The Earth is not flat. Are plants and plant canopies flat?

Cosine diffuser as used to measure irradiance. Off-the-shelf D7-H type from Bentham Instruments.

The problem

Irradiance or spectral irradiance on a horizontal plane is normally used to quantify energy or photons available for photosynthesis. Similar measurements of irradiance in narrow bands of the spectrum or spectral irradiance measurements are used to characterize radiation features perceived by plant through photoreceptors. Continue reading “The Earth is not flat. Are plants and plant canopies flat?”

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”.

The R Universe

My R packages are now listed at the R universe, a new web site with a repository of packages accesible in multiple ways.  It is implemented as a database rather than being static like CRAN.

The R Universe seems like a good tool to not only find packages but also to monitor their health. Its search engine based on package description should help find packages much more efficiently than a search with Google.

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?”

How did we work out that UVR8 is a solar-UV-B plus UV-A photoreceptor?

What were our findings?

We reported in two recent research papers and an update review, that functional UVR8 is required for the perception by plants of solar UV-radiation with wavelengths shorter than approximately 340 nm, which includes the whole UV-B band plus the shorter wavelengths in the UV-A band. In sunlight, cryptochromes are required for the perception by plants of blue light and the longer wavelengths within the UV-A band leading to changes in gene expression. In sunlight cryptochrome-mediated signalling is driven mostly by violet and blue light with wavelength longer than 400 nm. In comparison wavelengths between 350 nm and 400 nm of solar radiation seem to play only a minor role in the regulation of gene expression.

This is an important step forward in our understanding of the perception of different wavelengths of sunlight by plants as the former accepted view was that UVR8 is a UV-B photoreceptor that participated only in the perception of UV-B radiation while all wavelengths of UV-A radiation were perceived by cryptochromes and the other UV-A/Blue photoreceptors, phototropins and ZTL.

Continue reading “How did we work out that UVR8 is a solar-UV-B plus UV-A photoreceptor?”

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.


Cryptochromes and stomatal opening

Our recent paper, included in Fang Wang’s thesis:

Fang Wang, T Matthew Robson, Jorge J Casal, Alexey Shapiguzov, Pedro J Aphalo (2020) Contributions of cryptochromes and phototropins to stomatal opening through the day. Functional Plant Biology, 47, 226-238. DOI:

The role of phototropins in stomatal opening in response to blue light in well documented in the literature. Reports of a role for cryptochromes in this response have been few, and to some extent contradictory. Most studies on the daily patterns of stomatal opening date from the time when well described photoreceptor mutants were not yet available, so using these mutants was expected to reveal new features of stomatal responses.

Continue reading “Cryptochromes and stomatal opening”

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