Is targeted community DNA metabarcoding suitable for biodiversity inventories of lichen-forming fungi?

Comprehensive lichen inventories at biomonitoring reference sites provide valuable ecological information but are notoriously difficult to obtain. Due to the limited number of specialists and challenges with generating objective species inventories, investigating alternative or complementary strategies for compiling lichen inventories is paramount to improve biomonitoring strategies. The aim of this study was to determine if targeted community DNA metabarcoding provides an efficient, objective and reliable approach for characterizing lichen forming fungal diversity in biomonitoring research. To evaluate if reliable biodiversity data could be obtained efficiently and objectively, metacommunity samples were collected by trained field technicians and a professional lichenologist at a previously established biomonitoring reference site in east-central Nevada, USA. Using amplicon-based high-throughput sequencing of a portion of the fungal DNA barcoding marker, the internal transcribed spacer region, molecular operational taxonomic units (OTUs) were inferred and used as a proxy for species diversity. OTUs from individual sampling efforts and two DNA extraction methods were compared to data from the original, voucher-based inventory at the same site. Treating OTUs as a proxy for species diversity, a 1.6-fold increase in diversity of lichen-forming fungi was observed when comparing the targeted community DNA metabarcoding to the initial, voucher-based inventories - 72 OTUs vs. 43 species. Strikingly, substantial overlap in captured OTU diversity was observed between minimally trained technicians and a professional lichenologist metacommunity samples. Based on these results, targeted community DNA metabarcoding is a promising strategy for creating objective lichen inventories. However, metabarcoding cannot discriminate the presence of established thalli from that of spores or propagules (in absence of established thalli) present in the sample/area. Therefore, targeted community DNA metabarcoding for assessing lichen biodiversity offers a complementary, rather than a substitutive sampling strategy.