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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


The annual meeting of British Ecological Society

December 2017

Two of the members of Plant Ecology Lab participated in the annual meeting of British Ecological Society which was this year organized in collaboration with GFÖ, NecoV and EEF. Maarja Öpik gave oral presentation titled „Interactions between grassland plants and arbuscular mycorrhizal fungi are selective“and Kadri Koorem gave an oral presentation titled „Plant-soil feedback of range expanding plant species is influenced more by relatedness with the native species than by the origin of soil biota“. Thanks for the organizers, who packed the days between 11th to 14th of December in Ghent intensely with scientific talks and workshops! See more from the conference from Twitter.

Visit to Prof. Pål Axel Olsson lab in Lund University

November 2017

In November, PhD student Tanel Vahter visited the lab of Prof. Pål Axel Olsson in Lund University, Sweden. He learned how to quantify signature fatty acids of soil microorganisms for assessing their biomass. He worked with samples from his vegetation restoration experiment. This methodology is useful for tracking the growth dynamics of inoculated mycorrhizal fungi and provides an insight into the other micro-organism groups. This visit was part of the COST action Bio-Link activities.

Mycorrhizal symbiosis is associated with the realized niches of plant species

October 2017

Plant coexistence has puzzled scientists for a long time and one of the proposed underlying mechanisms is minimizing competition by niche differentiation. According to this, in order to coexist, species must differ in their realized niches (i.e. species must have distinct resource and habitat requirements). PhD student Maret Gerz with co-authors investigated whether and how the associations with mycorrhizal fungi could alter the realized niches of plant species. In a paper published in Journal of Ecology, it was found that, indeed, plants with different mycorrhizal statuses and types had distinct environmental preferences, but also that the range of environmental conditions which plant species tolerate, are dependent on whether they are obligately, facultatively or non-mycorrhizal, or which mycorrhizal type they form. Specifically, facultatively mycorrhizal, and ecto- and ericoid mycorrhizal plants had wider niches than other plants. These differences indicate that mycorrhizal symbiosis is an important contributing factor to plant coexistence.

Gerz, M.; Bueno, C. G.; Ozinga, W. A.; Zobel, M. & Moora, M. 2017. Niche differentiation and expansion of plant species are associated with mycorrhizal symbiosis. Journal of Ecology doi: 10.1111/1365-2745.12873.

Conference on Community Ecology

September 2017

John Davison recently attended the 1st International Conference on Community Ecology in Budapest (28-29 September). There he gave a talk describing recent work our group has carried out investigating arbuscular mycorrhizal fungi on islands worldwide.

Conference for network ecology and trophic interactions

September 2017

In September, Uppsala was the venue for two consecutive conferences, the 3rd Symposium on Ecological Networks and the 3rd Symposium on Molecular Analysis of Trophic Interactions. Our lab was represented by two members, senior researcher Maarja Öpik and her PhD student Siim-Kaarel Sepp, who presented a poster on his molecular analyses of AM fungal - plant interaction networks. Big thanks to the organisers, who managed to pull off a week-long event with topics ranging from hardcore theoretical ecology to identifying fish gut contents.

We welcome a new PhD student

September 2017

We are happy to announce that a new PhD student is joining our group. Daniela Leon Velandia studied and finished her Master thesis on microbiology in Colombia. Then, she decided to venture into plant mycorrhizal ecology in Estonia! She will work on the effect of land use in mycorrhizal trait composition of plant communities along large environmental gradients, under the supervision of Martin Zobel, Mari Mora and Guillermo Bueno. Welcome to Tartu!!

Increased sequencing depth by Illumina does not increase captured diversity of arbuscular mycorrhizal fungi compared to 454

August 2017

Doctoral student Martti Vasar with co-authors investigated how two sequencing platforms (454 and Illumina) compare with each other. To achive this, MaarjAM database with BLAST+ software was used. 454 sequencing is now discontinued and alternative had to be found. This raised a question how new sequencing platform results are comparable with previous platvorm. Both platforms were sequenced by same 12 samples from Järvselja forest. 454 sequences were at least 500+ base pair long, which filled interested amplicon of the SSU rRNA gene. Illumina have shorter sequences (previous generation 2x250bp, now 2x300bp), which have overlap at the end of sequence. Tagmentation was used for Illumina, which locates sequences at random location on the amplicon, but 454 sequences were starting from fixed position. Illumina produced 100x more raw sequences compared to 454, but catched fewer rare virtual taxon (VT – see MaarjAM database). After quality filtering, large portion of Illumina sequences were discarded, but this did not affect end results as the captured diversity was similar with 454.

Vasar, M.; Andreson, R.; Davison, J.; Jairus, T.; Moora, M.; Remm M.; Young, J. P. W.; Zobel, M. & Öpik, M. 2017. Increased sequencing depth does not increase captured diversity of arbuscular mycorrhizal fungi. Mycorrhiza doi: 10.1007/s00572-017-0791-y.

9th International Conference on Mycorrhiza

August 2017

ICOM9 was held in August in Prague, Czech Republic, with the overarching theme: „Mycorrhizal functioning: from wilderness to megacities”. Mari, Maarja, Guille, Inga, David, Lena, Maret and Tanel from our team and Leho and Petr from Tedersoo’s lab were presenting either posters or oral talks – indeed numerous participation! Mari gave a plenary talk on „Biogeography of mycorrhizal symbiosis: using plant mycorrhizal traits in space and time” and Maarja organized a workshop together with Tom Bruns and John Taylor and gave a lecture on „Molecular taxon concepts in AM fungi used in community ecology”. Thanks to the organizers for a great conference! See more from the conference Twitter.

Invertebrate herbivory in the tundra is widespread and sensitive to changes in climate

July 2017

Recent studies have shown that biotic interactions influence macroecological patterns and global dynamics, stressing the need to consider them beyond local and regional scales. In the context of global changes, we still know little about the role of key biotic interactions in the dynamics and fate of whole biomes. In this study, the intensity of background invertebrate herbivory (low intensity but chronic biomass removal) of a common tundra plant (Betula nana-glandulosa complex) was investigated in relation to latitude and climate. C. Guillermo Bueno from the University of Tartu was part of the research team led by Isabel C. Barrio and Mikhail V. Kozlov. They collected samples from 56 locations across the tundra biome in the first coordinated effort to measure invertebrate herbivory in tundra, outside the well-studied effects of insect outbreaks. Background herbivory was detected at nearly all tundra sites. The intensity of background herbivory, although low, was stronger with higher temperatures and, as such, is likely to increase in a warmer Arctic. This paper represents the first coordinated effort combining two international research networks in the tundra: the Herbivory Network (HN) and Network for Arthropods of the Tundra (NeAT).

Barrio, I.C., Lindén, E., Te Beest, M. et al. 2017. Background invertebrate herbivory on dwarf birch (Betula glandulosa-nana complex) increases with temperature and precipitation across the tundra biome. Polar Biol  doi:10.1007/s00300-017-2139-7




FACES workshop

July 2017

Tanel Vahter participated in FACES (Freely Accessible Central European Soil) workshop on 25.06-1.07 in Kaunas, Lithuania. During the week, course participants went through an intensive course about WRB (World Reference Base, FAO) soil classification. In addition, lectures on national soil classification systems in the partner countries were given. Fresh knowledge was tested during fieldwork on the various soils of Lithuania. Unlike national soil classification systems, WRB gives an opportunity for scientists across the world to describe and classify soils based on unified system. This gives opportunities for a better understanding and fruitful collaborations. University of Life Sciences scientist Endla Reintam, who was also an instructor on the course, led the Estonian team.

39th New Phytologist Symposium

June 2017

The 39th New Phytologist Symposium “Trait covariation: Structural and functional relationships in plant ecology” took place on June 27th to 29th in Exeter, UK. The symposium focused on trait relationships to plant and ecosystem function, fundamental limits on trait space, trait trade-offs and covariation, and predicting plant traits in response to changing environmental conditions. Coffee breaks provided opportunities to discuss plant mycorrhizal traits with several trait experts (Eric Garnier, Etienne Laliberté and Luke McCormack, among others). As a highlight, an improvised presentation of the FRED database (Fine-Root Ecology Database) was given by Luke McCormack. Overall the symposium identified the next generation trait questions, which relate to the development of root trait measurements and databases, including plant mycorrhizal traits. Our team was represented by Guillermo Bueno and Maret Gerz.

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

June 2017

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 mycorrhizal symbioses in plant communities. For instance, knowing that the proportion of arbuscular mycorrhizal (AM) plant species decreases at higher latitudes supports previous hypotheses about AM symbiosis 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, opens new 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. This first European exploration revealed that the share of plant mycorrhizal types (arbuscular, ecto-, ericoid or non-mycorrhizal plant species) varies along latitudinal but not along elevational gradients, while plant mycorrhizal status (obligately or facultatively mycorrhizal) varies in both. In particular, they found that obligately mycorrhizal plant species are more abundant in southern latitudes but also in higher elevations. This might indicate that glaciations may have influenced their distribution limiting its presence in northern latitudes.

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 26: 690–699.


Woody Root 7

June 2017

The 7th International Symposium on Physiological Processes in Roots of Woody Plants took place on June 26th to 29th in Tartu, organised by our colleague Ivika Ostonen. Our team was represented by Martin Zobel and PhD Student Siim-Kaarel Sepp. Martin gave a keynote lecture about the macroecology of arbuscular mycorrhizal fungi and Siim-Kaarel gave a presentation about his work on arbuscular mycorrhizal fungal diversity in Estonian habitats under different land use. We thank Ivika, EcolChange and other supporters for the inspiring event!

International journalists visited Muhu island

June 2017

On the 15th-16th of June, science journalists from several European countries visited the Life to Alvars project areas in Muhumaa. The journalist got an overview of the progress of alvar restoration and research involved. From our working group, Maarja Öpik and Tanel Vahter explained to the journalists the importance of mycorrhizal fungi and their effect on plant species richness. Tanel introduced his experiment of inoculating alvar grasslands with native arbuscular mycorrhizal fungi for habitat restoration. From the macroecology working group, Aveliina Helm and Sabrina Träger introduced their research. The meeting was part of the Estonian Research Council’s project „On the Fields of Estonian Research“.

Yearly excursion of the Estonian Soil Science Society

June 2017

On 13th-14th of June, the traditional soil excursion of the Estonian Soil Science Society took place. As a member of the society, our doctoral student Tanel Vahter also participated. During two days, an overview of the soils in Northern-Estonia with an emphasis on the national soil of the year 2017 – podzol, was given. Soil pits were dug to give a insight into the factors of soil formation and development in the area. The evening was spent exchanging thoughts and looking for ways of collaboration between soil scientists and ecologists.

Visiting natural and human-influenced sites in North-East Estonia

June 2017

In mid-June, members of the Plant Ecology Lab went on a trip to North-East Estonia in order to visit local natural communities as well as human-influenced oil shale mining sites. We visited the beautiful Kurtna Lake District and Saka cliff. The latter has a unique cliff forest community, which is an important habitat for rare Lunaria redidiva plants. We also confirmed that the experiment to study the revegetation of former oil-shale quarries has started successfully – seeds, which were sown in the end of April, are germinating! Near future will hold the truth about the role of mycorrhizal fungi in revegetation. In addition, we visited the Estonian Mining Museum in Kohtla-Nõmme, which took us to the exciting underground passages.

Jornal club outdoors meeting

May 2017

On the last of May, we had the final Journal club meeting for this academic year. To make it different we decided to have an outdoors event. We went to an adventure trail and hike in Elva-Vitipalu landscape reserve. After the hike, we went to Vapramäe Nature center to summarize this year and make plans for the coming academic year.

Beautiful spring in Estonian forests!

May 2017

In the end of May, Plant Ecology Laboratory went on a trip to learn about Estonian forest site types. Based on the legendary ordination scheme by Erich Lõhmus we identified various site types from dry heath forests to wet eutrophic boreal forests. The excursion was led by Prof. Martin Zobel, who stressed that in order identify the types correctly it is important to consider the understorey vegetation as well as soil conditions. Knowing the forest site types is crucial to understand forest ecosystem functioning.

Visit of Prof. J. Peter W. Young

May 2017

Prof. J. Peter W. Young visited Department of Botany and Centre of Excellence EcolChange to give a seminar and discuss with graduate students and post-docs. Prof. Young is based at York University, United Kingdom. He is Editor-in-Chief of open access journal Genes, and world-renown scientist for his research on bacterial genetics and biodiversity of arbuscular mycorrhizal fungi.

Experiment "arbuscular mycorrhizal fungi in restoration" is all set!

May 2017

Fieldwork to test the effect of inoculation with native arbuscular mycorrhizal fungi in plant community restoration is finished! As the main experiment in Tanel Vahters PhD project, a total of 432 test-plots have been set up in restored alvar grasslands, wooded meadows and depleted oil-shale quarries in Estonia. In each community type, plant seeds and a suitable native arbuscular mycorrhizal fungal inoculant was added. How the addition of a suitable fungal partner affects vegetation restoration speed and quality will be determined from the data collected during the following years. We thank the landowners, collaborators and everyone who took part in making this happen!

43. Theoretical Biology spring school

May 2017

This year’s Theoretical Biology spring school took place on May 12th-14th in Aluoja, North-Eastern Estonia and was dedicated to the 225th anniversary of Karl Ernst von Baer. During these three spring days, there were presentations about the life of Baer and his contribution to science, as well as about progress at the forefront of life sciences. Members of our working group participated actively in the spring school: PhD student Tanel Vahter gave a talk about issues related to practical applications of arbuscular mycorrhizal fungi and PhD student Siim-Kaarel Sepp wrote about the impacts of human activities on biodiversity of these fungi. We thank all participants and the organizers for superb weekend!

The papers presented at the spring school were published in Schola Biotheoretica XLIII, accessible here.

Visiting PhD student

May 2017

In May, PhD student Rita Filep visited our working group. She is studying in the University of Pécs, Hungary, where she is supervised by Ágnes Farkas. Rita investigates biogeography of invasive plant Helianthus tuberosus, including the role of arbuscular mycorrhizal symbiosis in the invasion process. During her stay at Plant Ecology Lab her supervisor was Mari Moora.

First International Bee Conference in Berlin

March 2017

Improving the protection of bees as pollinators and honey producers is a task to be tackled at international level. Therefore, the German Federal Ministry of Food and Agriculture (BMEL) and the German Beekeepers Association (DIB) were hosting an international conference on 28 and 29 March 2017 in Berlin.

The event was aimed at beekeepers, farmers, scientists and politicians from all over the world, in particular from Europe and America, and at representatives from relevant international organisations. All the speakers in the conference were specifically invited by organizers based on their scientific expertise. Mari Moora gave a presentation about the effect of climate change on biotic interactions (mycorrhizal symbiosis and pollination) and their interactive effect on plant diversity.

Visit of Francis M. Martin

May 2017

Prof. Francis M. Martin visited Department of Botany and Centre of Excellence EcolChange to give a seminar and discuss with graduate students and post-docs. Prof. Martin is Scientific Director of Laboratory of Excellence ARBRE at INRA-Nancy, France, editor at New Phytologist (and other journals), and world-renown scientist exploring fungal life styles using comparative genomics.

Vegetation zonation course on the Canaries

April 2017

Several members of our working group participated at a field course in Tenerife, financed by the Doctoral School of Earth Sciences and Ecology. Tenerife is a perfect model island to study ecological and evolutionary processes that shape vegetation due to a steep altitudinal gradient. The gradient stretches from the sea level up to 3700 meters on the top of the El Teide Volcano. During one week in April PhD students not only got to witness the main ecological theories in real life but also practice modern methods in plant ecology. Maret, Siim-Kaarel and Tanel participated as PhD students, and Inga as one of the main leaders of the expedition.

Science day in Tallinn’s Pae Secondary School

April 2017

On 20th of April, a Harry Potter themed science day called “Henry Lotter” took place in Tallinn’s Pae Secondary School. We were invited to do a workshop there. So, firstly we let the students to look for fungal structures in plant roots and afterwards explained them what did they see and why is mycorrhiza important not only for plants but also for us, humans.

Working group seminar

April 2017

This year’s Plant Ecology Laboratory seminar took place on 18th-19th of April near Palamuse. Working group members and invited guests gave talks about their ongoing projects. This year, there was also a small trait workshop lead by Carlos and Mari. The purpose of the workshop was to discuss which traits are plant mycorrhizal traits.

Tartu University’s Science day in Pärnu

April 2017

On 11th of April, University of Tartu science day took place in Pärnu. From our working group, Lena and Teele with Kersti from macroecology working group explained the students how plant communities are assembled and how to restore degraded communities. After that the students did a theoretical exercise about restoring an ecosystem – either wooded meadow, alvar grassland or raised bog.

PhD position in Plant Ecology

March 2017

We welcome applications from highly motivated and skilled people for a PhD position in Plant Ecology. The PhD student will work on the project titled ‘Land use induced variation in mycorrhizal trait composition of plant communities under different climatic and edaphic conditions’. The project is for 4 years (01.09.2017-31.08.2021). Additional information and the application deadline can be found from here.

Biodiversity workshops during Open Doors Day at the UT

March 2017

How far do the seeds disperse? How do the stomata look like? How can you get the DNA out of a plant? What’s the difference between overgrown or destroyed and restored habitats? Those were a few questions that high-school students could find answers in biodiversity workshops during the Open Doors day. This was the chance for them to find out what biologist and ecologist do in our University.

Conference and fieldwork in Chile

March 2017

March 6-9th took place a symposium on „Mycorrhizal Symbiosis in the Southern Cone of South America“ in Valdivia, Chile. Among the main conference organisers were some of our collaborators: Prof. Roberto Godoy and PhD student Cesar Marin (Austral University of Chile) and Patricia Silva Flores (University of Concepcion). Our team was represented by Guillermo Bueno and Maarja Öpik who were invited to give keynote lectures. Guillermo presented an overview of the conceptual framework and use of plant mycorrhizal traits with research examples from our group, from macroecological and plant community to plant species levels. Maarja gave an overview about DNA-based taxon recognition and identification of arbuscular mycorrhizal fungi, including the concept of Virtual Taxon used in our team, and MaarjAM database, curated by us, holding the information about AM fungal DNA-based diversity worldwide. After the conference, Guillermo and Maarja participated in fieldwork in Nahuelbuta National Park featuring amazing Araucaria forests. Maarja also visited University of Concepcion to give a seminar, hosted by Prof. Götz Palfner, and CEAF (Centro de Estudios Avanzados en Fruticultura), to visit Patricia’s field sites of Mediterranean matorral, give one more seminar, and discuss with the team of CEAF.

Kick-off meeting for BiodivERsA project SoilMan in Göttingen

March 2017

On 13 – 15. of March, the kick-off meeting for the six partner countries in BiodivERsa project SoilMan (Ecosystem services driven by the diversity of soil biota – understanding and management) was held in Göttingen, Germany. The Estonian team led by Maarja Öpik was represented at the meeting by PhD student Tanel Vahter. Working plans and general ideas were discussed for the following three years, in which the diversity of soil biota, agricultural management practices and socio-economic factors will be merged to provide added input to policy makers. Our task for the SoilMan project is to describe arbuscular mycorrhizal fungal diversity in the experimental sites all over Europe and provide context based explanations for the patterns we find.

Secondary succession in alvar grasslands – do changes in vascular plant and cryptogam communities correspond?

February 2017

The area occupied by semi-natural grasslands has constantly declined in Baltic region during the last century. Understanding how they naturally recover is crucial for conservation.  A lot is known about vegetation changes along time, but mosses and lichens are generally overlooked. This study looked how plant, moss and lichen communities develop after limestone quarry abandonment. We found that plants arrive fastest, then come the mosses, and the lichens are the slowest to arrive to a newly exposed habitat. We can conclude that during secondary succession the changes in vascular plant and cryptogam communities do not correspond.


García de León, D.; Neuenkamp, L.; Gerz, M.; Oja, E. & Zobel, M. 2017. Secondary succession in alvar grasslands – do changes in vascular plant and cryptogam communities correspond? Folia Geobotanica doi: 10.1007/s12224-016-9260-1.

Tallinn French Lyceum’s students visit UT

February 2017

On the 10th of February, students from Tallinn French Lyceum visited University of Tartu. Maarja Öpik and Inga Hiiesalu introduced the ongoing works in our workgroup. In addition, our colleagues Jane Oja and Sergei Põlme from chair of mycology introduced their work.


Plant Ecology Laboratory captured on a photo

February 2017

Members of the Plant Ecology Laboratory gathered recently to renew the group photo. From the top left: Maarja Öpik, Mari Moora, Lena Neuenkamp, Ede Oja, Maret Gerz, John Davison, Teele Jairus, Inga Hiiesalu, Guillermo Bueno, Siim-Kaarel Sepp, David Garcia de Leon, Martin Zobel, Tanel Vahter. Martti Vasar is missing from the photo.

Oikos Finland conference in Helsinki

February 2017

Oikos Finland hold a conference in Helsinki from 31st January to 1st February to celebrate 100 years of Finnish ecology. Our team was represented by Maarja Öpik who was invited to give a plenary. She spoke about AM fungal species pools and dark diversity. The conference was preceded by a symposium in memory of late academician Ilkka Hanski.

Scientist are planning to use AM fungi to restore plant species richness in alvar grasslands

January 2017

Our PhD student Tanel Vahter was interviewed by the newspaper Saarte Hääl. Tanel gave an overview of his experiments on the islands of Western-Estonia, where arbuscular-mycorrhizal fungi will be used for the restoration of alvar grasslands and wooded meadows.

COST Action ES1406 KEYSOM meeting

January 2017

Plant Ecology team together with Mari Ivask from Tallinn University of Technology Tartu College hosted a COST Action ES1406 KEYSOM (Soil fauna – Key to Soil Organic Matter Dynamics and Modelling) meeting from January 17 to 19th. There were participants from 24 countries discussing topics from fauna databases to soil food webs, biogeochemical processes, carbon modelling and of course soil arbuscular mycorrhizal fungal biodiversity, our favourite.

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