DOI: 10.5068/d1b688
title: Data from: Soil microbes generate stronger fitness differences than stabilization among California annual plants

description: 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.
description: 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.
description: 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:<br> 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.<br> 2. pot_id - the unique ID for each pot.
 soil_focalspecies_replicate<br> 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.<br> 4. focal_species: identity of the species growing
 in the pot.<br> 5. replicate: which block the pot came
 from.<br> 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.<br> 2. "pot_tag":
 The unique tag for each pot, in the format
 "v_SoilSource_FocalSpecies_Replicate"<br> 3.
 "experiment_id": Simply the letter "v" for all rows,
 to indicate that this is from the varitaion experiment<br> 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<br> 5. focal_species: identity of the species growing in
 the pot. Either FEMI or PLER.<br> 6. replicate: replicate number.
 Note that these were not randomized into blocks, but rather randomzied all
 together.<br> 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.