Advancing biodiversity assessments with environmental DNA: Long-read
technologies help reveal the drivers of Amazonian fungal diversity
Abstract
Fungi are a key component of tropical biodiversity. Due to their
inconspicuous and largely subterranean nature, they are however usually
neglected in biodiversity inventories. The goal of this study was to
identify the key determinants of fungal richness, community composition,
and turnover in tropical rainforests. We tested specifically for the
effect of soil properties, habitat, and locality in Amazonia. For these
analyses, we used high-throughput sequencing data of short and long
reads of fungal DNA present in soil and organic litter samples,
combining existing and novel genomic data. Habitat type
(phytophysiognomies) emerges as the strongest factor in explaining
fungal community composition. Naturally open areas – campinas – are
the richest habitat overall. Soil properties have different effects
depending on the soil layer (litter or mineral soil) and the choice of
genetic marker. We suggest that campinas could be a neglected hotspot of
fungal diversity. An underlying cause for their rich diversity may be
the overall low soil fertility, which increases the reliance on biotic
interactions essential for nutrient absorption in these environments,
notably ectomycorrhizal fungi–plant associations. Our results highlight
the advantages of using both short and long DNA reads produced through
high-throughput sequencing to characterize fungal diversity. While
short-reads can suffice for diversity and community comparison,
long-reads add taxonomic precision and have the potential to reveal
population diversity.