Using metabarcoding to ask if easily collected soil and leaf-litter samples can be used as a general biodiversity indicator

Abstract

The targeted sequencing of taxonomically informative genetic markers, sometimes known as metabarcoding, allows eukaryote biodiversity to be measured rapidly, cheaply, comprehensively, repeatedly, and verifiably. Metabarcoding helps to remove the taxonomic impediment, which refers to the great logistical difficulties of describing and identifying species, and thus promises to improve our ability to detect and respond to changes in the natural environment. Now, sampling has become a rate-limiting step in biodiversity measurement, and in an effort to reduce turnaround time, we use arthropod samples from southern China and Vietnam to ask whether soil, leaf litter, and aboveground samples provide similar ecological information. A soil or leaf-litter sample can be collected in minutes, whereas an aboveground sample, such as from Malaise traps or canopy fogging, can require days to set up and run, during which time they are subject to theft, damage, and deliberate contamination. Here we show that while the taxonomic compositions of soil and leaf-litter samples are very different from aboveground samples, both types of samples provide similar ecological information, in terms of ranking sites by species richness and differentiating sites by beta diversity. In fact, leaf-litter samples appear to be as or more powerful than Malaise-trap and canopy-fogging samples at detecting habitat differences. We propose that metabarcoded leaf-litter and soil samples be widely tested as a candidate method for rapid environmental monitoring in terrestrial ecosystems.