Visit to Universidad Austral de Chile

I recently visited Universidad Austral de Chile (UACh) located i n Valdivia. This trip is part of a colaboration with Daniel Calderini in a project about responses of wheat to planting density. My contribution is related to light quality in wheat canopies with plants at different spacing.

View of experimental wheat plots
View of experimental wheat plots

I also taught an intensive doctoral course titled “Ecología sensorial de plantas y aclimatación” and gave a seminar “Usando R en fotobiología”.

What is plant intelligence? and what it is not?

The opinions in this post are those of the author (Pedro J. Aphalo).

The scientific discussion about “plant intelligence” was started by Anthony Trewavas nearly 20 years ago, culminating with the publication of his book Plant Behaviour and Intelligence. The use of the word “intelligence” for plants was then controversial and remains nowadays still controversial. On the other hand the phenomena described and the experiments used as support used by Trewavas are not specially controversial.

In recent times the use of the term “plant intelligence” has reached the daily press and science popularization books in addition to videos in the internet. Much of this recent material is not only controversial in the meaning given to the word “intelligence” but also in the quality or strength of the evidence presented. This has led, in my view, to confusion and misinterpretations of what has been actually demonstrated with experiments versus what remians as tentative hypotheses in need of (further) testing. Continue reading “What is plant intelligence? and what it is not?”

Brighter times for our growth chambers

The latest LEDs from Nichia and other suppliers are game changers. I designed a replacement light source for our Aralab Fitoclima 1200 growth chambers and Nikolai Belevich (Biotechnology Institute) assembled a prototype before the start of the pandemic. This post was written time ago, but I am publishing it now that the final design of the light sources is ready for use after extensive testing. Nikolai Belevich also assembled the six light boxes for three growth chambers based on the final design, to which he also contributed.

In this post I briefly describe the prototype and some of the steps that led to the final design. I also discuss how the latest LED components, icnluding some specifically designed for horticulture, have qualitatively changed lighting possibilities in growth chambers and rooms.

Continue reading “Brighter times for our growth chambers”

Perception of solar UV radiation by plants: photoreceptors and mechanisms

Our Update article has been published in July’s issue of Plant Physiology. It summarizes the current state of knowledge including the new understanding and insights brought to light by the research by our group in Helsinki, done with the help of several collaborators.

Title: Perception of solar UV radiation by plants: photoreceptors and mechanisms

Authors: Neha Rai, Luis O. Morales, Pedro J. Aphalo

Neha Rai is now at the University of Geneva in Roman Ulm’s lab.

Luis O. Morales is at Örebro University leading his own research group.

DOI (open access):


About 95% of the ultraviolet (UV) photons reaching the Earth’s surface are UV-A (315–400 nm) photons. Plant responses to UV-A radiation have been less frequently studied than those to UV-B (280–315 nm) radiation. Most previous studies on UV-A radiation have used an unrealistic balance between UV-A, UV-B, and photosynthetically active radiation (PAR). Consequently, results from these studies are difficult to interpret from an ecological perspective, leaving an important gap in our understanding of the perception of solar UV radiation by plants. Previously, it was assumed UV-A/blue photoreceptors, cryptochromes and phototropins mediated photomorphogenic responses to UV-A radiation and “UV-B photoreceptor” UV RESISTANCE LOCUS 8 (UVR8) to UV-B radiation. However, our understanding of how UV-A radiation is perceived by plants has recently improved. Experiments using a realistic balance between UV-B, UV-A, and PAR have demonstrated that UVR8 can play a major role in the perception of both UV-B and short-wavelength UV-A (UV-Asw, 315 to ∼350 nm) radiation. These experiments also showed that UVR8 and cryptochromes jointly regulate gene expression through interactions that alter the relative sensitivity to UV-B, UV-A, and blue wavelengths. Negative feedback loops on the action of these photoreceptors can arise from gene expression, signaling crosstalk, and absorption of UV photons by phenolic metabolites. These interactions explain why exposure to blue light modulates photomorphogenic responses to UV-B and UV-Asw radiation. Future studies will need to distinguish between short and long wavelengths of UV-A radiation and to consider UVR8’s role as a UV-B/UV-Asw photoreceptor in sunlight.

Figure 5 from the paper at Plant Physiology web site

FBES/OEB/SenPEP weather station

Photograph of the station

We have a weather station at our experimental field that I look after. It started collecting data in 2015 and in 2020 it had a large upgrade. There is a full description of the equipment and measurements at

Photograph of the station
The weather station in November 2020

Differently to standard meteorological stations data are logged for most variables at 1 min intervals, as means of 12 measurements taken at 5 s intervals. Hourly and daily summaries are also stored.

Currently the station logs more than 40 variables, a few of them from multiple sensors. Special emphasis is on solar radiation, with measurements of photon irradiance for UV-B, UV-A, blue, red and far-red, and global energy irradiance. Differently to measurements of  erythemal, i.e., biologically effective UV radiation more commonly available, UV-A and UV-B irradiances are measured separately and without applying a spectral weighting function.

With the most recent upgrade we started measurements of the profile of soil temperature, water content and electrical conductivity. Surface temperature is measured on vegetation and/or bare soil with non-contact (infrared) sensors.

The usual air temperature, water vapour pressure, atmospheric pressure, wind speed, wind direction and rainfall are also recorded. The data are available on request. The radiation data for the winter period are less reliable than for the growth season, and there are also some gaps in past winters for all variables.


NEW BOOK: Learn R: As a Language

My book Learn R: As a Language was published some weeks ago by Chapman & Hall / CRC in the “The R Series”.

ISBN 9780367182533

As I a side note, I have typeset the whole book using R and LaTeX using the same approach as for reproducible data analyses. All code examples are run and their textual and graphical outputs generated each time the camera ready PDF is built. This ensures that all code is functional and that all output is up-to-date at the time the PDF is generated. In the spirit of openness and reproducibility, the source files used for generating the book PDF are available through the public Git repository at

R for photobiology packages

I have published through CRAN a suite of R packages for calculation and plotting tasks commonly needed in photobiology. Additional information and on-line documentation are available at The R for Photobiology Website.

This is open source, free to use and modify software that aims to make it easier for all photobiologists to do calculations correctly and play with example data. In addition, the example data facilitates the production of original illustrations for use in teaching and text books.

Continue reading “R for photobiology packages”

Perspectives on plant UV-research and its applications

An article, titled “A perspective on ecologically relevant plant-UV research and its practical application”, to be included in the PPS special issue, has been published on-line. It originated on discussions at the second UV4Plants Network meeting held in Bled last year, but writing and editing continued for several months. The article has been published under open access and is available through PPS’ web site. Several members of our research group and some of our collaborators are co-authors.

The graphical and text abstracts are reproduced below.

Graphical abstract from the article. Copyrighted (c) 2019.


Plants perceive ultraviolet-B (UV-B) radiation through the UV-B photoreceptor UV RESISTANCE LOCUS 8 (UVR8), and initiate regulatory responses via associated signalling networks, gene expression and metabolic pathways. Various regulatory adaptations to UV-B radiation enable plants to harvest information about fluctuations in UV-B irradiance and spectral composition in natural environments, and to defend themselves against UV-B exposure. Given that UVR8 is present across plant organs and tissues, knowledge of the systemic signalling involved in its activation and function throughout the plant is important for understanding the context of specific responses. Fine-scale understanding of both UV-B irradiance and perception within tissues and cells requires improved application of knowledge about UV-attenuation in leaves and canopies, warranting greater consideration when designing experiments. In this context, reciprocal crosstalk among photoreceptor-induced pathways also needs to be considered, as this appears to produce particularly complex patterns of physiological and morphological response. Through crosstalk, plant responses to UV-B radiation go beyond simply UV-protection or amelioration of damage, but may give cross-protection over a suite of environmental stressors. Overall, there is emerging knowledge showing how information captured by UVR8 is used to regulate molecular and physiological processes, although understanding of upscaling to higher levels of organisation, i.e. organisms, canopies and communities remains poor. Achieving this will require further studies using model plant species beyond Arabidopsis, and that represent a broad range of functional types. More attention should also be given to plants in natural environments in all their complexity, as such studies are needed to acquire an improved understanding of the impact of climate change in the context of plant-UV responses. Furthermore, broadening the scope of experiments into the regulation of plant-UV responses will facilitate the application of UV radiation in commercial plant production. By considering the progress made in plant-UV research, this perspective highlights prescient topics in plant-UV photobiology where future research efforts can profitably be focussed. This perspective also emphasises burgeoning interdisciplinary links that will assist in understanding of UV-B effects across organisational scales and gaps in knowledge that need to be filled so as to achieve an integrated vision of plant responses to UV-radiation.


Using R to acquire spectral data

My talk at the Nordic Ozone Group meeting. Although this is a video, I used it as one would use slides, with me speaking live. A true video with sound or subtitles will be produced in the future. The presentation is a demo of the R package ‘ooacquire’, which I have written. It is currently in use at the SenPEP research group, CanSEE research group and the Finnish Meteorological Institute (including at a station in India). The package implements algorithms developed by our collaborator Lasse Ylianttila at the Radiation Authority Finland.