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Current Microbiology Aug 2020During the exploration of microbial natural resources, two strains of Pseudomonas, PS14 and PS24, were isolated from samples taken from Izu Oshima, a volcanic island...
During the exploration of microbial natural resources, two strains of Pseudomonas, PS14 and PS24, were isolated from samples taken from Izu Oshima, a volcanic island located 120 km southwest of central Tokyo. Phylogenetic analysis based on 16S rRNA gene sequences showed that PS14 was most similar to Pseudomonas baetica a390 (99.6%) and Pseudomonas helmanticensis OHA11 (99.5%), and that PS24 was most similar to Pseudomonas qingdaonensis JJ3 (98.8%) and Pseudomonas lutea OK2 (98.7%). The major fatty acids of these two strains were C and C cyclo, summed feature 3 (C ω6c and/or C ω7c), and summed feature 8 (C ω7c and/or ω6c). The phylogenetic analyses, DNA-DNA hybridization results and phenotypic traits indicated that PS14 and PS24 constitute two novel species, Pseudomonas atagosis sp. nov. (type strain PS14 = CECT 9940, = LMG 31496) and Pseudomonas akappagea sp. nov. (type strain PS24 = CECT 9941, = LMG 31497), respectively. The sequence data of the draft genomes of PS14 and PS24 were deposited in the GenBank database under accession numbers VXCA00000000 and VXCP00000000, respectively, and the sequence data of their 16S rRNA genes were deposited in the GenBank database under accession numbers MN396717 and MN382268, respectively.
Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Genome, Bacterial; Islands; Nucleic Acid Hybridization; Phylogeny; Pseudomonas; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Tokyo; Volcanic Eruptions
PubMed: 32189049
DOI: 10.1007/s00284-020-01943-2 -
Scientific Reports Feb 2021Pseudomonas are ubiquitously occurring microorganisms and are known for their ability to produce antimicrobials. An endophytic bacterial strain NP-1, isolated from...
Pseudomonas are ubiquitously occurring microorganisms and are known for their ability to produce antimicrobials. An endophytic bacterial strain NP-1, isolated from Eucalyptus dunnii leaves, exhibits antifungal properties against five tested phytopathogenic fungi. The strain is a Gram-negative rod-shaped bacterium containing a single polar flagellum. It is strictly aerobic, grows at 4-37 °C, 2-5% NaCl, and pH 3-7. The 16S rRNA sequence analysis showed that NP-1 belongs to the Pseudomonas genus. Phylogenetic analysis based on four concatenated partial genes (16S rDNA, gyrB, rpoB and rpoD) and the phylogenomic tree indicated that NP-1 belongs to Pseudomonas fluorescens lineage but is distinct from any known Pseudomonas species. The G + C mol % of NP-1 genome is 63.96, and the differences between NP-1 and related species are larger than 1. The digital DNA-DNA hybridization and tetranucleotide signatures are 23.8 and 0.97, which clearly separates strain NP-1 from its closest neighbours, Pseudomonas coleopterorum and Pseudomonas rhizosphaerae. Its phenotypic and chemotaxonomic features confirmed its differentiation from related taxa. The results from this polyphasic approach support the classification of NP-1 as a novel species of Pseudomonas, and the name of Pseudomonas eucalypticola is thus proposed for this strain, whose type is NP-1 (= CCTCC M2018494 = JCM 33572).
Topics: Antifungal Agents; Base Composition; Eucalyptus; Genome, Bacterial; Humans; Phylogeny; Plant Leaves; Pseudomonas; RNA, Ribosomal, 16S
PubMed: 33542376
DOI: 10.1038/s41598-021-82682-7 -
Brazilian Journal of Microbiology :... Mar 2023The search for sustainable alternatives to the production of chemicals using renewable substrates and natural processes has been widely encouraged. Microbial surfactants... (Review)
Review
The search for sustainable alternatives to the production of chemicals using renewable substrates and natural processes has been widely encouraged. Microbial surfactants or biosurfactants are surface-active compounds synthesized by fungi, yeasts, and bacteria. Due to their great metabolic versatility, bacteria are the most traditional and well-known microbial surfactant producers, being Bacillus and Pseudomonas species their typical representatives. To be successfully applied in industry, surfactants need to maintain stability under the harsh environmental conditions present in manufacturing processes; thus, the prospection of biosurfactants derived from extremophiles is a promising strategy to the discovery of novel and useful molecules. Bacterial surfactants show interesting properties suitable for a range of applications in the oil industry, food, agriculture, pharmaceuticals, cosmetics, bioremediation, and more recently, nanotechnology. In addition, they can be synthesized using renewable resources as substrates, contributing to the circular economy and sustainability. The article presents a general and updated review of bacterial-derived biosurfactants, focusing on the potential of some groups that are still underexploited, as well as, recent trends and contributions of these versatile biomolecules to circular bioeconomy and nanotechnology.
Topics: Surface-Active Agents; Bacteria; Bacillus; Agriculture; Pseudomonas
PubMed: 36662441
DOI: 10.1007/s42770-023-00905-7 -
International Journal of Molecular... May 2022As one of the most widespread groups of Gram-negative bacteria, bacteria are prevalent in almost all natural environments, where they have developed intimate...
As one of the most widespread groups of Gram-negative bacteria, bacteria are prevalent in almost all natural environments, where they have developed intimate associations with plants and animals. is a novel species of with clinical, animal, and plant-associated isolates, closely related to human and animal health, plant growth, and bioremediation. Although genetic manipulations have been proven as powerful tools for understanding bacterial biological and biochemical characteristics and the evolutionary origins, native isolates are often difficult to genetically manipulate, thereby making it a time-consuming and laborious endeavor. Here, by using the CRISPR-Cas system, a versatile gene-editing tool with a two-plasmid strategy was developed for a native strain isolated from the model organism silkworm () gut. We harmonized and detailed the experimental setup and clarified the optimal conditions for bacteria transformation, competent cell preparation, and higher editing efficiency. Furthermore, we provided some case studies, testing and validating this approach. An antibiotic-related gene, , was knocked out, resulting in the slow growth of the deletion mutant in LB containing chloramphenicol. Fusion constructs with knocked-in exhibited intense fluorescence. Altogether, the successful construction and application of new genetic editing approaches gave us more powerful tools to investigate the functionalities of the novel species.
Topics: Animals; CRISPR-Cas Systems; Gene Editing; Plants; Pseudomonas
PubMed: 35628253
DOI: 10.3390/ijms23105443 -
Annals of Clinical Microbiology and... Mar 2022The carbapenem-resistance genes bla are widely disseminated in Pseudomonas, and frequently harbored within class 1 integrons that reside within various mobile genetic...
BACKGROUND
The carbapenem-resistance genes bla are widely disseminated in Pseudomonas, and frequently harbored within class 1 integrons that reside within various mobile genetic elements (MGEs). However, there are few reports on detailed genetic dissection of bla-carrying MGEs in Pseudomonas.
METHODS
This study presented the complete sequences of five bla-carrying MGEs, including two plasmids, two chromosomal integrative and mobilizable elements (IMEs), and one chromosomal integrative and conjugative element (ICE) from five different Pseudomonas isolates.
RESULTS
The two plasmids were assigned to a novel incompatibility (Inc) group Inc, which included only seven available plasmids with determined complete sequences and could be further divided into three subgroups Inc-1/2/3. A detailed sequence comparison was then applied to a collection of 15 MGEs belonging to four different groups: three representative Inc plasmids, two Tn6916-related IMEs, two Tn6918-related IMEs, and eight Tn6417-related ICEs and ten of these 15 MGEs were first time identified. At least 22 genes involving resistance to seven different categories of antibiotics and heavy metals were identified within these 15 MGEs, and most of these resistance genes were located within the accessory modules integrated as exogenous DNA regions into these MGEs. Especially, eleven of these 15 MGEs carried the bla genes, which were located within 11 different concise class 1 integrons.
CONCLUSION
These bla-carrying integrons were further integrated into the above plasmids, IMEs/ICEs with intercellular mobility. These MGEs could transfer between Pseudomonas isolates, which resulted in the accumulation and spread of bla among Pseudomonas and thus was helpful for the bacteria to survival from the stress of antibiotics. Data presented here provided a deeper insight into the genetic diversification and evolution of VIM-encoding MGEs in Pseudomonas.
Topics: Anti-Bacterial Agents; Chromosomes, Bacterial; Conjugation, Genetic; Integrons; Plasmids; Pseudomonas; beta-Lactamases
PubMed: 35264204
DOI: 10.1186/s12941-022-00502-w -
Molecular Plant Pathology Jan 2022Pseudomonas viridiflava is a gram-negative pseudomonad that is phylogenetically placed within the Pseudomonas syringae species complex. P. viridiflava has a wide host...
UNLABELLED
Pseudomonas viridiflava is a gram-negative pseudomonad that is phylogenetically placed within the Pseudomonas syringae species complex. P. viridiflava has a wide host range and causes a variety of symptoms in different plant parts, including stems, leaves, and blossoms. Outside of its role as a pathogen, P. viridiflava also exists as an endophyte, epiphyte, and saprophyte. Increased reports of P. viridiflava causing disease on new hosts in recent years coincide with increased research on its genetic variability, virulence, phylogenetics, and phenotypes. There is high variation in its core genome, virulence factors, and phenotypic characteristics. The main virulence factors of this pathogen include the enzyme pectate lyase and virulence genes encoded within one or two pathogenicity islands. The delineation of P. viridiflava in the P. syringae complex has been investigated using several molecular approaches. P. viridiflava comprises its own species, within the complex. While seemingly an outsider to the complex as a whole due to differences in the core genome and virulence genes, low average nucleotide identity to other of P. syringae complex members, and some phenotypic traits, it remains as part of the complex. Defining phylogenetic, phenotypic, and genomic characteristics of P. viridiflava in comparison to other P. syringae members is important to understanding this pathogen and for the development of disease resistance and management practices.
TAXONOMY
Kingdom Bacteria; Phylum Proteobacteria; Class Gammaproteobacteria; Family Pseudomonadaceae; Genus Pseudomonas; Species Pseudomonas syringae species complex, Genomospecies 6, Phylogroup 7 and 8.
MICROBIOLOGICAL PROPERTIES
Gram-negative, fluorescent, aerobic, motile, rod-shaped, oxidase negative, arginine dihydrolase negative, levan production negative (or positive), potato rot positive (or negative), tobacco hypersensitivity positive.
GENOME
There are two complete genomes, five chromosome-level genomes, and 1,540 genomes composed of multiple scaffolds of P. viridiflava available in the National Center for Biotechnology Information Genome database. The median total length of these assemblies is 5,975,050 bp, the median number of protein coding genes is 5,208, and the median G + C content is 59.3%.
DISEASE SYMPTOMS
P. viridiflava causes a variety of disease symptoms, including spots, streaks, necrosis, rots, and more in above- and below-ground plant parts on at least 50 hosts.
EPIDEMIOLOGY
There have been several significant disease outbreaks on field and horticultural crops caused by P. viridiflava since the turn of the century. P. viridiflava has been reported as a pathogen, epiphyte, endophyte, and saprophyte. This species has been isolated from a variety of environmental sources, including asymptomatic wild plants, snow, epilithic biofilms, and icepacks.
Topics: Phylogeny; Plant Diseases; Pseudomonas; Pseudomonas syringae; Virulence
PubMed: 34463014
DOI: 10.1111/mpp.13133 -
Scientific Reports Jun 2024A novel nano bio-fertilizer encapsulation method was developed to crosslink chitosan and alginate with humic acid. These nanocapsules, referred to as (Ch./Alg.HA.NPK) or...
A novel nano bio-fertilizer encapsulation method was developed to crosslink chitosan and alginate with humic acid. These nanocapsules, referred to as (Ch./Alg.HA.NPK) or (Ch./Alg.HA.NPK.PGPRs), were loaded with nanoscale essential agro-nutrients (NPK) and beneficial microorganisms Pseudomonas Fluorescence abbreviated as (P.Fluorescence). Structural and morphological analyses were conducted using FourierTransform Infrared, Thermogravimetric Analysis, Scanning Electron Microscopy, Malvern Zeta NanoSizer, and Zeta potential. Encapsulation efficiency and water retention were also determined compared to control non-crosslinked nanocapsules. The sustained cumulative release of NPK over 30 days was also investigated to 33.2%, 47.8%, and 68.3%, alternatively. The release mechanism, also assessed through the kinetic module of the Korsemeyer- Peppas Mathematical model, demonstrated superior performance compared to non-crosslinked nanocapsules (chitosan/alginate). These results show the potential of the synthesized nanocapsules for environmentally conscious controlled release of NPK and PGPRs, thereby mitigating environmental impact, enhancing plant growth, and reducing reliance on conventional agrochemical fertilizers.
Topics: Fertilizers; Chitosan; Agriculture; Alginates; Nanocapsules; Humic Substances; Pseudomonas
PubMed: 38871758
DOI: 10.1038/s41598-024-62973-5 -
Journal of Dairy Science Mar 2021Pseudomonas spp. are important spoilage bacteria that negatively affect the quality of refrigerated fluid milk and uncultured cheese by generating unwanted odors,...
Pseudomonas spp. are important spoilage bacteria that negatively affect the quality of refrigerated fluid milk and uncultured cheese by generating unwanted odors, flavors, and pigments. They are frequently found in dairy plant environments and enter dairy products predominantly as postpasteurization contaminants. Current subtyping and characterization methods for dairy-associated Pseudomonas are often labor-intensive and expensive or provide limited and possibly unreliable classification information (e.g., to the species level). Our goal was to identify a single-copy gene that could be analyzed in dairy spoilage-associated Pseudomonas for preliminary species-level identification, subtyping, and phenotype prediction. We tested 7 genes previously targeted in a Pseudomonas fluorescens multilocus sequence typing scheme for their individual suitability in this application using a set of 113 Pseudomonas spp. isolates representing the diversity of typical pasteurized milk contamination. For each of the 7 candidate genes, we determined the success rate of PCR and sequencing for these 113 isolates as well as the level of discrimination for species identification and subtyping that the sequence data provided. Using these metrics, we selected a single gene, isoleucyl tRNA synthetase (ileS), which had the most suitable traits for simple and affordable single-gene Pseudomonas characterization. This was based on the number of isolates successfully sequenced for ileS (113/113), the number of unique allelic types assigned (83, compared with 50 for 16S rDNA), nucleotide and sequence diversity measures (e.g., number of unique SNP and Simpson index), and tests for genetic recombination. The discriminatory ability of ileS sequencing was confirmed by separation of 99 additional dairy Pseudomonas spp. isolates, which were indistinguishable by 16S rDNA sequencing, into 28 different ileS allelic types. Further, we used whole-genome sequencing data to demonstrate the similarities in ileS-based phylogenetic clustering to whole-genome-based clustering for 27 closely related dairy-associated Pseudomonas spp. isolates and for 178 Pseudomonas type strains. We also found that dairy-associated Pseudomonas within an ileS cluster typically shared the same proteolytic and lipolytic activities. Use of ileS sequencing provides a promising strategy for affordable initial characterization of Pseudomonas isolates, which will help the dairy industry identify, characterize, and track Pseudomonas in their facilities and products.
Topics: Animals; Dairying; Food Contamination; Isoleucine-tRNA Ligase; Milk; Phylogeny; Pseudomonas
PubMed: 33455773
DOI: 10.3168/jds.2020-19283 -
Frontiers in Cellular and Infection... 2021and infections frequently co-localize in lungs of immunocompromised patients and individuals with cystic fibrosis (CF). The antifungal activity of has been described...
and infections frequently co-localize in lungs of immunocompromised patients and individuals with cystic fibrosis (CF). The antifungal activity of has been described for its filtrates. Pyoverdine and pyocyanin are the principal antifungal molecules active against biofilm metabolism present in iron-limited or iron-replete planktonic culture filtrates, respectively. Using various laboratory wild-type strains (PA14, PAO1, PAK), we found antifungal activity against colonies on agar. Comparing 36 PA14 and 7 PAO1 mutants, we found that mutants lacking both major siderophores, pyoverdine and pyochelin, display higher antifungal activity on agar than their wild types, while quorum sensing mutants lost antifungal activity. Addition of ferric iron, but not calcium or magnesium, reduced the antifungal effects of on agar, whereas iron-poor agar enhanced antifungal effects. Antifungal activity on agar was mediated by PQS and HHQ, MvfR. Among the MvfR downstream factors, rhamnolipids and elastase were produced in larger quantities by pyoverdine-pyochelin double mutants and showed antifungal activity on agar. In summary, antifungal factors produced by on agar differ from those produced by bacteria grown in liquid cultures, are dependent on quorum sensing, and are downregulated by the availability of ferric iron. Rhamnolipids and elastase seem to be major mediators of ' antifungal activity on a solid surface.
Topics: Aspergillus; Biofilms; Humans; Pseudomonas; Pseudomonas Infections; Pseudomonas aeruginosa; Pyocyanine; Quorum Sensing
PubMed: 34746024
DOI: 10.3389/fcimb.2021.734296 -
Scientific Reports Apr 2023Biodesulfurization (BDS) was employed in this study to degrade dibenzothiophene (DBT) which accounts for 70% of the sulfur compounds in diesel using a synthetic and...
Biodesulfurization (BDS) was employed in this study to degrade dibenzothiophene (DBT) which accounts for 70% of the sulfur compounds in diesel using a synthetic and typical South African diesel in the aqueous and biphasic medium. Two Pseudomonas sp. bacteria namely Pseudomonas aeruginosa and Pseudomonas putida were used as biocatalysts. The desulfurization pathways of DBT by the two bacteria were determined by gas chromatography (GC)/mass spectrometry (MS) and High-Performance Liquid Chromatography (HPLC). Both organisms were found to produce 2-hydroxy biphenyl, the desulfurized product of DBT. Results showed BDS performance of 67.53% and 50.02%, by Pseudomonas aeruginosa and Pseudomonas putida, respectively for 500 ppm initial DBT concentration. In order to study the desulfurization of diesel oils obtained from an oil refinery, resting cells studies by Pseudomonas aeruginosa were carried out which showed a decrease of about 30% and 70.54% DBT removal for 5200 ppm in hydrodesulfurization (HDS) feed diesel and 120 ppm in HDS outlet diesel, respectively. Pseudomonas aeruginosa and Pseudomonas putida selectively degraded DBT to form 2-HBP. Application of these bacteria for the desulfurization of diesel showed promising potential for decreasing the sulfur content of South African diesel oil.
Topics: Pseudomonas; Petroleum; Thiophenes; Sulfur Compounds; Gasoline; Pseudomonas putida; Pseudomonas aeruginosa; Biodegradation, Environmental
PubMed: 37055435
DOI: 10.1038/s41598-023-31951-8