rod-shaped, non-motile and halophilic bacterium, designated N53T, was isolated from a marine solar saltern in Wendeng, China. Cells of strain N53T were 0.3–0.4 µm wide and 2.0–5.5 µm long, catalase-positive and oxidase-positive. The bacterium grew optimally at 33 °C, at pH 7.0–8.0 and in the presence of 6.0 % (w/v) NaCl. Bacteriochlorophyll a was not found. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain N53T formed a phylogenetic lineage with members of the genus Roseovarius. Strain N53T exhibited the highest levels of similarity to Roseovarius pacificus (94.6 %) and Roseovarius confluentis (94.6 %), with a lower level to Roseovarius tolerans was 94.0 %. The percentage of conserved proteins and average nucleotide identity values between N53T and the type strain of the type species, Roseovarius tolerans , were 66.1 and 76.4 %, respectively. The genomic DNA G+C content was 68.1 mol%. The sole respiratory quinone was ubiquinone-10. The predominant cellular fatty acids (>10 %) were C18 : 1ω7c (54.0 %) and C16 : 0 (17.9 %). The polar lipids of strain N53T consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, an unidentified aminolipid, two unidentified phospholipids and two unidentified glycolipids. The differential phenotypic properties, together with the chemotaxonomic and genomic distinctiveness, revealed that strain N53T was separate from other recognized species of the genus Roseovarius. On the basis of the data presented here, strain N53T represents a novel species of the genus Roseovarius , for which the name Roseovarius salinarum sp. nov. is proposed. The type strain is N53T (=MCCC 1H00200T=KCTC 52886T).
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Description of Sansalvadorimonas verongulae gen. nov., sp. nov., a gammaproteobacterium isolated from the marine sponge Verongula gigantea
More LessA Gram-stain-negative, strictly aerobic, motile, rod-shaped bacterium, designated strain RKSG058T, was isolated from the marine sponge Verongula gigantea, collected off the west coast of San Salvador, The Bahamas. Phylogenetic analyses based on 16S rRNA gene sequences revealed that RKSG058T formed a distinct lineage within the family Hahellaceae (order Oceanospirillales , class Gammaproteobacteria ), and was most closely related to the genus Endozoicomonas , with sequence similarities to members of this genus ranging from 92.0 to 93.7 %. Optimal growth occurred at 30 °C, at pH 7 and in the presence of 2–3 % (w/v) NaCl. The predominant cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The major and minor respiratory quinones were Q-9 and Q-8, respectively. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified aminolipids, an unidentified phospholipid and five unidentified lipids. The DNA G+C content was 42.3 mol%. Biochemical, chemotaxonomic and phylogenetic analyses indicated that strain RKSG058T represents the first cultured isolate of a novel bacterial genus and species within the family Hahellaceae , for which the name Sansalvadorimonas verongulae gen. nov., sp. nov. is proposed. The type strain of Sansalvadorimonas verongulae is RKSG058T (=TSD-72T=LMG 29871T). An emended description of the genus Kistimonas is provided.
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Pannonibacter carbonis sp. nov., isolated from coal mine water
More LessTwo bacterial strains were isolated from coal mine water in China. Isolates were facultatively anaerobic, Gram-stain-negative, rod-shaped, motile by means of a single polar flagellum, and they did not produce bacteriochlorophyll α. Cells grew in tryptic soy broth with 0–5.5 % (w/v) NaCl, at 4–55 °C and pH 3.5–10.5. Isolates were positive for catalase, oxidase, urease, Voges–Proskauer test, gelatin hydrolysis and H2S production. Analysis of 16S rRNA gene sequences indicated that the closest relatives of strains Q4.6T and Q2.11 were the type strains Labrenzia suaedae DSM 22153T (97.4 %), Pannonibacter phragmitetus DSM 14782T (96.9 and 97.0 %) and Pannonibacter indicus DSM 23407T (96.8 %). The genomic average nucleotide identity (ANI) value for Q4.6T and Q2.11 was 100 %; however, this value was less than 77.7 % for the type strains P. phragmitetus and P. indicus , and less than 74.0 % for the type strain L. suaedae . The cellular fatty acid profile of strains Q4.6T and Q2.11 consisted primarily of C18 : 1ω7c. The principal quinone of the isolates was Q-10. The polar lipid profile consisted of diphosphatidyl glycerol, phosphatidyl glycerol, phosphatidyl ethanolamine and phosphatidyl choline. On the basis of phylogenetic analysis, genomic ANI analysis, DNA–DNA hybridization results, as well as phenotypic and chemotaxonomic data, strains Q4.6T and Q2.11 are assigned as a novel species within the genus Pannonibacter . The type strain is Pannonibacter carbonis Q4.6T (=CGMCC 1.15703T=KCTC 52466T).
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Terasakiella salincola sp. nov., a marine alphaproteobacterium isolated from seawater, and emended description of the genus Terasakiella
More LessA Gram-reaction-negative, S-shaped, motile, poly-β-hydroxybutyrate-accumulating, facultatively anaerobic, beige-pigmented bacterium, designated strain KMU-80T, was isolated from seawater collected from the Republic of Korea. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the novel isolate was affiliated with the family Methylocystaceae , of the class Alphaproteobacteria , and that it possessed the greatest sequence similarity (96.7 %) to Terasakiella pusilla NBRC 13613T. The DNA G+C content of KMU-80T was 48.3 mol%, and ubiquinone 10 was the sole respiratory quinone. The predominant cellular fatty acids consisted of C18 : 1 ω7c (60.2 %), C16 : 0 (13.4 %) and C16 : 1 ω7c and/or C16 : 1 ω6c (11.1 %). Strain KMU-80T had phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified aminolipid, an unidentified phospholipid and four unidentified lipids as polar lipids. Based on its distinct phylogenetic position and the combination of genotypic and phenotypic characteristics, this strain is considered to represent a novel species of the genus Terasakiella , for which the name Terasakiella salincola sp. nov. is proposed. The type strain of T. salincola sp. nov. is KMU-80T (= KCCM 90274T = NBRC 112846T). An amended description of the genus Terasakiella is also provided.
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Paracoccus fontiphilus sp. nov., isolated from a freshwater spring
More LessStrain MVW-1T, isolated from a freshwater spring in Taiwan, was characterized by using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain MVW-1T belongs to the genus Paracoccus and has the highest levels of sequence similarity to Paracoccus caeni MJ17T (97.6 %), Paracoccus sediminis CMB17T (97.4 %), Paracoccus angustae E6T (97.3 %) and Paracoccus acridae SCU-M53T (97.1 %). Cells were Gram-stain-negative, aerobic, poly-β-hydroxybutyrate-accumulating, non-motile, rod-shaped and formed light orange-coloured colonies. Optimal growth occurred at 20–25 °C, pH 6–7, and in the presence of 0–3 % NaCl. The major fatty acid of strain MVW-1T was C18 : 1ω7c. The polar lipid profile consisted of phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, diphosphatidylglycerol, an unidentified glycolipid, an unidentified aminolipid and three unidentified phospholipids. The predominant polyamines were spermidine, putrescine and cadaverine. The only isoprenoid quinone was Q-10. The genomic DNA G+C content of strain MVW-1T was 63.4 mol%. Strain MVW-1T exhibited less than 35 % DNA–DNA relatedness to P. caeni MJ17T, P. angustae E6T, P. sediminis CMB17T and P. acridae SCU-M53T. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain MVW-1T should be classified in a novel species of the genus Paracoccus , for which the name Paracoccus fontiphilus sp. nov. is proposed. The type strain is MVW-1T (=BCRC 80974T=LMG 29554T=KCTC 52239T).
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Marinicaulis flavus gen. nov., sp. nov., a novel stalked bacterium of the family Parvularculaceae
More LessA Gram-stain-negative, aerobic, ovoid or short rod-shaped bacterium with prosthecates and flagella, designated SY-3-19T, was isolated from the surface seawater of the South China Sea, and subjected to a polyphasic taxonomic study. The isolate grew at 4–40 °C and pH 5.0–9.0 (optimum 28 °C and pH 6.5–7.5), and with 0.5–16.0 % (w/v) NaCl (optimum 4 %). It was positive for oxidase and catalase activity. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SY-3-19T constituted a separate branch in the family Parvularculaceae , sharing the highest sequence similarities to the genera Aquisalinus (91.9 %), Amphiplicatus (91.1 %) and Parvularcula (91.0–89.4 %). The sole respiratory quinone was ubiquinone-10 and the principal fatty acids (>10 %) were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), 11 methyl C18 : 1 ω7c and C16 : 0. The polar lipids of strain SY-3-19T consisted of phosphatidylglycerol, nine unidentified glycolipids and four unidentified lipids. The DNA G+C content was 60.9 mol%. On the basis of morphological, physiological and chemotaxonomic characteristics, together with the results of phylogenetic analysis, strain SY-3-19T is described as a novel species in a novel genus, for which the name Marinicaulis flavus gen. nov., sp. nov. (type strain SY-3-19T=MCCC 1K03432T=KCTC 62156T) is proposed.
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Oceanisphaera avium sp. nov., isolated from the gut of the cinereous vulture, Aegypius monachus
A Gram-stain-negative, aerobic, catalase- and oxidase-positive, rod-shaped, flagellated bacterial strain, designated AMac2203T, was isolated from the gut of the cinereous vulture, Aegypiusmonachus, collected from the Seoul Grand Park Zoo, Republic of Korea. Strain AMac2203T grew optimally at 15–25 °C, pH 7–8 and in the presence of 3–5 % (w/v) NaCl. Phylogenetic analysis revealed 97.4–97.9 % and 96.9–97.3 % sequence similarities of the 16S rRNA genes to its counterparts in Oceanisphaera profunda SM1222T and Oceanisphaera ostreae T-w6T, respectively. The predominant fatty acids (>10 %) of strain AMac2203T were summed feature 3 (C16 : 0 ω7c and/or C16 : 1 ω6c, 33.6 %), summed feature 8 (C18 : 1 ω7c, 24.5 %) and C16 : 0 (19.9 %). The primary isoprenoid quinone was ubiquinone-8. Polar lipids included phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified amino lipid and an unidentified lipid. Based on complete genome sequencing of strain AMac2203T and the closest related type strain, O. profunda , the OrthoANI value is 77.5 %, which is below the 95 % cut-off for species demarcation. The genomic DNA G+C content of strain AMac2203T is 47.1 mol%. Thus, strain AMac2203T represents a novel species candidate of the genus Oceanisphaera . We propose the name Oceanisphaera avium sp. nov., with strain AMac2203T (=KCTC 62118T=JCM 32207T) as the type strain.
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Amylibacter lutimaris sp. nov., isolated from sea-tidal flat sediment
More LessA Gram-stain-negative, aerobic bacterial strain, designated strain m18T, was isolated from a sea-tidal flat in South Korea. Cells were non-motile short rods showing oxidase and catalase activities. Growth of m18T was observed at 10–40 °C (optimum, 30 °C), pH 5.5–10.0 (optimum, pH 7.0) and 0.5–7.0 % (w/v) NaCl (optimum, 3.0 %). The major respiratory quinone was ubiquinone-10 and the major fatty acids of were summed feature 8 (comprising C18 : 1ω7c/C18 : 1ω6c) and C16 : 0. The G+C content of the genomic DNA was 56.7 mol%. Phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, an unidentified phospholipid, an unidentified aminolipid and four unidentified lipids were detected in m18T. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that m18T formed a tight phyletic lineage with the members of the genus Amylibacter . Strain m18T was most closely related to Amylibactercionae H-12T, Amylibacter ulvae 6Alg 255T and Amylibacter marinus 2-3T with 98.9, 96.1 and 95.5 % 16S rRNA gene sequence similarities, respectively. The DNA–DNA hybridization value between m18T and the type strain of A. cionae was 43.6±3.4 %. On the basis of phenotypic, chemotaxonomic and molecular properties, m18T represents a novel species of the genus Amylibacter , for which the name Amylibacter lutimaris sp. nov. is proposed. The type strain is m18T (KACC 19229T=JCM 32051T).
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- Eukaryotic Micro-Organisms
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Papiliotrema plantarum sp. nov., a novel tremellaceous sexual yeast species
During a survey of the yeast community associated with the phylloplane of corn in Thailand, a basidiomycetous yeast strain belonging to the genus Papiliotrema was isolated. Analyses of the D1/D2 domains of the 26S (LSU) rRNA gene and complete ITS region supported the recognition of a novel species, for which the name Papiliotrema plantarum sp. nov. is proposed (type strain DMKU-CP801T=CBS 15220T=PYCC 7257T). Another strain of P. plantarum sp. nov., isolated in French Guiana, was found to be sexually compatible with the Thai isolate and mycelium with clamp connections, basidia and basidiospores were observed in culture. The basidial morphology of P. plantarum combined features previously observed for Papiliotrema bandonii and Papiliotrema fuscus, which represent the only sexual species hitherto known in the genus, i.e. transversely septate basidia, with sexual structures of the Tremella type.
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Yarrowia brassicae f.a., sp. nov., a new yeast species from traditional Chinese sauerkraut
More LessTwo strains of a novel yeast species were isolated from traditional Chinese sauerkraut samples collected in Nanyang, Henan Province, central China. Phylogenetic analysis based on the concatenated sequences of the D1/D2 domains of the large subunit rRNA gene and the internal transcribed spacer (ITS) regions showed that these strains belong to the Yarrowia clade, with seven clones of uncultured Yarrowia as their closest phylogenetic neighbours. They differed from their closest known species, Yarrowia divulgata CBS 11013T, by 3.2 % sequence divergence (14 substitutions and 2 gaps) in the D1/D2 domains and by 5.4 % sequence divergence (12 substitutions and 5 gaps) in the ITS regions. The two strains of novel species reproduced asexually, and no ascospores could be found. The name Yarrowia brassicae f.a., sp. nov. is proposed to accommodate these strains, with NYNU 17218T (=CICC 33263T=CBS 15225T) as the type strain.
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Metschnikowia maroccana f.a., sp. nov., a new yeast species associated with floral nectar from Morocco
More LessWild flowers, and in particular, nectar of flowers, have been shown to be a rich reservoir of yeast biodiversity. In a taxonomic study of yeasts recovered from floral nectar in Morocco, nine strains were found to represent a novel species. Morphological and physiological characteristics and sequence analyses of the D1/D2 region of the large subunit rRNA gene as well as the internal transcribed spacer region showed that the novel species belonged to the genus Metschnikowia. The name Metschnikowia maroccana f.a., sp. nov. (EBDCdVMor24-1T=CBS 15053T=NRRL Y-63972T) is proposed to accommodate this new species. Metschnikowia maroccana was isolated from floral nectar of Teucrium pseudochamaepitys, Teucrium polium and Gladiolus italicus. The ascosporic state of the novel species was not found. Metschnikowia maroccana was phylogenetically distinct from any currently recognized species and forms a well-supported subclade (bootstrap value 81 %) containing species associated with flowers and flower-visiting insects, including Metschnikowia gruessii, Metschnikowia lachancei and Metschnikowia vanudenii. The close genealogical relationship of M. maroccana with the M. gruessii clade is also consistent with the striking similarity of their ‘aeroplane’ cells morphologies and the lack of utilization of the α-glucoside trehalose. The ecology of these novel species and its probable endemicity are discussed.
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- Evolution, Phylogeny and Biodiversity
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Identification of a ‘Candidatus Phytoplasma hispanicum’-related strain, associated with yellows-type diseases, in smoke-tree sharpshooter (Homalodisca liturata Ball)
The 16SrXIII group from phytoplasma bacteria were identified in salivary glands from Homalodisca liturata, which were collected in El Comitán on the Baja California peninsula in Mexico. We were able to positively identify 15 16S rRNA gene sequences with the corresponding signature sequence of ‘Candidatus Phytoplasma ’ (CAAGAYBATKATGTKTAGCYGGDCT) and in silico restriction fragment length polymorphism (RFLP) profiles (F value estimations) coupled with a phylogenetic analysis to confirm their relatedness to ‘Candidatus Phytoplasma hispanicum’ , which in turn belongs to the 16SrXIII group. A restriction analysis was carried out with AluI and EcoRI to confirm that the five sequences belongs to subgroup D. The rest of the sequences did not exhibit any known RFLP profile related to a subgroup reported in the 16SrXIII group.
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- ICSP Matters
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- Corrigenda
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Corrigendum: Saliniramus fredricksonii gen. nov., sp. nov., a heterotrophic halophile isolated from Hot Lake, Washington, a member of a novel lineage (Salinarimonadaceae fam. nov.) within the order Rhizobiales, and reclassification of the genus Salinarimonas Liu et al. 2010 into Salinarimonadaceae
There was an error in the proposed genus name in the published article, in that the genus 'Salinivirga' was effectively published while this article was in review. Therefore, the genus 'Salinivirga' should be replaced with 'Saliniramus'. For the convenience of future readers, we have included the complete corrected article below, in which all occurrences of the incorrect genus name have been amended: A halophilic bacterial strain, HL-109T, was isolated from the unicyanobacterial consortium UCC-O, which was obtained from the photosynthetic mat of Hot Lake (Washington, USA). A polyphasic approach using phenotypic, genotypic and chemotaxonomic data was used to classify the strain within the order Rhizobiales . The organism stained Gram-negative and was a moderate thermophile with a growth optimum of 45 °C. It was obligately aerobic, heterotrophic and halophilic, growing in both NaCl and MgSO4 brines. The novel isolate had a polymorphic cellular morphology of short rods with occasional branching, and cells were monotrichous. The major fatty acids detected were C18 : 1, C18 : 0, C16 : 0 and C18 : cyc. Phylogenetic analysis of the 16S rRNA gene placed the strain in the order Rhizobiales and it shared 94 % identity with the type strain of its nearest relative, Salinarimonas ramus . Morphological, chemotaxonomic and phylogenetic results did not affiliate the novel organism with any of the families in the Rhizobiales ; therefore, HL-109T is representative of a new lineage, for which the name Saliniramus fredricksonii gen. nov., sp. nov. is proposed, with the type strain HL-109T (=JCM 31876T=DSM 102886T). In addition, examination of the phylogenetics of strain HL-109T and its nearest relatives, Salinarimonas ramus and Salinarimonas rosea , demonstrates that these halophiles form a clade distinct from the described families of the Rhizobiales . We further propose the establishment of a new family, Salinarimonadaceae fam. nov., to accommodate the genera Saliniramus and Salinarimonas (the type genus of the family).
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