RMQS: The French Soil Quality Monitoring Network (RMQS) is a national program for the assessment and long-term monitoring of the quality of French soils. This network is based on the monitoring of 2,240 sites representative of French soils and their land use. These sites are spread over the whole French territory (metropolitan and overseas) along a systematic square grid of 16 km x 16 km cells. The network covers a broad spectrum of climatic, soil and land-use conditions (croplands, permanent grasslands, woodlands, orchards and vineyards, natural or scarcely anthropogenic land and urban parkland). The first sampling campaign in metropolitan France took place from 2000 to 2009. Dataset: This dataset contains 16S (Archaea and Bacteria) microbial habitats of 1,798 sites of the RMQS. Soil 16S rDNA gene was sequenced using pyrosequecing (GS FLX Titanium - Roche 454) at Genosocope. Bioinformatics analysis was performed using BIOCOM-PIPE metabarcoding pipeline. OTUs were clustered at 95% using a post-clustering strategy Terrat et.al. (2019) across the whole dataset, producing 188,030 robust OTUs. Habitats were identified by fitting a multivariate regression tree (MRT) with the OTU matrix (10.57745/ZZWKGQ) as response matrix and the set of environmental descriptors (10.15454/QSXKGA) as explanatory variables (land-use type, climatic factors, soil texture, pH, soil chemistry, elevation). Sixteen habitats were identified. See associated articles for details.

Figure 2 from Karimi et.al. 2020

File structure:

rmqs1_16S_habitats.tsv: two columns file with id_site linked to its habitat rmqs1_16S_habitats.metadata.tsv: three columns file with habitat code, habitat name and habitat pH-based complex

Details:

Some sites sample could not be collected, they do not appear in dataset. Some sites did not pass laboratory or bioinformatics steps to attain 10,000 sequences before post-clustering, so they did not appear in the dataset. Supplementary filtering was applied (removing OTU with a total abundance of one, also called single-singleton) and some samples were removed from the initial 1,842 available. One can link this dataset with 10.15454/QSXKGA to get each sample physico-chemical property, landuse, coordinates, or filtering sites using its site_officiel column. Sites with ID longer than 4 number are supplementary sites that are not in the center of the cells (e.g. 10797 and 20797 that came from cell 797).