Genetic Potential of the Biocontrol Agent Pseudomonas brassicacearum (Formerly P. trivialis) 3Re2-7 Unraveled by Genome Sequencing and Mining, Comparative Genomics and Transcriptomics

Abstract

The genus Pseudomonas comprises many known plant-associated microbes with plant growth promotion and disease suppression properties. Genome-based studies allow the prediction of the underlying mechanisms using genome mining tools and the analysis of the genes unique for a strain by implementing comparative genomics. Here, we provide the genome sequence of the strain Pseudomonas brassicacearum 3Re2-7, formerly known as P. trivialis and P. reactans, elucidate its revised taxonomic classification, experimentally verify the gene predictions by transcriptome sequencing, describe its genetic biocontrol potential and contextualize it to other known Pseudomonas biocontrol agents. The P. brassicacearum 3Re2-7 genome comprises a circular chromosome with a size of 6,738,544 bp and a GC-content of 60.83%. 6267 genes were annotated, of which 6113 were shown to be transcribed in rich medium and/or in the presence of Rhizoctonia solani. Genome mining identified genes related to biocontrol traits such as secondary metabolite and siderophore biosynthesis, plant growth promotion, inorganic phosphate solubilization, biosynthesis of lipo- and exopolysaccharides, exoproteases, volatiles and detoxification. Core genome analysis revealed, that the 3Re2-7 genome exhibits a high collinearity with the representative genome for the species, P. brassicacearum subsp. brassicacearum NFM421. Comparative genomics allowed the identification of 105 specific genes and revealed gene clusters that might encode specialized biocontrol mechanisms of strain 3Re2-7. Moreover, we captured the transcriptome of P. brassicacearum 3Re2-7, confirming the transcription of the predicted biocontrol-related genes. The gene clusters coding for 2,4-diacetylphloroglucinol (phlABCDEFGH) and hydrogen cyanide (hcnABC) were shown to be highly transcribed. Further genes predicted to encode putative alginate production enzymes, a pyrroloquinoline quinone precursor peptide PqqA and a matrixin family metalloprotease were also found to be highly transcribed. With this study, we provide a basis to further characterize the mechanisms for biocontrol in Pseudomonas species, towards a sustainable and safe application of P. brassicacearum biocontrol agents.

Friend or foe? Exploring the fine line between Pseudomonas brassicacearum and phytopathogens

“…Twenty-one P. brassicacearum genomes have been sequenced to date and are publicly available, including an isolate involved in stress tolerance of wheat and potato, P. trivialis 3Re2-7, that was recently reclassified as P. brassicacearum [20] ( Table 1). Analysis of the hierarchical relationship of the 21 P. brassicacearum strains revealed that 19 cluster into four main branches [20]. The representative strain, NFM421, belongs to the largest group, which is comprised of TM1A3, Delaware, Wood1, BS3663, 3Re2-7, PP1_210F, L13-6-12, PA1G7, LBUM300, 51MFCVI2.1 and 93F8.…”

“…There are currently no metadata associated with BS3663 and to the best of our knowledge, there are no peer-reviewed publications available on this or strain 51MFCVI2.1. The second group includes DF41, a well-characterized biocontrol isolate from canola root [22,23,9,24,25], as well as two strains isolated from Wyoming soil, 36B7 and 36D4 which have high (98.3 and 98.5 %) pairwise amino acid identities (AAIs) with DF41 [20]. Two other soil isolates from Wyoming, 38D4 and 38D7, form the third group, while the fourth group consists of 37D10 and 48H11, isolated from soils in Wyoming and Wisconsin, respectively.…”

“…While there is a limited number of published studies regarding TM1A3, Delaware, Wood1, and 93F8, 38D4, 38D7, 37D10, 48H11 and Wood3, early investigations show that these strains exhibit biocontrol activity against phytopathogenic nematodes, fungi and bacteria [21,[26][27][28][29]. Based on the pairwise AAIs of 2331 core genes, all strains from the first and second groups, as well as LZ-4 and Wood3, show conservation with the P. brassicacearum representative strain, NFM421 [20]. However, AAIs of 37D10, 48H11, 38D7 and 38D4 with NFM421 are only 88.6-89.5 %, which is below the suggested species threshold of 95 % [20,30].…”

“…Based on the pairwise AAIs of 2331 core genes, all strains from the first and second groups, as well as LZ-4 and Wood3, show conservation with the P. brassicacearum representative strain, NFM421 [20]. However, AAIs of 37D10, 48H11, 38D7 and 38D4 with NFM421 are only 88.6-89.5 %, which is below the suggested species threshold of 95 % [20,30]. Because of this, it has been proposed that the classification of 37D10, 48H11, 38D7 and 38D4 as P. brassicacearum species should be reanalysed [20].…”

“…However, AAIs of 37D10, 48H11, 38D7 and 38D4 with NFM421 are only 88.6-89.5 %, which is below the suggested species threshold of 95 % [20,30]. Because of this, it has been proposed that the classification of 37D10, 48H11, 38D7 and 38D4 as P. brassicacearum species should be reanalysed [20].…”