Metabarcoding and mitochondrial metagenomics of endogean arthropods to unveil the mesofauna of the soil

Biological communities inhabiting the soil are among the most diversified, complex and yet most poorly studied terrestrial ecosystems. The greatest knowledge gaps apply to the arthropod mesofauna (0·1–2 mm body size) because conventional morphological and molecular approaches are in many cases insufficient for the characterisation of these complex communities. The development of high-throughput sequencing (HTS) methodologies is required to solve current impediments and to further advance our understanding of below-ground biodiversity.
We propose a flotation–Berlese–flotation (FBF) protocol for sampling and specimen processing to obtain ‘clean’ DNA extractions of arthropod mesofauna from the soil. In addition, we developed and tested HTS protocols for the characterisation of arthropod communities from these bulk DNA extractions using cox1 metabarcoding and shotgun metagenomic sequencing on the MiSeq Illumina platform.
The FBF protocol provided DNA of soil arthropods from sufficiently l...