The 3D lab

An efficient way to obtain soil texture data

Posted on April 27, 2023 by lembrechtsjonas

When we designed our large-scale citizen science project ‘CurieuzeNeuzen in de Tuin’, we soon realized we had a problem on our hands: if we wanted to get an accurate idea of soil temperature and especially soil moisture from our 5000 measurement locations, we needed to have data on local soil conditions, and at least the soil texture.

That was not entirely impossible, we thought, as we had a laser diffraction device in the lab to assess soil fractions that could be used. We just had to ask all citizens to take a soil sample and send it to us. The problem came to the surface when we calculated our time investments: most laser diffraction analyses – at least those we knew of – could handle four samples per hour. And that was at their best behaviour only, excluding errors, cleaning of lenses, replacing of components etc.

Sampling the soil around our ‘garden dagger’

Now, four samples an hour for 5000 samples gives a total of 1250 hours of soil texture analyses, which is 156 days of relentless work, or 8 months of continuous labwork for a lab technician; if not beaten to death halfway through by the extreme dullness of the task at hand.

A delivery to our university of 1276 boxes with soil samples, frankly hammering home the message that this was quite the amount of samples to deal with

It was obvious that we needed a better solution. That solution was found with our colleagues at the Earth and Life Institute of UCLouvain. They had a different way of measuring soil texture, using visible near-infrared spectroscopy. This technique was much faster – in a blink of an eye a soil sample could be scanned.

Laser diffraction involves boiling soil in acid, which is pretty cool at first, but can be rather time-consuming, especially for soils rich in organic material

Spectroscopy works fast, but the results need to be calibrated. For a subset of the data – say 10% – the traditional laser diffraction method still needs to be used, which can then provide you with a calibration curve to identify the fractions of clay, silt, and sand in your sample.

The spectroscopical analysis is as simple as putting a scanner on top of such a dried soil sample and processing the result

In a new paper together with the team at UCLouvain, we now provide a better calibration formula for this spectroscopical analysis, which takes into account one mathematical issue with texture data: the sum of clay, silt and sand is always 100%, so you need to model them together to avoid impossible soils with more (or less) than 100% of volume.

That issue has now been solved and published in the journal ‘Soil and tillage research’. Thanks to this fabulous method, our citizen participants also had to wait only four months to get information on their garden soil texture on their dashboard, a most remarkable achievement they are probably not even aware of.

One enthusiastic citizen – probably largely oblivious of the massive undertaking it would be to get their soil sample analyzed in time.

Posted in Belgium | Tagged Citizen science, Ecology, Gardens, Labwork, Science, Soil, Urban soils | Leave a comment

Microclimate can save plant species from population migration

Posted on April 24, 2023 by lembrechtsjonas

Global warming would force plant species to move dozens of kilometres north at breakneck speed to still find suitable habitat. “A failure for flora,” was the scientific consensus for a long time. Recent research suggests that such population relocation would not be necessary in many cases. Plants could seek refuge in ‘microrefugia’: oases in the landscape where the climate is relatively cooler than in the surrounding area.

Those who look at the climatology models hold their breath. Global warming is pernicious for greenery in this world. In fact, temperatures would rise so fast that plants would not have the chance to seek cooler places in time.

Although two recent papers in the journal Nature Climate Change outline a less grim prospect. “So-called microrefugia, such as a dense patch of forest where temperatures under the canopy are much lower than in the open areas around it, can provide (temporary) shelter for species fleeing rising temperatures.” explains ecologist Jonas Lembrechts (University of Antwerp). Lembrechts is the author of one of the papers and helped note that so far the consequences have turned out to be less severe than expected. “Thanks to those cooler locations, plants over the last 20 years eventually had to move no more than one km northwards, Maclean and Early calculated, while traditional models indicated another 50 km or so.”

One type of warming is not the other

“The temperature as perceived by plants, close to the ground or under the canopy of a forest, is very different from what we are used to from our weather stations,” Lembrechts explains. For instance, trees form an insulating layer above the forest, and photosynthesis in leaves causes water to evaporate, drawing heat from the environment.

Now it gets really interesting when those microrefugia are not only cooler than their surroundings, but also heat up more slowly. This makes them a buffer against climate change for much longer. “Such slower warming now also appears to be effectively possible,” Lembrechts explains. “For instance, in previous research, we showed that temperatures warm up more slowly in forests than in the surrounding countryside, because the cooling effect of (healthy) forests increases even more when temperatures rise.”

The influence of microclimate. A representation of the rate of microclimate change resulting in species range shifts. Three scenarios are shown: increased urbanization, unchanged land use, and increased forestation. The macroclimate will warm by 2 °C between 2020 and 2040. Each microhabitat may experience a unique rate of warming, ranging from 0 °C to 4 °C per pixel. Increased urbanization accelerates microclimate warming and requires faster species range shifts, while increased forestation slows microclimate warming and may maintain viable species populations. Protecting natural areas and creating new ones, especially in urban settings, is essential. The graph (bottom right) shows microclimate temperature increase variation over the 20-year period in different land-use scenarios (red, yellow, and blue).

Smart nature management as a solution

Such findings show that local nature can play an important role in combating the effects of global warming. At the same time, it is also fragile and human intervention can cause significant damage. Lembrechts: “Cutting down a forest will kill that local air conditioning, resulting in a local rise in temperature. That warming process can be much faster locally than what we expect from global climate change.” As a result, plant species will still have to rush off to cooler places.

But things can be different: smart nature management is able to firmly slow down warming at the local level. “So from nature’s perspective, it is not just about to what extent we can limit climate change by reducing our CO2 emissions, for example,” Lembrechts stresses. “Certainly as important is what we do with our limited green space. If we let it become more and more urbanised, the temperature in the microrefugia will rise much faster than if we bet on more forests, marshes, and other greenery.”

Posted in Science | Tagged Botanical garden, climate change, Ecology, Gardens, Microclimate, Nature, Plants, Science | Leave a comment

Botanical scouting

Posted on April 12, 2023 by lembrechtsjonas

I spent a beautiful spring day last week in one of Brussels’ most fairy-tale-like places: the botanical garden Jean Massart.

Springtime visits to the botanical garden, that’s abundant flowers wherever you look! Here: Fritillaria meleagris, a rare species planted – and thriving – in the botanical garden

This little piece of biodiversity sits in a picturesque valley bordering the E411 highway and that famous chunk of Brussels forest called the Sonian Forest.

Of course, I wasn’t there just for the picture-perfect flowers: I was there to do some scouting for a potential new – and pretty exciting – project. If we get it all figured out, we’d be using this beautiful garden as our laboratory for an important research question: can botanical gardens play a role as microclimate refugia in urban areas?

The botanical garden hosts some replicas of highly biodiverse grasslands, so typical – and endangered – for Flanders. One of the show-offs on this April afternoon was this Primula veris

Requirements for this are two-fold: a vast range of microclimatic conditions, resulting from a highly heterogeneous landscape, and a high biodiversity.

A patch of relatively dense forest at the bottom of a valley, the dream-location for stable and relatively cool microclimatic conditions, even close to the city of Brussels

If all goes well, we’ll find both these requirements fulfilled at the botanical garden Jean Massart, but the extent of both remains to be quantified. That’s all I’ll say about it now, so stay tuned for hopefully the start of something new and promising!

Anemone nemorosa was thriving in the forest understory

If you say Flemish forest in spring, you say Hyacinthoides non-scripta

Posted in Belgium | Tagged Botanical garden, Botany, Ecology, Flowers, Forest, Hiking, Microclimate, Nature, Outdoors, Plants, Spring, Walking | 1 Comment

ForestClim – bioclimatic variables for forest understory

Posted on April 7, 2023 by lembrechtsjonas

Those bioclimatic variables that we ecologists all love so much, but at a higher resolution and from right there where your study organisms are living? Wouldn’t that be a dream come true?

Time to pinch yourself, as we now released ‘ForestClim’, a dataset of all the familiar temperature-related bioclimatic variables, at a 25 x 25 m resolution. These bioclimatic variables are representative of conditions at 15 cm above the ground under all of Europe’s’ forest canopies, making them the perfect tool for anyone studying forest understory plants.

*Overview of the different bioclimatic variables in the ForestClim database.*

Now, for the attentive follower, these maps might look familiar. And, indeed, you might have seen at least one of them before: the underlying maps are building further on an earlier publication – by the same amazing PhD candidate Stef Haesen – where we showed a proof-of-concept for these forest microclimate models, based on data from the beloved – at least by me – SoilTemp microclimate database. In that first paper, the model was used to calculate mean annual temperature, but quite some more computer power needed to be consumed before we could create the other bioclimatic layers as well.

Now they arrived, and they are free for all to use, as it should be. So, off you go, go model some forest plant distributions using this neat new toy!

What temperatures are the bluebells of the famous Flemish ‘Hallerbos’ truly experience? Ask our high-resolution ForestClim-maps!

Posted in Science | Tagged Climate, Forests, Microclimate, Nature, Outdoors | Leave a comment

The efficiency of microbes

Posted on April 5, 2023 by lembrechtsjonas

In order to truly understand climate change, we have to understand the carbon cycle – which describes where that notorious element called ‘C’ is moving to. In order to understand that carbon cycle, we need to know who is using that carbon, when and how much. As it turns out, that’s a rather complicated knot to disentangle.

In a recent paper led by Anita Risch, we took a look at the role of some of the more elusive players in that whole business of carbon cycling: soil microbes. Soil microbes play a surprisingly big role in that story, but exactly hów big remains – as so often – hard to grasp. What is known is that soil microbial processes play an important role in the build-up and maintenance of the big chunk of carbon that’s stored in our soils. At the same time, however, soil microbes RELEASE a bunch of carbon into the air via a process called ‘heterotrophic respiration’, best understood as the breathing out we humans also do.

Grassland soils (here at an experimental site in South-Africa) store surprising amounts of carbon (All pictures by the NutNet-network)

From a climate change perspective, one would want microbes to store as much carbon in the soil, and to ‘breath out’ as little as possible. That balance can roughly be considered the ‘efficiency’ of the soil microbial respiration. In a recent paper, we set out to test what defines that efficiency.

For this assessment, we made use of a fantastic global experiment called NutNet, where scientists took natural grasslands and manipulated the amount of nutrients and herbivores. Then, the scientists from 23 grassland sites took a soil sample and sent it to the lab for a five-week laboratory experiment to assess microbial respiration.

So what did we find? Microbes – at least those in grassland soils – did not seem to care too much about nutrient addition and/or exclusion of herbivores. Indeed, both factors did not significantly affect their efficiency. What they did care about, however, was the local soil and microclimate conditions, which strongly affected that illustrious efficiency.

Herbivory in action in Kilpisjärvi (Finland)

So what to do with this information? Most importantly, perhaps, it explains why local studies across the globe have been finding such contradictory results on the matter. If it is indeed all local soil and microclimate conditions that decide how much microbes respire, it makes sense that each regional study will find a different effect of disturbance factors like nutrient addition or herbivory. A wise lesson again for us all: ecology can be darn complicated.

Posted in Science | Tagged Carbon, climate change, Ecology, Grasslands, Nature, Nature photography, Science | Leave a comment

Smart time management for the overwhelmed postdoc

Posted on April 4, 2023 by lembrechtsjonas

Look, I am an ambitious young scientist, but I don’t want to be swamped by work. Witha young family, I know all too well how challenging it can be to juggle work and personal responsibilities. I dream of doing all the science I want without sacrificing precious time with my family.

Enter: smart time management. When my wife introduced me to Motion, a smart time management app that calls itself an “AI executive assistant,” I immediately knew that was EXACTLY what I wanted.

After trying Motion out for a week, I was hooked. Although the app does cost money, I am 100% certain that it pays for itself by increasing my productivity and enabling me to achieve my goals without sacrificing quality family time.

Those two will always come first, and smart time management is key to make that work

Motion is essentially a combination of a smart calendar and a to-do list. You input your tasks, estimate how long they will take, and give each one a deadline. Then, you link the app to your calendar and specify when you don’t want to work, and let the artificial intelligence work its magic. Based on your importance rating and deadlines, Motion provides you with the best possible schedule of when to do each task.

The app shuffles your tasks in such a way that as many of them as possible get done before their deadline. It even warns you when certain tasks won’t fit in your schedule, enabling you to adjust and prioritize your to-do list. With Motion, you can swiftly work through tasks with high urgency without losing sight of your long-term plans.

I LOVE IT!

I love that Motion allows you to see immediately if you’ve taken on too many tasks. You no longer have to worry about biting off more than you can chew, as the app makes it clear which tasks you’ll need to drop to stay on track. Additionally, Motion adjusts instantly to changes in your plan, ensuring that you’re always working on the most important tasks.

My schedule for next week. I’m taking two days off for Easter (we had the family holiday last week already), and leave it to the app to figure out how to arrange my tasks around it

Another great feature of Motion is that it enables you to work on low-priority tasks guilt-free, knowing that the high-priority tasks will also be taken care of. This frees up time for me to work on tasks like writing this blog post, which is definitely not a top priority, but still important to me.

Motion also helps you tackle difficult tasks that you might otherwise avoid by breaking them down into manageable chunks and showing you the reward that comes after completion. This makes it easier to stay motivated and work through challenging projects.

However, there are a few downsides to Motion. If you’re too ambitious with your task list, the app might not be able to schedule certain tasks at all, even with a two-week delay. The AI tends to then simply abandon these asks, regardless of how desperately you needed to do them. It thus remains important to keep track of all your tasks to see nothing crucial gets abandoned.

You also need to be good at estimating how long tasks will take. Although I happen to have a knack for this, others may find it stressful to estimate their workload in advance. And finally, you need to have a certain routine to your weeks to make the most of the app. As a father of two young kids, there is some teeth-grinding involved when I see ambitions dropping off the cliff of hopes into the sea of ‘not gonna happen’. Especially a few days of unexpected sick kids at home can make all the apps’ alarms go off. ‘Good’ thing is: all of that would have been in shambles anyway even without the app, and the app allows you to pick up the pieces much more easily.

Despite my overall positive experience with the app, I have not been able to effectively apply it to non-work related tasks, such as painting the garden shed, due to the unpredictable nature of my schedule with young children. It’s difficult to find a window of time when I can fully dedicate myself to these tasks without interruptions, making it challenging to integrate them into the app’s scheduling system.

In short, I think this app is truly what keeps my ambitious to do-list afloat, without sacrificing my family time, and as a scientist with two part-time postdoctoral positions, this app is what keeps me sane.

I’m not saying you should buy it. I’m just saying I will never ever unbuy it :)!