Metabarcoding soil microarthropods for soil quality assessment: importance of integrated taxonomy, phylogenetic marker selection and sampling design

Abstract

Soil microarthropods are ubiquitous and ecologically significant in terrestrial environments. Collembola and Oribatida are the two most abundant and diverse representatives of microarthropods and are commonly targeted biological indicators of soil quality. Traditional methods for studying these groups have provided taxonomic and functional data for individuals but are inefficient for large scale biomonitoring applications. The adoption of molecular methods like metabarcoding is predicted to improve the efficiency of biomonitoring microarthropods but can be limited by the availability of reference specimens in sequence databases, and the importance of barcode selection and sampling design for this approach in plot-level experiments has not been explored. Demonstrated here, the inclusion of locally derived specimen barcodes to reference libraries significantly improved the quality of metabarcoding data. Also, targeting two barcodes (18S and COI) improved microarthropod richness estimates, and 10 samples with >10 m separation between each is recommend to increase the proportion of diversity detected.