For years, I have been teaching a practical course on the measurement of plant stress to our master students. In that course, we introduce them to the magical ecological process called ‘fluorescence’ to investigate stress in their studied plant species. Now, finally, the ultimate field guide on how to measure this fluorescence is out, thanks to our ambitious ‘ClimEx’-handbook paper (see this earlier post).

PAM-2000 fluorescence measurement

Chlorophyll fluorescence sensor

Yes, I am really talking about fluorescence, the physical process in which objects emit light, even when the light source is already gone. No, this does not result in leaves glooming like eyes of a cat in the dark, unfortunately. Leaves send out light at a wavelength invisible for the eye: infrared.

Dark adaption clip fluorescence

Clips for fluorescence measurement

In the practical course, students find out that the fluorescence of a leaf is the result of an excess of light in the plant: more that they can use for photosynthesis. It serves hence as an indirect way of measuring how much light energy the plants can use, which is then a measure for their ‘happiness’ level, as I tell the students.

 Plant efficiency analyser fluorescence

With an ingenuous sequence of light pulses to activate and deactivate the photosynthesis apparatus of the leave, we can find out how much a plant is suffering.

 Dark adaption clips and infrared light source

This years of teaching to the students now culminated in a whole chapter on ‘Chlorophyll fluorescence’ in the recent Handbook on Climate Change Experiments. It is a complicated procedure, but there is tens of thousands of scientific papers talking about it. Now, we provide the easy gateway into the complex science behind the fluorescence. From now on, the magic of fluorescence will have no mysteries anymore to both students and scientists using the technique and, hopefully, the results of the next tens of thousands of papers should be much more comparable.

Want to read more? Chapter 5.1 in ‘Halbritter et al. (2019) The handbook for standardised field and laboratory measurements in terrestrial climate-change experiments and observational studies (ClimEx). Methods in Ecology and Evolution.’

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Welcoming Eduardo

Ecology is a global science, and one that can only be done together. Understanding our world’s nature indeed needs collaborations between ecologists from all over the world, each from their own environment and perspective.


The Belgian team (Jonas and Jan on the left), visiting the Chilean team (Eduardo and Aníbal, on the right) in January

That is exactly why we are very happy to have Eduardo visiting our Antwerp lab for 3 months. Eduardo is a PhD-student from Concepcíon, Chile, and closely working with us within the Mountain Invasion Research Network.


The fabulous landscape – with volcano in the background – where Eduardo studies the effect of mountain roads on invasive plant species

After we visited them in Chile, collecting data for our global project on mycorrhizal fungi in mountain roads, Eduardo is now returning the favour with a visit to Antwerp. Less pretty landscapes here, yet we hope to make up for that with fun science!

Plan is to work on papers together on the invasion of alien plant species along mountain roads, a topic close to all of our hearts.

Stay tuned for more!

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The much-needed handbook

Let me tell you a little story. Imagine that you are an ambitious young PhD-student, worried about climate change and dedicated to spend the next 4 years performing an experiment that will answer critical questions on the future of our planet.


Climate change experiments, so crucial to understand the future of our rapidly changing world. Yet how to do them well?

You prepare your project thorougly, sitting together with your supervisors to decide which techniques to use, and browsing the literature for inspiration. You make important decisions that fit your specific case perfectly, setting up a unique and well-designed experiment that will answer your critical research question once and for all.

And then, results come in. And they are inconclusive. As in, climate change will have major implications for your study system, but results just don’t match up with what other people find. Bummer. Not only for you, when you try putting your results in perspective. Also for the whole scientific community, when trying to unify, summarize and synthesize results. But most importantly so for our whole society: how to communicate clearly about the impacts of climate change for the functioning of our planet if studies do not seem to hopelessly disagree with each other?


Measuring photosynthesis using a LI-COR

But then you dig deeper into the literature. Turns out that experiment B had a different tactic of measuring leaf traits, while experiment C worked with an entirely different definition of what exactly ‘plant stress’ entails. Research group D on the other hand has a different measurement tool alltogether, explaining their different results. Finally, the results of experiment E turned out only to be valid for rainforests, and not for the Arctic tundra where you did your precious experiment.


Did you measure leaf litter fall the same way as the other researchers in your field? 

What is lacking, clearly, is uniformity. Individual research projects invest considerable resources in collecting data for a number of environmental and biotic variables and in developing protocols for field measurements. This leads to a diversity of similar but not quite identical protocols, and hence to a diversity of ways to measure and quantify the same underlying effects and responses. While some of this variability may be due to good scientific reasons, protocol selection is often based on traditions and habits.


Climate change experiments need to strive for uniformity, to make results comparable and easier to interpret between studies. 

And this issue, ladies and gentlemen, is exactly what we solved! With 115 experts in the field, we created a handbook for climate change experiments (found here) that brings best practices together. Incomparability should now forever be in the past, where it belongs.



Halbritter et al. (2019) The handbook for standardised field and laboratory measurements in terrestrial climate-change experiments and observational studies (ClimEx). Methods in Ecology and Evolution.

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Death is life

Halloween has passed, with rain and wind and falling autumn leaves. And all over the forest: the very spooky ‘consumers of the death’, the creatures of the dark soils feasting on what has fallen: the saprotrophs and detritivores. What better time is there to put them in the spotlight, than All Hallow’s Eve.


A mushroom sprouting from a rotten log in a Danish forest. In autumn, the death burst of life

When visiting Aarhus in Denmark last week, I had a little walk through a seaside forest, where this spooky destruction was in full swing. The forest floor was covered with piles of dead leaves, logs, and branches, and the variety of organisms feasting on them was astonishing.


Autumn on the Danish seaside

Yet what we get to see on the outside – mostly cute little mushroom heads- isonly the tip of a dark and soily iceberg. The soil microbial community hosts countless organisms underneath the surface, many of them never see the light. There is the mycelia of the fungi, there is wiggly worms of all sorts and kinds, there is beetles, bacteria, springtails and such. When a leaf has fallen, it journey has only just begun…


With modern techniques and global collaborations, scientists are diving deeper into this dark and secret world than ever before. Yet every new discovery reveals how much there is still to learn. For example, a recent long-awaited paper in Science finally describes the global distribution of earthworm diversity (showing that their diversity is highest at higher lattitudes).


When a leaf falls, its journey has only just begun…

Earthworms, you might say, are they much of a secret? They live right under our very own eyes in the soil of our gardens! True, yet there is so little we knew about their global distributions, and which species of them are occurring where. An earthworm is not just an earthworm, mind you!

Yet there they are again: the fruits of increasing global collaboration! Now we do have a map of global earthworm diversity, as we do for nematodes (even tinier worms) and mycorrhizae (fungi living in roots of plants). But those are the easy ones to tackle, what about all this diversity that hardly anybody has ever even heard off?


The road is long, yet the blackbox that our soils are is slowly, day by day, loosing parts of its spooky unfamiliarity. In return, we get an even more spooky sense of wonder: what a mysterious bunch of creatures and ecologies we find belowground, and how intricately are their communities woven together!


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On the barricades for Arctic insects

Climate change is no joke, and the Arctic is feeling it. We know this, and have to act accordingly. What we also know, is that Arctic biodiversity is going to take a big part of the blow. What we know a lot less about, however, is what’s going to happen to this Arctic biodiversity once this blow hits it full in the face.

That is one of the main reasons why we gathered in the cute Danish city of Aarhus this week, with specialists from all over the world working with Arctic insects (and other arthropods). Unified in the NeAT-network (Network for Arthropods of the Tundra), we aim to understand these tiny creatures and their relation with the changing climate.


Aarhus city center on a rainy autumn day, still charming as ever

But there is still so much to learn! In many cases, we barely know where all of these species are, let alone how they are dealing with the tough conditions they are facing. Yet help is on the way, for example in the form of fantastic technology: NeAT-scientists are for example developing a formidable camera that can automatically photograph and identify hundreds of insects in a matter of minutes, where it traditionally costs specialists days to get the same job done.


NeAT, an ambitious network aiming to save some of the worlds’ toughest arthropods

At least as interesting is the use of cameras that continuously monitor flowers or mushrooms for visitors, saving the researchers countless weeks in the field. Artifical intelligence then helps sieving through the pictures and extracting the ecological information from them.

The biggest step forward of all, however, would be the teamwork: scientists from Greenland, Iceland, Scandinavia, Russia, Canada, Alaska, Antarctica and so many other places joining forces to exchange ideas, optimize protocols and share data. Our own SoilTemp database will also benefit tremenduously from this group effort, when all of them start measuring the climate there where it matters for the arthropods: close to the surface and under the snow.


Aarhus is not the Arctic, but a great city to meet and discuss science anyway

Now, back to work, there is a changing Arctic to be saved!

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European tree species in decline

Close to half of Europese tree species are threatened, according to a recent report by the IUCN, the groupin charge of the so-called ‘species red lists’. Causes of this dramatic number? Ongoing forest cutting of course. Yet, most importantly and rather surprisingly: invasive species topped the list of suspected culprits.

Horse chestnut: early autumn for the species all over Europe

Both invasive deseases (for example the horse-chestnut leaf miner, a little moth living in the leaves of the chestnut) and invasive tree species (like the American cherry, ruler of the forest understory) are threatening our native trees. Once again, this highlights the critical impacts of our diversity on the move.

Largest problems are in southern Europe: there, we find the highest amount of threatened tree species, among others due to the much higher tree species diversity in the south, especially in mountain regions. Additionally, however, important knowledge is lacking on many of these southernmost species, making their future particularly hard to predict.

Hallerbos - 11

Young beech seedling (Fagus sylvatica). Invasive tree species can cause fierce competition for the native tree seedlings (yet for now, the beech is safe).

So what to do now? More space for forests, and aiming for diverse, natural forests will be key. Botanical gardens can also help conserving endangered genotypes, while we frantically keep working to improve the knowledge of our most threatened tree species.

I got interviewed about this report by our local newspaper recently (here, yet in Dutch and behind a paywall), a great opportunity to spread these important warnings to the broader public.

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Scaling the elevation gradient of mount Nuolja, Abisko, northern Sweden

I might not have been able to enjoy the breathtaking wildness of Mount Nuolja myself this summer, yet I am getting the next best thing: its soil.

Set-up for pH analyses on mountain soils

We received a precious package in the mail last month, with more than 30 kg of soil. Soil dug out from the mountains of northern Scandinavia, to help us open that black box: what’s happening belowground that defines where our mountain plants are growing?

With this particular 30 kg of soil, we have some important plans, together with our colleagues at the Climate Impact Research Center of the Abisko Research Station: we want to use it to get a better understanding of the rapidly changing tundra and its plant communities.

Weighing in soil samples for nitrogen analysis

The big question: how much is the local plant community defined by the climate – and thus prone to more rapid changes now climate is warming – and how much by the growing conditions in the soil?

The latter part requires a lot of digging, but our team is on it to uncover the truth hiding under the soil surface!

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