This repository contains open-source code, data, & text files for the Stormwater Denitrification project (Town Creek, Greenville, North Carolina)
For information regarding the project, please visit: (update when manuscript is published)
-
Aim 1.): Examine the relationship between bacterial community composition, phylogenetic diversity, and denitrification potential along an urban stream reach during base and stormflow.
-
Aim 2.): Measure the phylogenetic diversity-function relationship in this urban stream ecosystem.
-
Aim 3.): Identify bacterial associations according to sediment or water sample type.
-
analyses:: An R Markdown file that includes R script written by Mario Muscarella 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 plant community composition) generated according to R script located in R Markdown file.
-
mothur:
- DatabaseDownload.sh - Downloads needed reference databases for mothur analysis. Also trims the alignment reference to improve performance.
- TC.Bacteria_A.Batch - First part of mothur analysis, includes alignment and chimera removal
- TC.Bacteria_B.Batch - Second part of mothur analysis, includes de novo OTU picking
- TC.files - Files file which assigns raw input into sample contigs
Dr. Ariane Peralta: Associate Professor, Department of Biology, East Carolina University. Principal Investigator of the Peralta Lab
Dr. Mario Muscarella: Assistant Professor, Institute or Arctic Biology, University of Alaska Fairbanks. Principal Investigator of the Muscarella Lab.
Dr. Eban Z. Bean: Assistant Professor, Department of Agricultural and Biological Engineering, University of Florida.