Data from: DNA from soil mirrors plant taxonomic and growth form diversity

Ecosystems across the globe are threatened by climate change and human
activities. New rapid survey approaches for monitoring biodiversity would
greatly advance assessment and understanding of these threats. Taking
advantage of next-generation DNA sequencing, we tested an approach we call
metabarcoding: high-throughput and simultaneous taxa identification based
on a very short (usually less than 100 base pairs) but informative DNA
fragment. Short DNA fragments allow the use of degraded DNA from
environmental samples. All analyses included amplification using
plant-specific versatile primers, sequencing and estimation of taxonomic
diversity. We tested in three steps whether degraded DNA from dead
material in soil has the potential of efficiently assessing biodiversity
in different biomes. First, soil DNA from eight boreal plant communities
located in two different vegetation types (meadow and heath) was
amplified. Plant diversity detected from boreal soil was highly consistent
with plant functional and structural diversity estimated from conventional
above-ground surveys. Second, we assessed DNA persistence using samples
from formerly cultivated soils in temperate environments. We found that
number of crop DNA sequences retrieved strongly varied with years since
last cultivation, and crop sequences were absent from nearby, uncultivated
plots. Third, we assessed the universal applicability of DNA metabarcoding
using soil samples from tropical environments: a large proportion of
species and families from the study site was efficiently recovered. The
results open unprecedented opportunities for large-scale DNA-based
biodiversity studies across a range of taxonomic groups using standardized
metabarcoding approaches.