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International Journal of Systematic and... Jan 2009Strain 78-123T was isolated from a sample of a bird's nest situated on the bank of Qiongtailan River in the region of Tuomuer Peak of Tianshan Mountain in the Xin-jiang...
Strain 78-123T was isolated from a sample of a bird's nest situated on the bank of Qiongtailan River in the region of Tuomuer Peak of Tianshan Mountain in the Xin-jiang Uygur Autonomous Region in north-western China. Phylogenetic analysis based on 16S rRNA gene sequence similarity showed that strain 78-123T was related to members of the genus Pseudomonas. 16S rRNA gene sequence similarity between strain 78-123T and Pseudomonas mendocina ATCC 25411T, Pseudomonas pseudoalcaligenes JCM 5968T and Pseudomonas alcaliphila AL15-21T was 97.1, 97.4 and 97.5 %, respectively. The major cellular fatty acids were C(16 : 0), C(16 : 1)omega7c and/or iso-C(15 : 0) 2-OH, C(18 : 1)omega7c and C(12 : 0). The G+C content was 60.4 mol%. On the basis of the phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness data, the novel species Pseudomonas tuomuerensis sp. nov. is proposed, with the type strain 78-123T (=CGMCC 1.1365T =JCM 14085T).
Topics: Animals; Bacterial Typing Techniques; Base Composition; Birds; China; DNA, Bacterial; DNA, Ribosomal; Fatty Acids; Genes, rRNA; Housing, Animal; Nucleic Acid Hybridization; Phenotype; Phylogeny; Pseudomonas; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Species Specificity
PubMed: 19126738
DOI: 10.1099/ijs.0.000547-0 -
Archives of Microbiology Oct 2012A Gram-negative, non-mobile, polar single flagellum, rod-shaped bacterium WZBFD3-5A2(T) was isolated from a wheat soil subjected to herbicides for several years. Cells...
A Gram-negative, non-mobile, polar single flagellum, rod-shaped bacterium WZBFD3-5A2(T) was isolated from a wheat soil subjected to herbicides for several years. Cells of strain WZBFD3-5A2(T) grow optimally on Luria-Bertani agar medium at 30 °C in the presence of 0-4.0 % (w/v) NaCl and pH 8.0. 16S rRNA gene sequence analysis revealed that strain WZBFD3-5A2(T) belongs to the genus Pseudomonas. Physiological and biochemical tests supported the phylogenetic affiliation. Strain WZBFD3-5A2(T) is closely related to Pseudomonas nitroreducens IAM1439(T), sharing 99.7 % sequence similarity. DNA-DNA hybridization experiments between the two strains showed only moderate reassociation similarity (33.92 ± 1.0 %). The DNA G+C content is 62.0 mol%. The predominant respiratory quinine is Q-9. The major cellular fatty acids present are C(16:0) (28.55 %), C(16:1ω6c) or C(16:1ω7c) (20.94 %), C(18:1ω7c) (17.21 %) and C(18:0) (13.73 %). The isolate is distinguishable from other related members of the genus Pseudomonas on the basis of phenotypic and biochemical characteristics. From the genotypic, chemotaxonomic and phenotypic data, it is evident that strain WZBFD3-5A2(T) represents a novel species of the genus Pseudomonas, for which the name Pseudomonas nitritereducens sp. nov. is proposed. The type strain is WZBFD3-5A2(T) (=CGMCC 1.10702(T) = LMG 25966(T)).
Topics: Base Composition; Microscopy, Electron, Transmission; Molecular Sequence Data; Phylogeny; Pseudomonas; RNA, Ribosomal, 16S; Soil Microbiology; Species Specificity; Triticum
PubMed: 22918457
DOI: 10.1007/s00203-012-0838-6 -
Current Microbiology Nov 2012A strain of genus Pseudomonas, LYBRD3-7(T) was isolated from long-term sulfonylurea herbicides applied wheat-field soil in Linying located in Henan province of China....
A strain of genus Pseudomonas, LYBRD3-7(T) was isolated from long-term sulfonylurea herbicides applied wheat-field soil in Linying located in Henan province of China. This strain is a strictly aerobic and Gram-negative short rod-shaped bacterium with single flagellum. Phylogenetic evaluation based on 16S rRNA gene sequence analysis placed this isolate as a member of Pseudomonas, and most closely to Pseudomonas tuomuerensis CGMCC 1.1365(T) (97.1 %) and P. alcaligenes IAM12411(T) (97.1 %). Morphological characters and chemotaxonomic data confirmed the affiliation of strain LYBRD3-7(T) to the genus Pseudomonas. The results of phylogenetic analysis, physiological and biochemical studies, and DNA-DNA hybridization allowed the differentiation of genotype and phenotype between strain LYBRD3-7(T) and the phylogenetic closest species with valid names. The name proposed for the new species is Pseudomonas linyingensis sp. nov. The type strain is LYBRD3-7(T) (=CGMCC 1.10701(T ) =LMG 25967(T)).
Topics: China; Herbicides; Molecular Sequence Data; Phylogeny; Pseudomonas; Soil Microbiology; Soil Pollutants; Triticum
PubMed: 22878554
DOI: 10.1007/s00284-012-0187-3 -
Applied and Environmental Microbiology Jan 2016The Pseudomonas genus contains a metabolically versatile group of organisms that are known to occupy numerous ecological niches, including the rhizosphere and endosphere...
The Pseudomonas genus contains a metabolically versatile group of organisms that are known to occupy numerous ecological niches, including the rhizosphere and endosphere of many plants. Their diversity influences the phylogenetic diversity and heterogeneity of these communities. On the basis of average amino acid identity, comparative genome analysis of >1,000 Pseudomonas genomes, including 21 Pseudomonas strains isolated from the roots of native Populus deltoides (eastern cottonwood) trees resulted in consistent and robust genomic clusters with phylogenetic homogeneity. All Pseudomonas aeruginosa genomes clustered together, and these were clearly distinct from other Pseudomonas species groups on the basis of pangenome and core genome analyses. In contrast, the genomes of Pseudomonas fluorescens were organized into 20 distinct genomic clusters, representing enormous diversity and heterogeneity. Most of our 21 Populus-associated isolates formed three distinct subgroups within the major P. fluorescens group, supported by pathway profile analysis, while two isolates were more closely related to Pseudomonas chlororaphis and Pseudomonas putida. Genes specific to Populus-associated subgroups were identified. Genes specific to subgroup 1 include several sensory systems that act in two-component signal transduction, a TonB-dependent receptor, and a phosphorelay sensor. Genes specific to subgroup 2 contain hypothetical genes, and genes specific to subgroup 3 were annotated with hydrolase activity. This study justifies the need to sequence multiple isolates, especially from P. fluorescens, which displays the most genetic variation, in order to study functional capabilities from a pangenomic perspective. This information will prove useful when choosing Pseudomonas strains for use to promote growth and increase disease resistance in plants.
Topics: Comparative Genomic Hybridization; Genetic Variation; Genome, Bacterial; Phylogeny; Plant Roots; Populus; Pseudomonas; Pseudomonas aeruginosa; Pseudomonas fluorescens; Pseudomonas putida; Rhizosphere; Sequence Analysis, DNA
PubMed: 26519390
DOI: 10.1128/AEM.02612-15 -
International Journal of Systematic and... Apr 2006A novel Pseudomonas species, for which the name Pseudomonas otitidis sp. nov. is proposed, was identified from clinical specimens of infected human ears. Forty-one...
A novel Pseudomonas species, for which the name Pseudomonas otitidis sp. nov. is proposed, was identified from clinical specimens of infected human ears. Forty-one pseudomonads (34 from patients with acute otitis externa, six from patients with acute otitis media with otorrhoea and one from a patient with chronic suppurative otitis media) were recovered that did not match any known species. On the basis of genetic analyses and biochemical characterization, these isolates were shown to belong to the genus Pseudomonas. 16S rRNA gene sequence analysis and DNA-DNA hybridization studies indicated that this novel bacterium is closely related to, but different from, Pseudomonas aeruginosa. A description of this species is based on polyphasic studies of 11 clinical isolates. The type strain of Pseudomonas otitidis is MCC10330T (=ATCC BAA-1130T = DSM 17224T).
Topics: DNA, Bacterial; Humans; Molecular Sequence Data; Otitis Media; Pseudomonas; RNA, Ribosomal, 16S
PubMed: 16585681
DOI: 10.1099/ijs.0.63753-0 -
Genome Biology and Evolution Dec 2019Many of the soil-dwelling Pseudomonas species are known to produce secondary metabolite compounds, which can have antagonistic activity against other microorganisms,...
Many of the soil-dwelling Pseudomonas species are known to produce secondary metabolite compounds, which can have antagonistic activity against other microorganisms, including important plant pathogens. It is thus of importance to isolate new strains of Pseudomonas and discover novel or rare gene clusters encoding bioactive products. In an effort to accomplish this, we have isolated a bioactive Pseudomonas strain DTU12.1 from leaf-covered soil in Denmark. Following genome sequencing with Illumina and Oxford Nanopore technologies, we generated a complete genome sequence with the length of 5,943,629 base pairs. The DTU12.1 strain contained a complete gene cluster for a rare thioquinolobactin siderophore, which was previously described as possessing bioactivity against oomycetes and several fungal species. We placed the DTU12.1 strain within Pseudomonas gessardii subgroup of fluorescent pseudomonads, where it formed a distinct clade with other Pseudomonas strains, most of which also contained a complete thioquinolobactin gene cluster. Only two other Pseudomonas strains were found to contain the gene cluster, though they were present in a different phylogenetic clade and were missing a transcriptional regulator of the whole cluster. We show that having the complete genome sequence and establishing phylogenetic relationships with other strains can enable us to start evaluating the distribution and evolutionary origins of secondary metabolite clusters.
Topics: Biosynthetic Pathways; Metabolomics; Phylogeny; Pseudomonas; Quinolines; Soil Microbiology; Whole Genome Sequencing
PubMed: 31800028
DOI: 10.1093/gbe/evz267 -
BioMed Research International 2015Very few studies have been conducted on alkaline adaptation of Gram-negative alkaliphiles. The reversed difference of H(+) concentration across the membrane will make... (Review)
Review
Very few studies have been conducted on alkaline adaptation of Gram-negative alkaliphiles. The reversed difference of H(+) concentration across the membrane will make energy production considerably difficult for Gram-negative as well as Gram-positive bacteria. Cells of the alkaliphilic Gram-negative bacterium Pseudomonas alcaliphila AL15-21(T) grown at pH 10 under low-aeration intensity have a soluble cytochrome c content that is 3.6-fold higher than that of the cells grown at pH 7 under high-aeration intensity. Cytochrome c-552 content was higher (64% in all soluble cytochromes c) than those of cytochrome c-554 and cytochrome c-551. In the cytochrome c-552-dificient mutant grown at pH 10 under low-aeration intensity showed a marked decrease in μ max [h(-1)] (40%) and maximum cell turbidity (25%) relative to those of the wild type. Considering the high electron-retaining abilities of the three soluble cytochromes c, the deteriorations in the growth of the cytochrome c-552-deficient mutant could be caused by the soluble cytochromes c acting as electron storages in the periplasmic space of the bacterium. These electron-retaining cytochromes c may play a role as electron and H(+) condenser, which facilitate terminal oxidation at high pH under air-limited conditions, which is difficult to respire owing to less oxygen and less H(+).
Topics: Adaptation, Physiological; Alkalies; Bacterial Proteins; Cytochrome c Group; Energy Metabolism; Hydrogen-Ion Concentration; Oxidation-Reduction; Pseudomonas
PubMed: 25705691
DOI: 10.1155/2015/847945 -
Journal of Agricultural and Food... Apr 2019In this study, we isolated and characterized the bacterial strain Pseudomonas sp. BYT-1, which is capable of degrading pymetrozine and using it as the sole carbon source...
In this study, we isolated and characterized the bacterial strain Pseudomonas sp. BYT-1, which is capable of degrading pymetrozine and using it as the sole carbon source for growth. Strain BYT-1 could degrade 2.30 mM pymetrozine within 20 h under the optimal conditions of 30 °C and pH 7.0. Investigation of the degradation pathway showed that pymetrozine was oxidatively hydrolyzed to 4-amino-6-methyl-4,5-dihydro-2 H-[1,2,4]triazin-3-one (AMDT) and nicotinic acid (NA). The former accumulates as the end product in the culture, whereas the latter was hydroxylated to 6-hydroxynicotinic acid (6HNA) and subjected to further degradation. The transformation of pymetrozine to AMDT and NA by the cell-free extracts of strain BYT-1 also supported that the oxidative hydrolysis of the C═N double bond in pymetrozine was the initial degradation step. This is the first report on a pure bacterial culture with the ability to degrade pymetrozine. These findings enhance our understanding of the microbial degradation mechanism of pymetrozine.
Topics: Biodegradation, Environmental; Niacin; Pseudomonas; Sewage; Triazines
PubMed: 30912660
DOI: 10.1021/acs.jafc.8b06155 -
Archives of Microbiology Dec 2013A Gram-staining-negative, rod-shaped and motile with several polar flagellums bacterium, designated WM-3(T), was isolated from a rice paddy soil in South China. Growth...
A Gram-staining-negative, rod-shaped and motile with several polar flagellums bacterium, designated WM-3(T), was isolated from a rice paddy soil in South China. Growth occurred with 0-3.0 % (w/v) NaCl (optimum 2.0 %), at pH 5.5-9.0 (optimum pH 7.0) and at 25-42 °C (optimum 30-37 °C) in liquid Reasoner's 2A medium. Analysis of the 16S rRNA gene and gyrB gene sequences revealed that strain WM-3(T) was most closely related to the type strains of the species Pseudomonas linyingensis and Pseudomonas sagittaria. Its sequence similarities with P. linyingensis CGMCC 1.10701(T) and P. sagittaria JCM 18195(T) were 97.4 and 97.3 %, respectively, for 16S rRNA gene, and were 94.1 and 94.2 %, respectively, for gyrB gene. DNA-DNA hybridization between strain WM-3(T) and these two type strains showed relatedness of 35.6 and 30.9 %, respectively. G+C content of genomic DNA was 69.4 mol%. The whole-cell fatty acids mainly consisted of C16:0 (30.0 %), C16:1 ω6c and/or C16:1 ω7c (19.3 %) and C18:1 ω6c and/or C18:1 ω7c (16.3 %). The results of phenotypic, chemotaxonomic and genotypic analyses clearly indicated that strain WM-3(T) belongs to genus Pseudomonas but represents a novel species, for which the name Pseudomonas oryzae sp. nov. is proposed. The type strain is WM-3(T) (=KCTC 32247(T) =CGMCC 1.12417(T)).
Topics: Bacterial Typing Techniques; Base Composition; China; DNA Gyrase; Fatty Acids; Molecular Sequence Data; Nucleic Acid Hybridization; Phylogeny; Pseudomonas; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil; Soil Microbiology; Species Specificity
PubMed: 24142159
DOI: 10.1007/s00203-013-0930-6 -
FEMS Microbiology Letters Sep 2018
Topics: Adaptation, Biological; Adaptation, Physiological; Congresses as Topic; Drug Resistance, Bacterial; Gene Expression Regulation, Bacterial; Host-Pathogen Interactions; Pseudomonas; Signal Transduction; Virulence Factors
PubMed: 30184124
DOI: 10.1093/femsle/fny159