Use of real-time quantitative PCR to investigate root and gall colonisation by co-inoculated isolates of the nematophagous fungus Pochonia chlamydosporia

The fungus Pochonia chlamydosporia is a potential biological control agent for plant parasitic nematodes, but to date, there has been little investigation of interactions (competitive, antagonistic or synergistic) between different isolates that occur together on roots and nematode galls. Real-time quantitative PCR (qPCR) has greatly improved the study of many fungi in situ on plant and nematode hosts, but distinguishing closely related isolates remains difficult. In this study, primers to discriminate P. chlamydosporia var. chlamydosporia and P. chlamydosporia var. catenulata were used to measure the relative abundance of isolates of the two varieties when inoculated singly or together on tomato plants. Also, sequence-characterised amplified polymorphic regions were identified to distinguish two different isolates of P. chlamydosporia var. chlamydosporia. Individual 1-cm root segments and nematode galls were excised, DNA extracted and subjected to real-time qPCR with the discriminatory primers. The qPCR method proved sensitive and reproducible and demonstrated that roots and nematode galls were not uniformly colonised by the fungi. Results indicated that the P. chalmydosporia var. catenulata isolate was more abundant on roots and eggs than P. chlamydosporia var. chlamydosporia, but all the isolates infected a similar proportion of nematode eggs. There was an indication that the abundance of each fungal isolate was reduced in co-inoculation experiments compared with single inoculations, but the number of root segments and galls colonised was not statistically significantly different.