WG 7 – Microbial and Molecular Data

WG 7 – Microbial and Molecular Data


Žaklina Marjanović
Department of Life Sciences, Institute for Multidisciplinary Research, Belgrade University, Republic of Serbia

Achim Schmalenberger
University of Limerick, Biological Sciences, Ireland


The objectives of this WG are to integrate morphological, ecological and molecular data of soil microorganisms into Edaphobase. This will be achieved in a stepwise manner.

  1. We will focus on taxonomic morphological data on fungal fruit bodies and microbial molecular data based on DNA sequencing, i.d. Operational Taxonomic Units (OTU), Sequence Variance etc. at lowest possible taxonomic level (genus level). Functional genes (DNA or RNA) analyses based on the closest match possible. For this, Edaphobase needs taxonomic trees of microorganisms such as bacteria, fungi, archaea, oomycetes, and protists.
  2. For analyses of functional traits, Edaphobase has to be modified to have such data included. This can be achieved by including data based on functional analyses such as enzymatic activities, soil respiration, microbial and metabolic quotients, soil microbial biomass and phospholipid fatty acid (PLFA) content. Environmental variables such as pH, nutrient availablity or texture can be easily incorporated in EUdaphobase as well.


The existing data have to be standardized in order to match the Edaphobase data model regarding taxonomy and ecological data, while Edaphobase has to be modified to accommodate molecular data. Initially, WG7 will establish and discuss with WG1 standardised and well-defined vocabularies and formats for data fields to be covered in the Edaphobase data warehouse. 

WG7 will specify a minimum data set as described in WG2: Guideline for requesting data for EUdaphobase – draft 2019-11-10.docx and What kind of data does EUdaphobase need.docx, including taxon, i.d. OTU, site of occurrence including soil type and land-use practice, sampling date, soil depth, source, methodology if available (DNA extraction method, sequencing platform, variable region amplified, primers used, other repository where the data are stored such as NCBI), promoting future data identification and re-use. This will include but not be limited to introducing specific attributes/variables in the existing EUdaphobase system. After the integration of microbial molecular data in EUdaphobase, integration and combined analyses of microbial, soil fauna and physical/chemical data will be made possible. 

The second main task of WG7 will be to develop procedures and protocols for data integration. By developing principles for the harmonisation, use and mapping of existing information on soil biodiversity in Europe, the quality of the data will increase the credibility of use by all partners, stakeholders and end-users. An important additional issue to be addressed in WG7 in collaboration with WG1WG3 is how data from microbiological and soil fauna databases can be integrated, which has never been achieved before. Integration of microbial data already deposited in other databases such as data from UNITE, LUCAS and EU projects as EcoFINDERS should be made possible.

Intended Outcomes

WG7 will (1) provide of standardised vocabularies, protocols and checklists for microbial soil-biodiversity data. These will be made available to all data providers, users and stakeholders at European and national levels. (2) Data quality-control processes for microbial data will be defined, which harmonize metadata for individual datasets to comply with overall criteria.