Tana about moderating a workshop in EcolChange PhD conference

Text by Tana Wuyun

A fun experience as one of the workshop moderators in EcolChange PhD Conference 2019 “EcolChange in World of Synergies”

Few weeks ago, I gladly participated the annual EcolChange conference in Voore, East Estonia. It went well, without saying, with a lot of sunshine from the sky and my heart.

As one of the organizing members, I was involved from the very beginning on all the details discussed. I felt so lucky for being with the team, since everyone was eager to share their thoughts and offer their knowledge. As a first year PhD, it was definitely a great learning experience.

In the afternoon workshop, I was the moderator for the group “Biogeochemistry Cycling in Ecosystems ‘To Growth or To Adapt? Carbon Cycling Under Stress’”. I came up with this idea because the topic of how plants react under different current and future climate stresses is a big concern nowadays and is quite relevant to the aim of the EcolChange team. With consideration of the different research areas in the organization, I intentionally made the topic fairly flexible, hoping everyone can share some thoughts so people could widen their horizon after the discussion and enlighten by each other. Overall, it was quite successful, each of the sub-group had come up with the answers for the broad questions.

Personally, I enjoyed this conference very much both as a PhD student organizer and audience. I hope there will be more conferences like this in the future that PhD students could take the initiative!


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EcolChange seminar – John Davison about the niches of mycorrhiza

Seminars of Department of Botany and Centre of Excellence EcolChange

Speaker: Dr. John Davison is senior researcher at the Plant Ecology Laboratory, Department of Botany, University of Tartu. His research addresses the role of biotic interactions in shaping biodiversity.

Title of the talk: The realised niches of arbuscular mycorrhizal fungi

Time: Thursday, 28. November 2019 at 14.15

Place: Tartu, Lai 40-218 (Vaga auditorium)

Summary: Understanding the ecology of unculturable soil microbes is extremely challenging. Here I make use of a stable molecular taxonomy and global datasets to investigate the abiotic and biotic niches of different arbuscular mycorrhizal fungal taxa. I identify patterns of phylogenetic correlation in niche characteristics throughout the diversity of the group.

“Phylogenetic trees of Glomeromycota and other fungi. A. Bayesian tree based on 1539 bp of small subunit rDNA sequences” (from Redecker & Raab 2017 Mycologia; https://doi.org/10.1080/15572536.2006.11832618)

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EcolChange seminar – Rauno Lust about nitrate removal from water

Seminar of Department of Geography, UT and Centre of Excellence EcolChange

Speaker: Rauno Lust is a PhD student in the Department of Geography, University of Tartu.

Title of the talk: Enhancing nitrate removal from waters with low organic carbon concentration using bioeletrochemical systems

Time: Wednesday, 27. November 2019 at 16.00

Place: Tartu, Vanemuise 46-327 (JG Granö auditorium)

Summary: Assesments of groundwater aquifiers made around the world show that in many cases nitrate concentrations are exceeding the safe drinking water threshold. This seminar will give overview how microbial electrosynthesis could be used to enhance nitrate removal from waters with low organic carbon concentration.


That´s how nitrogen gets to groundwater, honestly… (pic from here)

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EcolChange annual conference underlines its attractivity for young researchers

The Estonian Centre of Excellence EcolChange investigates global change ecology from molecular to biome-level in both natural and managed ecosystems. Annual meeting provides a great chance to meet and discuss current research questions in a cross-discipline environment. In 2019, team formed of PhD students from all research groups participating in EcolChange organised the annual doctoral conference, which took place on November 12th in Voore, Jõgevamaa. Target audience was EcolChange PhD students and junior scientists, but students and researchers outside the centre of excellence were also welcomed, and more than 70 participants followed the invitation of the organisers to listen and discuss the newest trends and highlights of EcolChange´s research groups.

In addition to presentations from the group leaders, there were intensive group discussions in the afternoon – three workshops with the following focuses: carbon cycle pathways in future climate scenarios; how to work on the challenge of big data in eco-sciences; and the increasing importance of internal and external communication in scientist’s everyday activities. PhD student and postdocs from all over the world gathered together, shared their knowledge and experiences, and found new friends and collaborators within and beyond EcolChange.

ecolch doc summit Voore 2019 nov

Participants (all pics by Aurele Toussaint)

The Centre of Excellence EcolChange involves research groups from the Estonian University of Life Sciences and University of Tartu. The conference was supported by the EU Regional Development Fund through the Center of Excellence EcolChange and the ASTRA project.



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EcolChange seminar – Colin Averill about forest fungi and the future of the Earth

Seminars of Department of Botany and Centre of Excellence EcolChange

Speaker: Dr. Colin Averill is a Senior Scientist at ETH Zürich, Switzerland, where he studies how the soil microbiome affects forest carbon sequestration and forest community ecology.

Title of the talk: Forests and Their Fungi: Mycorrhizal Symbiosis and the Future of Earth

Time: Monday, 11. November 2019 at 12.00

Place: Tartu, Lai 40-218 (Vaga auditorium)

Forest fungi and the past of Earth (pic from here)


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EcolChange seminar – Jiska van Dijk about human-wildlife conflicts

Seminars of Department of Botany and Centre of Excellence EcolChange

Speaker: Jiska Joanneke Van Dijk is a researcher in NINA – Norwegian Institute for Nature Research

Title of the talk: Human-wildlife conflicts or human-human conflicts – what’s in the name?

Time: Wednesday, 30. October 2019 at 14.15

Place: Tartu, Lai 40-218 (Vaga auditorium)

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EcolChange PhD Conference 2019 “EcolChange in World of Synergies”

Our Center of Excellence will have it´s annual conference in Voore puhkekeskus entitled: “EcolChange in World of Synergies“. It will also have several workshops. (link to conference home page). Registration is open until the end of October (link to registration).


Conference Day:  November 12th, 2019

General Aim and Outcome

The conference highlights the Centre of Excellence EcolChange activities of 2018/2019. In addition, all participants are kindly invited to stipulate enthusiastic contribution in the further development of Centre of Excellence EcolChange. Hereby, actively sharing their knowledge and experiences, and discussing cross-disciplined ideas in EcolChange relevant, specified topics during selected workshops is the key of success. Underlining the importance of Estonian Centre of Excellence EcolChange it will become a great chance to widen our research scope and meet domestic partners for future collaborations.

Target Audience

Primarily PhD students and junior scientists (incl. Post-docs) plus supervisors and other experienced scientists from EcolChange Centre of Excellence.

In addition: limited number of external PhD Students, junior scientists, and interested specialists/experts.

Program overview:

09:30 Welcome coffee

09:45 – 10:00 Welcome and introduction

10:00 – 10:30 Facts and figures of EcolChange 2019 Ülo Niinemets

10:30 – 12:00 Research Group Activities – Group Highlights 2019

Workshop preparation: grouping and gathering in workshop areas

12:00 – 13:00 Lunch Break

13:00 – 16:00 Workshop Session (parallel workshop subjects)

Individual Coffee break

16:00 – 17:30 Workshop Outcomes to all audience (prepared by each workshop group)

Wrap up, socialising, light dinner


Biogeochemistry Cycling in Ecosystems

“To Grow or To Adapt? Carbon Cycling Under Stress”

AIM We will look at different carbon cycling pathways in terms of different future climate scenario, to understand plant’s role under global change. Hereby, we brainstorm with junior scientists from different EcolChange fields on possible ways to cope with the future biotic and abiotic stress challenge in the context of plant management (identify or cultivate more adaptive species, more cutting-edge study on specialized metabolites).

OUTCOME We will briefly put together plant carbon cycling pathways under stress and conclude the possible ways of dealing with various stress in terms of plant management.

Communicating Science/EcolChange/Global Change to Society

“Communicating EcolChange – by who and to whom”

AIM We want to openly discuss a sample scheme of science communication – should it be organised or is it enough letting people do it on their own initiative? Should we follow the model of action groups to communicate as much as possible about everything, or do we have to be careful, whereas, what is too careful then?

OUTCOME Showing importance and preparing sensitivity, we will highlight relevant aspects of our open discussion briefly to the overall audience.

Open Data / Open Science

“Open Science – from state supported projects to piracy”

AIM Open Science is aimed to make research more accessible, which is accomplished through free distribution of publications, raw data, software, data production procedures and even physical samples. The implementation of Open Science principles makes research more efficient, visible and transparent, increases reproducibility, stimulates collaboration and, therefore, benefits the society as a whole. In the workshop we will take a look on several successful applications that are heavily based on Open Data, and will discuss problems that emerge in the transition between “Closed” and Open Science.

OUTCOME We will outline Open Science principles and supply them with with real-life examples, and briefly discuss benefits and challenges that come along with Open Science advance.

Big Data

“Handling Big Data in Eco Sciences”

AIM Ecology, together with many other sciences, has entered the world of big data as a result of rapid growth in data volumes worldwide. Growing amounts of data from remote sensing, automated sensor networks, global community data resources or citizen-science initiatives create exciting opportunities as well as many challenges related to data management and analyses. In this workshop, we explore these new opportunities and challenges, and look for the common approaches that may be useful in several branches of EcolChange.

OUTCOME Brief take-home messages about big data storage, management and analyzing solutions shall be provided to overall audience by workshop attendants.


“Centre of Excellence EcolChange Mid-Terms – Critical Review from Student’s perspective”

AIM Centre of Excellence EcolChange is now almost in its project mid-terms, worth to internally critically review. This session aims to become an open discussion forum rather a workshop about past, present and future of EcolChange from a student’s perspective. Sample questions that may be addressed: how PhD student were, are, or would like to be involved in further development of EcolChange. What are pros and cons of being part of EcolChange ? How see PhD students EcolChange benefits and what might become improved in the future?

OUTCOME At the end, it is intended to share generalised impressions with the overall audience.

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EcolChange seminar – Alexandre Fruleux about belowground interactions in the forests

Seminars of Department of Botany and Centre of Excellence EcolChange

Speaker: Alexandre Fruleux is Post-doctoral researcher at Department of Botany, Tartu University in the team of adaptive ecology of agricultural landscapes (led by Dr. Jaan Liira).

Title of the talk: Belowground interspecific interactions in European temperate forests

Time: Thursday, 17. October 2019 at 14.15

Place: Tartu, Lai 40-218 (Vaga auditorium)

Summary: The aim of this work was to study the belowground processes in order to better understand (a) the higher aerial growth of European beech (Fagus sylvatica) in mixed stands, relative to pure ones and (b) the successful invasion of American black cherry (Prunus serotina) in Europe. One key result is the report of ectomycorrhizae in invasive populations of P. serotina and its potential ecological implications.

No black flowers for black cherry… (pic from here)


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EcolChange seminar – Enn Lust about hydrogen infra and fuel cells

Seminars of Department of Botany and Centre of Excellence EcolChange

Speaker: Enn Lust is professor and head of chair of physical chemistry at the Institute of Chemistry, University of Tartu, member of Estonian Academy of Sciences and head of Centre of Excellence „Advanced materials and high-technology devices for energy recuperation systems“.

Title of the talk: Development of hydrogen infrastructure and fuel cells/electrolysers for sustainable energetics

Time: Thursday, 10. October 2019 at 14.15

Place: Tartu, Lai 40-218 (Vaga auditorium)

Summary: The talk will analyse recent progress in development of hydrogen infrastructure in the world-leading regions such as USA, Japan, European Union, Korea Republic, Canada. Examples of high-energy efficiency electrochemical power sources (supercapacitors, fuel cells, Na-ion batteries and solid oxide devices) for sustainable energy generation/storage complexes powered by wind and solar cells will be discussed.

Image may contain: 2 people, indoor

Enn Lust (left) with the former president of Estonia, Toomas H. Ilves (pic from Facebook)

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New publication – Are stomata in ferns and allies sluggish? Stomatal responses to CO2, humidity and light and their scaling with size and density

Text by Liisa Kübarsepp

Recently our lab published a new paper in New Phytologist on the stomatal reactions of ferns and allies. In this paper, we question the overall sluggishness that is assumed of evolutionarily older plants, and study thoroughly the reactions of many fern species both from physiological, morphological and evolutionary perspective.

Stomata – microscopic pores on the leaf surface – are highly significant in the functioning of a plant. Stomatal pores enable gas exchange between the leaf inner structures and the atmosphere, which is otherwise minimal. The epidermal cells covered by a cuticular layer protect the plant from desiccation, pathogens, pollutants etc. however, some gas exchange between the plant and outside environment is crucial. The gradient between water concentrations in the intercellular airspaces inside the leaf and the atmosphere is one of the important factors creating the water flow from the roots to the leaves. Closed stomatal pores also prohibit CO2 from reaching the mesophyll cells – thus inhibiting photosynthesis. The opening and closing of stomatal pores are controlled by stomatal guard cells, which respond to different environmental cues such as light, CO2 concentration, and humidity (both in soil and air). 

Stomatal reactions have been studied thoroughly, however, most studies focus on the model species Arabidopsis thaliana or other angiosperms. More recently other plant species have caught more attention, and it has been demonstrated these reactions can significantly differ even within one genus. Digging even deeper and comparing angiosperms to phylogenetically more distant species, like gymnosperms, ferns or lycophytes, the differences are even more drastic. Some studies have even found no or very slow stomatal responses to factors like CO2 concentration and light in these older plant groups. Therefore, it has long been thought that the stomata of evolutionarily older species, like ferns, are sort of sluggish when it comes to any other environmental factor apart from water deficiency. However, when giving a closer look some studies have shown that it might not be quite that simple. Stomatal reactions of evolutionarily older species are controlled by other mechanisms, not just lack of water, which causes water potential decrease in the plant and thus induces the stomatal closure. 

In our study, we focused on ferns and allies (altogether 29 species), and their stomatal reactions to environmental factors. We compared their reactions also to two angiosperm species, one woody and one herbaceous (Alnus subcordata and Phaseolus vulgaris). In our experiment, we used the same set of species to measure reactions to different environmental stimuli: changes in CO2 concentration, air humidity and light. Most studies only focus on one environmental factor at a time, making it difficult to make generalizations about the stomatal reactions. Indeed, we discovered that the stomatal reactions of ferns and allies are dependent on the environmental conditions, the reactions were fastest in response to low air humidity, and slower in response to CO2 concentration and light. What was also very interesting – in many cases, the stomata of ferns are not sluggish at all, in fact, they are often quite similar to angiosperms. 

One important part of this study is also looking for the explanations behind the stomatal reactions. Why are some stomata reacting faster than others? Mainly we looked at morphology – the size and density of stomata. It appears that in some cases, the reactions of smaller stomata are indeed faster like many studies have previously found. These include reactions to low CO2 concentration, high light intensity and low air humidity. However, this is not universal to all reactions leading to the conclusion that different mechanisms should control the stomatal reactions in ferns – not only passive regulation by water content in the plant as many other studies have stated.

To search for the reasons behind the differences in stomatal reactions we went even further and used the phylogenetic signal analysis to see if perhaps there is a relationship between the phylogenetic distance of species and the differences in stomatal reactions. However, we did not manage to find such relations in our species set for any of the environmental condition changes. This would not necessarily mean that such a correlation could not exist, however, a much broader set of species would be needed to perform such analysis in the future.


To read further see the paper: Kübarsepp, L., Laanisto, L., Niinemets, Ü., Talts, E., & Tosens, T. (2019). Are stomata in ferns and allies sluggish? Stomatal responses to CO2, humidity and light and their scaling with size and density. The New phytologist, https://doi.org/10.1111/nph.16159 (link to full text)


Stomata of Microsorum diversifolium (pics by Liisa Kübarsepp)



Fast stomatal reactions enable plants to successfully cope with constantly changing environment yet there is an ongoing debate on the stomatal regulation mechanisms in basal plant groups.

We measured stomatal morphological parameters in 29 fern and allies species from temperate to tropical biomes and two outgroup angiosperm species. Out of these, stomatal dynamic responses to environmental drivers were measured in 16 ferns and the two angiosperms using gas‐exchange system. PCA analyses were used to further reveal the structure ‐function relationships in stomata.

We show more than 10‐fold variation for stomatal opening delays and 20‐fold variation for stomatal closing delays in ferns. Across species, stomatal responses to VPD were the fastest, while light and [CO2] responses were slower. In most cases the outgroup species’ reaction speeds to changes in environmental variables were similar to those of ferns.

Correlations between stomatal response rate and size were apparent for stomatal opening in light and low [CO2] while not evident for closing reactions and changes in VPD. No correlations between stomatal density and response speed were observed. Altogether, this study demonstrates different mechanisms controlling stomatal reactions in ferns at different environmental stimuli, which should be considered in future studies relating stomatal morphology and function.

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