Making Sense of the Mysterious Green Box

Imagine yourself as a newly-enrolled plant science graduate student, fresh from the first of many meetings with your supervisor. During that meeting you hashed out a rather vague project timeline which will involve generating several mutants of your species-of-interest containing a modified gene which, based on prior evidence, may confer increased resistance to drought stress. Among several other measurements that you’re to perform on your transformed plants (a transformation process which is supposed to take a couple of months, but will end up requiring nearly a year of increasingly frustrating failures prior to success), at some point you will need to measure the “photosynthesis” of your new, hopefully drought-tolerant, plants.

Fast-forward to year two. You’re haggard and lab-bench weary from the year of low transformation success and a curveball power outage which killed all of the plants on your growth chamber shelf… but oddly enough, not the plants on any other shelf. After more cultures, seeds, and prayers, you’re armed with a new set of vigorous young plants and it’s time to measure that mysterious photosynthesis. A few days’ worth of reading The Literature leaves you with the idea that you should probably measure the water use efficiency and perhaps “Vcmax” of your plants (whatever that means). You dust off the mysterious green box (someone called it a “photosynthesis system”) hiding in a dark corner cabinet of the lab and buckle in for a wild ride.

This scene, with a great deal of variation in topic but fairly similar level of frustration, has doubtless played out thousands of times in plant biology labs worldwide. Many researchers, not only grad students but post-docs and technicians as well—let’s call them, collectively, novice gas exchangers—have found themselves in situations where they would like to use a photosynthesis system to understand the physiological effects that some treatment has on their plants. In the worst instances, the novice gas exchanger may have just powered on the photosynthesis system, shoved a leaf (or other plant appendage) inside the instrument’s “chamber”, and saved some data after waiting a few minutes. Later, after hundreds of these measurements, time came to make sense of the collected data. And as it turned out, the data made no sense because the novice gas exchanger had little-to-no idea what they really wanted to measure or how the photosynthesis system produced the numbers it did. Cue another year of frustration.

For the novice gas exchanger: Busch et al. have felt and witnessed this frustration firsthand, and have made a concerted effort to help you avoid your own year of unproductive photosynthetic bumblings. A guide to photosynthetic gas exchange measurements builds upon past works which were in many cases technique-specific (Busch, 2018; Evans & Santiago, 2014; Haworth et al., 2018; Long & Bernacchi, 2003; Parsons et al., 1997, among others); but the Guide manages to provide a more comprehensive compass to guide your own gas exchange journey. You won’t find set protocols here, because every experiment and species are unique and fraught with eccentricities that only the informed experimenter can fully understand. But you will be provided with an overview of and physiological context for key parameters measured by photosynthesis systems, detailed general guidelines for the types of measurements you’ll want to make (and how to make sense of those measurements), a comprehensive set of best practices, and pitfalls to avoid.

As it turns out, measuring “photosynthesis” mainly involves simply measuring some properties of gases flowing around a leaf. But with the right experimental context and measurement strategy, you can use these measurements to understand physiological processes happening deep within your plant material. You don’t need to be an engineer or a physicist to use a photosynthesis system as a tool for plant biology, but you do need to know your plant and just a little something about metrology, as Busch et al. make clear. By helping you understand the distinctions between instrument, plant, and environment, and the meaning of the many, many numbers output by modern commercial photosynthesis systems, the Guide will help you plan and execute a photosynthesis measurement strategy that helps you show the world that your drought-tolerance gene is indeed better than the control.

To learn more about taking photosynthetic gas exchange measurements, read ⁠Busch et al. publication for yourself or ⁠⁠visit our website for information regarding the LI-6800 Portable Photosynthesis System.

References

1. Busch, F.A., Ainsworth, E.A., Amtmann, A., Cavanagh, A.P., Driever, S.M., Ferguson, J.N. et al. (2024) A guide to photosynthetic gas exchange measurements: Fundamental principles, best practice and potential pitfalls. Plant, Cell & Environment, 47, 3344–3364. doi: https://onlinelibrary.wiley.com/doi/10.1111/pce.14815.