Soils encompass a huge diversity of organisms which mostly remains to be characterized due to a
number of methodological and logistical issues. Nonetheless, remarkable progress has been made in
recent years toward developing strategies to characterize and describe soil biodiversity, especially thanks
to the development of molecular approaches relying on direct DNA extraction from the soil matrix.
Metabarcoding can be applied to DNA from any environment or organism, and is gaining increasing
prominence in biodiversity studies. This approach is already commonly used to characterize soil microbial
communities and its application is now being extended to other soil organisms, i.e. meso- and
macro-fauna.
These developments offer unprecedented scientific and operational opportunities in order to better
understand soil biodiversity distribution and dynamics, and to propose tools and strategies for biodiversity
diagnosis. However, these opportunities also come with challenges that the scientific community
must face. Such challenges are related to i) clarification of terminology, (ii) standardisation of methods
and further methodological development for additional taxonomic groups, (iii) development of a common
database, and (iv) ways to avoid waste of information and data derived from metabarcoding. In
order to facilitate common application of metabarcoding in soil biodiversity assessment, we discuss these
opportunities and challenges and propose solutions towards a more homogeneous framework.