The precise fungal pathogens and their mixtures used as inoculants, along with the physical location of a tree have also been found to have a large effect on the yield and quality of agarwood. Plantation agarwood is now regularly harvested only a few years after inoculation and certain inoculants have resulted in significant production of agarwood after only 2 years. In Malaysia, indicated a rotation cycle of 4 to 8 years after inoculation, depending on the species, growth performance, site suitability, management techniques, and effectiveness of inducement.
Several fungus genera and species that result in agarwood production in Aquilaria spp. have been identified using various methods, and from the various species of Aquilaria, including the following genera: Cunninghamella, Curvularia, Fusarium (at least four species), Trichoderma, Paraconiothyrium, Botryosphaeria, Fomitopsis, Lasiodiplodia, Penicillium, Epicoccum, Alternaria, Acremonium, Colletotrichum, and Phaeoacremonium. Chhipa identified 82 species of fungus that result in agarwood, while cautioning that only 8% of fungi present in the trees have been studied for their roles in agarwood production, and many genera may not necessarily be responsible for the resin formation. In Malaysia, research has identified Aspergillus spp., Botryodiplodia spp., Diplodia spp., and Fusarium proliferatum as the key fungi resulting in agarwood. The types and combinations of fungi reported vary by tree species and geographic location, but consistent results for agarwood production occur with Fusarium spp. Santoso found that agarwood production in trees inoculated with Fusarium fungi varied according to the location within Indonesia where the fungi were sourced; they also found that F. solani was the best species to use.
Aromatic compound types and qualities may vary with the type and mixtures of fungi. Recent research from Malaysia that tested several combinations of fungi found that a combination of Trichoderma sp., Lasiodiplodia sp. and Curvularia sp. was the most productive inoculant for agarwood formation in Aquilaria spp., based on the coloration and length of the infected zone after 3- and 6-month inoculation periods. In China, where much of the current fungal research has been done, high quality oil production was reported within a period of just 8 to 18 months after inoculation