The rate of generation of gene sequence information now vastly outpaces our ability to characterise genes and determine their contributions to physiology, metabolism and ecology. Saturation transposon mutagenesis techniques, such as Transposon Directed Insertion Sequencing (TraDIS) provide new information on gene essentiality, gene function and genetic interactions. TraDIS uses a dense library of randomly generated loss-of-function mutants combined with massive parallel sequencing to simultaneously study all non-essential genes in the genome and identify genes which are important in conditions of interest. Whilst initial applications of this technique were largely focused on characterising genes associated with pathogenicity, this approach can be used to identify genetic factors involved in a range of ecological processes.
The interactions between plant commensal bacteria, their hosts and co-occurring microorganisms are important to agriculture and ecosystem health, but many aspects of this are still poorly understood. Our group has applied TraDIS to identify genetic factors critical for plant surface colonisation and persistence. Using this approach, we have identified ~50 genes important in attachment to plant surfaces, many of these genes are associated with cell wall/membrane/envelope biogenesis. Conditionally responsive genes of interest are being investigated to elucidate functions and determine their role in attachment. We are currently investigating genes associated with rhizosphere persistence and in interactions with other soil microbes, including fungal pathogens. This work demonstrates the utility of TraDIS for probing complex ecological interactions.