Data and code from: Local conspecific density affects the relationship between species abundance and plant-soil feedback in a subtropical forest
Data files
Oct 01, 2026 version files 19.11 KB
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code_for_analysis.R
2.71 KB
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PSF_GROUP.csv
5.07 KB
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PSF_PATHOGEN.csv
7 KB
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README.md
4.33 KB
Abstract
Increasing evidence suggests that plant-soil feedback (PSF) is essential in shaping species abundance and promoting the coexistence of common and rare species. Yet, empirical studies have yielded inconsistent results regarding the relationship between species abundance and PSF strength. To reconcile the debate on the species abundance–PSF relationship (SAPR), we propose a conceptual framework that decomposes PSF into two components: PSF1 caused by the focal tree and PSF2 caused by the nearby conspecific neighbors. These two components drive community assembly and diversity maintenance processes, respectively. Moreover, our framework emphasizes that local species density is critical for measuring species PSF in natural communities. We then conducted a shade-house experiment involving 14 subtropical tree species to test the SAPR in a subtropical forest. We found a significant negative relationship between species abundance and PSF only when inoculum soils were collected from areas with high local conspecific density. The fungal pathogens in the soil and roots were identified as the key driver of this pattern. Our study provides direct experimental evidence that local conspecific density affects the SAPR, which may clarify discrepancies across studies and advance our understanding of how PSF contributes to species coexistence in forest ecosystems. Integrating a conceptual framework with a multi-species soil inoculation PSF experiment, we reveal intensifying negative PSF from rare to common species in a subtropical forest community, with local density influencing this pattern. Consequently, our study suggests that the intricate relationship between species abundance and PSF is closely implicated in the dynamics of local species coexistence. We propose that previous controversies regarding the SAPR primarily stemmed from the neglect of local species density and the confusion of distinct ecological processes across studies.
Dataset overview
This dataset contains data associated with a plant--soil feedback (PSF) experiment examining the relationship between species abundance, local conspecific density, soil fungal pathogens, and PSF in a subtropical forest.
The dataset contains two comma-separated value (CSV) files:
PSF_Group.csv--- biological-replicate-level PSF data used to examine the relationship between species abundance and PSF under different soil inoculum treatments.PSF_Pathogen.csv--- sample-level data describing fungal pathogen metrics, PSF, species identity, and local conspecific density associated with the source locations of the soil inocula.code_for_analysis.R--- R script to analyze these datasets
File descriptions and variable definitions
1. PSF_Group.csv
This file contains experimental results at the biological-replicate level.
Variable: Description
Species: Plant species name.Treatment: Soil inoculum treatment.PSFHD_total,PSFLD_total, andPSFCON_total: represent PSF under the high local conspecific density (HD), low local conspecific density (LD), and heterospecific control (CON) treatments, respectively.Replicates: Biological replicate number. Integer values identify individual biological replicates within each species and treatment.PSF: Plant--soil feedback (PSF) value for each biological replicate.LN_AB: Natural logarithm of the abundance of the corresponding species. Species abundance was measured at the whole-plot scale.
2. PSF_Pathogen.csv
This file contains sample-level measurements used to examine associations among fungal pathogen metrics, PSF, species identity, and local conspecific density.
Variable: Description
Sample_code: Sample identifier composed of the species and treatment codes.rhizo_PAshannon: Shannon diversity index of fungal pathogens in the rhizosphere soil.rhizo_PARA: Relative abundance of fungal pathogens in the rhizosphere soil.root_PAshannon: Shannon diversity index of fungal pathogens within roots.root_PARA: Relative abundance of fungal pathogens within roots.PSF_total: Overall plant--soil feedback strength experienced by the individual plant sample.Species: Latin name of the plant species.R30_Den: Number of conspecific individuals within a circular area with a radius of 15 m centred on the source location of the soil inoculum used for the sample.LN_R30: Transformed local conspecific density, calculated asln(R30_Den) + 1, wherelndenotes the natural logarithm. The constant 1 was added after log transformation so that observations withR30_Den = 1have a transformed value of 1 rather than 0.
Key terms and treatment codes
- PSF: Plant--soil feedback.
- LCD: Local conspecific density.
- HD: High local conspecific density treatment (
PSFHD_total). - LD: Low local conspecific density treatment (
PSFLD_total). - CON: Heterospecific control treatment (
PSFCON_total). - Shannon diversity index: Diversity metric used to quantify fungal pathogen diversity.
- Rhizosphere: Soil directly associated with plant roots.
- Biological replicate: An independent experimental replicate associated with a distinct soil inoculum source.
Data relationships
PSF_GROUP.csv contains PSF values at the biological-replicate level and is used for analyses of the species abundance--PSF relationship under different soil inoculum treatments.
PSF_PATHOGEN.csv contains measurements for individual plant samples and links PSF values with fungal pathogen metrics and local conspecific density associated with the corresponding soil inoculum source.
Species abundance and local conspecific density
Species abundance in PSF_Group.csv is represented by LN_AB, the natural logarithm of species abundance measured at the whole-plot scale.
Local conspecific density in PSF_Pathogen.csv is represented by R30_Den, the number of conspecific individuals within a circular area with a radius of 15 m centred on the source location of the soil inoculum. LN_R30 is the transformed local-density variable and was calculated as ln(R30_Den) + 1.