To save our world’s biodiversity

Posted on June 19, 2022 by lembrechtsjonas

Today I will be presenting our SoilTemp project at the World Biodiversity Forum in Davos, Switzerland. That place might ring a bell from many a global convention, and the conference name even sounds familiar to the World Economic Forum hosted here. In fact, we are here with a same ambitious goal: bringing together some of the worlds’ experts on biodiversity towards a globally coordinated effort to save as much of it as we can.

View of Davos and – for those who know where to look – its conference center

High ambitions, for sure, but high stakes as well.

An important line of thought throughout the conference, however, is that there is surprisingly much about the sheer numbers of biodiversity that we simply don’t know yet. Especially in remote areas like mountains, and for more ‘obscure’ organisms like soil micro-organisms, we simply do not know yet what is out there, let alone how much of it we are loosing as a result of global change.

Rampion flower in a trailside in the Swiss Alps close to Davos, proudly reminding us what a wonderful biodiversity we can find in this world.

The good news is that this issue is more and more being voiced, and global efforts to monitor, map and predict global biodiversity are increasingly popping up. Many great examples of those were presented here this week.

Tomorrow, I will be showing how I think our work with SoilTemp can help in that regard: we are working hard to provide the necessary climatic baseline data to aid that mapping and predicting. Indeed, without good, accurate and most importantly relevant climate data – and all of that is also still rather patchy across the globe – it is even harder to get an idea of the fate of our worlds’ biodiversity.

Dactylorhiza orchid

For those in Davos, very much welcome to my talk at 16h15!

Campanula flower stubbornly holding on to the rocks of a road tunnel. Anthropogenic pressures are seriously threatening biodiversity, but there is still an awful lot to fight for!

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Trampling to save mountain plant diversity?

Posted on June 13, 2022 by lembrechtsjonas

By Ronja Wedegärtner and Jonas Lembrechts

What do you think about when you follow a hiking path up to the nearest mountain peak? When not thinking about the next chocolate break or the view, I spend my time thinking about ways that the trail that I am walking along might change the vegetation. 

As I walk up I am passing through different vegetation types. First, the last meters of mountain forest before entering a zone of willow shrubs, followed by a mosaic of low dwarf shrub tundra and alpine meadows. Up on the peak, the vegetation is sparse and close to the ground. 

The fact that trail hiking locally affects mountain vegetation is rather obvious. How exactly the vegetation reacts to this persistent trampling, that has up till now however been surprisingly unknown. 

Climate is considered the most important driver of where species grow at broader scales. How could those distribution patterns be changed by trails? Well, seeds can stick to boots and clothes and trampling on and along the trail can create gaps in the vegetation that might allow seeds to grow and establish. Alpine plants are considered especially vulnerable to new neighbor plants that might be moved in by hikers from the vegetation at lower zones. On the other hand, alpine species CAN grow in lower elevation zones – just think about those alpine plants thriving in lowland rock gardens. The climate is suitable for them, but the neighboring lowland plants are most often what hampers their lowland success: When they have to compete with faster growing lowland plants for light and nutrients, alpine species are usually outcompeted. When we remove those neighbors along trails by trampling on them, this could potentially improve alpine species chances in such locations?

With this in mind we surveyed almost 200 transects along 16 hiking trails in two popular hiking areas (Dovrefjell in Norway and Abisko, Sweden) and compared which species we found in trailsides and which in the vegetation away from trails. We identified all plant species and measured how disturbed the plots were.

We surveyed the vegetation along 16 hiking trails in the Scandinavian mountains of Abisko (Sweden) and Dovrefjell (Norway) to pinpoint the effects of hiking trails on the unique vegetation of those systems. The study is now published in the journal Diversity and Distributions.

Interestingly, we found a median of 4 plant species more in trailside plots than in those away from the trails, an average increase in diversity of 24%.

A simple figure but with important implications: trails have a higher plant species richness than the adjacent interior vegetation. A positive effect of disturbance on vegetation, perhaps a bit counter-intuitive to most?

Based on our more than 11000 species observations and a unique high-resolution climate data, we examined in which climate we found species along trails and away from them (their realized climatic niches) and checked if these niches had shifted along the trails.

Lead author Ronja immersed in dense willow shrubs along a mountain trail. Picture: I. Janssens.

We found that alpine species’ distributions shifted towards warmer locations along trails and that more species’ niches overlapped in trailsides – creating greater richness. As such, trails seemed to create interesting opportunities for range expansion for a variety of species. 

Importantly, trampling can create space for alpine plants and may help them persist in a changing climate. But we need to consider trails in context: disturbances may also destroy rare communities or rare and trampling-sensitive species.

So, think where you walk when you are next hiking in the mountains and maybe have a little look around for yourself – do you see more or different species along the trail than away from it?

Picture: I. Janssens

Reference:

Wedegärtner, R. E., Lembrechts, J. J., van der Wal, R., Barros, A., Chauvin, A., Janssens, I., & Graae, B. J. (2022). Hiking trails shift plant species’ realized climatic niches and locally increase species richness. Diversity and Distributions. https://doi.org/10.1111/ddi.13552

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The photobomber

Posted on June 8, 2022 by lembrechtsjonas

Now here is a little – and rather easy perhaps for most of those who follow me – botanical riddle: which tree has photobombed virtually all of my holiday pictures of Kotor, Montenegro?

Let me know in the comments if you know!

The Church of our Lady of Remedy on the mountain side in Kotor, Montenegro, flanked by a very characteristic tree
Vantage point over the city of Kotor
A cat in the hills above the ‘city of cats’, surrounded again by our by now very recognizable tree
Sprouts of the same tree, which followed us all the way to the Acropolis in Athens, Greece
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The energy balance of a leaf

Posted on May 12, 2022 by lembrechtsjonas

I am currently co-teaching the course on ‘environmental biophysics’ to our ecology masters, a largely theoretical course in which students get to know the physical equations behind ecology and the interaction between organisms and their environment. Besides this formula-juggling, the course contains a very nice little practicum which I inherited from my predecessors, which I wanted to share.

The goal is to calculate the full energy balance of a leaf: what kinds of energy are coming in, and which ones are going out again? Then, we go on an ‘excursion’ two meters out of the classroom door, take some real leaves and try to measure the necessary parameters to calculate that energy balance in real life.

Measuring the temperature of three ivy leaves, suspended in the air to simulate ‘normal’ conditions.

This involves a lot of environmental measurements: students measure air temperature, soil temperature, temperatures of the sky, short-wave radiation, wind speed and relative humidity, all these parameters who define the environment of a leaf and thus how it will regulate its energy.

Then of course, pretty important, they also measure the temperature of the surface of the leaf, which in itself relates to all these parameters but also to how well the leaf can regulate its temperatures. That temperature regulation works through two processes: energy loss through transpiration (water loss), and heat loss related to differences in temperature between leaf and environment.

Measuring leaf temperature (white pants), air temperature and wind speed (grey pants) and meticulously writing things down (jeans)

To get a good grip on those different parameters and how easy energy can be exchanged between a leaf and its environment (the so-called conductance of the leaf and its boundary layer), we did a little experiment: next to a control leaf, we had one leaf that we sprayed entirely wet. This situation greatly facilitates the transpiration of water, as now the air-water boundary is not inside the leave (forcing water vapour to go through the small stomata), yet on the outside of the leaf. The result? Significant multi-degree drop of temperature far below air temperature even (we had examples of air temperature at 23°C, and watered leaf temperature at 16°C!).

Additionally, we sprayed one leaf with ‘wilt-pruf’, a resin-based liquid that seals the stomata and thus effectively prevents any water loss. It’s traditionally used in horticulture when you want to prevent a vulnerable plant from loosing water, but here it served another purpose: sealing the stomata removes the transpiration process from the equation entirely. The result now? Take a second to think it through…

Measuring incoming shortwave radiation (device on the right). The ventilators are used to dry the resin-coated leaves.

Indeed, the leaf should start heating up, as it can’t loose energy through water loss anymore! This turned out to be hard to replicate in the field, as it is strongly dependent on weather conditions, wind speed and the question if stomata were open in the first place. Nevertheless, we managed to heat up a leaf 1°C as compared to the control this way!

It took us till we moved to a spot with low wind speed (enforced by wind screens left and right, resulting in a drop in wind from ~2 to 0.4 m/s) before we could successfully get the resin-covered leaf to heat up

So what’s the take home message of all of this? To me, it is that, indeed, you can describe the living world with mathematical equations. Nevertheless, the real world gets rapidly too complex to keep track of the formulas in it, which is why ecology so often works by proxy (and so often has strong noise in the data). An important piece of fundamental knowledge for aspiring ecologists, I would say!

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When does your elderberry bloom?

Posted on April 29, 2022 by lembrechtsjonas

Have you ever noticed that trees seem to green up earlier in cities than in the countryside? If yes, it is not just a feeling. Urban areas have higher temperatures earlier during the spring. Moreover, it is already known that plants have the tendency to leaf out and bloom earlier in cities.

The phenology of plants refers to the timing of events important in the life cycle of plants such as the bud bursting, leaf development, or the opening of flowers. Phenological studies aim to better understand how the timing of such events is influenced by variations in environmental conditions. However, phenological studies in urban environments usually rely on measurements of temperature and soil moisture at regional scales.

Phenological stages of the elderberry flower, from 0% open on the left to fully blooming on the right.

That’s a big limitation, but we realized that we were having a unique opportunity at hand: we could benefit from the incredible level of precision of the data acquired by the thousands of participants in the ‘CurieuzeNeuzen in de Tuin‘ citizen science project in Flanders and let them track phenology in their garden. This way, we can link the precise temperature and soil moisture data provided by the 3000 mini weather stations spread throughout Flanders to the exact timing of flowering of plants close to them.

Will these local patterns in daytime (left) or nighttime (right) temperatures be reflected in the timing of flowering onset? We’re going to find out!

The set-up is simple: participants with a mini weather station ánd an elderberry (Sambucus nigra) or butterfly bush (Buddleja davidii) in their garden are asked to report on the unfolding of the flowers of these shrubs every three days, until they are fully in bloom. This data on flowering time will then be linked to the actual temperatures in their garden.

Flower stages of the butterfly bush

What we hope to find? For example, we want to determine at what degree the temperature differences between the city environment and the countryside become sufficient to trigger earlier blooms.

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What microclimate sensor to use?

Posted on April 25, 2022 by lembrechtsjonas

I often get the question what microclimate sensor I would recommend. To facilitate my answer to that, I decided to summarize my ideas on the matter here. Note that this is a far from exhaustive musing on the different factors to take into account. And most importantly: I would love to hear from YOU what worked and what didn’t, and would gladly update this information here with your insights!

In SoilTemp, we are not using one standard sensor type, we are accepting data from all different kinds of sensors, as long as they measure with 4 hour intervals or less. Most common brands are TOMST, iButton, HOBO and Lascar, yet there is a myriad of other sensors, for example those integrated in weather stations, flux towers, or other long-term monitoring. My personal recommendation is still the TOMST TMS4, a sensor designed by and for ecologists that solves many of the issues one could have.

Some features:

  • Around 10 year memory space. This is the game changer for me! The TMS4 measures when it leaves the factory and never stops. It doesn’t overwrite data and simply keeps it all. You can always read out data from only your last measurement campaign or the whole thing. So no data losses as is ever so common with other sensors! Also, they easily measure every 15 minutes, whereas the cheap iButtons and HOBOs wouldn’t survive a whole year with their memory at ~60 minutes, even.
  • 4 sensors for the price of 1 (or 2-ish 🙂 ): the TMS4 mimics a little plant, measures temperature just above, at and just below the soil surface, and also measures soil moisture. This has proven véry useful, as the three temperature levels show highly different patterns and drivers in virtually all ecosystems (e.g. related to snow cover).
  • Around 10 year battery life, so no issues of sudden breakdown (without option to retrieve data) as with iButtons, and no struggling with replacing batteries as in HOBO
  • Standardization: no messing with home-made shields or installation methods, making measurements much more comparable between different studies.
  • Free software! iButton software is free as well, but I don’t like that I have to pay for HOBO software.
  • Rugged. The TMS4 is fully waterproof (no wrapping in Parafilm as with iButtons or fumbling with dessicant as in Hobo Pendant). The solar shields are the most vulnerable; TOMST provides rings now to secure it to the sensor, but the result is now that instead of disappearing they tend to break under duress). We still have some sensor deaths despite their ruggedness, which mostly relates to them sticking above the soil (e.g. mown down or burned).
  • The sensors unique number is written super clearly on the sensor, so messing up sensors and plots has become much less common. Perhaps more importantly even: the output file has a standardized naming that includes the sensor name, so you really have to put in effort to screw this up :).
  • Easy to handle data format: all datafiles are (mostly) exactly the same, so less of a mess than I’ve had with HOBOs but especially iButtons to get the data processed.
  • They look good. Admit it, it’s much more attractive to have this little mushroom in your plot than it is to have a buried soil temperature sensor.
The TOMST TMS4 can measure from -40 to +60°C, so that should be sufficient for most use cases

Some drawbacks, unavoidably:

  • Accuracy: as with most cheap sensors, the accuracy is not super high; I usually work with trusting it at 0.5°C. However, especially aboveground and on sunny days, there could be MASSIVE errors on the temperature readings, as the sensor heats up (see Maclean et al. 2021). As with all cheap sensors, extreme caution is thus warranted for interpretation of air temperature measurements. Soil temperatures shouldn’t have that issue. If you want to avoid this, you should work with small thermocouples, which don’t heat up (much) in the sun as they are so small. These are usually substantially more expensive, however. I heard of development of such a sensor within a similar price range, but haven’t seen it commercialized yet.
    The sensors come with optional solar shields, yet these don’t solve the issue (except that they are at least standardized, which is a great jump forward compared with homemade shielding). I especially am not that big of a fan of the lowest shield and prefer installing the sensor sufficiently deep so the middle-temperature sensor is just below the soil surface and as such avoids solar radiation. Here again, however, there is a risk of comparability with other studies, so it is tricky. Note also that having a different installation height of only a centimeter or so can dramatically change the readings on that surface sensor, as so much variation is happening close to the soil surface.
  • I’ve gotten repeated messages about read-out issues. Most of these seem to be software-related and TOMST is working very hard at solving those, but you have to stay on top of the software updates and if your sensor doesn’t respond, there is only so much you can do yourself to find the issue. TOMST has been very helpful in solving issues, though, and I have the feeling things have improved (we had a bunch of sensors in Congo that didn’t read out over there, but I managed reading out all of them back home).
  • This brings me to failure rates: I have the feeling the TMS4 is doing better than other sensors regarding percentage of erroneous measurements, but there is still a non-trivial amount of sensors that still provides erroneous data (e.g. all readings at -100°C, or sudden outliers of +80°C).
  • As for all sensors, you have to buy a reader as well. The TMD-adapter is the price of one sensor (so not better of worse than for the others, but you shouldn’t forget about it and it adds up if you can only buy a few sensors).
  • Visibility: the TMS4 sticks out of the soil. This makes it prone to damage by animals (e.g. wild boars are horrible). This can be solved by installing a metal wire frame around the sensor. But it also invites vandals. The latter in its turn can be solved by installing it out of sight of most humans or putting information signs next to it. In extreme cases (e.g., roadsides or agricultural fields), you could install the sensor fully belowground (TOMST even has shorter ‘dwarf’ versions of the sensor for this goal), but be warned that you then loose the important feature of comparability with other studies. They also have a (cheaper also!) smaller version called the ‘Thermologger’ which only measures one temperature. In theory, I think you can also install this one belowground and use it as you would a HOBO temperature logger, but I haven’t tried this. TOMST affirmed me, however, that it is sufficiently waterproof for this.
  • The soil moisture measurement is not super accurate. This is a whole big story on its own, but it boils down that there are different levels of uncertainty piling up onto each other (sensor-based, calibration, installation, soil heterogeneity, weather…) which in the end result in the fact that a measurement of 20% could be anything between 10% and 30%. However (!) we do get good result when looking at patterns across hundreds of sensors, so the noise seems mostly random, and we feel we can trust relative measurements (e.g. the slope of the curve when drying out, or the difference in moisture generated by a rain event). So, care is needed, but data still has many good uses. And again, very importantly, this issue is there for virtually all cheap soil moisture sensors.
  • Sending sensors across the globe: I’ve had DHL speak up against sending more than two sensors at once due to the Lithium content of the batteries. This made shipping very difficult and/or expensive. As the batteries cannot be removed, there wasn’t much I could do about that. I now however found a small local company who claims that DHL is misguided on the matter and that it’s actually ‘not worse than shipping a bunch of laptops’, so my shipping has resumed without much extra cost. I’ve heard of most collaborators that they simply don’t declare the Lithium when shipping, which solves the issue of course as well.
  • TOMST is a small company and the sensor has become very popular. Combine that with the global shortage in electronic equipment and the end result is that delivery could not always be guaranteed. I have the feeling that these issues (e.g. the shortage in equipment) has cleared up now and the company is on top of orders again. Also, I’ve had plenty of delivery issues with iButtons as well, despite the size of the Maxim Integrated company, so these hiccups simply exist.
iButtons

Some alternatives:

  • If you really only need one temperature, you can go cheaper than the TMS4. TOMST has the thermologger for that, as mentioned above, which could be of great help! But things like HOBO or iButton can go even cheaper. For example, I recently heard about iButtons (DS1921G) at a little bit over €20 which is of course unrivaled [UPDATE: looks like they sold out, which makes sense! Now they are much closer to TMS-prices]. However, failure rate is significantly higher there so you should take that into account, and you’d have to boost the measurement interval (we often used 4 hour intervals) to limit the amounts of time you have to go read them out.
  • If you want to measure air humidity, there are some good HOBO loggers out there that can do that job for you. They have proven robust to colleagues in the tundra, yet are significantly more expensive than alternatives from iButton and Kestrel. Rumours have been positive and negative about all options, so I can’t make any hard recommendations. In any case, be careful with relative humidity values close to 100%, as these are rarely accurate (and can show things like ‘drift’ in the data).
  • If you want to measure at >2 soil depths, you could obviously simply bury your TMS sensor (3 depths) or one of the dwarf versions. However, this limits you to the specific sensor depths of those. I haven’t tried anything else, yet I asked Twitter and got some good responses. I especially like the flexibility of the UGT, which can handle a temperature profile of up to 8 depths. However, I know nothing about the price.
  • The ultimate dream is of course remote data transmission using the Internet of Things. This allows you to track sensors on a daily basis, see when there are failures, dramatically reduces data loss due to sensor malfunctions, ánd ensures you are much more on top of microweather events, which in my opinion greatly improves mechanistic understanding of what’s happening. We have been working with TOMST to develop the TMS-NB for our citizen science project www.curieuzeneuzen.be, and these are truly game-changers to me. They are not commercialized yet as it is tricky to get them to work in other countries, and your price adds up (extra hardware, SIM-card, roaming costs, database connectivity…). We have a few secondhand available, though. We have also teamed up with the group of Pieter De Frenne (UGhent) on commercializing their modular (i.e., add whatever microclimate sensor you want) IoT-connected forest microclimate sensor MIRRA. NOT available yet for real usage, though!
  • If you want higher accuracy, especially above ground, or higher temporal resolution, you should consider thermocouples. I have little expertise there myself, however. Ilya Maclean (University of Exeter) is developing ‘the ultimate near-surface air temperature sensor’ using thermocouples and is close to commercializing this, but it’s not out in the open yet.

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