Motivating Methanogens - Exploring the Impact of Geometry on Anaerobic Digestion

Hello, my name is Ben Harper, and I'm from rural Southwestern Ontario. The goal of my project was to increase the amount of usable energy obtainable from anaerobic digestion by experimenting with different mesh geometries. During anaerobic digestion, methane is produced, which can be refined into natural gas for energy production.

To test this, I submerged mesh of various porosities in dairy cow slurry. I did this in the hopes of stimulating biofilm growth. Biofilm has been found to increase methane production and improve system stability.

I custom-made the equipment needed to evaluate gas production.

From this process, I found that my 30 PPI mesh produced 39% more methane than my Control.

Furthermore, I observed that all meshes produced more methane than my Control, but were less effective than the 30PPI.

This data also interestingly revealed that all meshes had an inverse effect on CO2 production. CO2 is another by-product of digestion, which is a greenhouse gas that can linger in the atmosphere for thousands of years.

These results suggest that optimizing reactor geometry can be used to make biogas systems more affordable for small farms.

PPI = Pores Per Square Inch.

Control = No mesh inside.

Purpose

Studies show that in a screening of nine biogas collection facilities, 30-50% of methane potential is lost due to inefficiencies [3].

Can efficiency be increased by changing the geometry of the anaerobic growing environment?

My project explored increasing the efficiency of anaerobic digestion by introducing different geometries. The purpose of these geometries is to stimulate biofilm growth. Biofilm not only produces more gas than free-floating bacteria, but also provides a more stable habitat for methanogens. Additionally, biofilm is resistant to temperature swings and pH drops [1].

To test the effect of geometry, aquarium foam disks with 30, 40, and 60 pores per square inch (PPI) were submerged in diluted dairy cow manure for 10 days. Each mesh type was tested separately in custom-designed anaerobic reactors (ARs) to isolate their effects. The sludge was sourced from a dairy farm and diluted with water, ensuring a large bacterial community was present.

Data was collected on pH, biogas production, and gas composition over the 10-day testing period on each jar, with double redundancy. This was compared to a Control (No mesh).

I hypothesize:

1)  Mesh made of medium-porosity aquarium foam at 40 PPI will perform better for methane production due to the balance of surface area, unobstructed sludge movement, and rapid gas expulsion.

2)  Any mesh added will perform better than the Control AR and produce increased CH4 production.

3)  Increased CH4 production in an AR will result in a decrease in CO2 production due to increased anaerobic efficiency.

To test the hypotheses, multiple custom-made apparatuses and processes were used to collect data about the anaerobic reactors (AR's). These include...

Water Displacement Chamber & Mesh Holder (Figure A2)

Gas produced by the ARs was captured in a custom 3D-printed chamber for later removal and testing. This chamber uses water displacement to store gas at low pressure, and has a capacity of 26.2mL of gas before overfilling.

The meshes tested were supported at the middle of the AR using a custom-made 3D-printed mesh holder. The main purpose of the mesh holder is to support the mesh above the accumulating particulates on the bottom of the AR.

Gas Testing (Figure A1)

The custom-built gas testing tool built for this experiment is a device for analyzing the ratio of CH4 using an MQ-4 sensor, H2S using an MQ-136 sensor, and CO2 using an MH-Z19B. MQ series gas sensors give a non-linear analog reading that can be used to calculate parts per million (PPM), while the MH-Z19B sensor gives true PPM and communicates to the microcontroller (ESP-32) through communication protocols rather than analog pins.

Gas Extraction Tool (Figure A3)

The gas extraction tool is a simple syringe with a balloon attached to the top. This tool uses atmospheric pressure to pull the trapped gas from the reservoir within the water displacement chamber. The process of transferring the gas sample from the water displacement chamber reservoir allows the trapped gas to be injected into the Handheld Gas Composition unit while protecting it from oxygen introduction.

Due to the CH4 and H2S data being collected in analog readings rather than PPM, conversions are necessary. This is done by calibrating the sensor to baseline air and using formulas to replicate the logarithmic curve of the sensor sensitivity.

Data Analysis

This data analysis is based on 746 data points collected from March 5th, 2026, to March 15th, 2026 (Table 1). These data points are split into mL of gas, baseline readings, and gas composition measurements. The mL of gas datapoints is the total amount of gas extracted using the gas extraction tool from each AR. Since the air in the gas dilution chamber isn’t totally uniform and can have a trace amount of biogas, a baseline reading is taken before 2mL of the gas sample is injected into the chamber. Then, after this reading stabilizes, the measured gas composition test is taken. The baseline readings and measured readings are 120 seconds of gas readings every 2 seconds, averaged out.

Table 2 is a summary of all gas composition measurements taken from March 5th, 2026, to March 15th, 2026. The CO2 sensor data is in true parts per million (PPM) readings; however, the H2S and CH4 readings are in analog, which are not converted to PPM yet.

Graph 1-4 represents the data in Table 1-4. The graphs are a combined line and bar graph that show the ratio of the gas samples behind the mL of gas produced by day. The PPM data in the table was turned into a percent ratio for this graph, which gives a more accurate picture of gas production. The tables display the PPM of CO2, H2S, CH4, and mL of gas produced over the 10-day test. The tables also show the total mL of gas produced and the total sample composition of each type of gas produced during testing.

Acidity/Alkalinity data were collected before and after the experiment on the manure in the ARs. Due to the AR being an isolated system, acidity from the hydrolysis, acidogenic, and acetogenesis bacterial community built up slowly. The starting pH of the sludge was 7.3, right in the middle of the methanogens' optimal range, which is 6.5-8. By the end of the experiment, the pH had dropped to 5.8 for the 30PPI tests, 5.69 for the 40PPI tests, 5.7 for the 60PPI tests, and finally 5.72 for the Control test. This is below the optimal range for methanogens, and therefore, CH4 production in the final days should be inhibited by acidity. It should also be noted that the 30PPI AR was less acidic at the experiment's end than every other test, showing that 30PPI might have less of a hydrolysis, acidogenic, and acetogenesis bacterial community.

The line graphs and tables in "SO WHAT" compare the AR's datapoints, making it easy to compare gas production and composition statistics. The composition data of each type of gas is represented as a percentage of the total PPM of the three gases.

The line graphs compare the percent ratio of gas composition and gas production of each AR category.

Overall Trends

The results show clear trends in gas composition and production across all experimental conditions.

-     The 30PPI mesh produced the highest amount of methane overall in raw PPM.

-     All meshes increased raw methane PPM compared to the Control AR.

-     Methane increased over time in all ARs.

-     All mesh’s appeared to inhibit CO2 production and, in this drop, produced more CH4.

Key Insights

Based on overall trends, key insights into the experiment's results were found.

-     Increasing porosity led to a decrease in gas production; however, all porosities performed better than the Control AR.

-     The Control AR had a larger hydrolysis, acidogenic, and acetogenesis bacterial community.

Conclusions

In conclusion, the 30PPI mesh produced the most CH4 in my experiment and, in total, produced around 39% more methane than my Control AR. My 40PPI mesh produced only a mild improvement, contrary to my hypothesis that it would yield the most CH4. I also found during my experiment that adding any mesh increased methane production compared to my Control AR, supporting my second hypothesis. CH4 and CO2 were observed to be inversely related; as CH4 production increased, CO2 production decreased, confirming my third hypothesis. Overall, these results show that the reactor geometry significantly affected the efficiency of anaerobic digestion.

This has many important real-world applications; improving methane output while reducing CO2 output through simple geometric structures can increase the profitability and accessibility of biogas systems.

Next Steps

Going forward with this experiment, I would upgrade the apparatus to allow for a larger amount of data collection. This would involve...

Real-time pH testing

More gas-detecting sensors

New water displacement chambers with sampling ports

More true PPM-based gas sensors

A float sensor or an ultrasonic water height sensor in the water displacement chamber

More porosities for testing would also be beneficial. This could be achieved by testing more porosities of aquarium foam, such as 20PPI or 50PPI. 3D printing using Bambu Studios infill patterns could allow for a massive number of interesting testing geometries beyond simple porosity.

Maggie & Wes

My project would not have been possible without Maggie & Wes's help, which allowed me to gather materials whenever I needed to run a test. Their support is greatly appreciated.

Jodi Stradeski

Special thanks to Jody for helping me with my grammar and improving the clarity of my writing when building my project report.

Jane Ho

Thanks to Jane for giving me valuable scientific feedback on my processes and apparatus.

Ms. Orr

Thanks to Ms. Orr. I appreciate her enthusiasm for my project and her continued support.

Family

Thanks to my family for supporting me and putting up with the smell of cow manure. I couldn't do my project without their support and tolerance for my wacky projects. Special thanks to my Dad for letting me set up my apparatus in the garage and to my Mom for letting me epoxy my stuff together in the house.

Webpages:

[1] National Library of Medicine. (2024, Dec). Biofilm application for anaerobic digestion: a systematic review and an industrial scale case. https://pmc.ncbi.nlm.nih.gov/articles/PMC11657524/

[2] EPA. (2026, Feb). Importance of Methane. https://www.epa.gov/gmi/importance-methane

[3] National Library of Medicine. (2022, Feb). Identifying targets for increased biogas production through chemical and organic matter characterization of digestate from full-scale biogas plants: what remains and why. https://pmc.ncbi.nlm.nih.gov/articles/PMC8830174/

[4] ScienceDirect. (2025, Oct). A critical review of anaerobic biofilm reactors for the renewable biogas production from food waste. https://www.sciencedirect.com/science/article/abs/pii/S2213343725029355

[5] National Library of Medicine. (2024, May). The Infected Polypropylene Mesh: When Does Biofilm Form and Which Antiseptic Solution Most Effectively Removes It? https://pmc.ncbi.nlm.nih.gov/articles/PMC12412129/

[6] EPA. (2026, Feb). The Benefits of Anaerobic Digestion. https://www.epa.gov/agstar/benefits-anaerobic-digestion

[7] ScienceDirect. (2025, Nov). Enhancing anaerobic digestion Efficiency: A comprehensive review on innovative intensification technologies. https://www.sciencedirect.com/science/article/pii/S0196890424009208

[8] ScienceDirect. (2019, Apr). Anaerobic digestion: A review on process monitoring. https://www.sciencedirect.com/science/article/abs/pii/S1364032118308359

[9] ScienceDirect. (2021, Dec). Impact of surface area and current generation of microbial electrolysis cell electrodes inserted into anaerobic digesters. https://www.sciencedirect.com/science/article/abs/pii/S138589472102862X

[10] EPA. Anaerobic Digester/Biogas System Operator Guidebook. https://www.epa.gov/sites/default/files/2020-11/documents/agstar-operator-guidebook.pdf

[11] ScienceDirect. (2010, Oct). Electroactive mixed culture biofilms in microbial bioelectrochemical systems: The role of temperature for biofilm formation and performance. https://www.sciencedirect.com/science/article/abs/pii/S0956566310003209

[12] EPA. (2020, Jul). AN OVERVIEW OF RENEWABLE NATURAL GAS FROM BIOGAS. https://www.epa.gov/sites/default/files/2020-07/documents/lmop_rng_document.pdf

[13] TEXAS A&M AGRILIFE EXTENSION. Hydrogen Sulphide in Drinking Water - Causes and Treatment Alternatives. http://soiltesting.tamu.edu/soiltesting/wp-content/uploads/sites/13/2023/05/L-5312.pdf

[14] National Library of Medicine. (2009, Jul). Bacterial Extracellular Polysaccharides Involved in Biofilm Formation. https://pmc.ncbi.nlm.nih.gov/articles/PMC6254922/

[15] ScienceDirect. (2024, Nov). Assimilatory sulphate reduction by acidogenesis: The key to prevent H2S formation during food and green waste composting for sustainable urbanization. https://www.sciencedirect.com/science/article/abs/pii/S138589472407640X

[16] Springer Nature. (2025, Dec). CO2 from biogas: valorization, economic and environmental impacts in circular carbon systems. https://link.springer.com/article/10.1007/s11157-025-09755-1#:~:text=Physical%20techniques%20like%20water%20scrubbing,towards%20more%20sustainable%20energy%20solutions

[17] National Library of Medicine. (2023, Apr). Removal of CO2 from Biogas during Mineral Carbonation with Waste Materials. https://pmc.ncbi.nlm.nih.gov/articles/PMC10177807/

[18] Government of Ontario. Hydrogen Sulphide in Agricultural Biogas Systems.

https://files.ontario.ca/omafra-hydrogen-sulphide-agri-biogas-systems-22-051-en-2022-12-08.pdf