Measuring DNA of soil-borne plant pathogens and biocontrol agents in soils in relation to disease and response to organic amendments

Abstract

Soilborne pathogens pose a significant threat to agricultural productivity, necessitating sustainable alternatives to chemical control methods. This study addresses the critical need to replace or complement chemical products with biologicals and organic amendments to mitigate soilborne pathogen pressure. Understanding the dynamics of soilborne pathogens and their interactions with biological controls is essential for enhancing food security and sustainable agriculture. This research employed various methodologies, integrating soil DNA extraction techniques, qPCR quantification, and metabarcoding analysis to investigate the effects of organic amendments on soilborne pathogens and beneficial organisms. Field trials conducted in raspberry, onion, daffodil, and asparagus crops evaluated the efficacy of various organic amendments, including manure, arbuscular mycorrhizal fungi (AMF), composts, digestates, and cover crops. The study revealed substantial variability in soil DNA extraction methods, influencing the comparability of results across studies. Although the selected methods correlated with quantified DNA in inoculated soils, validation in field conditions proved challenging. Field trials failed to establish inoculum density-disease incidence relationships or relate population changes to organic amendments. Site-specific variations dominated bacterial and fungal soil communities, suggesting the influence of unmeasured variables on soil microbiomes. Despite efforts to standardize molecular methods and control environmental variables, their impact persisted throughout the study. Future trials may require extended durations to assess long-term effects on soil health and pathogen populations with repeated application of organic amendments. Increased sampling frequency throughout the growing season is recommended to capture the dynamic nature of soil microbial communities. Molecular techniques, such as qPCR and metabarcoding, offer valuable insights into soil microbial interactions, guiding future testing options and informing sustainable agricultural practices. This thesis underscores the importance of considering soil characteristics, environmental factors, and field history in long-term management strategies.