Since isolating his first Pseudomonas from mushroom caps back in the 1980s Rainey has remained faithful to these wonderful weeds. The magical range of coloured pigments (siderophores, pyocanins and the like) released into the medium was enough to hook a young microbiologist.
During his second post doc at the now defunct NERC Institute for Virology and Environmental Microbiology in Oxford, Rainey worked in Mark Bailey’s team whose research focussed on assessing the risk of releasing genetically modified bacteria into the environment. For this purpose they isolated 1000s of phyllosphere and rhizosphere-colonising bacteria from sugar beet grown at the university farm in Wytham (adjacent to the famous Wytham Woods in which much pioneering ecology / behavioural ecology was — and is still — done). Isolate SBW25 (Sugar Beet Wytham, isolate 25) was typical of a common cluster of pseudomonads. It was genetically modified with an antibiotic resistance cassette and released into the environment!
Rainey’s role was generation of physical and genetic map of the beast’s chromosome, which was achieved after some years of slog by two-dimensional pulsed-field electrophoresis combined with end-labelling and published in Molecular Microbiology in 1996. How things have changed.
Having invested such effort in marking out the chromosome — and having, in his spare time, used SBW25 to continue work on adaptive radiation — Rainey embraced SBW25 when establishing his own lab as a BBSRC Advanced Fellow in the Department of Plant Sciences at the University of Oxford.
A primary focus during the first years at Plant Sciences was establishment of in vivo expression technologies (IVET) to identify SBW25 genes expressed specifically in the rhizosphere. He made one such system based on panB and Michaela Gal constructed a second much more powerful system based upon dapB.
Work on plant-microbe interactions continued with much building upon genes discovered using the IVET strategies. One notable finding was a type III secretion system that was previously known from pathogenic bacteria. Gail Preston performed super work on this system aided after some time by Rob Jackson who showed the system in SBW25 was functional. It turns out that such T3SSs are common among saprophytic bacteria. Just what their function is still not clear.
Also arising from application of IVET technologies was knowledge of the importance of the histidine uptake and degradation locus (hut). This was the focus of work by Xue-Xian Zhang and Rainey over many years of fruitful collaboration.
In the mean time it became possible to sequence genomes. One of the first non-pathogenic genome sequences funded by the BBSRC in 2002 was SBW25. The work performed at the Sanger Centre proved exceptionally challenging on account of numerous repeat sequences that hampered closure of the genome. Eventually new sequencing chemistries provided the necessary break through and the genome was eventually published alongside Pf0-1 including an extensive catalog of genes from IVET active in the plant environment.
Steve Giddens, Rob Jackson and Christina Moon took the genome sequence to an additional level through development of SPyVET — a cunning method for identifying regulators of plant-induced genes. Those were the days.
The bug, the genome and all its quirky behaviours remain at the heart of what we do with continual development of new approaches and tools for analysis.