Skip to main content
Dryad

Soil metabarcoding helps identify recalcitrant taxa from chaparral seed banks

Data files

Jan 30, 2026 version files 533.29 KB

Click names to download individual files

Abstract

Evaluating seed bank composition by germinating seeds from soil cores is a common technique used in ecological studies to identify the plant biodiversity reservoir of a site. However, failure to meet required germination cues or to correctly detect uncommon species are major hurdles to creating a comprehensive plant list from the soil seed bank. Identifying plant species from genetic material within the soil environment (eDNA or eRNA) via metabarcoding offers a potential solution that has not yet been widely utilized at least in part because interpretations of results are not always straightforward. To address this issue, we first assessed extraction and amplification protocols in a series of proof-of-concept experiments where we controlled the soil seed bank and soil environments. We found that barcodes from DNA were more consistently amplified than from RNA and adding a germination stimulant, such as water, did not significantly influence sequencing yield. We then compared our molecular methods to traditional methods of germinating seed banks using soil samples collected from a degraded chaparral site in southern California where germinating native plants ex situ is challenging. We found that the rbcL barcode identified the largest number of plant families while the ITS2 barcode identified the most plant genera. Species that are traditionally challenging to germinate, such as fire-followers and hemiparasitic plants, were among those identified by metabarcoding but not by traditional methods. Pairing molecular tools with ecological site familiarity will make the species identification process more efficient, complete, and especially conducive for identifying the recalcitrant species of soil seed banks.