mmuscarella / ReservoirGradient

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 Nelson.

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 functions change along a stream to lake gradient.

Repo Contents

• analyses:

  • ULReservoirGradient_MothurSummary.R: An R script to test mothur output and return basic information including sequence coverage and species richness. Used to determine if mothur pipeline returned logical output.

• data:

  • res.grad.metab.txt:
  • 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.bac.final.0.03.tax.summary
  • UL.bac.final.0.03.taxonomy:
  • UL.bac.final.0.05.tax.summarY:
  • UL.bac.final.0.05.taxonomy:
  • UL.bac.final.shared: Mothur output shared file. Used to generate the site-by-species matrix.
  • UL_euks.final.shared: Mothur output shared file for eukaryotes.

• bin:

  • MothurTools.R: An R script written by Mario Muscarella (Indiana University) containing functions used in the analysis of mothur raw files.

• figures:

  • Figure1.png: Microbial metabolism figure.

• maps:

• mothur:

  • UL.raw.seqs.sh: Shell script to download raw illumina data from () for Reservoir Gradient Project (work in progress).
  • UL.files: Mothur input file that organizes raw sequence files into read 1 and read 2 by sample design.
  • UL.Bacteria_A.Batch: Mothur batch script for the initial sequence processing. This script goes through chimera checking and the output is used by all subsequent batch scripts.
  • UL.Bacteria_B.Batch: Mothur batch script for analysis of bacterial sequences.
  • UL.Cyano.Batch: Mothur batch script for analysis of cyanobacteria only
  • UL.Euks.Batch: Mothur batch script for anlysis of eukaryotes based on plastid sequences
  • UL.Bacteria_A.sh: Torque script to execute UL.Bacteria_A.Batch on Mason (IU).
    Ends up submitting all subsequent torque scripts.
  • UL.Bacteria_B.sh: Torque script to execute UL.Bacteria_B.sh on Mason (IU).
  • UL.Cyano.sh: Torque script to execute UL.Cyano.Batch on Mason (IU).
  • UL.Euks.sh: Torque script to execute UL.Euks.Batch on Mason (IU).

Contributors

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

Megan Larsen: Ph.D. candidate in the Lennon Lab

Mario Muscarella: Ph.D. candidate in the Lennon Lab