Surveillance of crop-associated microbes using high-throughput sequencing of environmental and seed samples
Citation
Tremblay, É.D., Goulet, B.B., Lord, E., Samson, S., Liu, M., Tambong, J.T., Brunet, B.M.T., Khanal, R., Parent, J.-P., and Chen, W. (2023). Surveillance of crop-associated microbes using high-throughput sequencing of environmental and seed samples. In 12th International Congress Of Plant Pathology (Lyon, France).
Plain language summary
Plant pathogens and exotic species pose an increased risk to plant health and food security and threaten biodiversity. Their effects are amplified by climate change which can confer more permissive conditions for establishment in previously inhospitable areas. Repercussions of the establishment of unwanted/exotic species include more restrictive trade regulations. High-Throughput Sequencing (HTS) is a powerful approach to pre-screen plant pathogens. We used HTS and Whole-Genome sequencing to monitor fungal, oomycetes and bacterial plant pathogens and look for beneficial plant endophytes. First, preliminary results from a workflow that analyzed aerial spore samples will be introduced (abundance, diversity and distribution forecasting models). Then, results from the study of microbial endophytic community in barley seeds will be shared. Next, bacterial contents obtained by WGS on canola seed will be shown. Those results were compared with culture based results. This study could provide a baseline of Canadian microbes in crops/seed and become instrumental in trade disputes and crop improvement. Combined results will help understand pest incidence and improve risk readiness and response measures.
Abstract
Phytopathogens & Invasive Alien Species pose an increased risk to plant health & food security, threaten biodiversity and exacerbate phytosanitary issues. Their effects are amplified by climate change led by more permissive conditions for their establishment in previously inhospitable areas. More restrictive international trade regulations are among the repercussions of the establishment of adventive species. High-Throughput Sequencing is a powerful approach to pre-screen phytopathogens and locate hotspots. We use metabarcoding (fungi, oomycetes) & Whole-Genome Shotgun sequencing (WGS; bacteria) to develop surveillance tools, increase plant health and enhance agriculture sustainability (beneficial endophytes). First, preliminary results from a metabarcoding workflow for analyzing spore and suction trap samples collected biweekly will be introduced (abundance, diversity, incidence & distribution forecasting models). Then, results from the metabarcoding of endophytic community in barley seeds will be shared. Next, results obtained by WGS bacterial profiling of canola seed washes will be shown. Taxa detected by culture-independent methods were compared with culture-dependent communities. This study could provide a baseline of Canadian microbes in crops/seed washes which may be instrumental in international plant trade disputes and crop improvement (endophytes). Combined results will help understand pest incidence in space & time and improve risk readiness & response measures.