Coordinating Committee, Regulatory Working Group, Topical Leader in microbe classification system
Professor of Plant and Environmental Microbiology
Summary: We are exploring the potential of real-time DNA sequencing of plant-associated metagenomes using the Oxford Nanopore Technologies MinION in support of plant disease diagnostics. The goal is to provide same day results on the identity of the putative causal agent of diseased plants. The challenge lies in identifying the putative pathogen among the diversity of viruses, bacteria, fungi, and oomycetes present all the time on healthy as well as diseased plants. We currently focus on boxwood and on tomato.
Summary: Bacterial plant pathogen taxonomy is extremely challenging because of the existence of very closely related genetic lineages with different host range. This genetic and phenotypic diversity within groups of bacteria that are typically considered to be members to the same named species makes the application of traditional taxonomy to bacterial plant pathogens very difficult. We have thus developed a new genome-based system to circumscribe, describe, and name any group of organisms, be it a traditional named species or be it a single genetic lineage that caused a disease outbreak. We are currently developing a database and web-platform to implement this system for use in genome-based bacterial pathogen classification and identification. We are also exploring the use of the same database for the analysis of plant-associated microbiomes.
Summary: While the source of the plant root microbiome is obviously the soil, the source of the plant leaf microbiome is less obvious. Some evidence points to the soil as the main source of the leaf microbiome but the atmosphere and precipitation may very well play an important role also. As part of our research into ice nucleation active bacteria present in rain and soil and on plants, we are characterizing the microbial diversity of precipitation and we try to identify which bacteria present in precipitation are the most efficient colonizers of plant leaves. In a side project, we have also characterized the biocontrol potential of rain-borne bacteria, in particular, in regard to the control of fire blight on apple.