Miscanthus spp. Genotype Root Exudates

Overview

This repository contains protocols, notebooks, and resources for collecting and analyzing root exudates from Miscanthus spp. genotypes. Modified from a protocol from Rich Phillips.

Repository Structure

• data/: Contains raw (input/) and processed (output/) data files. Not all data is included due to size constraints. See GERMS lab Google Drive or request access.
• docs/: Documentation and supplementary materials. Poster presentations and other material in main GERMS lab Google Drive.
• protocols/: What did Bolívar do things? Contains detailed protocols for exudate collection.
  • mxg_exudate_collection_protocol.qmd: Comprehensive protocol for soluble root exudate collection (Version 6)
• notebooks/: How did Bolívar do things? Analysis notebooks and experimental documentation
  • pilot_mxg_greenhouse.md: Documentation for pilot greenhouse experiments
• R/: R scripts for import and cleaning data for metabolomic analysis and greenhouse carrying capacity for the lab.
• renv/: R environment configuration for reproducible analysis
• R/: R scripts for data analysis
• data/: Raw and processed data files

Read DATA_DICTIONARY and DMP_REPORT for more details on how the data was collected and managed.

Getting Started

Prerequisites

• R and RStudio for data analysis
• Quarto for rendering .qmd documents
• Laboratory equipment as detailed in the protocols

Setup

This project uses renv for managing R package dependencies. To set up the environment:

1. Clone this repository
2. Open the project in RStudio
3. Run renv::restore() to install the required packages

Protocols

Mxg Exudate Collection Protocol

The main protocol protocols/LDRD_Root_Exudates_Protocol-v6.docx or protocols/mxg_exudate_collection_protocol.html provides detailed instructions for collecting soluble root exudates from Miscanthus x giganteus. The protocol includes:

• Materials and equipment lists
• Step-by-step collection procedures
• Sample preservation methods
• Quality control considerations

View the full protocol in the protocols/ directory.

Pilot Experiments

Documentation for pilot experiments in greenhouse settings can be found in the notebooks/ directory. These include:

• Materials needed for Mxg rhizome preparation
• Growth conditions
• Experimental setup
• Data collection procedures

Contributors

• John Field, Ph.D (Oak Ridge National Laboratory)
• Bolívar Aponte Rolón, Ph.D (Iowa State University)
• Phillip de Lorimier (Iowa State University)