Workgroup and EcolChange seminar – Valentina Zolotarjova about nitrogen dynamics in crops

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

Valentina Zolotarjova is a junior researcher and PhD-student in the Estonian University of Life Sciences.

Title of the talk: Nitrogen change in agricultural plants during growth stages

Time: Monday, 29. April 2019 at 14.00

Place: Tartu, Kreutzwaldi 5 – D143 (Metsamaja)


Cartoon appearing as an advertisement for nitrogen fertilizer from the Spencer Chemical Company of Kansas City, Missouri, in the July 15, 1950, issue of Nebraska Farmer. (pic from here)


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Spring is coming!

The snow has finally ​melted, and our lab people (Evi, Steffen and Valentina) participated in running season opening with 7 km distance! (Results can be found here.)


Valentina and Steffen (pic by Evi)

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Workgroup and EcolChange seminar – Merili Toom & Keyvan Esmaeilzadeh Salestani about crop selection

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

Merili Toom and Keyvan Esmaeilzadeh Salestani are PhD students in the Estonian University of Life Sciences.

Titles of the talks: “Selecting winter cover crop species for Estonian conditions” & “Impact of Farming Systems on Barley Nutrient Use Efficiency

Time: Monday, 8. April 2019 at 14.00

Place: Tartu, Kreutzwaldi 5 – D143 (Aquarium Room in Metsamaja)


Crop field in Canada (pic from here)


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New member – welcome Hanna!

Text by Hanna Hõrak, gif by Pille Meilson


I am Hanna Hõrak, I started as a postdoctoral researcher in Ülo Niinemets’ lab in the Estonian University of Life Sciences in the beginning of the year. I got my first lab experiences as a second-year student in Tanel Tenson’s lab in the Institute of Technology in the University of Tartu. I studied the mechanisms of translational regulation in the popular model bacterium Escherichia coli and acquired many useful skills in molecular biology under the supervision of Ülar Allas. I carried out my Masters’ project in the same institute, but with a different subject – I studied the role of the protein ERD15 in stomatal regulation in the widely used model plant Arabidopsis thaliana in Hannes Kollist’s lab.

I fell in love with stomata (here are some of monocots, just look at them!) and stayed on for nearly seven years to complete a PhD project supervised by Hannes Kollist and Mikael Brosché in the same lab, which (completely different to the original plan, of course) became a part of the group effort to untangle the signalling pathways that control plant stomatal closure in response to elevated CO2 concentrations. We identified the mitogen-activated protein kinases MPK12 and MPK4 as key regulators of stomatal signalling that inhibit the HT1 protein kinase, thus enabling the activation of the guard cell anion channel SLAC1 and consequent CO2-induced stomatal closure. You can have a look at my PhD thesis, proclaimed elegant by the Estonian Academy of Sciences, here. During my PhD studies, I improved my skills in molecular biology and acquired additional expertise in plant genetics, physiology and gas exchange analysis.

After completing my PhD, I carried out a 1.5-year postdoctoral project in the lab of Julie Gray in the University of Sheffield, UK. During this project, I gained a lot of new knowledge about stomatal development and plant-pathogen interactions and learned the new skills of working with the Arabidopsis thaliana-Pseudomonas syringae plant-pathogen interaction model system and using chlorophyll fluorescence analysis for assessing plant disease. I became interested in systemic responses to abiotic and biotic stress factors, in terms of stomatal regulation as well as changes in plant photosynthetic capacities.

Currently I am discovering the exciting world of plant stress responses and related volatile organic compound emissions in the lab of Ülo Niinemets. I aim to bring together my skills in molecular biology and plant physiology, and knowledge of stomatal regulation and plant-pathogen interactions and apply them to better understand the local and systemic responses to bacterial infection in plants. In longer term, I hope to return to my old love, stomata, and the mechanisms that control their behaviour.

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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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New publication – Lichen chemistry is concordant with multilocus gene genealogy in the genus Cetrelia (Parmeliaceae, Ascomycota)

Text by Kristiina Mark

Lichens are symbiotic organisms formed in a mutualistic symbiosis between a terrestial green algae or cyanobacteria and (usually ascomycetous) fungus. Traditionally lichens are named after their fungal partner and thus their classification is based on the fungal counterpart. Likewise to plants, fungi also produce variety of natural products of ecological importance, also called the secondary metabolites. These substances are often used in delimiting taxa when morphological characters are scarce, however, the use of chemical characters in taxonomy is under ongoing debate.

Research investigating the utility of secondary metabolites in molecular taxonomy of lichen genus Cetrelia (Parmeliacea, Ascomycota) revealed clear correlation between lichen chemistry and phylogeny, suggesting to include information from secondary metabolites when identifying taxa in the genus Cetrelia. These organisms produce a constant set of  polyphenolic compounds, specifically orcinol-type depsides and depsidones, with still unknown function. Character state analyses affirmed metabolite evolution in Cetrelia towards more complex substances, which could indicate evolutionary importance of the chemical compounds in species survival or functioning.


Citation: Mark, K., Randlane, T., Thor, G., Hur, J.-S., Obermayer, W. & Saag, A. (2019). Lichen chemistry is concordant with multilocus gene genealogy in the genus Cetrelia (Parmeliaceae, Ascomycota). Fungal Biology 123(2): 125-139, (link to full text)


Fig. 2 from the paper. The three morphotypes in Cetrelia: sorediate (A, B), isidiate and/or lobulate (C, D), and without vegetative propagules (E, F). Scale bars 2.8 mm (A), 1.3 mm (B, C), 6.4 mm (D), 5.4 mm (E), and 6.3 mm (F). Photographed specimens: (A) Cetrelia olivetorum DNA-CKM59, Randlane and Saag, Estonia (TU); (B) C. chicitae DNA-25878, Thor, Japan (UPS, TU); (C) C. braunsiana, Kärnefelt, Russia (LD-1040527); (D) C. orientalis DNA-AT406, Skirina, Russia (LD-1062494); (E) C. alaskana DNA-CKM66, Obermayer, China (GZU); (F) C. sanguinea, Indonesia, Sumatra (TU).


The lichen genus Cetrelia represents a taxonomically interesting case where morphologically almost uniform populations differ considerably from each other chemically. Similar variation is not uncommon among lichenized fungi, but it is disputable whether such populations should be considered entities at the species level. Species boundaries in Cetrelia are traditionally delimited either as solely based on morphology or as combinations of morpho- and chemotypes. A dataset of four nuclear markers (ITS, IGS, Mcm7, RPB1) from 62 specimens, representing ten Cetrelia species, was analysed within Bayesian and maximum likelihood frameworks. Analyses recovered a well-resolved phylogeny where the traditional species generally were monophyletic, with the exception of Cetrelia chicitae and Cetrelia pseudolivetorum. Species delimitation analyses supported the distinction of 15 groups within the studied Cetrelia taxa, dividing three traditionally identified species into some species candidates. Chemotypes, distinguished according to the major medullary substance, clearly correlated with clades recovered within Cetrelia, while samples with the same reproductive mode were dispersed throughout the phylogenetic tree. Consequently, delimiting Cetrelia species based only on reproductive morphology is not supported phylogenetically. Character analyses suggest that chemical characters have been more consistent compared to reproductive mode and indicate that metabolite evolution in Cetrelia towards more complex substances is probable.


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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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