Two EcolChange seminars this week with three presenters – Prinzing/Santonja/Young

Seminar of Department of Botany and Centre of Excellence EcolChange

This week we have not one, but two EcolChange seminars:

First, on Tuesday, 23. May  2017 at 15.15 in Tartu, Lai 40-218 (Vaga auditorium)

Andreas Prinzing will do a presentation “Do good neighbors compensate for bad climate?”

And Mathieu Santonja will talk about “Plant diversity mitigates the negative effects of climate change, via soil biota and litter decomposition”


Andreas Prinzing is Professor at the University of Rennes 1, France.

Do good neighbors compensate for bad climate?


Evolutionary proximate neighborhoods reduce vulnerability of seedlings to climatic stress and soil fungi mediate this effect

Climate is changing and is becoming warmer and drier in large part of Europe. As a result, tree species such as oaks (Quercus petraea) are at a risk of strong decline. The classic strategy of foresters is to introduce genotypes coming from warmer or drier provenances and likely being adapted to warm and dry climates. However, this strategy results in the loss of local genotypes and it does not account for non-climatic constraints, such as biotic interactions – the impact of tree neighbors or natural enemies. We focus here on oaks (Quercus petraea) and their most vulnerable stage, seedlings. We studied germination, survival, growth and budburst of seedlings within a natural mosaic of soil microclimates and manipulated the biotic neighborhood: the distance of seeds / seedlings to adult oaks, the species identity of these oaks, the evolutionary distance of the ambient canopy, the density of seeds / seedlings and the presence of pathogenic fungi. The results suggest that germination and first year growth show particularly strong relationships to neighborhood, environment and their interaction. Specifically, seedlings develop better in moist soils and under an evolutionarily proximate canopy and such a canopy in addition reduces the negative impact of dry soils. Overall, the impact of climate change on regeneration of this major forest tree-species might be mitigated by changing the evolutionary neighborhood in which the regeneration takes place.


Quercus petraea forest (pic from here)

Mathieu Santonja is Teaching and Research Assistant at the University of Rennes 1, France.

Plant diversity mitigates the negative effects of climate change, via soil biota and litter decomposition


We tested how plant community diversity and climate change (through decreased precipitation) impacts soil biota and litter decomposition in two Mediterranean ecosystems: a shrubland dominated by Quercus coccifera and a forest dominated by Quercus pubescens.

In the shrubland, multi-species litter showed higher microbial abundance, lower bacterial diversity and higher fungal diversity compared to single-species litter. C and N release increased with increasing litter species richness. Drier conditions increased microbial diversity, reduced net N release from litter and led to higher and more frequent synergistic effects on C release. The results suggests that shifts in plant community composition may have stronger impacts on litter decomposition and nutrient cycling than relatively subtle changes in precipitation.

In the forest, drier conditions affected decomposers negatively, directly by reducing fungal biomass and detritivorous mesofauna, and also indirectly by increasing the predation pressure on detritivorous mesofauna by predatory mesofauna. Increased drought strongly decreased decomposition but the presence of several plant species in the litter mitigated this effect. Hence, faster decomposition in diverse litter mixtures might compensate slower decomposition under drier condition in this ecosystem.


Bacterial stamp – 9th Microbiology Congress in Moscow in 1966 (pic from here)

And then, on Thursday, 25. May  2017 at 15.15 in Tartu, Lai 40-218 (Vaga auditorium

J. Peter W. Young will do a talk about “Do bacteria have species?”

J. Peter W. Young is professor emeritus at York University, UK. He is a guest of Doctoral School of Earth Sciences and Ecology and in addition to the seminar he will hold round-table discussion with PhD students and early career scientists: Thursday May 25th, 10.30 in Lai 40 coffee room



We classify all organisms into species, but bacteriologists have always done it a little differently.  In the past two decades, we have acquired major new insights into bacterial genomes, diversity and evolution, and I believe it is time to rethink the species concept as applied to bacteria.  On the one hand, bacteria have species equivalent to the species of sexual eukaryotes, defined by recombination and barriers to recombination.  On the other hand, the dynamic nature of the bacterial accessory gene pool leads to high genetic and phenotypic diversity among members of the same species.   We can define species in a consistent and stable way, but the species name will not tell us all we need to know about a bacterium.  We also need a list of its most relevant accessory gene modules.  This has important implications for current attempts to describe the diversity of bacterial communities, as well as for our understanding of pathogens and their evolution.  I will illustrate these ideas with our own evidence from rhizobia, the symbiotic nitrogen-fixing bacteria.

Kumar N, Lad G, Giuntini E, Kaye ME, Udomwong P, Shamsani NJ, Young JPW, Bailly X (2015) Bacterial genospecies that are not ecologically coherent: population genomics of Rhizobium leguminosarum. Open Biology, 5: 140133. doi: 10.1098/rsob.140133

Remigi P, Zhu J, Young JPW, Masson-Boivin C (2016) Symbiosis within symbiosis: evolving nitrogen-fixing legume symbionts. Trends in Microbiology 24: 63-75 doi:10.1016/j.tim.2015.10.007


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Taavi Paal defended his PhD thesis: congratulations!

Text by Lauri Laanisto

Author: Taavi Paal

Title: Immigration limitation of forest plants into wooded landscape corridors

Supervisor: Dr Jaan Liira, University of Tartu, Estonia

Dissertation was accepted for the commencement of the degree of Doctor
philosophiae in plant ecology and ecophysiology at the University of Tartu on
March 6, 2017 by the Scientific Council of the Institute of Ecology and Earth
Sciences, University of Tartu.

Opponent: Prof. Lander Baeten, Ghent University, Belgium

Commencement: Council hall of the University of Tartu, 18 Ülikooli Street,
Tartu, on 10 May 2017 at 10.15 a.m.

Full text of the thesis can be found here.

Thesis is based on following publications:

Liira, J. & Paal, T. (2013) Do forest-dwelling plant species disperse along
landscape corridors? Plant Ecology 214:455–470. (link to full text)

Paal, T., Kütt, L., Lõhmus, K. & Liira, J. (2017) Both spatiotemporal
connectivity and habitat quality limit the immigration of forest plants into
wooded corridors. Plant Ecology 218:417–431. (link to full text) (link to blog post)

Lõhmus, K., Paal, T. & Liira, J. (2014) Long-term colonization ecology of
forest-dwelling species in a fragmented rural landscape – dispersal versus
establishment. Ecology and Evolution 4(15):3113–3126. (link to full text)

Paal, T., Zobel, K. & Liira, J. Plant traits indicate that various ecological
filters limit forest species use of wooded green corridors. Manuscript.


Taavi on stage (though, not defending the thesis…) (pic from here)


Large-scale agricultural and sylvicultural activities have led to the fragmentation and isolation of both ancient and recent forests in landscape. In afforested areas, the formation of forest-specific vegetation is impeded by the inhospitable surrounding agricultural matrix and by poor dispersal ability of many forest plants. Landscape corridors are proposed as a means to increase the connectivity between species source and target habitats, therein wooded corridors should enhance the dispersal of forest-specific species. The aim of this thesis was to evaluate the functionality of wooded landscape corridors as dispersal enhancing landscape elements for forest plants of deciduous forests. The results of this thesis indicate that wooded corridors in their present state do not perform well as dispersal enhancing structures for specialist forest plants. Even in well-connected corridors, most of forest specialists colonised only the first 5–10 m of the corridor, and only very few species could migrate to isolated corridors. Mainly those forest plants are successful that utilise long-distance dispersal vectors, such as mammals or birds, and those that can tolerate habitat edge mediated conditions dominating in corridors. Positive signals of the use of corridors by forest-dwelling plants were mostly created by shade tolerant generalist species. Analysis results showed that forest species can be supported only by wide corridors that are directly connected to ancient (source) forest, and those that have structures reducing edge effects. Such structures are formed in corridors with a double line of mature trees (e.g. old alleys) that have wide-arching canopies and lateral side branches. Landscape planning and conservation management of rural landscapes should target first on existing wooded corridors before planting new tree lines, as the formation of suitable habitat conditions takes decades or centuries.

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EcolChange seminar – Alar Rosentau about sea-level changes and coastal settlements in Baltics

Seminar of the Centre of Excellence EcolChange + Seminar of Department of Botany and Doctoral School of Earth Sciences and Ecology

Alar Rosentau is senior researcher at the Department of Geology, Tartu University.

Title of the talk: Sea-level change and early coastal settlements in Eastern Baltic

Time: Thursday, 18. May 2017 at 15.15

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


Depiction of Stone Age settlement in our region (pic from here)


Results of the interdisciplinary research which combines palaeo sea-level and Stone Age settlement data from the Narva-Luga area in Eastern Baltic will be presented during the seminar. The oldest traces of human activity in Narva-Luga dated to 8.5–7.9 cal. ka BP are associated with the palaeo-Narva River in the period of low water level in the Baltic basin at the beginning of the Litorina Sea transgression. The coastal settlement associated with the Litorina Sea lagoon, presently represented by 33 Stone Age sites, developed in the area c. 7.1 cal. ka BP and existed there for more than 2000 years. Transformation from the coastal settlement back to the river settlement indicates a change from a fishing-and-hunting economy to farming and animal husbandry c. 4.4 cal. ka BP

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New paper published – Dispersal limitation determines large-scale dark diversity in Central and Northern Europe

Text by Kersti Riibak

The inability of many plant species to disperse to environmentally suitable sites after the Last Glacial Maximum limits plant diversity within Europe. Dispersal may also limit species occupancy of potentially suitable sites within their distribution ranges, resulting in a large proportion of species being absent from those sites (i.e. these sites have high dark diversity). Dark diversity has already been mapped at the European scale (see Ronk et al. 2015 and a blog post), however, in our recent study (Riibak et al. 2017, Journal of Biogeography) we take a step further to explore the ecological mechanisms determining large-scale dark diversity.

We used vegetation data on ca. 10 x 10 km grid cells across seven regions in Central and Northern Europe to compare dispersal-related traits of observed and dark diversity. Our results show that poor dispersal ability (i.e. low seed production and short dispersal distance) restricts largely species dispersal to potentially suitable sites in Europe (Fig. 1). However, dispersal limitation decreased with increasing human population size and agricultural land use, showing that human activities have helped to disperse many plant species in Europe.


Fig.1. The log-ratio of seed production (upper graph) and potential dispersal distance (lower graph) between observed and dark diversity. Positive values indicate that absent plant species produce fewer seeds and have shorter potential dispersal distance than observed species (i.e. dispersal limited sites). Different lower case letters in the graph indicate significant differences between study areas.

Our results also indicate that the importance of dispersal limitation decreases either with strong abiotic stress or biotic resistance by resident vegetation. This means that in very stressful conditions, biodiversity is rather restricted by the establishment of poorly adapted species than dispersal. If the global change will be accompanied by warmer and moister conditions at high latitudes, dispersal limitation may become more dominant in the sparsely human inhabited regions of Northern Europe.

Citation: Riibak, K., Ronk, A., Kattge, J., Pärtel, M. (2017) Dispersal limitation determines large-scale dark diversity in Central and Northern Europe. Journal of Biogeography, doi: 10.1111/jbi.13000 (link to full text)



The square means of dispersal (pic from here)



Previous studies indicate that many plant species present in a surrounding region are absent from potentially suitable sites (i.e. they constitute dark diversity). However, quantitative analyses are lacking where and why dispersal limitation occurs within species occurrence range at the continental scale. We test if species characteristics related to dispersal limitation, that is, low seed production and short potential dispersal distance, affect the formation of dark diversity at large spatial scales. In addition, we explore how the levels of dispersal limitation are affected by climate, landscape heterogeneity and anthropogenic activity.


Seven study areas in Central and Northern Europe – Iceland, Finland, Estonia, the British Isles, the Netherlands, Germany and Switzerland.


We used data on vascular plant species occurrences in ca. 10 × 10 km grid cells from each study area. To estimate dark diversity for each grid cell, we applied geographical, biogeographical and environmental filters. Seed production was estimated directly (number of seeds per ramet), and indirectly from seed mass. We used several plant traits in combination (e.g. dispersal syndrome and seed characteristics) to estimate potential dispersal distance of seeds.


Species contributing to dark diversity produced generally fewer seeds and had shorter potential dispersal distances than observed species. Dispersal limitation tended to decrease with increasing environmental stress, human population density and agricultural land use.

Main conclusions

Many species are absent from potentially suitable sites in Central and Northern Europe because of dispersal limitation, induced by low seed production and short potential dispersal distances. However, strong abiotic stress, biotic resistance and human activities have reduced the importance of dispersal limitation. This knowledge can be considered in the predictions of how changes in climate and land use affect biodiversity in the future.

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EcolChange seminar – Lander Baeten about long-term changes of forest biodiversity

Seminar of the Centre of Excellence EcolChange + Seminar of Department of Botany and Doctoral School of Earth Sciences and Ecology

Lander Baeten is professor at the Department of Forest and Water Management, Ghent University, Belgium. He visits Department of Botany as opponent of PhD defence of Taavi Paal on May 10th at 10.15 in the Senate hall (Ülikooli 18).

Title of the talk: Plant biodiversity change in the Anthropocene – the value of multiple-site community resurvey data

Time: Thursday, 11. May 2017 at 16.15

Place: Tartu, Ülikooli street 17


Global biodiversity is in decline, but this crisis does not necessarily filter down to the local scale. Indeed, globally distributed data sets have shown that increases and decreases in plant diversity can be equally likely. But even if the net diversity change is zero, this does not imply communities don’t change over time. However, we often lack appropriate data to study the potentially dramatic shifts in composition, especially over decadal time scales. This is where ‘legacy data’ come in. Resurveys of historical vegetation records provide invaluable information to study biodiversity dynamics, especially if multiple data sets are combined to cover broad gradients in climate and other drivers of change. I will discuss the opportunities and challenges related to such data and illustrate this with the forestREplot initiative, a database of forest understorey resurvey studies.

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New paper published – Genetic consequences of landscape change for rare endemic plants–A case study of Rhinanthus osiliensis

Text by Tsipe Aavik

Saaremaa yellow rattle (Rhinanthus osiliensis) is the only endemic species of the island of Saaremaa, Estonia. This rare insect-pollinated plant prefers to grow in calcareous spring fens, which are naturally relatively rare and have largely disappeared due to severe land use change during the last century. These changes included extensive drainage of wetlands and consequent overgrowth of former fens with trees and bushes. Such landscape changes may have serious impact on the persistence of species growing in these habitats. For example, habitat loss is often accompanied by reduced population size, which has detrimental effects on the genetic diversity of plant populations. This, in turn, reduces the fitness of plants. Furthermore, at landscape scale, populations become isolated and are separated by hostile habitats, which may jeopardize the exchange of genes via pollen and seed flow between these populations. Lack of gene flow may further contribute to the extinction vortex of species endangered by habitat fragmentation.

We examined the effects of current landscape composition and landscape change during the last century on the genetic diversity of the endemic R. osiliensis. The study revealed that all examined populations of this rare species have recently experienced a severe bottleneck, i.e. a strong decline in population size. Furthermore, most populations suffered from high levels of inbreeding. These findings most likely reflect the consequences of the loss of the preferred habitats of R. osiliensis. We also found that a higher proportion of forests surrounding the populations caused a notable decrease in the genetic diversity within these populations.

Our study demonstrated that, most likely because of habitat fragmentation, rare species, such as the endemic R. osiliensis, are facing serious genetic consequences. To effectively organize the management of species endangered by fragmentation, it is important to keep in mind that in addition to the area and connectivity of suitable habitats, dispersal and pollen flow between populations is largely affected by the characteristics of the landscape matrix between suitable habitats.

Citation: Aavik, T., Talve, T., Thetloff, M., Uuemaa, E., Oja, T. (2017) Genetic consequences of landscape change for rare endemic plants – A case study of Rhinanthus osiliensis. Biological Conservation 210: 125-135. (link to full text)


Rhinanthus osiliensis (pic from here)


During the last hundred years European landscapes have experienced an extensive change in structure including a substantial loss of wetland habitats. In the current study we examined the influence of landscape change and current landscape composition on the genetic diversity of Rhinanthus osiliensis, a very rare endemic plant with narrow distribution range restricted to calcareous spring and species-rich fens in western part of the island of Saaremaa, Estonia. We observed very high inbreeding in some study populations of R. osiliensis. Furthermore, bottleneck analysis revealed that in fact all examined populations had experienced a severe decline in population size in the recent past. This result indicates that the high levels of inbreeding in R. osiliensis are not only the consequence of the mixed mating system common in this species, but may at least partly be attributed to habitat loss. Indeed, the analysis of landscape change revealed a substantial decrease in the area of mires during the last century in all study landscapes. Unexpectedly, current habitat availability did not influence the measures of genetic diversity. Nevertheless, the allelic richness of R. osiliensis was negatively affected by the amount of forests, which may have acted as a barrier for pollen flow in this insect-pollinated plant. We conclude that the populations of habitat-specialist rare plants such as R. osiliensis are endangered not only by the loss of habitats but also by other changes in landscape composition, e.g. afforestation, leading to strong declines in population size accompanied by genetic bottlenecks, decreased genetic diversity and high inbreeding



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New paper published – Despite admixing two closely related Carex species differ in their regional morphological differentiation

Text and pics by Lisanna Schmidt

Researchers from Estonia and Switzerland studied regional morphological differentiation of two closely related hybridising (and “taxonomically difficult”) species – Carex flava and Carex viridula. We asked whether due to genetic admixing of the two species within regions, variation between species within regions may be small and variation within species between regions similar between the two. Alternatively, as one of the studied species, C. flava, is more common and the other, C. viridula, has more of a patchy distribution and smaller populations, regional differentiation could be more pronounced in C. viridula.

lisanna flava

Carex flava

We show that, despite their admixing, the two closely related Carex species differ in their regional morphological differentiation, which was less pronounced in the more common species. The study implies that understanding morphological variation of hybridising species requires addressing variation for large geographic areas.

In addition, our study clarifies the morphological differences between the two species, which are considered as notoriously difficult to distinguish.

Citation: Schmidt, L., Fischer, M., Schmid, B., & Oja, T. Despite admixing two closely related Carex species differ in their regional morphological differentiation. Plant Systematics and Evolution, DOI 10.1007/s00606-017-1420-0 (link to full text)

lisanna viridula

Carex viridula


Rarer species are expected to show stronger geographic differentiation than more common species. However, if rare species hybridize with common species, differentiation may be quite similar between the two due to genetic admixing via backcrossing. We studied morphological differentiation of plants of 21 natural populations of the more common Carex flava, 16 of the less common Carex viridula and 6 of their hybrids from 27 sites in three climatically different regions, Estonia, Lowland Switzerland and Highland Switzerland. Univariate ANOVA and multivariate principal component analysis of 14 morphological characters, describing both vegetative and reproductive characters, allowed to clearly distinguish C. flava from C. viridula. Carex viridula populations showed stronger regional variation than C. flava. Hybrids had both intermediate and transgressive characters in Switzerland and Estonia. On average, hybrids from Lowland Switzerland were more similar to Swiss C. flava than to C. viridula, while hybrids from Estonia were morphologically intermediate between plants of Estonian populations of the parental species. The results suggest that within-region genetic admixing between species has limited potential to lead to region-specific similarity between species, at least in our model system of the C. flava complex. We conclude that C. flava and C. viridula are clearly distinct species and that, despite hybridization, geographic differentiation is more pronounced in the less common C. viridula than in C. flava.

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New paper published – Disproportionate photosynthetic decline and inverse relationship between constitutive and induced volatile emissions upon feeding of Quercus robur leaves by large larvae of gypsy moth (Lymantria dispar)

Text by Lauri Laanisto

Another paper by Ülo´s former postdoc Lucian, who does a lot of small experiments, where they measure all sorts of factors that could affect organic volatile emissions in plants. This time the focus is on the interplay between an oak and a moth. The topic is actually pretty interesting, or more precisely – it is something that we need to study. Climate change and the loss of ecosystem services like pest control (whether due to climate change or not) will change the invertebrate herbivore dynamics on plants in forseeable future. How significantly will it change the things, especially on small scale. So far we have very little idea about that. And this study tries to take the first steps in this direction.

As a remark I have to say that studying gypsy moth feels very-very Romanian thing to do;) I´m sure that soon the common name will be changed (like blackboys in Australia are now known as grasstrees etc). Maybe the Romani representatives have not yet had time to deal with such racial taxonomy…

Citation: Copolovici, L., Pag, A., Kännaste, A., Bodescu, A., Tomescu, D., Copolovici, D., … & Niinemets, Ü. (2017). Disproportionate photosynthetic decline and inverse relationship between constitutive and induced volatile emissions upon feeding of Quercus robur leaves by large larvae of gypsy moth (Lymantria dispar). Environmental and Experimental Botany, 138: 184–192. (link to full text)


Progressive spread of the gypsy moth (L. dispar) across north east US from 1900–2007; compiled from county data by US Forest Service (pic from here)


Gypsy moth (Lymantria dispar L., Lymantriinae) is a major pest of pedunculate oak (Quercus robur) forests in Europe, but how its infections scale with foliage physiological characteristics, in particular with photosynthesis rates and emissions of volatile organic compounds has not been studied. Differently from the majority of insect herbivores, large larvae of L. dispar rapidly consume leaf area, and can also bite through tough tissues, including secondary and primary leaf veins. Given the rapid and devastating feeding responses, we hypothesized that infection of Q. robur leaves by L. dispar leads to disproportionate scaling of leaf photosynthesis and constitutive isoprene emissions with damaged leaf area, and to less prominent enhancements of induced volatile release. Leaves with 0% (control) to 50% of leaf area removed by larvae were studied. Across this range of infection severity, all physiological characteristics were quantitatively correlated with the degree of damage, but all these traits changed disproportionately with the degree of damage. The net assimilation rate was reduced by almost 10-fold and constitutive isoprene emissions by more than 7-fold, whereas the emissions of green leaf volatiles, monoterpenes, methyl salicylate and the homoterpene (3E)-4,8-dimethy-1,3,7-nonatriene scaled negatively and almost linearly with net assimilation rate through damage treatments. This study demonstrates that feeding by large insect herbivores disproportionately alters photosynthetic rate and constitutive isoprene emissions. Furthermore, the leaves have a surprisingly large capacity for enhancement of induced emissions even when foliage photosynthetic function is severely impaired.

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EcolChange seminar – Francis M. Martin about mycorrhiza

Seminar of the Centre of Excellence EcolChange

Francis M. Martin is head of Cluster of Excellence ARBRE at INRA-Lorraine in Nancy, France; as a guest of doctoral school, F.M.Martin will also hold two discussion groups for PhD students and early career scientists:

Title of the talk: Unearthing the roots of mycorrhizal symbioses

Time: Thursday, 4. May 2017 at 15.15

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


F. M. Martin (pic from here)


The ability of fungi to form mycorrhizas with plants is one of the most remarkable and enduring adaptations to life on land. The establishment of the mycorrhizal mutualistic lifestyle represented a critical stage in the history of land plants. Molecular phylogenetics and phylogenomics are revolutionising our understanding of plant-microbe interactions and the development of timetrees (calibrated phylogenies) linked with the growing understanding of fungal genomes provide remarkable insights into the origins of key interactions between plants and mycorrhizal fungi. By unrolling the thread of our current knowledge of the evolutionary history of these interactions, I will demonstrate how plants and fungi evolved in tight partnerships, developing and diversifying into the mycorrhizal associations, which are a fundamental part of modern ecosystems. I will discuss the evolutionary histories of mycorrhizal symbioses that have been revealed by our paleogenomic studies, including the functions that have been lost by genome erosion and the genes that have been acquired to facilitate mutualistic interaction with host plants. I will consider how such an intersection of genomics and evolutionary biology can inform our understanding of the biological principles intrinsic to AM and ECM symbioses.

By reconstructing how these mutualistic fungi have adapted to environmental changes during the past more than 400 Mya of evolution, we may be able to predict how they are likely to adapt to future anthropogenic climate changes. Finally, I will advocate that a better understanding of the molecular/cellular mechanisms driving fungal mutualistic symbioses should contribute to our overall comprehension of the multitude of associations taking place between endophytic microbes and their respective host plants.

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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.

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