I've read about endophytic fungi that grows in between the cell walls of a plant's cells and offers some protection against bacterial and fungal parasites. Are there are any commercially available spawns that may be used to protect fruit trees against rusts and other fungal attacks? If there aren't any commercially available, have there been any experiments that have isolated certain species that I might be able to retrieve from the wild to experiment with myself?
It is true that some endophytic fungi have antimicrobial effects on their microscopic counterparts be it of fungal or bacterial origin.
This paper whose study employed the use of fungal extracts from Indigofera suffruticosa points out that Nigrospora sphaerica and Pestalotiopsis maculans inocula performed well in a rice culture medium against gram positive and negative bacteria like of the species Staphylococcus aureus.
Antifungal activity by endophytic fungi has also been observed in recent scientific studies. One study for instance, used fungal extracts (whose species were not specified in the abstract of the paywalled article) from Pinus strobus and exhibited antifungal biochemical characteristics against the rust and Microbotryum violaceum A.K.A anther smut fungus.
Another study in a paper by Mousa et al (2015) used extracts from finger millet to perform bioassay experiments that showed antifungal activity against Fusarium fungal species (like F. graminearum and three others). The strain(s) of anti Fusarium fungi was predicted to be of the Phoma genus.
Research on bioactive components from endophytic mycoflora from Sesbania grandiflora was conducted using bacterial and fungal indicator organisms. Of the isolated fungi in this study acremonium and fusarium species exhibited the most potency (Powthog et al, 2013).
This study further suggests that Schizophyllum commune fungal species produces proteolytic enzymes in which inhibit growth of phytopathogens in Piper hispidum.
I have not come across information on the commercial availability of the endophytic fungi mentioned above. However, studies can be conducted on their viability with particular tree (like fruit trees since most fungi are host specific) species upon acquiring samples from the wild.
Edit: I did not include antifungal endophytic fungi in the initial answer as I missed that [fundamental] part of the question. I hope this little edit answers the question and helps.