Members of the genus Pseudomonas inhabit a wide variety of environments, which is reflected in their versatile metabolic capacity and broad potential for adaptation to fluctuating environmental conditions. Here, we examine and compare the genomes of a range of Pseudomonas spp. encompassing plant, insect and human pathogens, and environmental saprophytes. In addition to a large number of allelic differences of common genes that confer regulatory and metabolic flexibility, genome analysis suggests that many other factors contribute to the diversity and adaptability of Pseudomonas spp. Horizontal gene transfer has impacted the capability of pathogenic Pseudomonas spp. in terms of disease severity (Pseudomonas aeruginosa) and specificity (Pseudomonas syringae). Genome rearrangements likely contribute to adaptation, and a considerable complement of unique genes undoubtedly contributes to strain- and species-specific activities by as yet unknown mechanisms. Because of the lack of conserved phenotypic differences, the classification of the genus has long been contentious. DNA hybridization and genome-based analyses show close relationships among members of P. aeruginosa, but that isolates within the Pseudomonas fluorescens and P. syringae species are less closely related and may constitute different species. Collectively, genome sequences of Pseudomonas spp. have provided insights into pathogenesis and the genetic basis for diversity and adaptation.

Pseudomonas genomes: diverse and adaptable

The use of plant growth promoting bacterial inoculants as live microbial biofertilisers provides a promising alternative to chemical fertilisers and pesticides. Inorganic phosphate solubilisation is one of the major mechanisms of plant growth promotion by plant associated bacteria. This involves bacteria releasing organic acids into the soil which solubilise the phosphate complexes converting them into ortho-phosphate which is available for plant up-take and utilisation. The study presented here describes the ability of endophytic bacterial isolates to produce gluconic acid, solubilise insoluble phosphate and stimulate the growth of Pea plants (Pisum sativum). This study also describes the genetic systems within three of these endophyte isolates thought to be responsible for their effective phosphate solubilising abilities. The results showed that many of the endophytic isolates produced gluconic acid (14-169 mM) and have moderate to high phosphate solubilisation capacities (~ 400-1300 mg L-1). When inoculated to Pea plants grown in sand/soil under soluble phosphate limiting conditions, the endophyte isolates that produced medium to high levels of gluconic acid also displayed enhanced plant growth promotion effects.

/pdf/plant-growth-promotion-induced-by-phosphate-solubilizing-y44kwa1bqe.pdf

Plant growth promotion induced by phosphate solubilizing endophytic Pseudomonas isolates

If living organisms are to survive, they must cope with ever-changing environments. One solution is the evolution of sensing mechanisms allowing modulation of the phenotype in response to specific cues. A simpler alternative is stochastic or random phenotype switching — 'hedging your bets'. A study of Pseudomonas fluorescens bacteria exposed to a fluctuating regime with similarities to environments such as the vertebrate immune system demonstrates the evolution of bet-hedging behaviour in real time. The P. fluorescens strain evolved the capacity to switch randomly between colony types, ensuring survival in an artificial environment that constantly favoured different colonies. The presence of bet hedging in these simple organisms, and the identification of the mutations involved, show how a changing environment can reward risk-spreading behaviour. Such strategies may have been among the earliest evolutionary solutions to life in fluctuating environments. In the face of fluctuating environmental conditions, bet hedging — stochastic switching between phenotypes — can be an advantageous strategy. But how does bet hedging evolve? The de novo evolution of bet hedging in experimental bacterial populations subjected to an environment that continually favoured new phenotypic states is now reported. The findings suggest that risk-spreading strategies may have been among the earliest evolutionary solutions to life in fluctuating environments. Bet hedging—stochastic switching between phenotypic states1,2,3—is a canonical example of an evolutionary adaptation that facilitates persistence in the face of fluctuating environmental conditions. Although bet hedging is found in organisms ranging from bacteria to humans4,5,6,7,8,9,10, direct evidence for an adaptive origin of this behaviour is lacking11. Here we report the de novo evolution of bet hedging in experimental bacterial populations. Bacteria were subjected to an environment that continually favoured new phenotypic states. Initially, our regime drove the successive evolution of novel phenotypes by mutation and selection; however, in two (of 12) replicates this trend was broken by the evolution of bet-hedging genotypes that persisted because of rapid stochastic phenotype switching. Genome re-sequencing of one of these switching types revealed nine mutations that distinguished it from the ancestor. The final mutation was both necessary and sufficient for rapid phenotype switching; nonetheless, the evolution of bet hedging was contingent upon earlier mutations that altered the relative fitness effect of the final mutation. These findings capture the adaptive evolution of bet hedging in the simplest of organisms, and suggest that risk-spreading strategies may have been among the earliest evolutionary solutions to life in fluctuating environments.

/pdf/experimental-evolution-of-bet-hedging-3s8qr1uaft.pdf

Experimental evolution of bet hedging

Cyclic-di-GMP is a ubiquitous second messenger in bacteria. The recent discovery that c-di-GMP antagonistically controls motility and virulence of single, planktonic cells on one hand and cell adhesion and persistence of multicellular communities on the other has spurred interest in this regulatory compound. Cellular levels of c-di-GMP are controlled through the opposing activities of diguanylate cyclases and phosphodiesterases, which represent two large families of output domains found in bacterial one- and two-component systems. This review concentrates on structural and functional aspects of diguanylate cyclases and phosphodiesterases, and on their role in transmitting environmental stimuli into a range of different cellular functions. In addition, we examine several well-established model systems for c-di-GMP signaling, including Pseudomonas, Vibrio, Caulobacter, and Salmonella.

Mechanisms of Cyclic-di-GMP Signaling in Bacteria

We provide here a comparative genome analysis of ten strains within the Pseudomonas fluorescens group including seven new genomic sequences. These strains exhibit a diverse spectrum of traits involved in biological control and other multitrophic interactions with plants, microbes, and insects. Multilocus sequence analysis placed the strains in three sub-clades, which was reinforced by high levels of synteny, size of core genomes, and relatedness of orthologous genes between strains within a sub-clade. The heterogeneity of the P. fluorescens group was reflected in the large size of its pan-genome, which makes up approximately 54% of the pan-genome of the genus as a whole, and a core genome representing only 45–52% of the genome of any individual strain. We discovered genes for traits that were not known previously in the strains, including genes for the biosynthesis of the siderophores achromobactin and pseudomonine and the antibiotic 2-hexyl-5-propyl-alkylresorcinol; novel bacteriocins; type II, III, and VI secretion systems; and insect toxins. Certain gene clusters, such as those for two type III secretion systems, are present only in specific sub-clades, suggesting vertical inheritance. Almost all of the genes associated with multitrophic interactions map to genomic regions present in only a subset of the strains or unique to a specific strain. To explore the evolutionary origin of these genes, we mapped their distributions relative to the locations of mobile genetic elements and repetitive extragenic palindromic (REP) elements in each genome. The mobile genetic elements and many strain-specific genes fall into regions devoid of REP elements (i.e., REP deserts) and regions displaying atypical tri-nucleotide composition, possibly indicating relatively recent acquisition of these loci. Collectively, the results of this study highlight the enormous heterogeneity of the P. fluorescens group and the importance of the variable genome in tailoring individual strains to their specific lifestyles and functional repertoire.

/pdf/comparative-genomics-of-plant-associated-pseudomonas-spp-4to1ni5jw7.pdf

Comparative Genomics of Plant-Associated Pseudomonas spp.: Insights into Diversity and Inheritance of Traits Involved in Multitrophic Interactions

Pseudomonas fluorescens are common soil bacteria that can improve plant health through nutrient cycling, pathogen antagonism and induction of plant defenses. The genome sequences of strains SBW25 and Pf0-1 were determined and compared to each other and with P. fluorescens Pf-5. A functional genomic in vivo expression technology (IVET) screen provided insight into genes used by P. fluorescens in its natural environment and an improved understanding of the ecological significance of diversity within this species. Comparisons of three P. fluorescens genomes (SBW25, Pf0-1, Pf-5) revealed considerable divergence: 61% of genes are shared, the majority located near the replication origin. Phylogenetic and average amino acid identity analyses showed a low overall relationship. A functional screen of SBW25 defined 125 plant-induced genes including a range of functions specific to the plant environment. Orthologues of 83 of these exist in Pf0-1 and Pf-5, with 73 shared by both strains. The P. fluorescens genomes carry numerous complex repetitive DNA sequences, some resembling Miniature Inverted-repeat Transposable Elements (MITEs). In SBW25, repeat density and distribution revealed 'repeat deserts' lacking repeats, covering approximately 40% of the genome. P. fluorescens genomes are highly diverse. Strain-specific regions around the replication terminus suggest genome compartmentalization. The genomic heterogeneity among the three strains is reminiscent of a species complex rather than a single species. That 42% of plant-inducible genes were not shared by all strains reinforces this conclusion and shows that ecological success requires specialized and core functions. The diversity also indicates the significant size of genetic information within the Pseudomonas pan genome.

/pdf/genomic-and-genetic-analyses-of-diversity-and-plant-2hx3plbt8m.pdf

Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens

Understanding the connections among genotype, phenotype, and fitness through evolutionary time is a central goal of evolutionary genetics. Wrinkly spreader (WS) genotypes evolve repeatedly in model Pseudomonas populations and show substantial morphological and fitness differences. Previous work identified genes contributing to the evolutionary success of WS, in particular the di-guanylate cyclase response regulator, WspR. Here we scrutinize the Wsp signal transduction pathway of which WspR is the primary output component. The pathway has the hallmarks of a chemosensory pathway and genetic analyses show that regulation and function of Wsp is analogous to the Che chemotaxis pathway from Escherichia coli. Of significance is the methyltransferase (WspC) and methylesterase (WspF) whose opposing activities form an integral feedback loop that controls the activity of the kinase (WspE). Deductions based on the regulatory model suggested that mutations within wspF were a likely cause of WS. Analyses of independent WS genotypes revealed numerous simple mutations in this single open reading frame. Remarkably, different mutations have different phenotypic and fitness effects. We suggest that the negative feedback loop inherent in Wsp regulation allows the pathway to be tuned by mutation in a rheostat-like manner.

https://www.genetics.org/content/genetics/176/1/441.full.pdf

Adaptive divergence in experimental populations of Pseudomonas fluorescens. III. Mutational origins of wrinkly spreader diversity.

Pseudomonas fluorescens SBW25 is a gram-negative, fluorescent pseudomonad that is able to colonise the roots and leaves of a wide range of plants. PfSBW25 has been widely adopted as a model organism for investigations into the molecular basis of plant colonisation, plant growth promotion and biocontrol, and is also used as a model organism in studies of biofilm formation and experimental evolution. The 6.7 Mb genome of PfSBW25 is currently being sequenced at the Sanger Institute. We have developed two in vivo expression technology (IVET) systems for P. fluorescens SBW25, and have used IVET as a functional genomics approach to identify and characterise more than a hundred plant-induced genes from P. fluorescens SBW25. The predicted functions of many of these genes can be assigned to broad functional categories such as nutrient acquisition, surface colonisation, stress tolerance, antibiotic biosynthesis, protein secretion and transcriptional regulation. We have begun the process of analysing the function and expression of some of these plant-induced genes in depth, focusing in particular on genes encoding a rhizosphere-induced type III protein secretion system (TTSS) that is similar to the Hrp TTSS of P. syringae. Functional genomic analyses of P. fluorescens SBW25 have provided insight into the biology and ecology of plant-colonising Pseudomonas, and into the utility and limitations of functional genomic techniques in understanding the biology of bacteria in complex environments.

Pseudomonas in the underworld: the secret life of Pseudomonas fluorescens SBW25

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Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens

Adaptive divergence in experimental populations of Pseudomonas fluorescens. III. Mutational origins of wrinkly spreader diversity.

Pseudomonas in the underworld: the secret life of Pseudomonas fluorescens SBW25