Ecologist’s Diary: From Peaks to Pipettes, or The Bull In the China Shop

It’s a cold and rainy morning, and I enter NIOO and a new world opens up to me: I am spending the next two months in the Netherlands Institute of Ecology in Wageningen.

Ecology for me, so far, has covered counting plants in the field or growing them in pots, digging in the dirt of mires and mountains, tracing ants in the sand and watching birds in forests and at lakeshores, and eventually some root-washing and treatment of soil samples with chemicals in the lab. Now I will go a bit deeper – and it really feels like it is not just one level. For this experience, I am changing my hiking boots for a lab coat, and my beloved Swiss Alps for the flat, wide landscape of central-East Netherlands. From the window of my apartment, I can spot the highest ‘mountain’ in the surroundings rising prominently out of the empty fields – for an approximated 30 metres of elevation. So why on earth would anyone come here to study decomposition on alpine summits?

Photo of the Netherlands Institute of Ecology in Wageningen
Netherlands Institute of Ecology in Wageningen (

The answer is inside the impressive modern building just across the road from the new campus of Wageningen University and Research. Constructed exclusively from re-usable materials following Cradle-to-Cradle principles and finished in 2010, the NIOO’s square-edged structure of glass, wood and steel is an ecological statement by itself. An intelligent heating/cooling system effectively regulates temperature whilst minimising energy consumption. All wastewater is treated, with the intention to become drinking water quality again. Further, the estate contains a high variety of different habitats, hosting diverse fauna and flora. And on top of this, it hosts the most generous and well-equipped research facilities I have ever encountered in an ecological institute (whatever that may mean in comparison to others). All in all, a quite impressive combination!

Importantly, the building hosts many nice, smart people at the Department of Terrestrial Ecology, who all have a profound knowledge of plant and soil processes. And this is exactly what my project is about: I study the decomposition of leaf litter in the alpine environment. This ecosystem is truly extreme and highly variable, showing temperature differences of multiple degrees within just a couple of metres. More importantly, it is projected to warm quickly with climate change, causing rapid distribution shifts of alpine species. So, incorporating these special features, how is the result of decay process influenced by litter identity, by temperature variation, or by bedrock and soil characteristics – and what could that mean for the future?

These are the questions I tried to answer during my Masters project in the Mountain Ecology group at SLF Davos, making use of the widely-applied teabag method. And we got back some surprising results, as decomposition was not at all controlled by temperature, but rather driven by soil properties. However, due to limitations in time, money, and facilities at SLF, our belowground measurements were quite rough and included only chemical and physical parameters, not incorporating the hidden billions of tiny creatures which are actually the main actors in cold-environment decay processes.

Teabag being buried
Teabag being buried

Time to catch up with that! By studying microbial community composition, we hope to increase our understanding of differences in the biotic environment between sites – and whether the foreign substrate of tea actually changes microbial communities locally. Fortunately, sampling is not very complicated: when you take a teabag out of the ground it leaves behind a nice hole, from which you can easily scratch the soil that has formerly been in contact with the teabag. Put that soil in a ziplock bag, stuff all the samples as well as an ice pack into a Styrofoam box, strap it onto your already overloaded backpack – and take it on a train ride to the little town of Wageningen in the Dutch countryside. Even if there’s not a lot around, given the expertise of both the University and NIOO in soil ecology, it seems like the right place to learn about molecular analyses of soil microorganisms.

And there is definitely a lot for me to learn. Most of all: precision. Every tiny air bubbles might ruin your analysis, every extra microliter of primer would mean having to repeat the whole procedure for the sample. Of course, that should not be a major issue (at least, as long as you don’t run out of soil), but still, every move you make, every pipetting step you perform, feels somehow irrevocable. Did I really ever think molecular lab work would be relaxed, compared to climbing alpine summits? Well, after the first days in the lab, when I come home absolutely crushed, not to speak of the muscle pain in the thumbs on the days after… I definitely learned my lesson there.

Above all, lab work seems to have developed its very own language, which can be quite hard to understand. Luckily for molecular immigrants like me, there are such things as lab protocols guiding you through the maze and making it relatively easy to apply the methods – and eventually gain some deeper understanding of the processes along the way. And then, of course, there are extremely helpful (and far more experienced) people around – cheers to Freddy, Emilia, Tanja, and all others! – who will pick me up and guide me back on track if I get lost.

Still, and despite all exhaustion, molecular biology remains a fascinating matter. Dissolve your soil in a pre-mixed liquid, combine with some other molecules in a little plastic tube, shake, filter and heat them in the right manner – and, as if little mechanics operated inside, you get the desired mixture at the end of the pipeline, enabling a computer to tell you about the specific composition of your sample. Just brilliant! Obviously, an astonishing evolutionary process in lab techniques has taken place over the past just 40 years, with scientists trying over and over to find the right substances and combinations. And after just four hours, you have millions of copies of every piece of DNA in your sample – in just one drop of colourless liquid.

And yet, at least for myself, I’m afraid lab work cannot compete with open-air fieldwork. No matter whether it’s raining or bright sunshine, a fresh breeze during worktime is just an invaluable plus. At times, I really miss that feeling, which results in me spending my lunchbreak alone outside on the chilly, yet eventually sunny, roof terrace. Not to say that we never have sun inside the lab – actually, it is sometimes too much for the self-regulating, glass-covered building to keep the inside temperature at a convenient level. Such a shame you have to leave the lab coat on… Sometimes, my inherent environmental conscience will also pinch me about the impressive loads of plastic waste being produced from pipette tips and used containers (though of course, I understand the necessity). And, with all due respect to Dutch radio stations, I think I still prefer the diversity of the outdoor soundscape over listening to the same 15 songs and commercials again and again.

But even if I don’t become any more of an enthusiastic molab worker, I am looking forward to analysing the results of the sequencing I’m currently running, and I am extremely grateful for the opportunity to have this learning experience. Thank you, Ciska and Sonja, for setting up this great project and entrusting me with it, and thank you, NIOO, and everybody inside for hosting me over these two months and demonstrating how comfortable, productive and inspiring a research environment can be.

I mean, could anybody state differently, if they were fortunate enough to have a cake baking contest happening on the afternoon of your goodbye? 🙂

Jonathan von Oppen

Read more Ecologist’s Diary posts here!

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