Gearing up our city microclimate plans

Yesterday, we had a new member joining the team! It was a virtual first day at work, but we are very happy nonetheless to have her on board now: Camille will be managing our citizen science project on garden microclimates, and will ensure we roll smoothly through the test phase this summer while building towards the full project for next year.

We are tremenduously happy to have her strengthen our team while we are frantically working backstage on getting everything ready for this ambitious plan.

In the meantime, our first batch of TMS4 ‘garden daggers’ for the season – introduced here– is happily logging microclimate data from crispy frozen April mornings and sunny afternoons. Keep an eye out on this place for some first data on the microclimate variability in my own backyard soon!


Our TMS-logger catching the first sun of the morning with their feet in a crispy frozen lawn

As we are all locked up now anyway, we decided to spread the love for garden sciencing across the world, and launched a call on Twitter for our fellow scientists with idle microclimate loggers to start measuring their own gardens as well.

There was a lucky few for which the loggers were not inaccessible in the office, just enough to give our trial project the global flare that it deserves.



Cat and TMS-logger bathing in the April sun

That said, we really hope to see all in person again soon in the future! Luckily, the 3D Lab has already gained quite some experience with ‘virtual labbing’, so we are not going to let this homeworking get us down!


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Knowledge synthesis communities as the answer?

Another guest post from 3DLab-member Ronja Wedegärtner on how we can do better science in these times of global change, and include the whole of society from the start.

We are producing much science, but not using it effectively enough – this is how I would summarize my last blogpost after the OIKOS 2020 conference, which left me wondering what we can do as ecologists to find answers to global issues. “Knowledge synthesis is the key to changing the world.”, was a statement in the final discussion that has kept my head spinning through the last weeks. (At those moment when the COVID-19-the-world-is-breaking-down-and-I-am-in-quarantine spinning came to a brief rest.)

The wonderful thing is that there are many of us out there think along these lines. I was therefore super-excited when I saw the article “A new ecosystem for evidence synthesis” by Shinichi Nakagawa and colleagues that proposes a new framework for knowledge synthesis.

They are envisioning a community of empiricists (data collectors) and synthesists working together from the start, thereby making sure that data is meaningful to answer big questions, is not pre-filtered by publication bias and synthesized in a timely manner.

The authors suggest a web-based synthesis platform to connect researchers and to communicate the findings of this “living system of synthesis” to the interested public.

It is a wonderful and timely article and I suggest you go and read it here (

And now I am going to venture in into an adventure. I am going to share my thoughts about the solution they propose. Much of my thinking on how we can solve global challenges as a collective has gone into similar directions. I see the building of communities as a central foundation for finding the solution for global challenges as well. And I completely agree with the authors that a web platform that connects people might be an integral part of finding solutions.

But one thing struck me when reading through the article – stakeholder engagement was through consumption of synthesized data only. Maybe the engagement of stakeholders in identifying the most pressing questions for which we need knowledge synthesis is implicit for them. But I think that this is a key foundation of making synthesis that matters. I think that we need to extend the community framework to include the non-scientific community. This is challenging and we need to think as a community about how we can do this and still gather our synthesis about pressing global issues at the speed that is necessary to actually face them and not only do an autopsy of a collapsed system.

What gave me most hope when reading through the article? The fact that initiatives such as the Evidence Synthesis Hackathon exist. After a brief stint in the start-up world before I started my PhD I have come to love hackathons. Hackathons originated in the tech-world and bring together interested people for a purpose – this can be solving a global challenge as much as developing an app. The participants bring their knowledge, experiences and creativity and collaborate over a fixed timeframe (often a weekend) very intensely on this topic and try to find solutions. I think that coming together for a short time, working extremely focused and solution-oriented, is very rewarding, often with great outcomes. The article discussed above is just one point of evidence in that regard.

I am going to keep an eye out for new opportunities to move things quickly on the website of the Evidence Synthesis hackathon: and will see if I can secure a spot in their next hackathon.

And I am closing this post with the question: Should we have a have a (digital, socially-distanced) hackathon about how we can involve non-researchers in such knowledge synthesis communities? Having students, policy makers, and holders of Traditional Knowledge involved from the start and throughout the process? – if you think ‘yes, this is exactly what we need!’, then get in touch and we will try to make this happen!

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Where do soil microbes live?

If we want to model where soil microbes are living, and why, traditional distribution models will not do. In a new paper in FEMS Microbiology Ecology, we suggest that accuracy can be achieved, if we just change our mindset and start thinking from the soil microbes’ perspective. Our three key points in that regard: measure hierarchically, interpolate local variability, and don’t forget biotic interactions!

Ecologists are getting increasingly better at describing and predicting where species live, especially thanks to a now widely famous class of models called ‘habitat suitability and distribution models’ (HSDMs). Indeed, we see global databases of species distributions becoming more and more established, and remote sensing data, for example from better and better satellites, adding to our knowledge of the enviroment. This, combined with a wider and better range of modelling tools, has caused an explosion of studies looking at where species live, and why.

Afbeeldingsresultaat voor lembrechtsjonas soil

Despite this rapid surge in knowledge on species distributions, there is one group of species that has remained particularly underexplored: soil microbes. The reasons for this are perhaps rather obvious: it is just so much more difficult to know what’s happening belowground, let alone model which microbes are living where.

In a new paper in the journal FEMS Microbiology Ecology, we argue however that there is no need anymore to leave soil microbe distributions understudied anymore. We can do this, we just have to approach the question with a local-scale, ‘microbe-specific’ mindset. In our conceptual paper, we provide the necessary details on how that mindset should look.

Afbeeldingsresultaat voor the3dlab soil

If we want to model where soil microbes are living, and why, a different approach is needed. Our three key points in that regard: measure hierarchically, interpolate local variability, and don’t forget biotic interactions!

First of all, and perhaps most importantly: soil microbes operate on a much smaller scale than aboveground organisms. That means that the environmental data we link their distributions to needs to be much more local as well. The coarse global climate data at 1 km resolution that is traditionally used for HSDMs is even less useful than it is for aboveground organisms. And even worse, climate measured in standardized weather stations is completely meaningless for soil microbes, where temperatures are often several degrees different from what is measured in that white box above the lawn. And then we are not even including all these other important abiotic variables yet, like soil moisture or acidity.

Figure 1

Overview of our proposed framework to tackle the distribution modelling of soil microbes, including nested sampling, modelling of local variation in environmental conditions, and the inclusion of biotic interactions. For more details, see the paper!

Importantly, however, there is no way that one can increase the resolution of the environmental data to be exactly at the level of what these microbes ‘see’: we can’t plug loggers in every centimeter of soil over a vast area. We argue however that such a dramatic hunt for a higher resolution is not necessary. Using a hierarchical sampling approach, where high resolution data is collected in a selection of plots, which can then be linked to a broad range of plots across the landscape, one can improve the resolution of environmental data, and model and predict the local variation in environmental conditions, without the need to measure it everywhere.

Figure 2

Details of our hierarchical sampling approach for environmental conditions and the microbial community. For more details, see the paper.

Finally, for soil microbes even more than for any other organism group, their distributions are not only affected by the environment, but at least as much by other species living in their neighbourhood. These interactions are a lot harder to incorporate in HSDMs, but are nevertheless critical to really understand where and why these species can be found. Luckily, the necessary modelling tools are now available to incorporate these interactions when modelling distributions, for example using Joint Distribution Models, which analyze the distribution of several species at once, and take their co-occurrence into account.

We hope that our conceptual paper encourages scientists to tackle the spatial distribution of soil microbes, as this knowledge is from critical importance to predict how these important components of our living world are dealing with the challenges of our times.


Lembrechts JJ, Broeders L, De Gruyter J, Radujković D, Ramirez-Rojas I, Lenoir J, Verbruggen E (2020), A framework to bridge scales in distribution modelling of soil microbiota, FEMS Microbiology Ecology, , fiaa051,

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Sciencing at home

With all the social distancing across the world keeping us all at home, a lot of our fieldwork is being delayed. And that’s a bummer, as we just received a beautiful batch of ‘daggers’ to measure microclimate, and had fantastic plans with them for important science.


Our favourite scientific toy: the TOMST TMS4-logger, a pretty dagger that measures temperature and soil moisture

We are not letting this virus take us down, though. Many of our plans are flexible, as fieldwork is all about adapting to the unexpected anyway. But of course we don’t want these good loggers sit there idle in their boxes, do we? So I kindly asked my wife if she would mind a bunch of mushrooms in her garden, and set to work.


Spreading the loggers through my garden to measure microclimatic variability in a suburban setting. Fences, houses, shrubs and concrete will all affect the local conditions. And we are here to find out how much!

I distributed 10 of these loggers through the garden; front and back, middle and side, next to the fence and in the middle of the lawn. All to see how much variability in microclimate there is within such a garden.


This serves as a little, local trial for our big citizen science project that we are frantically preparing in the background, in which we hope to get 5000 gardens in Flanders equiped with these loggers, to get the biggest and most detailed dataset ever of garden resilience against extreme climatic events. With an unseen joint effort by the whole community, we hope to measure how droughts and heatwaves are felt in gardens, from cities to rural areas, from the smallest city lawn till the largest golf courses.


This little piece of sand at the southern side of our house, right against the wall, should give logger readings several degrees warmer than those in the rest of the garden

We hope things stabilise sufficiently in the coming weeks so we can at least roll out the real trial for the project over summer. Until then, we are full on sciencing at home!

Will hopefully be continued soon!

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The baby goes to Reykjavik

As a parent in academia, travelling – and leaving wife and kid behind – is far from easy. That is why we decided to take an ambitious plunge when I had to go to Reykjavik for the conference of the Nordic Society Oikos: the whole family would come!


Our little family enjoying the views in Iceland

Oh, boy, that was an adventure! Baby’s first international travel, baby’s first airplane flight, baby’s first scientific conference… While conferencing an sich is already a challenge (let’s face it, days packed with social interactions and high-impact science are fun, but take a mental and physical toll), conferencing with a baby is next-level stuff.

Of course these were unforgettable times! Exploring the wild beauty of Icelands’ winter wonder land with wife and baby resulted in fantastic memories of happiness in a breathtaking setting. Those pictures coming out of this week will forever have a prominent place in our albums. Having my loved ones close also meant I did not have to miss them – and they did not have to miss me. Fantastic for me, close to lifesaving for them: we were all in it together.

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Visiting Icelands’ volcanic beauty with a baby in a sling. Unforgettable!

This adventure of course did not come without its challenges. There was a reduced time for social interactions (as in: oh no I will not go to the bar with you after this long day of talks, there is a cute baby waiting for me at home!). Most important challenge, however: conferencing with a baby is TIRING!

It already started on the way to Iceland. Our plane suffered a five hour delay, so we had to spend a whole afternoon at the airport. The flight only left after baby’s bedtime in the end, so that meant me walking up and down the isle to keep her asleep. Baby didn’t notice – best day ever! – but the tiredness was kicking in.


Turning the departure hall into a playground

And then the baby tumbled right off her schedule. New house, new place, different time zone, a totally different routine: sleeping became problematic. Struggling at night to get her to sleep, back to sleeping in my arms or in our bed instead of quietly in her own, you definitely feel that harder after a day of conferencing.

So, how bad was that sleeping? I know it felt pretty tough, but I wouldn’t be the data scientist I am if I wouldn’t dive right into the numbers again. So I expanded on the graph I made for an earlier post to see how sleeping really went.

Figure NS

Proxy of how much sleep we have been getting at night over time, using two different methodologies. In pink: the hours between the two main night feedings. In purple: the length of the main block of sleep. Note that we started tracking actual sleep only later, and currently only track the sleeping, so lines do not fully overlap in time. Lines are the rolling mean with a window of 10 days. Pink vertical zones mark our trip to Reykjavik

So what does the data show? As in my earlier post here, her sleep was gradually improving up till around 15 weeks, when we dropped into the ‘4-month sleep regression’. Using a rigorous sleep schedule, we fought our way out of this slump, up till we got a block of 8 hours of sleep again at around week 20.


Family dinner at the famous ‘Hofnin’ restaurant

But then, with the trip to Iceland approaching, sleep gradually worsened again, with a new low the week before her trip (both baby and mother were ill, while daddy was at a meeting in Sweden). We thus started our Iceland-adventure with a deficit, partly caused already by my earlier academia-related travelling. The trip to Iceland created another slump on top of what was already pretty much going wrong (note the set of nights where we didn’t get blocks longer than 2 (!) hours). These things get you.

I have to say the downfall was less steep than it felt to us at the time, but I think that is exactly the thing of taking your baby on an international trip: things are worse, but you also just have much less energy to deal with it all.

All in all, I would recommend this. Being a dad in academia inevitably means that time needs to be divided more stringently between home and work, so keeping up that spirit at the conference isn’t that much of a difference. But did I loose ‘conferencing-ability’? I bet you I did! And an important side-note is the following: we had some extra much-needed help on this trip, as my wife’s parents travelled to Iceland with us. Without them, I do not think any of this would have been possible.

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Baby loving the winter hikes close to her mommy

PS: I acknowledge these things can be tremenduously harder even for moms in academia. But there is other people who can tell those stories.



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Can collaboration help us tackle the big issues of ecology?

Ronja Wedegärtner, PhD student at NTNU in Norway and in The 3D Lab, takes you on a reflective tour of the key discussion point of last weeks’ meeting in Reykjavik, Iceland: how we as ecologists can take up our task to preserve our biodiversity in a rapidly changing world, and doing so before things get too far out of hand. More on Ronja’s work here!

During the last week I had the chance to attend OIKOS 2020 the fourth conference of the Nordic Society Oikos with the overarching topic “Ecology in the Anthropocene”. Attending the conference made me reflect not only about our research, but about our responsibility as ecologists and private people. How can we contribute solutions?

We are living in tumultuous times for ecology. Land-use change, and the climate crisis are changing and endangering nature as we know and love it. The issues seem so enormous, dark, and threatening that they can appear like a “black hole” as writer Andri Snær Magnason poignantly formulated in the wrap-up of the OIKOS conference in Reykjavik. And while a black hole cannot be seen directly, rather must be inferred from near surroundings we can observe its pull. Our “black hole”, our global threats to the environment are already pulling at our research, spinning and accelerating it.


Seaside view of Reykjavik, pictures by Jonas Lembrechts

At the OIKOS conference over 300 participants joined to hear 4 great keynotes, more than 120 talks and speed-talks in parallel sessions and browsed a multitude of posters. Each of the contributions was shining its light into one corner of our ecological universe, providing some enlightenment on one issue or ecological sub-question. Together, we produce many blips in the darkness of the unknown, clustering around our galaxies of interest. But our blips are spread out far and wide.

The OIKOS conference brought together many great scientists, but also many great people. Kind and caring for ecology, the environment and their surroundings. We listened to many contributions, but one thing was lacking for me until the last day: an open discussion about the issues we face and what we can do.


More than 300 ecologists gathered in the Harpa Concert Hall in beautiful Reykjavik

So, how do we look at the pressing issues of nature degradation and the climate crisis then? And how do we do so in a timely manner? As Vigdis Vandvik remarked in the final discussion: “Knowledge synthesis is the key to changing the world”. Examples such as The IPBES report show us, how much impact we as ecologists can have, if we join forces, coordinate well, and set ourselves tough deadlines. Therefore, I think that we, as ecologists, should take the challenge. We should identify the most pressing and relevant questions together with policy makers and the people who are impacted by the changes. And then we should follow the example of the physicists that produced the first image of a black hole: band together and collaborate.


Vigdis Vandvik showing how nature-related risks like climate change and the global biodiversity crisis (in green) made it to the top of the list of risks to the global economy

We should come together, virtually or in real life, and discuss how we can solve those challenges as a group and at least approximate solutions. Ideally joining forces with social scientists, traditional knowledge holders … maybe even economists. I think at our conferences we need more time to discuss and exchange in larger groups, not only to present and take notes. And we need to follow up on these discussions with work.

Still, if we want to produce results in a timely manner, I am wondering if we can stick to the academic model as we know it to find and make available these results.

It may sound crazy, but this conference and the discussions after it have me thinking about abandoning the traditional publishing process for a while – of course preserving peer review as the pillar of our community.


As a research community, we should make sure that the road to our ultimate goal does not get snowed under by a blind acceptance of ‘how we always did things’

I suggest that we as community, take our big challenges, divide it into smaller proportions, and in the end into bite-size peer reviewable work packages that we assign “merit points” to. Then we as the community who peer-reviews and contributes could still gain visibility and earn scientific merits even though we publish less or no journal articles for a while.

There will not be a perfect solution. But after the OIKOS conference I am more certain than ever: We must talk about the future. Because, as Magnason pointed out: Those who we love will be alive far beyond the horizon that we comfortably think in.


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This week brought three members of The 3D Lab (Jonas, Ronja and Jan) to the 4th meeting of Oikos, the Nordic Society for Ecology, in beautiful Reykjavik. As ecologists rooted in northern Scandinavia with most of our fieldwork and research topics, this bi-annual gathering of nordic ecologists seemed like the perfect place to learn.


The Harpa concert hall in beautiful Reykjavik, the venue of this year’s Oikos meeting

And oh yes, were we right! With the theme of this year’s meeting ‘Ecology in the Anthropocene’, the meeting focused on how we can study and save our biodiversity in Scandinavia and beyond in a time with rapid global changes. And no setting is better suited for that than wild and fragile Iceland.

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With its impressive waterfalls, geysers, mountains and volcanoes, Iceland is the place to be to admire the indestructable power of nature. On the other hand, however, it is part of the vulnerable Arctic, more than any place on earth suffering from rapid climate changes.

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Warm water under the soil surface makes this place the perfect dramatized ‘artists impression’ of a world affected by large-scale climate change

This wild winter wonderland provides the perfect backdrop for a group of 350 ecologists to discuss ways in which we can conserve our precious nature. And The 3D Lab was happy to contribute.

Ronja presented her work on how non-native plant species are moving into the mountains along hiking trails, while Jan showed his results on the role of mycorrhizal fungi and their interaction with plant roots in defining how high these invasive species can move up in the mountains.


I myself will present in tomorrow morning’s session the first results of our global SoilTemp database initiative, arguing that in these times of global change, more than ever ecologists need the correct climate data to answer their questions. Not what’s measured in these standardized weather stations, yet what is actually felt by the biodiversity we are studying.

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The Gullfoss waterfall displaying the magnificence of Icelandic nature


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