Comparative Profiling of Wood Canker Pathogens from Spore Traps and Symptomatic Plant Samples within California Almond and Walnut Orchards

Fungi causing wood canker diseases are major factors limiting productivity and longevity of almond and walnut orchards. The goal of this study was to compare pathogen profiles from spore traps with those of plant samples collected from symptomatic almond and walnut trees and assess if profiles could be influenced by orchard type and age, rainfall amount and frequency, and/or neighboring trees. Three almond orchards and one walnut orchard with different characteristics were selected for this study. Fungal inoculum was captured weekly from nine trees per orchard using a passive spore trapping device, during a 30-week period in the rainy season (October-April) and for two consecutive years. Fungal taxa identified from spore traps were compared with a collection of fungal isolates obtained from 61 symptomatic wood samples collected from the orchards. Using a culture-dependent approach coupled with molecular identification, we identified eighteen known pathogenic species from ten fungal genera ( , , , , , , , , , , , , , , , , , and ), plus two unidentified and species. However, only four species were identified with both methods ( , , and ), albeit not consistently across orchards. Our results demonstrate a clear disparity between the two diagnostic methods and caution against using passive spore traps to predict disease risks. In particular, the spore trap approach failed to capture; (i) insect-vectored pathogens such as that were often recovered from almond trunk and scaffold; (ii) commonly isolated from wood samples likely because species have a spatially restricted dispersal mechanism, since spores are exuded in a cirrus; and (iii) pathogenic species with low incidence in wood samples such as and . We propose that orchard inoculum is composed of both endemic taxa that are characterized by frequent and repeated trapping events from the same trees and isolated from plant samples, as well as immigrant taxa characterized by rare trapping events. We hypothesize that host type, orchard age, precipitation, and alternative hosts at the periphery of orchards are factors that could affect pathogen profile. We discuss the limitations and benefits of our methodology and experimental design to develop guidelines and prediction tools for fungal wood canker diseases in California orchards.