Data accompanying the manuscript:
Tedersoo L, Liao Y, Mõttus A, Lorenz C, Halling E, Friberg H, Hiiesalu I, Lees J, Mazina-Šinkar J, Kupagme J, Tammik K, Nolfi L, Leinus M, Kõiv M, Dulia O, Tabacchioni S, Vahter T, Annuk T, Mikryukov V, Bevivino A, Männistö M, Yli-Hemminki P, Loit K (2026) Soil health components, indicators and analytical solutions for croplands.
The study developed a multi-component Soil Health Index (SHI) for croplands and evaluated agrochemical, functional and DNA-based indicators of soil health. Soil samples were collected from 30 winter wheat fields in Estonia at two depths (0-10 cm, in two replicates, and 0-20 cm), giving 90 samples for DNA analyses.
| File | Marker | Target group | Sequencing | Features |
|---|---|---|---|---|
MultiSoil_16S.xlsx |
16S rRNA gene, V4-V5 (515F / 926R) | Bacteria and Archaea | Illumina NovaSeq | 48,126 ASVs |
MultiSoil_ITS.xlsx |
Full-length ITS (ITS9mun / ITS4ngsUni) | Fungi and protists | PacBio Revio | 23,948 OTUs (98% similarity) |
MultiSoil_Metazoa.xlsx |
COI (mlCOIintF / jgHCO2198) | Metazoa | Illumina NovaSeq | 1,147 OTUs (97% similarity) |
Each table contains one row per ASV/OTU, read counts per sample (columns MS*), and taxonomic annotation.
The 16S table also includes functional assignments (e.g., ammonification, nitrogen fixation, plant pathogens),
and the ITS table includes fungal guild and trait annotations (primary guild, plant pathogenicity, thallus type, biocontrol potential).
Bioinformatic processing:
- 16S: Cutadapt, USEARCH, DADA2; taxonomy against GTDB; tag-jump removal with UNCROSS2
- ITS: NextITS v1.2.0; taxonomy against EUKARYOME v2.0
- COI: DADA2 workflow in PipeCraft2 v1.2.2; taxonomy with SINTAX against CO1Classifier v5.1.0; non-metazoan, chordate and putative NUMT sequences removed
See the Methods section of the manuscript for details.
DNA sequences recovered in this study (amplicons and shotgun metagenomes) were deposited in the European Nucleotide Archive (ENA) under project accession PRJEB129066 (accession numbers ERR18091531-ERR18091826).
| Target | ENA accession numbers |
|---|---|
| 16S rRNA | ERR18091531 - ERR18091620 |
| COI | ERR18091621 - ERR18091708 |
| Total metagenome | ERR18091709 - ERR18091738 |
| ITS | ERR18091739 - ERR18091826 |
The study was funded by the EU Horizon grant MultiSoil.