DOI: 10.5061/dryad.ffbg79d67
title: Soil and biomass data from: Soil, competition, and niche shifts shape the floral mosaic of an annual plant diversity hotspot

description: Plant species with affinity for harsh substrates often have well-defined
 edaphic (soil) niches and are ideal for exploring questions of community
 assembly. Vertic clay soils are chemically and physically challenging to
 plant establishment and productivity, and annual plant communities
 associated with these soils of the San Joaquin Desert (California, USA)
 form a distinctive mosaic pattern of species that reflects differences in
 soil properties across the landscape. We conducted field sampling and a
 pot study with 12 native annual forb species with an affinity for vertic
 clay soils to determine how heterogeneous soils at two sites in the San
 Joaquin Desert differed between realized niches of species, to test if
 species differed in their realized and fundamental edaphic niches, and to
 examine the competition effects of an invasive annual grass (Bromus
 rubens) on these species’ edaphic niches. From our field study, we found
 some differences in the vertic clay soils between the realized niches of
 species at both sites. In our pot study, we found species exhibited
 similar fundamental edaphic niche optima on our treatment soils, and that
 species’ competitive ability differed across the gradient of edaphic
 stress in our treatment soils. For some species, differences in
 competitive ability led to shifts in edaphic niche optima, likely
 contributing to more divergent realized niches. We found that the
 combination of competitive pressure and abiotic stress drove differences
 between the realized niche and fundamental niche for species in a novel,
 heterogeneous study system.
description: <strong>Data
 in "dryad_fieldsoilsweighted_sitesseparate.csv"
 and "dryad_fieldsoilsweighted.csv" was collected as
 follows":</strong> Field-collected soil
 samples from the species patches for each study species (hereafter
 referred to as their “home soils”) were collected from sites at Cantua
 Creek, Carrizo Plain, or both, based on species distribution and
 verifiability of species patches during field visits. For each species, we
 sampled approximately 0.5 L of rhizosphere soil from a maximum depth of 25
 cm within the centroid of a species patch dominated by that species.
 Replicate sampling (n ≥ 5) for a single species was done at a minimum
 distance of 15 m and efforts made to ensure patches sampled for a single
 species were separated by one or more patches dominated by other species
 to avoid pseudo-replication. All soil samples were air-dried and sieved to
 2 mm prior to analysis. Soil samples collected from
 field sites and soils used for the pot study were analyzed by A&L
 Western Laboratories (Modesto, California, USA) for saturated paste pH
 (Rhoades and Miyamoto, 1990), KCl (2 M) extractable
 NO<sub>3</sub><sup>-</sup> (Keeney and Nelson,
 1982), Weak Bray P1 extractable
 HPO<sub>4</sub><sup>-2</sup> (Bray and Kurtz,
 1945), and bicarbonate extractable
 HPO<sub>4</sub><sup>-2</sup> (Olsen and Sommers,
 1982), ammonium acetate (1M, neutral pH) extractable
 K<sup>+</sup>, Ca<sup>2+</sup>,
 Mg<sup>2+</sup>, Na<sup>+</sup> (Thomas, 1982),
 Cation Exchange Capacity (CEC) calculated as the sum of extracted cations,
 and soil texture. Phosphorus content values used in data analysis were
 from either Weak Bray P1 or Olson/sodium bicarbonate results, as
 appropriate for each soil samples’ pH (Olsen et al., 1954; Frank et al.,
 1998). Molar ratios of Na:K and Ca:Mg were calculated from extractable
 elemental analysis. Coefficient of linear extension
 (COLE) was used as a measure of shrink-swell potential following the
 method of Schafer and Singer (1976). For each sample, 100 g of sieved soil
 was wetted to a saturated paste and allowed to equilibrate. The soil paste
 for each sample was then extruded from a 25 cm<sup>3</sup>
 syringe into 1-cm diameter rods, and length measured before being allowed
 to dry. Once dry, rod length was measured again, and COLE was calculated
 as: COLE = ((saturated rod length - dry rod length)/(dry rod
 length)). <strong>Data
 in "dryad_biomass.csv" was collected as
 follows:</strong> Seeds for all study species
 were provided by the Bureau of Land Management Central Coast Field Office,
 except for <em>Layia munzii</em>. All seed collections made by
 the Bureau of Land Management for species in this study were made from a
 minimum of 100 parent plants in collections of a minimum of 1000 seeds
 total that were homogenized post-collection. Seed collections were made
 from parent plants growing at or near one of our field sites (collection
 site was determined by species distributions). Parent plants for all
 species were growing on vertic clay soils. For <em>L.
 munzii,</em> we collected approximately 800 seeds from approximately
 50 parent plants in July 2020 at Carrizo Plain. The pot
 study was conducted outdoors in Fresno, California, from December 2020 to
 July 2021. The city of Fresno is located at the far eastern edge of the
 San Joaquin Desert and has a Köppen climate classification of BSk (cold
 semi-arid) to Csa (hot summer Mediterranean; Beck et al., 2023). Pots were
 set up outdoors in full sunlight, on a 1m high platform to ensure even and
 continuous sun exposure throughout daylight hours.
 Three soil types were selected for use in this study to capture a
 gradient of soil chemical stress present at field sites (Table 3). Clay
 soils are susceptible to pore collapse when the soil moisture content
 exceeds the plastic limit (the lowest moisture content at which a soil can
 undergo deformation without cracking), and passive watering of potted clay
 soils is often ineffective. For this reason, soils were manually wetted to
 ensure homogenous wetting throughout the soil for each pot. Each soil type
 was mixed with water by hand to achieve a consistent, homogeneous level of
 moisture within a semi-solid state without exceeding the plasticity limit.
 Soils were wetted manually until stable, moist 6–8 mm crumb aggregates
 formed. Plastic tree pots with dimensions 12.7 x 12.7 x 30.5 cm were
 filled to the top with the moistened soil. Soil was settled into the pots
 by lifting pots from the top edges and lightly tapping the bottom of the
 pot on a solid surface. Additional moistened soil was added to all pots so
 that the soil surface was within 2 cm of top edge of the pot. The pots
 were then placed in 29.5 x 54.6 x 6.4 cm plastic subirrigation trays which
 were filled with water to a depth of approximately 5 cm. The potted soils
 were left for 24 hours to rest and allow the soil to further moisten to
 field capacity by capillary action. Due to low germination rates in
 germination trials, the pots were heavily seeded (50–100 seeds; seedlings
 were thinned to one per pot following germination) for all study species
 in December 2020. Seeds were left uncovered by soil and misted from above
 daily for four weeks, in addition to subirrigation.
 Each of the 12 focal species was seeded in four replicate pots
 for every combination of soil treatment and competition treatment for n =
 24 pots per species total (Figure 2). Pots were separated following
 seedling thinning into four blocks of replicates (one replicate of each
 species × soil treatment × competition treatment per block) and pots
 within each block were randomized in placement within the block. To ensure
 there was no possibility of dissolved minerals from one soil type leaching
 into the subirrigation tray’s water and affecting another soil type, each
 block was internally randomized into sub-blocks of one soil type within a
 tray. Prior to seeding in pots, all seeds were
 cold-stratified at 3 °C for a 3-month period. For species with low
 germination rates during prior germination trials (<em>Benitoa
 occidentalis, Caulanthus anceps, Deinandra halliana, Layia munzii,
 Monolopia major, M. stricta,</em> and <em>Phacelia
 ciliata</em>), backups were seeded in potting soil in 3.8 cm x 3.8
 cm-celled seedling trays on the same date all pots were seeded.
 Transplants for one or more pots were necessary for <em>B.
 occidentalis, C, anceps, D. halliana, L. munzii, M. major, M.
 stricta,</em> and <em>P. ciliata,</em> and were
 transplanted within five weeks of seeding in all cases. Following
 germination, study species seedlings were thinned to one individual per
 pot. Pots with the competition treatment were thinned to three individual
 <em>B. rubens</em> seedlings surrounding one focal species
 seedling, per pot.  Overhead watering was conducted to
 keep the soil surface moist through seed germination and establishment.
 Following seedling establishment, overhead watering was reduced and
 applied as needed for all pots (watered in a uniform manner to all pots
 when applied). All overhead watering was tapered off after three months
 (late February 2021), and watering was limited to subirrigation for the
 remainder of the study. Beginning in May 2021, subirrigation watering was
 tapered down to reflect field conditions by gradually reducing the
 frequency of refilling the subirrigation trays with water. Beginning in
 June 2021, the volume of water used to refill subirrigation trays was also
 reduced. By July 2021, all plants had senesced, shortly before
 subirrigation tray refills were scheduled to be completely
 halted. Plant biomass was harvested following
 senescence of each plant. For the purposes of this study, senescence was
 defined as having occurred when either the last flower had bloomed and
 withered, with no developing buds remaining, or over 50% of leaves on the
 plant had browned over at least one third of their surface area,
 regardless of fruit development on the last flowers. To reduce loss of
 reproductive parts that might alter final biomass, flowers were bagged
 with cinchable polyester organza exclusion bags enclosing the flower and
 top of the pedicel after petals began to wither or after the innermost
 disk flowers had been open for a minimum of 24 hours. For Asteraceae, bags
 enclosed the capitulum and top of the peduncle. If a plant had not yet met
 our definition of senescence but had mature fruits, the fruits and flower
 parts captured in the bag were removed and dried early to prevent loss of
 that biomass. Following senescence, plant stems were
 cut at the soil surface and shoot biomass was collected. Roots were
 cleaned of soil immediately following shoot material collection. Root
 biomass was cleaned of soil residue using a method modified from Rechel
 (1993). For each plant, the entire soil mass from the pot was fully
 submerged and soaked in a dilute (≤ 0.25%) HCl solution for 15–45 minutes
 to loosen the soil by dissolution of carbonates, in combination with
 sonication at 70 KHz. Sonication was run for 15-minute intervals, as
 needed, to loosen the clay soil particles from the roots. Initial soaking
 and sonication were followed by further sonication and rinsing with water,
 as needed, in combination with manual agitation of the root mass over a 2
 mm sieve. Controlled agitation and rinsing with water over the sieve were
 repeated as necessary to prevent roots from tearing or any substantial
 loss of root mass, until the roots were entirely free of soil particles.
 Roots of competition-treated plants were painstakingly and carefully
 separated from <em>B. rubens</em> roots by hand. All collected
 and cleaned plant materials (reproductive parts, shoots, and roots) were
 dried to constant mass at 41°C for 24–48 hours and the combined total
 biomass of all three was recorded. Citations:
 Beck, H. E., T. R. McVicar, N. Vergopolan, A. Berg, N. J. Lutsko,
 A. Dufour, A. Zeng, et al. 2023). High-resolution (1 km) Köppen-Geiger
 maps for 1901–2099 based on constrained CMIP6 projections.
 <em>Scientific Data</em> 10: 724. Bray, R.
 H., and L. T. Kurtz. 1945. Determination of total, organic, and available
 forms of phosphorus in soils. <em>Soil Science</em> 59:
 39–45. Frank, K., D. Beegle, and J. Denning, J. 1998.
 Recommended phosphorus tests. <em>In</em> J. R. Brown [ed.],
 Recommended chemical soil test procedures for the North Central Region.
 Missouri Agricultural Experiment Station, Columbia, Missouri,
 USA. Keeney, D. R., and D. W. Nelson. 1982. Nitrogen:
 inorganic forms. <em>In</em> A. L. Page, R. H. Miller, and D.
 R. Keeney [eds.], Methods of soil analysis. Part 2. Chemical and
 microbiological properties, 643–689. American Society of Agronomy,
 Madison, Wisconsin, USA. Olsen, S. R., C. V. Cole, F.
 S. Watanabe, and L. A. Dean. 1954. Estimation of available phosphorus in
 soils by extraction with sodium bicarbonate. United States Department of
 Agriculture, Washington, District of Columbia, USA.
 Olsen, S. R., and L. E. Sommers. 1982. Phosphorus.
 <em>In</em> A. Klute [ed.], Methods of soil analysis, part 2:
 Chemical and microbiological properties, 403–430. American Society of
 Agronomy, Madison, Wisconsin, USA. Rechel, E. A. 1993.
 Using acetic acid to wash roots from calcareous soil.
 <em>Communications in</em> <em>Soil Science and Plant
 Analysis</em> 24: 1845–1848. Rhoades, J. D., and
 S. Miyamoto. 1990. Testing soils for salinity and sodicity.
 <em>In</em> R. L. Westerman [ed.], Soil testing and plant
 analysis, 3<sup>rd</sup> ed., 299–336. Soil Science Society of
 America, Madison, Wisconsin, USA.
description: # Soil and biomass data from: Soil, competition, and niche shifts shape
 the floral mosaic of an annual plant diversity hotspot Dataset DOI:
 [10.5061/dryad.ffbg79d67](https://doi.org/10.5061/dryad.ffbg79d67) ##
 Description of the data and file structure We examined 12 native annual
 forb species associated with vertic clay soils in this study over two
 components: an observational field sampling campaign and an experimental
 pot study. To explore whether these species had realized niches defined by
 edaphic properties, we sampled soils from 5–10 patches per species at both
 Cantua Creek (Fresno County, California) and Carrizo Plain (San Luis
 Obispo County, California). We then analyzed the soil samples for physical
 and chemical properties to characterize the edaphic realized niche along
 the axes of those soil properties. If differences in edaphic properties
 were the primary determinant of the realized edaphic niches of our study
 species, we anticipated finding significant differences between species
 for the soils sampled from species patches. We then used the dominant
 species of the patches from which those soils were sampled to conduct a
 pot study to experimentally test for 1) differences between species in
 fundamental edaphic niche within the range of edaphic factors captured in
 our pot study soils, 2) edaphic niche shifts when competition from *B.
 rubens* was present and 3) species-level differences in the effect of
 competition over soil treatments. To do so, we grew 12 species on three
 different field-collected vertic clay soils that captured a chemical
 stress gradient of several soil properties that varied across our field
 sites, to determine whether these species differ in their fundamental
 edaphic niche optima, using biomass to measure performance. We
 hypothesized that these species would differ in their performance when
 competition was absent over the three soils (i.e., we would observe
 differences in fundamental edaphic niche optima among species). To test
 whether competition from *B. rubens* led to niche shifts, a duplicate set
 of replicates in the pot study were seeded with *B. rubens* in addition to
 the study species, across all treatment soils. We hypothesized that
 competition from *B. rubens* would reduce performance of our study
 species, but that its effect would vary by soil treatment, resulting in
 niche shifts as edaphic stress modifies competition. We further
 anticipated species-level differences therein, as species likely differ in
 their specific edaphic specializations and would therefore also differ in
 how biotic-abiotic interactions influence their performance. ### Files and
 variables #### File: dryad_fieldsoilsweighted_sitesseparate.csv
 **Description:** data on soil properties of soil samples collected in the
 field, where soil samples were collected from the centroid of different
 species patches ##### Variables * origin: which species was growing in the
 patch the soil was sampled from. * site: site from which soils were
 collected. * pH: pH of the soil sample. * Pppm: Phosphorus content of the
 soil sample, in ppm. * Kppm: Potassium content of the soil sample, in ppm.
 * Mgppm: Magnesium content of the soil sample, in ppm. * Cappm:
 Calcium content of the soil sample, in ppm. * Nappm: Sodium content of the
 soil sample, in ppm. * COLE: Coefficient of linear extension of the soil
 sample (unitless value). * nitrogen: Nitrogen content of the soil sample
 in ppm. * percentclay: percentage of soil sample that was clay. * CEC:
 cation exchange capacity of the soil sample. * weight: weight applied to
 that replicate in the PCA to adjust for unequal sample sizes between
 species, for site-specific PCAs. #### File: dryad_fieldsoilsweighted.csv
 **Description:** data on soil properties of soil samples collected in the
 field, where soil samples were collected from the centroid of different
 species patches. The data is the same as
 in dryad_fieldsoilsweighted_sitesseparate.csv, but the weights are
 different (adjusted based on which samples went into which PCA) #####
 Variables * origin: which species was growing in the patch the soil was
 sampled from. * site: site from which soils were collected. * pH: pH of
 the soil sample. * Pppm: Phosphorus content of the soil sample, in ppm. *
 Kppm: Potassium content of the soil sample, in ppm. * Mgppm:
 Magnesium content of the soil sample, in ppm. * Cappm: Calcium content of
 the soil sample, in ppm. * Nappm: Sodium content of the soil sample, in
 ppm. * COLE: Coefficient of linear extension of the soil sample (unitless
 value). * nitrogen: Nitrogen content of the soil sample in ppm. *
 percentclay: percentage of soil sample that was clay. * CEC: cation
 exchange capacity of the soil sample. * weight: weight applied to that
 replicate in the PCA to adjust for unequal sample sizes between species,
 for PCA with both sites pooled. #### File: dryad_biomass.csv
 **Description:** biomass data from the greenhouse study conducted for 12
 species, with two competition treatments and three soil treatments. #####
 Variables * species: Study species. * treatment: Competition treatment. C
 = competition present (from *Bromus rubens*), NC = no competition present.
 * soil: Soil treatment. NS = non-sodic soil, S = somewhat sodic soil, ES =
 sodic soil. * tot_mass: Total biomass of the replicate after drying
 (includes reproductive biomass, shoot biomass, and root biomass) * block:
 Which block the replicate was in within the pot study's blocked
 layout. #### File: dryad_soils_finalscript.R **Description:** Script for
 soil data analyses (all PCAs and statistical tests conducted on soil
 samples' coordinates within the PCAs) and code for Figures 3, 4, and
 5. #### File: dryad_biomass_finalscript.R **Description:** Script for
 biomass data analyses (model and posthocs) and code for Figure 6. ##
 Code/software We used R (version 3.6.2, revisions done in version 4.5.2)
 in Rstudio (version 2022.7, revisions done in version 2025.09) for
 statistical analyses and generating figures. Superficial revisions to
 figures generated in R were made in Clip Studio Paint Pro (version 2.0).
 "dryad_biomass_finalscript.R" is the code used for analysis and
 figure generation for the biomass data from our pot study
 ("dryad_biomass.csv"). "dryad_soils_finalscript.R" is
 the code used for analysis and figure generation for the soils data from
 our field study ("dryad_fieldsoilsweighted_sitesseparate.csv"
 and "dryad_fieldsoilsweighted.csv"). These scripts use following
 packages: * car (version 3.1-3) * ggplot2 (version 3.5.2) * ggthemes
 (version 5.1.0) * WCluster (version 1.3.0) * tidyverse (version 2.0.0) *
 emmeans (version 1.11.2) * afex (version 1.5-0) * lme4 (version 1.1-37)