Burkholderia Adaptation to multiple hosts: exploring frontiers between eukaryotic mutualist and pathogens for the development of risk assessment tools – BURKADAPT

Modern agriculture needs to change its practices in order to become more sustainable and to limit its impact on the environment by the heavy use of chemical inputs and the emission of greenhouse gases. Microbial inoculants that contain bacteria with plant growth promoting properties are among the solutions that are proposed. There is an ongoing intensive search for appropriate bacterial species or species consortia that have properties as biostimulants, i.e. directly promoting plant growth, or as biopesticides, i.e. preventing the development of infectious plant diseases. A major issue with the large scale application of bacteria on crops or in environmental biotechnological applications such as bioremediation is the potential biohazard of the bacteria used.
The genus Burkholderia is composed of environmental bacteria with extraordinarily versatile ecological states. Many species are well-known for their beneficial properties on plants with large potential as biostimulants or biopesticides. However, the application of Burkholderia strains in biotech and agroecology is blocked by the presence of opportunistic human pathogens within the genus that cause high morbidity and mortality in immune-compromised individuals and cystic fibrosis patients. Thus, the widespread agricultural use of Burkholderia needs to be approached with extreme caution. In order to fully exploit the beneficial potential for applications within this remarkable genus, there is an urgent need to dispose of reliable methods to determine for any Burkholderia isolate its potential hazard for human and animal health.
The BURKADAPT project will explore the frontiers between the different ecological states of Burkholderia and uncover the genetic bases that underlie the differences between mutualism and pathogenicity in different hosts. From this fundamental knowledge, the project will further develop a predictive bioinformatics tool that will allow the rapid evaluation if potentially beneficial strains represent a risk for health, based on the presence and absence of pathogenicity marker genes.
The first objective of the project is dedicated to the screening of a selected panel of Burkholderia strains isolated from rice plants, insect guts and human infections, to evaluate their capacity to develop symbiotic, commensal or pathogenic interactions in a diversity of eukaryotic hosts. We will use Oryza sativa (rice) and Riptortus pedestris (bean bug) as models for symbiosis in plants and insects respectively, and human cells, Galleria mellonella (greater wax moth) and Danio rerio (zebrafish) as established models to test pathogenicity. The second objective uses comparative genomics tools to establish gene repertoires specific or in common between genomes of strains developing contrasting interactions with hosts. With the aim to identify genes that are differentially regulated and provide fitness benefit during their interaction with the respective host models, we will perform high-throughput transcriptomics (RNA-seq) and genetic screens (Tn-Seq), respectively, on a panel of selected Burkholderia strains during host-infection. The putative infection-related gene sets identified for each infection host will be compared with the gene repertoire determined by the in silico analysis. We further propose to develop a predictive tool to detect rapidly potential biohazard strains, based on the presence of infection-related genes in a given Burkholderia genome. The prediction tool will be tested on collections of strains from the four partners of the project, and predictions will be challenged with tests in the hosts used in the project to refine the prediction reliability of the tool.
The results of the BURKADAPT project will provide new insights in the genetic basis of Burkholderia to infect eukaryotic hosts and will contribute to obtaining solutions that will make Burkholderia with high agronomic and biotechnological potential acceptable for commercial use in the field.