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 molecul..., MATERIALS and METHODS
 
Sequencing known seed bank (Proof-of-concept)
We tested the accuracy and efficiency of metabarcoding methods across a combination of different soil complexities, added plant species, and soil preparations, for a total of 12 treatment groups with five replicates each. We first tested how efficiently S. leucophylla seeds could be sequenced from the simplest soil matrix - sterilized sand - under three germination treatments prior to nucleotide extraction, which included no treatment, 24 hour incubation with deionized (DI) water, and 24 hour incubation with gibberellic acid (GA). We expected stimulation for germination with water or GA would increase RNA transcription and yield. S. leucophylla seeds were chosen as our control species since their seeds had been recently collected from the wild and were abundantly available for testing.
Next, we tested how accurately and efficiently S. leucophylla seeds could be sequenced with metabarcoding from sterilized field s..., , # Soil metabarcoding helps identify recalcitrant taxa from chaparral seed banks

[https://doi.org/10.5061/dryad.hdr7sqvsw](https://doi.org/10.5061/dryad.hdr7sqvsw)

## Description of the data and file structure

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 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. Here, we provide the files necessary to perform the statistical analyses included in a submitted manuscript, curren...,