Tropical rainforest conversion into rubber plantations results in changes in soil fungal composition, but underling mechanisms of community assembly remain unchanged

•Forest conversion resulted in changes in soil fungal composition.•Forest conversion reduced β diversity and resulted in a net loss of landscape level diversity.•Rubber plantations and rainforest had similar mechanisms of community assembly.•Fungal community were highly niche-structured at regional scales.•Fungal community were largely neutrally structured at fine scales. Fungi play an important role in maintaining tropical forest diversity. However, little research to date has examined the effects of forest conversion (from rainforest to rubber plantation) on fungal community composition and diversity. In this study, we used Illumina MiSeq sequencing to assess soil fungal community composition and diversity for both rubber plantations and rainforest. We found: (1) Distinct differences in soil fungal community composition between rainforest and rubber plantation sites, indicating an important effect of forest conversion. The Ascomycota (36.71%) was the most abundant phylum in the rubber plantations, followed by the Basidiomycota (12.43%); these two phyla reversed in abundance in the tropical rainforest. (2) The OTU richness and Faith’s phylogenetic diversity were comparable in the plantations and rainforest, suggesting that conversion did not result in a reduction in α diversity. However, conversion resulted in a reduction in β diversity and a net loss of total diversity. (3) Community similarity of rubber plantations and rainforests declined with the distance among sample points at the fine scale, suggesting that dispersal limitation (a neutral process) was the main mechanism of fungal community assembly. Spatial variables (i.e., site location and elevation) accounted for 28% of the total variance in diversity, and therefore habitat filtering (a niche process) may drive fungal community assembly at the regional scale. In conclusion, the conversion of tropical rainforest to rubber plantations altered the composition of soil fungal communities, and reduced β diversity which resulted in a net loss of landscape level diversity. However, the underling mechanisms of community assembly remain unchanged. Neutral processes may explain fungal community assembly at fine scales, whereas niche processes likely drive patterns of assembly at the regional scale.