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Long-term Potentiation

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A practical guide to long-term field PAM chlorophyll fluorescence measurements: setup, installation, data processing

Chao Zhang1, Erhard E Pfündel2, Jon Atherton1

  • 1Optics of Photosynthesis Laboratory, Institute for Atmospheric and Earth System Research (INAR)/Forest Sciences, Viikki Plant Science Centre (ViPS), University of Helsinki, Helsinki, 00014, Finland.

Photosynthesis Research
|September 4, 2025
PubMed
Summary

Long-term field measurements of pulse-amplitude modulated (PAM) chlorophyll fluorescence (ChlF) are now feasible. New guidelines and an R-package (LongTermPAM) simplify data analysis, improving photosynthesis research.

Keywords:
Monitoring PAMNon-photochemical quenchingNorway sprucePhotochemical quenchingScots pineSeasonality of photosynthesis

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Area of Science:

  • Plant physiology and photosynthesis research.
  • Ecology and environmental monitoring.
  • Remote sensing and biophysical modeling.

Background:

  • Pulse-amplitude modulated (PAM) chlorophyll fluorescence (ChlF) is crucial for understanding photosynthesis regulation.
  • Long-term field PAM ChlF studies are limited by environmental and data processing challenges.
  • PAM ChlF links in-situ measurements to remotely sensed fluorescence for broader ecological insights.

Purpose of the Study:

  • To provide practical guidelines for establishing and maintaining long-term field PAM ChlF monitoring systems.
  • To introduce the LongTermPAM R-package for efficient filtering and analysis of long-term fluorescence data.
  • To enhance the interpretation of PAM ChlF data by addressing environmental interferences and physiological factors.

Main Methods:

  • Development of specialized field installation supports for PAM ChlF systems.
  • Utilizing the LongTermPAM R-package to process and filter long-term ChlF datasets.
  • Demonstration with MONI-PAM data from Scots pine and Norway spruce in a boreal forest.

Main Results:

  • Successful filtering of spurious data caused by dew, ice, and snow using the LongTermPAM R-package.
  • Accurate calculation of photochemical (PQ) and non-photochemical quenching (NPQ) parameters and their yields.
  • Illustration of how PQ and NPQ influence the ChlF-photochemical yield relationship.

Conclusions:

  • Long-term field PAM ChlF monitoring is achievable with appropriate installation and data handling strategies.
  • The LongTermPAM R-package significantly improves the reliability and interpretability of field ChlF data.
  • Understanding factors like PAR absorption and energy partitioning is vital for accurate ChlF interpretation in diverse environments.