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Journal of Molecular Evolution Jun 2023In recent years, evolutionary biologists have developed an increasing interest in the use of barcoding strategies to study eco-evolutionary dynamics of lineages within...
In recent years, evolutionary biologists have developed an increasing interest in the use of barcoding strategies to study eco-evolutionary dynamics of lineages within evolving populations and communities. Although barcoded populations can deliver unprecedented insight into evolutionary change, barcoding microbes presents specific technical challenges. Here, strategies are described for barcoding populations of the model bacterium Pseudomonas fluorescens SBW25, including the design and cloning of barcoded regions, preparation of libraries for amplicon sequencing, and quantification of resulting barcoded lineages. In so doing, we hope to aid the design and implementation of barcoding methodologies in a broad range of model and non-model organisms.
Topics: Pseudomonas fluorescens; Biological Evolution
PubMed: 37186220
DOI: 10.1007/s00239-023-10103-6 -
MSystems Feb 2023A major source of pseudomonad-specialized metabolites is the nonribosomal peptide synthetases (NRPSs) assembling siderophores and lipopeptides. Cyclic lipopeptides...
A major source of pseudomonad-specialized metabolites is the nonribosomal peptide synthetases (NRPSs) assembling siderophores and lipopeptides. Cyclic lipopeptides (CLPs) of the Mycin and Peptin families are frequently associated with, but not restricted to, phytopathogenic species. We conducted an analysis of the NRPSs encoded by lipopeptide biosynthetic gene clusters in nonpathogenic Pseudomonas genomes, covering 13 chemically diversified families. This global assessment of lipopeptide production capacity revealed it to be confined to the Pseudomonas fluorescens lineage, with most strains synthesizing a single type of CLP. Whereas certain lipopeptide families are specific for a taxonomic subgroup, others are found in distant groups. NRPS activation domain-guided peptide predictions enabled reliable family assignments, including identification of novel members. Focusing on the two most abundant lipopeptide families (Viscosin and Amphisin), a portion of their uncharted diversity was mapped, including characterization of two novel Amphisin family members (nepenthesin and oakridgin). Using NMR fingerprint matching, known Viscosin-family lipopeptides were identified in 15 (type) species spread across different taxonomic groups. A bifurcate genomic organization predominates among Viscosin-family producers and typifies Xantholysin-, Entolysin-, and Poaeamide-family producers but most families feature a single NRPS gene cluster embedded between cognate regulator and transporter genes. The strong correlation observed between NRPS system phylogeny and -based taxonomic affiliation indicates that much of the structural diversity is linked to speciation, providing few indications of horizontal gene transfer. The grouping of most NRPS systems in four superfamilies based on activation domain homology suggests extensive module dynamics driven by domain deletions, duplications, and exchanges. Pseudomonas species are prominent producers of lipopeptides that support proliferation in a multitude of environments and foster varied lifestyles. By genome mining of biosynthetic gene clusters (BGCs) with lipopeptide-specific organization, we mapped the global Pseudomonas lipopeptidome and linked its staggering diversity to taxonomy of the producers, belonging to different groups within the major Pseudomonas fluorescens lineage. Activation domain phylogeny of newly mined lipopeptide synthetases combined with previously characterized enzymes enabled assignment of predicted BGC products to specific lipopeptide families. In addition, novel peptide sequences were detected, showing the value of substrate specificity analysis for prioritization of BGCs for further characterization. NMR fingerprint matching proved an excellent tool to unequivocally identify multiple lipopeptides bioinformatically assigned to the Viscosin family, by far the most abundant one in Pseudomonas and with stereochemistry of all its current members elucidated. In-depth analysis of activation domains provided insight into mechanisms driving lipopeptide structural diversification.
Topics: Pseudomonas; Pseudomonas fluorescens; Lipopeptides; Phylogeny
PubMed: 36719227
DOI: 10.1128/msystems.00988-22 -
Microbial Pathogenesis Dec 2022Dactylogyrus extensus and Pseudomonas fluorescens are serious pathogens in Cyprinus carpio aquaculture causing severe impacts and substantial economic losses. During the...
Dactylogyrus extensus and Pseudomonas fluorescens are serious pathogens in Cyprinus carpio aquaculture causing severe impacts and substantial economic losses. During the early spring of 2021, abnormal mortalities were reported among farmed C. carpio. Moribund fish showed anorexia, respiratory distress, dermal ulcers, and septicemia. The water analysis revealed low dissolved oxygen (3.4 mg/L), and high un-ionized ammonia levels (0.65 mg/L). Seventy moribund C. carpio specimens were collected and subjected to parasitological and bacteriological examinations. The monogenetic trematode D. extensus was discovered in wet mounts from the gills of all the examined fish samples (100%). The identity of recovered parasites was confirmed by sequencing and alignment of the 28S rDNA gene. P. fluorescens was concurrently identified in the infested fish samples (58.5%) based on phenotypic characteristics using the API20 E. The identity of bacterial isolates was confirmed further by sequencing and alignment of 16S rRNA gene. The IL-1β and MHCII were upregulated in infested fish in tandem with the severity of infections. P. fluorescens isolates displayed high resistance to most of the tested antibiotics. The study is one of the earlier reports on D. extensus and P. fluorescens co-infections in farmed C. carpio and highlights the need of effective control programs to protect fish health and minimize losses.
Topics: Animals; Carps; Pseudomonas fluorescens; RNA, Ribosomal, 16S; Fish Diseases; Trematoda
PubMed: 36334863
DOI: 10.1016/j.micpath.2022.105867 -
Food Microbiology Feb 2023We investigated the function of pyoverdine in the biofilm formation, motility, and spoilage potential of Pseudomonas fluorescens. We targeted and identified two major...
We investigated the function of pyoverdine in the biofilm formation, motility, and spoilage potential of Pseudomonas fluorescens. We targeted and identified two major genes (pvdA and pvdE) that are involved in the biosynthesis of siderophores. We next constructed ΔpvdA and ΔpvdE mutants of P. fluorescens PF08 and found that the deletion of pyoverdine led to a biofilm-to-motivity transition as both ΔpvdA and ΔpvdE mutants displayed enhanced motility, reduced level of exopolysaccharides (EPSs), and attenuated biofilm formation. In addition, the lack of synthesis of pyoverdine promoted the spoilage of fish fillets stored at 4 °C. Based on the effect of pyoverdine deletion on the phenotype; we report that pyoverdine regulates the transcription levels of htpX, phoA, flip, flgA, and RpoS, suggesting that pyoverdine-mediated iron absorption may affect the regulation of flagellum and stress resistance. This study emphasizes the important role of pyoverdine in the formation of biofilm, motility, and spoilage of P. fluorescens PF08.
Topics: Animals; Siderophores; Pseudomonas fluorescens; Biofilms
PubMed: 36309448
DOI: 10.1016/j.fm.2022.104151 -
International Journal of Environmental... Sep 2020Bioremediation technology is one of the most profitable and sustainable strategies for remediating soils contaminated with hydrocarbons. This study focuses on assessing...
Bioremediation technology is one of the most profitable and sustainable strategies for remediating soils contaminated with hydrocarbons. This study focuses on assessing the influence of biostimulation and bioaugmentation with to contribute to the removal of total petroleum hydrocarbons (TPHs) of a soil. Laboratory studies were carried out (measurements of emitted CO, surface tension, and residual TPH) to select the best bioaugmentation and biostimulation treatment. The sources of C, N, and P were glucose-yeast extract, NHCl-NaNO, and KHPO-KPO, respectively. The effect of culture conditions on the reduction of TPH and respiratory activity was evaluated through a factorial design, 2, in a solid culture system. After 80 days of incubation, it was observed that treatments of yeast extract-NHCl-KHPO (Y4) and glucose-NaNO-KPO (Y5) presented a higher level of TPH removal (20.91% and 20.00% degradation of TPH, respectively). Biostimulation favors the production of biosurfactants, indirectly measured by the change in surface tension in the soil extracts. The treatments Y4 and Y5 showed a lower change value of the surface tension (23.15 and 23.30 mN·m at 25 °C). A positive correlation was determined between the change in surface tension and the removal of TPH; hence there was a contribution of the biosurfactants produced to the removal of hydrocarbons.
Topics: Biodegradation, Environmental; Biological Availability; Environmental Restoration and Remediation; Humans; Hydrocarbons; Nutrients; Petroleum; Pseudomonas fluorescens; Soil; Soil Microbiology; Soil Pollutants
PubMed: 32977570
DOI: 10.3390/ijerph17196959 -
MSphere Mar 2021LuxR solos are related to quorum sensing (QS) LuxR family regulators; however, they lack a cognate LuxI family protein. LuxR solos are widespread and almost exclusively...
LuxR solos are related to quorum sensing (QS) LuxR family regulators; however, they lack a cognate LuxI family protein. LuxR solos are widespread and almost exclusively found in proteobacteria. In this study, we investigated the distribution and conservation of LuxR solos in the fluorescent pseudomonads group. Our analysis of more than 600 genomes revealed that the majority of fluorescent spp. carry one or more LuxR solos, occurring considerably more frequently than complete LuxI/LuxR archetypical QS systems. Based on the adjacent gene context and conservation of the primary structure, nine subgroups of LuxR solos have been identified that are likely to be involved in the establishment of communication networks. Modeling analysis revealed that the majority of subgroups shows some substitutions at the invariant amino acids of the ligand-binding pocket of QS LuxRs, raising the possibility of binding to non-acyl-homoserine lactone (AHL) ligands. Several mutants and gene expression studies on some LuxR solos belonging to different subgroups were performed in order to shed light on their response. The commonality of LuxR solos among fluorescent pseudomonads is an indication of their important role in cell-cell signaling. Cell-cell communication in bacteria is being extensively studied in simple settings and uses chemical signals and cognate regulators/receptors. Many Gram-negative proteobacteria use acyl-homoserine lactones (AHLs) synthesized by LuxI family proteins and cognate LuxR-type receptors to regulate their quorum sensing (QS) target loci. AHL-QS circuits are the best studied QS systems; however, many proteobacterial genomes also contain one or more LuxR solos, which are QS-related LuxR proteins which are unpaired to a cognate LuxI. A few LuxR solos have been implicated in intraspecies, interspecies, and interkingdom signaling. Here, we report that LuxR solo homologs occur considerably more frequently than complete LuxI/LuxR QS systems within the group of species and that they are characterized by different genomic organizations and primary structures and can be subdivided into several subgroups. The group consists of more than 50 species, many of which are found in plant-associated environments. The role of LuxR solos in cell-cell signaling in fluorescent pseudomonads is discussed.
Topics: Gene Expression Regulation, Bacterial; Genome, Bacterial; Pseudomonas fluorescens; Quorum Sensing; Repressor Proteins; Signal Transduction; Trans-Activators
PubMed: 33789944
DOI: 10.1128/mSphere.01322-20 -
World Journal of Microbiology &... Dec 2022Pseudomonas fluorescens is considered among the main spoilage microorganisms due to its ability to produce proteases. Food deterioration caused by spoilage...
Pseudomonas fluorescens is considered among the main spoilage microorganisms due to its ability to produce proteases. Food deterioration caused by spoilage microorganisms has a major impact on food quality and the environment. The inactivation of Pseudomonas fluorescens growth and protease production was intensively investigated with the use of Salmide®, A Sodium Chlorite-Based Oxy-halogen Disinfectant. A unique M9 media was also developed to assure sufficient protease productions with different mutants of Pseudomonas fluorescens as a microbioreactor. Mutations were induced by classical whole-cell mutagenesis using N-methyl-N'- nitro-N-nitrosoguanidine (NTG). A dramatic decrease occurred in protease activity when different Salmide concentrations (5, 10, and 15 ppm) were added to the growth culture followed by a complete inhibition concentration (20, 25, 50, and 100 ppm) of Salmide. However, no significant inhibition occurred once it is secreted out of cells. Some mutants were resistant and remains highly stable with high protease production under stressful conditions of Sodium Chlorite-Based Oxy-halogen. The production of the protease showed a linear correlation with the increase in incubation time using a continuous culture bioreactor system and recorded maximum protease activity after 40 h. Our findings would offer alternative antimicrobial procedures for food and industrial sectors.
Topics: Pseudomonas fluorescens; Endopeptidases; Peptide Hydrolases; Halogens
PubMed: 36469174
DOI: 10.1007/s11274-022-03471-6 -
Annual Review of Microbiology Sep 2020Biofilms are the dominant bacterial lifestyle. The regulation of the formation and dispersal of bacterial biofilms has been the subject of study in many organisms. Over... (Review)
Review
Biofilms are the dominant bacterial lifestyle. The regulation of the formation and dispersal of bacterial biofilms has been the subject of study in many organisms. Over the last two decades, the mechanisms of biofilm formation and regulation have emerged as among the best understood of any bacterial biofilm system. Biofilm formation by occurs through the localization of an adhesin, LapA, to the outer membrane via a variant of the classical type I secretion system. The decision between biofilm formation and dispersal is mediated by LapD, a c-di-GMP receptor, and LapG, a periplasmic protease, which together control whether LapA is retained or released from the cell surface. LapA localization is also controlled by a complex network of c-di-GMP-metabolizing enzymes. This review describes the current understanding of LapA-mediated biofilm formation by and discusses several emerging models for the regulation and function of this adhesin.
Topics: Adhesins, Bacterial; Bacterial Proteins; Biofilms; Cyclic GMP; Gene Expression Regulation, Bacterial; Pseudomonas fluorescens
PubMed: 32689917
DOI: 10.1146/annurev-micro-011520-094214 -
Brazilian Journal of Biology = Revista... 2022Pseudomonas fluorescens is one of the main causes of septicemic diseases among freshwater fish, causing severe economic losses and decreasing farm efficiency. Thus, this...
Pseudomonas fluorescens is one of the main causes of septicemic diseases among freshwater fish, causing severe economic losses and decreasing farm efficiency. Thus, this research was aimed to investigate the occurrence of P. fluorescens in Nile Tilapia (O. niloticus) fish in Egypt, gene sequencing of 16SrDNA gene, and antimicrobial susceptibility. P. fluorescens strains were detected in 32% (128\400) of apparently healthy (9%; 36\400) and diseased (23%; 92\400) Nile tilapia fish. The highest prevalence was observed in gills of fish, 31.3% followed by intestine 26.9%, liver 24.2%, and kidneys 17.6%. The PCR results for the 16SrDNA gene of P. fluorescens showed 16SrDNA gene in 30% of examined isolates. Moreover, Homogeny and a strong relationship between strains of P. fluorescens was confirmed using 16SrDNA sequences. Beside the responsibility of 16SrDNA gene on the virulence of P. fluorescens. The results of antimicrobial susceptibility tests revealed that all strains were resistant to piperacillin (100%), followed by ceftazidime (29.7%), and cefepime (25.8%). The strains of P. fluorescence were highly sensitive to cefotaxime (74.2%), followed by ceftriaxone and levofloxacin (70.3% each). Interestingly, 29.7% of strains of P. fluorescens were multiple antimicrobial-resistant (MAR).
Topics: Animals; Anti-Bacterial Agents; Cichlids; Drug Resistance, Bacterial; Egypt; Pseudomonas fluorescens
PubMed: 35293547
DOI: 10.1590/1519-6984.257144 -
Current Opinion in Microbiology Jun 2017Manipulation of the soil microbiome holds great promise for contributing to more environmentally benign agriculture, with soil microbes such as Pseudomonas promoting... (Review)
Review
Manipulation of the soil microbiome holds great promise for contributing to more environmentally benign agriculture, with soil microbes such as Pseudomonas promoting plant growth and effectively suppressing pathogenic microorganisms. Next-generation sequencing has enabled a new generation of research into soil microbiomes, presenting the opportunity to better understand and exploit these valuable resources. Soil bacterial communities are both highly complex and variable, and contain vast interspecies and intraspecies diversity, both of which respond to environmental variation. Therefore, we propose that a combination of whole microbiome analyses with in-depth examination of key microbial taxa will likely prove the most effective approach to understanding rhizosphere microbial interactions. This review highlights recent efforts in this direction, based around the important biocontrol bacterium Pseudomonas fluorescens.
Topics: Microbiota; Plant Development; Plant Roots; Pseudomonas fluorescens; Soil Microbiology
PubMed: 28437662
DOI: 10.1016/j.mib.2017.03.005