EcolChange seminar – Bengt-Gunnar Jonsson about the forest cover changes in Scandinavia

Seminar of Department of Botany and Centre of Excellence EcolChange

Speaker: Bengt-Gunnar Jonsson is Professor of Plant Ecology at Mid Sweden University. His research focuses on forest history and dynamics and its role in maintaining forest biodiversity. He has played an active role in several national conservation projects initiated by the Swedish Environmental Protection Agency and the Swedish Forest Agency. He is the author and editor of number of books, including “Biodiversity in dead wood“. Prof. Jonsson is also a lead author of IPBES (Intergovermental Science-Policy Platform on Biodiversity and Ecosystem Services) European and Central Asia assessment, focusing on topics of forestry and forest land use.

Title of the talk: Coping with the loss of the last – the Scandinavian Green Belt and boreal forest green infrastructure in the northern Sweden

Time: Wednesday, 17. October 2018 at 15.15

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


Boreal forest (pic from here)

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Two more global citizen science networks calling for participants – FunLeaf and FunHome

Last week we had a post about DarkDivNet, a global network to explore the dark diversity of plant communities, instigated by Meelis Pärtel´s macroecology workgroup in the University of Tartu.

Now the Natural History Museum in Tartu, led by Urmas Kõljalg, has started with two global citizen science networks: FunLeaf to study the diversity of fungi and bacteria living in and on plant leaves; and FunHome to study the diversity of microscopic organisms living in the dusty corners of our homes.

Below you can find a little overview of both projects, for more information click the links to project web pages.

Cleaner dusts the letters of a book.

This is literally how you can do science, although not all the are nucleotides depicted with the right letter symbols… (pic from here)

FunLeaf (link to project page)

All parts of plants harbour many microscopic organisms. Especially plant leaves are an important habitat for many fungal and bacterial species that live inside or on the surface of these organs. Yet, very little is known about the diversity and distribution of these microorganisms in relation to habitat, seasonality and geographical space.

This citizen science project, led by well-recognized researchers, aims to describe the biodiversity of organisms associated with plant leaves across the globe. By using DNA-based methods for identification, scientists aim to determine the environmental features that lead to increase or loss of leaf biodiversity. Mathematical models enable to estimate total species richness of microorganisms on leaves to add one piece to the puzzle of global biodiversity.

This project seeks for volunteers who wish to contribute to understanding of complexity of life on the Earth. Participants are given simple protocols for collecting and sterilizing and posting leaf samples. The DNA of dead organisms is analysed only for identification purpose in one or more central laboratories. The results are communicated to participants over the web in each major analysis step. The principal idea of involving citizen science is to bridge frontline research and common people and to shed light on global issues among the public.


FunHome (link to project page)

Households of families harbour dust, which is comprised of particles of fibers and skin and many other biological components including pollen, parts of arthropods and various microscopic organisms. These nutrient-rich substances serve as a substrate for mites and moulds, many of which are severe allergens. Some information exists about the diversity of bacteria and fungi in dust in US homes (doi:10.1073/pnas.1420815112), but information about other organisms and from the entire world is almost lacking (doi:10.1073/pnas.1000454107).

The FunHome citizen science project extends from another public project focused on homes in USA (, which has received abundant public feedback and resulted in international scientific publications. The FunHome project is initiated by leading researchers in microbial ecology, with an objective to describe the biodiversity of microbes, plants and animals in household dust across the globe. By using DNA-based methods for identification, scientists aim to determine the global distribution patterns of dust-associated organisms with a focus on particularly toxin-producing species.

Hereby, the project leaders invite volunteers to contribute to a global understanding about the biological composition of dust in the home environment. Participants are provided simple protocols for collecting and storing and posting dust samples. The DNA from dust is analysed in a single central laboratory in the University of Tartu, Estonia. The results are communicated to participants over the web after major analysis steps.


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New publication – Non-native species led to marked shifts in functional diversity of the world freshwater fish faunas

Text by Aurele Toussaint

The biodiversity of freshwater fish fauna disturbed by invasive species

Non-native species introductions are recognized as one of the major drivers responsible of the ongoing sixth biodiversity crisis, along with climate change, pollution and habitat loss. However, this factor is most often only addressed in terms of increasing or decreasing in number of species, leaving unclear its impact on the functional diversity of communities (i.e. the diversity of ecological roles provide by species in ecosystems). An international team of researchers from the Institute of Ecology and Earth Sciences (Department of Botany/ University of Tartu/ Estonia), the Evolution and Biodiversity Laboratory (EDB – CNRS / University of Toulouse III Paul Sabatier / IRD) and the Center for Marine Biodiversity, Exploitation and Conservation (MARBEC – CNRS / University Montpellier / IRD / Ifremer) has just shown that while the number of fish species per river increased on average by 15% in the world’s rivers, the diversity of their functional attributes increased on average by 150% under the pressure of non-native fish introductions. These results, published in the November issue of the journal Ecology Letters, highlight the need to consider different facets of biodiversity in order to evaluate the impact of biological invasions on ecosystems.

Human activities has promoted biotic exchanges between regions for centuries, for food, commercial, ornamental and even involuntary purposes by carrying organisms unknowingly. As a result, several hundreds of species of freshwater fish are now established outside their native area. The survey of these introductions in the rivers of the world is rather well known and has already shown that the non-natives species introductions have resulted in an increase of about 15%, on average, of the number of species per river. However, it remained to be tested whether these non-native species share or not similar ecological characteristics to the species already present (native species) and therefore have or not led to an increase in the functional diversity of the communities. Toward this goal researchers have measured the morphological traits associated with locomotion and nutrition for more than 9,000 species of freshwater fish out of the 13,000 currently known. We demonstrated in this study that the 15% average increase in the number of species per river simultaneously caused an unexpected 150% increase of the functional diversity of the community!

While the very large rivers, such as the Amazon or Mississippi, have undergone few functional changes under the introduction of non-native species, the small rivers have undergone an explosion of their functional diversity because the introduced species have very different ecological traits from those of the species already present. This trend is particularly striking in arid and Mediterranean rivers, which naturally host few highly specialized species. Thus, in the Alpes-Maritimes for example, the Siagne river hosts historically 9 fish native species, but received under the effect of the human activities 6 non-native species. Among them the Carp, originating from Asia and Black Bass native to North America which have multiplied the original functional diversity of the community by more than 40.

More generally, at the world scale, we observed an increase in the average body size of fishes and an overrepresentation of laterally flattened species (such as carp or black bass) in communities under the introduction pressure. These functional changes are probably related to the effects of dams that favor the establishment of non-native species able to move and survive in a stagnant environment.

As conclusion of this study, we already knew that non-native species have a strong impact on the taxonomic diversity worldwide but we here demonstrate that considering the functional role of organisms is clearly a key point in order to better understand the impact of non-native species on biological communities.

aurele fish

World maps representing the changes in biodiversity due to non-native species introductions in terms of number of species (top) and in functional diversity (low)

Citation: Toussaint, A., Charpin, N., Beauchard, O., Grenouillet, G., Oberdorff, T., Tedesco, P. A., … & Villéger, S. (2018). Non‐native species led to marked shifts in functional diversity of the world freshwater fish faunas. Ecology Letters, 21: 1649–1659 (link to full text)



Global spread of non‐native species profoundly changed the world biodiversity patterns, but how it translates into functional changes remains unanswered at the world scale. We here show that while in two centuries the number of fish species per river increased on average by 15% in 1569 basins worldwide, the diversity of their functional attributes (i.e. functional richness) increased on average by 150%. The inflation of functional richness was paired with changes in the functional structure of assemblages, with shifts of species position toward the border of the functional space of assemblages (i.e. increased functional divergence). Non‐native species moreover caused shifts in functional identity toward higher body sized and less elongated species for most of assemblages throughout the world. Although varying between rivers and biogeographic realms, such changes in the different facets of functional diversity might still increase in the future through increasing species invasion and may further modify ecosystem functioning.

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New publication – Didymocyrtis trassii sp. nov. and other lichenicolous fungi on Cetraria aculeata

Text by Lauri Laanisto

Time for another taxonomy paper about fungi. (The previous blogpost about that can be found from here.) This time about new species that grow on lichens, specifically Cetraria aculeata. Genus Cetraria is called cuckoo´s ear in Estonian, by the way… One of the species that was found from these cuckoo ears in Ukranian sand dunes appeared to be new to species. And this species is now called Didymocyrtis trassii. Another trivia fact about names – Didymocyrtis is both a genus of fungi, but also a genus of Radiolaria (protozoa).


Didymocyrtis the radiolara (pic from here)


Didymocyrtisthe fungus (pic from here)

But in our case, the most important name here is trassii, the epithet of the new fungus species. The species is named after recently deceased Hans Trass (1928-2017), a renowned Estonian lichenologist. By the way he was first to publish how certain lichen species indicate air quality – e.g. bioindicators. Hans Trass was also the head of Botany and Ecology department for more than 30 years, and most of the PIs of EcolChange still work or have previously worked in this department under the Peremees – this was his nickname. (Including yours truly.)


Hans Trass (pic from here)

Citation: Khodosovtsev, A., Darmostuk, V., Suija, A., & Ordynets, A. (2018). Didymocyrtis trassii sp. nov. and other lichenicolous fungi on Cetraria aculeata. The Lichenologist, 50(5), 529-540. (link to full text)


Recently, nine species of lichenicolous fungi were found growing on Cetraria aculeata (Parmeliaceae) in a sand dune system in the Ukraine. One of them, Didymocyrtis trassii, is described here as new to science. This species is similar to D. pseudeverniae but differs in having smaller pycnidia, smaller obpyriform to clavate conidia as well as its DNA sequence. The new monotypic lichenicolous genus Katherinomyces is described here. Acremonium lichenicola s. l., Eonema pyriforme, Didymocyrtis cladoniicola and Lichenoconium erodensare reported for the first time on Cetraria aculeata. Furthermore, E. pyriforme is reported for the first time from lichen thalli. Acremonium lichenicola, E. pyriforme and Taeniolella rolfiiare new for the mycobiota of the Ukraine. A key to the eleven known lichenicolous species on Cetraria aculeata is provided.

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EcolChange seminar – Nele Ingerpuu about the new trends in bryology

Seminar of Department of Botany and Centre of Excellence EcolChange

Speaker: Nele Ingerpuu is senior researcher at the Department of Botany, Tartu University.

Title of the talk: Some new trends in bryology 

Time: Tuesday, 04. October 2018 at 15.15

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

Summary: New developments in bryophyte taxonomy are presented. Some studies on growth of mosses and diaspore banks are introduced. An overview about the new red data list of Estonian bryophytes and monitoring methods is given.


The most famous Moss was pretty trendy! (pic from “The IT Crowd“)


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DarkDivNet – Call for participants

DarkDivNet is a global network to explore the dark diversity of plant communities.

Why are some species present and others absent in a locality? To answer this central ecological and biogeographical question, we have to explore biodiversity at different spatial scales while also considering species’ habitat preferences. Only a subset of all species in a region can tolerate the ecological conditions of a given site (the site-specific species pool). Of those, not all are realized in local communities. The absent part of the species pool forms the dark diversity of a community.


Why dark diversity?

If we know the size and composition of dark diversity, we are better equipped to understand and protect biodiversity. Information about the dark diversity allows:

  • to estimate site relative diversity: how many suitable species are present compared to those that are absent (community completeness)
  • to compare of diversity across regions and habitat types
  • to detect processes shaping species presences and absences
  • to evaluate the conservation value and restoration potential


Why DarkDivNet?

In the last years, several coordinated global samplings have advanced our understanding of global biodiversity patterns. DarkDivNet is a global collaboration of researchers interested in dark diversity. It includes globally replicated vegetation surveys comprising both local and regional scales with the main aims:

  • to determine observed and dark diversity, species pool and community completeness, and link them to geographical and environmental gradients, anthropogenic disturbance, and interactions with soil biota (sampled with eDNA)
  • to test different methods to predict dark diversity
  • to evaluate whether locally collected empirical information on species co-occurrences can be substituted by the use of available large vegetation databases
  • to expand the dark diversity concept from purely taxonomy-based approaches to include the functional and phylogenetic aspects of diversity.

DarkDivNet is currently open to add new participants from all over the world. Read the protocols about guidelines for participation, the sampling methods, and the publication plan from the webpage. We devise that DarkDivNet will result in several major publications.

The network is coordinated by the Steering Committee of researchers at the University of Tartu: Meelis Pärtel, Carlos P. Carmona, Martin Zobel, Mari Moora, Kersti Riibak, Riin Tamme. The network activities are advised by a panel of international experts: Jon Bennett (Canada), Milan Chytrý (Czechia), Ove Eriksson (Sweden), Susan Harrison (United States), Rob Lewis (Denmark), Angela Moles (Australia), Maarja Öpik (Estonia), Jodi Price (Australia)

Contact us at


The Steering Committee: (from left) Riin Tamme, Carlos P. Carmona, Mari Moora, Kersti Riibak, Martin Zobel, Meelis Pärtel

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New publication – Genetic differentiation, phenotypic plasticity and adaptation in a hybridizing pair of a more common and a less common Carex species

Text and pic by Lisanna Schmidt

Species experience heterogeneous environments across their distribution area. Different biotic and abiotic factors affect populations within species and often result in regional differentiation. Under differing selection pressures, populations vary in their plastic and adaptive response. Life history traits and population characteristics shape the direction and strength of the response, among others commonness and frequency of species and populations size. Besides, hybridization between closely related taxa may affect their regional differentiation.

We performed a reciprocal transplant experiment with two closely related sedge species Carex flava and C. viridula, who differ in their commonness and population size. Putative hybrid individuals collected in the sites where the two taxa co-occurred were added to the experiment. This paper demonstrates the effect of environment and climatic factors on the phenotype and performance of two hybridizing sedge taxa and their putative hybrid. The two taxa showed some common evolutionary patterns where they co-occur in the same region, but also differences suggesting a high degree of independent evolution. Hybrids performed well in all transplant sites. Moreover, differential adaptation and maladaptation were detected and reasons discussed. Overall, our results indicate that plasticity, genetically determined variation and GxE interactions all contribute to regional differentiation of the closely related study species. Hybridization did not lead to completely parallel evolutionary patterns, but the less common species´ showed slightly more genetic differentiation between populations than the more common species, while the latter showed more evidence for regional adaptation.


Citation: Schmidt, L., Schmid, B., Oja, T., & Fischer, M. (2018). Genetic differentiation, phenotypic plasticity and adaptation in a hybridizing pair of a more common and a less common Carex species. Alpine Botany, (link to full text)lisanna sept 2018

C. flava, C. viridula and their putative hybrid, independent of their origin region, responded to the environmental conditions in high elevation transplant garden (Schynige Platte, Switzerland 1976 m.a.s.l.) with reduced growth



Phenotypic variation may be genetically determined or reflect phenotypic plasticity. More common plants are expected to be less differentiated between and within regions and more adapted than less common ones. However, such differences might not develop in hybridizing species which cannot evolve completely independently. We collected 311 genets of Carex flava, 215 of C. viridula and 46 of their hybrid C. × subviridula from 42 natural populations in cold temperate Estonia, mild temperate Lowland Switzerland and alpine Highland Switzerland. Three plantlets from each genet were planted to three experimental gardens, one in each region. We measured survival, growth, reproduction and morphological traits. The experimental transplants showed strong plasticity and grew smallest in the alpine garden. The less common C. viridula was slightly more differentiated between regions of origin than the more common C. flava and the hybrid. However, this depended on the experimental garden. Significant origin-by-garden-by-taxon and taxon-by-garden interactions suggest differential adaptation among populations and taxa. Regional differed from non-regional plants in several traits indicating both adaptations and, especially for C. viridula, maladaptations to the home regions. For C. flava, plant seed production was higher when mean annual temperature and precipitation were more similar between population of origin and garden, suggesting local adaptation to climate. Hybrids were intermediate between parental taxa or more similar to one of them, which was retained across gardens. We conclude that plasticity, genetic variation and genotype–environment interactions all contributed to regional differentiation of the closely related species. Hybridization did not completely align evolutionary patterns, and the less common species showed slightly more genetic differentiation between populations and more maladapted traits than the more common one.

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New publication – Inoculation of Brevibacterium linens RS16 in Oryza sativa genotypes enhanced salinity resistance: impacts on photosynthetic traits and foliar volatile emissions

Text by Ülo Niinemets

A collaboration between the scientists from Estonian University of Life Sciences and Chungbuk National University, South Korea demonstrates how plant growth-promoting bacteria enhance plant salinity tolerance

Soil salinity is one of the key abiotic stress factor affecting agricultural productivity worldwide. Every day, nearly 2000 hectares of fertile agricultural land degrades due to salinity. There are only limited agricultural options to cope with increasing salinification of soils, especially in the case of salt sensitive staple crops such as rice and wheat, productivity of which is seriously curbed due to salinity in many Earth locations. Among the possible options, plant growth-promoting bacteria (PGPB) have a large potential to improve crop plant productivity under salinity, but the progress in application of PGPB has been slow due to lack of non-invasive methodology for testing the efficiency of different bacteria in increasing plant salt resistance. The present collaborative study by scientists of Chungbuk National University, South Korea and the Estonian University of Life Sciences looked at foliage volatile emission and photosynthetic traits as potential non-invasive markers to estimate improvements in salinity resistance upon inoculation of rice plants with plant growth-promoting rhizosphere bacterium (PGPR) Brevibacterium linens RS16 .

This work was mainly focused on controlling the volatile organic compound (VOC) emission of plants. Though VOC emission is a part of plant defense, but it has a large impact to the environment and climate change, so the control of VOC emission from plants is still a complex and open question. “This study gives us a preliminary idea about the efficiency of 1-aminocyclopropane-1-carboxylate (ACC) deaminase producing plant growth promoting bacteria Brevibacterium linens RS16 in altering volatile emission and photosynthetic traits in conjunction with ameliorating salt stress. It also shows a strong negative relationship with foliage ethylene and volatile emission responses and a strong positive correlation with net carbon assimilation rate” said Poulami Chatterjee, the doctoral student from Chungbuk National University.

Enhanced salinity induces oxidative stress in plants, primarily by reducing the osmotic potential of soil water. Salt stress-driven accumulation of cellular Na+ above a threshold in chloroplasts causes tissue damage and increases the rate of chlorosis. The enhanced salinity above a threshold in soil declines osmotic potential of mesophyll cells and in turn, it curbs photosynthetic electron transport activities, ultimately leading to a significant reduction in photosynthesis. In the present study, we used IR29 (salt-sensitive) and FL478 (moderately salt resistant) rice cultivars, to assess foliage carbon assimilation and stress volatile emission rates in response to inoculation by the halotolerant PGPB B. linens RS16 followed by the application of salt in soil.

Inoculation of rice plants with ACC deaminase-containing B. linens RS16 alleviated the severity of salt-stress, characterized by enhanced foliage photosynthetic traits and decreased stress volatile emissions after stress applications, greater changes detected for salt-sensitive cultivar IR29 than for moderately salt resistant genotype FL478. In addition, maintenance of high level of Fv/Fm in bacterially-inoculated salt-stressed plants suggests that the integrity of photosynthetic apparatus was maintained upon bacterial inoculation. In fact, reduction in Na+ uptake from saline-soil water is likely associated with the ability of bacteria to bind Na+ with surface polysaccharides since the sequestration of Na+ into the vacuole is also a key strategy for adjusting osmotic potential.

“Salt stress is observed to have a strong effect on photosynthetic traits and volatile emissions, thus screening photosynthetic characteristics and volatile emissions as non-invasive tools under salinity can provide illuminative insight into the severity of stress as well as induction of various primary and secondary metabolic pathways through progression of stress” said Professor Ülo Niinemets of Estonian University of Lifesciences, who led the present study along with Professor Tong-Min Sa of Chungbuk National University.


In addition, this study showed that salt stress negatively affected foliage photosynthetic characteristics in both rice cultivars with more progressive reduction observed in salt sensitive cultivar, IR29 than moderately salt resistant, FL478. Moreover, salinity enhanced the emission rates of foliage stress volatiles, particularly ethylene, lipoxygenase pathway volatiles, light-weight oxygenated volatiles, long-chained saturated aldehydes, benzenoids, geranylgeranyl diphosphate pathway products, and mono- and sesquiterpenes. However, B. linens RS16 inoculation significantly improved photosynthetic characteristics and reduced the volatile emission in salt stressed rice cultivars, compared to control plants. The decrease in volatile emission upon bacterial inoculation may likely be associated with reduced foliar ACC accumulation and ACC oxidase activity catalyzed by ACC deaminase. “Overall, this work will be useful to explore novel characteristics of PGPR under saline environments and further outlines the feasibility of foliage spray of B. linens RS16 in realistic biological settings in fields as a cost-effective strategy to cope with salt-stress, associated with greater economic losses in salt-sensitive crops” mentioned by Prof. Tongmin Sa, from Chungbuk National University.


 A – healthy rice plants, and B- salt-affected rice plants (Photo courtesy: IRRI, Philippines)


 C – salt-affected rice field, and B – healthy rice field (Photo courtesy: Chungbuk National University, South Korea)

The collaboration among the participating teams was supported by a collaboration with the framework of European Research Council (ERC) – Korean National Science Foundation collaborative agreements that allowed the Estonian partner team led Prof. Ülo Niinemets working in the field of plant stress biology and volatile emissions to team up with the Korean microbiology team led by Prof. Tongming Sa.


Citation: Chatterjee, P., Kanagendran, A., Samaddar, S., Pazouki, L., Sa, T. M., & Niinemets, Ü. (2018). Inoculation of Brevibacterium linens RS16 in Oryza sativa genotypes enhanced salinity resistance: Impacts on photosynthetic traits and foliar volatile emissions. Science of the Total Environment, 645, 721-732. (link to full text)



The emission of volatiles in response to salt stress in rice cultivars has not been studied much to date. Studies addressing the regulation of stress induced volatile emission by halotolerant plant growth promoting bacteria containing ACC (1-aminocyclopropane-1-carboxylate) deaminase are also limited. The objective of the present study was to investigate the salt alleviation potential of bacteria by regulating photosynthetic characteristics and volatile emissions in rice cultivars, and to compare the effects of the bacteria inoculation and salt responses between two rice genotypes. The interactive effects of soil salinity (0, 50, and 100 mM NaCl) and inoculation with Brevibacterium linens RS16 on ACC accumulation, ACC oxidase activity, carbon assimilation and stress volatile emissions after stress application were studied in the moderately salt resistant (FL478) and the salt-sensitive (IR29) rice (Oryza sativa L.) cultivars. It was observed that salt stress reduced foliage photosynthetic rate, but induced foliage ACC accumulation, foliage ACC oxidase activity, and the emissions of all the major classes of volatile organic compounds (VOCs) including the lipoxygenase pathway volatiles, light-weight oxygenated volatiles, long-chained saturated aldehydes, benzenoids, geranylgeranyl diphosphate pathway products, and mono- and sesquiterpenes. All these characteristics scaled up quantitatively with increasing salt stress. The effects of salt stress were more pronounced in the salt-sensitive genotype IR29 compared to the moderately salt resistant FL478 genotype. However, the bacterial inoculation significantly enhanced photosynthesis, and decreased ACC accumulation and the ACC oxidase activity, and VOC emissions both in control and salt-treated plants. Taken together, these results suggested that the ACC deaminase-containing Brevibacterium linens RS16 reduces the temporal regulation of VOC emissions and increases the plant physiological activity by reducing the availability of ethylene precursor ACC and the ACC oxidase activity under salt stress.

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New publication – Acclimation of Fine Root Systems to Soil Warming: Comparison of an Experimental Setup and a Natural Soil Temperature Gradient

Text by Kaarin Parts

Global warming is predicted to impact high-latitude and high-altitude forests severely, jeopardizing their overall functioning and carbon storage, both of which depend on the warming response of tree fine root systems. This paper investigates the effect of soil warming on the biomass, morphology and colonizing ectomycorrhizal community of spruce fine and absorptive fine roots. Spruce was chosen for this study due to its economical importance and wide distribution in temperate and boreal European forests, while its shallow root system makes it especially susceptible to soil surface warming. We compared the responses of spruce roots growing at a man-made long-term soil warming (+ 4°C) experiment to results obtained from a geothermal soil temperature gradient (+ 1 to + 14°C) extending to the forest die-off edge, to shed light on the generalizability of the warming response and reveal any thresholds in acclimation ability.

Trees in warmer soils formed longer and less-branched absorptive roots with higher specific root length and area, and lower root tissue density in both spruce stands, irrespective of warming method and location. We attribute these changes to diminished root tip proliferation and reduced lifetime of absorptive roots, but also higher metabolic activity. Soil warming at the experimental warming site also supported the occurrence of a more varied ectomycorrhizal community and an increase in the abundance of Tomentella spp., indicating a shift in nutrient foraging. Fine and absorptive fine root biomass decreased toward warmer soil, with a sharp reduction occurring between + 4 and + 6°C from the ambient and leading to the collapse of the fine root system at the geothermal gradient. At the experimental warming site, the applied + 4°C warming had no effect on fine and absorptive fine root biomass. The similar fine root responses at the two warming sites suggest that the observations possibly reflect general acclimation patterns in spruce forests to global warming.

Citation: Parts, K., Tedersoo, L., Schindlbacher, A., Sigurdsson, B. D., Leblans, N. I. W., Oddsdottir, E. S., Borken, W., Ostonen, I. (2018). Acclimation of Fine Root Systems to Soil Warming: Comparison of an Experimental Setup and a Natural Soil Temperature Gradient. Ecosystems, DOI: 10.1007/s10021-018-0280-y (link to full text)

'Ha ha, stop tickling me, Billy!'

The real fine-root dynamics in trees.. (pic from here)

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New paper out – Structure and function of the global topsoil microbiome

/Editor´s note: It´s been silence in the blog throughout summer, as we all had a lot of field and lab work. But we´re back now!/

The first global study of soil genomics revealed a battle right under our feet. The clash between fungi and bacteria and research into this topic may benefit both farmers and the pharmaceutical industry.

The microscopic fungi that inhabit soil are essential for plant growth, but they are constantly at war with bacteria in order to survive. The discovery was made by an international research team led by the European Molecular Biology Laboratory (EMBL) and the University of Tartu in Estonia. The results of the study were recently published in Nature.

The lead authors of the study are Mohamad Bahram from the University of Tartu and Falk Hildebrand from the EMBL. They are the first scientists to study bacteria and fungi found in soil all across the world.

The research showed that only 0.5% of the millions of genes found in soil are familiar to us from gut and ocean microbiomes. “The number of unknown genes is overwhelming, but the ones we can interpret clearly point to a global war between bacteria and fungi in soil,” says Peer Bork, EMBL group leader and corresponding author of the paper.

This new knowledge can help predict the impact of climate change on soil and help us make better use of natural soil components in agriculture. This is important because climate change and extensive use of synthetic fertilisers have considerably decreased the diversity of the soil microbiome. The soil microbiome is a microsystem that consists of bacteria, microfungi, unicellular organisms and other microorganisms that are invisible to the naked eye. The reduction in the biodiversity of this system has made crop cultivation increasingly difficult.

A better understanding of the interaction between fungi and bacteria in soil could help to reduce the use of soil fertilisers in agriculture. This would give beneficial microorganisms a better chance of survival in their natural habitat.

The study also showed that fungi and bacteria that are in constant competition for nutrients produce a variety of antibiotics such as penicillin in order to gain an upper hand over one another. This can be survived only by bacteria that have sufficiently effective antibiotic-resistant genes.

This knowledge can be used to predict the spread of genes that lead to antibiotic resistance in different ecosystems and the ways they may reach human pathogens, i.e. disease-producing agents. This in turn can be used to pinpoint locations with high levels of natural antibiotic producers. This can greatly benefit the medical industry, as the rapid development of resilient bacteria has made finding effective antibiotics more complicated.

In order to produce such results, scientists had to get their hands dirty and analyse 58,000 soil samples collected over five years from 1,450 carefully selected sites all over the world. Forty samples were collected from each site. All of the sites had to be untouched by human activity, including by agriculture. Of the 1,450 sample sites, 189 were selected for in-depth analysis, covering the world’s most important biomes on all continents from tropical forests to tundra.

Original post by the University of Tartu (Link to post)


Bacterial robot (this one made in the University of Pennsylvania) for the future soilwars (photo from here)

Citation: Bahram, M., Hildebrand, F., Forslund, S. K., Anderson, J. L., Soudzilovskaia, N. A., Bodegom, P. M., Anslan, S., Pent, M., Põlme, S., Harend, H. …Tedersoo, L. & Huerta-Cepas, J. (2018). Structure and function of the global topsoil microbiome. Nature, 560: 233–237 (link to full text)

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