Monthly Archives: December 2016

Short term trends in long term research?

By Alexandra Linz 

It’s 4:00AM. Between prepping equipment and anxiety about today’s experiments, I only got a couple hours of sleep last night, but I’m full of adrenaline and ready to go. My undergraduate student and I drive to our first sampling site in beautiful northern Wisconsin, USA. The sun isn’t up yet, but the loons are laughing as we disturb Sparkling Lake’s calm waters, paddling our way to the buoy at its center. We drop our instruments into the water and wait a few minutes until exactly 5:00AM. In a flurry of motion, we begin to collect our samples – lake water concentrated through filters that must be collected in under 5 minutes and immediately frozen in liquid nitrogen. It’s over as quickly as it began, and the sun finally makes its way over the horizon. One timepoint down, thirty-five more to go.2016-07-07-04-35-12

I’m an LTER grad student, but this past summer, I ran an experiment on short-term changes in bacterial metabolism. Bacteria are crucial and beneficial members of lake ecosystems, where they recycle nutrients, harvest energy from sunlight, and decompose organic matter. My lab has studied freshwater bacteria in Wisconsin lakes for over a decade. I’m interested in carbon cycling specifically, and to find out what carbon sources are being used by the bacterial community at any given moment, you can collect a molecule called RNA. RNA is a messenger molecule in cells, and deciding what RNA to make and how much is a major way that bacteria regulate their metabolisms. Essentially, it’s the middle step between “I have the enzymes I need to eat this” and “I have the instructions to make those enzymes.” But because it would not be helpful for a cell to have all these old messages hanging around, RNA degrades fast. To collect it, we need to filter our samples quickly and immediately freeze them in the field. On top of that, our bodies make enzymes that degrade RNA as a defense against viruses, so while sampling, you are constantly spewing enzymes with the potential to destroy your experiment. RNA work is not something to embark on lightly.2016-07-09-14-57-32

We initially considered adding RNA sampling to our long-term time series, but there was one major problem: we didn’t know if there were short-term dynamics of RNA in freshwater. I’d just read a study in the ocean where huge changes in RNA were observed at different times of the day, as the bacteria adapted their metabolisms to take advantage of changing light conditions. I was concerned that if we tried to add RNA to our long-term sampling, we’d get different results depending on what time of day we sampled throughout the year. My professor’s response? “You should write a grant to study that!”

Fast-forward a year and a half. I did write a grant, and that grant got funded (!), and here I was at the crack of dawn attempting to sample three lakes every 4 hours for 48 hours each, all within two weeks. See, that ocean study that inspired me used a sampling torpedo. They dropped it off in their current of choice and picked it up a week later, all samples safely stowed on board. I, on the other hand, convinced/begged/harassed everyone I could to help me with the fieldwork. With my amazing volunteers, all the equipment I could haul in a university vehicle, and much trepidation, we began sampling.dsc_0188

I was keenly aware of everything that could go wrong. But after that first timepoint, I felt like I had done everything I could, like I had pushed a start button and now just had to sit back and let events unfold. And amazingly, the field work went quite smoothly! Well, we had to reschedule one timepoint due to thunderstorms, and once the boat flooded and nearly sank in high winds, and there was the time I got stopped by law enforcement on suspicion of illegal night fishing – but I was ready for these things. Call me a pessimist, but that’s how field work is supposed to happen. You react and revise your plans, and you come back with your samples and some crazy stories.

By this point, the samples I collected last summer are nearly all processed and I’m just waiting on the RNA data. I’m excited to learn if bacteria in lakes show the same changes during the day as they do in oceans, and to see how their short term trends compare to the long-term trends we’ve been studying at LTER for years. And then maybe the next LTER grad student can take what I’ve learned and plan a super awesome multi-year RNA experiment!


Alexandra Linz is a PhD student in the Microbiology Doctoral Training Program at the University of Wisconsin – Madison. She works with Prof. Katherine McMahon studying bacterial carbon cycling in Wisconsin lakes. Alex is passionate about science outreach and also writes for her lab’s blog, When not doing crazy experiments, Alex enjoys photography, playing guitar and piano, and reading science fiction.

Plants and Nitrogen – a love & hate relationship

Author: Melanie Batista of Universidade de Lisboa

Hi there!

I want to tell you about my visit to the LTER site at Whim Bog, Edinburgh, Scotland. The Centre for Ecology & Hydrology, based on the Natural Environment Research Council, manages a LTER site with facilities to study the effects of dry and wet nitrogen deposition. Nitrogen is an essential element for plant growth, however, like everything in life, too much is just too much. Wet deposition occurs when nitrogen enters the system in the form of precipitation, and dry deposition refers to forms of nitrogen dissolved in the atmosphere. Excess of nitrogen can lead to severe changes in ecosystems, especially if they are oligotrophic – meaning that they are adapted to low nutrient conditions. Studying these changes is exactly what this LTER site is about. The site is a peatland ecosystem, dominated by the shrub Calluna vulgaris and the  sedge Eriophorum vaginatum.


During my visit I studied the effects of dry deposition of nitrogen in the plant community – I assessed plant diversity and structure, using a set of transects along a gradient of ammonia (NH3). This gradient is imposed to the plant community by an automated free air release facility that releases gaseous ammonia. The  system fumigates only when wind speed and direction are within determined values, creating an ammonia gradient covering about 60 m in extend, with ammonia values ranging between ambient (c. 0.5 NH3 µg m-3) and 100 µg NH3 m-3 (annual averages).

One last thing about the Scottish experience. You ever heard about midges? Before my trip to Edinburgh I never heard about them. And, until my last day of my field work, when I was starting to think the midges were little more than a myth, they appeared in full force. It seems that until then there were never the perfect conditions. But, on that last afternoon, the sun shone brightly after a light rain, the wind had stopped blowing, and from one second to another, millions of little flying dots appeared from under the shrubs to land on our hands, faces, ears… everywhere. So I learned what midges are.


Melanie is a fellowship researcher at the Centre for Ecology, Evolution and Environmental Changes, Universidade de Lisboa. She studies plant functional diversity, mainly of the Mediterranean vegetation in Portugal, in response to different environmental changes, such as desertification and grazing.




In the realm of blueberries and moss… radiometry measurements at Kindla Integrated Monitoring site, Sweden

By Jan Pisek, Senior Research Fellow, Tartu Observatory, Estonia

The BRACE project (Background Reflectance ACross Europe) is one of 23 small projects supported by the eLTER H2020 project’s Transnational Access scheme (which is funded by the European Union). The objective of the project is to collect in situ measured background/understory reflectance data across diverse ecosystem research sites in Europe. The results should be particularly useful for validating remotely sensed data and for producing Northern hemisphere maps of seasonal forest dynamics, enabling analysis of understory variability, one of main contributors to uncertainty in present estimates of spring leaf emergence and fall senescence. Our data can also be used as an input for improved retrieval of biophysical parameters and for modelling local carbon and energy fluxes.

Our equipment for making understory spectra measurements at Kindla (from right to left): portable spectrometer; controlling unit (laptop); measuring tape and forest flags for laying out and marking transects; white Spectralon reference panel.

First stop was the Kindla Integrated Monitoring site in Sweden, which my colleague, Krista Alikas, and I visited in July 2016.  Kindla is one of the most inaccessible and wild areas in Örebro county, and it is also a large nature reserve (over 900 hectares).  To get good quality data, we have to collect our measurements in overcast, diffuse light conditions. You cannot do much when the sky is blue and the sun is shining, and during such moments we explored our surroundings and gorged on huge quantities of ever-present blueberries.

Our first 100 m long transect is laid out and ready to be measured in the forests of Kindla, Sweden (orange flags mark every 4 m along the transect). Notice the blueberry bushes (Vaccinium myrtillus) all around.

There are 15 km of paths in the nature reserve area, allowing individual walks of 7-10 km – just perfect to fit within the windows of our (in)activity when there was no hope of sudden increased cloudiness. Kindla’s summit, 425 meters above sea level, is also one of the county’s highest points. There is an additional 11-meter viewing tower, which allows you to rise over the treetops to get a fantastic view over the green sea of surrounding forests.

The splendid vista from the Kindla’s summit (426 meters above sea level).

We were told that you can find traces of bear, wolf, lynx and wolverine in Kindla, but the animals are clearly very shy and maybe unsurprisingly we failed to make a closer encounter with any of these animals. On the other hand, we were apparently sharing our accommodation with another typical local representative. We were staying in a nice and cosy barn-turned-into-hostel (we were the only guests all week) in the nearby tiny village of Nyberget. During nights we could often hear a strange, not entirely unpleaseant murmur coming from the base or underneath the building. Upon our departure we were told that it was most likely a badger.

Interesting teeth bite pattern from an incognito visitor (a fellow researcher, perhaps?).

With support from the eLTER H2020 project, we are looking forward to making similar measurements from two other European LTER sites this year: Montado in Portugal and Zöbelboden, Austria.

Author: Jan Pisek


Jan got his PhD. degree from University of Toronto, Canada. He is currently a senior research fellow at Tartu Observatory, Estonia. Jan is primarily interested in field- and space-based multi-spectral and multi-angle optical remote sensing, biophysical parameter and vegetation structure mapping. Jan would like to thank Lars Lundin and Stefan Löfgren of Swedish University of Agricultural Sciences (SLU) for providing excellent supplementary materials and introduction to the Kindla Integrated Monitoring Site.