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Cell Reports Jul 2021Bacterial communities are in a continuous adaptive and evolutionary race for survival. In this work we expand our knowledge on the chemical interplay and specific...
Bacterial communities are in a continuous adaptive and evolutionary race for survival. In this work we expand our knowledge on the chemical interplay and specific mutations that modulate the transition from antagonism to co-existence between two plant-beneficial bacteria, Pseudomonas chlororaphis PCL1606 and Bacillus amyloliquefaciens FZB42. We reveal that the bacteriostatic activity of bacillaene produced by Bacillus relies on an interaction with the protein elongation factor FusA of P. chlororaphis and how mutations in this protein lead to tolerance to bacillaene and other protein translation inhibitors. Additionally, we describe how the unspecific tolerance of B. amyloliquefaciens to antimicrobials associated with mutations in the glycerol kinase GlpK is provoked by a decrease of Bacillus cell membrane permeability, among other pleiotropic responses. We conclude that nutrient specialization and mutations in basic biological functions are bacterial adaptive dynamics that lead to the coexistence of two primary competitive bacterial species rather than their mutual eradication.
Topics: Adaptation, Physiological; Alleles; Anti-Infective Agents; Bacillus; Bacterial Proteins; Drug Resistance, Bacterial; Microbial Sensitivity Tests; Mutation; Permeability; Pseudomonas
PubMed: 34320359
DOI: 10.1016/j.celrep.2021.109449 -
Applied and Environmental Microbiology Jul 2019is a bacterial pathogen that causes severe chronic infections in immunocompromised individuals. This bacterium is highly adaptable to its environments, which frequently...
is a bacterial pathogen that causes severe chronic infections in immunocompromised individuals. This bacterium is highly adaptable to its environments, which frequently select for traits that promote bacterial persistence. A clinically significant temporal adaptation is the formation of surface- or cell-adhered bacterial biofilms that are associated with increased resistance to immune and antibiotic clearance. Extensive research has shown that bacterial flagellar motility promotes formation of such biofilms, whereupon the bacteria subsequently become nonmotile. However, recent evidence shows that antibiotic-tolerant nonattached bacterial aggregates, distinct from surface-adhered biofilms, can form, and these have been reported in the context of lung infections, otitis media, nonhealing wounds, and soft tissue fillers. It is unclear whether the same bacterial traits are required for aggregate formation as for biofilm formation. In this report, using isogenic mutants, we demonstrate that aggregates in liquid cultures are spontaneously formed independent of bacterial flagellar motility and independent of an exogenous scaffold. This contrasts with the role of the flagellum to initiate surface-adhered biofilms. Similarly to surface-attached biofilms, these aggregates exhibit increased antibiotic tolerance compared to planktonic cultures. These findings provide key insights into the requirements for aggregate formation that contrast with those for biofilm formation and that may have relevance for the persistence and dissemination of nonmotile bacteria found within chronic clinical infections. In this work, we have investigated the role of bacterial motility with regard to antibiotic-tolerant bacterial aggregate formation. Previous work has convincingly demonstrated that flagellar motility promotes the formation of surface-adhered biofilms in many systems. In contrast, aggregate formation by was observed for nonmotile but not for motile cells in the presence of an exogenous scaffold. Here, we demonstrate that both wild-type and mutants that genetically lack motility spontaneously form antibiotic-tolerant aggregates in the absence of an exogenously added scaffold. Additionally, we also demonstrate that wild-type (WT) and nonmotile bacteria can coaggregate, shedding light on potential physiological interactions and heterogeneity of aggregates.
Topics: Anti-Bacterial Agents; Biofilms; Carbenicillin; Drug Resistance, Bacterial; Gentamicins; Pseudomonas Infections; Pseudomonas aeruginosa
PubMed: 31076438
DOI: 10.1128/AEM.00844-19 -
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 -
Viruses Jun 2022More than 20% of all are infected with Pf4-related filamentous phage and although their role in virulence of strain PAO1 is well documented, its properties related to...
More than 20% of all are infected with Pf4-related filamentous phage and although their role in virulence of strain PAO1 is well documented, its properties related to therapy are not elucidated in detail. The aim of this study was to determine how phage and antibiotic therapy induce Pf4, whether the released virions can infect other strains and how the phage influences the phenotype of new hosts. The subinhibitory concentrations of ciprofloxacin and mitomycin C increased Pf4 production for more than 50% during the first and sixth hour of exposure, respectively, while mutants appearing after infection with obligatory lytic phage at low MOI produced Pf4 more than four times after 12-24 h of treatment. This indicates that production of Pf4 is enhanced during therapy with these agents. The released virions can infect new strains, as confirmed for models UCBPP-PA14 (PA14) and LESB58, existing both episomally and in a form of a prophage, as confirmed by PCR, RFLP, and sequencing. The differences in properties of Pf4-infected, and uninfected PA14 and LESB58 strains were obvious, as infection with Pf4 significantly decreased cell autoaggregation, pyoverdine, and pyocyanin production, while significantly increased swimming motility and biofilm production in both strains. In addition, in strain PA14, Pf4 increased cell surface hydrophobicity and small colony variants' appearance, but also decreased twitching and swarming motility. This indicates that released Pf4 during therapy can infect new strains and cause lysogenic conversion. The infection with Pf4 increased LESB58 sensitivity to ciprofloxacin, gentamicin, ceftazidime, tetracycline, and streptomycin, and PA14 to ciprofloxacin and ceftazidime. Moreover, the Pf4-infected LESB58 was re-sensitized to ceftazidime and tetracycline, with changes from resistant to intermediate resistant and sensitive, respectively. The obtained results open a new field in phage therapy-treatment with selected filamentous phages in order to re-sensitize pathogenic bacteria to certain antibiotics. However, this approach should be considered with precautions, taking into account potential lysogenic conversion.
Topics: Anti-Bacterial Agents; Biofilms; Ceftazidime; Ciprofloxacin; Inovirus; Pseudomonas; Pseudomonas Phages; Pseudomonas aeruginosa; Tetracyclines
PubMed: 35746731
DOI: 10.3390/v14061261 -
Molecules (Basel, Switzerland) Jul 2023The pollution of industrial wastewater has become a global issue in terms of economic development and ecological protection. has been studied as a bacterium involved in...
The pollution of industrial wastewater has become a global issue in terms of economic development and ecological protection. has been studied as a bacterium involved in the treatment of petroleum pollutants. Our study aimed to investigate the physicochemical properties and drug resistance of isolated from industrial wastewater with a high concentration of sulfate compounds. Firstly, was isolated and then identified using matrix-assisted flight mass spectrometry and 16S rDNA sequencing. Then, biochemical and antibiotic resistance analyses were performed on the , and a microbial high-throughput growth detector was used to assess the growth of the strain. Finally, PCR and proteomics analyses were conducted to determine drug-resistance-related genes/proteins. Based on the results of the spectrum diagram and sequencing, the isolated bacteria were identified as and were positive to reactions of ADH, MTE, CIT, MLT, ONPG, and ACE. was sensitive to most of the tested antibiotics, and its resistance to SXT and CHL and MIN and TIM was intermediate. The growth experiment showed that had a good growth rate in nutrient broth. Additionally, was the resistance gene, and mdtA2, mdtA3, mdtB2, mdaB, and emrK1 were the proteins that were closely associated with the drug resistance of . Our results show the biochemical properties of from industrial wastewater with a high concentration of sulfate compounds and provide a new perspective for to participate in biological removal of chemical pollutants in industrial wastewater.
Topics: Pseudomonas oleovorans; Pseudomonas; Wastewater; DNA, Ribosomal; Environmental Pollutants
PubMed: 37513278
DOI: 10.3390/molecules28145403 -
Frontiers in Cellular and Infection... 2021Bacterial biofilms are important medically, environmentally and industrially and there is a need to understand the processes that govern functional synergy and dynamics...
Bacterial biofilms are important medically, environmentally and industrially and there is a need to understand the processes that govern functional synergy and dynamics of species within biofilm communities. Here, we have used a model, mixed-species biofilm community comprised of PAO1, Pf-5 and KP1. This biofilm community displays higher biomass and increased resilience to antimicrobial stress conditions such as sodium dodecyl sulfate and tobramycin, compared to monospecies biofilm populations. is present at low proportions in the community and yet, it plays a critical role in community function, suggesting it acts as a keystone species in this community. To determine the factors that regulate community composition, we focused on because of its pronounced impact on community structure and function. Specifically, we evaluated the role of the N-acyl homoserine lactone (AHL) dependent quorum sensing (QS) system of PAO1, which regulates group behaviors including biofilm formation and the production of effector molecules. We found that mixed species biofilms containing QS mutants had significantly altered proportions of and populations compared to mixed species biofilms with the wild type . Similarly, inactivation of QS effector genes, e.g. and , also governed the relative species proportions. While the absence of QS did not alter the proportions of the two species in dual species biofilms of and , it resulted in significantly lower proportions of in dual species biofilms with . These observations suggest that QS plays an important role in modulating community biofilm structure and physiology and affects interspecific interactions.
Topics: Acyl-Butyrolactones; Biofilms; Pseudomonas; Pseudomonas aeruginosa; Quorum Sensing
PubMed: 33869078
DOI: 10.3389/fcimb.2021.646991 -
Cellular and Molecular Life Sciences :... Feb 2020Microorganisms acquire energy and nutrients from dynamic environments, where substrates vary in both type and abundance. The regulatory system responsible for... (Review)
Review
Microorganisms acquire energy and nutrients from dynamic environments, where substrates vary in both type and abundance. The regulatory system responsible for prioritizing preferred substrates is known as carbon catabolite repression (CCR). Two broad classes of CCR have been documented in the literature. The best described CCR strategy, referred to here as classic CCR (cCCR), has been experimentally and theoretically studied using model organisms such as Escherichia coli. cCCR phenotypes are often used to generalize universal strategies for fitness, sometimes incorrectly. For instance, extremely competitive microorganisms, such as Pseudomonads, which arguably have broader global distributions than E. coli, have achieved their success using metabolic strategies that are nearly opposite of cCCR. These organisms utilize a CCR strategy termed 'reverse CCR' (rCCR), because the order of preferred substrates is nearly reverse that of cCCR. rCCR phenotypes prefer organic acids over glucose, may or may not select preferred substrates to optimize growth rates, and do not allocate intracellular resources in a manner that produces an overflow metabolism. cCCR and rCCR have traditionally been interpreted from the perspective of monocultures, even though most microorganisms live in consortia. Here, we review the basic tenets of the two CCR strategies and consider these phenotypes from the perspective of resource acquisition in consortia, a scenario that surely influenced the evolution of cCCR and rCCR. For instance, cCCR and rCCR metabolism are near mirror images of each other; when considered from a consortium basis, the complementary properties of the two strategies can mitigate direct competition for energy and nutrients and instead establish cooperative division of labor.
Topics: Carbon; Catabolite Repression; Escherichia coli; Glucose; Humans; Phenotype; Pseudomonadaceae
PubMed: 31768608
DOI: 10.1007/s00018-019-03377-x -
The American Naturalist Sep 2019Predicting the evolution of expanding populations is critical to controlling biological threats such as invasive species and cancer metastasis. Expansion is primarily...
Predicting the evolution of expanding populations is critical to controlling biological threats such as invasive species and cancer metastasis. Expansion is primarily driven by reproduction and dispersal, but nature abounds with examples of evolution where organisms pay a reproductive cost to disperse faster. When does selection favor this "survival of the fastest"? We searched for a simple rule, motivated by evolution experiments where swarming bacteria evolved into a hyperswarmer mutant that disperses ∼100% faster but pays a growth cost of ∼10% to make many copies of its flagellum. We analyzed a two-species model based on the Fisher equation to explain this observation: the population expansion rate () results from an interplay of growth () and dispersal () and is independent of the carrying capacity: . A mutant can take over the edge only if its expansion rate () exceeds the expansion rate of the established species (); this simple condition ( ) determines the maximum cost in slower growth that a faster mutant can pay and still be able to take over. Numerical simulations and time-course experiments where we tracked evolution by imaging bacteria suggest that our findings are general: less favorable conditions delay but do not entirely prevent the success of the fastest. Thus, the expansion rate defines a traveling wave fitness, which could be combined with trade-offs to predict evolution of expanding populations.
Topics: Biological Evolution; Green Fluorescent Proteins; Models, Theoretical; Mutation; Pseudomonas aeruginosa; Selection, Genetic
PubMed: 31553215
DOI: 10.1086/704594 -
Journal of Medical Microbiology Feb 2020During infections, bacterial pathogens can engage in a variety of interactions with each other, ranging from the cooperative sharing of resources to deadly warfare. This... (Review)
Review
During infections, bacterial pathogens can engage in a variety of interactions with each other, ranging from the cooperative sharing of resources to deadly warfare. This is especially relevant in opportunistic infections, where different strains and species often co-infect the same patient and interact in the host. Here, we review the relevance of these social interactions during opportunistic infections using the human pathogen as a case example. In particular, we discuss different types of pathogen-pathogen interactions, involving both cooperation and competition, and elaborate on how they impact virulence in multi-strain and multi-species infections. We then review evolutionary dynamics within pathogen populations during chronic infections. We particuarly discuss how local adaptation through niche separation, evolutionary successions and antagonistic co-evolution between pathogens can alter virulence and the damage inflicted on the host. Finally, we outline how studying bacterial social dynamics could be used to manage infections. We show that a deeper appreciation of bacterial evolution and ecology in the clinical context is important for understanding microbial infections and can inspire novel treatment strategies.
Topics: Animals; Coinfection; Humans; Microbial Interactions; Opportunistic Infections; Pseudomonas Infections; Pseudomonas aeruginosa
PubMed: 31961787
DOI: 10.1099/jmm.0.001134