Soil metabarcoding helps identify recalcitrant taxa from chaparral seed banks

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.