Active microbes in forest soils differ from the total community yet are shaped by the same environment

This project is maintained by ZakLab-Soils

Title: Active microorganisms in forest soils differ from the total community yet are shaped by the same environmental factors: the influence of pH and soil moisture

Authors: Karl J. Romanowicz, Zachary B. Freedman, Rima A. Upchurch, William A. Argiroff, and Donald R. Zak

Accepted in FEMS Microbiology Ecology on July 6, 2016
Link to the article: http://femsec.oxfordjournals.org/content/92/10/fiw149.abstract?ijkey=1zbz8LGUdUkZ3SC&keytype=ref

This repository is associated with the manuscript "Active microorganisms in forest soils differ from the total community yet are shaped by the same environmental factors: the influence of pH and soil moisture" written by Karl J. Romanowicz, Zachary B. Freedman, Rima A. Upchurch, William A. Argiroff, and Donald R. Zak at the University of Michigan. Links are provided to the original raw sequencing data stored in the Sequence Read Archive at NCBI. Data stored in this repository include all .oligos files for extracting sample plot data from barcoded sequencing runs, final output files generated from the MOTHUR bioinformatic pipeline and used in all downstream statistics, and the RMarkdown dynamic document with rendered statistical code. The full MOTHUR batch files and associated reference databases are also included for reproducibility purposes.

Link to the rendered code file for production of all figures and statistical analyses (created with MI-Gradient-Romanowicz-2016.Rmd): http://rpubs.com/kjromano/MI_Gradient_Romanowicz_2016

Direct any questions regarding this repository to lead author Karl J. Romanowicz.

Information about this repository

Original .fastq files:

The original .fastq files were submitted to the NCBI Sequence Read Archive under BioProject PRJNA222775 with SRA accession numbers SRR1944476 and SRR1944477.

Directories:

  1. Data: Includes final output files from MOTHUR necessary to run statistics in R as well as the environmental metadata env.txt necessary for PERMANOVA analyses.

    • Bacteria: all .oligos files for separating bacterial reads by plot
    • Fungi: all .oligos files for separating fungal reads by plot
    • mothur.reference: 16S and 28S reference database files used for alignment and taxonomy assignment purposes for bacteria and fungi.
    • mothur.output: final MOTHUR files created from pipeline and used in all downstream statistics. Provided here for reproducibility.
      • MOTHUR cons.tax.summary files
      • MOTHUR groups.summary files
      • MOTHUR .shared files

    ZIP files need to be extracted and all resulting files placed directly in their corresponding directory folder for batch files to operate correctly.

  2. MOTHUR_batch: includes two batch files for processing raw PacBio sequencing data through a custom MOTHUR bioinformatic pipeline.

    • bacteria.master.list.subsample.batch Bacteria MOTHUR batch file
    • fungi.master.list.subsample.batch Fungi MOTHUR batch file

  3. MI-Gradient-Romanowicz-2016.Rmd: RMarkdown dynamic document with rendered code for complete statistical reproducibility within the R environment.

Note: This project is under the General MIT Public License.