PARbars: Cheap, Easy to Build Ceptometers for Continuous Measurement of Light Interception in Plant Canopies

Successful implementation of the protocol outlined here for building ceptometers (PARbars) depends most sensitively on two steps: 1.5 (gluing photodiodes in place) and 1.6 (soldering photodiodes to the copper wire). Step 1.5 is prone to error by aligning the photodiodes incorrectly with respect to their intrinsic polarity. For the photodiodes that we used, and which we recommend as essential specific items, the polarity is identified by virtue of the two electrical connector tabs on the diode having clearly different sizes. Thus, before applying cyanoacrylate glue and soldering the photodiodes in place, it is strongly advised to double-check that all diodes are placed with the large connector tabs facing in one direction and the small tabs facing in the other direction. Step 1.6 is prone to failure due to poor soldering technique and formation of a cold soldered junction. This can be avoided by applying thin solder flux using a flux pen immediately before soldering and ensuring that both the wire and the photodiode tab are heated with the solder tip (at approximately 350-400 ^oC) before soldering itself is applied to the junction. Problems with electrical connections in a PARbar typically manifest in the form of a calibration slope distinctly different from those of other PARbars. Such problems can be caught early by testing each electrical connection during construction (as described in Step 1.6), and again after all connections have been soldered, but before they have been encased in epoxy (Step 1.9). A third potential source of error arises from the failure to use a low temperature-coefficient precision resistor, whose resistance is insensitive to temperature; using an ordinary resistor will cause the error as the resistance, and hence the voltage output per unit of light absorbed by the diodes, changes with ambient temperature. The final major source of error is not unique to PARbars, but applies to all ceptometry measurements: namely, the inference of effective plant area index or leaf area index from light capture depends on features of canopy structure (notably mean leaf absorptance and leaf angle distribution; a and c in Eqns 1 and 2) that may vary during plant development and between genotypes.

There are two main areas in which the protocol described here could be modified or adapted. First, the PARbars that we present here were designed specifically for use in row crops, such as wheat and barley, but the design could easily be modified for other applications. For example, a shunt resistor with larger resistance could be used to enhance gain (mV output per unit PAR) at lower PAR ranges. For versatility, a low-temperature coefficient precision potentiometer (variable resistor) could be used to modify the PARbar's sensitivity range as needed or to make small adjustments to gain so that each of many PARbars have identical calibration slopes. Second, the photodiodes could also be used individually as quantum sensors, allowing the user to capture spatial as well as temporal variation within individual canopies for a much lower cost than possible using commercially available quantum sensors. This could be particularly valuable given the growing interest in dynamic photosynthesis under fluctuating light conditions¹². Third, although we used a conventional (and expensive) datalogger for the data presented in this study, there is scope for dataloggers to instead be built using off-the-shelf componentry, enabling the creation of a combined ceptometry and datalogger system on a limited budget. The popularity of so-called maker platforms, such as Arduino and Raspberry Pi, offer great promise in this area; we suggest the open-source Arduino-based Cave Pearl project¹³ as a starter for further development. Cave Pearl dataloggers were designed for environmental monitoring of cave ecosystems, so ruggedness and low power demand were key considerations in their design. Similar considerations are relevant for implementation to plant phenotyping work. Cave Pearl datalogger components are inexpensive (less than USD $50 per unit) and small, which could enable them to be directly incorporated into PARbars.

Application of the PARbars described here faces three main limitations. First, the inference of plant area index or leaf area index from measured light capture is hampered by strong time-dependent biases, particularly in row crops⁷. This can be overcome by making repeated or continuous measurements over a day. Second, inexpensive photodiodes do not have a spectral output that is exactly proportional to photon flux (the variable of greatest interest in photosynthesis research). This can cause bias when light quality changes greatly through a canopy, although previous estimates of the resulting error indicate that it is on the order of a few percent⁷. Third, PARbars cannot distinguish between the direct beam and diffuse components of incoming PAR above the canopy. As diffuse radiation penetrates deeper into the canopy than direct sunlight¹⁴, transmittance will be increased and PAI_eff will be underestimated as the diffuse fraction of total irradiance increases. When all radiation is diffuse, PAI_eff is directly proportional to the logarithm of 1/τ  rather than the relationship shown in Equation 1¹⁵. Cruse et al. (2015)¹⁶ noted that currently available commercial instruments that can measure direct and diffuse PAR are expensive and require regular maintenance, so they designed a simple and inexpensive apparatus to address this issue. Their system consists of a quantum sensor that is routinely shaded by a motorized, moving shadowband and allows for continuous measurement of total, direct and diffuse PAR. The sensor used in the Cruse et al.¹⁶ system could be replaced with the same photodiode used in PARbars to further reduce cost and may be easily incorporated into the existing PARbar setup. These measurements could be integrated into the data processing pipeline and would further enhance the reliability of estimates of PAI_eff.

The major advantage of PARbars relative to existing commercial ceptometers is their low cost, which makes it feasible to produce them in large numbers. Recently, there has been a growing interest in novel high-throughput plant phenotyping technologies for the estimation of canopy traits (for review see Yang et al., 2017¹⁷). Whilst these methods are promising in that they produce huge amounts of data they are typically very indirect and require validation against conventional techniques. PARbars could serve as a cost-effective, ground-based validation tool for these new techniques.

The low production cost of PARbars also make them a viable option for continuous measurements in the field. This could be useful for several reasons. For example, continuous measurements can be used to characterize row-orientation biases to develop time-specific correction functions for instantaneous measurements (for more information see Salter et al. 2018⁷). Continuous ceptometry can also capture short fluctuations in canopy light capture over time (sunflecks and shadeflecks) caused by clouds passing overhead, movement of the canopy, etc. Photosynthesis is known to be highly sensitive to small changes in environmental conditions and ‘dynamic’ changes in photosynthesis are now thought to be important in driving crop yield (for review see Murchie et al., 2018¹²). PARbars installed in the field with a suitably short logging interval could be used to capture these short fluctuations and provide better understanding of the dynamic nature of plant canopies.