The 3D lab

The rhododendron that can be tracked from space

Posted on November 1, 2021 by lembrechtsjonas

In the alpine tundra of the Changbai Mountains in Northeast China, on the border with North Korea, climate has warmed significantly over the last few decades (at a rate of 0.28 °C/decade, from 1959 to 2017, to be precise). It’s a pity that we can’t go back in time to see how this has affected the mountain and its ecosystem! Or can we…?

A unique time series

In a new paper, led by Shengwei Zong and published just now in Remote Sensing and the Environment, we dug up an extraordinary time series of 54 (!) years of satellite data, starting with declassified KeyHole camera data from a US Defense satellite from 1963, and then all the way up to the most recent, high-resolution satellite imagery. The goal? Analyzing these images for changes in snow and vegetation cover on the mountain. For the latter, we focused specifically on a unique little shrub: Rhododendron aureum, an alpine shrub that conveniently stands out in autumn as it’s the only shrub in the region that keeps its green leaves when winter approaches.

Fig. 1 — Changbai Mountains, on the border with North Korea, providing the back-drop for our study. Noteworthy is the top-right picture (A), where you can see patches of Rhododendron (in dark green) stand out from a brown autumn vegetation on the mountain.

Rhododendron in retreat

In short: we show that climate change has advanced the melting of snow in spring over the last 54 years of satellite data, while it resulted in a general upward retreat in the distribution of R. aureum over the last 30 years (of applicable satellite data). This makes sense, as the species needs a good spring snow cover to survive against cold temperatures! Take away the spring snow, and conditions get much harsher.

Fig. 10 — We used our model – calibrated on the current modelled link between Rhododendron and snow cover (a), to predict its future distribution as climate keeps warming (b). While we already observe a small upward retreat now (not shown here), we expect significant further declines in area (c) and shifts in elevational optimum (d) in the future.

So, our study provides a good example of how climate change is actively affecting species distributions under our very own eyes (or at least those of our satellites), in this case through changes in snow cover. We can expect those changes to be happening all around us. However, as long-term biodiversity monitoring is still rare and far-between, these changes are often hard to proof.

Complexity abound

We here show that the increasingly long-term satellite record can provide a great alternative to long-term surveys on the ground to record such changes over decadal periods. However, and we can’t stress this enough, accurately reading satellite data and getting this information out of them is NOT easy. You’ll see this if you browse through the paper, which has an impressive methods section (cheers and applause for Shengwei Zong for persisting with the analyses), and has gone through a few rounds of deep peer review helping us to clean up loose ends and making the methodology more air-tight.

Fig. 2 — Did I say complexity? This figure gives an overview of the methodological steps taken to extract Rhododendron aureum (RA) distribution data and link it to environmental data through species distribution models.

Just to give one example of the complexities: in the Changbai Mountains, we were pretty lucky to have fairly large patches of one specific species – the Rhododendron of interest – that stand out on satellite images in autumn, while the rest of the vegetation is green. And even then, it is far from straightforward to tell your algorithm which color of green represents your species of interest, and which is noise, as often enough there are other plants intermingled with the Rhododendron.

Fig. 4 — Linking the ‘greenness value’ of the satellite images (here called ‘NDVI’) to distinguish between a large cover of herbs (brown line) or Rhododendron (green line) in autumn

And then I’m not even talking yet about the aligning of images from different satellite sources, which gets especially tricky when one dives back as deep in time as the KeyHole camera data from back in the days when accurately monitoring environmental change was most certainly not the main goal of the imagery.

In short, we hope this rather complex methodological paper holds lessons for ecologists and remote sensing specialists in the future, and can help put us further on track to use satellite data to analyze vegetation change in these times of increasingly rapid global changes.

More details:

Zong et al. (2021) Upward range shift of a dominant alpine shrub related to 50 years of snow cover change. Remote Sensing of Environment

Posted in China | Tagged climate change, Ecology, Global change, Mountains, Nature, Plants, Remote sensing, Satellite, Science | Leave a comment

Happy hunting

Posted on October 14, 2021 by lembrechtsjonas

Finding ‘daddy’s little mushrooms’ has become one of the favourite activities of our oldest

I spent a happy, sunny, warm autumn Saturday on the farm with my oldest. The goal? Finding back the microclimate sensors we installed there together in early spring, and taking soil samples for soil microbial analysis. And learning about farm life, of course!

Taking a soil sample at the sensor location. Samples will be sent to ‘BiomeMakers’ in Spain, a company analyzing agricultural soils for their microbial diversity with which we partnered up

The fieldwork is part of our ‘CurieuzeNeuzen’ citizen science project, for which we also installed 500 sensors in potato fields and other farmlands all across Flanders. Goal is to see the spatial variability in microclimatic conditions across farmlands, and link these to the growth of the potato plants and the health of the soil.

This doesn’t look much like a potato field, but they are there – belowground! The diversity of plants (weeds, so you want) is the result of the organic farm methods used here.

We are participating with our community farm, where we weekly get our own vegetables. Across the farm, we installed ten sensors. The farm is small-scale and organic, so it will be especially interesting to compare with large-scale more industrial potato production we cover elsewhere.

The soil on the farm was beaming with life, perhaps thanks to the organic farming? We’ll take a look at the microbial communities and see if an organic footprint can be found back. In any case: plenty of little crawlers and creepers to show to the kid!

With that, another great day spend in nature, combining curiosity with science!

Searching sensors in a dense field of yacón

Microclimate in action: this tire is really warm, daddy!

Posted in Belgium | Tagged Agriculture, Climate, Farming, Microclimate, Nature photography, Science, Soil, Toddler | Leave a comment

Much-missed interactions

Posted on October 11, 2021 by lembrechtsjonas

Oh, finally! Finally, after such a long time: a research visit!

The waterfront of Amiens, host town of this weeks’ research visit

I’m spending two very short days in Amiens, visiting the lab of friend and SoilTemp co-founder Jonathan Lenoir, and meeting up with two other partners in SoilTemp-crime while there. The main goal: real-life science discussions! No Teams, no Zoom, no Skype, just sitting in a room – at a safe distance from each other – and let the minds roam free.

I truly felt this was necessary to spark some fires, focus some thoughts, and solidify some research directions; things that are a lot harder to achieve in virtual meetings or over emails. I really wanted to get some priorities straight, as in my enthusiasm for the sciences it’s often tricky to see what should be done first and – perhaps more importantly – convince the funders of those priorities.

The campus of the Université de Picardie Jules Verne, an inspiring backdrop to think about science

And just the mere fact of being here has already made a massive difference: we established the backbone for my next research proposal, one that should keep me on the rails for again a little bit longer, and one that should – if the Gods of Money are Generous – allow us to turn our plans into reality.

We also had some great meandering discussions on the scientific topics of interest, those kind of creative jumps and bousts of inspiration that are so much easier to realize over a shared cup of tea than when staring at each others’ pixelated face over crappy webcams.

The cathedral of Amiens, a stony giant and a landmark all across the city

While staring up at Amiens cathedral, I realized: I am not that ambitious that I need to build such a stony monster for myself, but I do strongly feel that our world needs a ‘cathedral of science’ to tackle the ongoing climate and biodiversity crisis, and that we need it fast. And I think I have a few more crucial bricks that I could contribute to the pile, and would love to get that chance!

Posted in France | Tagged Amiens, City, Citytrip, Ecology, Microclimate, Science, Travel, urban photography | 1 Comment

The first map of the air-conditioning effect of European forests

Posted on October 4, 2021 by lembrechtsjonas

Press release

Forest canopies cool summer temperatures with up to 10°C. An international team of scientists led by researchers from the KU Leuven in Belgium now mapped the temperature of all European forest patches to quantify the airco function of each and every one of them. You can explore how that looks for Flanders at https://www.sglobelab.com/forestairco/

Mini-weather stations on the forest floor

On a hot summer day, forests can feel a lot cooler than the surrounding area. Yet how much cooler a certain forest patch could be has been a lot harder to quantify for ecologists. Up till now, as an international team of researchers, led by PhD student Stef Haesen and Prof. Koenraad Van Meerbeek from the KU Leuven, Belgium, has now quantified the temperature of each and every European forest at a resolution of 25 meters, a resolution much finer than any of the 1-km resolution datasets that were currently available.

Using a unique dataset of more than 1200 mini-weather stations across all of Europe’s forests, the 52 researchers from more than 10 European countries quantified the difference in temperature between the forest understory and the existing weather station network. “This network of sensors on the forest floor is unique,” explains Stef Haesen, lead author from the study, “as it accurately captures the true temperature under the forest canopy, for forests big and small.”

Forests as thermal insulation

The data show that the maximum summer temperature in forests across Europe are on average 2°C (and up to 10 degrees) lower than outside forests. Similarly, minimum temperatures in winter can be 2°C (up to 12 degrees) higher than outside forests.

“With their foliage and branches in the canopy, trees create a thermal insulating layer above the forest floor”, explains Haesen. “For this reason, summer maximum temperatures are much lower inside forests than outside. Summer heat waves are thus strongly moderated below the tree canopy.” Forest canopies provide as such an effective air conditioning, increasingly important in a warming climate.

“Now this is the first time we have such a map at such a high resolution and over such a large spatial extent,” says Haesen. “This is a real scientific and technical breakthrough that will undoubtedly improve predictions from distribution models for forest species,” he adds. As the researchers worked at a higher resolution than ever before, their analyses also revealed never seen differences between and within forests: no two forests are the same, and differences in canopy cover, topography or tree species composition create significant variation in temperatures.

The new high-resolution forest temperature maps thus provide crucial information for researchers to analyse impacts of climate on and in forests across Europe. Haesen summarizes: “If we want to know why certain forest species grow where they are growing, we cannot use climate data from weather stations outside forests, we need the information from the location where the organisms live. These maps here are a real revolution in terms of information accuracy to know, but also to manage, the temperatures as felt by the tree saplings that constitute the forests of tomorrow.” That information becomes more important every year, as this protective shield is weakened by climate change and the increased frequency of extreme weather events (droughts and storms) that threaten the integrity of the canopy.

Unique high-resolution predictions of forest temperatures of all European forests reveal the significant temperature buffering caused by the forest canopy. Here shown for the ‘Meerdaalwoud’ close to Leuven in the centre of Belgium. On the left, you see the existing temperature data based on weather stations, on the right the new high-resolution temperature data product for all of Europe’s forests.

More information

The paper in Global Change Biology: https://onlinelibrary.wiley.com/doi/full/10.1111/gcb.15892

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

The impact of extreme weather on the cultivation of potatoes

Posted on September 29, 2021 by lembrechtsjonas

Blogpost written by Bart Deronde, and originally published (in a much prettier shape) on the blog of VITO.

In spring 2021, the largest citizen science campaign ever on the impact of heat and drought in Flanders’ gardens & fields ‘CurieuzeNeuzen in de Tuin’ took off, assuming that we would again suffer from heat waves and long dry spells as we got used to in the past years. But, weather isn’t predictable over a whole season and hence it turned out differently …

In this blog we dig into the meteorological observations, the measurements by the CurieuzeNeuzen sensors installed on the potato fields, the impact of the extreme weather on the cultivation of potatoes, and we give an outlook on the analyses planned.

CITIZEN SCIENCE ON DROUGHT! WAIT, WHAT?

In spring 2021, ‘CurieuzeNeuzen in de Tuin’ was kicked off. Led by the University of Antwerp and De Standaard, this massive citizen science project wants to gain insight in the microclimate and measures to which extent our gardens, public green spaces, and agricultural fields are susceptible to heat and drought. Expecting again a dry and hot summer season, 5000 “gazondolken” or “lawn daggers” were installed to measure the temperature and soil moisture between April and October 2021. But … the summer of 2021 will be remembered as the wettest summer ever in Belgium. What does this mean for a citizen science campaign on heat & drought?

Sentinel-1 satellite images of 9 and 15 July 2021 clearly show the effects of the exceptional rainfall.

The meteorological observations tell the story of this summer. We had to cope with intense and heavy rainfall. After a warm and dry onset during the first two weeks of June, the weather pattern drastically changed. Pouring rain was on the menu almost every week, with regularly days of more than 15 mm. In Brussels, the Royal Meteorological Institute recorded 410 mm of rain during the meteorological summer (June-Aug) while the average is only 234 mm. But there were also major regional differences. As we all know, the South-east of Belgium suffered from extreme rainfall, leading to catastrophic floods, while the North of Belgium experienced rather normal weather conditions.

Daily amount of rain in Brussels during the summer of 2021.

500 SOIL AND TEMPERATURE SENSORS IN VARIOUS FIELDS

Within the CurieuzeNeuzen project we’re not only looking to private gardens and public green spaces, we’re also gathering data on fields to learn more about the impact of extreme weather, either dry or wet, on our agriculture. In June 2021, at the start of the growing season, we installed almost 500 sensors in 295 potato fields spread over Flanders. Additionally, we installed 30 sensors in orchards (pear, strawberry, blueberry and vineyard) as a side experiment.

Installation of 500 soil and temperature sensors in several potato fields spread over Flanders.

Why do we focus on potatoes? Not only because it’s the favourite crop of many Belgians. The potato plant is also highly susceptible to extreme weather. Most potato varieties cultivated in western Europe prefer air temperatures between 20-25°C and soil (root) temperatures between 15-20°C, while the soil is preferably moist but not too wet. On average, Flanders is blessed with these moderate weather conditions. However, periods of drought, heat waves, or excessive rainfall, can all impact the quality and quantity of the yield.
Thanks to the highly professional know-how throughout the entire chain, constant innovation and a detailed quality system to ensure excellent potato quality, the Belgian potato industry plays a significant role in the Belgian economy. Belgium is for example the largest exporter of processed frozen potato products in the world. Being able to anticipate and to respond to changing weather conditions in order to guarantee the availability of potatoes is therefore utmost important.

THE EFFECT ON THE CULTIVATION OF POTATOES

This summer the major threat for the potato cultivation was the combination of persistent high humidity and moderate temperatures, resulting in severe disease stress. Late blight, Phytophthora and Alternaria were widely observed. Erosion gullies and difficulties to access the field with heavy machinery were other problems farmers faced. However, regular precipitation and moderate temperatures result also in favourable growing conditions. After a cold start in the spring with initially low yield predictions, a period of rapid growth followed in June and July. As a result, the expected potato yields are still more or less at the level of the multi-year average, as shown by samples taken by FIWAP / Carah in Wallonia and Inagro / PCA in Flanders between 6 and 8 September 2021 for the storage varieties like Fontane and Challenger.

But high quantity doesn’t always mean good quality. On the contrary, the quality will be inferior on many fields this year. The large amount of precipitation, often in combination with the presence of a lot of nitrogen in the soil, caused an explosive growth of the tubers, resulting in growth cracks and hollowness, mainly with Fontane. Some Fontane plots even started to flower again indicating new leaf and tuber growth. This will result in immature tubers. Where the ridges were washed away by runoff we see lots of green tubers. Quality checks during storage will be extremely important to timely detect rotten tubers and avoid losing large quantities.

READY TO ANALYZE THE SENSOR DATA

Unlike the measurements of the sensors in private gardens and public green spaces, which are collected and visualized in a personal dashboard, the measurements in the potato fields are stored in WatchITgrow, our online platform supporting growers to monitor their crops in view of increasing yields in a sustainable way. WatchITgrow allows combining remote sensing data with in-situ data using big data analytics and machine learning to provide growers with more timely and personalized advice.

Looking at the sensor measurements we already see that these low-cost devices were able to capture very precise and accurate measurements. Growers can easily access the soil moisture and soil temperature data, next to already available satellite images, greenness derived from Sentinel data, rainfall and temperature data.

Evolution of the greenness (fAPAR based on Sentinel 1 & 2 > CROPSAR technology) of a potato field in the North of Belgium, indicated in green. Daily amount of rainfall shown in blue bars, and the soil moisture as measured by the CurieuzeNeuzen sensors indicated with a blue line.

Once the harvest is over we will collect all sensors and start a detailed analysis of all measurements. Our remote sensing experts will combine all sensor data and link the soil sensor time series and soil properties measured in the field with:

meteorological observations
the greenness of the vegetation derived from satellite images
soil properties derived through soil sampling

Time series analyses of satellite derived greenness and soil sensor measurements will elucidate factors contributing to crop development and performance during the season. Machine learning methods will be applied to realize multivariate time series forecasting in aid of yield estimation.

115_Agro-CNIDT_FigANALYSES — The temperature and soil moisture data captured by the CurieuzeNeuzen sensors will be combined with satellite data, meteorological observations and soil analyses to assess crop performance and harvest.

This will yield insight in the crop development and crop quality during the extreme weather conditions we experienced. Although the prime objective of CurieuzeNeuzen was to measure the impact of heat and drought on the cultivation of potatoes, also the impact of extreme precipitation is very relevant as projected to occur more often in the future. First results of this analysis will be shared in December 2021. Stay tuned!

Posted in Belgium | Tagged Agriculture, climate change, Microclimate, Potatoes, Science, Weather | Leave a comment

Another year of microclimate citizen science!

Posted on September 22, 2021 by lembrechtsjonas

‘CurieuzeNeuzen in de Tuin’ (CNidT), the large-scale citizen science project on drought, heat and moisture in gardens is playing extensions. After a summer that was exceptionally wet, the project hopes to collect additional data on heat and drought. Find out all in the original story in De Standaard (here a shortened translation).

An ailing summer that never really got off the ground, with extreme flooding in large parts of Flanders in July. It was not the ideal setting for ‘the largest citizen survey on drought and heat ever’ in Flanders. Nevertheless, CuriousNoses in the Garden, a project by De Universiteit Antwerpen, De Standaard and many partners, was an unexpected success. We collected unique information on temperature differences between gardens, with data from cold freezing nights in April to insights into urban heat islands. The wettest summer in 200 years came as an unexpected godsend: the 5,000 sensors in garden soils give us a unique insight into the role of gardens as sponges during extreme rainfall, which will be reported in detail in October.

The one of a kind pluche ‘garden dagger’

Drier and wetter

But to live up to the baseline of research on heat and drought, more information is needed. The researchers at the University of Antwerp are curious about the interaction between drought and heat, want to find out how gardens work as air conditioners during heat waves and how long gardens retain water during drought. That’s why the citizen research with the ‘garden daggers’ is being extended for a year. There is a real chance that we will have a drier and hotter summer next year. In that case, the questions above can be answered, and we can compare data: how do gardens experience a warm day in a wet year versus a warm day in a dry year?

With climate change, scientists predict that we will get more of both: longer periods of drought and heat, interspersed with periods of heavy rainfall. This trend has already manifested itself in recent years. The extension of the citizen survey provides a unique opportunity to cover the whole picture and map the effects of both drought and flooding on a large scale and in fine detail. But even if 2022 has another ailing summer in store, it would provide relevant insights, for example about rain infiltration and groundwater.

1,000 candidates

The extension of the citizen survey provides a unique opportunity to map the effects of drought and flooding on a large scale and in a detailed manner.
To obtain this data, the researchers are looking for at least 1,000 participants who want to continue the climate survey in their garden.