Catching carabids and measuring microclimate

Last week, we started our monitoring campaign for carabid beetles in the botanical garden Jean Massart.

Pitfall traps to catch carabid beetles

I already introduced that beautiful oasis in the city of Brussels before, and the idea that within this nice, cool and wet patch of nature on the edge of Brussels’ greyest greyness, species might be able to find some crucial microrefugia against the increasingly blasting heat of the urban center.

The green oasis of the botanical garden Jean Massart

To tackle this, we installed an extensive network of microclimate sensors across the garden, which will allow us to model microclimate heterogeneity with a high resolution. Next to that, we are checking our hypotheses for two distinct groups of organisms: plants and carabid beetles.

Reading out microclimate sensor data

Now, the carabid beetle hunt has gone into full swing. We chose this group because they are relatively straightforward to monitor using pitfall traps, and there was an extensive survey of carabids back in 2015, which can give us very interesting temporal information.

Microclimate sensor (left) and pitfall trap (right) were always placed close together

Now, it’s waiting for our first harvest of beetles. For now, the record of being caught the fastest is held by a worm…

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Proximal microclimate

Spatial resolution is one thing. Temporal resolution an other. The microclimate community has been working hard to improve both, in a continuous search for better microclimate data.

However – and this might be slightly shocking – both are largely missing the point. What we should be aiming for instead, is an improved climate proximity.

The three dimensions of microclimate: spatial and temporal resolution, and proximity.

This ‘climate proximity’ s a new term we introduce in a paper just published in Global Ecology and Biogeography, and it refers to how well climate data represent the actual conditions that an organism is exposed to. This could, but doesn’t have to, relate to the spatial and temporal resolution of your climate data. More importantly, it integrates the important biophysical mechanisms that create the microclimate conditions your study organism is exposed to.

‘Ok, nice theory, Jonas,’ you might say. ‘But can you prove this actually works?’ Oh, yes, we can, and in this new paper, we do so. We compare the accuracy of two macroclimate data sources (ERA5 and WorldClim) and a novel mechanistic microclimate model (microclimf) in predicting soil temperatures (using data from the SoilTemp database. Then, we use ERA5, WorldClim and microclimf to test ecological models in three case studies: temporal (fly phenology), spatial (mosquito thermal suitability) and spatiotemporal (salamander range shifts) ecological responses. In all three cases, one would expect the more proximal microclimate model to do a better job.

The spatial and temporal resolution, and proximity, of the three climate sources used in our study. On the right, you see a list of proximal mechanisms, and how much they are included in the different climate sources

And, oh boy, did that microclimate model live up to our expectations! For predicting soil temperatures, microclimf had 24.9% and 16.4% lower absolute bias than ERA5 and WorldClim, respectively. Even more mindboggling, across the case studies, we find that increasing proximity (from macroclimate to microclimate) yields a 247% (yes, you read that correctly) improvement in performance of ecological models on average! That is compared to a meager 18% and 9% improvements from increasing spatial resolution 20-fold, and temporal resolution 30-fold, respectively.

Emergency rate predictions for ground-dwelling larvae of two crop pest insects in Canada, showing how our microclimate model (microclimf) gets substantially closer at predicting the emergency of the flies.

Temperature predictions (panel a) by ERA5, WorldClim and microclimf  were similar, yet marginal differences among the three temperature products yielded disparate calculations of growing degree days (panel b). The end result were substantial differences in estimates of insect emergence (panel c): the microclimate model had an average error of 6.57 days, while the next best macroclimate one had already 17.0 days of error.

The paper thus concludes that increasing climate proximity, even if at the sacrifice of finer climate spatiotemporal resolution, may be the way to go to improve ecological predictions. Importantly, that implies we have to use biophysically informed approaches, rather than generic formulations, when quantifying ecoclimatic relationships. Mechanisms first, data second!

Here also, differences in traditional variables like Bio1 were minimal, but for ecologically relevant parameters like fecundity, microclimf generated highly different predictions, with 50% more eggs/female/day than the two other climate sources.

Klinges et al. (2024) Proximal microclimate: Moving beyond spatiotemporal resolution improves ecological predictions. Global Ecology & Biogeography. https://doi.org/10.1111/geb.13884

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The peculiar case of the Rallarvägen

Gaining a long-term perspective on ecosystem changes is challenging. Even when ecologists describe changes as happening “remarkably fast,” they are often difficult to observe within a single scientific career, let alone the lifespan of a project.

Occasionally, however, we can catch a rare glimpse of long-term evolutions, and these invaluable “blasts from the past” can lead to groundbreaking discoveries. An example of this is a new paper we recently published in the Nordic Journal of Botany, thanks to the diligent efforts of master’s student Dymphna Wiegmans.

In this paper, we unearthed historical vegetation surveys conducted after the creation of the ‘Rallarvägen’ (or ‘The Material Road’). This trail, established at the very beginning of the 20th century, was used to construct the vital railroad line connecting the mining town of Kiruna in northern Sweden to the Atlantic Ocean at the Norwegian town of Narvik.

Train on the historical railroad track, from the iron ore mine of Kiruna to the Atlantic Ocean in Narvik.

At the dawn of the 20th century, northern Sweden was an incredibly remote and pristine area. The construction of this railroad, decades before the first real road opened up the region, was thus nothing short of a monumental achievement. The Rallarvägen trail was used by navvies (railway construction workers, known as “rallare” in Swedish) to transport materials and equipment necessary for building the railway.

The railroad project, known as the Iron Ore Line (Malmbanan in Swedish), began in the late 19th century and was completed in 1903. This line was essential for transporting iron ore from the rich deposits in Kiruna to the ice-free port of Narvik, enabling year-round shipping. The construction of the railroad through such a challenging and rugged landscape required significant human labor and ingenuity. Workers had to deal with harsh weather conditions, difficult terrain, and the logistical challenges of transporting heavy materials through an undeveloped wilderness.

Daydreaming about the achievements of these early railroad builders, we were now more actively interested in this historic disturbance and its impact on ruderal plant species, which thrive in disrupted environments but had up till then only few opportunities in this largely untouched landscape. Specifically, we wanted to understand the dynamics of both native and non-native ruderal species and how their distributions have evolved from that major railroad building project back in 1903 till now.

A map of a route

Description automatically generated
Map of the study region between Riksgränsen and Abisko in subarctic Sweden, with transects along hiking trails Rallarvägen (yellow dots), Björkliden (blue), and Låktatjåkka (red).

To our surprise, our research uncovered some unexpected findings. Using historical botanical records from 1903, 1913, and 1983, along with our own resurvey in 2021, we were able to partially reconstruct the long-term dynamics of these species. We initially hypothesized that the low levels of non-native ruderal species observed today indicated that their introduction was relatively recent, likely after the construction of the main highway (the ‘E10’ in the 1980s, compounded by increased tourism and climate change in recent decades.

Our historical sources tell an entirely different story, however. Many ruderal species were already present and common during the creation of the Rallarvägen. Remarkably, there were even more non-native species back then than there are now, and we have observed a consistent decline since then. Even more surprisingly, this decline has led to the current ruderal community having fewer warm-adapted species than during the era of railroad construction. This implies that warm-adapted species are disappearing rather than emerging. This pattern holds true for both native and non-native ruderals.

A remarkable decline in warm-adapted non-native species over time, as reflected by the range of ‘temperature indicator values’ by all species in each of the survey years.

The conclusion is clear: a major historical disturbance, such as the construction of the railroad back in 1903, can send shockwaves through an ecosystem that are still felt a century later. In this case, the impact of that disturbance has been even greater than that of contemporary climate change, as evidenced by the decline in both species richness and the temperature affinity of the community over time.

Our historical data is incomplete, so there remains some uncertainty about the exact sequence of events. Nonetheless, we could piece together a remarkable history that begins with gardens, stables, and foreign soil filled with ruderal seeds, followed by a steady decrease in disturbance levels and a corresponding decline in non-native ruderal species richness. The construction of the highway in the 1980s and its use since then has not yet resulted in an increase in ruderals along the Rallarvägen, likely because the Rallarvägen was not used as a construction road for the building of the highway. Nor has the recent warming climate led to a resurgence of these species.

Nowadays, ruderal species are as expected most strongly related to hotspots of introductions, such as the small train stations scattered along the tracks. Interestingly, here again disturbance trumps climate: the relationship of ruderal species was much stronger with disturbance than with climate.

A final interesting observation to point at here is that only very few ruderals, and especially non-native ruderals, have found their way from the Rallarvägen in the valley to higher elevations. Despite the presence of some well-visited hiking trails crossing the Rallarvägen, the uphill expansion of non-natives is limited. That is remarkable, given that they have had more than a hundred years to do so. The conclusion should thus be that most of these species are currently truly at their climatic limits here in the high north. Only a change in climate could thus make them move higher up…

Let that unfortunately exactly be what is happening…

The paper, published in the Nordic Journal of Botany, can be found here: https://nsojournals.onlinelibrary.wiley.com/doi/10.1111/njb.04382

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36.000 tea bags for science

It has become the go-to technique for many ecologists who need a cheap and simple method to measure decomposition rates in the soil: burying tea bags. However, it is still rather mindboggling that the team behind the international Tea Bag Index collected data from 36.000 (!) of these cups of soil tea from across the globe. The key conclusions from this monitoring project with perhaps one of the more unusual sources of data in ecology (although clearly rivaled by ‘operation underpants’, where underwear is used for the same purpose) now got published in Ecology Letters. As contributor of my own set of these brews to the mix, I happily took part in this endeavor.

A pile of tea bags, ready to be buried for science

Burying tea bags is appealing for two reasons: you know the litter type, and you know the exact quantity of it. Standardizing both across all of the worlds’ soils can provide a unique insight in differences in the rate of decomposition across these soils. Indeed, for a fair comparison of litter decomposition, one needs to standardize the type and quantity of buried plant material. The choice of Lipton tea bags, consistent in plant species and weight worldwide, resolved this methodological challenge.

The global spread of the mindboggling 36.000 tea bags

The study participants buried both the very leafy green tea and the more recalcitrant rooibos tea. After a predetermined time, the partially decomposed tea bags were excavated and weighed to ascertain weight loss. Subsequent analyses aimed to disentangle the influence of climate variations and anthropogenic land use on both decomposition rates and the extent of material breakdown (and thus the resulting stabilization of the remaining material).

Tea bag decomposition is strongly influenced by local climate conditions (which are rather unusual in the depicted Icelandic landscape).

One would hypothesize that the initial rate of decomposition and the amount of mass loss correlate pretty well at a global scale. Using our thousands of tea bags, we found this to be true, indeed, yet with some intriguing nuances, particularly in cold regions, where decomposition dynamics defied conventional expectations.

Indeed, especially in cold regions, we often observed initially relatively quick breakdown of a portion of organic material, yet high remaining mass loss. This mismatch between loss rate and stabilisation is important, and could for example result from different drivers of two main competing pathways responsible for said mass loss: simple leaching of soluble components into the soil, versus breakdown by soil microbes. While the latter is rather sluggish in cold environments, the former can still result in rapid mass loss. While our correlational study cannot be conclusive regarding the exact driver at play – and we discuss some alternative hypotheses in the text – these findings do underscore the intricate region-specific complexities of these biogeochemical processes.

Global patterns in mass loss rates (kTBI) and stabilisation (STBI) as modelled using the 36.000 tea bags. Bottom panels indicate areas with lower accuracy (higher CoV).

In conclusion, our study sheds light on the intricate relationship between climatic factors and litter decomposition rates, emphasizing their vital role in ecosystem carbon cycling, particularly in the face of climate change. By uncovering context-dependent effects, we highlight the need for nuanced approaches in global carbon modeling. Our findings underscore the significance of empirical data in refining our understanding of these complex dynamics and in improving the accuracy of carbon models.

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Filling the gaps

Anyone working with microclimate data is familiar with time series data – repeated measurements over time at the same location.

And anyone working with time series has bumped into an important potential issue with them: gaps. More often than not, time series are incomplete. There could be erroneous measurements, sensor malfunctioning, sensor replacement, data transfer issues, memory issues and so on.

Over time, a whole toolbox of techniques has emerged to fill those gaps and make those time-series whole again. In a recent paper, we tested a series of these gap-filling methodologies for their accuracy. That question is important especially for microclimate networks, as here not only the temporal but also the spatial relationship between time series is playing a role, and filling gaps is thus not a trivial exercise.

In this paper, we applied and evaluated 12 such gap-filling methods to complete the missing values in a dataset originating from large-scale environmental monitoring. For this, we used the unique dataset of 4400 IoT-connected microclimate sensors that were deployed across Flanders as part of ‘CurieuzeNeuzen in de Tuin’, our large-scale citizen science project on heat and drought.

(a) The TMS-NB microclimate sensor was used in a large-scale citizen science project on microclimate monitoring. The sensor measures temperature at three heights, as well as soil moisture. Data transmission occurred via NB-IoT. (b) The WSN covered 4400 gardens across Flanders. Sensor locations are colored based on whether time series were complete (green) or had missing records (red).

Methods evaluated included Spline Interpolation, MissForest, MICE, MCMC, M-RNN, BRITS, and others, and the performance of these imputation methods was evaluated for different proportions of missing data (ranging from 10% to 50%), as well as a realistic missing value scenario.

Accuraccy estimates (Root Mean Square Error and Mean Absolute Error) for the twelve tested imputation methods

Interestingly, techniques leveraging the spatial features of the data (such as MC, MCMC and MissForest in the graph above) tended to outperform the time-based methods. Importantly, as well, real scenarios of missing values – with gaps often occurring in larger blocks – often resulted in a lower performance of the models than artificial scenarios with randomly missing points, especially for more traditional techniques such as MICE.

Of course, this result is not the final conclusion on the debate which gap-filling technique to use. The outcome strongly depends on the specifics of the datasets at hand, in our case a dataset of microclimate data of fairly short duration (only little seasonality), with relatively sparse temporal resolution (every 15 minutes) and unusually high spatial density (4400 sensors across Flanders). These features work in favour of techniques that take the spatial features of the data into account, and reduce the applicability of e.g., deep-learning techniques that might prove more robust for more complex time series with longer temporal window and higher temporal resolution.

So, let’s hope this exercise in gap-filling can help other microclimate enthusiasts in their search for good solutions!

 Source: Decorte et al. (2024) Missing value imputation of wireless sensor data for environmental monitoring. Sensors.

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A wealth of wildflowers

One could wonder if the microclimate-based models of Haesen et al. would have predicted such a wealth of wildflowers in the garden of our new home!

Wild garlic

This is our first spring in our new garden, and we could thus have hardly foreseen that so many beautiful decorations would spring up in our little patch of forest!

Lily of the valley

Of course, that is if our distribution models would not have said so. In this recent paper in Ecology Letters, we used our high resolution (5 x 5 m) maps of forest microclimate to improve distribution models of forest understory plants.

5 x5 m might just be enough to give our garden its own little pixel on the maps, so it could be worthy to investigate…

Of course, I should not tell you that all that greenery was one of the reasons why we bought the place, so I am beyond excited that the garden is rewarding our decision so handsomely!

Bluebell
Wild garlic
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