Nutritional niche overlap analysis as a method to identify potential biocontrol fungi against trunk pathogens

Biological control agents possess various mechanisms to limit pathogens including ability to outcompete pathogens for resources and occupy shared niches. However, measuring this competition between putative biocontrol agents and pathogens for the same resources remains difficult. To evaluate carbon and nitrogen source utilization as a measure of competitiveness, we used phenotype microarrays on three endophytes (Trichoderma atroviridae, Trichoderma harzianum and Lecanicillium lecanii) with reported biological control activity and five stem-infecting fungal pathogens (Diplodia seriata, Eutypa lata, Neofusicoccum parvum, Phaeomoniella chlamydospora, and Phaeoacremonium minimum) that infect grapevine and other important woody plant hosts. The faster growing N. parvum and D. seriata utilized a greater number of the 190 assessed carbon and 380 assessed nitrogen sources than the relatively slower growing pathogens E. lata, P. chlamydospora, and P. minimum. All three endophytes had a greater niche overlap of carbon and nitrogen resource use than E. lata and P. chlamydospora. However, only T. harzianum and L. lecanii were determined to be able to equally compete or slightly outcompete N. parvum and D. seriata over carbon or nitrogen sources. Therefore, based on these results involving carbon and nitrogen source niche utilization, T. harzianum and L. lecanii would be advanced to additional biological control agent screening. Furthermore, according to plate bioassays, both Trichoderma spp. exhibited significant growth reduction of all pathogens except P. minimum, and L. lecanii significant reduced growth of D. seriata, E. lata, and N. parvum. Therefore, a combination of direct antagonism and ability to outcompete over resources is important in selecting biocontrols. Regardless, these results demonstrated the capacity of phenotype microarrays to assess the ability of endophytes to outcompete pathogens over shared resources in in vitro conditions as a complement to traditional plate assays.