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Annual plant competition experiment results and associated mycobiome ASV tables

Cite this dataset

Collings, Jeremy; Cook, Emily; Delevich, Carolyn; Diez, Jeff (2024). Annual plant competition experiment results and associated mycobiome ASV tables [Dataset]. Dryad. https://doi.org/10.5061/dryad.cfxpnvxfp

Abstract

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.

README: Competition and Mycobiome Similarity

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.  

Funding

National Science Foundation, Award: 2125586