High-throughput eDNA monitoring of fungi to track functional recovery in ecological restoration

Abstract

Fungi are key functional components of ecosystems (e.g. decomposers, symbionts), but are rarely included in restoration monitoring programs. Many fungi occur belowground, making them difficult to observe directly, but are observable with environmental DNA (eDNA) methods. Although eDNA approaches have been proposed as ecological monitoring tools for microbial diversity, their application to restoration projects is very limited. We used eDNA metabarcoding of fungal ITS barcodes on soil collected across a 10-year restoration chronosequence to explore fungal responses to restoration. We observed a dramatic shift in the fungal community towards that of the natural fungal community after just 10 years of active native plant revegetation. Agaricomycetes and other Basidiomycota – involved in wood decay and ectomycorrhizal symbiosis – increased in rarefied sequence abundance in older restored sites. Ascomycota dominated the fungal community, but decreased in rarefied sequence abundance across the restoration chronosequence. Our results highlight eDNA metabarcoding as a useful restoration monitoring tool that allows quantification of changes in important fungal indicator groups linked with functional recovery and, being underground, are normally omitted in restoration monitoring.