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International Journal of Systematic and... Mar 2023Two bacterial strains, designated 5GH9-11 and 5GH9-34, were isolated from greenhouse soil sampled in Wanju-gun, Jeollabuk-do, Republic of Korea. Both strains formed...
Two bacterial strains, designated 5GH9-11 and 5GH9-34, were isolated from greenhouse soil sampled in Wanju-gun, Jeollabuk-do, Republic of Korea. Both strains formed yellow colonies and were aerobic, rod-shaped and flagellated. The 16S rRNA gene sequence similarity between 5GH9-11 and 5GH9-34 was 98.6 %. Strain 5GH9-11 showed the highest sequence similarities to ATSB10 (98.1 %) and DSM 6220 (97.7 %) while strain 5GH9-34 revealed the highest sequence similarity to DSM 6220 (98.3 %) and ATSB10 (98.3 %). Phylogenetic analysis on the basis of the 16S rRNA gene sequence showed that strains 5GH9-11 and 5GH9-34 formed a robust cluster with MAH-13 and NBRC 104236. The phylogenomic tree also showed that strains 5GH9-11 and 5GH9-34 formed a robust cluster with DSM 26515 and MAH-13. Strain 5GH9-11 showed the highest orthologous average nucleotide identity (OrthoANI; 88.5 %) and digital DNA-DNA hybridization (dDDH) values (35.5 %) with MAH-13, and strain 5GH9-34 revealed highest OrthoANI (88.1 %) and dDDH (34.2 %) values with MAH-13. The orthoANI and dDDH values between strain 5GH9-11 and 5GH9-34 were 87.7 and 33.9 %, respectively. Their major respiratory quinone was ubiquinone 8, and the major cellular fatty acids were iso-C, summed feature 9 (iso-C ω9 and/or C 10-methyl) and iso-C. The major polar lipids of both strains were composed of large or moderate amounts of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified aminolipid and an unidentified aminophospholipid. Based on these data, strains 5GH9-11 and 5GH9-34 should represent two independent novel species of , for which the names sp. nov. (type strain 5GH9-11=KACC 16943=JCM 35197) and sp. nov. (type strain 5GH9-34=KACC 16945=JCM 35198) are proposed.
Topics: Phylogeny; RNA, Ribosomal, 16S; Fatty Acids; Sequence Analysis, DNA; DNA, Bacterial; Bacterial Typing Techniques; Base Composition; Pseudomonadaceae
PubMed: 36862578
DOI: 10.1099/ijsem.0.005759 -
PloS One 2015Non-selective effects, like genetic drift, are an important factor in modern conceptions of evolution, and have been extensively studied for constant population sizes...
Non-selective effects, like genetic drift, are an important factor in modern conceptions of evolution, and have been extensively studied for constant population sizes (Kimura, 1955; Otto and Whitlock, 1997). Here, we consider non-selective evolution in the case of growing populations that are of small size and have varying trait compositions (e.g. after a population bottleneck). We find that, in these conditions, populations never fixate to a trait, but tend to a random limit composition, and that the distribution of compositions "freezes" to a steady state. This final state is crucially influenced by the initial conditions. We obtain these findings from a combined theoretical and experimental approach, using multiple mixed subpopulations of two Pseudomonas putida strains in non-selective growth conditions (Matthijs et al, 2009) as model system. The experimental results for the population dynamics match the theoretical predictions based on the Pólya urn model (Eggenberger and Pólya, 1923) for all analyzed parameter regimes. In summary, we show that exponential growth stops genetic drift. This result contrasts with previous theoretical analyses of non-selective evolution (e.g. genetic drift), which investigated how traits spread and eventually take over populations (fixate) (Kimura, 1955; Otto and Whitlock, 1997). Moreover, our work highlights how deeply growth influences non-selective evolution, and how it plays a key role in maintaining genetic variability. Consequently, it is of particular importance in life-cycles models (Melbinger et al, 2010; Cremer et al, 2011; Cremer et al, 2012) of periodically shrinking and expanding populations.
Topics: Biological Evolution; Genetic Drift; Models, Biological; Pseudomonas putida; Selection, Genetic
PubMed: 26274606
DOI: 10.1371/journal.pone.0134300 -
Microbiology Spectrum Aug 2023Ginseng is a popular medicinal herb with established therapeutic effects such as cardiovascular disease prevention, anticancer effects, and anti-inflammatory effects....
Ginseng is a popular medicinal herb with established therapeutic effects such as cardiovascular disease prevention, anticancer effects, and anti-inflammatory effects. However, the slow growth of ginseng due to soilborne pathogens has been a challenge for establishing new plantations. In this study, we investigated root rot disease associated with the microbiota in a ginseng monoculture model system. Our results showed that a collapse of the early microbiota community inhibiting root rot disease was observed before the disease became severe, and nitrogen fixation was necessary to support the initial microbiota community structure. Furthermore, changes in the nitrogen composition were essential for the suppression of pathogen activity in early monoculture soils. We hypothesize that , a population built up by aspartic acid, can inhibit the occurrence of root rot disease in ginseng and that specific management practices that maintain a healthy microbiome can be implemented to prevent and mitigate the disease. Our findings provide insights into the potential use of specific members of the microbiota for controlling root rot disease in ginseng cultivation. Understanding the initial soil microbiota and community shifts in a monoculture system is critical for developing disease-suppressive soils for crop production. The lack of resistance genes against soilborne pathogens in plants highlights the need for effective management strategies. Our investigation of root rot disease and initial microbiota community shifts in a ginseng monoculture model system provides valuable insight into the development of conducive soil into specific suppressive soil. With a thorough understanding of the microbiota in disease-conducive soil, we can work toward the development of disease-suppressive soil to prevent outbreaks and ensure sustainable crop production.
Topics: Soil; Pseudomonadaceae; Soil Microbiology; Plant Diseases; Panax
PubMed: 37404179
DOI: 10.1128/spectrum.01150-23 -
Microbiology (Reading, England) Mar 2019Pseudomonas syringae is best known as a plant pathogenic bacterium that causes diseases in a multitude of hosts, and it has been used as a model organism to understand...
Pseudomonas syringae is best known as a plant pathogenic bacterium that causes diseases in a multitude of hosts, and it has been used as a model organism to understand the biology of plant disease. Pathogenic and non-pathogenic isolates of P. syringae are also commonly found living as epiphytes and in the wider environment, including water sources such as rivers and precipitation. Ice-nucleating strains of P. syringae are associated with frost damage to crops. The genomes of numerous strains of P. syringae have been sequenced and molecular genetic studies have elucidated many aspects of this pathogen's interaction with its host plants.
Topics: Genome, Bacterial; Host-Pathogen Interactions; Phylogeny; Plant Diseases; Pseudomonas syringae; Water Microbiology
PubMed: 30427303
DOI: 10.1099/mic.0.000715 -
Journal of Environmental Science and... Feb 2017This study aimed to isolate and characterize bacteria able to use sulfentrazone in the commercial formulation as their sole carbon source. The isolation of the potential...
This study aimed to isolate and characterize bacteria able to use sulfentrazone in the commercial formulation as their sole carbon source. The isolation of the potential sulfentrazone-degrading bacteria was made from soil samples with a recent history of herbicide application and from isolates identified through rDNA sequencing. Subsequently, we assessed the growth of the isolates and their sulfentrazone degradation ability using high-performance liquid chromatography. Twenty-six potential sulfentrazone-degrading bacterial isolates were obtained in pure culture. Through analysis of the rDNA sequences, the predominance of bacterial species of the genus Pseudomonas was found. The isolates presented a differentiated ability of sulfentrazone degradation. The presence of herbicide in the culture medium reduced the log phase of four isolates. Pseudomonas putida, Pseudomonas lutea, Pseudomonas plecoglossicida and three isolates of Pseudomonas sp. showed higher sulfentrazone degradation capacity, which varied from 4 to 15%. This is the first report of the Pseudomonas genre capable of sulfentrazone degradation. The isolates obtained present potential use in bioremediation programs for soil contaminated with sulfentrazone.
Topics: Biodegradation, Environmental; Culture Media; DNA, Ribosomal; Herbicides; Pseudomonas; Pseudomonas putida; Soil Microbiology; Soil Pollutants; Sulfonamides; Triazoles
PubMed: 27820678
DOI: 10.1080/03601234.2016.1248136 -
International Journal of Systematic and... Sep 2021Strain F2A, isolated from the cricket , was subjected to a polyphasic taxonomic characterization. Cells of the strain were rod-shaped, Gram-stain-negative and catalase-...
Strain F2A, isolated from the cricket , was subjected to a polyphasic taxonomic characterization. Cells of the strain were rod-shaped, Gram-stain-negative and catalase- and oxidase-positive. It did not assimilate any carbohydrates. The strain's 16S rRNA gene sequence showed highest similarity to QZS01 (96.4 %). The next highest similarity values were found to representatives of related genera (<93 %). The genome size of strain F2A was 3.2 Mbp and the G+C content was 36.4 mol%. Average nucleotide identity values based on blast and MUMmer and average amino acid identity values between strain F2A and QZS01 were 74.29/74.43, 83.88 and 74.70 %, respectively. The quinone system predominantly contained ubiquinone Q-8. In the polar lipid profile, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified phospholipid were detected. The polyamine pattern consisted of the major compounds putrescine and spermidine. Major fatty acids were C ω7 and C and the hydroxyl acids were C 3-OH, C 2-OH and C 3-OH. The diagnostic diamino acid of the peptidoglycan was -diaminopimelic acid. Due to its association with the only species of the genus but its distinctness from we here propose the novel species sp. nov. F2A (=CCM 9136=LMG 32211).
Topics: Animals; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Diaminopimelic Acid; Fatty Acids; Gryllidae; Nucleic Acid Hybridization; Peptidoglycan; Phospholipids; Phylogeny; Pseudomonadaceae; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone
PubMed: 34516367
DOI: 10.1099/ijsem.0.004997 -
Clinical Microbiology Reviews Oct 2014Pseudomonas fluorescens is not generally considered a bacterial pathogen in humans; however, multiple culture-based and culture-independent studies have identified it at... (Review)
Review
Pseudomonas fluorescens is not generally considered a bacterial pathogen in humans; however, multiple culture-based and culture-independent studies have identified it at low levels in the indigenous microbiota of various body sites. With recent advances in comparative genomics, many isolates originally identified as the "species" P. fluorescens are now being reclassified as novel Pseudomonas species within the P. fluorescens "species complex." Although most widely studied for its role in the soil and the rhizosphere, P. fluorescens possesses a number of functional traits that provide it with the capability to grow and thrive in mammalian hosts. While significantly less virulent than P. aeruginosa, P. fluorescens can cause bacteremia in humans, with most reported cases being attributable either to transfusion of contaminated blood products or to use of contaminated equipment associated with intravenous infusions. Although not suspected of being an etiologic agent of pulmonary disease, there are a number of reports identifying it in respiratory samples. There is also an intriguing association between P. fluorescens and human disease, in that approximately 50% of Crohn's disease patients develop serum antibodies to P. fluorescens. Altogether, these reports are beginning to highlight a far more common, intriguing, and potentially complex association between humans and P. fluorescens during health and disease.
Topics: Genomics; Host-Pathogen Interactions; Humans; Phenotype; Pseudomonas Infections; Pseudomonas fluorescens; Quantitative Trait, Heritable; Virulence Factors
PubMed: 25278578
DOI: 10.1128/CMR.00044-14 -
Metabolic Engineering Jul 2023The emergence of next-generation sequencing (NGS) technologies has made it possible to not only sequence entire genomes, but also identify metabolic engineering targets...
The emergence of next-generation sequencing (NGS) technologies has made it possible to not only sequence entire genomes, but also identify metabolic engineering targets across the pangenome of a microbial population. This study leverages NGS data as well as existing molecular biology and bioinformatics tools to identify and validate genomic signatures for improving phenazine biosynthesis in Pseudomonas chlororaphis. We sequenced a diverse collection of 34 Pseudomonas isolates using short- and long-read sequencing techniques and assembled whole genomes using the NGS reads. In addition, we assayed three industrially relevant phenotypes (phenazine production, biofilm formation, and growth temperature) for these isolates in two different media conditions. We then provided the whole genomes and phenazine production data to a unitig-based microbial genome-wide association study (mGWAS) tool to identify novel genomic signatures responsible for phenazine production in P. chlororaphis. Post-processing of the mGWAS analysis results yielded 330 significant hits influencing the biosynthesis of one or more phenazine compounds. Based on a quantitative metric (called the phenotype score), we elucidated the most influential hits for phenazine production and experimentally validated them in vivo in the most optimal phenazine producing strain. Two genes significantly increased phenazine-1-carboxamide (PCN) production: a histidine transporter (ProY_1), and a putative carboxypeptidase (PS__04251). A putative MarR-family transcriptional regulator decreased PCN titer when overexpressed in a high PCN producing isolate. Overall, this work seeks to demonstrate the utility of a population genomics approach as an effective strategy in enabling the identification of targets for metabolic engineering of bioproduction hosts.
Topics: Pseudomonas chlororaphis; Metagenomics; Genome-Wide Association Study; Pseudomonas; Phenazines; Bacterial Proteins
PubMed: 37369325
DOI: 10.1016/j.ymben.2023.06.008 -
The ISME Journal Jun 2021Bacteria and fungi secrete many natural products that inhibit each other's growth and development. The dynamic changes in secreted metabolites that occur during...
Bacteria and fungi secrete many natural products that inhibit each other's growth and development. The dynamic changes in secreted metabolites that occur during interactions between bacteria and fungi are complicated. Pyochelin is a siderophore produced by many Pseudomonas and Burkholderia species that induces systemic resistance in plants and has been identified as an antifungal agent. Through imaging mass spectrometry and metabolomics analysis, we found that Phellinus noxius, a plant pathogen, can modify pyochelin and ent-pyochelin to an esterification product, resulting in reduced iron-chelation and loss of antifungal activity. We also observed that dehydroergosterol peroxide, the fungal metabolite, is only accumulated in the presence of pyochelin produced through bacteria-fungi interactions. For the first time, we show the fungal transformation of pyochelin in the microbial interaction. Our findings highlight the importance of understanding the dynamic changes of metabolites in microbial interactions and their influences on microbial communities.
Topics: Antifungal Agents; Fungi; Iron; Pseudomonas; Pseudomonas aeruginosa; Siderophores
PubMed: 33619352
DOI: 10.1038/s41396-020-00871-0 -
Current Topics in Medicinal Chemistry 2021Modulators of quorum sensing pathways in Pseudomonas aeruginosa (PA) gain attention due to their potential therapeutic applications. These chemical agents are viewed as... (Review)
Review
Modulators of quorum sensing pathways in Pseudomonas aeruginosa (PA) gain attention due to their potential therapeutic applications. These chemical agents are viewed as anti-virulence agents capable of increasing the existing therapeutic agents' efficacy against resistant clinical strains. Additionally, they can be utilized in developing anticancer therapeutics, whole-cell biosensors, and artificial biological systems. In this mini-review, we summarize recent (2015-2021) publications on PA's QS modulation.
Topics: Antineoplastic Agents; Biosensing Techniques; Pseudomonas aeruginosa; Quorum Sensing; Virulence
PubMed: 34561982
DOI: 10.2174/1568026621666210924160004