SoilTemp: towards a global map and database of soil temperature and climate

Short: we are looking for soil temperature data from all over the world for inclusion in our global database. Update: find the SoilTemp-website here!

Many questions in ecology revolve around climate: what climatic requirements do organisms have, how do they survive in extreme climatic conditions, and – increasingly relevant – how do they deal with the rapid changes in climate we are experiencing?

Despite climate thus being a crucial component of today’s ecological research, we are still very much limited in the climatic data we have to our disposal to actually answer these questions, especially at the global scale. Most of the data we do have comes from weather stations (or interpolations based on those): coarse-grained data measured at two meter above the ground.

SoilTemp - soil temperature and climate

Climate and temperatures are and have always been a crucial factor in ecological research

For many organisms, however, these free-air climatic averages are far from relevant: many species operate at much smaller spatial or temporal scales, for example. Free-air temperature and climate patterns also differ significantly from what happens at the soil surface, or a few centimeters below it. For many organisms in the soil and close to the surface (soil micro-organisms, ground beetles, herbs, forbs, mosses or tree seedlings, for example) there is thus a large mismatch between the climatic data we have, and the climate they actually experience.

Soil temperature forest understory

For forest understory species, free-air temperature is meaningless, as temperatures at the forest floor will differ several degrees from what happens above the forest canopy

However, while the quality and resolution of free-air and surface temperature data at the global scale is rapidly improving thanks to elaborated networks of weather stations and satellite data, the availability of soil temperature datasets is still largely limited. That is the rationale behind our launch of SoilTemp, a global effort to develop a database of soil temperature data and build global maps of soil climate that answer to the pressing needs of modern ecologists.

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For alpine species, temperatures close to the surface are what matters, especially in winter, when they can hide from the frost under a protective snow cover

Yet for such a global effort, we will need your help! If you feel one or more of the following statements apply to you, please e-mail jonas.lembrechts [at] uantwerpen.be for more information:

1) You have georeferenced soil temperature data (0 till 10 cm below the surface) for a period of at least 1 month with maximum a 4-hour interval, and would like it to be part of this open access global database/map.
2) You have associated species (plants or other taxa) composition or trait data from the same location.
3) You know other possible partners with interesting soil temperature datasets, or working on similar topics, who might be interested in collaborating.
4) You are interested to be involved in this project in any other way.
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Small and cheap temperature loggers (like these iButtons) have recently made such a global-scale endeavour as ‘SoilTemp’ possible

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City life

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Take this proudly walking pigeon in the port of Barcelona as an announcement for next week’s talk about life in the city, which I’ll be giving for the biologist students at the University of Antwerp.

In a session in a series of after-hour events on fauna and flora in our region, I will be introducing them to how climate and land use change together create novel ecosystems, with an unseen combination of climatic, environmental and biotic conditions. A novel ecosystem that requires a lot of flexibility of species trying to survive there.

No better example of that city environment than the built-up mess that is Flanders, where we are studying the effect of the Urban Heat Island on newly introduced species. Tbe students are lucky enough to get a sneak peak on some of our newest results in that regard, on how plant species from a warm origin prefer this city climate and use cities as a gateway to the rest of the country. More on that soon!

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Manzano

Please allow me some nostalgic feelings today. If I show you the pictures I was browsing through, you’ll immediately realize why:

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It is nostalgia for that fabulous day on the steep mountain road heading out of el Manzano up to the slopes of the dry Argentinian Andes, and it was fieldwork with such stunning views that they will forever remain in my memories.

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Scouting for plants on the slopes of the Andes around Mendoza, Argentina

It was our one but last fieldwork day in South America, beginning of February, and we were determined to get the most out of it. In the morning, it was up, up, up to the top of the road, thanks to the skilled mountain road driving of Agustina, one of our amazing hosts in Mendoza.

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Travellers on horseback on their way down from the Chilean border

The road took us to the rocky world at close to 4000 meters above sea level. Only a bit higher, the road eventually stopped dead, limiting travel over the pass to the Chilean border to  sure-fooded horses only.

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Amazing succulent Viola (was it ‘atropurpurea’?) in the high Andes. Not the best season to see them, but you can still see remnants of the cute circle of Viola flowers surrounding the rosette

This rocky high-elevation environment not only brought stunning views, yet also some of the most intriguing plant species I have ever seen. Oh, alpine vegetation is stunning everywhere, but the high Andes in Mendoza has some wonders that you would have to see for yourself to share my excitement.

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Fluffy grass waving its little horsetail-like flowers in the wind

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The spiky branches of Mulinum spinosum

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Large cushion plants of Adesmia subterranea scattered the rocky slopes

One could never get enough of this stunning environment, I promise you. We worked our way down along the road back to the valley, studying the impact of the road on the alpine vegetation all along the way.

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Road building uprooted a centuries-old cushion plant

Another of the roads from our global MIREN-network that I could now add to the list of study areas I visited. Another unique environment so different from the other mountain roads I have seen all over the world. Yet interestingly, many of the road effects are comparable in all of them, a fact that hits home a lot harder when you see all these unique places in real life.

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When evening came, after a long day of sampling, the light deepened and the shadows of the mountains lenghtened. Another beautiful summer evening arrived, and wildlife slowly emerged.

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A curious fox circled around our fieldsite for a while

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The wonderful ‘torrent duck’, playfully rafting in the strong currents of mountain streams

Better times to remember on this ‘Throwback Thursday’ might be hard to find. And all of that thanks to the fantastic scientists from the MIREN Mendoza-team, without whom nothing like this would have been possible!

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Our fieldwork team in the evening sun, after an unforgettable fieldwork day

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The footlands of the Andes, flat as a biljart table, just after sunset

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Linguistic wonders

So, I had a little question: did my English vocabulary improve after 5 years of paper writing? Good question, I thought, and nothing our good friend R could not help me answer! So I dove into the data, read in all 10 of my first-author publications (8 published, 2 in the review stage) into R (after cleaning away references and figures), and asked R boldly: is there more unique words in my more recent work? I went for the easy answer at first: I took a sample of 2000 words (to unify the length of each paper) from every paper and calculated how many unique words could be found in each one of them. The results were… disappointing (Fig. 1):

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Figure 1: The number of unique words in a standardized sample of 2000 words (app. 3/4 of most papers) for each of my first-author publications, chronologically ordered (paper 1 published in 2014, paper 9 and 10 currently in the review stage).

A linear model on that data was far from significant: no trend at all could observed here. Perhaps I was not getting more eloquent after all?

But then my wife pointed out that, yes, sampling 2000 words is an attempt to standardize between papers, but the length of each paper will still strongly affect the amount of words used, with longer papers allowing for a more variable word use.

Could that be true?

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Figure 2: The number of unique words in the same standardized sample of 2000 words, yet now as a function of the total length of the paper

Oh, yes, it was true! Longer papers indeed – perhaps obviously so – allowed for a higher diversity in words, even within that sample of 2000 words!

So what to do next? I still wanted to know if, if corrected for that bias, my vocabulary was increasing. After a brief over-dinner consult with my linguistically trained sister-in-law, I came up with the following:

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Figure 3: cumulative unique word count throughout each paper (gray/reddish is old, greener is new, black is the most recent paper)

This graph wonderfully solves the issue, in my opinion. By plotting the cumulative unique word count in the order of the paper, I neatly take into account changes in structure in the writing, as per linguistic advice, while correcting for the length of the paper. Steeper curves would suggest a more elaborate use of the English language, even when they stopped earlier due to shorter paper length.

And indeed: my more recent papers (in green in Fig. 3) all but one (paper 6) show a steeper curve compared to the older papers. Especially paper 10 (the black line) is an interesting case, as it was a clear low outlier in Fig. 1. This time, it revealed a steep curve, together with the other recent papers, showing a great variety in word use despite its shorter length.

The trend is perhaps not too shocking, but of course none of these papers are ever written by me alone. There is a whole team of professionals behind each of them, giving me advice along the way, and likely suggesting new vocabulary to use, especially early on in my career.

So my vocabulary improved (a bit) over time. But how did the use of specific words change? Can we visualise changes in my topics of interests from the early stages of my PhD to my time as a postdoc now? As I now I had all this papers elegantly read in into R, this could easily be done. Check out the following:

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Figure 4: Frequency of words in my 3 most recent papers (from my postdoc, so to speak), compared to word frequency in my 3 first papers (2014-2016). Colors indicate overall frequency of the word in question, the dashed line indicates a constant use in both datasets. Not all words are visualised.

And oh, is that interesting! There seems to be a constant interest in ‘change’, ‘anthropogenic’ and ‘conditions’ (as these are close to the dashed line). But my overal interest clearly shifted from a focus on ‘survival’ (of plants), ‘gaps’ (caused by disturbance), ‘native’ (and ‘non-native’ species) and ‘alpine’ and ‘elevational’-related questions to ‘soil’, ‘air’ and ‘microclimate’, and ‘temporal’ and ‘spatial’ patterns in ‘distributions’ at the ‘local’ ‘scale’.

Take this last one as a ‘spoiler’: from this recent papers, only one is currently published, so you can expect some more cool things about microclimate in the near future, as we are finally opening the black box that is the soil. Please stay tuned if you like those words above the dashed lines, cause you will see a lot more of them! If you are more of a fan of what happens below the dashed lines: don’t worry, there will be more of those as well, yet perhaps less often with me as a first author. That’s why we have students on board now!

Want to answer similar questions? The ‘Text mining in R‘-book from Julia Silge and David Robinson is a great source of code!

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Dark diversity

Spring finally arrived here in Belgium, and with that spring the  fieldwork vibe inevitably starts blossoming as well.

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The ‘Kalmthoutse Heide’, north of Antwerp, on a grey day just before the start of spring

To get that fieldwork vibe up to speed, we headed north of Antwerp, to the ‘Kalmthoutse Heide’, a large swath of semi-natural heathland on the border with the Netherlands, and – in my opinion – the jewel on nature’s crown around Antwerp. There, we had a meeting with a forester of the Agency of Nature and Forest (ANB) to scout for plots for a new and exciting experiment for this summer, with a fascinating name: Dark Diversity.

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A sandy road through typical heathland vegetation

No, we will not be monitoring orcs, trolls and other dark spawn, dark diversity simply refers to those species that are NOT present in a certain place, although they theoretically could be there. The absent biodiversity, so to speak. To get a formal idea of which species are not present in a certain area, we joined the global DarkDivNet Network, who will be monitoring this absent diversity all over the world.

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Some colour on that grey day: a garden variety of Erica tetralix, with Narcissus in the background

The idea is to monitor the vegetation in a typical natural or semi-natural ecosystem in your region, and compare that with the total plant species diversity in the whole are. That should show that only a subset of all species in a region can tolerate the ecological conditions of a given site. Of those, not all are realized in local communities. The absent part of the species pool forms the dark diversity of a community.

It is for this reason that we drove north to the heathland area in Kalmthout, a fascinating ecosystem with high conservation interest. Including this vegetation type as flagship of our Flemish nature into the global network sounded like a great decision.

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Dramatic landscape where recently a forest has been cut, aiming for heathland recovery

To study those processes that influence the dark diversity, we will compare the typical  heathland vegetation with a side that has seen recent anthropogenic disturbance. We went for a drastical disturbance: the complete removal of a pine forest – complete with invasive shrubs and all – for heathland restoration.

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This site is still far from the target heathland vegetation, yet will over time hopefully slowly converge. This should reveal some cool dynamics in the dark diversity as well.

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For now, we stuck to a short scouting mission. We will return in summer for the real deal: vegetation surveys and soil sampling, hopefully under a sunny summer sky! Stay tuned!

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Kalø

Yes, that title looks very Danish! I just returned from a short trip to the beautiful-yet-rainy east coast of Danmark, at the Aarhus University in Rønde. Besides for some outstanding Danish cuisine (did you try their amazing rye bread lunches?), we mostly met up their to talk microclimate.

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The ‘Gl. Løgten Strandkro’, strongly recommended if you can get excited about the idea of a good, windy Danish seaside

Topic of our little meeting was how one could measure the local climate for insects and other arthropods in the tundra. For our global SoilTemp-project, this is a very interesting question, as these little creatures are one of the key organism groups for which we believed our initiative very important: a ground beetle crawling through an Arctic moss bed will not have the faintest idea about the climate conditions at 2 meter in the air as measured in a weather station, making it very urgent to go measure there where it matters.

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The fairytale-like forest tracks around the Aarhus University in Rønde

Our meeting was short yet very productive: we got much closer to what kind of data we need, what challenges lie ahead if one wants to measure exactly ‘what the beetle feels’, and to how the available microclimatic measurement devices can get us the closest to that answer.

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Very Danish view from my hotel window

If all goes well, our knowledge of the environment as experienced by these little, often neglected, creatures in a changing Arctic and Antarctic will soon start increasing, as data will flow in over the coming field seasons.

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Sunset at the National Park Mols Bjerge

And that feels good: witnessing the start of such an ambitious, yet much needed plan to improve our understanding of a crucial component of cold-climate biodiversity. In a few years from now, when we will have our answers, we will look back on this Danish meeting with fond memories, as here it was where it all started.

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The all-seeing eyes of the guanaco

This is the 6th post in a series of stories from our fieldtrip to South America. Check out the arrival in Concepcion, the first, second and third fieldwork day and this post on pine invasions <–

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MIREN study plot at high elevations in the dry Andes around Mendoza

We are now making a major jump compared to the previous posts on this fieldtrip to South America: from the lush and very European looking vegetation at the feet of the Andes in central Chile to the very(!) dry lands around Mendoza, Argentina.

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Rolling hills with patchy grass vegetation, a typical view in the area

Our first fieldwork day over there immediately felt like the jackpot: rolling hills, amazing views, and working under the all-seeing eyes of guanaco’s, the uncrowned kings and queens of the Andes.

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A guanaco overlooking its mountain realm from the top of a cliff

The latter are fascinating creatures. They have a strong preference for viewpoints, and thus keep popping up on the most stunning mountain ridges, cliffs and rocks. They always keep a watchful eye out for us, but did not care too much about human passage. And their ears are just plain adorable.

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A guanaco on the road in the mist, a funnily spooky sight

As you can see from the pictures above, our first fieldwork day in the Andes slowly and surely turned more cloudy. Our first plots in the morning, at the top of our study road for the day, were conveniently situated high above the clouds. However, as the day proceeded, we drove deeper and deeper into a foggy soup of greyness.

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Old ‘candles’ of Verbascum thapsus kept popping up through the fog

This weather was rather unusual, so our local guides warned us. And rightfully so, as we had been preparing for baking summer suns in the desert climate around Mendoza, where scorching temperatures were the rule. Not so on our first fieldwork day; we even got some rain, and temperatures low enough to consider putting on a jacket. For those of us used to summers in the Norwegian subarctic, it again felt surprisingly much like home (albeit with guanacos appearing in the mist instead of the traditional reindeer).

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A nandu on a mountain ridge, high above the clouds

From a scientific viewpoint, that first day in Mendoza also turned into a success. Our protocol – thought up at home with mostly Scandinavian heathland as a reference – managed to withstand the totally different vegetation structure in the region. But, oh boy, how many plant species do they have there!

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Part of the MIREN Mendoza team sampling leaf traits

It might not appear as such in the pictures, but these alpine grasslands hosted a diversity that was far too much for me to learn in one week. The shrublands in the valleys were an even bigger challenge, with time and time again several different species of shrubs in every plot. Luckily, we could again count on an enthusiastic team of local experts, without whom this would have been an impossible challenge.

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And with that, the remaining fieldwork time was getting shorter, but the dataset – and our sample bag – was steadily growing. Fieldwork is most certainly rewarding!

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KittenR

I finally got an opportunity to put my R skills to ‘good use for society’: I visualised the numbers of kittens that were brought to our local animal shelter throughout the season, and modelled how much milk, kitten food, and foster homes are needed to take care of them .

Aantal kittens per dag

And, oh dear, these numbers! Season only slowly starts in April-May, but then numbers rapidly take off to over 80 kittens present in the shelter at the peak of the season in July. If you know that all these kittens need to be raised by foster parents until they are old enough to be adopted, you can imagine there is a big team of volunteers needed (ideally around 25 foster families, especially in the summer months).

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The animal shelter takes care of over 200 foster kittens each year (picture credit Kami St.)

To make the life of this team of kitten lovers and the animal shelter a bit easier, I visualised how much kitten food they would need throughout the season on a daily basis. Herefore I linked up the age of each kitten on each day with the average amount of milk, wet or dry food a kitten should eat at that age.

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Eten per dag

The conclusion? A stock of 231 liter of kittenmilk, over 1000 kg of dry food and around 400 kg of wet food should last them through the season, based on last years numbers.

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The youngest kittens still get their milk from a bottle every few hours, day and night

Interestingly, these graphs visualise some distinct patterns within the season. Our first graph already showed three peaks: a first big one with the bulk of the kittens in July, but a clear second wave around October, and a last little bump in December.

These peaks are even clearer in the graphs of the necessary food supplies. As kittenmilk is only needed for the youngest, and wet food when they are transitioning from milk to dry food, peaks in the different food needs stand out clearly throughout the season. The youngest kittens peak in June, August and October, yet at the height of our kitten season in July, there is virtually no need for kittenmilk. At that point, the cohort of youngest kittens – which will stay longer in their foster families and now transition to wet and then dry food, are now joined by older kittens (perhaps thrown out of their homes when they are approaching the age of vaccination and sterilisation, an unwanted expense for many unvoluntary kitten owners). The result is a group of older kittens, mostly eating dry food, that are largely gone to their forever homes by the time the new wave of kittens arrives around August.

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Last year’s foster kitten (left) taking care of a little fluffball from this year’s bunch

This is the first year that I have such detailed information on kittens at hand. I hope to continue monitoring this in the future however, as I am curious to see if there is a climate signal in the data. For example, this second and third bump in the number of kittens (especially visible for the milk-loving youngest ones) could relate to an increase (and delay) in the length of our summers here in Belgium. It would be fascinating to link this up to interannual variation in weather, to see if long and warm summers indeed increase the length of the kitten season at our shelter.

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Freshly fed kittens, with the milk still on their noses

PS: no, this post was not an excuse to finally post some of these cute kitten pictures on this otherwise very scientific website!

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