Characterizing Crustose Lichen Communities—DNA Metabarcoding Reveals More than Meets the Eye

Abstract

Biodiversity inventories are important for informing land management strategies, conservation efforts, and for biomonitoring studies. For many organismal groups, including lichens, comprehensive, accurate inventories are challenging due to the necessity of taxonomic expertise, limitations in sampling protocols, and the commonplace occurrence of morphologically cryptic species and other undescribed species. Lichen communities in arid regions are often dominated by crustose lichens, which have been particularly difficult to incorporate into biodiversity inventories. Here, we explore the utility of DNA metabarcoding for characterizing the diversity of lichen-forming fungi at a typical crustose lichen-dominated site on the Colorado Plateau in the southwestern USA. We assessed the consistency of independent sampling efforts to comprehensively document lichen diversity, evaluated the capability of minimally trained technicians to effectively sample the lichen communities, and provide a metagenomic-based inventory of lichen diversity, including representative sequence data, for a diverse, crustose-dominate lichen community on the Colorado Plateau. Our results revealed that crustose lichen communities in the southwestern USA are more diverse than traditionally thought, and community metabarcoding is a promising strategy for characterizing the lichen-forming fungal diversity more thoroughly than other methods. However, consistently sampling the diversity of crustose lichen communities, even at small spatial scales, remains difficult. Interpreting these results within a traditional taxonomic context remains challenging without the use of vouchers.

Keywords

• amplicon sequencing
• biodiversity
• biomonitoring
• ecological sampling
• Illumina
• internal transcribed spacer region (ITS)