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International Journal of Systematic and... Feb 2020A Gram-stain-negative, non-motile, coccobacillus-shaped bacterium, designated CPCC 101021, was isolated from a sandy soil sample collected from Badain Jaran desert,...
A Gram-stain-negative, non-motile, coccobacillus-shaped bacterium, designated CPCC 101021, was isolated from a sandy soil sample collected from Badain Jaran desert, China. Its 16S rRNA gene sequence was closely related to those of members of the genus showing high similarities with THG-N2.22 (98.0 %), KCTC 42542 (97.9 %), YW11 (97.9 %) and S1 (97.8 %). In the phylogenetic tree based on 16S rRNA gene sequences, strain CPCC 101021 formed a distinct subclade with KCTC 42542 within the genus . Growth of the isolate occurred at 15-37 °C and pH 6.0-8.5, with optimal growth at 30 °C and pH 7.0. The major cellular fatty acids were Cω, summed feature 8 (Cωc/Cω), summed feature 3 (Cωc/Cω) and Cω. Q-10 was detected as the main component in the respiratory quinone system, with Q-9 as a minor component. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, an unidentified phospholipid, an unidentified aminolipid and an unidentified glycolipid were found in the polar lipid profile. The genomic DNA G+C content was 68.7 mol%. The average nucleotide identity was 84.6 % when comparing the draft genome sequences of strain CPCC 101021 with KCTC 42542. On the basis of genotypic, chemotaxonomic and phenotypic characteristics, strain CPCC 101021 is proposed to represent a novel species of the genus with the name sp. nov. Strain CPCC 101021 (=J1A743=KCTC 62043) is the type strain of the species.
Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Desert Climate; Fatty Acids; Glycolipids; Methylobacteriaceae; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sand; Sequence Analysis, DNA; Ubiquinone
PubMed: 31860433
DOI: 10.1099/ijsem.0.003898 -
International Journal of Systematic and... Jan 2016A Gram-stain-negative, aerobic, short rod-shaped, non-endospore-forming, ivory-pigmented and non-motile bacterium, designated strain BUT-5T, was isolated from activated...
A Gram-stain-negative, aerobic, short rod-shaped, non-endospore-forming, ivory-pigmented and non-motile bacterium, designated strain BUT-5T, was isolated from activated sludge of an herbicides-manufacturing wastewater treatment facility in Jiangsu Province, China. The major fatty acids (>5 % of total fatty acids) were C16 : 0, C18 : 1 2-OH and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The predominant respiratory quinone was ubiquinone Q-10. The polar lipids profile of strain BUT-5T included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and two unknown aminolipids. The DNA G+C content was 67.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain BUT-5T showed the highest sequence similarities to Roseomonas soli 5N26T (97.5 % 16S rRNA gene sequence similarity), followed by Roseomonas lacus TH-G33T (97.3 %) and Roseomonas terrae DS-48T (97.1 %). Strain BUT-5T showed low DNA-DNA relatedness with Roseomonas soli KACC 16376T (41 %), Roseomonas lacus KACC 11678T (46 %) and Roseomonas terrae KACC 12677T (42 %), respectively. On the basis of phenotypic and genotypic properties, as well as chemotaxonomic data, strain BUT-5T represents a novel species of the genus Roseomonas, for which the name Roseomonas eburnea sp. nov. is proposed. The type strain is BUT-5T ( = CCTCC AB2013276T = KACC 17166T).
Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Methylobacteriaceae; Molecular Sequence Data; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sewage; Ubiquinone; Wastewater
PubMed: 26530339
DOI: 10.1099/ijsem.0.000728 -
Antonie Van Leeuwenhoek Dec 2023Strain CN29, isolated from the stem of 5- to 6-year-old Populus tomentosa in Shandong, China, was characterized using a polyphasic taxonomic approach. Cells of CN29 were...
Strain CN29, isolated from the stem of 5- to 6-year-old Populus tomentosa in Shandong, China, was characterized using a polyphasic taxonomic approach. Cells of CN29 were Gram-stain negative, aerobic, nonspore-forming, and nonmotile coccoid. Growth occurred at 20-37 °C, pH 4.0-9.0 (optimum, pH 6.0), and with 0-1% NaCl (optimum, 1%). Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain CN29 was closely related to members of the genus Roseomonas and closest to Roseomonas pecuniae N75 (96.6%). This classification was further supported by phylogenetic analysis using additional core genes. The average nucleotide identity and digital DNA‒DNA hybridization values between strain CN29 and Roseomonas populi CN29 were 82.7% and 27.8%, respectively. The genome size of strain CN29 was 5.87 Mb, with a G + C content of 70.9%. The major cellular fatty acids included summed feature 8 (C ω7c/C ω6c), C cyclo ω8c and C. The major respiratory quinone was Q-10. The polar lipids were phosphatidylcholine, aminolipid, phosphatidylglycerol, and diphosphatidylglycerol. Strain CN29 can utilize acetate as a carbon source for growth and metabolism. Additionally, it contains acid phosphatase (2-naphthyl phosphate), which catalyzes the hydrolysis of phosphoric monoesters. The CN29 strain contains several genes, including maeB, gdhB, and cysJ, involved in carbon, nitrogen, and sulfur cycling. These findings suggest that the strain may actively participate in ecosystem cycling, leading to soil improvement and promoting the growth of poplar trees. Based on the phylogenetic, phenotypic, and genotypic characteristics, strain CN29 is concluded to represent a novel species of the genus Roseomonas, for which the name Roseomonas populi sp. nov. is proposed. The type strain is CN29 (= JCM 35579 = GDMCC 1.3267).
Topics: Acetates; Phylogeny; Populus; RNA, Ribosomal, 16S; Methylobacteriaceae; Plant Stems; China; Nucleic Acid Hybridization; DNA, Bacterial; Bacterial Typing Techniques
PubMed: 38147266
DOI: 10.1007/s10482-023-01911-3 -
Systematic and Applied Microbiology May 2021Two Gram-negative, aerobic, rod-shaped and yellow-orange pigmented bacterial strains (LMG 31523 and LMG 31524) were isolated from roots of wild-growing Alkanna tinctoria...
Two Gram-negative, aerobic, rod-shaped and yellow-orange pigmented bacterial strains (LMG 31523 and LMG 31524) were isolated from roots of wild-growing Alkanna tinctoria plants collected near Thessaloniki, Greece. Analysis of their 16S rRNA gene sequences revealed that they form a separate cluster related to the genus Roseomonas. A comparative whole genome analysis of the two strains and the type strains of related Roseomonas species revealed average nucleotide identity values from 78.84 and 80.32%. The G + C contents of the genomic DNA of strains LMG 31523 and LMG 31524 were 69.69% and 69.74%, respectively. Combined data from phenotypic, phylogenetic and chemotaxonomic studies indicated that the strains LMG 31523 and LMG 31524 represent a novel species of the genus Roseomonas. Genome analysis of the new strains showed a number of genes involved in survival in the rhizosphere environment and in plant colonization and confirmed the endophytic characteristics of LMG 31523 and LMG 31524. Since the strains LMG 31523 and LMG 31524 were isolated from a plant collected in Greece the name Roseomonas hellenica sp. nov. is proposed. The type strain is LMG 31523 (=CECT 30032).
Topics: Bacterial Typing Techniques; Base Composition; Boraginaceae; DNA, Bacterial; Endophytes; Greece; Methylobacteriaceae; Phylogeny; Pigmentation; Plant Roots; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 33945925
DOI: 10.1016/j.syapm.2021.126206 -
International Journal of Systematic and... Jul 2017Three light-brown-coloured, Gram-stain-negative, small rod- to oval-shaped, motile bacteria were isolated from lagoon sediments collected from North Carolina, USA. The...
Three light-brown-coloured, Gram-stain-negative, small rod- to oval-shaped, motile bacteria were isolated from lagoon sediments collected from North Carolina, USA. The strains (S1T, AS3 and AS6) grew aerobically at 13-42 °C (optimum, 30-35 °C) and pH 6.5-9.1 (optimum, pH 7.0-7.5). All three strains were positive for catalase and oxidase activity, and no added NaCl was required for growth. C18 : 1ω6c/C18 : 1ω7c, C16 : 1ω6c/C16 : 1ω7c, C18 : 1ω7c 11-methyl and C16 : 0 were the predominant fatty acids (>5 %). Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and an unidentified glycolipid were the major polar lipids. The genomic DNA G+C content of strains S1T, AS3 and AS6 was 70.5, 70.1 and 70.8 mol%, respectively. Strain S1T showed 16S rRNA gene sequence similarity of 99.1 % with Roseomonas rubra S5T, 98.7 % with Roseomonas rhizosphaerae YW11T, 98.5 % with Roseomonas cervicalis E7107T, 97.8 % with Roseomonas aestuarii JC17T, 97.2 % with Roseomonas oryzae JC288T, 97.2 % with Roseomonas ludipueritiae 170/96Tand <97 % with other members of the genus Roseomonas. Strains AS3 and AS6 shared 99.9 % 16S rRNA gene sequence similarity with strain S1T. DNA-DNA hybridization values among strains S1T, AS3 and AS6 were >89 %, while all the three strains showed <56 % relatedness with the most closely related type strains. Distinct phenotypic, genotypic and phylogenetic differences from the previously described taxa support the classification of strain S1T as a representative of a novel species in the genus Roseomonas, for which the name Roseomonas suffusca sp. nov. is proposed. The type strain is S1T (=KEMB 563-465T=JCM 31176T). Strains AS3 and AS6 serve as additional strains of the newly proposed species.
Topics: Bacterial Typing Techniques; DNA, Bacterial; Fatty Acids; Geologic Sediments; Methylobacteriaceae; North Carolina; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Water Microbiology
PubMed: 28714843
DOI: 10.1099/ijsem.0.001966 -
International Journal of Systematic and... Mar 2023A strictly aerobic bacteriochlorophyll -containing alphaproteobacterium, designated strain S08, was isolated from a biofilm sampled at Tama River in Japan. The...
A strictly aerobic bacteriochlorophyll -containing alphaproteobacterium, designated strain S08, was isolated from a biofilm sampled at Tama River in Japan. The non-motile and rod-shaped cells formed pink-beige pigmented colonies on agar plates containing organic compounds and showed absorption maxima at 798 and 866 nm in the near-infrared region, typical for the presence of bacteriochlorophyll . The new bacterial isolate is Gram-negative, oxidase-negative and catalase-positive. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain S08 was closely related to species in the genus . The closest phylogenetic relative of strain S08 was TH-G33 (98.2 % sequence similarity). The major cellular fatty acids were C, C 2-OH and summed feature 8 (C 7/C 6). The predominant respiratory quinone was ubiquinone-9. The major polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and an aminolipid. The G+C content of the genomic DNA was 70.6 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain S08 and the related type strains were all far lower than the cut-off value for the delineation of species. The results of polyphasic comparisons showed that strain S08 was clearly distinguishable from other members of the genus . Therefore, we propose a new species in the genus , namely, sp. nov. The type strain is S08 (=DSM 111902=NBRC 112025).
Topics: Fatty Acids; Rivers; Bacteriochlorophyll A; Phylogeny; RNA, Ribosomal, 16S; DNA, Bacterial; Base Composition; Bacterial Typing Techniques; Sequence Analysis, DNA; Ubiquinone; Methylobacteriaceae; Biofilms; Phospholipids
PubMed: 37009860
DOI: 10.1099/ijsem.0.005810 -
International Journal of Systematic and... Aug 2017A Gram-stain-negative, aerobic, non-motile and coccoid to short-rod-shaped bacterial strain (THG-N2.22T) was isolated from the rhizosphere of Mugunghwa (Hibiscus...
A Gram-stain-negative, aerobic, non-motile and coccoid to short-rod-shaped bacterial strain (THG-N2.22T) was isolated from the rhizosphere of Mugunghwa (Hibiscus syriacus). Growth occurred at 20-40 °C (optimum 28 °C), at pH 5-9 (optimum 7) and with 0-4 % (w/v) NaCl (optimum 1 %). Based on 16S rRNA gene sequence analysis, the nearest phylogenetic neighbours of strain THG-N2.22T were identified as Roseomonas rhizosphaerae YW11T (98.5 % similarity), Roseomonas rubra S5T (98.5 %), Roseomonas cervicalis ATCC 49957T (98.2 %), Roseomonas aestuarii JC17T (97.8 %), Roseomonas oryzae JC288T (97.3 %) and Roseomonas ludipueritiae 170/96T (97.3 %); levels of similarity with the type strains of other Roseomonas species were lower than 97.0 %. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, two unidentified aminolipids, three unidentified phospholipids and three unidentified lipids. The major quinone was ubiquinone-10. The major fatty acids were C16 : 0, C18 : 1 2-OH, C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The DNA G+C content of strain THG-N2.22T was 64.1 mol%. DNA-DNA hybridization values between strain THG-N2.22T and R. rhizosphaerae YW11T, R. rubra S5T, R. cervicalis ATCC 49957T, R. aestuarii JC17T, R. oryzae JC288T and R. ludipueritiae 170/96T were 43.1 % (30.2 %, reciprocal analysis), 39.0 % (24.7 %), 34.4 % (15.2 %), 18.0 % (14.5 %), 14.7 % (9.7 %) and 11.0 % (5.6 %), respectively. On the basis of the phylogenetic analysis, chemotaxonomic data, physiological characteristics and DNA-DNA hybridization data, strain THG-N2.22T represents a novel species of the genus Roseomonas, for which the name Roseomonas hibiscisoli sp. nov. is proposed. The type strain is THG-N2.22T (=KACC 18935T=CCTCC AB 2016176T).
Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Hibiscus; Methylobacteriaceae; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Republic of Korea; Rhizosphere; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone
PubMed: 28820105
DOI: 10.1099/ijsem.0.002036 -
International Journal of Systematic and... Nov 2017A novel strain, designated EM302, was isolated from a soil sample collected from farmland located in Yesan-gun in the Republic of Korea. The cells were...
A novel strain, designated EM302, was isolated from a soil sample collected from farmland located in Yesan-gun in the Republic of Korea. The cells were Gram-stain-negative, aerobic, non-motile without flagella and coccobacilli-shaped. Colonies were circular with entire edges, convex, opaque and pink. The strain grew at 15-40 ˚C (optimum, 35 ˚C) and pH 6.0-9.0 (optimum, 7.0). The strain grew in R2A medium without the addition of NaCl. Based on 16S rRNA gene sequences analysis, strain EM302 was found to be phylogenetically related to Roseomonas wooponensis WW53 (96.5 % 16S rRNA gene sequence similarity), Roseomonas arcticisoli MC 3624 (95.2 %), Roseomonas aerilata 5420-30 (94.5 %), Roseomonas pecuniae N75 (94.4 %) and Roseomonas vinacea CPCC 100056 (94.4 %). The major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The predominant respiratory quinone was Q-10. The major polar lipids were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminolipid. The DNA G+C content of the type strain was 65.7 mol%. On the basis of data presented here, strain EM302 is considered to represent a novel species of the genus Roseomonas, for which the name Roseomonasterricola sp. nov. is proposed. The type strain is EM302 (=KACC 13942=KCTC 42906=NBRC 111477).
Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Methylobacteriaceae; Phospholipids; Phylogeny; Pigmentation; RNA, Ribosomal, 16S; Republic of Korea; Sequence Analysis, DNA; Soil Microbiology
PubMed: 28984215
DOI: 10.1099/ijsem.0.002389 -
International Journal of Systematic and... Oct 2020A Gram-stain-negative, non-motile, coccus-shaped, catalase- and oxidase-positive, facultatively anaerobic and pink-pigmented bacterium, designated strain CQN31, was...
A Gram-stain-negative, non-motile, coccus-shaped, catalase- and oxidase-positive, facultatively anaerobic and pink-pigmented bacterium, designated strain CQN31, was isolated from sediment of Changqiaohai Lake, Yunnan Province, China. Growth occurred at 4-45 °C (optimum, 37 °C), at pH 6.5-9.5 (optimum, pH 8.0) and with 0-1 % (w/v) NaCl (optimum, 0 %). C 7/C 6 and C were the predominant fatty acids. Phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), phosphatidyldimethylethanolamine (PME) and one unidentified aminolipid (AL) were the major polar lipids. The G+C content of the genomic DNA was 71.5 %. 16S rRNA gene sequence comparisons indicated that strain CQN31 shared 96.8 % similarity with JCM 19527 and 95.9 % with EM0302. Digital DNA-DNA hybridization values between strain CQN31 and DSM 19981, DSM 14916 and NCTC 13291 were 21.0, 19.4 and 19.8 %, respectively. Average amino acid identity and average nucleotide identity values between strain CQN31 and DSM 19981, DSM 14916 and NCTC 13291 were 73.7, 63.4 and 61.9 %, and 79.2, 77.1 and 77.5%, respectively. Distinct morphological, physiological and genotypic differences from previously described taxa support the classification of strain CQN31 as a representative of a novel species in the genus , for which the name sp. nov. is proposed. The type strain is CQN31 (=KCTC 62447=MCCC 1H00309).
Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Geologic Sediments; Lakes; Methylobacteriaceae; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Pigmentation; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 32886590
DOI: 10.1099/ijsem.0.004436 -
Antonie Van Leeuwenhoek Mar 2018A novel pale pink-coloured, strictly aerobic, Gram-stain negative bacterial strain, designated strain KER25-12, was isolated from a laboratory air-conditioning system in...
A novel pale pink-coloured, strictly aerobic, Gram-stain negative bacterial strain, designated strain KER25-12, was isolated from a laboratory air-conditioning system in South Korea. Cells were observed to be non-motile cocci showing positive catalase and oxidase reactions. Strain KER25-12 was found to grow at 10-30 °C (optimum, 25-30 °C), at pH 4.0-9.0 (optimum, pH 6.0-7.0) and in the presence of 0-2% (w/v) NaCl (optimum, 0%). Ubiquinone-10 and spermidine were detected as the sole respiratory quinone and the predominant polyamine, respectively. The major fatty acids were identified as summed feature 8 (comprising C ω7c and/or C ω6c), summed feature 3 (comprising C ω7c and/or C ω6c), C and C. The genomic DNA G+C content of strain KER25-12 was determined to be 70.0 mol%. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and an unidentified aminolipid. Phylogenetic analysis based on 16S rRNA gene sequence comparison revealed that strain KER25-12 belongs to the genus Roseomonas and shows high sequence similarity to Roseomonas aerilata 5420S-30 (98.57%), Roseomonas pecuniae N75 (97.44%) and Roseomonas vinacea CPCC 100056 (97.40%). Based on the morphological, physiological, chemotaxonomic and phylogenetic features, strain KER25-12 is concluded to represent a novel species of the genus Roseomonas, for which the name Roseomonas aeriglobus sp. nov. is proposed. The type strain is KER25-12 (= KACC 19282 = JCM 32049).
Topics: Air Microbiology; Bacterial Typing Techniques; Base Composition; Environmental Microbiology; Methylobacteriaceae; Phenotype; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 28983692
DOI: 10.1007/s10482-017-0956-x