Shrub and Sedge Rhizosphere communities display distinct affinities toward Exudates and soil organic matter degradation: A quantitative stable Isotope probing analysis (2022 - 2025)

This experiment examined substrate preferences and biological strategies from microbial taxa belonging to shrub and sedge rhizosphere communities, as well as uninoculated permafrost communities. Using quantitative stable isotope probing, we identified taxon-specific growth rates for bacteria and fungi across rhizosphere/permafrost communities and substrate treatments. Substrate treatments consisted of daily synthetic exudate additions or water additions, which served as our soil organic matter treatment.
Specific aims of the study included the following:
1) Measure taxon-specific growth rates for rhizosphere and permafrost microbes.
2) Identify the strategies of rhizosphere and permafrost microbes by looking for microbial communities associated with degrading exudates and soil organic matter (SOM).
3) Determine whether strategies of permafrost microbes change in the presence of rhizosphere microbes.
4) Determine whether the intrusion of rhizosphere communities alters SOM degradation rates.
The primary data types for this study consist of metadata, respiration data, DNA sequencing data, isotopic enrichment data, and qPCR data. The qSIP pipeline utilizes and synthesizes all of this with the exception of respiration data. 16S and ITS refer to the primers used in generating amplicon sequences and represent bacteria and fungi, respectively.
A couple of quick notes about the data repositories:
· Most of the data provided here is relevant to recreating the workflow and the qSIP pipeline. I highly recommend using the R scripts as a guide and using the datasets as needed in R environments for context.
· If you are interested in using data on taxon-specific growth rates then I suggest opening the growth_summary_compiled_subset dataframes (separate for 16S and ITS).