Soil biodiversity - DNA Bacteria and Fungi

The dataset includes bacterial 16S data and fungal ITS raw DNA sequences for 885 samples collected as part of LUCAS 2018 Soil survey (Biodiversity module).
Soil biodiversity - DNA Bacteria and Fungi
Resource Type: 
Datasets
Soil Functions Data
Registration is requested: 
Yes
Year: 
2023
Themes: 
Soil Biodiversity
Keywords: 
Biodiversity

The dataset includes 16S and ITS raw DNA sequences 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 PRJNA952168. 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.

The “METADATA_LUCAS18_BIODIVERSITY_885ID_COMPLETED” table includes values for soil properties, extracted climatic data (1970-2000 average) and extracted soil moisture data4 associated to the 885 samples, as well as information on the sampling month. To combine single file of DNA sequences with data in the metadata table (“METADATA_LUCAS18_BIODIVERSITY_885ID_COMPLETED” Excel table), 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, and the protocols for measuring soil properties and sources of climatic data can be found in Labouyrie et al. 2023 “Patterns in soil microbial diversity across Europe.”1.

All R scripts used for the analyses presented in Labouyrie et al. are available for download. Associated READ.ME document mentions the libraries needed and the purposes of each script in the workflow.

Metadata:

Title: Soil biodiversity - DNA Bacteria and Fungi
Description: The dataset includes bacterial 16S data and fungal ITS raw DNA sequences for 885 samples collected as part of LUCAS 2018 Soil survey (Biodiversity module).
Spatial coverage: European Union
Type: DNA sequences, R Scripts
Temporal coverage:  2018
More information: EU Science update on soil biodiversity.

Note: You cal also download the Soil Biodiversity - DNA Eukaryotes

Important note: when sequencing 16S LUCAS samples, the sequencing-adapters and barcodes were added after the PCR with the 16S primers. Due to this, the 16S insert can be in both orientations. The downloadable 16S files have not been subjected to such a re-orientation

Data are available for download

References

  1. 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.
  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. NASA-USDA Enhanced SMAP Global Soil Moisture Data. https://developers.google.com/earth-engine/datasets/catalog/NASA_USDA_HSL_SMAP10KM_soil_moisture#description

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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:

  1. The data provided has been prepared for use by internal research activities in the Joint Research Centre (JRC) Ispra in collaboration with University of Zurich and University of Tartu . In addition, other research organisations have participated in this research:  Agroscope Reckenholz, Swedish University of Agricultural Sciences, Uppsala (SE), MWSchmid GmbH (CH). The research activities support the LUCAS soil campaign. The LUCAS Soil sample collection is supported by the Directorate‐General Environment (DG‐ENV), Directorate‐General Agriculture and Rural Development (DG‐AGRI) and Directorate‐General Climate Action (DG‐CLIMA) of the European Commission. 
  2. 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.
  3. 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.
  4. In case the data are used for EU assessments, you are kindly request to inform the JRC.
  5. The user agrees to:
    • make proper reference to the source of the data when disseminating the results to which this agreement relates;
    • 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) :

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

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