DNA barcodes for soil biodiversity
JRC scientists published a joint study on the use of metabarcoding to characterise soil biodiversity. The published paper presents the opportunities and challenges of this relatively new methodology, and proposes solutions to facilitate its common application. Metabarcoding is a molecular approach based on the assumption that Operational Taxonomic Units can be unequivocally identified through a specific sequence of DNA (barcode). The ability to extract and store soil DNA for prolonged periods of time provides a unique opportunity to assess the evolution of soil biodiversity over time in relation to global change, and to develop concrete measures to preserve these features
Soils encompass a huge diversity of organisms which mostly remains to be characterised. Nonetheless, remarkable progress has been made in recent years toward developing strategies to describe soil biodiversity, especially thanks to the development of molecular approaches relying on direct DNA extraction from the soil matrix - the assemblage of mineral particles and organic materials in various stages of decomposition and living soil populations. This approach is already commonly used to characterise soil microbial communities (i.e. fungi and bacteria) and its application is now being extended to other soil organisms, i.e. meso- and macro-fauna (i.e. insects and earthworms).
Soil biodiversity data collected by means of DNA barcoding is likely to increase in the coming years. This requires the development of Standard Operating Procedures (SOP's) for soil analyses and referential methods for the interpretation and comparison of the results depending on the soil type, climate, and land use.
To reach this goal, the scientists call for a joint effort of the soil community to clarify the terminology, further develop and standardise the methods and set-up a common database of data derived from barcoding.
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.
More infomration (References):
Orgiazzi A., Dunbar M.B., Panagos P., de Groot G., Lemanceau P. 2015. Soil biodiversity and DNA barcodes: opportunities and challenges. Soil Biology and Biochemistry. Vol. 80, Pages 244–250.
Fig. 1: Concept of step-by-step workflow for studies on soil biodiversity