Root-associated fungi modulate plant recruitment in Mediterranean forests
Data files
Oct 08, 2026 version files 813.43 KB
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dataset_FE-2025-01276.xlsx
805.61 KB
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README.md
7.82 KB
Abstract
Established plants affect directly and indirectly the success of juvenile plants recruiting in their close vicinity, what is defined as a canopy-recruit interaction. Such interactions affect plant species demography and community dynamics. Root‑associated fungi (RAF) can influence plant performance and survival, thus contributing to the sign and intensity of canopy-recruit interactions. Pathogenic RAF negatively affect individual plants and their neighbours, while mycorrhizal fungi can positively counteract those effects. Additionally, saprotrophic RAF decompose organic matter, modifying nutrient availability in the soil, possibly enhancing recruitment. Therefore, understanding the role of RAFs in canopy-recruit interactions will help us understand their potential effect on the dynamics of natural plant communities.
We combined information on canopy-recruit interactions for 24 woody species in two Mediterranean mixed forests with high-throughput sequencing of root DNA from each species. We determined the relationships between plant recruitment and the similarity and richness of RAF communities among woody species associated with different mycorrhizal types.
The probability of canopy-recruit interactions decreased between plants sharing more similar pathogenic RAF communities. However, their effect on the frequency of recruitment was modulated by the mycorrhizal association of the recruit, being negative for plant species associated with AM fungi but not significant for those associated with ECM. At the plant species level, plants hosting higher richness of pathogenic RAF presented scarcer recruitment and recruited under a narrower set of canopy species; on the other hand, canopy species associated with ECM fungi or hosting higher richness of saprotrophic RAF, promoted denser recruit banks of any species in their vicinity.
Our findings provide evidence of the importance of RAF for plant recruitment in natural habitats, and thus for plant population and community dynamics. They support the hypothesis that pathogenic RAF interact with mycorrhizal associations, and that plant species susceptibility to multiple pathogens limits its recruitment success. They also suggest that the positive effect of certain plant species on the recruitment of others (i.e., nurse effect) is likely mediated by a higher diversity of saprotrophic RAF.
This dataset contains the root-associated fungal (RAF) community data used in the paper "Root-associated fungi modulate plant recruitment in Mediterranean forests" (Pajares-Murgó, Perea, Bastida, López-García, Garrido & Alcántara; [JOURNAL, YEAR, DOI]).
Roots of 24 woody plant species were sampled in two Mediterranean mixed forests in southern Spain (Jaén and Segura; 147 samples in total). Fungal DNA was extracted from the roots and sequenced by high-throughput sequencing (HTS) of [MARKER, e.g. ITS2 region] to obtain amplicon sequence variants (ASVs). Each ASV was assigned a taxonomy and a functional guild (saprotroph, pathogen, ectomycorrhizal, arbuscular mycorrhizal or endophyte). The data allow reconstructing the RAF community of each plant species, which was used in the paper to test whether RAF community similarity and richness, by functional guild, influence plant recruitment under different canopy species.
Description of the data and file structure
The dataset is a single Excel workbook (dataset_FE-2025-01276.xlsx) with four sheets: OTU_table, Taxonomy, Variables and README (a short version of this file). Tables are linked by two identifiers:
ASVlinksOTU_tableandTaxonomy.sample_IDlinksOTU_table(column names),TaxonomyandVariables.
Sheet OTU_table
Matrix of raw read counts: 1,174 rows (one per ASV) x 147 sample columns.
| Column | Description |
|---|---|
ASV |
Unique code of each fungal ASV (e.g. ASV00016). |
rhizo_... (147 columns) |
One column per sample; the column name is the sample_ID defined in Variables. Each value is the number of sequencing reads of that ASV in that sample (integer, reads). |
A value of 0 means the ASV was not detected in that sample. Total reads per sample range from 78 to 161,775 (mean ~35,900). Counts are raw: no rarefaction or normalisation has been applied.
Sheet Taxonomy
Taxonomic and functional annotation of the ASVs. The table is in long format: it has one row for each ASV detected in a sample (6,319 rows, matching the number of non-zero cells in OTU_table). The annotation of an ASV is therefore repeated in every sample where it occurs, and is identical across rows of the same ASV (1,174 unique ASVs).
| Column | Description |
|---|---|
sample_ID |
Sample in which the ASV was detected (see Variables). |
ASV |
ASV code (see OTU_table). |
guild4 |
Functional guild of the ASV: saprotroph, pathogen, em (ectomycorrhizal), endophyte or am (arbuscular mycorrhizal). Assigned with [FungalTraits / other database, version]. |
Kingdom, Phylum, Class, Order, Family, Genus, Species |
Taxonomy assigned with the UNITE database. The UNITE rank prefixes are kept (k__, p__, c__, o__, f__, s__); the species epithet is given without the genus. Empty cells mean the ASV could not be classified at that rank (Order: 54 rows, Family: 134, Genus: 372, Species: 2,747). |
Sheet Variables
Sample metadata: 147 rows, one per sample, no missing values.
| Column | Description | Values |
|---|---|---|
sample_ID |
Unique sample label. Matches the column names of OTU_table. Prefix rhizo_ECM_ + rhizo_S |
|
site |
Study forest. | Jn = Jaén; Sg = Segura |
num_sample |
Sample number within [plant species / zone]: | integer, 0-8 |
zone |
Sampling zone within the site: | Jaén: CHAZ_ALTO, CHAZ_BAJO, CHIMBA, CREA, HAZ, Q1, Q2. Segura: MADERA, N.ESPINO, N_CAB, RESERVA |
plant_species |
Host plant species sampled, as a six-letter code (first three letters of genus + first three of epithet). See the key below. | 24 codes |
Plant species key (please check the names marked with ?):
| Code | Species | Code | Species |
|---|---|---|---|
ACEMON |
Acer monspessulanum | QUEFAG |
Quercus faginea |
BERHIS |
Berberis hispanica ? | QUEILE |
Quercus ilex |
CISALB |
Cistus albidus | QUEPYR |
Quercus pyrenaica |
CRALAC |
Crataegus laciniata ? | RHALYC |
Rhamnus lycioides |
DAPLAU |
Daphne laureola | ROSJAE |
Rosa sp.in Jaén |
GENCYN |
Genista cinerea | ROSOFF |
Rosmarinus officinalis |
LAVLAT |
Lavandula latifolia | ROSSEG |
Rosa sp.in Segura |
PHIANG |
Phillyrea angustifolia | THYMAS |
Thymus mastichina |
PHILAT |
Phillyrea latifolia | THYZYG |
Thymus zygis |
PHLPUR |
Phlomis purpurea | ULEPAR |
Ulex parviflorus |
PINHAL |
Pinus halepensis | PISLEN |
Pistacia lentiscus |
PINNIG |
Pinus nigra | PRUSPI |
Prunus spinosa |
Number of samples per plant species ranges from 3 to 19.
Abbreviations
RAF: root-associated fungi. ASV: amplicon sequence variant. HTS: high-throughput sequencing. EM / ECM: ectomycorrhizal. AM: arbuscular mycorrhizal.
Sharing/Access information
Links to other publicly accessible locations of the data:
- None.
Data was derived from the following sources:
- UNITE database, version v. 8.2 (taxonomic assignment): https://unite.ut.ee
- FungalTraits database (functional guilds): https://doi.org/10.1007/s13225-020-00466-2
Code/Software
None.
