Soil microorganisms influence a variety of processes in plant communities. Many theoretical and empirical studies have shown that dynamic feedbacks between plants and soil microbes can stabilize plant coexistence by generating negative frequency-dependent plant population dynamics. However, inferring the net effects of soil microbes on plant coexistence requires also quantifying the degree to which they provide one species an average fitness advantage, an effect that has received little empirical attention. We conducted a greenhouse study to quantify microbially mediated stabilization and fitness differences among fifteen pairs of annual plants that co-occur in southern California grasslands. We found that although soil microbes frequently generate negative frequency-dependent dynamics that stabilize plant interactions, they simultaneously generate large average fitness differences between species. The net result is that if the plant species are otherwise competitively equivalent, the impact of plant-soil feedbacks is to often favor species exclusion over coexistence, a result that only becomes evident by quantifying the microbially mediated fitness difference. Our work highlights that comparing the stabilizing effects of plant-soil feedbacks to the fitness difference they generate is essential for understanding the influence of soil microbes on plant diversity.

Data are from a greenhouse experiment in which individuals of six annual plant species were grown in pots containing soil inocula that was previously cultivated by conspecific or heterospecific plants.

File 1: phase2-harvest.csv

This file contains the biomass for all pots grown in the second phase of the experiment. There are six columns:
1. "number" - this just has a unique number for each pot, and was used to randomize the map. Not really meaningful for data analysis, except as a way to keep track of each pot.
2. pot_id - the unique ID for each pot. soil_focalspecies_replicate
3. Source soil - identifies which soil was used to inoculate the pot. Eight unique soils: AC, FE, HO, SA, PL, UR, and two controls. The two controls are "aastr" and "abfld" and refer to sterile and field soil, respectively.
4. focal_species: identity of the species growing in the pot.
5. replicate: which block the pot came from.
6. abg_dry_g: dry aboveground biomass, in grams.

File 2: variation-harvest.csv

This file contains the biomass of all plants grown for the variation experiment (described in Appendix S2). In this experiment, each pot was inoculated with soil cultivated by a single PLER phase 1 monoculture (soils were homogenized across 5 replicate monocultures for the main experiment). There are seven columns:

1. "pot_id": this is a unique number associated with each pot; was used for randomizing the pots but not relevant for the analysis.
2. "pot_tag": The unique tag for each pot, in the format "v_SoilSource_FocalSpecies_Replicate"
3. "experiment_id": Simply the letter "v" for all rows, to indicate that this is from the varitaion experiment
4. Source soil - identifies which soil was used to inoculate the pot. Five unique soils, each representing a single PLER Phase 1 monoculture: PL1, PL2, PL3, PL4, PL5
5. focal_species: identity of the species growing in the pot. Either FEMI or PLER.
6. replicate: replicate number. Note that these were not randomized into blocks, but rather randomzied all together.
7. abg_dry_g: dry aboveground biomass, in grams.

File 3: psf-greenhouse-analysis-script.R

This R script generates all of the figures and tables in the manuscript.