EcolChange seminar – Elin Org about mice and men and microbiota

Seminars of Department of Botany, Doctoral School of Earth Sciences and Ecology and Centre of Excellence EcolChange

Speaker: Dr. Elin Org is senior researcher in genomics and microbiomics at the Institute of Genomics of University of Tartu.

Title of the talk: Host-gut microbiota interactions and metabolic traits in mice and human

Time: Thursday, 14. February 2018 at 15.15

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

After the seminar everyone is welcome to coffee/tea and snacks in the seminar room (coffee room, ground floor).

Insert a colonial joke here. Or colonal… (pic from here)


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Blogyear summary 2018

Text Lauri Laanisto

It is already February. Nearly a month too late. But as the years go by, more and more reports are required every January, which is why the summaries of voluntary nature tend to get delayed or even fail to appear completely.

Our second year of blogging resulted in 55 blog posts by 26 different authors (last years numbers were 69 and 21, respectively). Blog was reached by 2200 unique visitors with 3390 clicks, from 75 countries and territories (Estonia, USA, HongKong, Germany and UK had the most visitors from). The blog has 250 followers, mostly through accompaniying Twitter account.

The most popular post from last year was written by Ivika Ostonen about root-foraging strategies in forests, a paper that was published in New Phytologist.

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Not one, but again two seminars: Marc-André Selosse & Benoît Perez-Lamarque about mycorrhiza

Holiday season is thankfully over, and time to get back to science!

Seminars of Department of Botany, Doctoral School of Earth Sciences and Ecology and Centre of Excellence EcolChange

Speaker1Prof. Selosse is based at the National Museum of Natural History (Muséum National d’Histoire Naturelle) in Paris, France.

Title of the talk: A case study of plant-fungal cointroduction: a pantropically introduced tree was followed by pseudovertically transmitted mycorrhizal fungi

Speaker2MSc Perez-Lamarque is his PhD student at Ecole Normale Supérieure in Paris. They are visiting plant ecology work group of Department of Botany.

Title of the talk: Constraints on the emergence of cheating mycoheterotrophic plants in the arbuscular mycorrhizal symbiosis

Time: Thursday, 10. January 2019 at 15.15

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

N.B. After the second seminar everyone is welcome to coffee/tea and snacks in the seminar room (coffee room, ground floor).

'Mom, Dad -  this is Jeremy.'

Introducing fungi (pic from here)

Calendar of the department’s events:

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Additional information: Maarja Öpik,


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Ilkka Hanski´s “Messages from Islands” now in Estonian

Text by Lauri Laanisto

In a tiny country like Estonia scientists are probably more concious about progeny than in more populated places where the flow of potential students is much more steady. So, most of Estonian scientists are involved in various activities promoting science in general and their specific discipline more narrowly.

My niche in this field, in addition to blogging, is translating. I´m trying to make science more accessible for young people like I was when growing up, or people who do not speak English.

And just today my latest translation hit the already overloaded shelves of bookstores. It´s Ilkka Hanski´s posthumously published “scientific testament” called “Messages from Islands” (University of Chicago Press 2016). In Estonian (which is the second language after Finnish – naturally – it has been translated into) it is called “Sõnumeid saartelt”. Here is the cover:

Ilkka Hanski collaborated with members of EcolChange, and the concept of extinction debt (link to Helm, Hanski and Pärtel 2005 in EcolLetters) is quite thouroughly discussed also in this book.

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Soil biodiversity training school

/Here´s an announcment about slightly EcolChange-related soil biodiversity training school that will take place in Tartu in January. But it´s important to stress out that the registration deadline is already on 15th of December!/


COST Action “KEYSOM” – 3rd Training School

Soil fauna – Key to Soil Organic Matter Dynamics and Modelling. Interactions with other components of soils – Mycorrhizal fungi

Tartu, Estonia, 22-24 January 2019

'Just think...our pies feed the soil,the soil feeds the grass,the grass feeds us...'

Once you start thinking about the interactions… (pic from here)

Linking Soil Biodiversity with Soil Organic Matter Dynamics

Framed within the objectives of the COST ACTION KEYSOM (Soil fauna – Key to Soil Organic Matter Dynamics and Modelling – see this third Training School aims at linking the role of the soil biodiversity with the soil organic matter dynamics. This school will provide a comprehensive overview of the tools available to assess the soil biodiversity (including macrofauna, mesofauna, microfauna and microorganisms), such as classical taxonomic approaches and novel soil DNA metabarcoding. The originality of this training school lies in the interdisciplinarity of its subjects, from molecular biology to soil science, and its trainers, getting together soil ecologists, biogeochemists and modellers.

Dr. Maarja Öpik and Prof. Alar Astover will be hosting this third KEYSOM Training School. A selection of relevant speakers (see below) are invited to provide their knowledge and experience in themes ranging from soil biodiversity, soil function, and SOM interaction. Targeted mainly at PhD students and young post-doctoral fellows (ECIs), this training school also aims at stimulating collaborative research among participants and with the guest lecturers.


PARTICIPATION & REGISTRATION (30 participants max.):

The participation in this Training School has no registration fees. Participants will be selected based on their CV and motivation letter. Applications (one single pdf), including a CV and a motivation letter, should be sent by e-mail to Maarja Öpik ( until December 15, 2018.

Selected participants will receive a “trainee grant” as a contribution to their expenses regarding travelling, accommodation and meals, according to COST regulations. Trainees eligible for reimbursement are those from all COST countries, approved Near Neighbour Countries’ institutions and approved European RTD Organisations (see COST rules in the vademecum at:

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New publication – Fungal diversity regulates plant-soil feedbacks in temperate grassland

Text and pic by John Davison and Marina Semchenko

Ecologists have long suspected that one key to explaining plant diversity lies with their enemies, including pathogenic soil microbes. Plant–soil feedback describes a process whereby plants shape the microbial communities living alongside them in the soil; and the microbes then have a ‘feedback’ effect on the performance of subsequent generations of plants. Feedback effects can be negative if driven by pathogenic microbes or positive if driven by beneficial microbes, such as mycorrhizal fungi. However, we remain largely in the dark about the mechanism involved, especially concerning the identity and diversity of microbes that could drive plant-soil feedbacks.

An international collaboration involving Dr John Davison (Ecolchange, University of Tartu) and led by Dr Marina Semchenko (University of Manchester, UK; formerly University of Tartu) has shed light on the drivers of plant-soil feedbacks in a study published in Science Advances. The team identified the microbes responsible for feedback effects and discovered why some plants live fast and die young whilst others have long and healthy lives. Their experiment consisted of a ‘conditioning phase’ where 14 different grassland plant species were grown for 3 years in field-based mesocosms containing natural grassland soil. The microbial communities in the soil were then described using high-throughput sequencing, and a ‘feedback’ experiment was conducted where plant species were grown on soil conditioned by the same or different species.

They found that the fungal communities present in conditioned soil varied considerably, with some plant species promoting different plant pathogenic fungi, and others favouring more beneficial fungi. The balance between pathogenic and beneficial fungi was dependent on plant functional traits and soil characteristics. Plants with more nutrient-acquisitive traits attracted more diverse communities of pathogenic fungi and associated with fewer mycorrhizal fungi. Soil microbial communities inhabiting fertile soils were more conducive to antagonistic interactions with plants, and plants were more susceptible to pathogens when grown on fertile soils. In the feedback stage, plant performance was negatively related to the diversity of harmful fungi rather than to the abundance of any particular specialist pathogens. It was also positively related to the diversity of mycorrhizal fungi. Lead author, Dr. Semchenko said: “We found that plant growth is strongly controlled by how many different harmful and beneficial fungi are attracted to plant roots. Some plants are slow to grow but enjoy a long life by cooperating with beneficial fungi; others grow fast and are initially successful, but then they are brought down by diseases caused by harmful fungi.”

The results could pave the way for new approaches in agriculture to achieve the right microbial balance for the production of healthy crops. The study also helps us understand how plant diversity is maintained. This, in turn, could help improve nature conservation and natural habitat restoration. Richard Bardgett, Professor of Ecology at The University of Manchester, said: “While these results come from grasslands in northern England, it is likely that the same mechanisms occur in other ecosystems around the world.” Dr. Semchenko added: “Soil microbes are known to be sensitive to human interference, such as intensive agriculture, and our findings suggest that negative impacts on soil microbes may have knock-on effects on the conservation of plant diversity.”

The study involved a collaboration between nine institutions including the Universities of Berlin, Colorado, Edinburgh, Lancaster, Manchester and Tartu.

Citation: Semchenko, M., Leff, J. W., Lozano, Y. M., Saar, S., Davison, J., Wilkinson, A., … & Mason, K. E. (2018). Fungal diversity regulates plant-soil feedbacks in temperate grassland. Science Advances, 4(11), eaau4578. (link to full paper)

marina ja john seened

Fungal diversity may be key to the maintenance of plant diversity in grasslands


Feedbacks between plants and soil microbial communities play an important role in vegetation dynamics, but the underlying mechanisms remain unresolved. Here, we show that the diversity of putative pathogenic, mycorrhizal, and saprotrophic fungi is a primary regulator of plant-soil feedbacks across a broad range of temperate grassland plant species. We show that plant species with resource-acquisitive traits, such as high shoot nitrogen concentrations and thin roots, attract diverse communities of putative fungal pathogens and specialist saprotrophs, and a lower diversity of mycorrhizal fungi, resulting in strong plant growth suppression on soil occupied by the same species. Moreover, soil properties modulate feedbacks with fertile soils, promoting antagonistic relationships between soil fungi and plants. This study advances our capacity to predict plant-soil feedbacks and vegetation dynamics by revealing fundamental links between soil properties, plant resource acquisition strategies, and the diversity of fungal guilds in soil.

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Not one, but two seminars: Björn Lindahl about symbiotic composition in boreal soils & Paul Ashton about genes and grasses in meadow

Seminars of Department of Botany, Doctoral School of Earth Sciences and Ecology and Centre of Excellence EcolChange

Speaker1: Prof. Björn Lindahl is based at Swedish University of Agricultural Sciences, Uppsala, Sweden. He is visiting the Department of Botany to act as opponent at the PhD defence of Petr Kohout on December 10th, at 9:15 AM in Vaga auditorium, Lai 40-218, Tartu.

Title of the talk: Symbiotic decomposition in boreal forest soils

Time: Tuesday, 11. December 2018 at 10.15

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

Speaker2: Prof. Paul Ashton is based at Edge Hill University, United Kingdom. He is visiting the Department of Botany to act as opponent at the PhD defence of Lisanna Schmidt on December 12th, at 9:15 AM in Vaga auditorium, Lai 40-218, Tartu.

Title of the talk: Let the grass grow and the genes flow! Lessons learned from research into hay meadow vegetation

Time: Tuesday, 11. December 2018 at 15.15

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

N.B. After the second seminar everyone is welcome to coffee/tea and snacks in the seminar room (coffee room, ground floor).


Instead of a joke, a little addition to the commandments: let the grass grow, the genes flow, and keep the aspidistra flying! (pic from here

Calendar of the department’s events:

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Additional information: Maarja Öpik,

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Annual update on our share of most influencal scientist

Text by Lauri Laanisto

Last year, when Clarivate Analytics published the list of most influential scientists in the world, we in EcolChange were rather happy about it, because: “From those 7 most influential Estonian researchers 4 (!!!) are members of our centre of excellence: Ülo Niinemets, Martin Zobel, Urmas Kõljalg and Leho Tedersoo. So one can say that EcolChange really is the dominant force in Estonian science.” (link to last year´s blogpost).

Well – new list was published about a week ago (link to the list). And this year we have even more influencers! Among the 6,000 most cited researchers of the world are the following EcolChange (associated) scientists: Ülo Niinemets from Estonian University of Life Sciences; Urmas Kõljalg, Leho Tedersoo, Martin Zobel (in two fields: plant and animal sciences and environment and ecology), Meelis Pärtel, Mari Moora, Kessy Aberenkov and Mohammad Bahram from Tartu Ülikool.

Thus, we have doubled our influence! Considering that EcolChange will run for five more years, we could expect about 256 people in that list by the end of 2023…


Although, we are pretty far away from the impact of “actual” influencers… (pic from here)


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New publication – Global trait–environment relationships of plant communities

Text by Martin Luther University in Halle via EurekaAlert

/Ed: This new macroecological paper includes Meelis Pärtel and Ülo Niinemets from EcolChange as coauthors./

Which plant species grow where, alongside which others – and why? The diversity of global vegetation can be described based on only a few traits from each species. This has been revealed by a research team led by Martin Luther University Halle-Wittenberg (MLU) and the German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig. In a new study published in the scientific journal Nature Ecology & Evolution, they present the world’s first global vegetation database which contains over 1.1 million complete lists of plant species sampled across all Earth’s ecosystems. The database could help better predict the consequences of global climate change.

All plants face the same challenges, whether they are small grasses, shrubs or trees. “For example, they have to find an efficient way to conduct photosynthesis in order to obtain the energy they need. At the same time, they compete with neighbouring plants for limited resources in the soil, like water and nutrients,” explains Professor Helge Bruelheide from the Institute of Biology / Geobotany at MLU and co-director of iDiv.

Currently around 390,000 plant species are known to science. Over time, each species has developed very different traits in reaction to external factors at their location. These include the plant’s size, the thickness and the chemical constituents of its leaves. These properties are also referred to as functional plant traits. “These functional traits directly influence a plant’s ecosystem function, such as how much biomass it produces or how much carbon dioxide it absorbs from the air,” says Bruelheide.

Until now, researchers have primarily investigated different combinations of these functional traits from the perspective of individual plant species. “In reality, however, plant species rarely occur alone; plants live in communities,” says Bruelheide. Therefore, so-called vegetation databases are needed that contain data on all of the plants growing at a specific location. The German Vegetation Reference Database is an example. It is managed at MLU by Dr. Ute Jandt, a member of Helge Bruelheide’s research group. It contains about data on about 200,000 vegetation plots from published and unpublished vegetation studies. Similar databases exist, or are being compiled, in many other countries.

Up until now there has been no database of databases, to compile and harmonize all these different datasets. As a result, the “sPlot” initiative was launched at the iDiv research centre to develop and set up the first global vegetation database, unifying and merging the existing datasets. “sPlot” currently contains more than 1.1 million vegetation lists from every continent, collected over the past decades by hundreds of researchers from all over the world. “Each point in our database is a real place with precise coordinates and information about all the plant species that co-exist there,” explains Bruelheide.

The research group combined this massive dataset with the world’s largest database for plant traits called “TRY” which is also an iDiv database platform. “It has enabled us to answer questions that nobody has been able to tackle before,” Bruelheide continues. The research tested, for instance, to what extent global factors influence the functional traits of plant communities. Contrary to current opinion, they found that temperature and precipitation play a relatively limited role. “Surprisingly, these two macro-factors are not so important. Our analysis shows, for example, that plant communities are not consistently characterised by thinner leaves as the temperature increases – from the Arctic to the tropical rainforest,” says Bruelheide. Instead the researchers found a close tie between climate variables and the phosphorus supply in the leaves, reflected in the ratio between nitrogen and phosphorus content in the leaf, which is an indicator of plants’ nutritional status. For example, the longer the vegetation period, the lower the phosphorus supply – which also affects leaf thickness. Local land use and the interaction of different plants at a specific location have a much greater impact on the functional traits of plant communities. According to Bruelheide, these findings show that future calculations of plant production in a region cannot only be determined on the basis of simplistic temperature-precipitation models.

The study published in Nature Ecology & Evolution is the first of a series of upcoming papers by the “sPlot” consortium. Being available on request to other scientists, the “sPlot” database is disclosing unprecedented opportunities to tackle numerous biodiversity questions at the global scale, including the issues pertaining to the distribution of non-native plant species and the similarities and differences of plant communities across world regions.

Citation: Bruelheide, H., Dengler, J., Purschke, O., Lenoir, J., Jiménez-Alfaro, B… Pärtel, M…, Niinemets, Ü…., & Hennekens, S. M. (2018). Global trait–environment relationships of plant communities. Nature Ecology and Evolution, (link to full text)


Plant functional traits directly affect ecosystem functions. At the species level, trait combinations depend on trade-offs representing different ecological strategies, but at the community level trait combinations are expected to be decoupled from these trade-offs because different strategies can facilitate co-existence within communities. A key question is to what extent community-level trait composition is globally filtered and how well it is related to global versus local environmental drivers. Here, we perform a global, plot-level analysis of trait–environment relationships, using a database with more than 1.1 million vegetation plots and 26,632 plant species with trait information. Although we found a strong filtering of 17 functional traits, similar climate and soil conditions support communities differing greatly in mean trait values. The two main community trait axes that capture half of the global trait variation (plant stature and resource acquisitiveness) reflect the trade-offs at the species level but are weakly associated with climate and soil conditions at the global scale. Similarly, within-plot trait variation does not vary systematically with macro-environment. Our results indicate that, at fine spatial grain, macro-environmental drivers are much less important for functional trait composition than has been assumed from floristic analyses restricted to co-occurrence in large grid cells. Instead, trait combinations seem to be predominantly filtered by local-scale factors such as disturbance, fine-scale soil conditions, niche partitioning and biotic interactions.

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Martin Novak about Isotope constraints on N2-fixation and denitrification

Seminar Centre of Excellence EcolChange

Speaker: Dr. Martin Novak from Czech Geological Survey, Prague

Title of the talk: Isotope constraints on N2-fixation and denitrification in Central European peatlands

Additionaly: local PhD students – Alisa Krasnova, Thomas Schindler, Mohit Masta – will make presentations on nitrogen cycling research; and there will be given information about the BIOGEOMON 2020 conference in Tartu

Time: Tuesday, 20. November 2018 at 16.00

PlaceDepartment of Geography, UT, Vanemuise 46, J.G. Granö auditory (327)


Presentations about nitrogen are all about entertainment! (pic from here)


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