Plant Root Exudates and Microbe Competition

ISEF Category: Microbiology

Subcategory: Other  ·  Difficulty: Advanced  ·  Setup: University Lab  ·  Time: Full Year

The Hook

Plants do not just feed themselves. Their roots leak chemicals that can change which microbes win nearby. That means a houseplant may quietly steer a tiny bacterial turf war. You can test whether those root signals shift competition on agar plates.

What Is It?

This project asks whether plant root exudates change how two bacteria compete. Root exudates are chemicals that roots release into water and soil. Citrate and malate are two common organic acids in that mix. You are asking if those molecules act like a nudge that helps one microbe grow faster, slow down, or lose ground.

Think of it like two teams racing on the same track. The track itself changes if you spray it with a chemical that one team handles better than the other. Bacillus and Pseudomonas can respond differently to carbon sources, acids, and stress. If you track colony expansion over time, you can turn that race into numbers and compare the outcome across treatments.

The math side comes from a generalized Lotka-Volterra model. That model describes how each species affects the other’s growth. In simple terms, it helps you estimate whether the relationship looks like competition, interference, or a weaker bias under certain exudates. You are not just watching plates grow. You are testing how chemical signals reshape the rules of the game.

Why This Is a Good Topic

This makes a strong science fair topic because you can change one chemical factor, measure a clear outcome, and compare models across conditions. It connects to real problems in agriculture, soil health, and microbial ecology, where plant roots can shape which bacteria thrive. You can also learn useful skills, including experimental design, time-lapse imaging, image quantification, and model fitting. A careful student can turn a simple-looking plate experiment into serious quantitative biology.

Research Questions

• How does citrate exposure change the relative expansion rate of Bacillus and Pseudomonas on agar plates??
• How does malate exposure change the competitive outcome between Bacillus and Pseudomonas on agar plates??
• What is the effect of hydroponic runoff from different houseplants on the pairwise growth dynamics of Bacillus and Pseudomonas??
• To what extent does adding citrate or malate alter the fitted interaction coefficients in a generalized Lotka-Volterra model??
• Which exudate treatment produces the largest change in colony boundary area over time for each bacterium??
• Does the presence of plant-derived organic acids shift the final spatial dominance pattern between the two species??

Basic Materials

• Petri dishes with suitable agar for the selected BSL-1 strains.
• Verified BSL-1 Bacillus strain and verified BSL-1 Pseudomonas putida strain.
• Sterile inoculation loops or sterile swabs.
• Micropipettes with sterile tips.
• Sterile saline or broth for suspensions.
• Citrate and malate standards or prepared stock solutions from a school or university lab.
• Hydroponic runoff or plant root exudate samples collected under supervised conditions.
• Parafilm or plate sealing film.
• Smartphone or camera with a fixed mount.
• Ruler or calibration target for image scaling.
• Incubator with appropriate access and supervision.
• Nitrile gloves, lab coat, and eye protection.
• Disinfectant approved by the lab supervisor.

Advanced Materials

• Certified BSL-1 Bacillus strain and certified BSL-1 Pseudomonas putida strain.
• Sterile agar media with defined carbon conditions for comparison.
• Spectrophotometer for standardizing inoculum density.
• Benchtop incubator with stable temperature control.
• Time-lapse imaging setup with fixed lighting and camera position.
• Image analysis computer with calibration reference.
• Analytical balance for preparing exudate standards.
• Sterile filtration setup for plant runoff samples.
• pH meter to track acid effects separately from carbon effects.
• Shaking platform or orbital mixer for sample preparation if permitted by the lab.

Software & Tools

• ImageJ: Measures colony area, edge expansion, and spatial overlap from time-lapse images.
• Python: Fits growth curves, calculates interaction terms, and plots model outputs.
• R: Runs statistical tests, mixed models, and figure-ready comparisons across treatments.
• Google Sheets: Organizes image dates, treatment labels, and replicate tracking.
• PubMed: Finds review articles and primary papers on microbial interactions and root exudates.

Experiment Steps

1. Define the exact competition question, then choose one plant exudate or one synthetic analog as your main variable.
2. Decide how you will standardize both bacteria so the starting matchup is fair.
3. Plan a plate layout that separates treatment effects from random position effects and edge effects.
4. Build an image plan that gives you the same field of view, lighting, and scale across every time point.
5. Choose the growth metrics you will extract, such as colony area, boundary speed, or overlap ratio.
6. Fit a simple interaction model first, then compare it with a generalized Lotka-Volterra version.

Common Pitfalls

• Using unverified environmental isolates instead of confirmed BSL-1 strains, which creates safety and interpretation problems.
• Treating hydroponic runoff as a single chemical signal when its pH, salt level, and sugar content can all change the result.
• Photographing plates under shifting light or at different distances, which makes colony area measurements drift.
• Comparing only end-point colony size, which misses early competitive shifts that explain the interaction.
• Fitting a generalized Lotka-Volterra model before checking whether your images and replicates actually support that level of complexity.

What Makes This Competitive

A strong version of this project goes beyond asking which plate looks bigger at the end. You would quantify growth over time, separate chemical effects from pH effects, and compare more than one exudate source. Strong entries also use enough replicates to fit interaction models and test whether the model actually explains the data. That kind of design turns a simple competition assay into a real ecological analysis.

Project Variations

• Swap the synthetic citrate and malate for filtered runoff from different houseplants and compare which plant causes the biggest shift.
• Test one bacterium at a time against a no-competitor control to separate direct growth stimulation from true competition effects.
• Add a pH-matched control so you can tell whether the exudate effect comes from the organic acid itself or from acidity alone.

Learn More

• PubMed: Search for review articles on root exudates, microbial competition, and generalized Lotka-Volterra models.
• NIH NCBI Bookshelf: Look for free textbook chapters on microbial ecology and growth modeling.
• NOAA educational resources: Review basic experimental design ideas and data interpretation methods used in environmental science.
• MIT OpenCourseWare: Search for microbiology and ecology course materials that explain growth curves and interaction models.
• USDA research pages: Find background on plant-microbe interactions, rhizosphere chemistry, and agricultural microbiology.
• Applied and Environmental Microbiology: Search recent papers on plant-associated bacteria and competition experiments.