CropDiversity

This repository contains open-source code, data, & text files for

For information regarding the project, please visit: Peralta, A. L., Y. Sun, M. D. McDaniel, and J. T. Lennon. 2018. Crop rotational diversity increases disease suppressive capacity of soil microbiomes. Ecosphere 9(5):e02235. 10.1002/ecs2.2235

Raw sequence files can be found at NCBI SRA BioProject ID PRJNA472091.

We address the following questions

• Aim 1.): What is the relationship between crop diversity and soil microbial community composition and PPS potential?

• Aim 2.): What is the role of changes in soil physicochemical properties on the crop diversity effect on soil microbial community composition and PPS populations?

Repo Contents

• analyses:: An R Markdown file that includes R script written by Mario Muscarella, Yanmei Sun, and Ariane Peralta containing functions used in analysis of soil and microbial sequence data.

• bin:

  • MothurTools.R: An R script written by Mario Muscarella (Indiana University, now at University of Illinois) containing functions used in the analysis of community sequence data.

• data:: Files associated with soil and microbial data sets.

• figures:: Figures (of soil, microbes) generated according to R script located in R Markdown file.

• mothur:: Files containing script for bioinformatic analysis of 16S rRNA gene sequences (Illumina MiSeq platform) using mothur pipeline.

Contributors

Dr. Ariane Peralta: Principal Investigator, Assistant Professor, Department of Biology, East Carolina University. Principal Investigator of the Peralta Lab

Dr. Mario Muscarella: Postdoc in the O'Dwyer Lab at the University of Illinois at Urbana-Champaign