New publication – How do arbuscular mycorrhizal fungi travel

Text by Guillermo Bueno

Two of the members of the department of Botany (C. Guillermo Bueno and Mari Moora) were invited to write a commentary on a recently published paper in New Phytologist (Correia et al 2019). The paper commented showed the first evidence of co-dispersal of AM fungi and AM plants by birds. The commentary highlights the need for more research on the dispersal mechanisms of this important group of fungi (associated with around 80 % of plant species) and pose interesting lines of future prospect.

Citation: Bueno, C. G., & Moora, M. (2019). How do arbuscular mycorrhizal fungi travel?. New Phytologist, 222(2), 645-647. (link to full text)


About to disperse mycorrhiza. Though, not AM, but EcM… (pic from here)


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EcolChange seminar – Guillermo Bueno about plant mycorrhizal traits

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

Speaker: Guillermo Bueno is research fellow at the Plant Ecology Laboratory, Department of Botany, Tartu University. He explores how biotic interactions shape plant communities.

Title of the talk: Plant mycorrhizal traits: from concepts to applications

Time: Thursday, 25. April 2018 at 15.15

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

Summary: Applying trait-based frameworks to fundamental biotic interactions has the potential to unveil their patterns and processes at multiple spatial scales, ultimately defining their relevance and dynamics. Among plant biotic interactions, mycorrhizal symbiosis is an association between plant roots and soil fungi, present in around 80 % of the plants, and expected to be essential for plant species survival and distribution. I will present work on plant mycorrhizal traits, from concepts to applications, highlighting the limitations and challenges to categorize and measure these relevant traits in mycorrhizal ecology and biogeography.


The left one is the one with mycorrhiza, of course (pic 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 – Are biotic as relevant as abiotic factors to determine the functional and phylogenetic diversity of communities at a biome scale?

Text by Guillermo Bueno

Taking as a reference the distribution of herbivores in the Arctic, James Speed with the contribution of 22 researchers of the herbivory network (including Guillermo Bueno from the Botany department of the UT) have tried to answer this question. Similar to large-scale diversity patterns, functional and phylogenetic diversities are commonly assumed to be driven by abiotic factors (i.e. climate), while few efforts have attempted to analyze whether biotic factors (i.e. trophic interactions) can have a role in large (functional and/or phylogenetic) diversity patterns. Here we estimated the functional diversity, considering herbivore traits including diet, digestive system type, group and body size, wintering strategy, mobility, habitat, population dynamics and litter size, and phylogenetic diversity through building an Arctic herbivore phylogeny using nucleotide sequences accessed from GenBank. We tested whether the spatial pattern of both diversities is driven by abiotic: climate severity (f.e. winter temperatures) and landscape heterogeneity, or biotic (trophic; predator diversity or vegetation productivity). In addition, we calculated the functional convergence (which is the functional similarity among species after taking into account their relatedness). Functional convergence will happen if a large functional diversity occurs within a group of closely related species (low phylogenetic diversity) and functional divergence in the opposite situation, when low functional diversity is not much clustered in the phylogeny. Convergence can indicate that the trait evolution has had certain constrains. In fact, our results showed that the assemblages of herbivores were functionally convergent in some parts of the Arctic, like Victoria Island and Subarctic Quebec region (see bottom figure), possibly indicating some weak environmental limitations. Overall, we found a predominant role of biotic interactions, both predators (top-down) and vegetation productivity (bottom-up) to herbivore functional and phylogenetic diversity, which along with winter temperature are driving the spatial patterns of functional and phylogenetic diversity (see figure below). These results highlight the need to consider biotic interactions at larger scales and under current changes in winter climate.

guillermo april2019

Figure including at the top – Hypothetical pairings of Arctic herbivores demonstrating high and low levels of functional (browsers and grazers) and phylogenetic diversity (Aves and Artiodactyla) and functional divergence to convergence (ratio of functional diversity to phylogenetic diversity); and at the bottom, the standardised effect sizes of phylogenetic and functional diversity and functional convergence (full details can be found in the paper

Citation: Speed, J. D., Skjelbred, I. Å., Barrio, I. C., Martin, M. D., Berteaux, D., Bueno, C. G., … & Grytnes, J. A. (2019). Trophic interactions and abiotic factors drive functional and phylogenetic structure of vertebrate herbivore communities across the Arctic tundra biome. Ecography, (link to full text)


Communities are assembled from species that evolve or colonise a given geographic region, and persist in the face of abiotic conditions and interactions with other species. The evolutionary and colonisation histories of communities are characterised by phylogenetic diversity, while functional diversity is indicative of abiotic and biotic conditions. The relationship between functional and phylogenetic diversity infers whether species functional traits are divergent (differing between related species) or convergent (similar among distantly related species). Biotic interactions and abiotic conditions are known to influence macroecological patterns in species richness, but how functional and phylogenetic diversity of guilds vary with biotic factors, and the relative importance of biotic drivers in relation to geographic and abiotic drivers is unknown. In this study, we test whether geographic, abiotic or biotic factors drive biome‐scale spatial patterns of functional and phylogenetic diversity and functional convergence in vertebrate herbivores across the Arctic tundra biome. We found that functional and phylogenetic diversity both peaked in the Western North American Arctic, and that spatial patterns in both were best predicted by trophic interactions, namely vegetation productivity and predator diversity, as well as climatic severity. Our results show that both bottom‐up and top‐down trophic interactions, as well as winter temperatures, drive functional and phylogenetic structure of Arctic vertebrate herbivore assemblages.. This has implications for changing Arctic ecosystems; under future warming and northward movement of predators potential increases in phylogenetic and functional diversity in vertebrate herbivores may occur. Our study thus demonstrates that trophic interactions can determine large‐scale functional and phylogenetic diversity just as strongly as abiotic conditions.

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EcolChange seminar – John Clarke about fish macroevolutionary dynamics

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

Speaker: John Clarke is research fellow at the chair of entomology, Department of Zoology, Tartu University. He explores evolution, including diversification, using fishes as model systems.

Title of the talk: Polyploidy, historical expectations and habitat shifts: revealing macroevolutionary dynamics underpinning half of vertebrate diversity

Time: Thursday, 11. April 2018 at 15.15

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

Summary: Why are some groups extremely diverse in morphology, while other groups vary little in morphology? To address this fundamental question, I use actinopterygian fishes (~33000 species today) as a model system, testing classic expectations regarding their morphological evolution through time, ranging from genome duplication to the role of habitat type.


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EcolChange seminar – Anne Kull about the role of religion in studying nature

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

Speaker: Anne Kull, she explores relationships between science and religion. She is based at the School of Theology and Religious Studies of the Faculty of Arts and Humanities of Tartu University.

Title of the talk: Struggling over Nature

Time: Thursday, 4. April 2018 at 15.15

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


Pic from here


Nature stands at the very centre of an intense struggle today. We witness it in passionate controversy over basic questions. People often turn to religions to add weight to their opinions and strategies.

Lynn White, Jr., in his very influential essay in Science „The Historical Roots of our Ecologic Crisis“ (1967) claimed that due to „orthodox Christian arrogance toward nature,“ Christianity „bears a huge burden of guilt“ for the contemporary environmental crisis. There had been other critics long before, e.g., Ludwig Feuerbach, etc. Is traditional Christian thought about nature ecologically bankrupt? And anyway, what is the role of the idea of nature in our understandings of technology, theology, God, laws of nature, etc? While we are near consensus that nature is not a script from which we can read off values and meanings, there are also good reasons to insist that nature and sciences (rather than inherited philosophies and theologies), should serve as baseline for our thinking. If our perennial traditions have the same status as poetry – how does one bring poetry to bear on scientific knowledge? And, do we know what we are talking about, when we talk about Christian understanding of nature?


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EcolChange seminar – Piibe Piirma and Taavi Suisalu about mixing art and science

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

Speakers: Piibe Piirma and Taavi Suisalu are artists, with interests in interfaces between art and science. (link to their joint Maalabor page)

Titles of the talks: I Hybrid Practice. Art and Science in Artistic Research // II Art and Science: flirt, data fiction and poetic encounters

Time: Thursday, 28. March 2018 at 15.15

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

Summary: I Our cultural symbolism has vastly expanded thanks to science and interdisciplinary approaches to research that are continually increasing in popularity. Due to science, we can think of a person as a fragment of the universe continuing to exist and succeed in this vast entity. I will talk about collaboration between scientists and artists, focusing on my artistic practice and doctoral dissertation titled HYBRID PRACTICE. Art and Science in Artistic Research (Estonian Academy of Arts, 2015).

II In the constellation of art and science collaborations, interdisciplinary and hybrid practices, we experience a wide range of approaches, ranging from speculative research and data visualization to poetic narratives and absurd flirts. In this presentation I will introduce a varied spectrum of art projects fascinated by scientific research, methods or mindset, highlighting the broad nature of possible encounters.


Mushroom hacking at Maalabor (pic from Maalabor FB page)

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 – Ozone and Wounding Stresses Differently Alter the Temporal Variation in Formylated Phloroglucinols in Eucalyptus globulus Leaves

Text by Bin Liu

Eucalyptus globulus Labill. is a fast growing tree species with great economic and ecological values. In addition, the existence of wide range of foliar terpenoids and phenolics makes E. globulus an ideal reference plant for the study of specialized metabolites in plants. Our previous colleague Arooran Kanagendran and the team led by Prof. Ülo Niinemets have elaborately investigated the temporal response of terpenoids in E. globulus foliage upon ozone and wounding stresses (see also Kanagendran et al. 2018a, b). As an extension of previous study, in collaboration with colleagues from University of Copenhagen, we continued to dig out more about the other group of special phenolic metabolites, formylated phloroglucinol compounds (FPCs) in E. globulus foliage subjected to ozone and wounding stresses.

FPCs are a group of specialized metabolites consisting of a phloroglucinol-based derivative often attached with mono- or sesquiterpene moiety such as macrocarpals and euglobals. In fact, for the last two decades, much studies have been focusing on FPCs, particularly for elucidating chemical structures of novel FPCs, discovering pharmaceutical values, and elaborating herbivore deterring properties. However, the potential role of FPCs in plant resistance to environmental stresses has poorly been studied and that has motivated us to carry out the current study on exploring temporal variation in formylated phloroglucinols in E. globulus leaves in response to ozone and wounding stresses. In this study, we detected two groups of FPCs, macrocarpals and sideroxylonals in E. globulus leaf extracts, using a state-of-the art analytical instrument UHPLC-DAD-ESI-Q-TOF-MS/MS. The results indicated that there are differential and temporal regulations of different types of macrocarpals and sideroxylonals observed under separate and combined ozone and wounding treatments.

Moreover, considering the special chemical structure of FPCs, the pathway involved in in vivo synthesis of FPC would be deactivated to channel the enhanced biosynthesis of both terpenoids and phenolics, particularly upon stresses. Surprisingly, we explored that there were negative correlations between terpenoid emissions and FPC concentrations, which shed light on the first hint that competitions might exist for the biosynthesis of FPCs and terpenoids. Further studies investigating the temporal variation of FPCs in E. globulus upon different abiotic stresses and in different Eucalyptus species such as Eucalyptus nitens are highly warranted.

Citation: Liu, B., Marques dos Santos, B., Kanagendran, A., Neilson, E. H. J., & Niinemets, Ü. (2019). Ozone and Wounding Stresses Differently Alter the Temporal Variation in Formylated Phloroglucinols in Eucalyptus globulus Leaves. Metabolites, 9(3), 46. (link to full text)


You can heal your wounds with eucalypts, or you can wound eucalypts to see how they heal… (pic from Amazon)


Formylated phloroglucinol compounds (FPCs) are a class of plant specialized metabolite present in the Myrtaceae family, especially in the genus Eucalyptus. FPCs are widely investigated due to their herbivore deterrence properties and various bioactivities of pharmaceutical relevance. Despite the increasing number of studies elucidating new FPCs structures and bioactivity, little is known about the role of those compounds in planta, and the effects of environmental stresses on FPC concentration. Ozone (O3) and wounding are key stress factors regularly confronted by plants. In this study, we investigated how O3, wounding, and their combination affected individual and total FPC foliar concentration of the economically important species Eucalyptus globulus. Six individual FPCs, including five macrocarpals and one sideroxylonal, showed different response patterns to the single and combined stresses. Total macrocarpals only increased under single O3 treatment, whereas total sideroxylonals only increased in response to wounding treatment, suggesting different physiological roles played by the two groups of FPCs predominantly existing in E. globulus foliage. Total FPCs increased significantly under individual wounding and O3 treatments but not under the combined treatment. A principal component analysis indicated that all different treatments had unique FPC fingerprints. Total phenolic contents increased in all O3 and wounding treatments, and a marginally positive correlation was found between total FPCs and total phenolic contents. We suggest that, depending on the concentration and composition, FPCs play multiple physiological roles in planta, including serving as antioxidants to scavenge the reactive oxygen species brought about by O3 and wounding stresses.


Kanagendran, A., Pazouki, L., & Niinemets, Ü. (2018a). Differential regulation of volatile emission from Eucalyptus globulus leaves upon single and combined ozone and wounding treatments through recovery and relationships with ozone uptake. Environmental and experimental botany145, 21-38.
Kanagendran, A., Pazouki, L., Bichele, R., Külheim, C., & Niinemets, Ü. (2018b). Temporal regulation of terpene synthase gene expression in Eucalyptus globulus leaves upon ozone and wounding stresses: relationships with stomatal ozone uptake and emission responses. Environmental and experimental botany155, 552-565.
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EcolChange seminar – Veljo Kisand about aDNA perspective in paleoecoloy

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

Speaker: Dr. Veljo Kisand is senior researcher at the Institute of Technology of Tartu University.

Title of the talk: Paleoecology: an aDNA prespective

Time: Thursday, 14. March 2018 at 15.15

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


the alphabet of DNA (pic from here)


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EcolChange seminar – Andras Zlinszky about LIDAR mapping of habitats, biodiversity and ecosystem services

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

Speaker: Dr. Andras Zlinszky is reasearcher at the Center for Ecological Research of the Hungarian Academy of Sciences. He is visiting Department of Botany for scientific collaboration with Aveliina Helm.

Title of the talk: Airborne LIDAR for mapping habitat conservation status, biodiversity and ecosystem services

Time: Thursday, 7. March 2018 at 15.15

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

Summary: Airborne LIDAR delivers 3D models of the landscape and is available across all Estonia. We present case studies of using LIDAR for ecosystem assessment at various scales. These include Natura 2000 habitat conservation status mapping in an alkali grassland, wetland vegetation ecosystem service potential assessment and nationwide species richness prediction with high resolution.


LIDAR map (pic from here)

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New publication – Anatomical constraints to nonstomatal diffusion conductance and photosynthesis in lycophytes and bryophytes

Text by Kristiina Mark

Bryophytes – polyphyletic group consisting liverworts, hornworts and mosses – and lycophytes (also known as ‘fern allies’) are considered the earliest living relatives to ancient land plants that first migrated from aquatic environment to land. Both, bryophytes and lycophytes, are known for their simple structure, reproduction by spores, and tendency to prefer moist and shady environment. Being the second largest group of land plants (topped only by angiosperms), bryophytes contribute substantially to primary productivity in high latitude ecosystems where conditions for vascular plants are unsuitable.

Photosynthesis is the key process in primary metabolism and is often limited by CO2 concentration at carboxylation sites in chloroplast, which is determined by CO2 diffusion through plant tissues. Bryophytes and lycophytes show low photosynthetic capacity compared to vascular plants, however, contribution of specific constraining factors remained unexamined. Global collaborative study between seven research institutes from six countries (Spain, Australia, Chile, Estonia, USA, Indonesia) hypothesized that bryophyte and lycophyte lower rate of photosynthesis is largely due to constrained CO2 diffusion through photosynthetic tissues, specifically, limited by nonstomatal diffusion conductance (gnsd).

Research concluded that low photosynthesis rate in bryophytes and lycophytes is indeed related to their specific anatomical characteristics, especially their very thick cell walls and low chloroplast exposure to intercellular air spaces. Photosynthesis in mosses was mostly limited by gnsd and in lycophytes co-limited by gnsd and leaf photochemistry. These results support the suggested phylogenetic trend towards increasing photosynthesis and link to increasing stomatal and mesophyll/nonstomatal conductance.

kristiina samblad kaart

Study sites of the species included in this study (Fig 1 from the study)

Citation: Carriquí, M., Roig-Oliver, M., Brodribb, T. J., Coopman, R., Gill, W., Mark, K., Niinemets, Ü., Perera-Castro, A. V., Ribas-Carbó, M., Sack, L., Tosens, T., Waite, M., & Flexas, J. (2019). Anatomical constraints to non-stomatal diffusion conductance and photosynthesis in lycophytes and bryophytes. New Phytologist, (link to full text)



Photosynthesis in bryophytes and lycophytes has received less attention than terrestrial plant groups. In particular, few studies have addressed the non-stomatal diffusion conductance to CO2 (gnsd) of these plant groups. Their lower photosynthetic rate per leaf mass area at any given nitrogen concentration as compared to vascular plants suggested a stronger limitation by CO2 diffusion. We hypothesized that bryophyte and lycophyte photosynthesis is largely limited by low gnsd. Here we studied CO2 diffusion inside the photosynthetic tissues and its relationships with photosynthesis and anatomical parameters in bryophyte and lycophyte species in Antarctica, Australia, Estonia, Hawaii and Spain. On average, lycophytes and, specially, bryophytes had the lowest photosynthetic rates and non-stomatal diffusion conductance reported for terrestrial plants. These low values are related to their very thick cell walls and their low exposure of chloroplasts to cell perimeter. We conclude that the reason why bryophytes lie at the lower end of the leaf economics spectrum is their strong non-stomatal diffusion conductance limitation to photosynthesis, which is driven by their specific anatomical characteristics.

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