Indoor Air Microbiome Mapping With Settle Plates

ISEF Category: Microbiology

Subcategory: Environmental Microbiology  ·  Difficulty: Intermediate  ·  Setup: School Lab  ·  Time: 1 to 2 Months

The Hook

Your home is not empty air. It carries tiny biological traces from people, pets, plants, dust, and vents. That means two rooms can have different microbial fingerprints, even if they look the same. You can test that with a project that feels part ecology, part detective work.

What Is It?

Indoor-air microbiome mapping asks a simple question: what microbes are moving through the air in different rooms? A microbiome is the collection of microorganisms in a place, like a room, a leaf surface, or your skin. Passive settle plates catch particles that fall out of the air, so you can compare what lands in one room versus another.

Think of each room like a different pond, except the water is air and the fish are microscopic. A bedroom with a plant, a kitchen with cooking activity, and a room near a vent may each collect a different mix of spores, bacteria, and dust-borne cells. You are not trying to name every microbe by sight. You are testing whether the patterns of growth, colony count, and later sequence-based IDs match room features like HVAC mode and houseplant presence.

The phyllosphere is the surface of a plant leaf. Plants release and collect microbes from that surface, and some of those microbes can move into nearby indoor air. If you compare your indoor samples with public Earth Microbiome Project reference data, you can ask whether rooms with plants show a detectable plant-linked signal.

Why This Is a Good Topic

This is a strong science fair topic because you can measure real differences between rooms without needing a university lab. You can change one factor at a time, such as plant presence, vent status, or room use, and compare colony patterns or DNA-based classifications. The project connects to indoor air quality, building design, and microbial ecology, all of which matter in daily life. You will learn sampling design, contamination control, classification, and statistics.

Research Questions

• How does houseplant presence affect the number of colonies that settle on plates in a room?
• What is the effect of HVAC on versus HVAC off on indoor settle-plate colony diversity?
• Does a room with more foot traffic show a different colony count than a quieter room?
• To what extent do rooms with houseplants match phyllosphere reference profiles from public Earth Microbiome Project data?
• Which room feature, plant presence, vent proximity, or occupancy, best predicts the indoor microbial pattern?
• How does sampling location within the same room change the observed settle-plate community?

Basic Materials

• Sterile nutrient agar or pre-poured agar plates
• Permanent marker
• Measuring tape
• Notebook or data sheet
• Smartphone camera
• Digital thermometer-hygrometer
• Timer
• Gloves
• Mask
• Sealable bags for transport
• Household room map
• Labels and tape.

Advanced Materials

• Sterile swabs for follow-up sampling
• DNA extraction kit for environmental samples
• PCR reagents and primers for bacterial or fungal markers
• Gel electrophoresis setup
• Access to a sequencer or amplicon sequencing service
• Incubator with controlled conditions
• Autoclave or approved sterilization method
• Spectrophotometer or fluorometer for DNA quantification
• Environmental monitoring sensors for CO2, temperature, humidity, and particulate matter.

Software & Tools

• ImageJ: Measures colony area, density, and color features from plate photos.
• QIIME 2: Processes amplicon sequencing data and compares indoor samples with reference datasets.
• R: Runs statistics, plots comparisons, and tests whether room features predict microbial patterns.
• Google Sheets: Organizes sample metadata, room conditions, and colony counts.
• PubMed: Helps you find review articles on indoor microbiomes and plant-associated microbes.

Experiment Steps

1. Define one main comparison, such as plant versus no plant, so your project has a clear question.
2. Choose sampling sites that differ in only a few room features, and write down the features you will track.
3. Plan controls that separate room effects from contamination, human activity, and plate handling.
4. Decide how you will turn plate growth or sequence reads into numbers you can compare across rooms.
5. Build a reference plan for matching your indoor results with public phyllosphere and indoor microbiome datasets.
6. Set your analysis plan before collecting data, including replication, visualization, and the statistical test you will use.

Common Pitfalls

• Leaving plates open for different lengths of time, which makes samples impossible to compare.
• Sampling rooms at different times of day, which mixes up HVAC effects with daily activity patterns.
• Placing plates near people, pets, or open windows, which adds contamination that does not reflect the room.
• Counting colonies without a consistent rule for merged or fuzzy growth, which changes your data from plate to plate.
• Using only one room with plants and one room without plants, which makes the plant result too weak to trust.

What Makes This Competitive

A competitive version of this project does more than count colonies. You would use multiple rooms, repeated sampling, and a clear analysis plan that tests one prediction at a time. Strong projects also compare your indoor samples to public reference microbiome data instead of stopping at a simple visual comparison. If you add good metadata, careful controls, and a model that separates plant effects from HVAC and occupancy, your project gets much stronger.

Project Variations

• Compare a bedroom, kitchen, and living room to see whether room use predicts different indoor microbial patterns.
• Compare rooms with snake plants, pothos, or no plants to test whether plant type changes the indoor phyllosphere signal.
• Compare HVAC on, HVAC off, and window open conditions to see how airflow changes settle-plate growth and classification.
• Compare daytime and nighttime sampling in the same room to test whether human activity changes the indoor airborne microbiome.

Learn More

• Earth Microbiome Project: Search the project site for sample records and metadata on soil, leaf, and built-environment microbiomes.
• NIH PubMed: Search for review articles on indoor microbiomes, phyllosphere microbes, and built-environment microbiology.
• USGS Water, Energy, and Biogeochemical Budgets Program: Look for microbiome and environmental sampling methods that help with field-style study design.
• NOAA Climate Data Online: Find room-relevant weather and humidity context if you want to compare indoor and outdoor conditions.
• QIIME 2 Documentation: Read the official guides for amplicon sequence processing and community analysis.
• MIT OpenCourseWare: Search introductory microbiology and environmental biology materials for background on microbial ecology and sampling design.