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

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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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New publication – Plant diversity in oceanic archipelagos: realistic patterns emulated by an agent-based computer simulation

Text by Madli Jõks

Simulated islands help to untangle the secrets of biodiversity

Volcanic islands emerge empty from the sea and thus, offer a unique change to study how plant- and animal species colonize new areas. They have been in the focus on interest of biogeographers for centuries and are known as hotspots for biodiversity as well as for extinctions. Unfortunately, even several centuries are a time too short to observe evolution and dispersal processes in live. That often makes difficult to study the mechanisms behind the curious patterns of island biodiversity.

Computer simulations, which allow us to emulate the possible processes responsible for insular biodiversity development, might come in handy in this situation. Scientist of the macroecology workgroup in University of Tartu Madli Jõks and Meelis Pärtel used a computer simulation to study the plant communities of Hawaii, Galapagos, Canary Islands, Azores and Cape Verde. Their aim was to understand, which factors design species richness and composition on the islands: is it mainly island area, habitat diversity or the position in the archipelago?

The aim was approached by altering archipelago maps to create realistic and less realistic situations in which island biodiversity might have developed during the millions of years. These maps were then used as arena for simulations which emulated immigration and dispersal processes, as well as competition between the species, evolution and extinction. As these simulations are more than an ordinary computer can handle, the help of the High Performance Computing Centre of the University of Tartu was used.

It became apparent that the results were more realistic when the virtual islands contained many different habitats; scenarios where the islands were covered with one consistent habitat didn’t give results quite as accurate. From the results, it can be concluded that the diversity of the habitats has been a more important factor of island biodiversity than had been previously assumed.

To test the importance of the spatial configuration of islands, simulations with randomly relocated islands were used. The right positioning of the islands was found to be important for getting a realistic composition of species only in more elongated archipelagos: in Hawaii, Azores and Canary Islands. That also makes perfect sense: when the configuration of islands is randomly changed in an elongated archipelago, the islands are likely to be further away from their actual neighbours, and islands which were initially further away will become their new neighbours.

But why study oceanic islands in Estonia? Islands, especially oceanic islands, are primarily great model systems. Knowledge about how species disperse between habitat fragments or diverge due to geographic barriers can be applied to the study and protection of other island-like communities, e.g., patches of forest left between clear-cut areas.

Citation: Jõks. M, & Pärtel, M. (2018). Plant diversity in oceanic archipelagos: realistic patterns emulated by an agent-based computer simulation, Ecography, (link to full text)


Current primary dispersal corridors to Canary Islands (pic from here)


Although islands as natural laboratories have held the attention of scientists for centuries, they continue to offer new study questions, especially in the context of the current biodiversity crisis. To date, habitat diversity on islands and spatial configuration of archipelagos have received less attention than classical island area and isolation. Moreover, in the field where experiments are impossible, correlative methods have dominated, despite the call for more mechanistic approaches. We developed an agent‐based computer simulation to study the effect of habitat diversity and archipelago configuration on plant species richness and composition in five archipelagos worldwide (Hawaii, Galapagos, Canary Islands, Cape Verde and Azores) and compared simulated diversity patterns to the empirical data. Habitat diversity proved to be an important factor to achieve realistic simulation results in all five archipelagos, whereas spatial structure of archipelagos was important in more elongated archipelagos. In most cases, simulation results correlate stronger with spermatophyte than with pteridophyte data, which we suggest can be attributed to the different dispersal and evolution rates of the two species groups. Correlation strength between simulated and observed diversity also varied among archipelagos, suggesting that geological and biogeographic histories of archipelagos have affected the species richness and composition on the islands. Our study demonstrates that a relatively simple computer simulation involving just a few essential processes can largely emulate patterns of archipelagic species richness and composition and serve as a powerful additional method to complement empirical approaches.

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Andres Metspalu about biobanks and personalized medicine

Seminar of Department of Botany and Centre of Excellence EcolChange

Speaker: Andres Metspalu is professor of biotechnology at the Institute of Molecular and Cell Biology, University of Tartu, and head of Estonian Genome Centre.

Title of the talk: From biobanking to personalized medicine

Time: Thursday, 15. November 2018 at 15.15

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


Andres Metspalu (pic from

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DOI codes will be used parallel to species names

Text from Research in Estonia page (link to the original post)

Scientists at the University of Tartu created a new method for communicating species. The classification initiated by Carl von Linné, which has lasted for over 200 years, does not take current scientific methods into account.

The mycologists and taxonomists working under the Natural History Museum and the Botanical Garden of the University of Tartu have so far been known as the creators of the eBiodiversity portal and the PlutoF platform. But now we can say that 10 years of work has resulted in the creation of a new international system that facilitates the classification of species.

Let’s start from the beginning. When a new species is discovered and being described, it is given a scientific name in Latin (e.g., the Brachyzapus greengoblin discovered recently by scientists from Tartu), the species will belong to some specific genus and family, etc. Often, it later becomes apparent that the initial classification was incorrect and the species name has to be changed – more trouble than necessary.

Furthermore, new modern work methods are now being used to search for species in an environment without catching them. For example, a water sample from one lake contains the DNA of all the fish living there (through faeces, fish slime as well as other excretions). Thus, describing the species living in an environment through a DNA analysis of a sample from this environment is becoming the most common work method used by scientists.

This is also the work method for mycologists, for example, studying the fungi that form symbiotic relationships with plant roots. The amount of microfungi found in soil is immense and they can all be found by simply separating their DNAs from the soil sample in a laboratory. In its essence, DNA is only a code, a nucleotide sequence. However, knowing this code is not that helpful as not all the DNA sequences of the world’s species have been correlated with the species names and there is no database that would let you know the name of the species by entering the DNA sequence.

The research group led by the professor of mycology, Urmas Kõljalg, at the University of Tartu, developed a database just for this purpose. However, this database is initially only for fungi. “We created a communication system so these species found via DNA could be communicated without knowing the names of the taxon (e.g., species, genus, etc. – ed.)”, explained Kõljalg. “Many species are only known based on their DNA: for example, analysing microfungi in soil. A large part of these have also not been described for science. Some have been described between 50 and 100 years ago but only based on their visible portion and this cannot be connected to the DNA collected from the sample.”

To associate a DNA sample with a specific species, you will need to assign this sample a unique name or code as the DNA sequence itself is too cumbersome – long and varying. The DOI (Digital Object Identifier) code known from scientific literature was chosen as this code. Every research ever published has its own unique DOI code that is constant in time, so this code can always be used to find the one specific research from the databases of scientific literature all over the world. DOI codes are given out by the International Certification Centre and the right of issuing DOI codes (in this instance, to fungal species or more specifically to their DNA samples instead of articles) was also granted to the Natural History Museum.

“For this purpose, we have a separate global database named ‘UNITE’, which we started and manage, and employs hundreds of people. Certain gene sequences have been gathered together from all over the world, and based on these, species and DNA-based species have been calculated. Then we simply built a communication system on top of it, which is an alternative to Linné’s system and based on DOIs, the same as journal articles. Every species has its own DOI code, which is an identifier that is stable in time.”

Scientists basically managed to develop a tool, which will tell the researcher who lives in the environment they are studying solely on the basis of DNA samples.

“That’s right”, said Kõljalg. “And it works almost on all fungi in the world. Little by little, we will start with other groups as well.”

The receipt of the right to issue DOI codes is also an interesting story – it happened as recently as during the years 2013–2014.

“Before DOIs, we created our own unique and stable identifiers. But the internationally recognised system is much better. And when we got the right to issue an indefinite number of DOIs, we issued half a million of them at the first go. And then these went to the headquarters in Germany, where they register these DOIs, and it was silent for a while. These DOIs are meant for scientific data and at that time there were only a couple of thousands of codes issued for scientific data in the world. And then we barged in with half a million. And then they looked at it for a while and said that ‘oh, this is a clever idea indeed’ (Urmas laughs).”

The DOI codes issued to species (and to be precise, to species hypothesis) enable the scientists working with wildlife classification to enter the modern world of data. Systematists constantly work with species names and the definition of one species often changes a couple of times a year. Now, however, every DOI code marks one definition made at a given moment in time, and all the old and new definitions are linked in databases.

“For example, if someone carries out a study of soil biota today and finds out who (whose DNA) is found in the soil somewhere, and then, 10 years later, someone conducts the same study and wants to compare the results of the two studies, then it is possible, because even if the species have been relocated in the interim, the digital connections between the new and old species have been retained. All of this is possible thanks to digital solutions”, exclaimed Urmas Kõljalg with anticipation for the use of the new system.

'Turn right at the Robinia pseudoacacia, pass the garden with the salvia officinalis, cross the road when you see the stranvaesia davidinia and the pub is on the left!'

DOIs will be DOIs! (pic from here)


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EcolChange seminar – Melissa McCormick about orchid mycorrhiza

Seminar of Department of Botany and Centre of Excellence EcolChange

Speaker: Melissa McCormick is ecologist at the Smithsonian Environmental Research Center, USA. She visitis Department of Botany to act as opponent at the PhD defence of Jane Oja on November 8th, at 9.15 AM in Vaga auditorium, Lai 40-218, Tartu.

Title of the talk: The fungal half of the mycorrhizal equation: how fungi affect orchid population dynamics

Time: Wednesday, 7. November 2018 at 16.15

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

Say it with Flowers: 'Late - daffs. Drunk - roses. Stag party - carnations. Adultery - orchids.'

Some orchid-related semiotics (pic from here)

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EcolChange seminar – Ebe Merilo about stomatal regulation of crops

Seminar of Department of Botany and Centre of Excellence EcolChange

Speaker: Ebe Merilo is senior researcher at the Institute of Technology, University of Tartu.

Title of the talk: Stomatal regulation of crops

Time: Thursday, 25. October 2018 at 15.15

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

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