Exploring Fungal Diversity Through COI Primers: A Nontargeted eDNA Approach

The broad amplification potential of COI primers, typically designed for arthropods, unexpectedly revealed fungal DNA alongside arthropod data in our assessment of fungal communities across tropical (Hainan, China) and nontropical (Guizhou, China) rainforests using eDNA metabarcoding of 96 samples. This nontarget finding demonstrates the ability of COI‐based metabarcoding to capture fungal diversity in previously unexplored ambient samples. Our results showed very different biogeographical patterns. For example, in Hainan, mixed land use (MIX) resulted in a complete collapse of diversity (Shannon = 0.00), whereas in Guizhou, some diversity remained (Shannon = 0.28). In the tropics, diversity decreased by 90%; in the nontropics, by 64%. This increased sensitivity was associated with pronounced habitat specialization, as organic matter (OM) environments exhibited the highest diversity in Hainan (Shannon = 3.73). A GLM showed that OM had the biggest positive effect (estimate = 3.815, p < 0.001), with Hainan having 5.3 times as many habitat‐specialist OTUs (64 vs. 12) and soil/tree (ST) habitats acting as important refuges (34 indicator OTUs, correlation strength = 0.966). We detected temporal asymmetry, with Hainan retaining consistent regional diversity despite fluctuations (interannual Δ = −1.45, p = 0.653). However, 33% of the Guizhou samples revealed a continuous lack of diversity over the years, indicating population extinction. The primary driver of community structure was habitat type, as confirmed by PERMANOVA ( R 2 = 0.301, p = 0.001). In the tropics, MIX resulted in an 87% loss of diversity, whereas in Guizhou the effects were nonsignificant ( p = 0.207). This indicates that tropical mushrooms are at risk of catastrophic collapse due to niche specialization, necessitating immediate protection of OM‐rich habitats. On the other hand, nontropical systems require restoration to address the instability caused by dispersal limitation.