coming soon: a low-cost, user-expandable kit to study biological nitrogen fixation!
The Pretty-Good Philosophical Instrument (“Pretty-Good PI” or “PI” for short) uses on-board Python software to make various measurements related to biological nitrogen fixation. “Philosophical Instrument” was an old name for things like microscopes and barometers. PI are square!
A user-supplied host computer (like a Raspberry Pi) runs downloaded open-source Python code to send commands to the PI, display graphs, and save data. To measure hydrogen production by root nodules (a proxy for nitrogen fixation), you will need an inexpensive 12-volt power supply. To measure optical density of bacterial cultures (or light transmittance by leaves, a proxy for nitrogen content), download a file to 3-D print an attachment that connects to fiber-optic components on the PI. You can add components like miniature solenoid valves to increase throughput and support more-complex assays (Oono et al., 2020; Denison & Layzell, 1991).
Is “Pretty Good” Good Enough?
The PI should not be used for medical diagnosis or other applications where limited accuracy could lead to health risks or economic loss.
The PI’s software-centered approach greatly reduces costs and expands potential uses, but this flexibility comes with tradeoffs. The PI may be less accurate or less portable than more-expensive devices optimized for some subset of the measurements the PI can make. For example, adding a $59 CO2 sensor to the PI would let you expand measurement options to include photosynthesis or respiration, but its reported accuracy of +/- 30 ppm might limit it to relative comparisons of genotypes or treatments. However, plants of the same genotype vary so much that absolute accuracy may not be as important as controls and replication.
Some specific limitations are addressed below. If you don’t understand these limitations (or are too busy to read on), the PI is not for you. Soldering is only required if you want to add something to the prototype area. But if downloading software, using a screwdriver, learning a little Python, or rearranging the flexible-tubing connections on the back of the PI (to increase throughput or add gas mixing) sound like overwhelming hassles rather than educational or research opportunities, please don’t order a PI. You might be happier with the instruments and support from Qubit Systems.
The PI’s central function is to measure production of hydrogen gas, a byproduct of nitrogen fixation (Schubert and Evans, 1976). Measuring hydrogen production is faster, easier, and less dangerous than the old actetylene-reduction method to estimate nitrogen-fixation rate. However, some nitrogen fixers recycle hydrogen — most cyanobacteria and about 20% of soybean-nodulating rhizobia strains (Keyser et al., 1984) — so hydrogen release is not always a useful proxy for nitrogen fixation. Even when nodules don’t recycle hydrogen, uptake of hydrogen by bacteria in field soils could be a problem.
Another limitation applies to both the hydrogen and acetylene methods. In saturating (10%) acetylene, 100% of nitrogenase activity goes to reduction of acetylene to ethylene, which can be measured by gas chromatography. Similarly, in a nitrogen-free atmosphere (Ar:O2), 100% of nitrogenase activity goes to hydrogen production. In each case, measured activity should match nitrogen fixation in air — for a few minutes. However, either approach prevents actual N fixation, often triggering host “sanctions” against nonfixing nodules (Kiers et al., 2003). These sanctions can decrease nitrogenase activity, making measurements increasingly unrepresentative of undisturbed plants.
To prevent this “acetylene- or argon-induced decline” (Minchin et al., 1983) you can measure hydrogen production in air (or use subsaturating acetylene). However, using those measurements to estimate the nitrogen-fixation rates of undisturbed plants in air requires assuming or measuring the EAC or Electron Allocation Coefficient (Maloney et al., 1994). For example, if hydrogen production doubles after switching from air to Ar:O2, then half of nitrogenase activity in air went to to nitrogen fixation and half to hydrogen production. Measuring N-per-CO2 nitrogen-fixation efficiency, including EAC, requires additional components and compressed gases (Oono et al., 2020).
Because the sensitivity of the PI’s sensor to hydrogen depends on the background gas (Layzell et al., 1984), the PI hardware and software support electrolytic generation of hydrogen to calibrate the sensor in the humid air returning from plants (in each gas mix, if you add gas-mixing capability).
The sensor also responds to methane, ethanol, or carbon monoxide, so it will not be useful if your samples contain more than one of these gases. On the other hand, it might be possible to (for example) estimate methane production from soils where hydrogen production is negligible. Or, maybe you could use sensor response to PI-controlled hydrogen-production to measure oxygen concentration. The more exploring such options (or wire-wrapping your own components in the small user area) appeals to you, the more likely you are to be happy with a PI.
Pretty Good Philosophical Instruments 