RESUMO
The isolated Chryseobacterium ginsengiterrae sp. nov DCY68T was found to be Gram-negative, aerobic, non-motile, non-flagellate and rod-shaped. Their size was approximately 0.40-0.46 × 1.0-1.27 µm. The colonies were yellow-pigmented, convex, circular and 0.5-1.3 mm in diameter when grown on R2A agar for 2 days. DNA, esculin, skim milk, gelatine, starch, Tween 20, and Tween 80 were hydrolyzed, but not cellulose. The cells grew on R2A, TSA, and NA but not on MacConkey agars. Growth occured at 4-33 °C (optimum, 30 °C), at pH 5.0-8.0 (optimum, pH 6.5), and 0-2.5% NaCl. Nitrate was not reduced to nitrite. Oxidase and catalase activity were positive. Strain DCY68T contained ß-glucosidase activity in which ginsenoside Rb1 was enzymatically converted to ginsenoside F2. Analysis of the16S rRNA gene sequence revealed that strain C. ginsengiterrae sp. nov DCY68T belonged to the family Flavobacteriaceae and was most closely related to C. limigenitum SUR2T (97.4%). The genomic DNA G+C content was 42.0 mol%. The predominant quinones were MK-6 (74.5%) and MK-7 (25.5%). The major fatty acids were iso-C15:0, summed feature 3 (containing C16:1 ω7c and/or C16:1 ω6c) and iso-C17:0 3-OH. On the basis of these phenotypic, genotypic and chemotaxonomic studies, strain DCY68T represents a novel species of the genus Chryseobacterium, for which name C. ginsengiterrae sp. nov. is proposed. The type strain is DCY68T (=KCTC 32089T = JCM 18517T).
Assuntos
Chryseobacterium/enzimologia , Chryseobacterium/isolamento & purificação , Microbiologia do Solo , beta-Glucosidase/metabolismo , Aerobiose , Técnicas de Tipagem Bacteriana , Composição de Bases , Chryseobacterium/classificação , Chryseobacterium/genética , Análise por Conglomerados , Citosol/química , DNA Bacteriano/química , DNA Bacteriano/genética , DNA Ribossômico/química , DNA Ribossômico/genética , Ácidos Graxos/análise , Panax/crescimento & desenvolvimento , Filogenia , Quinonas/análise , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Cloreto de Sódio/metabolismo , TemperaturaRESUMO
Ginseng-cultivated soil is an excellent habitat for soil-borne bacteria to proliferate. A novel strain, DCY87T, was isolated from ginseng-cultivated soil in Gochang County, Republic of Korea, and subsequently characterized by polyphasic approach. Cells were rod shaped, non-motile, aerobic, Gram-reaction-positive, oxidase-negative and catalase-positive. 16S rRNA gene sequence analysis showed that strain DCY87T shared the highest similarity to 'Phycicoccus ochangensis' L1b-b9 (98.7 %). Closely phylogenetic relatives of strain DCY87T were identified: Phycicoccus ginsenosidimutans BXN5-13T (97.9 %), Phycicoccus soli THG-a14T (97.8 %), Phycicoccus bigeumensis MSL-03T (97.3 %), Phycicoccus cremeus V2M29T (97.3 %), Phycicoccus aerophilus 5516T-20T (97.3 %), Phycicoccus dokdonensis DS-8T (97.3 %) and Phycicoccus jejuensis KSW2-15T (97.1 %). The major polar lipids were classified as phosphatidylinositol and diphosphatidylglycerol. The major cellular fatty acids were composed of iso-C15 : 0, anteiso-C15:0, C17 : 0 and C17 : 1ω8c. The menaquinone was resolved as MK-8(H4). Strain DCY87T contained meso-diaminopimelic acid as diamino acid in the cell-wall peptidoglycan and glucose, xylose and rhamnose in the whole-cell sugar. The genomic DNA G+C content was calculated to be 72.7 mol%. DNA-DNA hybridization value between strain DCY87T and 'P. ochangensis' L1b-b9 was estimated to be 50 %. However, DNA-DNA hybridization value obtained between strain DCY87T and P. ginsenosidimutans BXN5-13T, P. soli THG-a14T and P. bigeumensis MSL-03T was well below 17 %. In general, polyphasic taxonomy demonstrated that DCY87T strain represented a novel species within the genus Phycicoccus. Accordingly, we propose the name Phycicoccus ginsengisoli sp. nov. The type strain is DCY87T (=KCTC 39635T=JCM 31016T).
Assuntos
Actinomycetales/classificação , Panax/microbiologia , Filogenia , Microbiologia do Solo , Actinomycetales/genética , Actinomycetales/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácido Diaminopimélico/química , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Peptidoglicano/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/químicaRESUMO
Traditional molecular methods have been used to examine bacterial communities in ginseng-cultivated soil samples in a time-dependent manner. Despite these efforts, our understanding of the bacterial community is still inadequate. Therefore, in this study, a high-throughput sequencing approach was employed to investigate bacterial diversity in various ginseng field soil samples over cultivation times of 2, 4, and 6 years in the first and second rounds of cultivation. We used non-cultivated soil samples to perform a comparative study. Moreover, this study assessed changes in the bacterial community associated with soil depth and the health state of the ginseng. Bacterial richness decreased through years of cultivation. This study detected differences in relative abundance of bacterial populations between the first and second rounds of cultivation, years of cultivation, and health states of ginseng. These bacterial populations were mainly distributed in the classes Acidobacteria, Alphaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, and Sphingobacteria. In addition, we found that pH, available phosphorus, and exchangeable Ca+ seemed to have high correlations with bacterial class in ginseng cultivated soil.
Assuntos
Bactérias/classificação , Biodiversidade , Panax , Microbiologia do Solo , Agricultura , Bactérias/genética , Análise por Conglomerados , Ecossistema , Evolução Molecular , Panax/crescimento & desenvolvimento , Filogenia , RNA Ribossômico 16S/genética , República da Coreia , Solo/química , Fatores de TempoRESUMO
A novel bacterial strain, designated DCY70(T), was isolated from soil of a ginseng field in Republic of Korea and was characterized in order to determine its taxonomic position. The strain was Gram-reaction negative, yellow-pigmented, rod-shaped and catalase- and oxidase-positive. Based on the 16S rRNA gene sequence similarity, strain DCY70(T) was shown to belong to the genus Flavobacterium, most closely related to Flavobacterium oncorhynchi 631-08(T) (98.4 %), Flavobacterium plurextorum 1126-1H-08(T) (97.9 %), Flavobacterium chilense LM-09-Fp(T) (97.9 %) and Flavobacterium chungangense CJ(T) (97.7 %). The chemotaxonomic characteristics showed only menaquinone-6 (MK-6), iso-C15:0, iso-C15:0 3OH, iso-C17:0 3OH and summed feature 3 as major cellular fatty acids. Polar lipids were phosphatidylethanolamine (PE), two unidentified aminolipids, four unidentified polar lipids and one unidentified phospholipid. The DNA G+C content was 34.9 mol%. Based on the phylogenetic, phenotypic and genotypic data, a novel species, Flavobacterium panacisoli sp. nov., is proposed (=KCTC 32393(T) = JCM 19162(T)).
Assuntos
Ácidos Graxos/análise , Flavobacterium , Fosfatidiletanolaminas/análise , Vitamina K 2/análogos & derivados , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Flavobacterium/classificação , Flavobacterium/genética , Flavobacterium/isolamento & purificação , Panax/microbiologia , Fosfolipídeos/análise , Filogenia , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Microbiologia do Solo , Vitamina K 2/análiseRESUMO
A novel, Gram-stain-negative, rod-shaped bacterial strain, designated as DCY109T, was isolated from the rhizosphere of rusty mountain ginseng root located on Hwacheon mountain of Gangwon province, South Korea. 16S rRNA gene sequence analysis revealed that strain DCY109T belonged to the genus Phenylobacterium and was related closely to Phenylobacterium muchangponense KACC 15042T (98.2 % similarity), Phenylobacterium immobile DSM 1986T (96.9 %) and Phenylobacterium koreense KCTC 12206T (96.7 %). The predominant isoprenoid quinone was ubiquinone (Q-10) and the DNA G+C content was 66.9 mol%. The major polar lipids were phosphatidylglycerol, an unidentified glycolipid and an unidentified lipid. The major fatty acids (>10 %) were C16 : 0, summed feature 3 (which comprised C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 8 (which comprised C18 : 1ω7c and/or C18 : 1ω6c). Mean DNA-DNA relatedness between strain DCY109T and its closest relative, P. muchangponense KACC 15042T, was 15.1±3.9 %. Based on the physiological, biochemical, chemotaxonomic and genetic analyses, strain DCY109T is considered to represent a novel species of the genus Phenylobacterium, for which the name Phenylobacterium panacis sp. nov. is proposed. The type strain is DCY109T (=KCTC 42749T=JCM 31045T).
Assuntos
Caulobacteraceae/classificação , Panax/microbiologia , Filogenia , Rizosfera , Microbiologia do Solo , Técnicas de Tipagem Bacteriana , Caulobacteraceae/genética , Caulobacteraceae/isolamento & purificação , DNA Bacteriano/genética , Ácidos Graxos/química , Glicolipídeos/química , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Ubiquinona/químicaRESUMO
A Gram-stain-negative, rod-shaped bacterium, designated DCY83T, was isolated from soil of a ginseng field in Gwangju Province, Republic of Korea. Cells were motile by means of flagella. Growth occurred at 4-40 °C (optimum 30 °C), at pH 6-8 (optimum pH 7.0) and with ≤ 0.4 % NaCl. Strain DCY83T was able to produce siderophore and was positive for phosphate solubilization. Indole-3-acetic acid production was 12.9 µg ml- 1 after 3âdays in culture. 16S rRNA gene sequence analysis showed that strain DCY83T belonged to the genus Duganella and was related most closely to Duganella sacchari Sac-22T (97.4 % similarity), Duganella zoogloeoides IAM 12670T (97.1 %) and Duganella radicis Sac-41T (97.1 %). The major fatty acids were C16 : 0 and summed feature 3 (containing C16 : 1ω7c and/or C16 : 1ω6c). The major polar lipids were phosphatidylglycerol and phosphatidylethanolamine. The only quinone was ubiquinone 8. The genomic DNA G+C content was 55.3âmol%. DNA-DNA relatedness between strain DCY83T and D. sacchari KCTC 22381T, D. zoogloeoides JCM 20729T and D. radicis KCTC 22382T was 27.7, 22.4 and 35.5 %, respectively. On the basis of the phenotypic and genotypic analysis, DCY83T is classified as representing a novel species in the genus Duganella, for which the name Duganella ginsengisoli sp. nov. is proposed. The type strain is DCY83T ( = KCTC 42409T = JCM 30745T).
Assuntos
Oxalobacteraceae/classificação , Panax/microbiologia , Filogenia , Microbiologia do Solo , Técnicas de Tipagem Bacteriana , DNA Bacteriano/genética , Ácidos Graxos/química , Dados de Sequência Molecular , Hibridização de Ácido Nucleico , Oxalobacteraceae/genética , Oxalobacteraceae/isolamento & purificação , Fosfatidiletanolaminas/química , Fosfatidilgliceróis/química , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Ubiquinona/químicaRESUMO
A novel Gram-staining-positive, rod-shaped bacterium, designated DCY100(T), was isolated from rhizome of mountain ginseng root in Hwacheon mountain, Gangwon province, Republic of Korea. The 16S rRNA gene sequence analysis showed that strain DCY100(T) belonged to the genus Microbacterium and was most closely related to Microbacterium ginsengisoli KCTC 19189(T) (97.9%), Microbacterium lacus JCM 15575(T) (97.2%) and Microbacterium invictum DSM 19600(T) (97.1%). The major menaquinones were MK-11 and MK-12. The major polar lipids were found to be diphosphatidylglycerol, phosphatidylglycerol and one unidentified glycolipid. The major fatty acids (>10.0%) were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The cell-wall peptidoglycan contained the amino acids ornithine, alanine, glutamic acid and glycine; whole-cell sugars consisted of glucose, galactose, rhamnose and ribose. The DNA G+C content was 63.6 ± 0.7 mol%. The DNA-DNA hybridization relatedness values between strain DCY100(T) and Microbacterium ginsengisoli KCTC 19189(T), Microbacterium lacus JCM 15575(T) and Microbacterium invictum DSM 19600(T) were 36.2 ± 0.4, 22.0 ± 3.0 and 15.3 ± 1.8%, respectively. On the basis of phenotypic, chemotaxonomic and genotypic analyses, the isolate is classified as a representative of a novel species in the genus Microbacterium, for which the name Microbacterium rhizomatis DCY100(T) is proposed. The type strain is DCY100(T) ( = KCTC 39529(T) = JCM 30598(T)).
Assuntos
Actinomycetales , Actinomycetales/classificação , Técnicas de Tipagem Bacteriana , Composição de Bases , Celulases/genética , DNA Bacteriano/genética , Ácidos Graxos/química , Genótipo , Glucosidases , Glicolipídeos/química , Lipídeos/análise , Dados de Sequência Molecular , Hibridização de Ácido Nucleico/genética , Panax/microbiologia , Peptidoglicano/química , Filogenia , RNA Ribossômico 16S/genética , República da Coreia , Rizoma , Análise de Sequência de DNA , Microbiologia do SoloRESUMO
A novel bacterium, designated DCY95T, was isolated from ginseng-cultivated soil in Quang Nam province, Vietnam. On the basis of 16S rRNA and gyrB gene sequence analysis, this isolate was assigned to the genus Paenibacillus and found to be closely related to Paenibacillus sacheonensis SY01T (97.1â% 16S rRNA gene sequence similarity) and Paenibacillus taihuensis THMBG22T (96.4â%). The partial gyrB gene of DCY95T possessed 69.6-83.9â% sequence identity to those of other members of the genus Paenibacillus. Strain DCY95T was Gram-reaction-negative, catalase-negative, oxidase-positive, strictly aerobic, rod-shaped and motile by means of peritrichous flagella. Ellipsoidal free spores or subterminal endospores were produced in sporangia. MK-7 was the diagnostic menaquinone. The cell-wall peptidoglycan contained meso-diamonopimelic acid as the diamino acid. Whole-cell sugars comprised ribose, mannose and glucose. The major cellular fatty acids were anteiso-C15â:â0, iso-C16â:â0 and C16â:â0. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, three unidentified aminophospholipids, and two unidentified phospholipids. The genomic DNA G+C content was 60.7 ± 0.9âmol%. Phenotypic and chemotaxonomic results placed strain DCY95T within the genus Paenibacillus. However, DNA-DNA relatedness values between strain DCY95T and P. sacheonensis KACC 14895T or P. taihuensis NBRC 108766T were lower than 36â%. The low DNA relatedness data in combination with phylogenetic and (GTG)5-PCR analyses, as well as biochemical tests, indicated that strain DCY95T could not be assigned to any recognized species. In conclusion, the results in this study support the classification of strain DCY95T as a representative of a novel species within the genus Paenibacillus, for which the name Paenibacillus panaciterrae is proposed. The type strain is DCY95T ( = KCTC 33581T = DSM 29477T).
Assuntos
Paenibacillus/classificação , Panax/microbiologia , Filogenia , Microbiologia do Solo , Técnicas de Tipagem Bacteriana , Composição de Bases , Parede Celular/química , DNA Bacteriano/genética , Ácido Diaminopimélico/química , Ácidos Graxos/química , Genes Bacterianos , Hibridização de Ácido Nucleico , Paenibacillus/genética , Paenibacillus/isolamento & purificação , Peptidoglicano/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vietnã , Vitamina K 2/análogos & derivados , Vitamina K 2/químicaRESUMO
The type strain DCY99(T) was isolated from soil collected from a ginseng field in Hwacheon, Republic of Korea. Strain DCY99(T) is Gram-negative, non-spore forming, motile, rod-shaped, and strictly aerobic. The bacteria grow optimally at 25-30 °C and pH 6.0-6.5. Phylogenetically, strain DCY99(T) is most closely related to Sphingomonas oligophenolica JCM 12082(T), followed by Sphingomonas asaccharolytica KCTC 2825(T), Sphingomonas mali KCTC 2826(T), Sphingomonas cynarae JCM17498(T), Sphingomonas pruni KCTC 2824(T), and Sphingomonas glacialis DSM 22294(T). The DNA-DNA relatedness between strain DCY99(T) and S. oligophenolica JCM 12082(T) was 15.6 ± 0.4 %, and the DNA G+C content of strain DCY99(T) was 64.4 mol%. An isoprenoid quinone was detected and identified as ubiquinone Q-10, and sym-homospermidine was identified as the major polyamine of DCY99(T). The major polar lipids were identified as sphingoglycolipid, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, and phosphatidylcholine. C14:02OH, C16:0, and summed feature 8 (C18:1 ω7c:/C18:1 ω6c) were identified as the major fatty acids present in DCY99(T). The results of physiological and biochemical tests allowed strain DCY99(T) to be differentiated phenotypically from other recognized species belonging to the genus Sphingomonas. Therefore, it is suggested that the newly isolated organism represents a novel species, for which the name Sphingomonas panacis sp. nov. is proposed with the type strain designated as DCY99(T) (=JCM 30806(T) =KCTC 42347(T)).
Assuntos
Panax/microbiologia , Microbiologia do Solo , Sphingomonas/classificação , Sphingomonas/isolamento & purificação , Aerobiose , Técnicas de Tipagem Bacteriana , Composição de Bases , Análise por Conglomerados , Citosol/química , DNA Bacteriano/química , DNA Bacteriano/genética , DNA Ribossômico/química , DNA Ribossômico/genética , Ácidos Graxos/análise , Concentração de Íons de Hidrogênio , Locomoção , Hibridização de Ácido Nucleico , Fosfolipídeos/análise , Filogenia , Quinonas/análise , RNA Ribossômico 16S/genética , República da Coreia , Rizosfera , Análise de Sequência de DNA , Espermidina/análise , Sphingomonas/genética , Sphingomonas/fisiologia , TemperaturaRESUMO
Strain DCY91(T), a Gram-stain-negative, rod-shaped, aerobic, non-motile bacterium, was isolated from soil of ginseng field in Gyeonggi province, South Korea. Strain DCY91(T) shared the highest 16S rRNA gene sequence similarity with Sphingomonas mucosissima DSM 17494(T) (98.55%), Sphingomonas dokdonensis KACC 17420(T) (98.11%) and Sphingomonas xinjiangensis DSM 26736(T) (96.68%). The strain DCY91(T) was found to able to grow best in trypticase soy agar at 28 °C, at pH 7 and at 0.5 % NaCl. Ubiquinone 10 was identified as the isoprenoid quinone. The major polar lipids were identified as sphingoglycolipid, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine. The major fatty acids of strain DCY91(T) were identified as unsaturated C18:1 ω7c and saturated C16:0. The major polyamine content was sym-homospermidine. The DNA G + C content was determined to be 65.8 mol% (HPLC). After 6 days of incubation, strain DCY91(T) produced 9.64 ± 1.73 and 33.73 ± 4.66 µg/ml indole-3-acetic acid, using media without L-tryptophan and supplemented with L-tryptophan, respectively. Strain DCY91(T) was also weakly solubilized phosphate and produced siderophores. On the basis of the phenotypic characteristics, genotypic analysis and chemotaxonomic characteristics, strain DCY91(T) is considered to represent a novel species of the genus Sphingomonas, for which the name Sphingomonas panaciterrae sp. nov. is proposed. The type strain is DCY91(T) (=KCTC 42346(T) =JCM 30807(T)).
Assuntos
Microbiologia do Solo , Sphingomonas/classificação , Sphingomonas/fisiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , Ácidos Graxos/análise , Panax/microbiologia , Filogenia , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Especificidade da Espécie , Sphingomonas/genética , Sphingomonas/isolamento & purificaçãoRESUMO
A novel bacterial strain DCY104(T) isolated from soil of a ginseng field in Yeoncheon County, Republic of Korea is described in this study. Cells were short rod-shaped, motile by mean of one polar flagellum, strictly aerobic, Gramreaction negative, oxidase and catalase-positive. 16S rRNA gene sequence analysis showed that strain DCY104(T) shared highest similarity 98.2 % to Paralcaligenes ureilyticus GR24-5(T), and from 97.7 to 97.1 % with other type strains belong to the genera Candidimonas, Pusillimonas and Parapusillimonas Otherwise, phylogenetic trees analyses indicated that strain DCY104(T) belongs to a single group with P. ureilyticus GR24-5(T) that was distinct to other genera. The major polar lipids were phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol. The major cellular fatty acids consisted of C16:0, cyclo-C17:0, and summed feature 8 (comprising C18:1 ω7c and/or C18:1 ω6c). The predominant polyamine was putrescine. The ubiquinone was Q-8. The genomic DNA G+C content was 55.9 mol%. These data in combination with the presence of one polar flagellum and positive activity of urease confirmed the placement of strain DCY104(T) in the genus Paralcaligenes. DNA-DNA relatedness between strain DCY104(T) and P. ureilyticus KACC 13888(T) was 40 %. The differences in the profiles of polar lipids, fatty acids and phenotypic characteristics in combination with DNA-DNA relatedness delineated strain DCY104(T) and P. ureilyticus KACC 13888(T). In summary, taxonomic analyses in this study demonstrated that strain DCY104(T) represents a novel species within the genus Paralcaligenes, for which we propose the name Paralcaligenes ginsengisoli. The type strain is DCY104(T) (= KCTC 42406(T) = JCM 30746(T)).
Assuntos
Alcaligenaceae/classificação , Alcaligenaceae/isolamento & purificação , Panax/crescimento & desenvolvimento , Microbiologia do Solo , Aerobiose , Alcaligenaceae/genética , Alcaligenaceae/fisiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , Catalase/análise , Análise por Conglomerados , Citosol/química , DNA Bacteriano/química , DNA Bacteriano/genética , DNA Ribossômico/química , DNA Ribossômico/genética , Ácidos Graxos/análise , Coreia (Geográfico) , Locomoção , Dados de Sequência Molecular , Hibridização de Ácido Nucleico , Oxirredutases/análise , Fosfolipídeos/análise , Filogenia , Putrescina/análise , Quinonas/análise , RNA Ribossômico 16S/genética , Análise de Sequência de DNARESUMO
Two novel Gram-staining-positive bacteria, designated DCY60T and DCY90T, were isolated from soil of a ginseng field in the Republic of Korea. 16S rRNA gene sequence comparisons showed the two novel strains were closely related to members of the genus Humibacter with greatest similarity to Humibacter antri KCTC 33009T (98.8 and 98.4% for DCY60T and DCY90T, respectively). The predominant menaquinones present were MK-11 and MK-12. The major fatty acids were anteiso-C17 : 0 and summed feature 8 containing C18 : 1ω7c and/or C18 : 1ω6c. The DNA G+C contents of strains DCY60T and DCY90T were 62.8 and 66.8âmol%, respectively. The peptidoglycan of both strains contained the amino acids ornithine, 2,4-diaminobutyric acid, alanine, glutamic acid and glycine. The cell-wall sugars of strain DCY60T comprised glucose, galactose, rhamnose and xylose, while strain DCY90T contained glucose, galactose, rhamnose and ribose. The major polar lipids of both strains were phosphatidylglycerol, an unidentified glycolipid, and an unknown phospholipid. On the basis of the phenotypic analysis strains DCY60T and DCY90T represent novel species of the genus Humibacter, for which names Humibacter ginsengiterrae sp. nov. (type strain DCY60T = KCTC 33520T = JCM 30079T) and Humibacter ginsengisoli sp. nov. (type strain DCY90T = KCTC 33521T = JCM 30080T) are proposed.
Assuntos
Actinomycetales/classificação , Panax/microbiologia , Filogenia , Microbiologia do Solo , Actinomycetales/genética , Actinomycetales/isolamento & purificação , Composição de Bases , Parede Celular/química , DNA Bacteriano/genética , Ácidos Graxos/química , Dados de Sequência Molecular , Peptidoglicano/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Vitamina K 2/químicaRESUMO
A novel bacterial strain, DCY86(T) (=KCTC 42053(T) = JCM 19890(T)) was isolated from soil of a ginseng field in Yeoncheon province (38°04'00â³N 126°57'00â³E), Republic of Korea using a serial dilution method. Strain DCY86(T) was observed to be Gram-stain negative, strictly aerobic, to grow optimally at 25-30 °C, at pH 7-7.5 and on tryptic soya agar medium. The cells were found to be sensitive to ceftazidine and tetracycline. Based on 16S rRNA gene sequence comparisons, strain DCY86(T) was found to be most closely related to Cupriavidus basilensis LMG 18990(T) (98.48 %), Cupriavidus numazensis LMG 26411(T) (98.34 %), Cupriavidus pinatabonesis KCTC 22125(T) (98.34 %) and Cupriavidus laharis KCTC 22126(T) (98.00 %). The G+C content was determined to be 64.23 mol %. The only isoprenoid quinone detected in strain DCY86(T) was ubiquinone Q-8. The major polar lipids were identified as diphosphatidylglycerol, phosphtidylethanolamine, phosphatidylglycerol, unidentified aminophosphoglycolipids and unidentified phospholipids. The major fatty acids were identified as C16:0 summed feature 3 (C16:1 ω7c/ω6c and/or iso-C15â:â0 2-OH) and summed feature 8 (C18:1 ω7c and/or C18:1 ω6c). These data support the affiliation of strain DCY86(T) to the genus Cupriavidus. Strain DCY86(T) was also found to be able to solubilize phosphate and produce siderophores. The results of physiological and biochemical tests enabled strain DCY86(T) to be differentiated genotypically and phenotypically from the recognized species of the genus Cupriaividus. Therefore, the novel isolate can be considered to represent a novel species, for which the name Cupriavidus yeoncheonense sp. nov. is proposed here. The type strain is DCY86(T) (=KCTC 42053(T) = JCM 19890(T)).
Assuntos
Cupriavidus/classificação , Cupriavidus/isolamento & purificação , Microbiologia do Solo , Aerobiose , Antibacterianos/farmacologia , Técnicas de Tipagem Bacteriana , Composição de Bases , Ceftazidima/farmacologia , Análise por Conglomerados , Meios de Cultura/química , Cupriavidus/genética , Cupriavidus/fisiologia , Citosol/química , DNA Bacteriano/química , DNA Bacteriano/genética , DNA Ribossômico/química , DNA Ribossômico/genética , Ácidos Graxos/análise , Glicolipídeos/análise , Concentração de Íons de Hidrogênio , Dados de Sequência Molecular , Panax/crescimento & desenvolvimento , Fosfolipídeos/análise , Filogenia , Quinonas/análise , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Temperatura , Tetraciclina/farmacologiaRESUMO
A novel bacterial strain, designated DCY94(T), was isolated from forest soil cultivated with ginseng in Vietnam. The strain was Gram-reaction-negative, facultatively anaerobic, non-motile, rod-shaped and catalase- and oxidase-positive. 16S rRNA gene sequence analysis demonstrated that strain DCY94(T) was closely related to Paracoccus sphaerophysae Zy-3(T) (97.5% 16S rRNA gene sequence similarity) and Paracoccus caeni MJ17(T) (96.9%). The fatty acid profile of strain DCY94(T) contained a predominant amount of summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 88.4%) and moderate to small quantities of C8 : 0 3-OH (1.0%), C10 : 0 3-OH (2.8%) and C18 : 0 (5.2%). Phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and one unidentified glycolipid were major polar lipids; one unidentified aminolipid, one unidentified aminophospholipid, one unidentified phospholipid and four unidentified polar lipids were minor components. The polyamine pattern comprised the major compounds putrescine and spermidine and minor amounts of sym-homospermidine and spermine. The ubiquinone of the strain was Q-10 and the G+C content of its genomic DNA was 68.3 mol%. All these results support the placement of strain DCY94(T) within the genus Paracoccus . Levels of DNA-DNA relatedness between strain DCY94(T) and P. sphaerophysae HAMBI 3106(T) and P. caeni KCTC 22480(T) were 52 and 50%, respectively. The results of phylogenetic analysis, phenotypic tests, chemotaxonomic characterization and DNA-DNA relatedness studies distinguished strain DCY94(T) from the closest recognized species of the genus Paracoccus , suggesting that this strain represents a novel species, for which the name Paracoccus panacisoli sp. nov. is proposed. The type strain is DCY94(T) (â=âKCTC 42086(T)â=JCM 30337(T)).
Assuntos
Panax/microbiologia , Paracoccus/classificação , Filogenia , Microbiologia do Solo , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Florestas , Dados de Sequência Molecular , Hibridização de Ácido Nucleico , Paracoccus/genética , Paracoccus/isolamento & purificação , Fosfolipídeos/química , Poliaminas/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Ubiquinona/análogos & derivados , Ubiquinona/química , VietnãRESUMO
Strain DCY56(T) was isolated from a soil sample taken from a ginseng field. The strain was Gram-reaction positive, catalase-positive, oxidase-negative, aerobic and non-motile. Phylogenetic analysis, based on 16S rRNA gene sequence analysis, indicated that strain DCY56(T) belonged to the genus Microbacterium. The closest relatives were Microbacterium azadirachtae AI-S262(T), Microbacterium aerolatum V-73(T) and Microbacterium phyllosphaerae DSM 13468(T) (98.0â%, 98.0â% and 97.5â% gene sequence similarity, respectively). The G+C content of the genomic DNA of strain DCY56(T) was 68.5 mol%. The DNA-DNA relatedness values between strain DCY56(T) and the most closely related type strains were lower than 36â%. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol and an unidentified glycolipid. The predominant fatty acids contained iso-C16â:â0, anteiso-C15â:â0 and anteiso-C17â:â0. The menaquinones were MK-12 and MK-13. The diagnostic diamino acid of strain DCY56(T) was ornithine. The dominant whole-cell sugars were glucose, rhamnose and ribose. The results of the genotypic analysis, in combination with chemotaxonomic and physiological data, demonstrate that strain DCY56(T) represents a novel species within the genus Microbacterium, for which the name Microbacterium panaciterrae sp. nov. is proposed. The type strain is DCY56(T) (â=âKCTC 19884(T)â=âJCM 17839(T)).
Assuntos
Actinomycetales/classificação , Panax/microbiologia , Filogenia , Rizosfera , Microbiologia do Solo , Actinomycetales/genética , Actinomycetales/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Glicolipídeos/química , Dados de Sequência Molecular , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/químicaRESUMO
A novel bacterial strain DCY89(T) was isolated from soil sample of ginseng field and was characterized using a polyphasic approach. Cells were Gram-reaction-positive, rod-shaped, spore-forming and motile with flagella. The strain was aerobic, esculin and starch positive, catalase- and oxidase-negative, optimum growth temperature, and pH were 25-30 °C and 6.0-7.5, respectively. On the basis of 16S rRNA gene sequence analysis, strain DCY89(T) was shown to belong to the genus Paenibacillus and the closest phylogenetic relatives were Paenibacillus cellulosilyticus KACC 14175(T) (98.2%), Paenibacillus kobensis KACC 15273(T) (98.1%), Paenibacillus xylaniclasticus KCTC 13719(T) (96.9%), and Paenibacillus curdlanolyticus KCTC 3759(T) (96.64%). The DNA G+C content was 52.5 mol%, and the predominant respiratory quinone was MK-7. The major fatty acids were iso-C15:0, iso-C16:0, and anteiso-C15:0. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylglycerol. The results of the genotypic analysis in combination with chemotaxonomic and physiological data demonstrated that DCY89(T) represented a novel species within the genus Paenibacillus, for which we propose the name Paenibacillus ginsengiterrae. The type strain is DCY89(T) (JCM 19887(T) = KCTC 33430(T)).
Assuntos
Ginsenosídeos/metabolismo , Paenibacillus/classificação , Filogenia , Microbiologia do Solo , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/análise , Lipídeos/análise , Dados de Sequência Molecular , Oxirredutases/metabolismo , Paenibacillus/química , Paenibacillus/genética , Paenibacillus/isolamento & purificação , Paenibacillus/metabolismo , Panax , RNA Ribossômico 16S/genética , Especificidade da EspécieRESUMO
A novel Gram-staining-negative, rod-shaped bacterium, designated DCY78(T), was isolated from soil of a ginseng field in Yeon-cheon province (38° 04' 00â³ N 126° 57' 00â³ E), Republic of Korea. The phylogenetic analysis based on 16S rRNA gene sequences showed that strain DCY78(T) belonged to the genus Epilithonimonas and was most closely related to Epilithonimonas lactis DSM 19921(T) (98.5â% sequence similarity) and Epilithonimonas tenax DSM 16811(T) (97.8â%). Growth occurred at 10-30 °C with an optimum temperature of 28 °C. The pH range for growth was pH 5.5-8.0. The major polar lipids were found to be phosphatidylethanolamine three unidentified amino lipids and one unidentified polar lipid. The only predominant quinone was MK-6. The major polyamines were sym-homospermidine and spermidine. The major fatty acids were summed feature 3 (comprising C16â:â1ω6c and/or C16â:â1ω7c), iso-C15â:â0 and iso-C17â:â0 3-OH. The DNA G+C content was 37.9 mol%. On the basis of the phenotypic and genotypic analysis, the isolate is classified as representative of a novel species in the genus Epilithonimonas, for which the name Epilithonimonas ginsengisoli is proposed. The type strain is DCY78(T) (â=âKCTC 32174(T)â=âJCM 19896(T)).
Assuntos
Flavobacteriaceae/classificação , Panax/microbiologia , Filogenia , Microbiologia do Solo , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Flavobacteriaceae/genética , Flavobacteriaceae/isolamento & purificação , Dados de Sequência Molecular , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Espermidina/análogos & derivados , Espermidina/química , Vitamina K 2/análogos & derivados , Vitamina K 2/químicaRESUMO
Strain DCY84(T), a Gram-stain positive, rod-shaped, aerobic, spore-forming bacterium, motile by means of peritrichous flagella, was isolated from humus soil from Yongin forest in Gyeonggi province, South Korea. Strain DCY84(T) shared the highest sequence similarity with Paenibacillus barengoltzii KACC 15270(T) (96.86 %), followed by Paenibacillus timonensis KACC 11491(T) (96.49 %) and Paenibacillus phoenicis NBRC 106274(T) (95.77 %). Strain DCY84(T) was found to able to grow best in TSA at temperature 30 °C, at pH 8 and at 0.5 % NaCl. MK-7 menaquinone was identified as the isoprenoid quinone. The major polar lipids were identified as phosphatidylethanolamine, an unidentified aminophospholipid, two unidentified aminolipids and an unidentified polar lipid. The peptidoglycan was found to contain the amino acids meso-diaminopimelic acid, alanine and D-glutamic acid. The major fatty acids of strain DCY84(T) were identified as branched chain anteiso-C15:0, saturated C16:0 and branched chain anteiso-C17:0. The cell wall sugars of strain DCY84(T) were found to comprise of ribose, galactose and xylose. The major polyamine was identified as spermidine. The DNA G+C content was determined to be 62.6 mol%. After 6 days of incubation, strain DCY84(T) produced 52.96 ± 1.85 and 72.83 ± 2.86 µg/ml L-indole-3-acetic acid, using media without L-tryptophan and supplemented with L-tryptophan, respectively. Strain DCY84(T) was also found to be able to solubilize phosphate and produce siderophores. On the basis of the phenotypic characteristics, genotypic analysis and chemotaxonomic characteristics, strain DCY84(T) is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus yonginensis sp. nov. is proposed. The type strain is DCY84(T) (=KCTC 33428(T) = JCM 19885(T)).
Assuntos
Paenibacillus/classificação , Paenibacillus/isolamento & purificação , Microbiologia do Solo , Aerobiose , Técnicas de Tipagem Bacteriana , Composição de Bases , Carboidratos/análise , Análise por Conglomerados , DNA Bacteriano/química , DNA Bacteriano/genética , DNA Ribossômico/química , DNA Ribossômico/genética , Ácido Diaminopimélico/análise , Ácidos Graxos/análise , Florestas , Concentração de Íons de Hidrogênio , Coreia (Geográfico) , Locomoção , Dados de Sequência Molecular , Paenibacillus/genética , Paenibacillus/fisiologia , Peptidoglicano/análise , Fosfolipídeos/análise , Filogenia , Poliaminas/análise , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Cloreto de Sódio/metabolismo , Temperatura , Vitamina K 2/análiseRESUMO
A Gram-staining-positive, catalase-positive, oxidase-negative, non-motile, non-flagellate and rod-shaped bacterium, was designated as DCY81(T), and isolated from soil of a ginseng field in Pocheon province, Republic of Korea. The 16S rRNA gene sequence analysis revealed that strain DCY81(T) belonged to the genus Arthrobacter. Major fatty acid was anteiso-C15:0, while major polar lipids were diphosphatidyglycerol, phatidyglycerol, phosphatidylinositol, monogalactosyldiacylglycerol (GL1), and dimannosyldiacylglycerol (GL2). The dominant quinone was MK-9(H2). The peptidoglycan type was A3α with an L-Lys-L-Ala-L-Thr-L-Ala interpeptide bridge. The DNA-DNA hybridization relatedness between strain DCY81(T) and Arthrobacter siccitolerans LMG 27359(T) (98.2 %), Arthrobacter sulfonivorans JCM 13520(T) (97.81 %), Arthrobacter scleromae DSM 17756(T) (97.59 %), Arthrobacter oxydans KCTC 3383(T) (97.3 %) was 39.1 ± 0.2, 62.2 ± 1.6, 36.8 ± 1.1 and 48.3 ± 1.6 %, respectively which show that the genotypic separation of strain DCY81(T) from the closest reference strain of the genus Arthrobacter. The DNA G+C content was 65.2 mol%. The genotypic analysis, physiological, and chemotaxonomic results indicate that strain DCY81(T) represents a novel species of the genus Arthrobacter. Therefore, Arthrobacter ginsengisoli sp. nov., is proposed as the type strain (=KCTC 29225(T) = JCM 19357(T)).
Assuntos
Arthrobacter/isolamento & purificação , Panax , Microbiologia do Solo , Arthrobacter/classificação , Arthrobacter/genética , Arthrobacter/fisiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/análise , Genes de RNAr , Lipídeos/análise , Dados de Sequência Molecular , Hibridização de Ácido Nucleico , Peptidoglicano/química , Filogenia , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNARESUMO
A novel Gram-staining-positive, aerobic bacterium, designed DCY80(T), was isolated from soil of a ginseng field in the Republic of Korea. 16S rRNA gene sequence analysis revealed that strain DCY80(T) belonged to the genus Brachybacterium (95.8-98.2â% similarity) and was most closely related to Brachybacterium faecium DSM 4810(T) (98.2â%). Colonies were circular, entire, low-convex, opaque and 0.5-1.0 mm in diameter after growth for 2 days on TSA at 30 °C. Growth occurred at 4-34 °C (optimum, 25 °C), at pH 5.0-10.0 (optimum, pH 6.5-7.0) and in the presence of 0-7.0â% NaCl. Strain DCY80(T) produced siderophores and was sensitive to penicillin G, erythromycin, cefazolin, oleandomycin, ceftazidime, vancomycin, tetracycline, novobiocin, carbamicillin, rifampicin and neomycin. The DNA G+C content was 71.0 mol%. Levels of DNA-DNA relatedness between strain DCY80(T) and B. faecium DSM 4810(T), B. paraconglomeratum KCTC 9916(T), B. saurashtrense DSM 23186(T) and B. conglomeratum KCTC 9915(T) were 46.9±0.5, 28.9±0.6, 20.4±0.9 and 17.3±0.4â%, respectively. The cell-wall peptidoglycan of strain DCY80(T) contained meso-diaminopimelic acid as the diagnostic diamino acid. The menaquinones were MK-7 (85.8â%) and MK-8 (14.2â%). The major cellular fatty acids were anteiso-C15â:â0 (69.1â%) and anteiso-C17â:â0 (12.2â%). Phosphatidylglycerol, diphosphatidylglycerol, an unidentified glycolipid, two unidentified phospholipids and five unidentified polar lipids were found. On the basis of our phenotypic and genotypic analyses, strain DCY80(T) represents a novel species of the genus Brachybacterium, for which the name Brachybacterium ginsengisoli sp. nov. is proposed (type strain DCY80(T)â=âKCTC 29226(T)â=âJCM 19356(T)).