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Plant Ecology Laboratory

Research in our lab focuses on diversity patterns in biological communities, and on the interactions underlying these patterns. The main questions we address are: how do communities vary along natural gradients and gradients of human impact? What are the major assembly rules shaping communities; and are they attributable to biotic interactions or environmental heterogeneity? What are the roles of different biotic interactions - including competition, facilitation, herbivory and symbiosis - in structuring communities? Read more


Mycological Society of America Annual Meeting in Berkeley, California

August 2016

The Annual Meeting of MSA took place this year in Berkeley, California. Our team was represented by Maarja Öpik, who was invited to talk in the symposium of fungal biogeography. Our good colleague Leho Tedersoo from Tartu University Natural History Museum also presented in the same session.

Annual Meeting of British Ecological Society in Liverpool

December 2016

The Annual Meeting of BES took place this year in Liverpool, bringing together over 1000 ecologists from UK and beyond. Out team was represented by three members: Maarja Öpik gave a talk about AM fungal species pools and dark diversity, Martti Vasar presented poster about AM fungal bioinformatics and Siim-Kaarel Sepp presented posted about AM fungal diversity patterns in different Estonian land use types.

Mosses mediate the influence of shrubs on soil properties and processes in alpine tundra

December 2016

Changes in soil properties and processes are key drivers behind shrub expansion in alpine and arctic tundra. However, apparently shrubs themselves do not change the soil conditions in the favorable direction, suggesting a role of other, yet unidentified, players. We tested whether moss cover interacting with shrubs can be the key player modulating the soil properties and processes. In an alpine area (Southwest Yukon, Canada), we manipulated experimentally the moss cover (removed or intact) under two main expanding shrub species in North America: Salix pulchra and Betula nana-gladulosa . We found effects of moss cover and shrub species alone, or differential effect of moss cover depending on shrub species on key soil properties and processes. We suggest that moss cover needs to be considered when predicting soil and tundra vegetation trends under the current and future environmental changes.

Bueno, C.G.; Williamson, S.N.; Barrio, I.C.; Helgadóttir, Á. & Hik, D.S. 2016. Moss mediates the influence of shrub species on soil properties and processes in alpine tundra. PloS One 11: e0164143.



PhD students conference

November 2016

The third biannual PhD student conference of the Department of Botany took place on November 17th and18th in Kubija. We had the opportunity to hear presentations from 16 PhD students from all working groups of the department. The presenters introduced their ongoing research and the newest results. Lena from our working group was awarded as the second best presenter. Congratulations!

New Phytologist's editor Maarja Öpik: "Be curious"

November 2016

New Phytologist made an Editor profile video of Maarja Öpik. She tells there about her role as an editor in New Phytologist, how did she become a scientist, who are her role models and says few words to scientists at the beginning of their careers.

Which AM fungi and plants colonize early successional sites first?

October 2016

There is little quantitative information about which arbuscular mycorrhizal (AM) fungi colonize early successional sites first and whether AM fungi or plants arrive quicker. In our new publication, we placed traps with natural sterilized substrate in a limestone quarry to measure dispersal of AM fungi and plants from surrounding calcareous grasslands. We found mostly AM fungi with ruderal traits to be the first and fast colonizers of early successional habitats. As for plants, we found fewer species further away from the propagule source and increasing number of plant species with more time. AM fungi were faster colonizers than plants.

García de León, D.; Moora, M.; Öpik, M.; Jairus, T.; Neuenkamp, L.; Vasar, M.; Bueno, C.G.; Gerz, M.; Davison, J. & Zobel, M. 2016. Dispersal of arbuscular mycorrhizal fungi and plants during succession. Acta Oecologica 77:128-135.


Plant Ecology laboratory welcomes visiting students

October 2016

Plant Ecology lab welcomes new visiting students Diana Navrátilová, Javier Puy and Mathieu Forget.


Diana is a PhD student in the Institute of Microbiology of the Academy of Sciences of the Czech Republic where she is supervised by Petr Baldrian. Diana is studying the phylogenetic covariation between vascular plants and soil microorganisms. During her stay with the Plant ecology lab she is supervised by Martin Zobel.



JavierJavier is a PhD student in the Functional Plant Ecology lab at the University of South Bohemia in Czech Republic.  He is supervised by Francesco de Bello and Carlos Perez Carmona. Javi's PhD thesis is focusing on the role of maternal effects in plant interactions. During his stay here he will be working with
Maarja, Mari and Inga.




Mathieu is a master student in Ecole Normale Supérieure, Paris, France, where he is supervised by Marc-André Selosse from Muséum National d’Histoire Naturelle. His master thesis is about Sebacinales diversity in plant roots. During his stay in the Plant ecology lab he is supervised by Maarja Öpik.

Plant Ecology laboratory welcomes a visiting PhD student

October 2016

Plant Ecology lab welcomes new visiting student Patricia Silva Flores, who is doing her doctoral degree in Biological Sciences in the Department of Botany at Concepción University in Chile. Her supervisor there is Dr. Götz Palfner. She is performing her research work in CEAF in the laboratory of Root-Microorganisms Interaction, where her supervisor is Dr. Rubén Almada. Patricia is studying in her PhD project the effect of host plant species, soil physicochemical factors and climatic seasons on the diversity and distribution of arbuscular mycorrhizal fungi of mediterranean sclerophyll forest. During her stay with plant ecology laboratory she is supervised by Maarja Öpik.

Biotic interactions drive herbivore richness in the Arctic

October 2016

This is the first collective effort and analytical paper of the Herbivory Network. Here, we collected information on the distribution of all 73 species of vertebrate herbivores that occur in the Arctic.  Vertebrate herbivores are particularly important as they affect the structure and dynamics of plant communities and provide food for higher trophic-level predators.  The results of this study showed that herbivore diversity in the Arctic is higher in areas with greater plant productivity and with higher diversity of predators.  The interactions between plants, herbivores and predators occurred over large spatial scales across the Arctic, in ecosystems where patterns of biodiversity were supposed to be affected mainly by temperature variation. Overall this paper is one of the first ones showing that biotic interactions can be relevant at large scales.


Map of herbivore distribution

Figure. Distribution maps of species richness of (a) all herbivores, (b) herbivorous birds, and (c) herbivorous mammals.
Barrio, I. C.; Bueno, C. G.; Gartzia, M.; Soininen, E. M.; Christie, K. S.; Speed, J. D. M.; Ravolainen, V. T.; Forbes, B. C.; Gauthier, G.; Horstkotte, T.; Hoset, K. S.; Høye, T. T.; Jónsdóttir, I. S.; Lévesque, E.; Mörsdorf, M. A.; Olofsson, J.; Wookey, P. A. & Hik, D. S. 2016. Biotic interactions mediate patterns of herbivore diversity in the Arctic. Global Ecology and Biogeography 25:1108–1118.


Defence of a PhD thesis

October 2016

On the 12th of October, Jaak-Albert Metsoja defended his PhD thesis titled "Vegetation dynamics in floodplain meadows: influence of mowing and sediment application", which is available from here. Congratulations!

Prof. David Gowing from Open University, United Kingdom, acted as an oponent for Jaak-Albert. The day before the defence, Prof. Goving gave a seminar titled "British floodplain meadows and the hydrological niche".

Trip to Öland

July 2016

Phd students and young scientists of the Botany and Geology institutes made a joint excusion to Sweden. Europe´s biggest alvar grassland ("Stora Alvar") on the swedish island Öland impressed botanists as well as geologists. Such easy and interesting interdisciplinary projects should be definitely repeated.

Trip to NW Estonia

July 2016

Summertime is the time for excursions and fieldwork! On 13th-14th of July, the team members of the plant ecology group, led by Martin Zobel, went to North-West Estonia and examined dry pine forests, wetland succession towards raised bogs, coastal areas as well as the high variety of berries Estonian forests have to offer in summer.

Assessment of the correlation in the composition of plant and AM fungal communities

May 2016

New paper is asking how efficiently plants and arbuscular mycorrhizal (AM) fungi disperse into early successional ecosystems, and which, if either of the two, symbiotic partner drives the successional dynamics. To study that, samples were collected from successional series in two islands in Eastern Baltic Sea. In the study sites, plant and AM fungal communities were strongly correlated at small spatial and temporal scales. The results of this study suggest that AM fungi may drive plant community composition.

Garcia de Leon, D.; Moora, M.; Öpik, M.; Neuenkamp, L.; Gerz, M.; Jairus, T.; Vasar, M.; Bueno, C. G.; Davison, J. & Zobel, M. 2016. Symbiont dynamics during ecosystem succession: co-occurring plant and arbuscular mycorrhizal fungal communities. FEMS Microbiology Ecology doi:10.1093/femsec/fiw097.

Mari Moora was a keynote speaker of the POPBIO

May 2016

Our workgroup member Mari Moora was asked to be a keynote speaker of the 29th POPBIO conference in Trebon, Czech Republic on 5-7 May. The POPBIO is a conference for plant ecologists studying plant populations in context. Mari spoke about the role of AM symbiosis in the life of plants’ and plant communities.

Plant Ecology lab's seminar

April 2016

This year’s seminar of Plant Ecology lab titled “Vegetation, global processes and biotic interactions” took place on April 21-22 in Haanja. PhD students presented their newest results and ongoing projects and Martin gave an overview of plant ecology in Tartu.

Plant Ecology laboratory welcomes a visiting PhD student

April 2016

We welcome new visiting student Iolanda Ramalho da Silva. During her stay with plant ecology laboratory she is supervised by Maarja Öpik. Iolanda comes from the Federal University of Pernambuco, Recife, Brazil, where she is supervised by Prof. Leonor Costa Maia. In her PhD project she studies molecular diversity of arbuscular mycorrhizal fungi along latitudinal gradient in coastal environments of Brazil.

Impact of alien pines on local arbuscular mycorrhizal fungal communities

April 2016

New paper is asking how the introduction of alien ectomycorrhizal plants influences local arbuscular mycorrhizal (AM) fungal communities and whether it differs in sites with different biogeographic histories. To study that, samples were collected from Argentina where ectomycorrhizal trees are naturally present, and from Republic of South Africa where ectomycorrhizal trees are historically absent. In Argentina, the AM fungal community composition and richness was similar in native forests and ectomycorrhizal pine plantations. However, in South Africa, the AM fungal richness was lower in pine plantations compared to native AM fynbos.

Gazol, A.; Zobel, M.; Cantero, J.J.;  Davison, J.; Esler, K.J.; Jairus, T.; Öpik, M.; Vasar, M. & Moora, M. 2016. Impact of alien pines on local arbuscular mycorrhizal fungal communities – evidence from two continents. FEMS Microbiology Ecology doi: 10.1093/femsec/fiw073.

Biodiversity workshops during Open Doors Day at the UT

March 2016

Department of Botany was revealing the secret life of plants to highschool students of Estonia at the Open Doors Day of University of Tartu. During multiple workshops students could extract DNA from bananas, stress out the plants, get acquainted with DNA barcoding, measure seed dispersal distances and vote for the prettiest and ugliest landscape. In addition, we set up microscopes to introduce diverse microorganisms – common mold fungi, microalgae and various types of mycorrhizae. We hope that the students enjoyed the hands-on activities and inspired them to study biology.

Mechanisms shaping AM fungal communities worldwide

March 2016

Lab members have published a paper showing how local AM fungal communities worldwide are shaped by multiple mechanisms at a range of scales. The study investigated phylogenetic diversity in fungal communities and used a hierarchical null model approach, generating random communities from taxon pools filtered according to some or all of spatial scale, ecosystem type and host plant identity. The results provide evidence that AM fungal communities are shaped by dispersal limitation and habitat filtering at wide spatial scales and mutualist partner selection at local scales. Intriguingly phylogenetic clustering of communities even in comparison with the finest-scale null model indicates that the plant-AM fungal symbiosis may be further influenced by genotypic selectivity or stochastic processes at very small scales.

Davison, J., Moora, M., Jairus, T., Vasar, M., Öpik, M. & Zobel, M. 2016. Hierarchical assembly rules in arbuscular mycorrhizal (AM) fungal communities. Soil Biology and Biochemistry, 97: 63-70.

Workshop on floodplain meadows

March 2016

Jaak-Albert Metsoja and Martin Zobel attended a workshop “One Ecosystem, Multiple Climates: floodplain meadows as a model system for investigating climatic resilience” at Open University, Milton Keynes, England on March 14-15. The workshop focussed on international collaboration of floodplain meadow scientists from a wide longitudinal gradient – from England to Western Siberia. More specifically, possibilities and needs for a unified database and different means for funding networking and cooperation were discussed.

Members of the Plant ecology lab received Estonian Science Award

March 2016

Our lab members Martin Zobel, John Davison, Mari Moora and Maarja Öpik received Estonian Science Award on bio- and geosciences for the studies on the topic ‘Factors underlying biodiversity patterns of plant and mycorrhizal fungal communities’. Congratulations!

Plant Ecology laboratory welcomes a visiting student from Czech Republic

March 2016

Bachelor student Lada Klimešova from the University of South-Bohemia in Czech Republic is visiting our workgroup for one month. For her Bachelor thesis she is studying orchid mycorrhiza. During her stay here she will work with root samples from the high Himalayas (> 5000 m asl) measuring the colonization of arbuscular mycorrhizal and endophytic fungi.

Land use changes affect alpine grasslands

February 2016

Guillermo Bueno investigated with co-authors how land use changes affect alpine grasslands during two decades at the Spanish Central Pyrenees. The study shows that the most recent changes of traditional management by grazing, with an overall decrease in livestock numbers and replacement of sheep with cattle, have lead to drastic changes. In areas with high livestock stocking rates (mainly cattle), grassland biomass and greenness decreased, while in areas with relatively low stocking rates, biomass and greenness increased. This indicates that two opposite processes are simultaneously occurring: over-grazing in cattle ranging areas, and under-grazing in abandoned areas. The findings suggest that a change in the livestock management is needed to prevent losing some of the most valuable and traditional semi-natural grasslands of Central Pyrenees.

Gartzia M.; Pérez-Cabello, F.; Bueno, C. G. & Alados, C. L. 2016. Physiognomic and physiologic changes in mountain grasslands in response to environmental and anthropogenic factors. Applied Geography DOI:10.1016/j.apgeog.2015.11.007.

Can we identify species of arbuscular mycorrhizal fungi on the basis of DNA sequences?

February 2016

Tom Bruns and John Taylor—mycologists at University of California, Berkeley—question in today’s issue of Science whether the Virtual Taxa as used by Davison et al. in Science last year, allow species level identification of arbuscular mycorrhizal fungi. Maarja Öpik, John Davison, Mari Moora, Meelis Pärtel and Martin Zobel explain in their response why and how the Virtual Taxon approach is appropriate for describing diversity patterns of Glomeromycota.



Applying a new toolkit to relate mycorrhization to soil properties and plant diversity

February 2016

Our PhD student Maret used a novel method (proposed by Moora 2014) to reveal contrasting patterns between arbuscular and overall mycorrhization depending on soil properties and plant diversity in the temperate zone. The approach tested on Estonian grasslands and forests shows promise for further description of larger-scale patterns of mycorrhizal symbiosis.

Gerz, M., Bueno, C. G., Zobel, M. & Moora, M. 2016. Plant community mycorrhization in temperate forests and grasslands: relations with edaphic properties and plant diversity. Journal of Vegetation Science 27:89–99.

Debate about the productivity and plant species richness

January 2016

Recent issue of „Science“ publishes  another debate about the relationship of productivity and plant species richness, which involves also researchers from our lab. A global dataset, which was published in Science in July, demonstrates that plant richness is biggest at intermediate productivity and decreases in high and low productivity. In the current issue, Treddnick et al. propose that using other methods to analyze this dataset, the relationship becomes weaker. Pither et al., including  Martin Zobel, Mari Moora and Kadri Koorem from our lab, therefore argue that the relationship as such still holds when analyzed differently and taht this is a highly important piece of evidence for this long-argued topic.

16th New Phytologist Workshop

January 2016

On January 24-27th, the teams of Plant Ecology and Macroecology organised a workshop on „Dark diversity of co-occurring arbuscular mycorrhizal fungi and host plants„. The workshop had 14 participants, including eight international participants from seven countries and six local participants from the Department of Botany. The workshop included discussions and empirical data analyses on how the application of concepts of dark diversity and species pool would improve understanding the biodiversity of arbuscular mycorrhizal and ectomycorrhizal fungi and its relationships with diversity of host plants. The workshop was funded by New Phytologist Trust. See more at and in Twitter #16NPW.

Plant ecology lab welcomes new member

January 2016

A new research fellow Inga Hiiesalu has joined the Plant Ecology Lab. Inga finished her PhD studies at the Macroecology workgroup at UT and after her post-doctoral research at the Czech Academy of Sciences she returned to join the Plant Ecology Lab. She will be examining the diversity patterns of AM fungi and host plants along altitudinal gradients in the arid Himalayas.

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