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, (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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EcolChange seminar – Adam Frew about how arbuscular mycorrhizal fungi impact belowground herbivores

Seminars of Department of Botany and Centre of Excellence EcolChange

Autumn is here. Which means seminars are back as well. The apples in Tartu have became extra sweet from night frost. And together with majority of life, mycorrhiza is winterizing. We´ll talk about them while they sleep…

Speaker: Adam Frew is Post-doctoral researcher at Charles Sturt University, Wagga Wagga, Australia. He studies interactions between plants, herbivores and soil microbiota. He is visiting Department of Botany, Tartu University in order to collaborate with the Plant Ecology Laboratory.

Title of the talk: How do arbuscular mycorrhizal fungi impact belowground herbivores?

Time: Thursday, 03. October 2019 at 14.15

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

Summary: Almost all terrestrial plants are attacked by one, if not many, species of invertebrate herbivore. Most of these plants associate with arbuscular mycorrhizal (AM) fungi. Despite our increasing understanding of these tripartite interactions involving aboveground herbivores, we know less about the impacts of AM fungi on root-feeders. Here I will present results from a combination of experiments investigating these belowground interactions.

Panel 1: Pirates of Hawaii – C. elegans lab variant, N2, was originally isolated in Bristol from a pineapple. This is a cartoon on how the polymorphic variant of N2, the Hawaiian strain, tries to conquer N2’s use as the common lab strain.
Panel 2: Game of worms: Tyrion Lannister is depicted by the fat and stout mutant in C. elegans called Dumpy. E. coli strain, OP50, is compared to Tryrion’s wine because C. elegans feeds on OP50 as much as Tyrion Lannister on his wine.
Panel 3: Mite wars: One major, eternal threat to C. elegans is posed by Mites! Here, mites are compared to dark forces/Sith army while worms are compared to the Jedi army. Fungi are also a source of contamination to C. elegans. Hence, fungi are shown as allies of the dark forces.
Panel 4: The usual suspects: The most common mutants used in C. elegans community – the wildtype (N2), the dumpy (dpy), the long (lon) and the uncoordinated (unc). (picture together with the legend from here)

After the seminar everyone is welcome to coffee/tea and snacks in the seminar room (coffee room, ground floor).
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New publication – Arbuscular mycorrhizal fungal community composition determines the competitive response of two grassland forbs

Anyone can name at least a couple of factors affecting plant growth, be it climate (drought, flooding, hail) or the presence of organisms feeding on plants (birds, insects, mammals, or plant diseases). Some might even think of the nutrients found in soil without which plants cannot grow. But few are probably aware that in addition to nutrients, there are microscopic fungi living in soil that are essential for plants. Furthermore, these fungi may be highly significant in determining the structure of plant communities.

Scientists from the Department of Botany at the University of Tartu Institute of Ecology and Earth Sciences recently published a study in the international journal PLOS ONE that found the microscopic Glomeromycota to have an important role in the development of plant community diversity.

For years, plant ecologists have been interested in the mechanisms influencing plant coexistence and diversity, and the importance of microorganisms is becoming ever clearer. The roots of many plants form arbuscular mycorrhizas (AM) with the microscopic Glomeromycota living in soil.

Glomeromycota are considered to be the oldest organisms living in symbiosis with terrestrial plants. They are widespread in ecosystems and an estimated 74% of plant species are arbuscular mycorrhizal.

The fungus obtains organic carbon from the plant via AM, and in turn, the fungus helps the plant obtain minerals and water from the soil. By dividing nutrients between plant species, Glomeromycota can determine plant-plant interactions by benefiting some plants and inhibiting the life of others.

Even though the influence of Glomeromycota in the competition between plants has already been studied for decades, most of the experiments have been conducted in laboratories using easily culturable fungi, which unfortunately represent only a small portion of the natural diversity of Glomeromycota. However, it is important to know that the communities of Glomeromycota vary in time and space, and therefore, the communities from different ecosystems may have different effects on plant growth.

As it is difficult to conduct experimental studies in nature, scientists from the UT Department of Botany studied the influence of natural Glomeromycota communities on plant-plant competition in a greenhouse growing two plant species – narrowleaf plantain (Plantago lanceolata) and rough hawkbit (Leontodon hispidus) – alone and with a competitor, the red fescue (Festuca rubra).

To avoid the influence of other microscopic soil organisms on plant growth, the plants were grown in sterilised soil to which scientists added Glomeromycota communities gathered from a calcareous grassland and a 60-year-old pine forest. In addition, plants were also grown in a soil without any symbiotic Glomeromycota, therefore, these plants were unable to form a mycorrhiza with the Glomeromycota.

Microscopic study of plant roots confirmed the formation of mycorrhiza but also showed that, in competitive conditions, Glomeromycota have a positive effect on plant growth – plants that formed the mycorrhiza had better competitive responses than non-mycorrhizal plants.

Furthermore, grassland and pine forest Glomeromycota communities had a different effect on plant growth. A species-rich grassland fungal community enhanced the competitive response of plants more (plants grew larger) than the species-poorer pine forest fungal community. The positive influence of the grassland Glomeromycota community was clearest with the narrowleaf plantain, which prefers to grow on grasslands. However, the competitive response of the rough hawkbit growing in grasslands as well as forests was not significantly influenced by the origin of the fungi.

Therefore, the great diversity of Western Estonian calcareous grasslands may be attributed to the microscopic fungi in the soil, as these fungi unify the competitiveness of many plant species in conditions where plants are competing for the same nutrients so individual species cannot dominate.

The results show that the origin of Glomeromycota communities is an important influencer of plant growth and competitive interactions. Knowing the role of Glomeromycota in plant-plant interactions might enable more accurate predictions about the development of plant communities, their diversity, sensitivity, resistance to disturbances, and to apply this knowledge in nature conservation, for example.


Citation: Neuenkamp, L., Zobel, M., Lind, E., Gerz, M., & Moora, M. (2019). Arbuscular mycorrhizal fungal community composition determines the competitive response of two grassland forbs. PloS one, 14(7), e0219527. (link to full text)


Lena Neuenkamp in lab (pic from Novaator)


We performed a greenhouse experiment to assess how differences in AM fungal community composition affect competitive response of grassland plant species. We used a full factorial design to determine how inoculation with natural AM fungal communities from different habitats in Western Estonia affects the growth response of two grassland forbs (Leontodon hispidus L., Plantago lanceolata L.) to competition with a dominant grass (Festuca rubra L.). We used AM fungal inocula that were known to differ in AM fungal diversity and composition: more diverse AM fungal communities from open grasslands and less diverse AM fungal communities from former grassland densely overgrown by pines (young pine forest). The presence of AM fungi balanced competition between forb and grass species, by enhancing competitive response of the forbs. The magnitude of this effect was dependent on forb species identity and on the origin of the AM fungal inoculum in the soil. The grassland inoculum enhanced the competitive response of the forb species more effectively than the forest inoculum, but inoculum-specific competitive responses varied according to the habitat preference of the forb species. Our findings provide evidence that composition and diversity of natural AM fungal communities, as well as co-adaptation of plant hosts and AM-fungal communities to local habitat conditions, can determine plant-plant interactions and thus ultimately influence plant community structure in nature.

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EcolChange seminar – Chun-Neng Wang about how pollinatiors affect plant flower color

Seminars of Department of Botany, Doctoral School of Earth Sciences and Ecology and Centre of Excellence EcolChange

Speaker: Chun-Neng Wang is associate Professor at Institute of Ecology and Evolutionary Biology of National Taiwan University, Taiwan. He studies plant development from genetic and evolutionary aspects. He is visiting Tartu University under the framework of Erasmus+ program.

Title of the talk: Over-dispersion of flower colour assembly due to possible competitions for pollinators in alpine community of Taiwan

Time: Thursday, 6. June 2019 at 15.15

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

Summary: Taiwan is a subtropical island yet mountains extending to 3900 m high with temperate origin species relic in alpine areas.  Alpine community species tend to be more divergent in floral color than expected by chance. Our analysis revealed that over-dispersion of floral color is probably driven by competitive exclusion for limited pollinators in alpine.

Current political climate changes (pic from here)

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EcolChange seminar – Jeanalle Eck about microbes that shape plant disease and diversity

Seminars of Department of Botany, Doctoral School of Earth Sciences and Ecology and Centre of Excellence EcolChange

Speaker: Jenalle Eck is post-doctoral researcher at the University of Zürich, Switzerland. She studies plant population and community ecology, with special emphasis on plant-microbial interactions. Jenalle is visiting Department of Botany for collaboration with Plant Ecology Laboratory.

Title of the talk: Genotype-specific microbes shape plant disease and diversity: from Panama to Plantago

Time: Thursday, 16. May 2019 at 15.15

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

Summary: Genotype is important in mediating interactions between plants and microbes, and genotype-specific interactions can create complex eco-evolutionary dynamics in plant populations and communities. In this talk, I describe insights on this topic from research in two study systems, the tropical forests of Panama and the temperate grasslands of Finland.


Diseases might shape bacteria too… (pic from here)


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