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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 -
Journal of Global Antimicrobial... Dec 2018Benzyldimethyldodecyl ammonium chloride (BDMDAC) is a quaternary ammonium compound (QAC) with bactericidal action that is used as an active molecule in detergent...
OBJECTIVES
Benzyldimethyldodecyl ammonium chloride (BDMDAC) is a quaternary ammonium compound (QAC) with bactericidal action that is used as an active molecule in detergent formulations. Pseudomonas fluorescens is a Gram-negative bacterium with versatile metabolism that is frequently present in biofilms on industrial surfaces. This work reports P. fluorescens adaptation to BDMDAC and subsequent concurrent reduced susceptibility to the QAC benzalkonium chloride (BAC) and the antimicrobial ciprofloxacin (CIP).
METHODS
Stepwise adaptation to increasing concentrations of BDMDAC was easily achieved and caused changes in the bacterial phenotype of P. fluorescens. Adaptation was evaluated through minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) determination and was subsequently confirmed by time-kill curves. Biofilm phenotype (biomass and number of cells) was characterised for the adapted and reference strains after treatment with BDMDAC, BAC and CIP.
RESULTS
Susceptibility to BAC and CIP was reduced in adapted P. fluorescens. Biofilms developed by the adapted strain had 20% more mass and a higher number of bacteria (2 log).
CONCLUSIONS
This study revealed that exposure to sublethal concentrations of BDMDAC may select tolerant strains to that product as well as to related products and unrelated antimicrobial agents.
Topics: Adaptation, Biological; Anti-Bacterial Agents; Benzalkonium Compounds; Biofilms; Drug Resistance, Bacterial; Microbial Sensitivity Tests; Phenotype; Pseudomonas fluorescens
PubMed: 30026133
DOI: 10.1016/j.jgar.2018.07.004 -
Applied Microbiology and Biotechnology Oct 2023Early blight of tomato caused by Alternaria solani results in significant crop losses. In this study, Bacillus subtilis J3 and Pseudomonas fluorescens J8 were...
Early blight of tomato caused by Alternaria solani results in significant crop losses. In this study, Bacillus subtilis J3 and Pseudomonas fluorescens J8 were co-cultured as a synthetic microbial community (BCA) for synergistic biocontrol of A. solani, and the inhibition mechanism was investigated. BCA presented an inhibition ration against A. solani at 94.91%, which lowered the disease incidence by 38.26-42.87%; reduced peroxidase, catalase, superoxide dismutase activity of tomatoes by 73.11-90.22%; and promoted the biomass by 66.91-489.21%. With BCA protection, the relative expression of tomato resistance genes (including gPAL2, SWRKY, PR-10, and CHI) in roots and leaves was 12.83-90.70% lower than without protection. BCA also significantly altered the rhizosphere and phyllosphere microbial community. The abundance of potentially beneficial bacteria, including Bacillus, Pseudomonas, Arthrobacter, Lysobacter, and Rhizobium, elevated by 6.58-192.77%. They were negatively correlated with resistance gene expression, indicating their vital involvement in disease control. These results provided essential information on the synergistic biocontrol mechanism of bacteria against pathogens, which could contribute to developing novel biocontrol strategies. KEY POINTS: • Bacillus and Pseudomonas present a synergistic biocontrol effect against A. solani. • Biocontrol prevents pathogen damage and improves tomato growth and systemic resistance. • Beneficial bacteria thrive in the rhizosphere is the key to microbial regulation.
Topics: Pseudomonas fluorescens; Bacillus subtilis; Solanum lycopersicum; Pseudomonas; Bacillus; Plant Diseases
PubMed: 37540249
DOI: 10.1007/s00253-023-12642-w -
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 -
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 -
PloS One 2016The Pseudomonas fluorescens complex includes Pseudomonas strains that have been taxonomically assigned to more than fifty different species, many of which have been...
The Pseudomonas fluorescens complex includes Pseudomonas strains that have been taxonomically assigned to more than fifty different species, many of which have been described as plant growth-promoting rhizobacteria (PGPR) with potential applications in biocontrol and biofertilization. So far the phylogeny of this complex has been analyzed according to phenotypic traits, 16S rDNA, MLSA and inferred by whole-genome analysis. However, since most of the type strains have not been fully sequenced and new species are frequently described, correlation between taxonomy and phylogenomic analysis is missing. In recent years, the genomes of a large number of strains have been sequenced, showing important genomic heterogeneity and providing information suitable for genomic studies that are important to understand the genomic and genetic diversity shown by strains of this complex. Based on MLSA and several whole-genome sequence-based analyses of 93 sequenced strains, we have divided the P. fluorescens complex into eight phylogenomic groups that agree with previous works based on type strains. Digital DDH (dDDH) identified 69 species and 75 subspecies within the 93 genomes. The eight groups corresponded to clustering with a threshold of 31.8% dDDH, in full agreement with our MLSA. The Average Nucleotide Identity (ANI) approach showed inconsistencies regarding the assignment to species and to the eight groups. The small core genome of 1,334 CDSs and the large pan-genome of 30,848 CDSs, show the large diversity and genetic heterogeneity of the P. fluorescens complex. However, a low number of strains were enough to explain most of the CDSs diversity at core and strain-specific genomic fractions. Finally, the identification and analysis of group-specific genome and the screening for distinctive characters revealed a phylogenomic distribution of traits among the groups that provided insights into biocontrol and bioremediation applications as well as their role as PGPR.
Topics: Base Sequence; DNA, Bacterial; Denitrification; Genetic Variation; Genome, Bacterial; Genomics; Phylogeny; Pseudomonas fluorescens; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Siderophores; Soil Microbiology
PubMed: 26915094
DOI: 10.1371/journal.pone.0150183 -
Scientific Reports Mar 2021The genome of Pseudomonas fluorescens F113, a model rhizobacterium and a plant growth-promoting agent, encodes three putative type VI secretion systems (T6SSs); F1-, F2-...
The genome of Pseudomonas fluorescens F113, a model rhizobacterium and a plant growth-promoting agent, encodes three putative type VI secretion systems (T6SSs); F1-, F2- and F3-T6SS. Bioinformatic analysis of the F113 T6SSs has revealed that they belong to group 3, group 1.1, and group 4a, respectively, similar to those previously described in Pseudomonas aeruginosa. In addition, in silico analyses allowed us to identify genes encoding a total of five orphan VgrG proteins and eight putative effectors (Tfe), some with their cognate immunity protein (Tfi) pairs. Genes encoding Tfe and Tfi are found in the proximity of P. fluorescens F113 vgrG, hcp, eagR and tap genes. RNA-Seq analyses in liquid culture and rhizosphere have revealed that F1- and F3-T6SS are expressed under all conditions, indicating that they are active systems, while F2-T6SS did not show any relevant expression under the tested conditions. The analysis of structural mutants in the three T6SSs has shown that the active F1- and F3-T6SSs are involved in interbacterial killing while F2 is not active in these conditions and its role is still unknown.. A rhizosphere colonization analysis of the double mutant affected in the F1- and F3-T6SS clusters showed that the double mutant was severely impaired in persistence in the rhizosphere microbiome, revealing the importance of these two systems for rhizosphere adaption.
Topics: Adaptation, Physiological; Gene Expression Regulation, Bacterial; Microbial Viability; Microbiota; Multigene Family; Phylogeny; Protein Domains; Pseudomonas fluorescens; Rhizosphere; Type VI Secretion Systems
PubMed: 33707614
DOI: 10.1038/s41598-021-85218-1 -
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 -
Veterinary Microbiology Apr 2015For pathogenic bacteria, the ability to acquire iron is vital to survival in the host. In consequence, many genes involved in iron acquisition are associated with...
For pathogenic bacteria, the ability to acquire iron is vital to survival in the host. In consequence, many genes involved in iron acquisition are associated with bacterial virulence. Pseudomonas fluorescens is a bacterial pathogen to a variety of farmed fish. However, the global regulatory function of iron in pathogenic P. fluorescens is essentially unknown. In this study, in order to identify proteins affected by iron condition at the expression level, we performed proteomic analysis to compare the global protein profiles of P. fluorescens strain TSS, a fish pathogen, cultured under iron-replete and iron-deplete conditions. Twenty-two differentially expressed proteins were identified, most of which were confirmed to be regulated by iron at the mRNA level. To investigate their potential involvement in virulence, the genes encoding four of the 22 proteins, i.e. HemO (heme oxygenase), PspB (serine protease), Sod (superoxide dismutase), and TfeR (TonB-dependent outermembrane ferric enterobactin receptor), were knocked out, and the pathogenicity of the mutants was examined in a model of turbot (Scophthalmus maximus). The results showed that compared to the wild type, the hemO, pspB, and tfeR knockouts were significantly impaired in the ability to survive in host serum, to invade host tissues, and to cause host mortality. Immunization of turbot with recombinant TfeR (rTfeR) and PspB induced production of specific serum antibodies and significant protections against lethal TSS challenge. Further analysis showed that rTfeR antibodies recognized and bound to TSS, and that treatment of TSS with rTfeR antibodies significantly impaired the infectivity of TSS to fish cells. Taken together, these results indicate for the first time that in pathogenic P. fluorescens, iron affects the expression of a large number of proteins including those that are involved in host infection.
Topics: Animals; Bacterial Outer Membrane Proteins; Bacterial Proteins; Carrier Proteins; Fish Diseases; Flatfishes; Gene Expression Regulation, Bacterial; Gene Knockout Techniques; Heme Oxygenase (Decyclizing); Host-Pathogen Interactions; Iron; Iron-Regulatory Proteins; Proteomics; Pseudomonas Infections; Pseudomonas fluorescens; Receptors, Cell Surface; Serine Proteases; Superoxide Dismutase; Virulence
PubMed: 25680811
DOI: 10.1016/j.vetmic.2015.01.020 -
Frontiers in Cellular and Infection... 2022Antagonistic coevolution between hosts and parasites, the reciprocal evolution of host resistance and parasite infectivity, has important implications in ecology and...
Antagonistic coevolution between hosts and parasites, the reciprocal evolution of host resistance and parasite infectivity, has important implications in ecology and evolution. The dynamics of coevolution-notably whether host or parasite has an evolutionary advantage-is greatly affected by the relative amount of genetic variation in host resistance and parasite infectivity traits. While studies have manipulated genetic diversity during coevolution, such as by increasing mutation rates, it is unclear how starting genetic diversity affects host-parasite coevolution. Here, we (co)evolved the bacterium SBW25 and two bacteriophage genotypes of its lytic phage SBW25ɸ2 in isolation (one phage genotype) and together (two phage genotypes). Bacterial populations rapidly evolved phage resistance, and phage reciprocally increased their infectivity in response. When phage populations were evolved with bacteria in isolation, bacterial resistance and phage infectivity increased through time, indicative of arms-race coevolution. In contrast, when both phage genotypes were together, bacteria did not increase their resistance in response to increasing phage infectivity. This was likely due to bacteria being unable to evolve resistance to both phage the same mutations. These results suggest that increasing initial parasite genotypic diversity can give parasites an evolutionary advantage that arrests long-term coevolution. This study has important implications for the applied use of phage in phage therapy and in understanding host-parasite dynamics in broader ecological and evolutionary theory.
Topics: Bacteriophages; Biological Evolution; Genotype; Host-Parasite Interactions; Pseudomonas Phages; Pseudomonas fluorescens
PubMed: 35310856
DOI: 10.3389/fcimb.2022.834406