Ülo Niinemets awarded with honorary doctor title

Text by EMÜ (link)

Without the robe (pic from here)

Last week, on November 8th, University of Life Sciences professor Ülo Niinemets received the highest recognition from the foreign university as a researcher. The academician was awarded with the honorary doctor titel (Doctor Honoris Causa) of the Aurel Vlaicu University of Arad from the Romanian University.

According to Professor Niinemets, cooperation with the University of Romania has lasted for a long time. “Together we have published nearly fifty articles. In particular with professor Lucian Copolovic, who at the time was a postdoctoral and senior researcher at the University of Life Sciences,” he said.

Certainly, collaboration between the two universities in the future will continue. Niinemets said that now he will focus more on the medical and crop-specific study of secondary metabolism of the plant.

Estonian University of Life Sciences congratulates professor Niinemets!

rumeenia audoktor

With the robe!

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Our workgroup participated in university´s sports competition

Text and pics by Evi Vaino

Every person who likes to be healthy, happy, and experience less stress has to make at least 10 000 steps every day in medium pace (citation missing…). Unfortunately, average office (and lab) working person typically makes only 3000 – 5000 steps, and that is not enough.


Evi (nr 3755)

In order to bring the numbers up, our university organizes annual competition “Iga kilomeeter loeb!” (Every kilometer counts!) that promotes moving around on foot, without any vehicle. Both the students and employees can participate.



This year plant physiologists took part with a team of four people:
Ülo Niinemets
Steffen Manfred Noe
Beate Regine Noe
Evi Vaino

spordifoto 2018


Altogether 24 teams with 82 competitors participated, and total of 7309.33 km was covered during the competition. Within 2 weeks, between 15th and 30th of October we covered altogether 673.29 km, and got the third place, although among employees we were the first!


Ülo (nr 87)


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New publication – A methodology to derive global maps of leaf traits using remote sensing and climate data

Text by Lauri Laanisto

We have a lot of robots nowadays. So why not give them fieldwork assignments? It´s not as simple. Remember how much problems Mars rover “Curiosity” has had. And there is no life in Mars! With all the vegetation and animals and destructive humans – no wonder that developing a fully operational field work robot has been a real challenge for people.

Another option is to use “extraterrestrial” robots. We have quite a lot of stuff hovering on the orbit, including remote sensing satellites. But is it possible to measure for example plant traits from satellites? This has been the direction in remote sensing research for quite a while now. And the paper, which is the basis of this blogspot as it includes Ülo as one of the authors, describes one novel way how to get SLA, LNC, LPC, LDMC and other traits from MODIS/Landsat data with spatial resolution of 500 meters.

So – read the paper how to do it! (Or why…)

Citation: Moreno-Martínez, Á., Camps-Valls, G., Kattge, J., Robinson, N., Reichstein, M., van Bodegom, P., … & Niinemets, Ü. (2018). A methodology to derive global maps of leaf traits using remote sensing and climate data. Remote Sensing of Environment, 218, 69-88. (link to full text)


This paper introduces a modular processing chain to derive global high-resolution maps of leaf traits. In particular, we present global maps at 500 m resolution of specific leaf area, leaf dry matter content, leaf nitrogen and phosphorus content per dry mass, and leaf nitrogen/phosphorus ratio. The processing chain exploits machine learning techniques along with optical remote sensing data (MODIS/Landsat) and climate data for gap filling and up-scaling of in-situ measured leaf traits. The chain first uses random forests regression with surrogates to fill gaps in the database (> 45% of missing entries) and maximizes the global representativeness of the trait dataset. Plant species are then aggregated to Plant Functional Types (PFTs). Next, the spatial abundance of PFTs at MODIS resolution (500 m) is calculated using Landsat data (30 m). Based on these PFT abundances, representative trait values are calculated for MODIS pixels with nearby trait data. Finally, different regression algorithms are applied to globally predict trait estimates from these MODIS pixels using remote sensing and climate data. The methods were compared in terms of precision, robustness and efficiency. The best model (random forests regression) shows good precision (normalized RMSE≤ 20%) and goodness of fit (averaged Pearson’s correlation R = 0.78) in any considered trait. Along with the estimated global maps of leaf traits, we provide associated uncertainty estimates derived from the regression models. The process chain is modular, and can easily accommodate new traits, data streams (traits databases and remote sensing data), and methods. The machine learning techniques applied allow attribution of information gain to data input and thus provide the opportunity to understand trait-environment relationships at the plant and ecosystem scales. The new data products – the gap-filled trait matrix, a global map of PFT abundance per MODIS gridcells and the high-resolution global leaf trait maps – are complementary to existing large-scale observations of the land surface and we therefore anticipate substantial contributions to advances in quantifying, understanding and prediction of the Earth system.

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New publication – Plant functional trait change across a warming tundra biome

Text by Anne Bjorkman, post originally published in Nature Ecology and Evolution blog

It takes a global village to write one paper – and nearly 200,000 hours of work to collect the data!

Our findings published today in Nature indicate that the traits of tundra plant communities, despite differing across biome-wide climate and soil moisture gradients, are not changing rapidly with warming… except for plant height.


There is great beauty to be found when you get up close and personal with tundra plants. Here, the seeds of Dryas integrifolia (Mountain Avens) twist as they develop. Photo credit: Anne D. Bjorkman

You know the saying ‘it takes a whole village to raise one child…’, the same could be true of writing a scientific paper. Sometimes the most exciting scientific questions can only be answered with huge amounts of data, and putting together those data requires a very big team of collaborators. Our study of functional trait change across the tundra biome, published this week in Nature, is a perfect example of the kinds of big-scale questions we can explore when 130 scientists from around the world work together.

The Arctic and alpine tundra are the most rapidly warming parts of the planet, but until recently plant trait data across this vast temperature-limited biome were lacking from global analyses. As a result, we had very little understanding of how climate shapes patterns in plant functional traits over space nor the speed with which traits are changing over time at the tundra biome scale. Plant traits are a critical link between vegetation change and ecosystem functions such as carbon storage and surface energy exchange. To quantify climate feedbacks, we need to understand climate-trait relationships.


Taller species like this Salix arctica (Arctic willow) are increasing in the rapidly warming tundra biome, leading to an increase in the height of tundra plant communities. Other key plant functional traits have not responded to warming despite strong relationships between climate and traits across spatial temperature gradients. Photo credit: Anne D. Bjorkman

Our study found that although many traits of the vegetation vary with climate over space, only community-level plant height has been increasing rapidly over time. Much of the community-level change we observed was due to new species entering long-term monitoring plots, rather than just changes in the abundance of resident species. For other plant traits, such as specific leaf area and leaf nitrogen content, soil moisture played a strong role moderating the strength and direction of temperature-trait relationships. Our results help inform projections of the rate at which tundra ecosystems will responding to warming, and thus contribute to global climate feedbacks.


On Qikiqtaruk – Herschel Island, we have observed a localized expansion of the grass species Alopecurus alpinus from the wider species pool (pictured here). This species was originally absent from the long-term plots and has increased the canopy height of the plant community more than four-fold over the past 20 years. Photo credit: Gergana N. Daskalova

Answering biome-scale questions about how tundra plant traits are responding to climate change requires information on changes in community composition at sites across the tundra biome combined with multiple trait observations for nearly every tundra species. Building such massive datasets requires many, many collaborators. This is what we set out to do by forming what we affectionately call the Tundra Trait Team through the sTundra working group of the German Centre for Integrative Biodiversity Research (iDiv). The Tundra Trait Team is a collaboration of over 100 scientists from dozens of countries all around the world, all of whom have collected data on the traits of tundra plant species. Combined with data contributed by members of the already-established TRY trait database our study includes exactly 56,048 trait records and community composition observations from 1,520 plots at 117 sites recorded across three decades as a part of the International Tundra Experiment and related efforts.

Our co-authors and collaborators were a generous lot! We wondered: If it took 26’950 km of hiking to collect 302 data points, how long does it take to collect over 606,748 data points (depending on how you count it)?


Plant traits encompass observations from plant height and leaf area to wood density, seed size, leaf chemistry, plant growth form and beyond.  Together all of these individual trait records help us understand how the form and function of plant communities change across climate gradients and over time. Photo credit: Gergana N. Daskalova

We estimated it takes on average 20 min to collect a trait record (probably much shorter for a plant height record or much longer for specific leaf area or wood density) and roughly one hour to monitor a community composition plot (depending on what method you use and the species diversity and canopy complexity of your site – some sites take over two hours per plot!). That adds up to 18,683 hours to collect the trait records and 4575 hours to collect the community composition data or together 1938 12-hour days of work (or over five years of the life of a plant ecologist or ~180 hours per co-author on our study). And that is not including the travel time to remote tundra locations, the five years of hard work it took to compile these data and conduct our analysis …and, well, you could keep counting.


Point-framing, the method recommended by the International Tundra Experiment protocols to measure community composition, is a painstaking and meditative activity – some love it and some hate it, but the data that result quantify how tundra plant communities are changing over time and responding to warming temperatures. Photo credit: Isla H. Myers-Smith

In summary, it takes an global village of researchers and nearly 20,000 hours to compile a dataset that spans the entire tundra biome and a consecutive decade of work to write one paper. When most of these data were originally collected, this particular study was not yet dreamed up. The data we collect every day as field ecologists have long-term value beyond this year’s or next year’s analysis. Sharing data and making them public ensures the hard work that went into data collection continues to yield scientific insight decades later.


In our second working group at iDiv, we are literally jumping for joy at all the tundra trait data that we were able to compile!

For more information:




Citation: Bjorkman, A.,… Niinemets, Ü., … & Weiher, E. (2018). Plant functional trait change across a warming tundra biome. Nature, doi.org/10.1038/s41586-018-0563-7 (link to full text)


The very jolly sTundra working group pictured at our first working group at the German Centre for Integrative Biodiversity Research (iDiv) – this group is only a part of the many contributors to this study.


The tundra is warming more rapidly than any other biome on Earth, and the potential ramifications are far-reaching because of global feedback effects between vegetation and climate. A better understanding of how environmental factors shape plant structure and function is crucial for predicting the consequences of environmental change for ecosystem functioning. Here we explore the biome-wide relationships between temperature, moisture and seven key plant functional traits both across space and over three decades of warming at 117 tundra locations. Spatial temperature–trait relationships were generally strong but soil moisture had a marked influence on the strength and direction of these relationships, highlighting the potentially important influence of changes in water availability on future trait shifts in tundra plant communities. Community height increased with warming across all sites over the past three decades, but other traits lagged far behind predicted rates of change. Our findings highlight the challenge of using space-for-time substitution to predict the functional consequences of future warming and suggest that functions that are tied closely to plant height will experience the most rapid change. They also reveal the strength with which environmental factors shape biotic communities at the coldest extremes of the planet and will help to improve projections of functional changes in tundra ecosystems with climate warming.

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Fieldwork report – Kaia and Astrid in Australia

Text by Kaia Kask

In front of EucFACE Experiment site (Photo by M. K)

From 28th of March to 13 of April senior scientist Astrid Kännaste and PhD student Kaia Kask were visiting professor David Ellsworth in the Western Sydney University in Hawkesbury, Australia. The purpose of the visit was to measure VOC-s and photosynthesis of 16 different species. Plant VOC-s were collected on multibed cartridges and photosynthesis was measured with Li-Cor 6400. Measured species were located in the EucFACE experimental site and in Davies park, Springwood.


Kaia measuring photosynthesis with Li-Cor 6400 (photo by Astrid)

Most of the time we were lucky to measure the whole day as there was no rain, but during hot and sunny days, especially after midday, we had to pause photosynthesis measurements as plants were not “collaborative” with us. Stomata closure and reduced net assimilation rate would give wrong numbers on measured species. Therewhile we continued work inside the station, weighted leaves and measured leaf area; or collected extra samples from each species for later analyses in Estonia.


Astrid in Davies park (photo by Kaia)

For measuring in the EucFACE site, long trousers, closed shoes and walkie-talkies were obligatory equipment for everyday measurements, as the most venomous black and brown snakes could be on the site territory. Actually we could not even distinguish snakes from the fallen branches and Eucalyptus bark, as these seemed also like snakes. Sometimes we used bigger branched to make some noise or check the area around us. Astrid was the lucky one to see a juvenile brown snake on the pathway in front of the station house. Also while looking for species for measurements we saw kangaroos. Hat and a water bottle were in our ever day equipment as well, because temperatures were mostly up to 35°C.


Equipment – hats and machine (photo by Kaia)

We also managed to visit some botanical gardens, like Blue Mountains Botanic Garden and the Royal Botanic Garden in Sydney. We were amazed from what we saw. Similarly, a visit to the Chinese Garden of Friendship was impressive.


With David (photo by M. K.)

We would like to thank David for his valuable time and suggestions and all his team members who helped us.


Hey, snake! (photo by Kaia)

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Workgroup and EcolChange seminar – Tom Sharkey about the Auxiliary pathways of the Calvin-Benson cycle

Seminar of Chair of Crop Science and Plant Biology and Centre of Excellence EcolChange, Estonian Univ of Life Sciences .

Thomas D. Sharkey is University Distinguished Professor in Michigan State University, and fellow of the AAAS. (Link to his homepage; link to his Wiki page); currently visiting our lab.

Title of the talk: Auxiliary pathways of the Calvin-Benson cycle

Time: Monday, 24. September 2018 at 10.15

Place: Tartu, Kreutzwaldi 5 – 2A41 (Metsamaja)

calvin ja benson

The Calvin-Benson cycle and auxiliary pathways


Tom Sharkey will give a lecture on carbon metabolism of photosynthesis. Tom has studied this topic for over 40 years and has recently written a review on the original discovery by Calvin and Benson of the pathway that converts carbon dioxide to sugars. Recent data from his laboratory indicate that there may be other pathways that work with the Calvin-Benson cycle. In addition to work on carbon metabolism of photosynthesis Tom studies the biochemistry of isoprene emission from trees and is currently visiting Crop Science and Plant Ecology at the Estonian University of Life Science to carry out experiments on isoprene emission.

Tom got his PhD at Michigan State University and returned there in 2008 to become chair of the Biochemistry Department. In between he worked as a post-doc with Graham Farquhar in Australia, then at the Desert Research Institute in Reno Nevada, then as a professor at the University of Wisconsin-Madison. He retired from UW-Madison (he is now emeritus professor of Botany) to return to Michigan.

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New member – welcome Yusuph!

Text and pic Yusuph Olawale Abiola

I would like to use this medium to introduce myself as the recipient of the DoRa+ Scholarship Programme and to also express my profound gratitude to the donor. I finished my master’s degree in Agricultural Sciences in June 2018 from Szent Istvan University, Godollo, Hungary with the support from joint scholarship programme sponsored by the Food and Agricultural Organization of United Nations (FAO) and the Ministry of Agriculture of Hungary. My master’s thesis focused on “Effect of abiotic stress on germination of rice (Orzya sativa L) varieties”.


I’m very excited to be here at Ülo Niinemets’ Lab and I couldn’t be happier than where I am now as it’s a perfect match that will allow me to continue my quest in the field of Agriculture and environmental sciences. In view of the prevailing global challenges of food insecurity and climate change, I really believe that I am at the perfect place with the group of scientists focusing on the alleviating those challenges under the esteemed leadership of Prof. Ülo Niinemets and I am also willing and ready to contribute my own quota. My PhD research will focus on “Comparative study of stress resistance of novel crops; Sweet potato and its resistance strategy to drought and pathogen stress”.

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