Sampling design and sample processing affect soil biodiversity assessments

This repository contains the code and resources used for analyzing the impact of sampling design on soil animal, bacterial, and fungal diversity estimates based on PacBio and Illumina amplicon sequencing. This repository eexplores the influences of sampling designs including sampling depth, sampling area, and sample size on the biodiversity estimation using individual samples, DNA and soil pooling samples.

Repository Contents

• get the tables.R: Script to rarefy the tables.
• get the sample size for 8 subsamples.R: Script to select 8 samples from GSMc62 (N62D0-5) sampling design and estimate the diversity for each combination.
• get the richness at different sequencing depths.R: Script to estimate diversity at various sequencing depths.
• effective number of designs.R: Script to estimate effective number at summary sequencing depth for unpooled sampling designs.
• visualization and significant test.R: Generates figures used in the manuscript (e.g., accumulation curve).

Calcuator link

https://mycology-microbiology-center.github.io/Soil_biodiversity_assessments/

Citation

Chen, M., Dulya, O., Mikryukov, V., Copot, O., Metsoja, M., & Tedersoo, L. (under review). Sampling design and sample processing affect soil biodiversity assessments.