Student scientists, bulk sampling and DNA metabarcoding demonstrate improved species detectability in lichen diversity inventories

Author:
Morgan G., Adams P., Robison A., St. Clair L.L. & Leavitt S.D.
Year:
2026
Journal:
Bryologist
Pages:
129(2): 106–119
Url:
https://doi.org/10.1639/0007-2745-129.2.106
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Lichens are present in nearly all terrestrial ecosystems. They often represent a substantial portion of the community-level species diversity, play important ecological roles, and are commonly used to monitor ecological health. Consistently and accurately detecting and representing lichen diversity remains challenging, even when standardized surveys are conducted by experts. In fact, recent work suggests that lichen detectability is unexpectedly low, even in some of the best-case scenarios, with striking differences among independent sampling efforts. DNA metabarcoding of bulk environmental samples holds promise for enhanced detectability of species in lichen inventory surveys. Here, we compare consistency in characterizing lichen community species diversity based on the independent bulk sampling efforts conducted by trained student scientists using high-throughput DNA sequencing. Each student was instructed to collect small lichen fragments representing the range of perceived lichen diversity in a narrow limestone canyon on the eastern edge of the Great Basin, Utah County, Utah. Metagenomic DNA was extracted from the independent bulk samples, and lichen-forming fungal diversity was inferred using Illumina high-throughput sequencing of ITS2 amplicons. Illumina short reads were processed using FROGS, a pipeline for inferring operational taxonomic units, and taxonomic assignments were made with a customized pipeline. Results of the metagenomic sampling approach were compared to a traditional, student-led lichen inventory completed in the early 1990s. The bulk sampling-metagenomic inventory captured three times the diversity documented in the traditional, morphology-based survey (190 species vs. 63). We observed high overlap in capturing species-level diversity between the two bulk sampling efforts, with nearly 70% similarity. Only limited overlap in species was observed between the composite bulk sampling lichen inventory and the decades-old, morphology-based inventory. Additionally, ca. one-third of the species-level lineages inferred from metagenomic reads could not be assigned to a known species with confidence. We discuss the implications of our results and the efficacy of using bulk sampling and metagenomic DNA barcoding as a protocol for conducting lichen biodiversity surveys. Keywords: Crustose lichens, dark taxa, detectability, high-throughput sequencing, next-generation biomonitoring, undergraduate research, Wasatch Front.
Id:
39540
Submitter:
zpalice
Post_time:
Monday, 20 July 2026 11:04