Analysis code for paper "Soil characteristics and land-use drive bacterial community assembly patterns"

This repository contains the code for analysis and figure generatation for the paper:

Barnett SE, Youngblut ND, Buckley DH. Soil characteristics and land-use drive bacterial community assembly patterns, FEMS Microbiology Ecology, 2020;96(1):fiz194, doi: 10.1093/femsec/fiz194

Contents

Here is a brief description of each of the files:

Diversity_measures.md: Examines alpha and beta diversity of the soil microbial communities including running CAP analysis to examine the how different soil properties explain variation in community composition.

• Figure 1
• Supplementary figure S2
• Supplementary figure S5

Neutral_model.md: Fits the Sloan neutral model to the regional dataset to assess how well this model explains OTU occupancy.

• Figure 2

Phylogenetic_signal.md: Assess the phylogenetic signal in niche preference for pH, percent SOM, and C:N ratio of the bacteria across the region.

• Supplementary figure S3

bNTI_calculation.md: Calculation of the βNTI metric (Deterministic proceses).

bNTI_soil_properties.md: Looking for correlations between βNTI and variation in soil parameters across all soil samples.

• Supplementary figure S4

bNTI_across_landuse.md: Testing if βNTI differes across land use regimes. Also looking for correlations between βNTI and variation in soil parameters within each land use regime.

• Figure 4

bNTI_across_pH_groups.md: Testing if βNTI differes between acidic or pH neutral soils.

Comm_assembly_processes.md: Calculating RCbray metric. Quantifying how different community assembly processes differ across land use regimes and pH groups (Deterministic: Homogeneous selection and variable selection, Stochastic: limited dispersal, homogenizing dispersal, and drift alone).

• Figure 3
• Figure 5

License

This is provided under the MIT license. See LICENSE for more information.