DOI: 10.5061/dryad.rxwdbrvjb
title: Data from: Arbuscular mycorrhizal fungi equalize differences in plant fitness and facilitate plant species coexistence through niche differentiation

description: Mycorrhizal fungi are essential to the establishment of the vast majority
 of plant species but are often conceptualized with contradictory roles in
 plant community assembly. On one hand, host-specific mycorrhizal fungi may
 allow a plant to be competitively dominant by enhancing growth. On the
 other, host-specific mycorrhizal fungi with different functional
 capabilities may increase nutrient niche partitioning, allowing plant
 species to coexist. To resolve the balance of these two contradictory
 forces, we used a controlled greenhouse study to manipulate the presence
 of two main types of mycorrhizal fungi, ectomycorrhizal fungi (EMF) and
 arbuscular mycorrhizal fungi (AMF) and used a range of conspecific and
 heterospecific competitor densities to investigate the role of mycorrhizal
 fungi in plant competition and coexistence. We find that the presence of
 AMF equalizes fitness differences between plants and stabilizes
 competition to create conditions for host species coexistence. Our results
 show how belowground mutualisms can shift outcomes of plant competition,
 and that a holistic view of plant communities which incorporates their
 mycorrhizal partners is important in predicting plant community dynamics.
description: # Data from: Arbuscular mycorrhizal fungi equalize differences in plant
 fitness and facilitate plant species coexistence through niche
 differentiation **Authors:** Claire E. Willing, Joe Wan, Jay J. Yeam, Alex
 M. Cessna, Kabir G. Peay  Authors for correspondence: Claire E. Willing
 ([willingc@uw.edu](mailto:willingc@uw.edu)) Kabir G. Peay
 ([kpeay@stanford.edu](mailto:kpeay@stanford.edu))  Access this dataset on
 Dryad:
 [https://doi.org/10.5061/dryad.rxwdbrvjb](https://doi.org/10.5061/dryad.rxwdbrvjb) # Description of the data and file structure Where data is missing, values are reported as NA. This includes where data was never measured due to sample missingness. For values that were measured beyond machine detection limits, these are also listed as NA. Units for all variables are reported below for each specific file type. | File Name | File description | | :-------------------------------------------------- | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | | IsotopeData\_CSIB\_UCB\_Willing\_15N13C\_MCTSamples | Data on leaf carbon and nitrogen concentrations and stable isotope ratios. These data were collected by the California, Berkeley Center for Stable Isotope Biogeochemistry. This facility uses an Isoprime100 continuous flow mass spectrometer using dual-element analysis mode interfaced with a CHNOS elemental analyzer. Long-term precision for C and N isotope determinations is ±0.10‰ and ±0.20‰, respectively. The δ13C results were reported in values relative to the Vienna Pee Dee Belemnite standard and the δ15N measure of the ratio of the two stable isotopes of nitrogen, 15N:14N and the standard is atmospheric N2 (0.3663 atom% \~ 15N). Values marked NA indicate a missing sample and thus no measurements were taken. % C and % N the percent leaf mass measured to as carbon and nitrogen, respectively based on the micrograms of N and micrograms of C (“µg N in capsule” and “µg C in capsule”) measured in each capsule and divided by the total mass of leaf tissue in each tin capsule of sample analyzed. | | LeafP\_Part1.csv and | Data on leaf phosphorus content. Dried and homogenized samples were also used to determine leaf P content at University of California, Davis Analytical Lab using a closed vessel microwave digestion in nitric acid/hydrogen peroxide and Inductively Coupled Plasma Atomic Emission Spectrometry (ICP-AES). Long-term method detection limits for P at this lab is 0.01%. Ground leaf tissue was sent to the Analytical Lab at the University of California, Davis ([http://anlab.ucdavis.edu](http://anlab.ucdavis.edu)). Due to small volumes of leaf material in this seedling experiment, no duplicate samples were run (every 10 samples, there is a Davis\_SampleID that is called “Duplicate” and each is read as NA. The column SampleIDnum matches the unique sample identification numbers for the study. Values are reported as a total percentage of P in leaf tissue. The first several rows contain metadata for sample submission and the lab’s standard operating protocols. | | PRS.xlxs | This is the data reported from the Plant Root Stimulator Probes (PRS; Western Ag. Innovations Inc., Saskatoon, Saskatchewan) which are designed to determine the plant available nutrients in the soil. PRS probes were placed in empty pots of soil in the experiment (no seedling) for the experiment for 9 weeks to measure soil nutrient availability. Data from Western Ag. analysis of the probes is reported here for each nutrient measured. Nutrient availability is recorded as (µg ion\*10cm^-2\*9 weeks^-1). | | Files beginning with 2020 | Files that begin with 2020 are data derived from the LI-COR 6800. The names of the files indicate the data that those data were collected. In the first several rows, the conditions for and settings for the LI-COR are reported; data collected starts on row 67. SampleID refers to the unique sample identifiers that match with the other types of data collected on individual focal plants. Descriptions of all measured variables, including explanations of units, can be found at: [https://www.licor.com/env/support/LI-6800/topics/symbols.html](https://www.licor.com/env/support/LI-6800/topics/symbols.html). Unique Sample IDs (sample identifiers) are included in the first column and all environmental conditions are recorded for each measurement across these columns. The column under GasEx (Gas Exchange) labeled ‘A’ refers to LI-COR calculated photosynthesis and ‘gsw’ refers to the calculated stomatal conductance. Because our samples didn’t entirely fill the leaf chamber, all values were adjusted to actual leaf area encapsulated which is reported here under the Const section as ‘S’ (measured in cm2). For all samples, 5 values were recorded once samples plateaued at their maximum photosynthetic capacity to capture full range of gas exchange variability and these were averaged in R for later calculations. Each file is named by the date that measurements were taken across a \~6 week period of measurement.     | | MCT\_BaBi\_FullDataSheet | This is our datalog for plant harvesting data; please see: | | MCT\_AMF.EMF.CompAnalyses\_2023.Rmd | This is our R markdown data analysis fil, also available on github as linked above. | ### ##Variables and units for MCT\_BaBi\_FullDataSheet | Variable | Units | Notes | | :----------------------------------- | :---------------------- | :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | SampleID | NA | Unique sample identifier code which refers to focal seedling. This includes a description of the different treatments which this seedling was a part of. | | SampleIDNum | NA | Unique sample identifier (extracted from SampleID) | | Mycotreatment | NA | Mycorrhizal treatments to which seedlings were exposed: arbuscular mycorrhizal fungi (AMF), ectomycorrhizal fungi (EMF), a mix of both mycorrhizal types (AMFEMF), and and no mycorrhizal fungi (Sterile). | | DensityTreatment | NA | This show the competition treatment assignment where seedlings were grown with different densities and focal plants were grown with either Baccharis (Ba) or Bishop pine (Bi). Numeric values refer to number of competitors present. | | FocalSpecies | NA | Focal plant species ID; either Baccharis pilularis (Ba) or Pinus muricata (Bi) | | Competitornum | NA | Number of competitors in pot; 0, 1, 4, or 8 competitors were present. | | CompetitionTreatment | NA | Focal plants were either growing with heterospecific or conspecific competitors as coded here | | Replicate | NA | Within each combination unique treatment groups (mycorrhizal treatment + competition type + density treatment + focal species), we replicated the full set of treatments 6 times. Replicate numbers were assigned to each unique pot. | | Dead? | NA | Reports if seedlings died during experiment. NA rows indicate that no seedlings in this pot died during the duration of the experiment. | | Roottrim\_28/08/2020 | NA | Roots that started to grow out of the pot (for Baccharis only) were trimmed on August 28, 2020. “Trimmed” indicates that roots were trimmed and dried for total seedling biomass. NA indicates that root trimming was not necessary for these pots. | | Rootmasstrimmed\_g | grams | Mass of dried roots trimmed prior to harvesting seedlings. | | Position | NA | Refers to the location of seedlings randomized within different potting trays. | | TrayNum | NA | Refers to the unique potting trays in which pots were grown. | | HarvestDate | Date (Month\_Day\_Year) | Seedlings were harvested during a \~6 week period and the data of harvest is reported here. | | Percol\_root | Proportion from 0-1 | This refers to the ectomycorrhizal colonization of Pinus muricata in the experiment. For seedlings with a 0 reported, this indicates that root colonization was measured and 0 colonized roots were encountered. Where a value is reported as NA, this indicates that root colonization was not measured either due to dead focal plant or time constraints. For some Baccharis, there are values here listed as “calculate” which indicates that root tissue was collected for these seedlings to be stained for determination of percent root colonization by arbuscular mycorrhizal fungi. | | AMFPercol\_rootmass | NA | Again refers to where Baccharis root tissue was collected to assess percent root colonization. NA indicates that samples were not collected for root staining. | | Percol\_wetmass\_g | Grams | Where roots were collected to stain for mycorrhizal colonization, the amount of wet root mass collected is reported here. | | Rootmass\_focal\_wet\_g\_minuspercol | Grams | Total wet root mass for Baccharis minus what was taken for later determination of percent colonization by staining | | Stemheight\_mm | Millimeters | Height of seedling from root cuff to tip of leader | | Shoot\_leaf\_mass\_g | Grams | Total dry biomass of leaves and stem, minus leaf material taken for determination of leaf mass per area and leaf mass for LI-COR 6800 | | WET\_LMA\_leafmass\_g | Grams | Total of leaf mass taken for determination of leaf mass per area | | Amax\_mass\_g | Grams | Total leaf mass of leaves encapsulated in LI-COR 6800 chamber during gas exchange measurements. | | DRY\_LMA\_leafmass\_g | Grams | Dry leaf mass taken for LMA (from the wet measurement above) | | Notes | NA | Where NA, no relevant notes were recorded | | Competitor biomass | Grams | Where 0, there were no (live) competitors present at the time of harvest. Where NA, competitor biomass was not recorded due to sample missingness. | | Hyphae | Count | From root staining for mycorrhizal colonization based on grid intersect method; number of hyphae counted at each intersect | | Arbuscules | Count | From root staining for mycorrhizal colonization based on grid intersect method; number of arbuscules counted at each intersect | | Vesicles | Count | From root staining for mycorrhizal colonization based on grid intersect method; number of vesicles counted at each intersect | | No Colonization | Count | From root staining for mycorrhizal colonization based on grid intersect method; number of intersects with no colonization | | Total | Count | From root staining for mycorrhizal colonization based on grid intersect method; total number of intersects counted | ### ## Code/Software All data were analyzed using R statistics. Data cleaning and analysis can be found at: [https://github.com/ClaireWilling/MycorrhizaCoexist.git](https://github.com/ClaireWilling/MycorrhizaCoexist.git)