Developing and Standardising Tools and Procedures for Assessment of Soil Biodiversity

WP leader Francis Martin (fmartin@nancy.inra.fr) INRA-Nancy, France.


  • Establishing standardised state-of-the-art morphology-, function- and molecular-based procedures for assessing the diversity and structure of soil-borne communities, including bacteria, archea, fungi, micro- and meiofauna.
  • Establishing a comprehensive reference database of DNA barcoding for soil micro-organisms.
  • Producing guidelines for standardised operating procedures.
  • Developing optimal soil sampling and storage, high-throughput next generation sequencing, and bioinformatics methods and tools to assess incremental levels of soil organism diversity and to explore ways to integrate this biological complexity into the physical and chemical structure and functioning of soils.
  • Standardising sampling procedures for morphology- and function-based methods of already existing indicators and to develop expert knowledge systems (media interactive identification keys) and trait-based identification approaches, which will be interconnected with molecular identification approaches.
  • Research and development in WP3 will be mostly based on samples collected at the LTOs and/or national survey sites.



To fulfil the project’s scientific objectives, it is necessary to develop new tools and analytical pipelines to assess the biodiversity of soil organisms in a functional context. This will be done by linking biodiversity with morphological and functional data using high throughput imaging and metagenomics/metatranscriptomics approaches, respectively.

WP3 is aimed to provide:

    – Protocols for soil DNA extraction, DNA purification, PCR amplification and DNA pyrosequencing using next generation sequencing technologies will be optimized for the microflora (bacteria, fungi) and micro- and meiofauna. These procedures will be standardized and compiled in a digital booklet.

    – Computerized expert systems (mainly based on digital image processing) to characterize enchytraeids and earthworms.

        – Study the decomposition of organic matter and the feeding activity in terms of applicability, practicability and ecological relevance, taking site and regional differences into account.

        – Produce an ISO-compliant discovery-level metadata catalogue, available via the project website.


 Minimum required standards of data stewardship will be specified for all relevant partners, e.g definition of standards for data ownership and IPR, standards for metadata and associated documentation (instrumentation, calibration process, units of measure, reference system), technical details of how data are stored (formats and media) and accessed, formal responsibilities for long-term curation and/or disposal.

A long-term data management strategy and distribution policy will be established, which will set-out agreed approaches to data back-up and archiving, periodic review of stored data, publicising and intention to dispose/destroy data.