Microbial Carbon Traits

This repository contains open-source code, data, & text files for the microbial carbon traits project currently titled: Trait-based approach to bacterial growth efficiency.

Publication

Muscarella, M.E., Howey, X.M. and Lennon, J.T. (2020), Trait‐based approach to bacterial growth efficiency. Environ Microbiol. Accepted Author Manuscript. doi:10.1111/1462-2920.15120

Goals

• Aim 1.) Determine metabolic profiles of HMWF culture collection using BioLog EcoPlates

• Aim 2.) Determine metabolic potential of HMWF culture collection using Genomic Functional Potential Evaluation

• Aim 3.) Measure physiological traits including productivity, respiration, and growth efficiency using defined carbon sources

Contents

• bin:

  • consenTRAIT.R: consenTrait function from Adam Martiny's group
  • curve_fit_fxs.R: Code for fitting growth curves
  • EcoPlate.R: Code for analyzing ecoplate data
  • grid.mle2.R: Code for fitting grid maximum likelihood
  • growthcurve_models.R: Growth Curve Analysis scripts
  • modified_Gomp.R: Modified gomphertz growth curve function
  • PresensInteractiveRegresssion.R: Code for moving window regression with R
  • PreSensRespiration.R: Code to process presense respirometer data
  • read.synergy.R: Functions to import data from synergy plate reader
  • ReadEcoPlate.R: Function to import ecoplate data
  • moleculetype_matrix.txt: EcoPlate Molecule Grouping Matrix
  • resource_matrix.txt: EcoPlate Well ID Matrix

• data:

  • CellCounts: Directory with cell count data from experiments
  • EcoPlate: Directory with EcoPlate data from experiments
  • Old Genomes: Directory with Amino Acid annotations for HMWF genomes (OLD Genome Annotations)
  • GrowthCurves: Directory with growth curve data and output
  • Maple: Directory with GenBank genome annotations and Maple output
  • Phylogeny: Directory with 16S sequences and RAxML phylogeny
  • Production: Raw data for bacterial production
  • Respiration: Raw data for bacterial respiration
  • RespiratoryQuotient: Raw CO2 data for RQ calculations
  • 16SrRNA.txt: rRNA copy number data
  • ABS-Cells.txt: Absorbance to cell density values
  • BGE_data.txt: Growth efficiency output data
  • BP_data.txt: Production output data
  • BR_data.txt: Respiration output data
  • eco.data.txt: Ecoplate output data
  • umax.txt: Maximum growth rate output data

• analyses:

  • CarbonTraits.Rmd
  • CarbonTraitsEcoPlate.R
  • CarbonTraitsGrowthRate.R
  • CarbonTraitsPreSens.R
  • CarbonTraitsProduction.R
  • CarbonTraitsRespiration.R

• figures:

  • OLD: Directory with all of the old figures (remove soon)
  • Figure1.png - Chemicals used in the incubations
  • Figure2.png - Phylogenetic tree with BGE values
  • Figure3.png - Physiological tradeoffs
  • Figure4.png - Respiration / Production relationship
  • FigureS1.png
  • FigureS2.png

Funding Sources

1. Huron Mountain Wildlife Foundation Grant (to JTL & MEM) - Browning of freshwater ecosystems: Will terrestrial carbon loading alter the diversity and function of aquatic microbial communities?
2. Indiana Academy of Sciences Grant (# 00375714 to MEM) - Metabolic Fate of Terrestrial Carbon Resources
3. National Science Foundation (DEB‐0842441 to JTL, DEB‐1442246 to JTL and DEB‐1501164 to JTL & MEM)

Sequencing Data

Isolate genomes are available on NCBI (BioProject PRJNA420393)

Contributors

Mario Muscarella: Postdoctoral Fellow in the del Giorgio Lab and Research Associate II in the Institute of Arctic Biology at the University of Alaska Fairbanks. Former Ph.D. candidate in the Lennon Lab. Conducted the experiments and analyzed the data

Xia Meng Howe: Former undergraduate Researchers in the Lennon Lab. Conducted the experiments

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