DNA metagenomes - Soil biodiversity

The dataset includes raw DNA sequences for 630 samples collected as part of the LUCAS 2018 Soil survey for the biodiversity module. The dataset includes DNA reads annotated as antibiotic resistance and biosynthesis genes (ARG and ABG, respectively) revealed in the metagenomes from 630 soil samples collected during the LUCAS 2018 Soil survey
Resource Type: 
Datasets
Soil Functions Data
Registration is requested: 
Yes
Year: 
2024
Themes: 
Soil Biodiversity
Soil Biodiversity›DNA barcodes for soil biodiversity

Description

The dataset includes raw DNA sequences for 630 samples collected as part of the LUCAS 2018 Soil survey for the biodiversity module. The raw DNA sequences have been deposited in the NCBI Sequence Read Archive (SRA) under the primary accession code PRJNA1032917 (BioSamples SAMN38018670 – SAMN38019327). Samples from four locations were re-sampled, and thus sequenced twice (i.e., 630 total samples from 626 sampling sites). Specifically, samples numbered 59, 102, 113, 116 were re-sequenced as samples numbered 138, 601, 717, and 258, respectively.

The “ABG_ARG_LUCAS” table includes the number of DNA reads annotated as antibiotic resistance and biosynthesis genes (ARG and ABG, respectively) revealed in the metagenomes from 630 soil samples collected during the LUCAS 2018 Soil survey (GENES sheet). To identify ARGs (genes that, if expressed, provide antibiotic resistance to their host), we employed the short-sequence model of DeepARG v.1.0.2 (Arango-Argoty et al., 2018). ABGs were identified using the eggNOG-mapper v.2.1.2 (Cantalapiedra et al., 2021) based on eggNOG orthology data v.5.0.2 (Huerta-Cepas et al., 2019). Details on the search parameters are available in the published paper "A trait-based ecological perspective on the soil microbial antibiotic-related genetic machinery".

The “ABG_ARG_LUCAS” table contains additional information on the DNA reads generated for each sample from which the ABG and ARG data were retrieved (SAMPLES sheet). To merge the “SAMPLES” and “GENES” sheets, one should use the column BARCODE_ID.

Additional details on DNA extraction and sequencing methods, as well as sources of climatic data, can be found in paper “A trait-based ecological perspective on the soil microbial antibiotic-related genetic machinery”. The source code used for data analyses in this study is available for public access on GitHub https://github.com/Mycology-Microbiology-Center/LUCAS_ABRG (DOI: 10.5281/zenodo.10039980).

Title: Soil biodiversity - DNA metagenomes
Description: The dataset includes link to raw metagenomic DNA sequences + a table reporting the number of DNA reads annotated as antibiotic resistance and biosynthesis genes (ARG and ABG, respectively) revealed in the metagenomes for 630 samples collected as part of LUCAS 2018 Soil survey (Biodiversity module).
Spatial coverage: European Union
Type: DNA sequences  
Temporal coverage:  2018.
 

Reference: Dulya, O., Mikryukov, V., Shchepkin, DV., Pent, M., Tamm, H., Guazzini, M., Panagos, P., Jones, A., Orgiazzi, A., Marroni, F., Bahram, M., Tedersoo, L. 2024. A trait-based ecological perspective on the soil microbial antibiotic-related genetic machinery. Environment International, 190, 108917, DOI:10.1016/j.envint.2024.108917.

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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 in the Joint Research Centre (JRC) Ispra in collaboration with University of Tartu. 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. 
  • 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) :

Dulya, O., Mikryukov, V., Shchepkin, DV., Pent, M., Tamm, H., Guazzini, M., Panagos, P., Jones, A., Orgiazzi, A., Marroni, F., Bahram, M., Tedersoo, L. 2024. A trait-based ecological perspective on the soil microbial antibiotic-related genetic machinery. Environment International, 190, 108917, DOI:10.1016/j.envint.2024.108917.

 

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