Seven strains were selected for genomic sequencing based upon their characterized and distinctive biological control properties and their isolation from different habitats (bulk or rhizosphere soil or aerial plant surfaces) (Table 1). The seven strains and three previously-sequenced strains (Pf-5, Pf0-1, and SBW25) evaluated in this study exhibited the conserved phenotypes of the P. fluorescens group: positive for fluorescence under UV light, arginine dihydrolase activity, and oxidase activity; and negative for growth at 41°C and induction of a hypersensitive response on tobacco, determined through standard methods [138] (Table S16). The ten strains were subjected to a panel of biochemical and biological assays (nitrate reduction, levan sucrase production, potato soft rot, gelatinase activity, and catabolic spectra) [138] , [139] to assign each to a biovar of P. fluorescens or to a species of Pseudomonas[129] (link) (Table 1 and Table S16). Strains A506, 30-84, SS101, and BG33R are rifampicin-resistant (100 µg/ml) derivatives of field isolates; previously, spontaneous mutants with resistance to rifampicin were selected to facilitate tracking of these strains in field studies. Strain A506 is known to have a single nucleotide insertion in rpoS, which causes a frameshift resulting in a truncated form of the stationary-phase sigma factor RpoS [140] (link). During the course of this work, we discovered that strain Pf0-1 has a mutation in gacA, which encodes a component of the GacA/GacS global regulatory system in Pseudomonas spp. [61] (link). We sequenced gacA and gacS from the strain Pf0-1 in our collection and confirmed that the sequences are identical to those in the published genome of Pf0-1 [32] (link). It is not possible to know whether the mutations in A506 and Pf0-1 were present in the strains prior to isolation or if they developed in the laboratory during storage, but all strains have been maintained as frozen stocks (−80°C) throughout this study and for many years preceding.
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