University Lake Reservoir Gradient Project

This repository contains open-source code, data, & text files for the Reservoir Gradient Project. This project is the product of the 2013 SSRP work done with N. Nelson at Indiana University.

Project Goals

• Aim 1) Determine if there is an underlying stream to lake gradient in small reservoirs.

• Aim 2) Determine if microbial communities change along a stream to lake gradient.

• Aim 3) Determine if microbial activity changes along a stream to lake gradient.

Repo Contents

• data:

  • res.grad.metab.txt: Metabolism data (bacterial production and respiration) along the gradient.
  • ResGrad_EnvDat.csv: Environmental data - Contains data collected from the hydrolab and calculated environmental data. This file includes the following:
    1. UTM lat/long; WGS84
    2. distance to dam (m)
    3. water temperature (°C)
    4. Specific conductivity (SpC; ms/cm)
    5. Dissolved Oxygen (DO; mg/L)
    6. pH
    7. Total Phosphorus (TP; µg P/L)
    8. Respiration Rate (µM O2 Hr-1)
    9. Chlorphyll a ()
  • ul_resgrad.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.opti_mcc.0.03.cons.tax.summary: Taxonomy summary from mothur
  • ul_resgrad.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.opti_mcc.0.03.cons.taxonomy: Taxonomy from mothur
  • ul_resgrad.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.opti_mcc.shared: Site-by-OTU matrix from mothur
  • ul_resgrad.tree: Phylogeny
  • UL.design.txt: Design corresponding to site by OTU matrix

• bin:

  • mothur_tools.R: An R script written by M. Muscarella and modified by N. Wisnoski containing functions used in the analysis of mothur raw files.
  • Chao_functions.R: R functions from Chiu and Chao to estimate richness in the presence of sequencing errors

• figures:

  • Includes a number of intermediate and final figures included in the manuscript.

• intermediate-data:

  • Includes intermediate output used in the main analysis file.

• maps:

  • Includes shapefiles of university lake

• mothur:

  • batch file and list of raw sequence files for sequence processing

• Miscellaneous cache and output files from knitr processing of the main ReservoirGradient.Rmd analysis file.

• ReservoirGradient.Rmd: main analysis file.

Contributors

Nathan Wisnoski.

Mario Muscarella.

Megan Larsen.

Ariane Peralta.

Dr. Jay Lennon: Principle Investigator, Professor, Department of Biology, Indiana University, Bloomington. Head of the Lennon Lab.