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Dynamic plant-soil microbe interactions: the neglected effect of soil conditioning time

Cite this dataset

Ke, Po-Ju; Zee, Peter; Fukami, Tadashi (2021). Dynamic plant-soil microbe interactions: the neglected effect of soil conditioning time [Dataset]. Dryad.


Plant-soil feedbacks (PSF) may change in strength over the life of plant individuals as plants continue to modify the soil microbial community. However, the temporal variation in PSF is rarely quantified and its impacts on plant communities remain unknown. 

Using a chronosequence reconstructed from annual aerial photos of a coastal dune ecosystem, we characterized >20-year changes in soil microbial communities associated with individuals of the four dominant perennial species, one legume and three non-legume. We quantified the effects of soil biota on conspecific and heterospecific seedling performance in a greenhouse experiment that preserved soil properties of these individual plants. We used a general individual-based model to explore the potential consequences of temporally varying PSF on plant community assembly.

In all plant species, microbial communities changed with plant age. However, plant's response to the turnover in microbial composition depended on the transplanted seedling species: only the soil biota effect experienced by the non-legume species became increasingly negative with longer soil conditioning. Model simulations suggested that temporal changes in PSF could affect the transient dynamics of plant community assembly.

These results suggest that temporal variation in PSF over the course of decades should be considered to understand how PSF structures plant communities.

Usage notes

Data description as follows:

Files related to bacterial community composition

1. BacteriaCommunityMatrix.csv --> community matrix of bacterial OTU characterized from each soil sample

2. BacteriaSampleData.csv --> Sample metadata and information for each soil sample where bacteria were sampled

3. BacteriaTaxInfo.csv --> Taxnomic assignment for each bacterial OTU 

4. BacteriaRepresentativeSequence.fasta --> Sequence for representative bacterial OTU

Files related to fungal community composition

1. FungiCommunityMatrix.csv --> community matrix of fungal OTU characterized from each soil sample

2. FungiSampleData.csv --> Sample metadata and information for each soil sample where fungi were sampled

3. FungiTaxInfo.csv --> Taxnomic assignment for each fungal OTU 

4. FungiRepresentativeSequence.fasta --> Sequence for representative fungal OTU

Files related to plant-soil feedback greenhouse experiment 

1. GreenhouseData.csv --> Plant performance data from the greenhouse experiment

Files related to the individual-based model

1. func_DemodynAssembly.R --> Main function for IBM simulation

2. defineFeed.R --> Supporting function for IBM simulation

3. generateDynFeedback.R --> Supporting function for IBM simulation

4. wavelets.RData --> Supporting information for IBM simulation

5. Run_DemogFeedbackAssembly.R --> Example of running the IBM simulation