Seedling community from Puerto Rico


Light is one of the most important and limiting resources for seedlings growing in tropical rainforest. In this study we want to quantify whether species differences in photosynthesis efficiency affect the distribution and coexistence of species through space and time.


Proton Motive Force via DIRK

Estimates the proton motive force through the ATP synthase, thereby estimating ATP production. The proton motive force is measured by measuring the electrochromic shift (ECS), the shift in the absorbance of chlorophyll at ~520nm in the thylakoid membrane due to a shift in the electric field. The electric field is created by the accumulation of hydrogen ions (H+) in the thylakoid, causing an electric field to be produced between the inside and outside of the thylakoid membrane. This measurement applies the ambient light level in the chamber to the sample, then shuts off the light, causing the intensity of the electric field to drop as the H+ ions drain from the thylakoid. This drop in electric field intensity is detected by the measuring light at 520nm. The method is called DIRK - Dark Induced Relaxation Kinetics. The size of the change in the electric field (and therefore 520 signal) is an indicator of the quantity of H+ ions which had accumulated in the thylakoid. The rate at which the electric field changes indicates the capacity of ATP synthase to release H+ from the thylakoid membrane.

The One Protocol (Phi2, PSI, NPQ) II

The One Protocol to rule them all! Phi2, PSI, NPQt, combined!

Changes from previous The One protocol: - no longer outputs signal from the far red period, which simplifies the signal output for the user - changed distance between measuring pulses from 10,000 to 2,000 which improves measurement resolution - has an initial stabilization period, so Fs has a chance to adjust to the actinic. - the measuring lights are used only when actually needed (before lights 15 and 10 were always pulsed, even when the values were not used in the macro outputs) - removed light 2 (650) on add-on board during the actinic periods so now actinic is just light 20 (650) on the main boards. This was causing the actinic to not match ambient, as the combination of two 650 lights was greater than the ambient value.

Chlorophyll content (SPAD) I

REQUIREMENTS: Firmware v0.38 or lower (used for older devices which do not have a SPAD calibration, generally device ID 87 and lower).Measures transmission at 940nm and 650nm in order to determine the 'greenness' of a leaf, an indicator of chlorophyll content and nitrogen content. The 940 is used to account for leaf thickness.


  1. species (Short Answer)
  2. Height (Multiple Choice)
  3. leaf damage (Multiple Choice)
  4. Cotyledon (Multiple Choice)
  5. age of the leaf (Multiple Choice)
  6. Substrate (Multiple Choice)
  7. Seedling Tag (Short Answer)
  8. Seedling Plot (Short Answer)




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