The European Research Council (ERC) celebrates a new milestone – the 10 000th researcher awarded an ERC grant

On May 6 European Research Council (ERC) celebrated a new milestone – the 10 000th researcher awarded an ERC grant. Who are these grantees? What are they doing? The ERC cites 15 examples of researchers who have truly changed science. One of them is Professor Ülo Niinemets of the Estonian University of Life Sciences.

Look at the article and podcast on the occasion of ERC 10,000th grantee celebration. It will be part of a story package ‘How the ERC transformed science’. Only 15 stories (among 10,000 ERC grantees) have been chosen to feature in this series.

Among the 15 stories is the story of Professor Ülo Niinemets.

The work of ERC grantee Ülo Niinemets has shown that monitoring plant stress emissions could help us to better understand atmospheric processes. This has led to a rethink on global climate modelling and strengthened research into crop resilience. His project’s successful international collaboration has also demonstrated how ERC funding can boost scientific excellence in smaller countries like Estonia.

Embed podcast here: h ]

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PhD position on cryptogam-associated microbial interactions biology and ecology

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New project – GAIN4CROPS

Nature-inspired solutions to sustainably increase crop yield

Estonian University of Life Sciences participates in the recently launched EU-funded project GAIN4CROPS aims to improve photosynthetic efficiency of the oil crop sunflower using nature-inspired solutions and innovative breeding techniques. The 5-year 8M € project, funded under the EU Horizon 2020 Framework Programme, will pave the way for the introduction of strategic crops which might decrease the use of major resources in agriculture: land, nitrogen, and water.

GAIN4CROPS ( is developing novel disruptive technologies to overcome one of the main constraints of photosynthesis: the photorespiration, a process that reduces CO2 assimilation efficiency, and thus biomass yield and agricultural productivity.

Most plants (85%), including rice, wheat, soybeans and all trees, perform photosynthesis according to the so-called C3 type. At higher temperatures, their photosynthetic efficiency is strongly impaired by photorespiration, which constrains yield. However, some plants have evolved metabolic strategies to bypass this effect: they actively accumulate the CO2 into specific compartments, thus creating an environment unsuitable for photorespiration.

GAIN4CROPS takes inspiration from one of these naturally occurring metabolic strategies and proposes a stepwise approach to enhance the efficiency of photosynthesis. The Consortium aims to optimize the process by designing novel metabolic pathways that make better use of cellular resources by avoiding the release of CO2 back into the atmosphere.

“Attempts to include new metabolisms into crops proved to be very complicated, primarily due to difficulties in introducing a de novo leaf anatomy and fitting in the complex regulatory networks of the cell.” explains the project coordinator Prof. Andreas Weber, from the Institute of Plant Biochemistry of the Heinrich Heine University Düsseldorf. “In GAIN4CROPS, instead, we build on the natural physiology of the sunflower – which has the innate capacity to evolve towards improved metabolisms, ultimately increasing agricultural productivity.”

Overall, the approaches pursued by GAIN4CROPS hold potential for decreasing the use of three major resources in agriculture: land, nitrogen, and water. A more efficient photosynthetic rate brings to greater crop yield per unit area land, which in turn limits the expansion of the arable land and the need for nitrogen fertilizers and water.

The benefits of GAIN4CROPS plants become even more evident at higher temperature, promoting the development of climate-resilient crops as needed to address the consequences of anthropogenic climate change.

“With GAIN4CROPS, we join the current efforts to align land use and food production to conserve biodiversity, reduce environmental impact of agriculture, and deliver sufficient amounts of healthy foods.” says prof. Weber. Indeed, the sunflower oil is a healthy alternative to other edible oils, like the palm one.

Prof. Ülo Niinemets says that EMÜ researchers are particularly experienced in analyzing plant leaf internal architecture and linking it to photosynthesis physiology using unique custom-made gas-exchange systems. This expertize contributes to identifying the best crop lines with advances photosynthetic physiology for future climates

The Consortium, composed of 3 research organizations (Max Planck Society, CEA and Agroscope), 6 academic institutions (Heinrich Heine University Düsseldorf, University of Rostock, University of Cambridge, University of Padua, Estonian University of Life Science and University of Groningen), 1 industry representative (Corteva Agriscience) and 3 SMEs (IN srl, NRGene Ltd and Genomix4Life), gathers a vast array of expertise and pulls together cutting-edge research on plant physiology, microbiology and system biology with groups that are highly experienced in genome sequencing, plant breeding and field-crops.

The experience gained with GAIN4CROPS will serve as a roadmap to attain similar performances in other plants and pave the way to innovative crops, which, thanks to their climate resilience and reduced resource consumption, might lead to a more sustainable agriculture.


Prof. Ülo Niinemets

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New publication – The triangular space of abiotic stress tolerance in woody species: a unified trade‐off model

Text by Lauri Laanisto

I felt like I was totally alone in an airport. Literally alone. It was half past one in the night. Tartu airport has just one arrival per day. Slightly after midnight from Helsinki. It had arrived, all the passengers came through the gate and left. Seemed like all the workers as well. Most lights had been shut off. Could not hear a single sound. And I was still waiting for Giacomo (I had to pick him up, because I had his keys – because of an ongoing urban ecology experiment). He was suppose to return from Bill Shipley´s trait course in Canada. His phone was off, I had been trying several times. If I hadn´t had a manuscript with me (which is still submitted to somewhere), that I could edit, I probably would have had already left, when finally some door in the darkness opened, and Giacomo came out. His luggage was lost, and he had been filling out the paperwork. And forgot to switch on the phone.

He started already in the airport. Triangle, he insisted, it´s always shaped like a triangle. I tried everything, he claimed, and it´s still triangular. My brain was already mostly asleep, it was way past my usual bedtime. And he had not been sleeping in the connecting flights. So it all felt a bit distant at that time.

Giacomo meant the interrelationships of different abiotic stress tolerance factors. Specifically drought, shade, watelogging and cold tolerance. These are the most omnipresent. (And have enough comparable data available as well.) Traditionally (e.g. Smith and Huston 1989 Vegetatio) it has been proposed that universal physiochemical constraints shape the polytolerance – capability of tolerating multiple stress factors at the same time. Of course, species tolerate a bit of everything, but according to the earlier stress models, a species can be adapted to either tolerate shade or drought, but not both at the same time. When it comes to conditions outside the moderate (a week without a rain is not yet drough, etc…). Physics does not allow it. However, some studies (e.g. Sack 2004 Oikos; Markesteijn et al. 2011 NewPhyt) found that there is seemingly no trade-off between, for example shade and drought (which is the most-studied stress-contrast in plants). And some studies (Laanisto & Niinemets 2015 GEB) have indicated that the supposed trade-off between shade and drought might be mitigated by other stress factors (cold and waterlogging), climatic conditions (length of vegetation season) or even adaptations (dormancy).

Couple of days later we´ll meet at work. And Giacomo continues with the triangle. Persistently. I finally start seeing it. I suggest that let´s just publish that. The triangle. It seems that it´s kind of a big deal – a significantly different approach to understanding the interrelationships of different stress factors. Plus, Giacomo´s triangle claims, among other things, that woody species´ shade and drought tolerance is actually independent from each other. Whether different life forms are analyzed separately, or leaf types, or evolutionary origins. Or even when random 100, 200, 300 etc. species are analyzed. The stress tolerance space is always triangular – drought versus waterlogging+cold tolerance on one PC axis, and shade on the other, alone (like me in the airport…).

But then we start thinking further – what is the types of trade-off that forms this stress tolerance space? Giacomo points out the recent review by Grubb. We add the third trade-off type – polytolerance (basically no boundaries in tolerating different types of abiotic stress). Then we ask Mike to join. He is supersceptical when we first describe it to him. He says he is too old for another spin-off of Grime and his stress triangle. We finally convince him that this is completly different stress triangle. And he comes on board as a third author. After all – it´s a triangle we´re trying to write…

Writing of the manuscript goes so quickly and smoothly (another shoutout to senior colleagues) that a few months later I do not remeber anything from the writing (might be from my own encroaching seniority…). It´s also quickly accepted in the first journal where it´s peer-reviewed. Well, that´s it…

Fig. 1 from the paper. Stress tolerance space (STS). STS is defined by combinations of tolerance to shade (ST), drought (DT), waterlogging (WT) and cold (CT) for 799 woody species from the northern hemisphere. Different colours define areas with different probabilities of species occurrence in the STS (red area, high probability; white area, low probability). The variance explained by each principal component (PC) is shown in parenthesis. Species-specific coordinates in the STS are reported in Supporting Information Table S1.

Citation: Puglielli, G., Hutchings, M. J., & Laanisto, L. (2020). The triangular space of abiotic stress tolerance in woody species: a unified trade-off model. New Phytologist;


  • Tolerance of abiotic stress in woody plants is known to be constrained by biological trade‐offs between different forms of stress, especially shade and drought. However, there is still considerable uncertainty on the relationship between tolerances and the limits on tolerance combinations.
  • Using the most extensive database available on shade, drought, waterlogging and cold tolerance for 799 northern hemisphere woody species, we determined the number of dimensions needed to summarise their tolerance combinations, and the best trade‐off model among those currently available, for description of the interdependence between tolerances.
  • Two principal component analysis (PCA) dimensions summarised stress tolerance combinations. They defined a triangular stress tolerance space (STS). The first STS dimension reflected segregation between drought‐tolerant and waterlogging‐tolerant species. The second reflected shade tolerance, which is independent of the other tolerances. Cold tolerance scaled weakly with both dimensions. Tolerance combinations across the species in the database were limited by boundary‐line trade‐offs.
  • The STS reconciles all major theories about trade‐offs between abiotic stress tolerances, providing a unified trade‐off model and a set of coordinates that can be used to examine how other aspects of plant biology, such as plant functional traits, change within the limits of abiotic stress tolerance.
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New publication – Global patterns of biomass allocation in woody species with different tolerance of shade and drought: evidence for multiple strategies

Text by Giacomo Puglielli

Can we solve a long-standing debate in plant ecology?

Plants are known to allocate the greatest proportion of biomass to the organs involved in the acquisition of the most limiting resource for growth. For example, if light is limiting plant growth then plants are expected to allocate more biomass to aboveground parts (i.e. leaves and stems) and less to roots. Conversely, when soil water is the limiting factor, then biomass allocation to roots is expected to be greater compared to that allocated to aboveground parts. Such model is also known as Optimal Partitioning Theory (OPT), and its first formulation dates back to 1960s. OPT has been formulated and it is valid at the intraspecific level, when a single species is exposed to different environmental conditions.

Plant species inherently differ in their habitat affinity, so that there are species that consistently perform the best in shaded or in dry environments. A long-standing debate in plant ecology is if OPT predictions can equally apply when addressing interspecific differences in biomass allocation between species differing in their habitat affinity. Nevertheless, results are scattered and often not consistent across studies. The greatest limitations of previous studies are: i) the sample size (differences among few species from a single ecosystem type are evaluated); ii) the considered range of total plant biomass that strongly influences biomass allocation patterns. Also differences between plant functional types could have further blurred previous results.

We used the most extensive database of biomass allocation available for woody species (Poorter et al., 2015) spanning more than 10 orders of magnitude in plant size, and complemented it with information on species ecological tolerance of shade and drought (i.e. habitat affinity in response to light and water availability), and on plant functional type (deciduous and evergreen broad-leaf and evergreen needle-leaf). The final dataset included 7377 observations of biomass allocation to leaves, stems and roots spanning 604 species worldwide from tropical to boreal ecosystems. We used this dataset to test if OPT predictions are equally valid at the interspecific level independently of developmental stages and plant functional types.

The main and most novel result we obtained is that plant functional type is the major determinant of biomass allocation patterns independently of the considered tolerance. Ifanything, differences between tolerant and intolerant species often run in opposite directions compared to OPT predictions. Also the total plant size at which the comparison was made strongly influenced the observed differences. We conclude that the detection of a given difference between tolerant and intolerant species strongly depends on the size at which the comparison has been made within each plant functional type.

Biomass allocation fractions to: (a-c) leaves (LMF); (d-f) stems (SMF); and (g-i) roots (RMF) at different shade tolerance levels (1 = intolerant; 3 = tolerant) at three fixed values of total plant dry mass at which differences were evaluated (Seedlings = 0.001 Kg; Small trees = 10 kg; Big trees = 1000 kg) for deciduous broad-leaf species.(Figure is from the paper.)

In the paper we also discuss other determinants of biomass allocation patterns between tolerant and intolerant species at the global scale, namely changes in organ morphology together with phenotypic plasticity and the effect of plant architecture on biomass allocation. Altogether, such factors allow tolerant and intolerant woody species to display multiple biomass allocation strategies in response to shade and drought.

While we partly solved a long-standing debate in plant ecology we could not challenge another one, biological patterns are not as easy as theory suggests….luckily for us!

Citation: Puglielli, G., Laanisto, L., Poorter, H., & Niinemets, Ü. (2020). Global patterns of biomass allocation in woody species with different tolerance of shade and drought: evidence for multiple strategies. New Phytologist,


  • The optimal partitioning theory predicts that plants of a given species acclimate to different environments by allocating a larger proportion of biomass to the organs acquiring the most limiting resource. Are similar patterns found across species adapted to environments with contrasting levels of abiotic stress?
  • We tested the optimal partitioning theory by analysing how fractional biomass allocation to leaves, stems and roots differed between woody species with different tolerances of shade and drought in plants of different age and size (seedlings to mature trees) using a global dataset including 604 species.
  • No overarching biomass allocation patterns at different tolerance values across species were found. Biomass allocation varied among functional types as a result of phenological (deciduous vs evergreen broad‐leaved species) and broad phylogenetical (angiosperms vs gymnosperms) differences. Furthermore, the direction of biomass allocation responses between tolerant and intolerant species was often opposite to that predicted by the optimal partitioning theory.
  • We conclude that plant functional type is the major determinant of biomass allocation in woody species. We propose that interactions between plant functional type, ontogeny and species‐specific stress tolerance adaptations allow woody species with different shade and drought tolerances to display multiple biomass partitioning strategies.
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Workgroup and EcolChange seminar – Keyvan about soil microbial diversity and Yusuph about tropical agriculture

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

There will be another two PhD-students taking about their thesis. And after the seminar, we´ll have the opportunity to congratulate professor Ülo on his 50th birthday (which was during the spring quarantine), and on a freshly ran new personal best in marathon – first time under 3 hours: 2:55:16.


Keyvan Esmaeilzadeh Salestani (PhD student, EMÜ):
 „Soil Microbial Diversity and Activity Under Organic and Conventional Farming“

Yusuph Olawale Abiola (PhD student, EMÜ)
„Tropical Agricultural species in changing climate“

Time: Thursay, 17. September 2020 at 10.00

Place: Tartu, Kreutzwaldi 5 – D143 (Metsamaja)

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Workgroup and EcolChange seminar – Chikodinaka, Banafsheh and Hassan about abiotic and biotic stress effects on different crops

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

New schoolyear is beginning and so are the seminars. The first seminar will have three talks from our Phd-students who study plant stress from agricultural point of view.


Chikodinaka Nkechinyere Okereke (PhD student, EMÜ):
 „Heat stress resistance drives coordination of emission suites of volatiles after severe heat stress and during recovery in five tropical crops“

Banafsheh Khalegh Doust (PhD student, EMÜ)
„Cereal valorization opportunities“

Hassan Yussuf Sulaiman (PhD student, EMÜ)
„Phloem-feeding insect infestation antagonizes volatile organic compound emissions and enhances heat stress recovery of photosynthesis in the aromatic herb Origanum vulgare“

Presenters are all PhD-students in the Estonian University of Life Sciences

Time: Thursay, 10. September 2020 at 10.00

Place: Tartu, Kreutzwaldi 5 – D143 (Metsamaja)

Generic picture of “agriculture+stress” search (pic from here)
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New publication – Contrasting co‐occurrence patterns of photobiont and cystobasidiomycete yeast associated with common epiphytic lichen species

Text by Lauri Laanisto

Spreading contingency on intimate relationships

The world of lichens seemed a pretty clear when I was a bachelor student of biology in late 90s. Pretty and clear, to be more precise. It´s difficult to like these strange creatures. Of course, we only studied species that could be identified with the eye or a little magnifying glass. All the species were in one book, and that was it.

A few years later things begun to get confusing. Suddenly appeared the term mycobiont and started dominating in lichen talk. There was no more symbiontic lichen – the holobiontic nature of this being was disentangled into two unequal parts. Fungus was the real deal, and algae (photobiont) was suddenly an outcast, marginal nobody hiding somewhere on the edge of the mycobiontic thallus. It was because sequencing came along. How do you identify the genetics of a symbiontic organism. You have scrap all but one of the partners.

The new system took a while, but we all got used to it. Identification in the field was based on the whole organism, and databases mainly used the genetics of the mycobiont.

But then came another blow by Spribille et al. Apparently the lichen was not so simple. There´s not just the fungus and algae – there is also some kind of shady yeast living in the lichen. Permanently. And very species-specifically, meaning that the the same myco-, photo-, and yeast biont species always lived together. Lichen became a conservative threesome, where all the partners are faithful and commited to a single thallus.

Our study, however, makes things more complicated. Sorry! Our analysis showed that mycobiont and photobiont are indeed basically always coupling up in the same combinations of species. But the yeast. That one is volatile. Sometimes it was one species living together with the same combination of myco- and photobiont, sometimes other. They were also taxonomically more variable than previously thought. We could not really put our finger to their distribution drivers. Our samples, collected by Kristiina, were from Estonia and Switzerland, showed completely different species (or OTUs, to be more precise) pool for these two countries. But why…

JH Lawton famously called community ecology collecting stamps. The same seems to be the case with lichens. It´s a symbiotic contingency. Once ecologists become interested in something, the contingency virus will spread and corrupt the pretty and clear systems established long time ago. This is why we cannot have nice things. Just ecology…

pic from here

Citation: Mark, K., Laanisto, L., Bueno, C. G., Niinemets, Ü., Keller, C., & Scheidegger, C. (2020). Contrasting co‐occurrence patterns of photobiont and cystobasidiomycete yeast associated with common epiphytic lichen species. New Phytologist, (link to full text)


The popular dual definition of lichen symbiosis is under question with recent findings of additional microbial partners living within the lichen body. Here we compare the distribution and co‐occurrence patterns of lichen photobiont and recently described secondary fungus (Cyphobasidiales yeast) to evaluate their dependency on lichen host fungus (mycobiont).

We sequenced the nuclear internal transcribed spacer (ITS) strands for mycobiont, photobiont, and yeast from six widespread northern hemisphere epiphytic lichen species collected from 25 sites in Switzerland and Estonia. Interaction network analyses and multivariate analyses were conducted on operational taxonomic units based on ITS sequence data.

Our study demonstrates the frequent presence of cystobasidiomycete yeasts in studied lichens and shows that they are much less mycobiont‐specific than the photobionts. Individuals of different lichen species growing on the same tree trunk consistently hosted the same or closely related mycobiont‐specific Trebouxia lineage over geographic distances while the cystobasidiomycete yeasts were unevenly distributed over the study area – contrasting communities were found between Estonia and Switzerland.

These results contradict previous findings of high mycobiont species specificity of Cyphobasidiales yeast at large geographic scales. Our results suggest that the yeast might not be as intimately associated with the symbiosis as is the photobiont.

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Kaia defended her PhD!

A general rise in air temperature damages plant photosynthesis. During a hot period, plants also emit an odour which indicates cellular damage, as is evident in a recently defended doctoral thesis by Kaia Kask.

Plants are susceptible to various abiotic factors during their growth, such as low and high temperatures, drought, and excess water and light. According to Kaia Kask, rising temperature is one of the most topical issues at this time, as it threatens the ecosystem as a whole.

Therefore, Kask decided to study plant species separately. She was interested in the effects of heat stress on the photosynthesis and volatile organic compound emissions in black mustard and tobacco.

“Both the black mustard and tobacco experienced strongly reduced stomatal conductance and negative carbon fixation at higher temperatures,” said Kask describing the results. According to her, this indicates extensive damage to the photosynthetic processes and the prevalence of respiration.

In the case of black mustard, heat stress caused the emissions of species-specific glucosinolate breakdown products together with green leaf volatiles. Both volatile groups indicate cellular damage.

Brassica nigra (pic from wiki)

At higher temperatures, tobacco also emitted similar green leaf volatiles. Furthermore, tobacco emitted other characteristic volatile compounds which indicate the increased heat stress it had to endure.

According to Kask, these results improve the understanding of species-specific responses of plant photosynthesis and volatile organic compound emissions. In particular, heat stress severity and type affect volatile organic compound emissions from the leaves.

“Volatile organic compounds play a key role in plant-plant, plant-insect and plant-insect-environment relationships,” added Kask.

The doctoral thesis defended at the Estonian University of Life Sciences can be found here.

The translation of this article from Estonian Public Broadcasting science news portal Novaator was funded by the European Regional Development Fund through Estonian Research Council.

Nicotiana tabacum (pic from wiki)

Articles in the thesis:

Kask K., Kännaste A. & Niinemets Ü. (2013) Emission of volatile organic compounds as a signal of plant stress. Scientific Bulletin of ESCORENA 8, 79–93.

Kask K., Kännaste A., Talts E., Copolovici L., Niinemets Ü. (2016) How specialized volatiles respond to chronic and shortterm physiological and shock heat stress in Brassica nigra. Plant, Cell and Environment 39, 2027–2042.

Turan S., Kask K., Kanagendran A., Li S., Anni R., Talts E., Rasulov B., Kännaste A., Niinemets Ü. (2019) Lethal heat stressdependent volatile emissions from tobacco leaves: what happens beyond the thermal edge? Journal of Experimental Botany, 70, Issue 18, 5017–5030.

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High School student made a research in the University of Life Sciences measuring volatile organic compound emissions in Brassica oleracea var sabellica

Text and pics by Urmas Tokko, Raffael Somelar, Kaia Kask

During the recent school year a student of Tartu Tamme Gymnasium (TTG), Raffael Somelar (11th Grade of nature science class), studied the effects of temperature rise and mechanical wounding on volatile organic compound emissions (VOCs) in kale (Brassica oleracea var. sabellica). The research was made by the supervision of Kaia Kask (PhD), specialist in the Institute of Agricultural and Environmental Sciences, and Urmas Tokko, teacher of biology in TTG. The cooperation between us was very good.

The student and the supervisors found the topic very interesting and promising in regards to better understanding the influence of climate changes in plant communities.

Lab work started in summer 2019, with planning and carrying out the experiments. Experiments were conducted with specialized equipment in the laboratory, which offered many new experiences. The main interest in this study was how the rate of VOCs emissions changes in young kale plants exposed to heat stress and mechanical wounding.

Kale under stress

The results were quite interesting, and in many cases went well together with the theoretical side. Comparisons with previously conducted research with different plants from the Brassicaceae family showed that kale does react slightly differently to heat stress. Moreover, mechanical wounding caused the nice bouquet of green leaf volatiles.

The defence of given research will take place at 25th of May 2020 in Tartu Tamme Gymnasium. The theme (plant stress, VOCs, etc) itself was very interesting to learn about for the participating student. Both the student and the school are very glad about the possibility to conduct an interesting scientific research with the help of its infrastructure and under the supervision of a good specialist, Kaia Kask. We would also like to thank Ü. Niinemets for providing this hands-on opportunity.

Raffael and Kaia
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