Soil biodiversity DNA archaea

The dataset includes archaeal 16S raw DNA sequences for 885 samples collected as part of LUCAS 2018 Soil survey (Biodiversity module).
Resource Type: 
Datasets
Soil Functions Data
Registration is requested: 
Yes
Year: 
2026
Themes: 
Soil Biodiversity
Keywords: 
Archea

Title: Soil biodiversity - DNA archaea.
Description: Archaea are an important group of soil organisms that play key roles in carbon and nitrogen cycling, particularly in nitrification (ammonia oxidation) and methanogenesis. However, there are knowledge gaps regarding their importance in ecosystem processes relative to other microbial groups and how they may be impacted by land-use and environmental changes. Here, by carrying out a continental-scale sample collection and utilising archaea-specific primers for metabarcoding and shotgun metagenomics, we aimed to decipher the structure and function of archaeal communities across various land-use types in Europe. Metagenomic data reveal that land-use intensification increases the relative abundance of archaea, whereas bacteria and eukaryotes show no increase. The dataset includes archaeal 16S raw DNA sequences1 for 885 samples collected as part of LUCAS 2018 Soil survey2,3 for the biodiversity module. Raw DNA sequences are deposited on NCBI Sequence Read Archive (SRA) database under BioProject ID PRJNA1118194. Samples from four locations were re-sampled, and thus sequenced twice, due to sampling issues (i.e., 885 total samples from 881 sampling sites): samples n° 59, 102, 113, 116 were re-sequenced as samples n° 138, 601, 717, 258 respectively.

Sampling site metadata can be found at the Soil Biodiversity - DNA Bacteria and Fungi data and the Soil Biodiversity - DNA Eukaryotes with further details on data acquisition in Labouyrie et al. 20234 and Köninger et al. 20235. To combine single file of DNA sequences with data in the metadata tables, one needs to take the number (from 1 to 885) in the file name and match it to the corresponding “BARCODE_ID” (numbers from 1 to 885) in the table.

Additional details on the DNA extraction, amplification and sequencing can be found in Bahram et al. 2026 “Intensive land use enhances soil ammonia-oxidising archaea at a continental scale”1.

Spatial coverage: EU27+ UK
Type:  DNA sequences
Temporal coverage:  2018
 

References: 

  1. Bahram, M., Lehtovirta-Morley, L., Mikryukov, V., Sveen, T.R., Grant, A., Pent, M., Hildebrand, F., Labouyrie, M., Köninger, J., Tedersoo, L., Jones, A., Panagos, P., Orgiazzi, A. 2026. Intensive land use enhances soil ammonia-oxidising archaea at a continental scale. Soil Biology and Biochemistry, 213: 110024.
  2. Orgiazzi, A. et al. LUCAS Soil, the largest expandable soil dataset for Europe: a review. Eur J Soil Sci 69, 140–153 (2018).
  3. Orgiazzi, A. et al. LUCAS Soil Biodiversity and LUCAS Soil Pesticides, new tools for research and policy development. European J Soil Science 73 (2022).
  4. Labouyrie, M., Ballabio, C., Romero, F., Panagos, P., Jones, A.,  Schmid, M., Mikryukov, V., Dulya, O., Tedersoo, L., Bahram, M., Lugato, E., van der Heijden, M.G.A., Orgiazzi, A. 2023. Patterns in soil microbial diversity across Europe. Nature Communications. 14, Article number: 3311, doi: 10.1038/s41467-023-37937-4.
  5. Köninger, J. Ballabio, C., Panagos, P., Jones, A., Schmid, M.W., Orgiazzi, A, Briones, M.J.I. 2023. Ecosystem type drives soil eukaryotic diversity and composition in Europe . Global Change Biology. 29(19): 5706-5719. DOI: 10.1111/gcb.16871

Subscribe to ESDAC Monthly newsletter

By sending these data, you declare that you have read & accept the notification below and that your personal data will be handled by the JRC only for statistical purposes (conform to privacy statement).

For any problem / question / comment on this dataset, please contact ec-esdac@ec.europa.eu

Notification:

  • The data provided has been prepared for use by internal research activities of the Joint Research Centre (JRC) in collaboration with Agricultural Sciences, Uppsala, Sweden ,  University of Tartu, T Estonia, Aarhus University, Denmark and other Institutions. 
  • The data are the result of JRC research activities and are primarily made available for further research. The JRC does not accept any liability whatsoever for any error, missing data or omission in the data, or for any loss or damage arising from its use. The JRC agrees to provide the data free of charge but is not bound to justify the content and values contained in the databases.
  • The permission to use the data specified above is granted on condition that, under NO CIRCUMSTANCES are these data passed to third parties. They can be used for any purpose, including commercial gain.
  • The user agrees to:
       a) Make proper reference to the source of the data when disseminating the results to which this agreement relates;
       b) Participate in the verification of the data (e.g. by noting and reporting any errors or omissions discovered to the JRC).


 

Reference of source (Citations) :

Bahram, M., Lehtovirta-Morley, L., Mikryukov, V., Sveen, T.R., Grant, A., Pent, M., Hildebrand, F., Labouyrie, M., Köninger, J., Tedersoo, L., Jones, A., Panagos, P., Orgiazzi, A. 2026. Intensive land use enhances soil ammonia-oxidising archaea at a continental scale. Soil Biology and Biochemistry, 213: 110024.


 

When making reference to the ESDAC

  • Panagos, P., Van Liedekerke, M., Borrelli, P., Köninger, J., Ballabio, C., Orgiazzi, A., Lugato, E., Liakos, L., Hervas, J., Jones, A.  Montanarella, L. 2022. European Soil Data Centre 2.0: Soil data and knowledge in support of the EU policies. European Journal of Soil Science, 73(6), e13315. DOI: 10.1111/ejss.13315
  • Panagos P., Van Liedekerke M., Jones A., Montanarella L., “European Soil Data Centre: Response to European policy support and public data requirements”; (2012) Land Use Policy, 29 (2), pp. 329-338. doi:10.1016/j.landusepol.2011.07.003
  • European Soil Data Centre (ESDAC), esdac.jrc.ec.europa.eu, European Commission, Joint Research Centre