DOI: 10.5061/dryad.cfxpnvxfp
title: Annual plant competition experiment results and associated mycobiome ASV tables

description: Major theories regarding microbe-mediated plant community dynamics assume
 that plant species cultivate distinct microbial communities. However, few
 studies empirically assess the role of species-associated microbial
 community dissimilarity in plant competitive dynamics. In this study, we
 paired a competition experiment between eight annual forbs with a
 characterization of species-associated fungal communities to assess
 whether mycobiome dissimilarity is associated with pairwise competitive
 dynamics. Using a quantitative approach informed by modern coexistence
 theory, we found that fungal dissimilarity was correlated with both
 increased stabilizing niche differences and fitness inequalities.
 Additionally, we found that the probability of coexistence increased with
 mycobiome dissimilarity. When subsetting the community into different
 fungal functional groups (pathotrophs, saprotrophs, symbiotrophs), overall
 relationships between dissimilarity and competitive dynamics were
 independent of these functional groups.  Synthesis: These results
 suggest that fungal community divergence may play an important role in
 mediating plant competitive dynamics. Although fungal community
 dissimilarity is associated with both niche and fitness differences,
 complex biotic and/or abiotic interactions belowground may result in an
 observed correlation between fungal community dissimilarity and plant
 coexistence. Ultimately, this study suggests a novel approach to better
 understanding how microbiome dissimilarity may impact host community
 dynamics.
description: # Competition and Mycobiome Similarity
 [https://doi.org/10.5061/dryad.cfxpnvxfp](https://doi.org/10.5061/dryad.cfxpnvxfp) These data were those used to assess the degree to which key metrics of competition (interaction coefficients, niche differences, fitness inequalities, and probability of coexistence) are related to the dissimilarity of plant species associated mycobiomes. A competition experiment between eight native annual plants from Willamette Valley prairies was paired with sequencing of rhizosphere soil associated with each plant species. Competition experiment data were used to fit population models and estimate species interaction terms, which were then used to calculate niche differences, fitness inequalities, and the probability of coexistence for each species pair. Rhizosphere samples went through DNA extraction, PCR, and library prep for Illumina sequencing of the ITS region. Sequences were run through DADA2 to assign ASVs, and subsquently filtered to generate the available ASV table. Further, ASVs were assigned taxonomy using the UNITE fungal taxonomy database and functional guilds using FunGuild. We estimated the average fungal Bray-Curtis dissimilarity (total as well as partitioned into functional group) for each species and fit models predicting competition strength, niche & fitness differences, and the coexistence probability as a function of fungal dissimilarity. Overall, we found that while there was no consistent effect of fungal dissimilarity on competition strength, niche and fitness differences both increased with fungal community dissimilarity. Further, we found a marginal increase in the probability of coexistence with increasing fungal community dissimilarity.  ## Description of the data and file structure The first set of files pertain to the competition common garden experiment. Focal plants of each of the eight species were sewn into low, medium, and high density background plots of each of the eight species as well as in alone plots. The number of individuals of the background species within an 19cm radius circle around each focal species is recorded within the "background.xlsx" file. Note that Lupinus bicolor and Madia elegans focals and subplots were removed from all analyses due to low germination counts.  Because we principally collected data at the inflorescence (or stem) level, and used a subset of individuals to calculate mean seed output per reproductive structure, we have multiple data files for the reproductive data of focal individuals. Plectritis was collected first, and while troubleshooting the subset data collection protocol, we collected additional data on the Plectritis collections. Further, Plectritis was the only species that consistently had one seed per flower, so there is no seed per fruit data for this species. Thus, these files are separate.  The additional reproduction files, "StructuresData.xslx", "FlowerData.xlsx", and "SeedsData.xlsx" contain the data for the remaining species. The "StructuresData.xlsx" contains the total number of reproductive structures (flowers, flower heads, or stems) for each focal plant within a sheet for each species. The "FlowersData.xlsx" contains the data for the subset of reproductive structures for which flower counts were conducted. Note that for the species which we did count all flowers (Acmpison americanus, Clarkia amoena, and Clarkia purpurea), there is no subset and thus no sheets within this dataset. Each row in this dataset is a single reproductive structure. The "SeedsData.xlsx" contains the data from the subset of fruits for which seed counts were conducted.  A complete list of column explanations for each of these excel files is contained within the table below: | File | Column Name | Description | | :---------------------- | :---------- | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | background.xlsx | foc | species of the focal plant ("AA" = Acmispon americanus, "CC" = Calindrinia ciliata, "CA" = Clarkia amoena, "CG" = Collomia grandiflora, "CP" = Clarkia purpurea, "LP" = Lupinus bicolor, "ME" = Madia elegans, "NI" = Navarretia intertexta, "PC" = Plectritis congesta, "PN" = Plagiobothrys nothofulvus) | | background.xlsx | id | unique id assigned to each focal individual | | background.xlsx | competitor | species of the background plot | | background.xlsx | dens | density treatment ("L" = low, "M" = medium, and "H" = high) within the background plot | | background.xlsx | count | count of background competitors | | PC\_StructureData.xlsx | ID | unique id assigned to each focal individual | |  PC\_StructureData.xlsx | foc | species of focal plant (always PC in this file) | | PC\_StructureData.xlsx | Comp | species of background plant ('NA' in the case of alone plants) | | PC\_StructureData.xlsx | Dens | density treatment ('NA' in the case of alone plants) | | PC\_StructureData.xlsx | Count | count of inflorescences | | PC\_FlowerData.xlsx | plant | unique id assigned to each focal individual | | PC\_FlowerData.xlsx | count | count of flowers | | PC\_FlowerData.xlsx | type | ordinal position of inflorescence on stem (ie is this a primary (1), secondary (2), tertiary (3), ... inflorescence) | | PC\_FlowerData.xlsx | ht | height of inflorescence in mm | | PC\_FlowerData.xlsx | whorls | number of  whorls composing the inflorescence | | PC\_FlowerData.xlsx | person | person who did data entry | | StructuresData.xlsx | ID | unique id assigned to each focal individual | | StructuresData.xlsx | Foc | species of focal plant | | StructuresData.xlsx | Comp | species of background plant ('NA' in the case of alone plants) | | StructuresData.xlsx | Dens | density treatment ('NA' in the case of alone plants) | | StructuresData.xlsx | N\_\* | number of reproductive structures; for AA, CA & CP, this is the number of fruits; for CG & NI, this is the number of flower heads; for CC & PN, this is the number of reproductive stems; for PN, the number of stems is further subdivided into small and large stems | | StructuresData.xlsx | Notes | additional notes | | FlowerData.xlsx | ID | unique id assigned to each focal individual | | FlowerData.xlsx | Foc | species of focal plant | | FlowerData.xlsx | Comp | species of background plant ('NA' in the case of alone plants) | | FlowerData.xlsx | Dens | density treatment ('NA' in the case of alone plants) | | FlowerData.xlsx | N\_flow | number of flowers | | FlowerData.xlsx | Notes | additional notes | | SeedsData.xlsx | ID | unique id assigned to each focal individual | | SeedsData.xlsx | Foc | species of focal plant | | SeedsData.xlsx | Comp | species of background plant ('NA' in the case of alone plants) | | SeedsData.xlsx | Dens | density treatment ('NA' in the case of alone plants) | | SeedsData.xlsx | N\_Seeds | number of seeds | | SeedsData.xlsx | Notes | additional notes | The remaining files are all related to the fungal sequence data. The "illumina_2023_asv-table.txt" file contains the table of fungal ASVs for each of our rhizosphere samples. The "ASVforFG.taxa.guilds.txt" file contains the output from our FunGuild run, assigning putative functional classifications to each fungal ASV. Finally, the "sample_order.csv" contains a table relating the sample names used in the illumina run to more informative sample IDs.  ## Code/Software All code associated with the generation and analysis of these data can be found at [https://github.com/jeremyacollings/CAMS](https://github.com/jeremyacollings/CAMS).