EcolChange seminar – Ave Suija about the (micro)cosmic properties of lichens

Seminar of the Centre of Excellence EcolChange

Ave Suija is researcher at the Department of Botany, University of Tartu.

The Lichen as a Microcosm

Time: Thursday, 27. April 2017 at 15.15

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


Fungal (though not lichen-forming fungal) art by Peeter Laurits (pic from here)


Lichens are increasingly regarded not simply as dual partnerships between fungi and algae, but as a microcosm comprised of diverse assemblages of specific fungal and microbial lineages. I give a brief overview about recent advances and incorporate some examples from my own work.

Posted in Event | Tagged , , , , , | Leave a comment

New paper accepted – Extremely thick cell walls and low mesophyll conductance: welcome to the world of ancient living!

Text and pics by Linda-Liisa Veromann-Jürgenson

I am overjoyed that I have my first article for my PhD accepted! It is now published in Journal of Experimental Botany.

a day in the lab

Linda-Liisa in the lab

As everyone in our group knows, mesophyll conductance is a key player in net assimilation rates in plants, but it’s not too well studied. Recent research, several from this department, has highlighted the importance of mesophyll structure in determining its conductance. Although several papers have been published on the mesophyll conductance of angiosperms and its underlying ultrastructural characteristics, only two studies had been conducted on gymnosperms that consider gas-exchange as well as mesophyll anatomy. We studied evolutionarily old plants including three divisions of gymnosperms, a whisk fern and a clubmoss to understand the role of mesophyll conductance on net assimilation rate as well as the impact of mesophyll anatomy on gas-exchange with an evolutionary perspective. Additionally, we examined the leaf economics spectrum (LES) correlations in these species as gymnosperms have been found to differ significantly from angiosperms in the LES parameters. We got several important results. Firstly, mesophyll conductance is a very important limiter of photosynthesis in gymnosperms and it depends on mesophyll anatomy. Secondly, the cell wall thickness as well as chloroplast area exposed to intercellular airspaces influence mesophyll conductance significantly and in opposite directions. Furthermore, chloroplast shape and size can play an important role in limiting CO2 diffusion in the liquid phase. Thirdly, although anatomy plays a key role, high leaf mass per area did not relate low net assimilation or high cell wall thickness. Interestingly, we measured extremely thick cell walls in several species, which may indicate a preservation of ancient traits through time due to some evolutionary constraints.

Citation: Veromann-Jürgenson, L. L., Tosens, T., Laanisto, L., & Niinemets, Ü. (2017) Extremely thick cell walls and low mesophyll conductance: welcome to the world of ancient living!. Journal of Experimental Botany, DOI: (link to full text)

Psilotum nudum TEM

Psilotum nudum transmission electron microscopy photograph


Mesophyll conductance is thought to be an important photosynthetic limitation in gymnosperms, but they currently constitute the most understudied plant group in regard to the extent to which photosynthesis and intrinsic water use efficiency are limited by mesophyll conductance. A comprehensive analysis of leaf gas exchange, photosynthetic limitations, mesophyll conductance (calculated by three methods previously used for across-species comparisons), and the underlying ultra-anatomical, morphological and chemical traits in 11 gymnosperm species varying in evolutionary history was performed to gain insight into the evolution of structural and physiological controls on photosynthesis at the lower return end of the leaf economics spectrum. Two primitive herbaceous species were included in order to provide greater evolutionary context. Low mesophyll conductance was the main limiting factor of photosynthesis in the majority of species. The strongest sources of limitation were extremely thick mesophyll cell walls, high chloroplast thickness and variation in chloroplast shape and size, and the low exposed surface area of chloroplasts per unit leaf area. In gymnosperms, the negative relationship between net assimilation per mass and leaf mass per area reflected an increased mesophyll cell wall thickness, whereas the easy-to-measure integrative trait of leaf mass per area failed to predict the underlying ultrastructural traits limiting mesophyll conductance.

Posted in New publication | Tagged , , , , , , , , , , , , | Leave a comment

New publications describing a new method to predict species establishment and invasion

Text by Jon Bennett

[This is a repost from Meelis Pärtel´s Macroecology Workgroup blog]

Understanding which species are going to establish within a given community (i.e. invasion) is one of the most fundamental pursuits in ecology. In today’s era of global change, this is especially important given the threat of exotic species to native biodiversity. Many hypotheses have been developed in attempts to answer this question, but two predominate. The first is that newly establishing species need to be similar enough to the species at the site to survive the environmental conditions at that site, but dissimilar enough to avoid strong competition with the resident species for the limited available resources (i.e. Darwin’s naturalization hypothesis). The second hypothesis is largely an extension of the first. It predicts that diverse plant communities should be more resistant to invasion because most of the available resources will already be in use due to the larger number of, presumably functionally distinct, species. However, there are flaws in these hypotheses that limit their applicability.

The first major flaw is that the species found at a given site are not entirely the product of interactions among those species: they are also influenced by the regional processes and environmental filtering which combine to shape the species pool for that site (Fig. 1). These processes also have their own effects on invasion. Sites that can support a greater number of species may also support a greater number of invaders (Fig. 1). Consequently, sites that are more diverse due to a larger species pool may also be more readily invaded, complicating any use of local diversity as an indicator of potential biotic resistance. However, if we make local richness proportional to the size of the species pool using the community completeness index (Fig. 1), we may find a more consistent relationship between diversity and invasion.

bennett fig1

Fig. 1. The multiple filters acting on community assembly and their influence on invasion

Using a large experiment, we tested this hypothesis by adding both native and exotic species to sites distributed throughout southern Estonia (Bennett et al. 2016 Ecology Letters). We found that by accounting for the size of the site-specific species pool and community completeness, we were better able to explain the variation in invasion than by using local richness alone. Interestingly, species pool size was not always a positive indicator of invasion rates. For exotic species, a larger species pool sometimes resulted in greater biotic resistance. A larger species pool may contain a larger number of strong competitors by random chance alone. However, if competition trades off with dispersal abilities, as it sometimes does, then species pools that remain small due to limited dispersal may be less likely to contain any species that can resist the invader.

The previous result highlights the importance of understanding the characteristics of the species in different species pools for predicting invasion. Darwin’s naturalization hypothesis attempts to do so, by comparing the characteristics of the potential invader to the resident community. However, this approach does not consider species pool effects on local diversity. Further, it is based on a flawed premise, as competition is not necessarily strongest between the most similar species. Instead competition will depend on the underlying assembly dynamics within the community. In a recent paper (Bennett and Pärtel 2017 Ecology and Evolution), we developed a new method that models environmental and biotic filtering by comparing species across multiple components of the regional species list (Fig. 2).

bennett fig2

Fig. 2. The comparisons used to model community assembly

We measure the similarity among species within the site-specific pool relative to the similarity between the site-specific pool and the remainder of the regional species list to model environmental filtering. Similarly, we compare local diversity to the species from the site-specific species pool that are currently absent (dark diversity) to model biotic filtering. Using these models, and the similarity between the invader and these two components of diversity, we can then predict which invaders should establish (Fig. 3). When we tested the method using data from experiments that added seed to Estonian grasslands, we were able to predict approximately 50% of establishment from seed – a very impressive result. This result was based on only native species, but we are working to test the model using exotic species as well.

bennett fig3

Fig. 3. A graphical reprentation of the method predicting inasion by modelling community assembly

These two papers provide strong evidence that species pools need to be considered when trying to understand and predict invasion. Further, they also indicate a strong need to re-evaluate many of the hypotheses in invasion biology in the light of current knowledge on community assembly.


Bennett, J. A., Riibak, K., Kook, E., Reier, Ü., Tamme, R., Guillermo Bueno, C., & Pärtel, M. (2016). Species pools, community completeness and invasion: disentangling diversity effects on the establishment of native and alien species. Ecology Letters, 19(12), 1496-1505. (link to full text)
Bennett, J. A., & Pärtel, M. (2017). Predicting species establishment using absent species and functional neighborhoods. Ecology and Evolution, DOI: 10.1002/ece3.2804. (link to full text)
Posted in New publication | Tagged , , , , , , , , , , , , , | Leave a comment

EcolChange seminar – Tsipe Aavik about the landscape genetics of plants

Seminar of the Centre of Excellence EcolChange

Tsipe Aavik is researcher in macroecology workgroup at the Department of Botany, University of Tartu.

Landscape genetics of plants: examples from semi-natural grasslands

Time: Thursday, 20. April 2017 at 15.15

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


The general scheme of how to do landscape genetics in plants (pic from this paper)


Landscape genetics is a field, which combines landscape ecology and population genetics. Using plants in semi-natural grasslands as an example, I will provide an overview about how landscape genetics can be used for tracking the dispersal and gene flow of plants. I will also briefly discuss, how landscape genetics can be applied for examining adaptive genetic diversity of plants.

Posted in Event | Tagged , , , , , , , | Leave a comment

New publication – Plant mycorrhizal status, but not type, shifts with latitude and elevation in Europe

Text by Guillermo Bueno

Understanding the distribution of plant mycorrhizal traits of the European flora should guide us to keep understanding and to expand our curiosity about the ecological roles and distribution of the mycorrhizal symbioses in plant communities. For instance, knowing that the proportion of AM plant species decreases at higher latitudes, may support previous hypotheses about AM symbioses claiming to be inefficient in cold conditions. As well, knowing that obligately mycorrhizal plants are poorly distributed in higher latitudes but not so poorly distributed at higher elevations and lower latitudes, open the hypothesis about the effect of glaciation on the distribution of plant mycorrhizal traits. Guillermo Bueno within the research group of Martin Zobel and Mari Moora, and with several collaborators from the University of Tartu, as well as with Prof. Ingolf Kühn (Helmholtz-Centre for Environmental Research, Halle, Germany) present in essence the first attempt to analyze the distribution of plant mycorrhizal traits at the European level.

Citation: Bueno, C. G., Moora, M., Gerz, M., Davison, J., Öpik, M., Pärtel, M., Helm, A., Ronk, A. Kühn, I. & Zobel, M. (2017). Plant mycorrhizal status, but not type, shifts with latitude and elevation in Europe. Global Ecology and Biogeography. (link to full text)


Latitudinal trends of plant mycorrhizal types on the left, and the distribution of the proportions of obligately mycorrhizal plant species in Europe on the right



Identifying the factors that drive large-scale patterns of biotic interaction is fundamental for understanding how communities respond to changing environmental conditions. Mycorrhizal symbiosis is a key interaction between fungi and most vascular plants. Whether plants are obligately (OM) or facultatively (FM) mycorrhizal, and which mycorrhizal type they form – arbuscular mycorrhizal (AM), ectomycorrhizal (ECM), ericoid mycorrhizal (ERM) or non-mycorrhizal (NM) – can have strong implications for plant species distribution at the continental scale and on the responses of plants to environmental gradients.


Europe, north of 43° latitude and excluding Russia, Belarus and Moldova.


Using published sources, we compiled the most complete dataset yet of plant mycorrhizal and geographical information for Europe, comprising 1442 plant species. We mapped the European distributions of plant mycorrhizal status (OM and FM) and type (AM, ECM, ERM and NM) and analysed their relationships with climatic, edaphic and plant productivity drivers on a 50 km × 50 km equal-area grid.


The distribution of mycorrhizal types in Europe was driven by mean temperature, soil pH and productivity. AM plant species predominated throughout the region, but at higher latitudes the share of NM and, to a lesser extent, ECM and ERM species increased. FM species predominated over OM species, and this increased with latitude and was dependent on temperature drivers. The high share of OM species in the central European mountains indicates a possible influence of historical glacial refugia.

Main conclusions

Our results challenge the prevailing view of parallel trends in the latitudinal and elevational distribution of mycorrhizal types and demonstrate distinctive responses of plants with different mycorrhizal status to climatic, edaphic and biogeographical drivers at the European scale.

Posted in New publication | Tagged , , , , , , , , , | Leave a comment

New publication – Predicting species establishment using absent species and functional neighborhoods

Text by Meelis Pärtel and Jonathan Bennett

Understanding which species establish in which habitats is fundamental to community ecology and to more applied pursuits, such as the restoration of degraded sites and the prevention of invasion by exotic species. Jonathan Bennett and Meelis Pärtel from macroecology workgroup of the University of Tartu developed a method that compares the characteristics of species across the regional species list, the site-specific species pool and locally observed species to predict which other species will be able to establish. As part of this method, we developed a new way to measure dissimilarity among species which we call functional neighborhood distances. Using this method in Estonian grasslands, we were able to predict approximately 50% of species establishment from seed, indicating that the new method may be a robust means to predict establishment and potentially invasion.

Citation: Bennett, J. A., & Pärtel, M. (2017). Predicting species establishment using absent species and functional neighborhoods. Ecology and Evolution, DOI: 10.1002/ece3.2804 (link to full text)

bennett ja pärtel

FIG 2 from the paper: A hypothetical example showing how different functional distance measures may affect our interpretation of establishment probabilities. Panel (a) shows the distribution of species in functional space, where gray circles represent biotically excluded species and white circles species present in the community. The letters A and B represent two potential colonists. Both species are similarly distant from their nearest neighbor (b). As species A is closer to the mean trait value for the observed community than species B, species B has a higher mean distance to species within the community than A (c). Using the mean distance to species within the functional neighborhood (dashed circles), there is little difference between species A and B (d)

Species establishment within a community depends on their interactions with the local environment and resident community. Such environmental and biotic filtering is frequently inferred from functional trait and phylogenetic patterns within communities; these patterns may also predict which additional species can establish. However, differentiating between environmental and biotic filtering can be challenging, which may complicate establishment predictions. Creating a habitat-specific species pool by identifying which absent species within the region can establish in the focal habitat allows us to isolate biotic filtering by modeling dissimilarity between the observed and biotically excluded species able to pass environmental filters. Similarly, modeling the dissimilarity between the habitat-specific species pool and the environmentally excluded species within the region can isolate local environmental filters. Combined, these models identify potentially successful phenotypes and why certain phenotypes were unsuccessful. Here, we present a framework that uses the functional dissimilarity among these groups in logistic models to predict establishment of additional species. This approach can use multivariate trait distances and phylogenetic information, but is most powerful when using individual traits and their interactions. It also requires an appropriate distance-based dissimilarity measure, yet the two most commonly used indices, nearest neighbor (one species) and mean pairwise (all species) distances, may inaccurately predict establishment. By iteratively increasing the number of species used to measure dissimilarity, a functional neighborhood can be chosen that maximizes the detection of underlying trait patterns. We tested this framework using two seed addition experiments in calcareous grasslands. Although the functional neighborhood size that best fits the community’s trait structure depended on the type of filtering considered, selecting these functional neighborhood sizes allowed our framework to predict up to 50% of the variation in actual establishment from seed. These results indicate that the proposed framework may be a powerful tool for studying and predicting species establishment.
Posted in New publication | Tagged , , , , , , , , , | Leave a comment

EcolChange seminar – Ülo Mander about the consequences of man-made changes to nitrogen cyclon

Seminar of the Centre of Excellence EcolChange

Ülo Mander is professor at the Department of Geography, University of Tartu.

Man-made alterations of nitrogen cycling: global and regional consequences

Time: Thursday, 16. March 2017 at 15.15

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


Ülo Mander with couple of manuscripts (pic from here)


During the last 70 years, the reactive nitrogen cycling in the biosphere has been significantly intensifying. Globally, about a half of this cycling is caused by anthropogenic activities. Among several environmental consequences, nitrate contamination of water bodies and groundwater, as well as increasing emission of nitrous oxide (N2O), the dangerous greenhouse gas and the main ozone layer depletion agent, can be highlighted. In this presentation results from three projects will be presented: (1) the global effect of peatland drainage on nitrogen cycling, especially focusing on relations between the N2O emissions and controlling environmental and microbiological factors (denitrification genes); (2) nitrogen budget dynamics in full-drained peatland forests in Estonia; (3) mitigation of nitrate contamination of intensively managed agricultural catchments using artificial wetlands (the French experience).

Posted in Event | Tagged , , , , , , , , | Leave a comment

New paper published – Arbuscular mycorrhizal fungal communities in forest plant roots are simultaneously shaped by host characteristics and canopy-mediated light availability

Text by Kadri Koorem

Recent years have been ground-breaking in describing the diversity patterns of arbuscular mycorrhizal (AM) fungi. These microscopic fungi live in plant roots and receive carbon compounds from the plant in exchange of nutrients. In natural conditions, one plant individual can harbour more than ten taxa of AM fungi. Interestingly, AM fungal communities in the roots of plants in same habitat can be remarkably different. However, we have little information what determines the composition of AM fungi in plant roots and with this study we aimed to contribute to filling this gap.

In the presence of forest canopy, shade-avoidant plant species have been shown to harbour less diverse AM fungal community in their roots than shade-tolerant plant species. We hypothesized that this due to carbon deficiency and in the absence of forest canopy, shade-avoidant plant species can increase their photosynthetic capacity and become associated to more diverse AM fungal community, similarly to shade-tolerant plants. We sampled shade-tolerant and shade-avoidant plant species in the presence and absence of forest canopy. In all plant individuals, we recorded photosynthetic capacity and the composition of AM fungal communities in their roots.

Results of this study indicated that all, but especially shade-avoidant plants have higher photosynthetic capacity in the absence of forest canopy. AM fungal communities, associated to shade-avoidant and shade-tolerant species remained distinctive under the canopy and indeed become more similar in the absence of forest canopy. Interestingly the change in the AM fungal communities was bigger in the roots of shade-tolerant plants, which experienced smaller increase in photosynthetic capacity. Thus it seems that host plant characteristics as well as environment influence AM fungal communities in plant roots but the mechanisms need to be examined further.

Citation: Koorem, K., Tulva, I., Davison, J., Jairus, T., Öpik, M., Vasar, M., Zobel, M, & Moora, M. (2017). Arbuscular mycorrhizal fungal communities in forest plant roots are simultaneously shaped by host characteristics and canopy-mediated light availability. Plant and Soil, 410(1-2), 259-271. (link to full text)


Kadri explaining some research-related stuff (pic from here)


Background and Aims The majority of terrestrial plant species associate with arbuscular mycorrhizal (AM) fungi, to exchange carbon compounds with nutrients. However, the factors that determine the composition of AM fungal communities in individual plant roots remain poorly understood. We hypothesized that AM fungal communities are simultaneously influenced by environmental conditions, such as light availability, and the photosynthetic capacity of host plant species.

Methods We sampled individuals of shade-tolerant and shade-avoidant plant species, growing in the presence and absence of forest canopy, representing conditions of low and high light availability. We recorded photosynthetic parameters, shoot biomass and root AM fungal colonisation of these plant individuals and used 454-sequencing to characterise AM fungal communities in the roots of these plants.

Results Shade-avoidant plant species increased their photosynthetic capacity more than shade-tolerant plant species as a response to increased light availability due to canopy removal. Root AM fungal colonisation of all plants was higher when the forest canopy was absent, but canopy status had little influence on AM fungal richness in plant roots. The composition of AM fungal communities associating with shade-tolerant plants was significantly influenced by canopy status, while a less pronounced difference was observed among shade-avoidant plants.

Conclusions We suggest that both environmental conditions and the ability of plant species to exploit available resources determine the dynamics of mutualistic associations between host plant species and AM fungal taxa.

Posted in New publication | Tagged , , , , , , , , , , , , , , , | Leave a comment

EcolChange seminar – Carlos Carmona on trait probability densities

Seminar of the Centre of Excellence EcolChange

Carlos P. Carmona is researcher at the macroecology workgroup of the Department of Botany, University of Tartu.

Trait probability densities: probabilistic hypervolumes in ecology and beyond

Time: Thursday, 9nd. March 2017 at 15.15

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


Somehow all the niche memes out there are of Eltonian nature…


Hutchinson’s idea of niches as multidimensional hypervolumes has long inspired ecologists. However, practical use of hypervolumes has not been feasible until recent times, when advances in computational resources and data availability are allowing to estimate them. In particular, functional-trait based ecologists have been attempting to incorporate this appealing concept for more than a decade. In this seminar, I will present an overview of existing hypervolume-based methods to estimate the functional niche of species, along with their respective strengths and weaknesses. I will then show how the adoption of a probabilistic-based idea of the niche can serve to build a unified framework that allows estimating any aspect of functional diversity at all scales while also considering the role of intraspecific variability. Finally, I will provide some examples of practical uses of this framework in a purely ecological context as well as in other fields.

Posted in Event | Tagged , , , , , , | Leave a comment

Congratulations – Martin Zobel 60!

Text by Lauri Laanisto

A week ago, academician, and the professor of Plant ecology in the University of Tartu, and also one the team leaders in EcolChange, Martin Zobel, celebrated his 60th birthday. All the best wishes to him!

Incidentally, his seminal paper about species pool: “The relative of species pools in determining plant species richness: an alternative explanation of species coexistence?” (link to full text) was published in TREE exactly 20 years ago. So, back then he was 40. It´s his most cited first author paper, which to this day gets nearly 50 new citations annually.

And on a personal note – this text is the most influencial for me. It has more or less set the ground rules to what and how I have been studying stuff. Thanks!


i don´t know for sure but that picture of MZ is probably taken around late 1990s


Posted in Other news | Tagged , , , | Leave a comment