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1,049 results for “Pseudomonas”
Data from: Social evolution of toxic metal bioremediation in Pseudomonas aeruginosa.
Bacteria are often iron-limited, and hence produce extracellular iron-scavenging siderophores. A crucial feature of siderophore production is that it can be an altruistic behaviour (individually costly but benefitting neighbouring cells), thus siderophore producers can be invaded by non-producing social 'cheats'. Recent studies have shown that siderophores can also bind other heavy metals (such as Cu and Zn), but in this case siderophore chelation actually reduces metal uptake by bacteria. These complexes reduce heavy metal toxicity, hence siderophore production may contribute to toxic metal bioremediation. Here, we show that siderophore production in the context of bioremediation is also an altruistic trait and can be exploited by cheating phenotypes in the opportunistic pathogen Pseudomonas aeruginosa. Specifically, we show that in toxic copper concentrations (i) siderophore non-producers evolve de novo and reach high frequencies, and (ii) producing strains are fitter than isogenic non-producing strains in monoculture, and vice versa in co-culture. Moreover, we show that the evolutionary effect copper has on reducing siderophore production is greater than the reduction observed under iron-limited conditions. We discuss the relevance of these results to the evolution of siderophore production in natural communities and heavy metal bioremediation.
Data from: Bacillus cereus AR156 activates defense responses to Pseudomonas syringae pv. tomato in Arabidopsis thaliana similarly to flg22
Bacillus cereus AR156 (AR156) is a plant growth promoting rhizobacterium capable of inducing systemic resistance to Pseudomonas syringae pv. tomato (Pst) in Arabidopsis thaliana (Arabidopsis). Here we show that when applied to Arabidopsis leaves, AR156 acted similarly to flg22, a typical pathogen-associated molecular pattern (PAMP), in initiating PAMP-triggered immunity (PTI). AR156-elicited PTI responses included phosphorylation of MPK3 and MPK6, induction of the expression of defense-related genes PR1, FRK1, WRKY22, and WRKY29; production of reactive oxygen species; and callose deposition. Pretreatment with AR156 still significantly reduced Pst multiplication and disease severity in NahG transgenic plants and mutants sid2-2, jar1, etr1, ein2, npr1, and fls2. This suggests that AR156-induced PTI responses require neither salicylic acid, jasmonic acid, and ethylene signaling; nor flagella receptor kinase FLS2, the receptor of flg22. On the other hand, AR156 and flg22 acted in concert to differentially regulate a number of AGO1-bound miRNAs that function to mediate PTI. A full-genome transcriptional profiling analysis indicated that AR156 and flg22 activated similar transcriptional programs, co-regulating the expression of 117 genes; their concerted regulation of 16 genes was confirmed by real-time quantitative PCR analysis. These results suggest that AR156 activates basal defense responses to Pst in Arabidopsis similarly to flg22.
Data from: The bacterium Pseudomonas aeruginosa senses and gradually responds to inter-specific competition for iron
Phenotypic plasticity in response to competition is a well-described phenomenon in higher organisms. Here, we show that also bacteria have the ability to sense the presence of competitors and mount fine-tuned responses to match prevailing levels of competition. In our experiments, we studied inter-specific competition for iron between the bacterium Pseudomonas aeruginosa (PA) and its competitor Burkholderia cenocepacia (BC). We focused on the ability of PA to phenotypically adjust the production of pyoverdine, an iron-scavenging siderophore. We found that PA up-regulates pyoverdine production early on during competition under condition of low iron availability. This plastic upregulation was fine-tuned in response to the level of competition imposed by BC, and seems to confer a relative fitness benefit to PA in the form of an earlier initiation of growth. At later time points, however, PA showed reduced growth in mixed compared to monoculture, suggesting that competitive responses are costly. Altogether, our results demonstrate that phenotypic plasticity in siderophore production plays an important role in inter-specific competition for iron. Upregulating siderophore production may be a powerful strategy to lock iron away from competing species, and to reserve this nutrient for strain members possessing the compatible receptor for uptake.
Data from: Dynamic social behaviour in a bacterium: Pseudomonas aeruginosa partially compensates for siderophore loss to cheats
Cooperation underlies diverse phenomena including the origins of multicellular life, human behaviour in economic markets and the mechanisms by which pathogenic bacteria cause disease. Experiments with microorganisms have advanced our understanding of how, when and why cooperation evolves, but the extent to which microbial cooperation can recapitulate aspects of animal behaviour is debated. For instance, understanding the evolution of behavioural response rules (how should one individual respond to another's decision to cooperate or defect?) is a key part of social evolution theory, but the possible existence of such rules in social microbes has not been explored. In one specific context (biparental care in animals), cooperation is maintained if individuals respond to a partner's defection by increasing their own investment into cooperation, but not so much that this fully compensates for the defector's lack of investment. This is termed 'partial compensation.' Here, I show that partial compensation for the presence of non-cooperating 'cheats' is also observed in a microbial social behaviour: the cooperative production of iron-scavenging siderophores by the bacterium Pseudomonas aeruginosa. A period of evolution in the presence of cheats maintains this response, whereas evolution in the absence of cheats leads to a loss of compensatory behaviour. These results demonstrate i) the remarkable flexibility of bacterial social behaviour; ii) the potential generality of partial compensation as a social response rule; and iii) the need for mathematical models to explore the evolution of response rules in multi-player social interactions.
Denitrification performance of pseudomonas fluorescens Z03 immobilized by GO modified PVA-SA gel bead at low temperature
<p>Experimental data monitoring results.</p>
Data from: Epistasis buffers the fitness effects of rifampicin-resistance mutations in Pseudomonas aeruginosa
Epistatic interactions between resistance mutations in antibiotic-free environments potentially play a crucial role in the spread of resistance in pathogen populations by determining the fitness cost associated with resistance. We used an experimental evolution approach to test for epistatic interactions between 14 different pairs of rifampicin mutations in the pathogenic bacterium Pseudomonas aeruginosa in 42 different rifampicin-free environments. First, we show that epistasis between rifampicin-resistance mutations tends to be antagonistic: the fitness effect of having two mutations is generally smaller than that predicted from the effects of individual mutations on the wild type. Second, we show that sign epistasis between resistance mutations is both common and strong; most notably, pairs of deleterious resistance mutations often partially or completely compensate for each others' costs, revealing a novel mechanism for compensatory adaptation. These results suggest that antagonistic epistasis between intragenic resistance mutations may be a key determinant of the cost of antibiotic resistance and compensatory adaptation in pathogen populations.
Data from: Evolutionary dynamics of interlinked public goods traits: an experimental study of siderophore production in Pseudomonas aeruginosa
Public goods cooperation is common in microbes, and there is much interest in understanding how such traits evolve. Research in recent years has identified several important factors that shape the evolutionary dynamics of such systems, yet few studies have investigated scenarios involving interactions between multiple public goods. Here we offer general predictions about the evolutionary trajectories of two public goods traits having positive, negative or neutral regulatory influence on one another's expression, and we report on a test of some of our predictions in the context of Pseudomonas aeruginosa's production of two interlinked iron-scavenging siderophores. First, we confirmed that both pyoverdine and pyochelin siderophores do operate as public goods under appropriate environmental conditions. We then tracked their production in lines experimentally evolved under different iron-limitation regimes known to favour different siderophore expression profiles. Under strong iron limitation, where pyoverdine represses pyochelin, we saw a decline in pyoverdine and a concomitant increase in pyochelin – consistent with expansion of pyoverdine-defective cheats derepressed for pyochelin. Under moderate iron limitation, pyochelin declined – again consistent with an expected cheat invasion scenario – but there was no concomitant shift in pyoverdine because cross-suppression between the traits is unidirectional only. Alternating exposure to strong and moderate iron-limitation caused qualitatively similar though lesser shifts compared to the constant-environment regimes. Our results confirm that the regulatory inter-connections between public goods traits can significantly modulate the course of evolution, yet also suggest how we can start to predict the impacts such complexities will have on phenotypic divergence and community stability.
Data from: Selection experiments reveal trade-offs between swimming and twitching motilities in Pseudomonas aeruginosa
Bacteria possess a range of mechanisms to move in different environments, and these mechanisms have important direct and correlated impacts on the virulence of opportunistic pathogens. Bacteria use two surface organelles to facilitate motility: a single polar flagellum, and type IV pili, enabling swimming in aqueous habitats and twitching along hard surfaces, respectively. Here, we address whether there are trade-offs between these motility mechanisms, and hence whether different environments could select for altered motility. We experimentally evolved initially isogenic Pseudomonas aeruginosa under conditions which favoured the different types of motility, and found evidence for a trade-off mediated by antagonistic pleiotropy between swimming and twitching. Moreover, changes in motility resulted in correlated changes in other behaviours, including biofilm formation and growth within an insect host. This suggests environmental origins of a particular motile opportunistic pathogen could predictably influence motility and virulence.
Data from: Adaptive landscapes in evolving populations of Pseudomonas fluorescens
The repeatability of adaptive evolution depends on the ruggedness of the underlying adaptive landscape. We contrasted the relative ruggedness of adaptive landscapes across two environments by measuring the variance in fitness and metabolic phenotype within and among genetically distinct strains of Pseudomonas fluorescens in two environments differing only in the carbon source provided (glucose vs. xylose). Fitness increased in all lines, plateauing in one environment but not the other. The pattern of variance in fitness among replicate lines was unique to the selection environment; it increased over the course of the experiment in xylose but not in glucose. Metabolic phenotypes displayed two results: (1) populations adapted via changes that were distinctive to their selection environment, and (2) endpoint phenotypes were less variable in glucose than in xylose. These results indicate that although the response to selection is highly repeatable at the level of fitness, the underlying genetic routes taken were different for each environment and more variable in xylose. We suggest that this reflects a more rugged adaptive landscape in xylose compared to glucose. Our study demonstrates the utility of using replicate selection lines with different evolutionary starting points to try and quantify the relative ruggedness of adaptive landscapes.
Data from: Linking system-wide impacts of RNA polymerase mutations to the fitness cost of rifampin resistance in Pseudomonas aeruginosa
Fitness costs play a key role in the evolutionary dynamics of antibiotic resistance in bacteria by generating selection against resistance in the absence of antibiotics. Although the genetic basis of antibiotic resistance is well understood, the precise molecular mechanisms linking the genetic basis of resistance to its fitness cost remain poorly characterized. Here, we examine how the system-wide impacts of mutations in the RNA polymerase (RNAP) gene rpoB shape the fitness cost of rifampin resistance in Pseudomonas aeruginosa. Rifampin resistance mutations reduce transcriptional efficiency, and this explains 76% of the variation in fitness among rpoB mutants. The pleiotropic consequence of rpoB mutations is that mutants show altered relative transcript levels of essential genes. We find no evidence that global transcriptional responses have an impact on the fitness cost of rifampin resistance as revealed by transcriptome sequencing (RNA-Seq). Global changes in the transcriptional profiles of rpoB mutants compared to the transcriptional profile of the rifampin-sensitive ancestral strain are subtle, demonstrating that the transcriptional regulatory network of P. aeruginosa is robust to the decreased transcriptional efficiency associated with rpoB mutations. On a smaller scale, we find that rifampin resistance mutations increase the expression of RNAP due to decreased termination at an attenuator upstream from rpoB, and we argue that this helps to minimize the cost of rifampin resistance by buffering against reduced RNAP activity. In summary, our study shows that it is possible to dissect the molecular mechanisms underpinning variation in the cost of rifampin resistance and highlights the importance of genome-wide buffering of relative transcript levels in providing robustness against resistance mutations. IMPORTANCE Antibiotic resistance mutations carry fitness costs. Relative to the characteristics of their antibiotic-sensitive ancestors, resistant mutants show reduced growth rates and competitive abilities. Fitness cost plays an important role in the evolution of antibiotic resistance in the absence of antibiotics; however, the molecular mechanisms underlying these fitness costs is not well understood. We applied a systems-level approach to dissect the molecular underpinnings of the fitness costs associated with rifampin resistance in P. aeruginosa and showed that most of the variation in fitness cost can be explained by the direct effect of resistance mutations on the enzymatic activity of the mutated gene. Pleiotropic changes in transcriptional profiles are subtle at a genome-wide scale, suggesting that the gene regulatory network of P. aeruginosa is robust in the face of the direct effects of resistance mutations.
Data from: Local adaptation is associated with zinc tolerance in Pseudomonas endophytes of the metal-hyperaccumulator plant Noccaea caerulescens
Metal hyperaccumulating plants, which are hypothesised to use metals for defence against pests and pathogens, provide a unique context in which to study plant–pathogen co-evolution. Previously, we demonstrated that the high concentrations of zinc found in leaves of the hyperaccumulator Noccaea caerulescens provide protection against bacterial pathogens, with a potential trade-off between metal-based and pathogen-induced defences. We speculated that an evolutionary arms race between zinc-based defences in N. caerulescens and zinc tolerance in pathogens might have driven the development of the hyperaccumulation phenotype. Here, we investigate the possibility of local adaptation by bacteria to the zinc-rich environment of N. caerulescens leaves and show that leaves sampled from the contaminated surroundings of a former mine site harboured endophytes with greater zinc tolerance than those within plants of an artificially created hyperaccumulating population. Experimental manipulation of zinc concentrations in plants of this artificial population influenced the zinc tolerance of recovered endophytes. In laboratory experiments, only endophytic bacteria isolated from plants of the natural population were able to grow to high population densities in any N. caerulescens plants. These findings suggest that long-term co-existence with zinc hyperaccumulating plants leads to local adaptation by endophytic bacteria to the environment within their leaves.
Data from: Pan-genome dynamics of Pseudomonas gene complements enriched across hexachlorocyclohexane dumpsite
Background: Phylogenetic heterogeneity across Pseudomonas genus is complemented by its diverse genome architecture enriched by accessory genetic elements (plasmids, transposons, and integrons) conferring resistance across this genus. Here, we sequenced a stress tolerant genotype i.e. Pseudomonas sp. strain RL isolated from a hexachlorocyclohexane (HCH) contaminated pond (45 mg of total HCH g−1 sediment) and further compared its gene repertoire with 17 reference ecotypes belonging to P. stutzeri, P. mendocina, P. aeruginosa, P. psychrotolerans and P. denitrificans, representing metabolically diverse ecosystems (i.e. marine, clinical, and soil/sludge). Metagenomic data from HCH contaminated pond sediment and similar HCH contaminated sites were further used to analyze the pan-genome dynamics of Pseudomonas genotypes enriched across increasing HCH gradient. Results: Although strain RL demonstrated clear species demarcation (ANI ≤ 80.03%) from the rest of its phylogenetic relatives, it was found to be closest to P. stutzeri clade which was further complemented functionally. Comparative functional analysis elucidated strain specific enrichment of metabolic pathways like α-linoleic acid degradation and carbazole degradation in Pseudomonas sp. strain RL and P. stutzeri XLDN-R, respectively. Composition based methods (%codon bias and %G + C difference) further highlighted the significance of horizontal gene transfer (HGT) in evolution of nitrogen metabolism, two-component system (TCS) and methionine metabolism across the Pseudomonas genomes used in this study. An intact mobile class-I integron (3,552 bp) with a captured gene cassette encoding for dihydrofolate reductase (dhfra1) was detected in strain RL, distinctly demarcated from other integron harboring species (i.e. P. aeruginosa, P. stutzeri, and P. putida). Mobility of this integron was confirmed by its association with Tnp21-like transposon (95% identity) suggesting stress specific mobilization across HCH contaminated sites. Metagenomics data from pond sediment and recently surveyed HCH adulterated soils revealed the in situ enrichment of integron associated transposase gene (TnpA6100) across increasing HCH contamination (0.7 to 450 mg HCH g−1 of soil). Conclusions: Unlocking the potential of comparative genomics supplemented with metagenomics, we have attempted to resolve the environment and strain specific demarcations across 18 Pseudomonas gene complements. Pan-genome analyses of these strains indicate at astoundingly diverse metabolic strategies and provide genetic basis for the cosmopolitan existence of this taxon.
Data from: Cheating and resistance to cheating in natural populations of the bacterium Pseudomonas fluorescens
Bacteria perform cooperative behaviours that are exploitable by non-cooperative cheats, and cheats frequently arise and coexist with cooperators in laboratory microcosms. However, evidence of competitive dynamics between cooperators and cheats in nature remains limited. Using the production of pyoverdine, an iron-scavenging molecule, and natural soil populations of Pseudomonas fluorescens, we found that (1) non-producers are present in the population; (2) they co-occur (<1cm3) with pyoverdine producers; (3) they retain functional pyoverdine receptors and (4) they can utilize the pyoverdine of on average 52% of producers. This suggests non-producers can potentially act as social cheats in soil: utilizing the pyoverdine of others while producing little or none themselves. However, we found considerable variation in the extent to which non-producers can exploit cooperators, as some cooperators appear to produce exclusive forms of pyoverdine or kill non-producers with toxins. We examined the consequences of this variation using theoretical modeling. Variance in exploitability leads to some cheats gaining increased fitness benefits and others decreased benefits. However, the absolute gain in fitness from high exploitation is lower than the drop in fitness from low exploitation, decreasing the mean fitness of cheats and subsequently lowering the proportion of cheats maintained in the population Our results suggest that although cooperator-cheat dynamics can occur in soil, a range of mechanisms can prevent non-producers from exploiting cooperators.
Data from: Co-evolutionary dynamics between public good producers and cheats in the bacterium Pseudomonas aeruginosa
The production of beneficial public goods is common in the microbial world, and so is cheating – the exploitation of public goods by non-producing mutants. Here, we examine co-evolutionary dynamics between cooperators and cheats and ask whether cooperators can evolve strategies to reduce the burden of exploitation, and whether cheats in turn can improve their exploitation abilities. We evolved cooperators of the bacterium Pseudomonas aeruginosa, producing the shareable iron-scavenging siderophore pyoverdine, together with cheats, defective in pyoverdine production but proficient in uptake. We found that cooperators managed to co-exist with cheats in 56% of all replicates over approximately 150 generations of experimental evolution. Growth and competition assays revealed that co-existence was fostered by a combination of general adaptions to the media and specific adaptions to the co-evolving opponent. Phenotypic screening and whole-genome re-sequencing of evolved clones confirmed this pattern, and suggest that cooperators became less exploitable by cheats because they significantly reduced their pyoverdine investment. Cheats, meanwhile, improved exploitation efficiency through mutations blocking the costly pyoverdine-signalling pathway. Moreover, cooperators and cheats evolved reduced motility, a pattern that likely represents adaptation to laboratory conditions, but at the same time also affects social interactions by reducing strain mixing and pyoverdine sharing. Overall, we observed parallel evolution, where co-existence of cooperators and cheats was enabled by a combination of adaptations to the abiotic and social environment and their interactions.
Data from: The path to re-evolve cooperation is constrained in Pseudomonas aeruginosa
Background. A common form of cooperation in bacteria is based on the secretion of beneficial metabolites, shareable as public good among cells within a group. Because cooperation can be exploited by "cheating" mutants, which contribute less or nothing to the public good, there has been great interest in understanding the conditions required for cooperation to remain evolutionarily stable. In contrast, much less is known about whether cheats, once fixed in the population, are able to revert back to cooperation when conditions change. Here, we tackle this question by subjecting experimentally evolved cheats of Pseudomonas aeruginosa, partly deficient for the production of the iron-scavenging public good pyoverdine, to conditions previously shown to favor cooperation. Results. Following approximately 200 generations of experimental evolution, we screened 720 evolved clones for changes in their pyoverdine production levels. We found no evidence for the re-evolution of full cooperation, even in environments with increased spatial structure, and reduced costs of public good production - two conditions that have previously been shown to maintain cooperation. In contrast, we observed selection for complete abolishment of pyoverdine production. The patterns of complete trait degradation were likely driven by "cheating on cheats" in unstructured, iron-limited environments where pyoverdine is important for growth, and selection against a maladaptive trait in iron-rich environments where pyoverdine is superfluous. Conclusions. Our study shows that the path to re-evolve public-goods cooperation can be constrained. While a limitation of the number of mutational targets potentially leading to reversion might be one reason for the observed pattern, an alternative explanation is that the selective conditions required for revertants to spread from rare are much more stringent than those needed to maintain cooperation.
Investigating the role of Pseudomonas dye-decolorizing peroxidases in quinone redox cycling for bio-design of a DypB-based lignin degrading enzyme cocktail
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The collapse of cooperation during range expansion of Pseudomonas aeruginosa [Source Data]
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Dataset of the bacterial fitness estimation values and mutation identifications from: Rapid decline of adaptation of Pseudomonas fluorescens to soil biotic environment
<p>Interactions between microbes can both constrain and enhance adaptation, but to date, most studies employ simplified communities and environments. We measured fitness of populations of the soil bacterium Pseudomonas fluorescens that have been evolved in both the presence and absence of a natural potting soil microbial community. Populations from both environments showed similar fitness increases with respect to the ancestor in the absence of the community, suggesting no significant cost of evolving with the community. By contrast, fitness in the presence of the community increased for community-evolved populations, but decreased considerably below the ancestral state for populations evolved in the absence of the community. This suggests some abiotic beneficial mutations are costly in the presence of the community, while others are not, with the former only selected against in the presence of the community. Most mutations underpinning fitness changes were clone specific, supporting the view that there are multiple genetic pathways to adaptation in this complex environment. Such extreme mutational effects have not been observed in comparable in vitro studies that employ much simpler abiotic and biotic environments, and suggest that a caution is need when extrapolating results from simplified in vitro systems to real-world contexts.</p>
Figure 9 from: Dorri K, Modaresi F, Shakibaie MR, Moazamian E (2022) Effect of gold nanoparticles on the expression of efflux pump mexA and mexB genes of Pseudomonas aeruginosa strains by Quantitative real-time PCR. Pharmacia 69(1): 125-133. https://doi.org/10.3897/pharmacia.69.e77608
Figure 9 Results of toxA gene replication in clinical isolates of Pseudomonas aeruginosa. Well 1: marker size 50 bp; Well 2–23: positive samples of size 85 bp; Well 24: negative control; Well 25: positive control of Pseudomonas aeruginosa PTCC 17589.
Figure 8 from: Dorri K, Modaresi F, Shakibaie MR, Moazamian E (2022) Effect of gold nanoparticles on the expression of efflux pump mexA and mexB genes of Pseudomonas aeruginosa strains by Quantitative real-time PCR. Pharmacia 69(1): 125-133. https://doi.org/10.3897/pharmacia.69.e77608
Figure 8 Results of Pela gene replication in clinical isolates of Pseudomonas aeruginosa. Well 1: marker size 50 bp; Well 2–23: positive samples of size 148 bp; Well 24: negative control; Well 25: positive control of Pseudomonas aeruginosa PTCC 17589.
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