Nutrient availability and invader density regulate the diversity–invasibility relationship mediated by soil microbes
Data files
Jul 23, 2025 version files 538.61 KB
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Li_et_al.__Fungi.xlsx
496.84 KB
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Li_et_al.__plant_biomass.xlsx
37.50 KB
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README.md
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Abstract
This dataset accompanies a study examining how native plant diversity, nutrient availability, and invader density interact to influence the growth of the invasive plant Phytolacca americana via soil microbial mechanisms in a temperate forest ecosystem. The dataset includes (1) aboveground biomass data of P. americana grown in soils conditioned by varying native plant diversity levels (1, 3, or 6 species), under different nutrient conditions (fertilized vs. non-fertilized) and invader planting densities (1, 2, or 4 individuals); and (2) soil fungal community data derived from high-throughput sequencing, including taxonomic profiles (from phylum to genus) and functional classifications assigned using FUNGuild (e.g., saprotrophs, pathogens, symbionts). These data support analyses of how plant–soil feedbacks and soil microbial composition mediate invasion success, and are valuable for researchers in the fields of invasion ecology, soil microbiology, and plant–microbe interactions.
Dataset DOI: 10.5061/dryad.1ns1rn95g
Description of the data and file structure
This dataset contains measurements of aboveground biomass of the invasive plant Phytolacca americana and fungal community composition from soil samples collected under varying diversity treatments. The experiment manipulated native plant diversity, nutrient availability, and invader density to examine their interactive effects on plant invasibility and soil microbial dynamics.
Methodological information
We collected plant samples manually, oven-dried them, and weighed the dry biomass using an electronic balance to obtain plant biomass data. We isolated the total genomic DNA from 250 mg of each homogenized soil sample using the EZNA® Soil DNA Kit (Omega Bio-tek, Norcross, GA, USA) and quantified DNA concentrations using a NanoDrop2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). The primers ITS1/ITS2 were used to amplify the ITS1 region to obtain data on soil fungal communities.
Files and variables
File: Li_et_al.__plant_biomass.xlsx
Variables
- Id: Row number for each data entry.
- Diversity: The level of native plant diversity in the treatment, with three levels: 1, 3, and 6 species.
- Identity: The identity of the native species used in the diversity-1 treatment, and the specific species combinations used in the diversity-3 and diversity-6 treatments. A total of 27 unique combinations were used.
- Density: The number of Phytolacca americana individuals (invader density) planted per pot, with three levels: 1, 2, or 4 plants.
- Nutrient: Nutrient availability treatment, where 1 indicates fertilised and 2 indicates non-fertilised conditions.
- Biomass: The aboveground dry mass (in grams) of Phytolacca americana per pot, measured after oven-drying and weighing.
File: Li_et_al.__Fungi.xlsx
Variables
- OTU: Operational Taxonomic Unit; a unique identifier for a cluster of similar fungal ITS sequences, typically approximating species-level resolution.
- sample1–sample27: Columns representing individual experimental soil samples. Each cell indicates the number of ITS sequence reads (i.e., abundance) assigned to a particular OTU in a given sample.
- Taxonomy: Microbial taxonomic classification (e.g., phylum, class, order, family, genus) assigned to each OTU based on ITS sequence similarity.
- Taxon: The scientific name of the fungal taxon assigned to each OTU, based on ITS classification.
- Taxon Level: The taxonomic rank at which the OTU was assigned.
- Trophic Mode: The primary ecological strategy of the fungus (e.g., saprotroph, symbiotroph, pathotroph), as defined by the FUNGuild database.
- Guild: The predicted ecological role or function of the fungal taxon (e.g., saprotroph, pathogen, endophyte), assigned based on FUNGuild classification.
- Growth Morphology: The general growth form of the fungus.
- Trait: Functional or ecological traits associated with the fungal taxon, such as host specificity, substrate preference, or ecological niche.
- Confidence Ranking: A qualitative indicator of confidence in the trophic/guild assignment (e.g., “Probable”, “Highly Probable”, or “Possible”), as provided by FUNGuild or other sources.
- Notes: Additional notes or clarifications regarding specific OTUs or functional assignments. This may include manual annotations, classification uncertainties, or contextual ecological information.
- Citation/Source: The literature or database used as the source for taxonomic or functional annotation.
Note: For all columns (except Notes), cells containing “–” indicate missing or unavailable data. This may be due to low sequence similarity, ambiguous taxonomy, or lack of functional annotation in reference databases.
Data was derived from the following sources:
Data was derived from the following sources: plant biomass data were manually recorded during the experiment, while soil microbial community data were generated by Meiji BioTech Co., Ltd. through high-throughput sequencing and analysis.