Soil biota sampling
Soil biodiversity was measured using environmental DNA (eDNA)
metabarcoding from the soil samples. In the field, we extracted eDNA
from a 15 g aliquot following Taberlet et al. (2012, 2018). The
remaining soil was sieved at 2 mm and used to measure soil
physico-chemical properties (Table 1).
We employed six DNA markers, including two universal markers (euka02 for
eukaryote, bact01 for bacteria) and four clade-specific markers (fung02
for fungi, inse01 for insect, olig01 for oligochaeta, and coll02 for
collembola) (Taberlet et al. 2018). Details regarding the markers
and molecular analyses are detailed in Appendix 2. A standardised
bioinformatic pipeline was applied to curate the retrieved sequences
from contaminants and errors (Calderón‐Sanou et al. 2020), using
the OBITools software (Boyer et al. 2016) and the ‘metabaR’ R
package (R Core Team 2020; Zinger et al. 2021). Sequences were
clustered into Molecular Operational Taxonomic Unit (MOTU) with
SUMACLUST (Mercier et al. 2013) using a clustering threshold of
97% for Euka02, Fung01 and Bacte01, 85% for Coll01, 88% for Olig01
and 95% for Inse01, following the recommendations in Bonin et
al. (2023). Taxonomic annotations were performed on MOTUs with the
SILVAngs pipeline (Quast et al. 2013) (SILVA version 138.1) for
ribosomal universal markers. For clade specific markers, we used the
ecotag program from the OBITools, and marker-specific databases built
with the ecoPCR program (Ficetola et al. 2010), from the EMBL
database version 136. Metazoan taxa not registered in the European
region were removed from the data (<1% of total reads) using
the GBIFfilter tool
(https://github.com/nleguillarme/gbif-filter-python).