Pseudomonas pan-genomic analysis informs the discovery of plant pathogen inhibitors Andrew Truman 1 , Alba Pacheco-Moreno 1 , Francesca L. Stefanato 1 , Jonathan J. Ford 1 , Jacob G. Malone 1,2 1 John Innes Centre, UK, 2 University of East Anglia, UK Pseudomonas spp. are one of the most abundant bacterial genera in the soil and rhizosphere, where they can have important roles in promoting plant health 1 . However, the genetic and metabolic determinants of this beneficial activity are only partially understood. In our work, we genetically and phenotypically characterise the Pseudomonas fluorescens population in a commercial potato field, which shows that this single field contains a hugely diverse and dynamic population of Pseudomonas bacteria, whose capacity to produce specialised metabolites is shaped both by plant colonisation and defined environmental inputs 2 . We identify strong correlations between specialised metabolism and antagonism of the potato pathogens Streptomyces scabies and Phytophthora infestans . Genetic and chemical analyses identified hydrogen cyanide and cyclic lipopeptides as key specialised metabolites associated with S. scabies inhibition, which was supported by in planta biocontrol experiments 2 . We used this genetic and phenotypic information to prioritise strains for specialised metabolite discovery 3 , which led to the discovery of the first Pseudomonas producer of 3,7-dihydroxytropolone. We genetically characterise this biosynthetic pathway to gain an insight into the interplay between primary and specialised metabolism for the production of 3,7-dihydroxytropolone in Pseudomonas . Our ongoing use of paired phenotypic-genomic data for the discovery of new bioactive specialised metabolites will also be discussed. We propose that systematic analyses of individual organisms within microbiomes will be crucial to help answer questions relating to microbial communities and host interactions that are difficult to address using global ‘omics approaches alone. For example, the role of many bacterial specialised metabolites in nature is poorly understood, especially for prolific producers such as the pseudomonads and the streptomycetes 4 . References 1. D. M. Weller, Phytopathology , 2007, 97 , 250–256. 2. A. Pacheco-Moreno, F. L. Stefanato, J. J. Ford, C. Trippel, S. Uszkoreit, L. Ferrafiat, L. Grenga, R. Dickens, N. Kelly, A. D. Kingdon, L. Ambrosetti, S. A. Nepogodiev, K. C. Findlay, J. Cheema, M. Trick, G. Chandra, G. Tomalin, J. G. Malone and A. W. Truman, eLife , 2021, 10 , e71900. 3. A. D. Moffat, A. Elliston, N. J. Patron, A. W. Truman and J. A. Carrasco Lopez, Synth. Biol. , 2021, 6 , ysab004. 4. A. van der Meij, S. F. Worsley, M. I. Hutchings and G. P. van Wezel, FEMS Microbiol. Rev. , 2017, 41 , 392–416.
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