RESUMO
Strain ELA7T, a novel Gram-negative, non-motile bacterium with a white pigment and rod-shaped morphology, was isolated from the faeces of an eland at Seoul Grand Park, a zoo in the Republic of Korea. The novel bacterial strain grew optimally in R2A medium under the following conditions: 0â% (w/v) NaCl, pH 8.0, and 34â°C. Based on phylogenetic analyses using 16S rRNA gene sequencing, strain ELA7T was found to have the closest relatedness to Pedobacter ginsengisoli Gsoil 104T (97.8â%), P. frigoris RP-3-15T (97.2â%), P. humi THG S15-2T (97.0â%), P. seoulensis THG-G12T (97.0â%), and P. foliorum LMG 31463T (96.9â%). The genome size and genomic DNA G+C content of strain ELA7T were 3.63 Mbp and 46.5â%, respectively. A whole genome-level comparison of strain ELA7T with P. ginsengisoli Gsoil 104T, P. frigoris RP-3-15T, P. africanus DSM 12126T, and P. psychroterrae RP-1-14T revealed average nucleotide identity values of 72.0, 71.8, 71.9, and 71.6â%, respectively. The major fatty acids were summed feature 3 (comprising C16â:â1 ω7c and/or C16â:â1 ω6c) and MK-7 was the predominant respiratory quinone. The major polar lipids of strain ELA7T were phosphatidylethanolamine, sphingolipid, unidentified aminolipid, unidentified phosphoglycolipid, unidentified glycolipid, and eight unidentified lipids. Considering our chemotaxonomic, genotypic, and phenotypic findings, strain ELA7T (=KACC 23137T=JCM 36003T) is identified as representing a novel species within the genus Pedobacter, for which the name Pedobacter faecalis sp. nov. is proposed.
Assuntos
Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano , Ácidos Graxos , Fezes , Pedobacter , Filogenia , RNA Ribossômico 16S , Análise de Sequência de DNA , Vitamina K 2 , Ácidos Graxos/análise , Ácidos Graxos/química , RNA Ribossômico 16S/genética , Fezes/microbiologia , DNA Bacteriano/genética , Pedobacter/genética , Pedobacter/isolamento & purificação , Pedobacter/classificação , República da Coreia , Animais , Vitamina K 2/análogos & derivados , Vitamina K 2/análise , Animais de Zoológico/microbiologia , Genoma Bacteriano , Hibridização de Ácido Nucleico , Ruminantes/microbiologiaRESUMO
An aerobic, Gram-stain-negative bacterium, designated as SYSU D00382T, was sourced from soil of Gurbantunggut Desert, PR China. The strain was short-rod-shaped, oxidase-positive and catalase-negative, with yellow-colored, convex, round, and smooth colonies on TSA plate. Growth and proliferation occurred at 4-37 °C (optimal: 28-30 °C), pH 5.0-8.0 (optimal: pH 6.0-7.0) and NaCl concentration of 0-2.5% (optimal: 0-0.5%). The 16S rRNA gene based phylogenetic assessment showed that SYSU D00382T belonged to the genus Pedobacter, and was most closely related to Pedobacter ginsengisoli Gsoil 104T with similarity of 97.7%. The genomic DNA G+C content of SYSU D00382T was 46.4%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between SYSU D00382T and P. ginsengisoli Gsoil 104T were 75.7% and 17.5%, respectively. The main polar lipid was phosphatidylethanolamine. The major fatty acids (> 5%) were iso-C15:0, iso-C17:0 3-OH, summed features 3 and 9. The sole respiratory quinone identified was MK-7. The phylogeny based on 16S rRNA gene and whole-genome sequences revealed that SYSU D00382T formed a robust lineage with P. ginsengisoli Gsoil 104T. Based on phenotypic, phylogenetic and genotypic data, a novel specie named Pedobacter deserti sp. nov. is proposed. The type strain is SYSU D00382T (= CGMCC 1.18627T = MCCC 1K04972T = KCTC 82279T).
Assuntos
Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano , Clima Desértico , Ácidos Graxos , Pedobacter , Filogenia , RNA Ribossômico 16S , Microbiologia do Solo , Pedobacter/genética , Pedobacter/classificação , Pedobacter/isolamento & purificação , Pedobacter/fisiologia , RNA Ribossômico 16S/genética , DNA Bacteriano/genética , Ácidos Graxos/análise , China , Hibridização de Ácido Nucleico , Análise de Sequência de DNARESUMO
Two novel bacterial strains, designated as SYSU D00823T and SYSU D00873T, were isolated from sandy soil of the Gurbantunggut Desert in Xinjiang, north-west China. SYSU D00823T and SYSU D00873T shared 99.0â% 16S rRNA gene sequence identity, and were both most closely related to Pedobacter xinjiangensis 12157T with 96.1â% and 96.0â% similarities, respectively. Phylogenetic and phylogenomic analyses revealed that the two isolates and P. xinjiangensis 12157T formed a separate distinct cluster in a stable subclade with the nearby species Pedobacter mongoliensis 1-32T, as well as the genera Pararcticibacter and Arcticibacter. Furthermore, P. mongoliensis 1-32T formed a separate deep-branching lineage and did not form a cluster with members of the genus Pedobacter. The average nucleotide identity and digital DNA-DNA hybridization values between SYSU D00823T and SYSU D00873T and related species were well below the thresholds for species delineation (<81.0â% and <24.0â%, respectively). The genomes of SYSU D00823T and SYSU D00873T were 6.19 and 6.43 Mbp in size with 40.4â% and 40.5â% DNA G+C contents, respectively. The predominant fatty acids (>10â%) of SYSU D00823T and SYSU D00873T were iso-C15â:â0, iso-C17â:â0 3-OH and summed feature 3 (C16â:â1 ω7c and/or C16â:â1 ω6c). Menaquinone-7 was the only respiratory quinone. The major polar lipids were phosphatidylethanolamine, glycosphingolipid, aminoglycolipid/glycolipid, aminophospholipid and three or four unidentified polar lipids. These data indicated that strains SYSU D00823T and SYSU D00873T should be assigned to two novel species of a new genus within the family Sphingobacteriaceae, for which the names Desertivirga arenae gen. nov., sp. nov. and Desertivirga brevis sp. nov. are proposed. The type strains are SYSU D00823T (=CGMCC 1.18630T=MCCC 1K04973T=KCTC 82278T) and SYSU D00873T (=CGMCC 1.18629T=MCCC 1K04974T=KCTC 82281T), respectively. Accordingly, the reclassification of P. xinjiangensis as Desertivirga xinjiangensis comb. nov., and P. mongoliensis as Paradesertivirga mongoliensis gen. nov., comb. nov. are also proposed.
Assuntos
Pedobacter , Filogenia , Microbiologia do Solo , Composição de Bases , China , Clima Desértico , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Pedobacter/genética , Pedobacter/classificação , Pedobacter/isolamento & purificação , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análogos & derivadosRESUMO
Two Gram-staining negative, catalase- and oxidase-positive, pinkish-colored and rod-shaped strains, designated SJ11T and HCMS5-2 T, were isolated from soil in South Korea. The growth of strain SJ11T was observed from 15â to 35â (optimum, 30â), from pH 6.0 to 11.0 (optimum, pH 6.0-7.0) and with NaCl 0-1% (w/v) (optimum, 0%) and that of strain HCMS5-2 T was observed from 4â to 40â (optimum, 25â), from pH 6.0 to pH 8.0 (optimum, pH 7.0) and with NaCl 0-5% (w/v) (optimum, 0-1%). Phylogenetic analysis based on 16S rRNA gene sequences showed that both strains belonged to the genus Pedobacter. Strain SJ11T had the highest 16S rRNA similarities with Pedobacter jejuensis THG-DR3T (98.5%) and strain HCMS5-2 T had the highest similarities with Pedobacter nototheniae 36B243T (98.7%). The digital DNA-DNA hybridization value of strain SJ11T with Pedobacter jejuensis THG-DR3T was 23.6%, with an average nucleotide identity value of 79.6%, and that of strain HCMS5-2 T with Pedobacter nototheniae 36B243T was 26.4%, with an average nucleotide identity value of 83.1%. The predominant cellular fatty acids (> 10%) of SJ11T and HCMS5-2 T were iso-C15:0, summed feature 3 (comprising C16:1ω7c and/or C16:1ω6c) and iso-C17:0 3-OH. The genome size of strain SJ11T was approximately 4.7 Mb with a G + C content of 37.7% and that of strain HCMS5-2 T was approximately 4.1 Mb with a G + C content of 36.4%. The major polar lipid and respiratory quinone of SJ11T and HCMS5-2 T were phosphatidylethanolamine and menaquinone NK-7, respectively. Results of this study showed that strains SJ11T and HCMS5-2 T belonged to the genus Pedobacter as novel species, of which the name Pedobacter rhodius sp. nov., with the type strain SJ11T (= KACC 22884 T = TBRC 16597 T) and Pedobacter punctiformis sp. nov., with the type strain HCMS5-2 T (= KACC 22863 T = TBRC 16598 T) were respectively proposed.
Assuntos
Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano , Ácidos Graxos , Hibridização de Ácido Nucleico , Pedobacter , Filogenia , RNA Ribossômico 16S , Microbiologia do Solo , Pedobacter/genética , Pedobacter/classificação , Pedobacter/isolamento & purificação , Pedobacter/fisiologia , RNA Ribossômico 16S/genética , DNA Bacteriano/genética , Ácidos Graxos/metabolismo , Ácidos Graxos/análise , República da Coreia , Análise de Sequência de DNA , Fosfolipídeos/análiseRESUMO
The extracellular polysaccharide (EPS) matrix embedding microbial cells and soil particles plays an important role in the development of biological soil crusts (BSCs), which is widely recognized as beneficial to soil fertility in dryland worldwide. This study examined the EPS-producing bacterial strains YL24-1 and YL24-3 isolated from sandy soil in the Mu Us Desert in Yulin, Shaanxi province, China. The strains YL24-1 and YL24-3 were able to efficiently produce EPS; the levels of EPS were determined to be 257.22 µg/mL and 83.41 µg/mL in cultures grown for 72 h and were identified as Sinorhizobium meliloti and Pedobacter sp., respectively. When the strain YL24-3 was compared to Pedobacter yulinensis YL28-9T using 16S rRNA gene sequencing, the resemblance was 98.6% and the strain was classified as Pedobacter sp. using physiological and biochemical analysis. Furthermore, strain YL24-3 was also identified as a subspecies of Pedobacter yulinensis YL28-9T on the basis of DNA-DNA hybridization and polar lipid analysis compared with YL28-9T. On the basis of the EPS-related genes of relevant strains in the GenBank, several EPS-related genes were cloned and sequenced in the strain YL24-1, including those potentially involved in EPS synthesis, assembly, transport, and secretion. Given the differences of the strains in EPS production, it is possible that the differences in gene sequences result in variations in the enzyme/protein activities for EPS biosynthesis, assembly, transport, and secretion. The results provide preliminary evidence of various contributions of bacterial strains to the formation of EPS matrix in the Mu Us Desert.
Assuntos
Matriz Extracelular de Substâncias Poliméricas/química , Pedobacter/isolamento & purificação , Pedobacter/fisiologia , Sinorhizobium meliloti/isolamento & purificação , Sinorhizobium meliloti/fisiologia , Técnicas de Tipagem Bacteriana , China , DNA Bacteriano/genética , Clima Desértico , Matriz Extracelular de Substâncias Poliméricas/genética , Matriz Extracelular de Substâncias Poliméricas/metabolismo , Espaço Extracelular/química , Ácidos Graxos/análise , Metais Pesados/farmacologia , Hibridização de Ácido Nucleico , Pedobacter/citologia , Pedobacter/efeitos dos fármacos , Filogenia , RNA Ribossômico 16S/genética , Sinorhizobium meliloti/citologia , Sinorhizobium meliloti/efeitos dos fármacos , Microbiologia do SoloRESUMO
An aerobic, Gram-stain-negative, weak-motile, short-rod-shaped bacterial strain, designated JBR3-12T, was isolated from halophyte Carex pumila plants, and its taxonomic position was investigated by using a polyphasic taxonomic approach. The strain produced a pink pigment on tryptic soy agar and grew optimally at 25 °C, pH 8 and in the presence of 3â% (w/v) NaCl. Results of phylogenetic analysis based on 16S rRNA gene sequences showed that strain JBR3-12T formed a lineage within the genus Pedobacter and was most closely related to Pedobacter sandarakinus DS-27T (98.0â%) and Pedobacter agri PB92T (97.6â%). The DNA G+C content of the genome was 41.3 mol%; the whole genome length was 5â426â070 bp. The major fatty acids of JBR3-12T were iso-C15â:â0, summed feature 3 (comprising C16â:â1 ω6c and/or C16â:â1 ω7c) and iso-C17â:â0 3-OH. The predominant polar lipid was phosphatidylethanolamine. The predominant quinone was menaquinone-7. Based on its phenotypic, phylogenetic and genotypic features, strain JBR3-12T is proposed to represent a novel species of the genus Pedobacter, for which the name is Pedobacter endophyticus sp. nov. The type strain is JBR3-12T (=KCTC 82363T=NBRC 114901T).
Assuntos
Carex (Planta)/microbiologia , Pedobacter/classificação , Filogenia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Pedobacter/isolamento & purificação , Fosfatidiletanolaminas/química , Pigmentação , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Microbiologia do Solo , Vitamina K 2/análogos & derivados , Vitamina K 2/químicaRESUMO
Dead fungal biomass is an abundant source of nutrition in both litter and soil of temperate forests largely decomposed by bacteria. Here, we have examined the utilization of dead fungal biomass by the five dominant bacteria isolated from the in situ decomposition of fungal mycelia using a multiOMIC approach. The genomes of the isolates encoded a broad suite of carbohydrate-active enzymes, peptidases and transporters. In the extracellular proteome, only Ewingella americana expressed chitinases while the two Pseudomonas isolates attacked chitin by lytic chitin monooxygenase, deacetylation and deamination. Variovorax sp. expressed enzymes acting on the side-chains of various glucans and the chitin backbone. Surprisingly, despite its genomic potential, Pedobacter sp. did not produce extracellular proteins to decompose fungal mycelia but presumably feeds on simple substrates. The ecological roles of the five individual strains exhibited complementary features for a fast and efficient decomposition of dead fungal biomass by the entire bacterial community.
Assuntos
Comamonadaceae/metabolismo , Enterobacteriaceae/metabolismo , Fungos/metabolismo , Pseudomonas/metabolismo , Actinobacteria/genética , Actinobacteria/isolamento & purificação , Actinobacteria/metabolismo , Biomassa , Quitina/metabolismo , Comamonadaceae/genética , Comamonadaceae/isolamento & purificação , Enterobacteriaceae/genética , Enterobacteriaceae/isolamento & purificação , Florestas , Genoma Bacteriano/genética , Micélio/metabolismo , Pedobacter/genética , Pedobacter/isolamento & purificação , Pedobacter/metabolismo , Proteobactérias/genética , Proteobactérias/isolamento & purificação , Proteobactérias/metabolismo , Proteômica , Pseudomonas/genética , Pseudomonas/isolamento & purificação , RNA Ribossômico 16S/genética , Solo/química , Microbiologia do SoloRESUMO
Fifteen isolates of the genus Pedobacter were obtained from Arctic soil samples. All isolates were Gram-stain-negative and rod-shaped. Cells were strictly aerobic, psychrotolerant and grew optimally at 15-20 °C. Phylogenetic analysis based on 16S rRNA gene sequences revealed that all the isolated strains formed a lineage within the family Sphingobacteriaceae and clustered as members of the genus Pedobacter. The sole respiratory quinone was MK-7 and the major polar lipid was phosphatidylethanolamine. The major cellular fatty acids were summed feature 3 (iso-C15 : 02-OH/C16 : 1ω7c/ω6c), iso-C15 : 0 and iso-C17 : 0 3-OH. The DNA G+C content of the novel strains was 33.9-41.8 mol%. In addition, the average nucleotide identity and in silico DNA-DNA hybridization relatedness values between the novel type strains and phylogenetically related type strains were below the threshold values used for species delineation. Based on genomic, chemotaxonomic, phenotypic, phylogenetic and phylogenomic analyses, the isolated strains represent novel species in the genus Pedobacter, for which the names Pedobacter cryotolerans sp. nov. (type strain AR-2-6T=KEMB 9005-717T=KACC 19998T=NBRC 113826T), Pedobacter cryophilus sp. nov. (type strain AR-3-17T=KEMB 9005-718T=KACC 19999T=NBRC 113827T), Pedobacter frigiditerrae sp. nov. (type strain RP-1-13T=KEMB 9005-720T=KACC 21147T=NBRC 113829T), Pedobacter psychroterrae sp. nov. (type strain RP-1-14T=KEMB 9005-721T=KACC 21148T=NBRC 113830T), Pedobacter hiemivivus sp. nov. (type strain RP-3-8T=KEMB 9005-724T=KACC 21152T=NBRC 113833T), Pedobacter frigidisoli sp. nov. (type strain RP-3-11T=KEMB 9005-725T=KACC 21153T=NBRC 113927T), Pedobacter frigoris sp. nov. (type strain RP-3-15T=KEMB 9005-726T=KACC 21154T=NBRC 113834T), Pedobacter psychrodurus sp. nov. (type strain RP-3-21T=KEMB 9005-728T=KACC 21156T=NBRC 113835T) and Pedobacter polaris sp. nov. (type strain RP-3-22T=KEMB 9005-729T=KACC 21157T=NBRC 113836T) are proposed.
Assuntos
Antioxidantes/análise , Pedobacter/classificação , Filogenia , Microbiologia do Solo , Regiões Árticas , Técnicas de Tipagem Bacteriana , Composição de Bases , Canadá , DNA Bacteriano/genética , Ácidos Graxos/química , Pedobacter/isolamento & purificação , Fosfatidiletanolaminas/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Svalbard , Vitamina K 2/análogos & derivados , Vitamina K 2/químicaRESUMO
A Gram-stain negative, aerobic, non-flagellated, rod-shaped bacterium, designated strain SM1810T, was isolated from deep-sea sediment collected from the Southwest Indian Ocean. Strain SM1810T grows at 15-40 °C (optimum, 28 °C), at pH 5.0-9.0 (optimum, pH 6.0-7.0) and with 0-8% (w/v) NaCl (optimum, 1.5%). Phylogenetic analysis of 16S rRNA gene sequences revealed that strain SM1810T is affiliated with the genus Pedobacter, sharing high sequence similarity (95.8%) with the type strain of Pedobacter bauzanensis. The major fatty acids of strain SM1810T are iso-C15:0, summed feature 3 (C16:1ω7c and/or C16:1ω6c) and iso-C17:0 3OH. The predominant respiratory quinone is MK-7. The polar lipids are phosphatidylethanolamine, an unidentified aminophospholipid, an unidentified phospholipid and eight unidentified lipids. The genomic DNA G + C content of strain SM1810T was determined to be 40.8 mol%. Based on the phylogenetic, chemotaxonomic and phenotypic data obtained in this study, strain SM1810T is concluded to represent a novel species of the genus Pedobacter, for which the name Pedobacter indicus sp. nov. is proposed. The type strain is SM1810T (KCTC 62798T = CCTCC AB 2018198T).
Assuntos
Organismos Aquáticos , Sedimentos Geológicos/microbiologia , Pedobacter/isolamento & purificação , DNA Bacteriano , Genoma Bacteriano , Genômica/métodos , Pedobacter/classificação , Pedobacter/genética , Fenótipo , Filogenia , RNA Ribossômico 16S/genéticaRESUMO
A strictly aerobic, Gram-stain-negative, rod-shaped, yellow, non-spore-forming bacterial strain, designated P-25T, was isolated from soil collected in Yantai, Shandong Province, PR China. The temperature, pH and NaCl concentration ranges for the growth of strain P-25T were 10-37 °C (optimum, 28-30 °C), pH 6.0-9.0 (optimum, pH 7.5-8.0) and 0-4â% (w/v) (optimum, 1â% w/v), respectively. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain P-25T was most closely related to Pedobacter xixiisoli S27T (98.1â% 16S rRNA gene sequence similarity), followed by Pedobacter chitinilyticus CM134L-2T (97.2â%) and Pedobacter ureilyticus THG-T11T (97.1â%). The genomic DNA G+C content of strain P-25T based on its draft genome sequence was 38.1â%. MK-7 was the major respiratory quinone, and iso-C15â:â0, C16â:â1ω7c and/or C16â:â1ω6c (summed feature 3) and iso-C17â:â0 3-OH were the major fatty acids. The major polar lipids were phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified phospholipid, two unidentified lipids, five unidentified aminolipids and two unidentified glycolipids. Average nucleotide identity values for the draft genomes between strain P-25T and strains S27T, CM134L-2T and THG-T11T were 81.8, 77.6 and 81.2â%, respectively, and the digital DNA-DNA hybridization (dDDH) values were 30.0, 19.2 and 27.6â%, respectively. Based on their phylogenetic and phenotypic characteristics, chemotaxonomic data, and dDDH results, strain P-25T is considered to represent a novel species of the genus Pedobacter, for which the name Pedobacter helvus sp. nov. is proposed; the type strain is strain P-25T (KCTC 62821T=CCTCC AB 2018185T).
Assuntos
Fazendas , Pedobacter/classificação , Filogenia , Microbiologia do Solo , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Glicolipídeos/química , Hibridização de Ácido Nucleico , Pedobacter/isolamento & purificação , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/químicaRESUMO
A Gram-negative, aerobic, non-motile, pink and rod-shaped bacterium, designated E01020T, was isolated from soil collected from the Chinese Great Wall Station, Antarctica. Comparative analysis of 16S rRNA gene sequences revealed that strain E01020T is a member of the genus Pedobacter, related to Pedobacter alluvionis DSM 19624T (96.8% similarity), Pedobacter agri JCM 15120T (96.5% similarity) and Pedobacter chinensis JDX94T (96.3% similarity). The dDDH values and ANI values of strain E01020T with closely related strains indicate that it can be distinguished from them as a novel species. The DNA G+C content was determined to be 35.2 mol%. The growth of strain E01020T was observed at 4-25 °C (optimal 20 °C), in the presence of 0-1% NaCl (w/v, optimal 0%) and at pH 6.0-8.0 (optimal pH 7.0). Strain E01020T was found to contained menaquinon-7 (MK-7) as only respiratory quinone, iso-C15:0, iso-C17:0 3-OH and Summed feature 3 (C16:1ω6c and/or C16:1ω7c) as major fatty acids. The major polar lipids were phosphatidylethanolamine, one unidentified lipid and two unidentified aminolipids. On the basis of the results of the phylogenetic and phenotypic analyses, it was suggested that strain E01020T represents a novel species of the genus Pedobacter, for which the name Pedobacter changchengzhani sp. nov. is proposed. The type strain is E01020T (= KCTC 62990T = MCCC 1H00357T).
Assuntos
Técnicas de Tipagem Bacteriana , Pedobacter/classificação , Pedobacter/isolamento & purificação , Filogenia , Microbiologia do Solo , Aerobiose , Regiões Antárticas , 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 , Pedobacter/genética , Pedobacter/fisiologia , Quinonas/análise , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Cloreto de Sódio/metabolismo , TemperaturaRESUMO
A novel bacterial strain, JDX94T, was isolated from tundra soil sampled north of the Yellow River station, Arctic. Cells were Gram-stain-negative, non-spore-forming, short rod-shaped and aerobic. The strain displayed growth at 4-37 °C with an optimum at 28 °C, with 0-1.0â% (w/v) NaCl (optimum, 0%) and at pH 6.0-9.0 (optimum, pH 7.0-7.5). Cells contained summed feature 3 (comprising C16â:â1ω7c and/or C16â:â1ω6c), iso-C15â:â0 and iso-C17â:â0 3-OH as its major cellular fatty acids and menaquinone-7 as the only respiratory quinone. The polar lipid profile of strain JDX94T consisted of phosphatidylethanolamine, two unidentified aminolipids and four unknown polar lipids. The DNA G+C content was 37.5 mol%. On the basis 16S rRNA gene sequence comparison, strain JDX94T showed the highest sequence similarity (96.7â%) to Pedobacteragri JCM 15120T, followed by Pedobacteralluvionis DSM 19624T (96.3â%). Furthermore, the average nucleotide identity and digital DNA-DNA hybridization values between strain JDX94T and related species of the genus Pedobacter were 74.6-79.2â% and 18.9-24.5â%, respectively. Based on the presented results, we propose a novel species for which the name Pedobacterchinensis sp. nov. is suggested, with the type strain JDX94T (=MCCC 1H00335T= KCTC 62850T).
Assuntos
Celulose/metabolismo , Pedobacter/classificação , Filogenia , Microbiologia do Solo , Tundra , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Pedobacter/isolamento & purificação , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Svalbard , Vitamina K 2/análogos & derivados , Vitamina K 2/químicaRESUMO
A pink pigmented, Gram-negative, rod-shaped, non-spore-forming bacterium (strain 36B243T), was isolated from the spleen of a black rock cod (Notothenia coriiceps, Richardson 1844) in the Chilean Antarctica. Strain 36B243T has a 5.26 Mb chromosome with a DNA G + C content of 35.4 mol%. The draft genome includes the prediction and annotation of 4585 coding genes, and 46 tRNA, 1 tmRNA, and 2735 hypothetical proteins. Phylogenetic analysis based on the 16S rRNA gene sequence placed strain 36B243T into the genus Pedobacter with high sequence similarity to the type strains of Pedobacter sandarakinus (97.5%) and Pedobacter petrophilus (97.1%). Sequence similarities to type strains of all other current Pedobacter species were below 97.1%. Predominant fatty acids are summed feature 3 (C16:1ω7c and/or C16:1ω6c) and iso-C15:0 followed by iso-C17:0 3-OH and C16:0. The major respiratory quinone was menaquinone MK-7. The polar lipid profile contained the major lipids phosphatidylethanolamine, five unidentified aminolipids, two lipids lacking a functional group and two minor glycolipids and one lipid lacking a functional group. An alkali-stable lipid was present. The polyamine pattern contained the predominant compound sym-homospermidine. Characterization by 16S rRNA gene sequence analysis, physiological parameters, pigment analysis, ubiquinone, polar lipid, and fatty acid composition revealed that strain 36B243T represents a new species of the genus Pedobacter. For this reason, we propose the name Pedobacter nototheniae sp. nov. with the type strain 36B243T (= LMG 30634T = CCM 8855T = CIP 111622T).
Assuntos
Pedobacter/classificação , Pedobacter/isolamento & purificação , Perciformes/microbiologia , Baço/microbiologia , Animais , Regiões Antárticas , Técnicas de Tipagem Bacteriana , Composição de Bases , Chile , Análise por Conglomerados , Citosol/química , DNA Bacteriano/química , DNA Bacteriano/genética , DNA Ribossômico/química , DNA Ribossômico/genética , Ácidos Graxos/análise , Genoma Bacteriano , Glicolipídeos/análise , Pedobacter/genética , Pedobacter/fisiologia , Fosfolipídeos/análise , Filogenia , Pigmentos Biológicos/metabolismo , Quinonas/análise , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análiseRESUMO
A Gram-stain negative, strictly aerobic, non-spore forming, non-motile, rod-shaped bacterium, designated TBBPA-24T, was isolated from tetrabromobisphenol A-contaminated soil in China. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain TBBPA-24T was most closely related to Pedobacter nanyangensis Q4T (96.5%) and Pedobacter 'zeaxanthinifaciens' TDMA-5T (96.1%). Chemotaxonomic analysis revealed that strain TBBPA-24T possessed MK-7 as the major respiratory quinone and lipid, aminolipid, phospholipid, phosphatidylethanolamine, and phosphoaminolipid as the major polar lipid. The major fatty acids were iso-C15:0 (40.2%), summed feature 3 (C16:1ω6c and/or C16:1ω7c, 25.6%) and iso-C17:0 3-OH (16.4%). The genomic DNA G+C content of strain TBBPA-24T was 43.9 mol%. Based on the phylogenetic, phenotypic characteristics, and chemotaxonomic data, strain TBBPA-24T is considered a novel species of the genus Pedobacter, for which the name Pedobacter pollutisoli sp. nov. is proposed. The type strain TBBPA-24T (= KCTC 62314T = CCTCC AB 2017244T) is proposed.
Assuntos
Pedobacter/classificação , Pedobacter/fisiologia , Filogenia , Bifenil Polibromatos/química , Microbiologia do Solo , Poluentes do Solo/química , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Pedobacter/química , Pedobacter/isolamento & purificação , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Solo/química , Especificidade da Espécie , Vitamina K 2/análogos & derivados , Vitamina K 2/químicaRESUMO
A Gram-stain-negative, aerobic, non-motile, rod-shaped and non-spore-forming bacterium, designated YXT, was isolated from wetland soil. Compared to strain YXT, Pedobacter yonginense HMD1002T had the highest 16S rRNA gene sequence identity (97.8%), and the remaining strains had the identities below 97%. Phylogenetic analysis of the 16S rRNA gene sequences showed that strain YXT grouped with P. yonginense HMD1002T. The values of DNA-DNA hybridization and genomic orthologous average nucleotide identity (orthoANI) between strain YXT and Pedobacter yonginense KCTC 22721T were 58.5% and 82.0%, respectively. The genome size of strain YXT was 5.0 Mb, comprising 4369 predicted genes with a DNA G+C content of 37.3 mol %. Strain YXT had menaquinone-7 as the only respiratory quinone and polar lipids of phosphatidylethanolamine, sphingolipid, aminolipid and three unidentified lipids. The predominant cellular fatty acids (> 10%) of strain YXT were summed feature 3 (iso-C15:0 2-OH and/or C16:1ω7c), iso-C15:0 and iso-C17:0 3-OH. Strain YXT could be distinguished from the other Pedobacter members based on the data of phylogenetic distance, DNA-DNA hybridization, genomic orthoANI, RecA MLSA, core-protein comparison, and hydrolyses of L-arginine, utilization of D/L-lactate, L-alanine, 5-ketonic gluconate and glycogen. Therefore, strain YXT represents a novel species of the genus Pedobacter, for which the name Pedobacter paludis sp. nov. is proposed. The type strain is YXT (= KCTC 62520T = CCTCC AB 2018029T).
Assuntos
Pedobacter , Microbiologia do Solo , Técnicas de Tipagem Bacteriana , Composição de Bases/genética , DNA Bacteriano/genética , Ácidos Graxos/análise , Hibridização de Ácido Nucleico/genética , Pedobacter/classificação , Pedobacter/genética , Pedobacter/isolamento & purificação , Fosfatidiletanolaminas/metabolismo , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Solo , Vitamina K 2/análogos & derivados , Vitamina K 2/metabolismo , Áreas AlagadasRESUMO
In a survey of endophytic bacteria in Miscanthus sinensis, a strain of Gram-negative, non-endospore-forming, rod-shaped, aerobic bacterium was isolated and designated as RS10T. Phylogenetic analysis based on its 16S rRNA gene sequence showed that the strain RS10T was affiliated with the genus Pedobacter and exhibited the highest sequence similarities to Pedobacter kyungheensis KACC 16221T (97.78â%), Pedobacter roseus KCTC 22187T (97.75â%), Pedobacter humicola KACC 18452T (97.29â%) and Pedobacter soli KACC 14939T (97.23â%). The novel strain contained iso-C15â:â0, iso-C17â:â0-3OH and summed feature 3 (C16â:â1ω7c and/or C16â:â1ω6c) as major fatty acids. The only isoprenoid quinone detected in strain RS10T was MK-7. Strain RS10T contains phosphatidylethanolamine and one kind of aminophospholipid as its major polar lipids. The DNA G+C content for RS10T was 39.8 mol%. Based on the results of phenotypic and genomic characterizations, we concluded that strains RS10T represents a novel species of Pedobacter, for which the name Pedobacter miscanthi sp. nov. is proposed. The type strain is RS10T (=KCTC 62786T=GDMCC 1.1415T).
Assuntos
Pedobacter/classificação , Filogenia , Poaceae/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Pedobacter/isolamento & purificação , Fosfolipídeos/química , Caules de Planta/microbiologia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/químicaRESUMO
A bacterium, designated strain CM134L-2T, was isolated from a chitin-enriched wheat leaf microbiome in Chengdu, Sichuan province, China. It was Gram-stain-negative, strictly aerobic, non-spore-forming, motile, rod-shaped, and bright yellow in colour. Strain CM134L-2T grew at 4-35 °C, at pH 6.0-9.0 and could use chitin as the only carbon resource. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CM134L-2T was most closely related to Pedobacter nanyangensis Q-4T (97.7â%) and Pedobacter zeaxanthinifaciens TDMA-5T (97.4â%). Digital DNA-DNA hybridization (dDDH) values between strain CM134L-2T with these two type strains were 26.8â and 20.8â%, respectively, and average nucleotide identity (ANI) values were 83.2 and 76.2â%; these values are lower than the proposed and generally accepted species boundaries of 70â% for dDDH and 95-96â% for ANI, which suggests strain CM134L-2T represents a novel species. The genomic DNA G+C content of strain CM134L-2T was 39.3 mol%, menaquinone-7 was the major respiratory quinone, phosphatidylethanolamine was the major polar lipid and the major components of the cellular fatty acids were iso-C15â:â0, and C16â:â1ω7c/C16â:â1ω6c (summed feature 3); these features supported the affiliation of strain CM134L-2T to the genus Pedobacter. Overall, strain CM134L-2T belongs to the genus Pedobacter, but can be classified as a novel species, for which the name Pedobacter chitinilyticus sp. nov. is proposed. The type strain is CM134L-2T (=CGMCC 1.16520T=KCTC 62643T).
Assuntos
Pedobacter/classificação , Filogenia , Triticum/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , China , Quitina/metabolismo , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Pedobacter/genética , Pedobacter/isolamento & purificação , Fosfatidiletanolaminas/química , Pigmentação , Folhas de Planta/microbiologia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/químicaRESUMO
A non-motile, pink-pigmented bacterial strain designated IMCC25679T, was isolated from freshwater Lake Chungju of Korea. Phylogenetic trees based on 16S rRNA gene sequences showed that the strain IMCC25679T formed a lineage within the genus Pedobacter. The strain IMCC25679T was closely related to Pedobacter daechungensis Dae 13T (96.4% sequence similarity), Pedobacter rivuli HME8457T (95.3%) and Pedobacter lentus DS-40T (94.3%). The major fatty acids of IMCC- 25679T were iso-C15:0, iso-C16:0 and summed feature 3 (comprising C16:1ω6c and/or C16:1ω7c). The major respiratory quinone was MK-7. The major polar lipids were phosphatidylethanolamine (PE), an unidentified sphingolipid (SL), an unidentified aminolipid (AL) and three unidentified polar lipids (PL). The DNA G + C content of IMCC25679T was 32.2 mol%. Based on the evidence presented in this study, the strain IMCC25679T represents a novel species within the genus Pedobacter, with the proposed name Pedobacter aquicola, sp. nov. The type strain is IMCC25679T (= KACC 19486T = NBRC113131T).
Assuntos
Água Doce/microbiologia , Pedobacter/genética , Pedobacter/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/análise , Lagos , Pedobacter/química , Pedobacter/classificação , Fosfatidiletanolaminas , Filogenia , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Esfingolipídeos/análise , Vitamina K 2/análiseRESUMO
A Gram-staining-negative, rod-shaped, strictly aerobic, non-motile, non-spore-forming, orange bacterium, which was designated strain YL28-9T, was isolated from sandy soil in the district of Yulin, Shaanxi province, PR China, and was characterized by using a polyphasic taxonomic approach. The optimal growth conditions of the strain were 30 °C, pH 7.0, 0â% (w/v) NaCl. Phylogenetic analysis, based on the 16S rRNA gene sequence, revealed that YL28-9T represented a member of the genus Pedobacter and showed the highest sequence similarity to Pedobacter rhizosphaeraeKACC 14938T (95.1â%). The genomic DNA G+C content of this strain was 50.4 mol%, which was out of the range reported for the other strains of members of the genus Pedobacter. The only respiratory quinone detected in YL28-9T was menaquinone-7 (MK-7). The predominant cellular fatty acids were identified as iso-C15â:â0, summed feature 3 (C16â:â1ω7c and/or C16â:â1ω6c) and iso-C17â:â0 3-OH. The major polar lipid was phosphatidylethanolamine. On the basis of the results of phenotypic, genotypic, chemotaxonomic and phylogenetic analysis, YL28-9T could be distinguished from the most closely related species of the genus Pedobacter. It is evident from the derived data that YL28-9T represents a novel species of the genus Pedobacter,for which the name Pedobacter yulinensis sp. nov. is proposed. The type strain is YL28-9T (=CGMCC 1.16050T=KCTC 62104T). An emended description of the genus Pedobacteris proposed.
Assuntos
Pedobacter/classificação , Filogenia , Microbiologia do Solo , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Pedobacter/genética , Pedobacter/isolamento & purificação , Fosfatidiletanolaminas/química , Pigmentação , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/químicaRESUMO
A Gram-stain-negative, aerobic, non-motile, non-spore-forming and rod-shaped bacterium, designated YHM-9T, was isolated from soil in Yangquan, Shanxi Province, PR China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YHM-9T belonged to the genus Pedobacter and shared the highest similarity (97.4â%) to the type strain Pedobacter lignilitoris W-WS13T. Strain YHM-9T exhibited low DNA-DNA relatedness with P. lignilitoris W-WS13T (21.7±1.3â%). The DNA G+C content was 38.9 mol%. The major fatty acids were iso-C15â:â0, summed feature 3 (C16â:â1ω7c and/or C16â:â1ω6c) and iso-C17â:â0 3-OH. The respiratory quinone was MK-7, the major polyamine was sym-homospermidine and the major polar lipids were phosphatidylethanolamine. Based on the morphological, physiological, biochemical and chemotaxonomic characteristics, strain YHM-9T was recognized as a representative of a novel species within the genus Pedobacter, for which the name Pedobacteragrisoli sp. nov. is proposed. The type strain is YHM-9T (=JCM 32093T=CCTCC AB 2017125T).