What happens to the mix of gases inside a sealed bottle with a plant growing in it? My current understanding of the gas exchange processes that take place inside the bottle is as follows:

Microbes in the soil consume dead organic material in the soil. They use oxygen from the air and produce CO2 and water from the organic material.

Some microbes in the soil fix nitrogen from the air - I don’t know much about this yet, and don’t know whether nitrogen levels in the air will be a factor that I need to consider over the timescales that I’m interested in (months).

During photosynthesis, plants in the bottle (moss and the carrot seedlings), take CO2 from the air and release oxygen (this also uses up water). The plants also respire - taking in oxygen and releasing CO2 and water. But so long as the plant is growing the net effect is to remove CO2 from the air and produce oxygen.

In the log entry “First Attempt” I noted that nothing germinated in two bottles that I set up at the beginning of November, and all weeds that sprouted subsequently died. I wondered whether this was due to the soil producing more CO2 than the plants could consume. 

I used an MHZ-14A CO2 sensor to measure the CO2 in one of the bottles described in the “First Attempt” log entry. Although this meant removing the cap of the bottle in order to attach the sensor, I thought that not much CO2 would escape when I did this. 

The MHZ-14A seems easy to use. The one that I ordered didn’t come with documentation, but I found some here and here. It has a UART with 5V TTL compatible IO, and has a command for directly returning the CO2 level in parts-per-million (ppm), so it is straightforward to hook it up to a laptop and display the CO2 level on the screen.

I have the sensor mounted in an enclosure with a bottle lid glued onto it so that I can easily screw it onto the top of a bottle to check the CO2 level in the bottle. The photos below shows the sensor and its enclosure, and the sensor attached to a bottle (with a MAX232 circuit attached so that it can be connected to a laptop).

I noticed that the CO2 level in my room was 1300ppm. When I opened the door to let in fresh air it went down to 750ppm in about 15 minutes. When I breathed into a bottle and attached the CO2 sensor it reported 5000ppm, indicating that the concentration was at or above the measurable range. I haven’t calibrated the sensors, but these levels seem reasonable.

The CO2 reading in one of the bottles described in the “First Attempt” log entry was greater than or equal to 5000ppm, so this is perhaps the reason why everything died.

How can CO2 production from the soil be slowed down? One way is to use less soil, another is to put enough plants in the bottle to absorb the CO2 produced, another strategy that might work is to limit the amount of water - perhaps drier soil will release less CO2. Limiting the water might not hamper plant growth because more water will be produced (from organic matter) by soil microbes at the same time that they produce CO2.