In Silico Characterization and Phylogenetic Distribution of Extracellular Matrix Components in the Model Rhizobacteria Pseudomonas fluorescens F113 and Other Pseudomonads

Abstract

Biofilms are complex structures that are crucial during host–bacteria interaction and colonization. Bacteria within biofilms are surrounded by an extracellular matrix (ECM) typically composed of proteins, polysaccharides, lipids, and DNA. Pseudomonads contain a variety of ECM components, some of which have been extensively characterized. However, neither the ECM composition of plant-associated pseudomonads nor their phylogenetic distribution within the genus has been so thoroughly studied. In this work, we use in silico methods to describe the ECM composition of Pseudomonas fluorescens F113, a plant growth-promoting rhizobacteria and model for rhizosphere colonization. These components include the polysaccharides alginate, poly-N-acetyl-glucosamine (PNAG) and levan; the adhesins LapA, MapA and PsmE; and the functional amyloids in Pseudomonas. Interestingly, we identified novel components: the Pseudomonas acidic polysaccharide (Pap), whose presence is limited within the genus; and a novel type of Flp/Tad pilus, partially different from the one described in P. aeruginosa. Furthermore, we explored the phylogenetic distribution of the most relevant ECM components in nearly 600 complete Pseudomonas genomes. Our analyses show that Pseudomonas populations contain a diverse set of gene/gene clusters potentially involved in the formation of their ECMs, showing certain commensal versus pathogen lifestyle specialization.

Beyond the Wall: Exopolysaccharides in the Biofilm Lifestyle of Pathogenic and Beneficial Plant-Associated Pseudomonas

“…Among all the exopolysaccharides that are produced by plant-associated Pseudomonas [ 72 ], those that have been mainly studied are alginate, cellulose, and Psl ( Table 1 ). A description of their functions in biofilm formation and architecture and their ecological significance during pathogenic and beneficial plant–bacteria interactions are listed below.…”

“…Several biosynthesis and regulation mechanisms have been described for bacterial cellulose, but a common role of this component is to facilitate the establishment of efficient host-bacteria interactions [ 95 ]. Previous studies reported that several plant-associated Pseudomonas species can produce cellulose, including the plant-associated pathogenic bacteria P. syringae , P. asplenii , P. marginalis , P. corrugate, and P. savastanoi and beneficial bacteria, such as P. fluorescens and P. putida [ 72 , 93 , 94 ]. Within the Pseudomonas genus, P. fluorescens SBW25 (SBW25) is traditionally used as the model strain for the study of bacterial cellulose.…”

“…This exopolysaccharide is involved in the formation of floating biofilms, also called pellicles, in many strains of the species mentioned above, including the SBW25 [ 31 , 93 , 96 , 97 , 98 , 99 ]. The P. aeruginosa species does not contain the cellulose operon [ 72 ]. In particular, P. aeruginosa PAO1 and PA14 strains, which have been traditionally used as model strains for conducting biofilm studies within the Pseudomonas genus, were tested for cellulose production, but in line with in silico observations [ 72 ], they were not found to produce this exopolysaccharide [ 94 ].…”

“…The P. aeruginosa species does not contain the cellulose operon [ 72 ]. In particular, P. aeruginosa PAO1 and PA14 strains, which have been traditionally used as model strains for conducting biofilm studies within the Pseudomonas genus, were tested for cellulose production, but in line with in silico observations [ 72 ], they were not found to produce this exopolysaccharide [ 94 ]. However, the PAO1 and PA14 strains contain a seven-gene operon that encodes Pel, which is a polymer composed of partially acetylated 1→4 glycosidic linkages of N-acetylgalactosamine and N-acetylglucosamine [ 100 ].…”

“…However, the PAO1 and PA14 strains contain a seven-gene operon that encodes Pel, which is a polymer composed of partially acetylated 1→4 glycosidic linkages of N-acetylgalactosamine and N-acetylglucosamine [ 100 ]. The pel operon is poorly conserved among environmental Pseudomonas [ 72 , 100 , 101 ]. Interestingly, Pel promotes the formation of pellicle biofilms, as has also been described for cellulose [ 102 ].…”