EcolChange seminar – Aveliina Helm about everyone’s nature conservation

Seminar of Department of Botany and Centre of Excellence EcolChange

Speaker: Aveliina Helm is senior researcher at macroecology workgroup of the Department of Botany.

Title of the talk: Everyone’s nature conservation – what it is and why it is needed?

Time: Thursday, 01. March 2017 at 15.15

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


Actions for protecting biodiversity need to be taken on the local scale, thus we need broad involvement of general public in conservation efforts. Everyone’s nature conservation is a concept that emphasizes the role of voluntary conservation efforts of individuals and small communities in improving the condition of habitats and species. I will introduce the conservation actions within everyone’s nature conservation and hope to have everybody’s input to the discussion about the possibilities of incentivizing general public in conservation actions.

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EcolChange seminar – Üllas Erlich about economic evaluation of nature

Seminar of Department of Botany and Centre of Excellence EcolChange

Speaker: Üllas Ehrlich is professor of environmental economics at the School of Business and Governance of Tallinn University of Technology.

Title of the talk: Economic evaluation of non-market values of nature

Time: Thursday, 22. February 2017 at 14.15

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


The ultimate market bubble (pic from here)


According to welfare economics, individuals are trying to use available goods and services in the manner and proportions that would maximize their welfare. Only some products and services have monetary equivalent or price and one can buy them on the market. Such goods are called market goods and their value or ability to raise an individual’s welfare is proportional to the market price. However, an individual’s welfare depends not only on market goods but a significant role in welfare is played also by such goods and services that are not traded in the market and therefore have no monetary equivalent in the market. Such goods are called non-market goods. Examples of non-market goods might be clean air, scenery, knowledge about biological species, for example, pandas (Ailuropoda melanoleuca). In economics, every good and service that increases an individual’s welfare has economic value. A problem is how to attribute value to non-market goods in order to make them comparable to other goods traded in the market in decision-making process. This is especially important in the case of a competitive or exclusive way of using a resource. The speaker discusses options and gives examples of the economic evaluation of non-market natural resources.

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New publication – Effects of land use on arbuscular mycorrhizal fungal communities in Estonia

Text by Siim-Kaarel Sepp

The type and intensity of land use are important drivers of local aboveground biodiversity. The same holds for arbuscular mycorrhizal (AM) fungi, but most research effort has been put into natural or, on the other hand, intensively managed habitat types. In this recent study, PhD student Siim-Kaarel Sepp and co-authors investigated the diversity patterns of AM fungi in a range of six common Estonian habitat types that also included semi-natural land use such as alvar grasslands or wooded meadows.

Surprisingly, mean AM fungal richness per sample did not differ among habitat types, but the AM fungal community composition clearly shifted with land use intensification (forest vs forest clear-cut). Meanwhile, abandonment and concurrent overgrowing of alvar grasslands only resulted in a marginal shift in AM fungal composition.

Furthermore, the study found that when comparing AM fungal communities in soil and in roots of a single host plant species, the AM fungi in roots are more similar among different habitat types. This could indicate that although little host specialization is expected in arbuscular mycorrhizal symbiosis (ca 300 AM fungal taxa interact with ca 80% of terrestrial plants), the host plant still may act as an additional filter in AM fungal community assembly by effectively selecting a suitable subset of AM fungi from the general soil species pool.

Citation: Sepp, S. K., Jairus, T., Vasar, M., Zobel, M., & Öpik, M. (2018). Effects of land use on arbuscular mycorrhizal fungal communities in Estonia. Mycorrhiza, DOI: 10.1007/s00572-018-0822-3. (link to full text)


Restored alvar grassland in Saaremaa, western Estonia (pic from here)


Arbuscular mycorrhizal (AM) fungal communities vary across habitat types, as well as across different land use types. Most relevant research, however, has focused on agricultural or other severely human-impacted ecosystems. Here, we compared AM fungal communities across six habitat types: calcareous grassland, overgrown ungrazed calcareous grassland, wooded meadow, farmyard lawn, boreonemoral forest, and boreonemoral forest clear-cut, exhibiting contrasting modes of land use. AM fungi in the roots of a single host plant species, Prunella vulgaris, and in its rhizosphere soil were identified using 454-sequencing from a total of 103 samples from 12 sites in Estonia. Mean AM fungal taxon richness per sample did not differ among habitats. AM fungal community composition, however, was significantly different among habitat types. Both abandonment and land use intensification (clearcutting; trampling combined with frequent mowing) changed AM fungal community composition. The AM fungal communities in different habitat types were most similar in the roots of the single host plant species and most distinct in soil samples, suggesting a non-random pattern in host-fungal taxon interactions. The results show that AM fungal taxon composition is driven by habitat type and land use intensity, while the plant host may act as an additional filter between the available and realized AM fungal species pool.


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Ülo Niinemets receives the national research award

Text excerpts from Research in Estonia

Last week, the Government of the Republic announced this year’s laureates of the national research awards. ERR Novaator has compiled an overview of what these scientists do.

Award in the field of geology and biology

Academic Ülo Niinemets (born 1970) is a professor with the Institute of Agricultural and Environmental Sciences at the Estonian University of Life Sciences and has been given the award for his cycle of research works, “Integration and adaptation mechanisms of plant photosynthesis: from foliage gradients to global patterns.

All organisms on Earth are dependant on plant photosynthesis – it is the foundation of life. Ülo Niinemets asks: Which structural and physiological properties of plants determine the speed of photosynthesis? By posing this question he is actually asking how global climate change affects the capability of Earth’s vegetation to provide us with clean air and sufficient food. Additionally, he offers insights for developing a new generation of climate models that can predict the production of vegetation and the processes of the biosphere, while also hinting at ways to increase the yield of plants.


Ülo Niinemets (pic from Scanpix)

Ülo Niinemets has previously been presented with the following awards:

  • 2000 national research award of the Republic of Estonia (together with Olevi Kull) in the field of geology and biology for the work, “Adaptation of photosynthesis in foliage”
  • 2006 national research award of the Republic of Estonia in the field of chemistry and molecular biology for the work, “Physiology of volatile organic compound emissions”
  • 2012 Order of the White Star of the Republic of Estonia, Fourth Class
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New publication – More bang for the buck? Can arbuscular mycorrhizal fungal communities be characterized adequately alongside other fungi using general fungal primers?

Text by Maarja Öpik

How to measure things? How to measure biodiversity? For organisms which are visible to human eye, detecting them is not an issue, though identifying the species might be. The situation is fully different for organisms we cannot see with our detector (human eye) or in cases when we wish to use other detection systems, such as sequencing DNA obtained from the organisms, and subsequent identification of the sequences.

The way how it most commonly works in the DNA-based detection and identification of organisms, be they microbial or macroscopic, is first getting their DNA in a small volume of a liquid (we call it DNA extraction, from, e.g., soil). Next, the amount of DNA of interest is increased (amplified) via PCR so that it is easier to work with it, such as to sequence the DNA and match the DNA sequences against others we already know. The result of this step is dependent on the specificity of primers, short DNA fragments, which selectively bind to the DNA in the sample only if they are of the same sequence. This is like fishing in the dark and only knowing which fish was out there once we check the hook. But is our fishing hook the right one? Could we use the same hook for different kinds of fish, or do we need separate hooks for all fishes?

In our new paper, led by Ylva Lekberg (MPG Ranch, Missoula, Montana, USA; University of Montana, Missoula, Montana, USA), we asked analogous question about soil fungi: can we use general fungal primers to characterise diversity of arbuscular mycorrhizal (AM) fungi sufficiently well, or do we need to use separate primers for these fungi? There has been a lab lore around for some time that the commonly used general fungal primers do not catch AM fungi sufficiently well, and thus would underestimate their diversity. This is a problem if we want to understand both the diversity patterns of all fungi in our system, and to zoom in to specific groups, such as fungi forming arbuscular mycorrhiza.

In this paper we made use of DNA sequence data obtained by using the two kinds of “fishing hooks” in parallel: sequencing AM fungi separately, by using AM fungal specific primers, and sequencing all fungi from the same samples with general fungal primers. What was our answer? As all too often, we learned that it depends… First, we detected higher diversity of AM fungi in our samples when using AM fungal specific primers. However, when we looked at how the AM fungal diversity responded to the experimental manipulations of soil moisture, or changed during the growing seasons in nature, our two detection systems revealed the same shifts in AM fungal diversity. Thus, the inaccuracy of AM fungal detection with the general fungal primers did not change the ecological conclusions regarding the responses of AM fungi to climate manipulations. However, using the higher accuracy of detection with the AM fungal specific system we can learn better which AM fungi respond in which ways, and in particular, we are better equipped to find fungi with differential behaviour.

This result is important. It means that we can learn about AM fungal responses to environmental changes in large datasets addressing big spatiotemporal scales and broad groups of organisms. It also means that there is no longer any reason to neglect AM fungi in these big datasets, and better so, because AM fungi carry important functions for all of us. Think of fresh air – the lungs of the planet, tropical rainforests, need AM fungi, and not just any, but the right ones. Or your next cup of coffee, slice of bread or an apple – all the same. Or your garden, organic farm or urban landscape. Still the same.

Citation: Lekberg, Y., Vasar, M., Bullington, L. S., Sepp, S. K., Antunes, P. M., Bunn, R., Larkin, B. G. & Öpik, M. (2018). More bang for the buck? Can arbuscular mycorrhizal fungal communities be characterized adequately alongside other fungi using general fungal primers?. New Phytologist, DOI: 10.1111/nph.15035. (link to full text)


Where does the buck stop?! (pic from here)



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New paper published – Two Closely Related Species Differ in their Regional Genetic Differentiation Despite Admixing

Text by Lisanna Schmidt

Genetic differences between regions are usually studied for individual species. However, many species can reproduce with each other. We studied whether gene flow between two closely related sedge species influences regional differences. Our molecular genetic data support considerable gene flow between the species. Still, we detected clear genetic differences between species and regions, and more pronounced regional differences for the less common one. Thus, gene flow between the species appeared too weak to neutralise differences between the regional genetic structure of our study species. We encourage further regional-differentiation studies in groups of cross-compatible species.

Citation: Schmidt, L., Fischer, M., & Oja, T. (2018). Two Closely Related Species Differ in their Regional Genetic Differentiation Despite Admixing. AoB PLANTS, DOI: 10.1093/aobpla/ply007. (link to full text)


Good old hybrid plant… (pic from here)


Regional genetic differentiation within species is often addressed in evolutionary ecology and conservation biology. Here, we address regional differentiation in two closely related hybridizing taxa, the perennial sedges Carex flava and C. viridula and their hybrid C. x subviridula in 37 populations in the north and centre of their distribution range in Europe (Estonia, Lowland (< 1000m a.s.l.) and Highland Switzerland) using ten putative microsatellite loci. We ask whether regional differentiation was larger in the less common taxon C. viridula or whether, possibly due to hybridization, it was similar between taxa. Our results showed similar, low to moderate genetic diversity for the three studied taxa. In total, we found 12 regional species-specific alleles. AMOVA, STRUCTURE and Multidimensional Scaling Analysis showed regional structure in genetic variation, where intraspecific differentiation between regions was lower for C. flava (AMOVA: 6.84%) than for C. viridula (20.77%) or C. x subviridula (18.27%) populations. Hybrids differed from the parental taxa in the two regions where they occurred, i.e. in Estonia and Lowland Switzerland. We conclude that C. flava and C. viridula clearly differ from each other genetically, that there is pronounced regional differentiation, and that, despite hybridization, this regional differentiation is more pronounced in the less common taxon, C. viridula. We encourage future studies on hybridizing taxa to work with plant populations from more than one region.

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EcolChange publications list 2017

Text by Lauri Laanisto, data by Tiia Kurvits, Pille Meinson

Here is hopefully rather complete, alphabetic list of publications from the members of EcolChange from 2017. There are altogether 83 peer-reviewed papers. You can also check the Publications tab, where you can now find the year-by-year publications lists since 2012, together with links to blog posts about some of them (25 publications from 2017 were blogged about).

Centre of Excellence EcolChange publications in 2017, classification 1.1 in ETIS

  1. Aavik, T.; Helm, A., (2017). Restoration of plant species and genetic diversity depends on landscape-scale dispersal. Restoration Ecology. 10.1111/rec.12634.
  2. Aavik, T.; Talve, T.; Thetloff, M.; Uuemaa, E.; Oja, T. (2017). Genetic consequences of landscape change for rare endemic plants – A case study of Rhinanthus osiliensis. Biological Conservation, 210, 125−135. 10.1016/j.biocon.2017.04.016.
  3. Bazzicalupo, A.L.; Buyck, B.; Saar, I.; Vauras, J.; Carmean, D.; Berbee, M.L. (2017). Troubles with mycorrhizal mushroom identification where morphological differentiation lags behind barcode sequence divergence. Taxon, 66, 4, 791−810. 10.12705/664.1.
  4. Bennett, J. A.; Riibak, K.; Tamme, R.; Lewis, R. J.; Pärtel, M. (2017). The reciprocal relationship between competition and intraspecific trait variation. Journal of Ecology, 1−23. 10.1111/1365-2745.12614.
  5. Bennett, Jonathan A.; Pärtel, Meelis (2017). Predicting species establishment using absent species and functional neighborhoods. Ecology and Evolution, 7, 2223−2237. 10.1002/ece3.2804.
  6. Bueno, C.G.; Moora, M.; Gerz, M.; Davison, J.; Öpik, M.; Pärtel, M.; Helm, A.; Ronk, A.; Kühn, I.; Zobel, Z. (2017). Plant mycorrhizal status, but not type, shifts with latitude and elevation in Europe. Global Ecology and Biogeography, 26 (6), 690−699. 10.1111/geb.12582.
  7. Bullock, James M.; Mallada González, Laura; Tamme, Riin; Götzenberger, Lars; White, Steven M.; Pärtel, Meelis; Hooftman, Danny A. P. (2017). A synthesis of empirical plant dispersal kernels. Journal of Ecology, 105 (1), 6−19. 10.1111/1365-2745.12666.
  8. Chytrý, Milan; Chiarucci, Alessandro; Pillar, Valério D.; Pärtel, Meelis; (2017). Applied Vegetation Science enters its 20th year. Applied Vegetation Science, 20 (1), 1−4. 10.1111/avsc.12286.
  9. Corrales, Adriana; Turner, Benjamin L.; Tedersoo, Leho; Anslan, Sten; Dalling, James W. (2017). Nitrogen addition alters ectomycorrhizal fungal communities and soil enzyme activities in a tropical montane forest. Fungal Ecology, 27, 14−23. 10.1016/j.funeco.2017.02.004.
  10. Ehrmann, Steffen; Liira, Jaan; Gärtner, S.; Hansen, K.; Brunet, J.; Cousins, S. A. O.; Deconchat, M.; Decocq, G.; De Frenne, P.; De Smedt, P.; Diekmann, M.; Gallet-Moron, E.; Kolb, A.; Lenoir, J.; Lindgren, J.; Naaf, T.; Paal, Taavi; Valdés, A.; Verheyen, K.; Wulf, M. … Scherer-Lorenzen, M. (2017). Environmental drivers of Ixodes ricinus abundance in forest fragments of rural European landscapes. BMC Ecology, 17 (1), 1−31. 10.1186/s12898-017-0141-0.
  11. García-Plazaola, J.I.; Portillo-Estrada, M.; Fernández-Marín, B.; Kännaste, A.; Niinemets, Ü. (2017). Emissions of carotenoid cleavage products upon heat shock and mechanical wounding from a foliose lichen. Environmental and Experimental Botany, 133, 87−97. 10.1016/j.envexpbot.2016.10.004.
  12. Gerz, Maret; Bueno, C. Guillermo; Ozinga, Wim A.; Zobel, Martin; Moora. Mari (2017). Niche differentiation and expansion of plant species are associated with mycorrhizal symbiosis. Journal of Ecology. 10.1111/1365-2745.12873.
  13. Hallik, L.; Kazantsev, T.; Kuusk, A.; Galmés, J.; Tomás, M.; Niinemets, Ü. (2017). Generality of relationships between leaf pigment contents and spectral vegetation indices in Mallorca (Spain). Regional Environmental Change, 17, 2097−2109. 10.1007/s10113-017-1202-9.
  14. Hari, Pertti; Kerminen, Veli-Matti; Kulmala, Liisa; Kulmala, Markku; Noe, Steffen; Petäjä, Tuukka; Vanhatalo, Anni; Bäck, Jaana (2017). Annual cycle of Scots pine photosynthesis. Atmospheric Chemistry and Physics, 17, 15045−15053. 10.5194/acp-17-15045-2017.
  15. He, Jinhong; Tedersoo, Leho; Hu, Ang; Han, Conghai; He, Dan; Wei, Hui; Jiao, Min; Anslan, Sten; Nie, Yanxia; Jia, Yongxia (2017). Greater diversity of soil fungal communities and distinguishable seasonal variation in temperate deciduous forests compared with subtropical evergreen forests of eastern China. FEMS Microbiology Ecology, 93. 10.1093/femsec/fix069.
  16. Hernández, L.; Lehtonen, A.; Moreno-Fernandez, D.; Marin, G.; Alberdi, I.; Cañellas, I.; Ostonen, I.; Kriiska, K.; Didion, M.; Varik, M.; Jandl, R.; Adermann, V.; Blujdea, V. (2017). Towards complete and harmonized assessment of soil carbon stocks and balance in forests: the ability of the Yasso07 model across a wide gradient of climatic and forest conditions in Europe. Science of the total environment, 599, 1171−1180. 10.1016/j.scitotenv.2017.03.298.
  17. Ingerpuu, Nele, Vellak, Kai (2017). Methods for monitoring threatened bryophytes. Biodiversity and Conservation, 26 (14), 3275 −3287. 10.1007/s10531-017-1405-x.
  18. Jardine, Kolby J; de Souza, Vinicius Fernandes; Oikawa, Patty; Higuchi, Niro; Bill, Markus; Porras, Rachel; Niinemets, Ülo; Chambers, Jeffrey (2017). Integration of C1 and C2 Metabolism in Trees. International Journal of Molecular Sciences, 18 (2045), 1−18. 10.3390/ijms18102045.
  19. Jiang Yifan, Veromann-Jürgenson Linda-Liisa, Ye Jiajan, Niinemets Ülo (2017). Oak gall wasp infections of Quercus robur leaves lead to profound modifications in foliage photosynthetic and volatile emission characteristics. Plant, Cell and Environment, 0−10. 10.1111/pce.13050.
  20. Jiang, Yifan; Jiayan, Ye; Li, Shuai; Niinemets, Ülo (2017). Methyl jasmonate-induced emission of biogenic volatiles is biphasic in cucumber: a high-resolution analysis of dose dependence. Journal of Experimental Botany, 68 (16), 4679−4694. 0.1093/jxb/erx244.
  21. Johansson V.; Bahram, M; Kõljalg, U.; Tedersoo, L. (2017). Specificity of fungal associations of Pyroleae and Monotropa hypopitys during germination and seedling development. Molecular Ecology, 26 (9), 2591−2604. 10.1111/mec.14050.
  22. Kaurilind, Eve; Brosché, Mikael (2017). Stress Marker Signatures in Lesion Mimic Single and Double Mutants Identify a Crucial Leaf Age-Dependent Salicylic Acid Related Defense Signal. PLoS ONE, 1−17. 10.1371/journal.pone.0170532.
  23. Kohout, P.; Bahram, M.; Põlme, S.; Tedersoo, L. (2017). Elevation, space and host plant species structure Ericaceae rootassociated fungal communities in Papua New Guinea. Fungal Ecology, 30, 112−121. 10.1016/j.funeco.2017.09.004.
  24. Kohout, P.; Tedersoo, L. (2017). Effect of soil moisture on root-associated fungal communities of Erica dominans in Drakensberg mountains in South Africa. Mycorrhiza, 27 (4), 397−405. 10.1007/s00572-017-0760-5.
  25. Koorem, Kadri; Tulva, Ingmar; Davison, John; Jairus, Teele; Öpik, Maarja; Vasar, Martti; Zobel, Martin; Moora, Mari (2017). Arbuscular mycorrhizal fungal communities in forest plant roots are simultaneously shaped by host characteristics and canopy-mediated light availability. Plant and Soil, 410, 259−271. 10.1007/s11104-016-3004-0.
  26. Kotilínek, Milan; Hiiesalu, Inga; Košnar, Jiri; Šmilauerová, Marie; Šmilauer, Petr; Altman, Jan; Dvorský, Miroslav; Kopecký, Martin Dolezal, Jiri (2017). Fungal root symbionts of high-altitude vascular plants in the Himalayas. Scientific Reports, 7, 6562. 10.1038/s41598-017-06938-x.
  27. Kuht, J.; Eremeev, V.; Talgre, L.; Madsen, H.; Toom, M.; Mäeorg, E.; Loit, E.; Luik, A. (2017). The content of weed seeds in the soil based on the management system. Agronomy Research, 15 (5), 1934−1943.
  28. Kukumägi, Mai; Ostonen, Ivika; Uri, Veiko; Helmisaari, Heljä-Sisko; Kanal, Arno; Kull, Olevi; Lõhmus, Krista (2017). Variation of soil respiration and its components in hemiboreal Norway spruce stands of different ages. Plant and Soil, 414, 265−280. 10.1007/s11104-016-3133-5.
  29. Kupper, P.; Rohula, G.; Inno, L.; Ostonen, I.; Sellin, A.; Sõber, A. (2017). Impact of high daytime air humidity on nutrient uptake and night-time water flux in silver birch, a boreal forest tree species. Regional Environmental Change, 17 (7), 2149−2157. 10.1007/s10113-016-1092-2.
  30. La Rosa A.; Bizio, E.; Saitta, A.; Tedersoo, L. (2017). Inocybe castaneicolor (Agaricales, Basidiomycota), a new species in section Splendentes. Phytotaxa, 316, 79−87. 10.11646/phytotaxa.316.1.8.
  31. Lee, Marissa R.; Bernhardt, Emily S.; van Bodegom, Peter M.; Cornelissen, J. Hans C.; Kattge, Jens; Laughlin, Daniel C.; Niinemets, Ülo: Penuelas, Josep; Peter B. Reich, Peter B.; Ygue; Benjamin; Wright, Justin P. (2017). Invasive species’ leaf traits and dissimilarity from natives shape their impact on nitrogen cycling: a meta-analysis. New Phytologist, 213 (1), 128−139. nph.14115.
  32. Lei, Yanbao; Jiang, Yonglei; Chen,Ke; Duan, Baoli; Zhang, Sheng; Korpelainen, Helena; Niinemets, Ülo; Li, Chunyang (2017). Reproductive investments driven by sex and altitude in sympatric Populus and Salix trees. Tree Physiology, 37 (11), 1503−1514. 10.1093/treephys/tpx075.
  33. Lewis, R. J.; Bello, F.; Bennett, J. A.; Fibich, P.; Finerty, G. E.; Götzenberger, L.; Hiiesalu, I.; Kasari, L.; Lepš, J.; Májeková, M.; Mudrák, O.; Riibak, K.; Ronk, A.; Rychtecká, T.; Vitová, A.; Pärtel, M. (2017). Applying the dark diversity concept to nature conservation. Conservation Biology, 31 (1), 40−47. 10.1111/cobi.12723.
  34. Li, Le; Ma, Zeqing; Niinemets, Ülo; Guo, Dali (2017). Three Key Sub-leaf Modules and the Diversity of Leaf Designs. Frontiers in Plant Science, 8 (Art No 1542), 1−8. 10.3389/fpls.2017.01542.
  35. Li, Shuai; Harley, Peter C.; Niinemets, Ülo (2017). Ozone-induced foliar damage and release of stress volatiles is highly dependent on stomatal openness and priming by low-level ozone exposure in Phaseolus vulgaris. Plant, Cell and Environment, 40 (9), 1984−2003. 10.1111/pce.13003.
  36. Lücking, R.; Thorn, R.G.; Saar, I.; Piercey-Normore, M.D.; Moncada, B.; Doering, J.; Mann, H.; Lebeuf, R.; Voitk, M.; Voitk, A. (2017). A hidden basidiolichen rediscovered: Omphalina oreades is a separate species in the genus Lichenomphalia (Basidiomycota: Agaricales: Hygrophoraceae). The Lichenologist, 49 (5), 467−481. 10.1017/S0024282917000378.
  37. Mander, Ülo; Ostonen, Ivika, Niinemets, Ülo (2017). Indicators of climate change adaptation from molecules to ecosystems. Regional Environmental Change, 17 (7), 2055−2059. 10.1007/s10113-017-1215-4.
  38. Menzel, Andreas; Hempel, Stefan; Klotz Stefan; Moora, Mari; Pyšek, Petr; Rillig, C. Mathias; Zobel, Martin; Kühn, Ingolf (2017). Mycorrhizal status helps explain invasion success of alien plant species. Ecology, 98 (1), 92−102. 10.1002/ecy.1621.
  39. Napa, Ülle; Ostonen, Ivika; Kabral, Naima; Kriiska, Kaie; Frey, Jane. (2017). Biogenic and contaminant heavy metal pollution in Estonian coniferous forests. Regional Environmental Change, 17 (7), 2111−2120. 10.1007/s10113-017-1206-5.
  40. Niinemets, Ü.; Kahru, A.; Mander, Ü.; Nõges, P.; Nõges, T.; Tuvikene, A.; Vasemägi, A. (2017). Interacting environmental and chemical pollutant stresses under global change in aquatic ecosystems: stress responses, adaptation and scaling. Regional Environmental Change, 1−17. 10.1007/s10113-017-1196-3.
  41. Niinemets, Ü.; Kahru, A.; Nõges, P.; Tuvikene, A.; Vasemägi, A.; Mander, Ü.; Nõges, T. (2017). Environmental feedbacks in temperate aquatic ecosystems under global change: why do we need to consider chemical stressors? Regional Environmental Change, 1−18. 10.1007/s10113-017-1197-2.
  42. Niinemets, Ülo; Berry, Joseph A.; von Caemmerer, Susanne; Ort, Donald R.; Parry, Martin A. J.; Poorter, Hendrik (2017). Photosynthesis: ancient, essential, complex, diverse … and in need of improvement in a changing world. The 17th International Congress on Photosynthesis Research – Photosynthesis in a Changing World, Maastricht, The Netherlands, August, 2016. New Phytologist, 213 (1), 43−47.
  43. Nuytinck, J.; Verbeken, A.; Saar, I.; Lambert, H.; Bérubé, J.; Voitk, A. (2017). Lactarius splendens, a second species with white latex in Lactarius section Deliciosi. Botany, 95 (8), 859−863. 10.1139/cjb-2017-0040.
  44. Oja, J.; Vahtra, J.; Bahram, M.; Kohout, P.; Kull, T.; Rannap, R.; Kõljalg, U.; Tedersoo, L. (2017). Local-scale spatial structure and community composition of orchid mycorrhizal fungi in semi-natural grasslands. Mycorrhiza, 27 (4), 355−367. 10.1007/s00572-016-0755-7.
  45. Onoda, Yusuke, Wright Ian, Evans John, Hikosaka Kouki, Kaoru, Kitajiama, Ülo Niinemets, Henrik Poorter, Tiina Tosens, Mark Westoby (2017). Physiological and structural tradeoffs underlying the leaf economics spectrum. New Phytologist, 147, 1447−1463. 10.1111/nph.14496.
  46. Ostonen, Ivika; Truu, Marika; Helmisaari, Heljä-Sisko; Lukac, Martin; Vanguelova, Elena; Godbold, Douglas L; Lõhmus, Krista; Zang, Ulrich, Tedersoo, Leho; Preem, Jens-Konrad; Rosenvald, Katrin; Aosaar, Jürgen; Armolaitis, Kestutis; Frey, Jane; Kabral, Naima; Kukumägi, Mai; Leppälammi-Kujansuu, Jaana; Lindroos, Antti-Jussi; Merilä, Päivi; Napa, Ülle; Nöjd, Pekka … Truu, Jaak (2017). Adaptive root foraging strategies along a boreal-temperate forest gradient. New Phytologist, 215 (3), 977−991. 10.1111/nph.14643.
  47. Paal, Taavi; Kütt, Laura; Lõhmus, Kertu; Liira, Jaan (2017). Both spatiotemporal connectivity and habitat quality limit the immigration of forest plants into wooded corridors. Plant Ecology, 218 (4), 417−431. 10.1007/s11258-017-0700-7.
  48. Peguero-Pina, José Javier; Sisó, Sergio; Flexas, Jaume; Galmés, Jeroni; García-Nogales, Ana; Niinemets, Ülo; Sancho-Knapik, Domingo; Ángel Saz, Miguel; Gil-Pelegrín, Eustaquio (2017). Cell-level anatomical characteristics explain high mesophyll conductance and photosynthetic capacity in sclerophyllous Mediterranean oaks. New Phytologist, 214 (2), 585−596. 10.1111/nph.14406.
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New publication – The role of plant mycorrhizal type and status in modulating the relationship between plant and arbuscular mycorrhizal fungal communities

Text by Lena Neuenkamp

Interactions between communities of plants and arbuscular mycorrhizal (AM) fungi shape fundamental ecosystem properties. Experimental evidence suggests that compositional changes in plant and AM fungal communities should be correlated, but empirical data from natural ecosystems is scarce.

PhD student Lena Neuenkamp and co-authors fill this gap of knowledge with their recently published study in New Phytologist, where they clearly show that compositional changes of plant and AM fungal communities were correlated across three stages of grassland succession. The authors also reveal that strength of plant-AM fungal correlation weakened during succession following cessation of grassland management, which was brought about by changes in the proportion of plants exhibiting different AM status. Plant-AM fungal correlation was strong when the abundance of obligate AM plants was high, and declined as the proportion of facultative AM plants increased.

The findings of this study indicate that the extent to which plants rely on AM symbiosis can determine how tightly communities of plants and AM fungi are interlinked, regulating community assembly of both symbiotic partners. Further, the results of this study imply that restoration of ecosystems with obligate AM plant dominated vegetation, such as calcareous grasslands, might benefit from the re-introduction of local AM fungal communities, especially if the ecosystem is already heavily degraded.

Citation: Neuenkamp, L., Moora, M., Öpik, M., Davison, J., Gerz, M., Männistö, M., Jairus, T., Vasar, M. & Zobel, M. (2018). The role of plant mycorrhizal type and status in modulating the relationship between plant and arbuscular mycorrhizal fungal communities. New Phytologist, DOI: 10.1111/nph.14995 (link to full text)


Graphical abstract: Showing how the strength of correlation between plant and AM fungal communities in grasslands depends on the abundance of obligatory AM plants in the plant community. The higher is the abundance of obligatory AM plants, the stronger are plant and AM fungal communities related.


  • Interactions between communities of plants and arbuscular mycorrhizal (AM) fungi shape fundamental ecosystem properties. Experimental evidence suggests that compositional changes in plant and AM fungal communities should be correlated, but empirical data from natural ecosystems are scarce. We investigated the dynamics of covariation between plant and AM fungal communities during three stages of grassland succession, and the biotic and abiotic factors shaping these dynamics.
  • Plant communities were characterised using vegetation surveys. AM fungal communities were characterised by 454-sequencing of the small subunit rRNA gene and identification against the AM fungal reference database MaarjAM. AM fungal abundance was estimated using neutral-lipid fatty acids (NLFAs).
  • Multivariate correlation analysis (Procrustes) revealed a significant relationship between plant and AM fungal community composition. The strength of plant–AM fungal correlation weakened during succession following cessation of grassland management, reflecting changes in the proportion of plants exhibiting different AM status. Plant–AM fungal correlation was strong when the abundance of obligate AM plants was high, and declined as the proportion of facultative AM plants increased.
  • We conclude that the extent to which plants rely on AM symbiosis can determine how tightly communities of plants and AM fungi are interlinked, regulating community assembly of both symbiotic partners.
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New publication – Mapping local and global variability in plant trait distributions

Text by Lauri Laanisto

Seems like macroecology has finally arrived to a crossroads where it might split so fundamentally, that two or more new disciplines will emerge. Finding global patterns, that would explain the world in one graph, like JH Brown once hoped for: “The promise of macroecology is that very general statistical patterns provide clues the operation of equally general mechanistic processes which govern the structure and dynamics of complex ecological systems.” (Brown 1999). It has not really come up to expectations. You can collect all the stamps, but the collection is still not making sense, if to paraphrase another classic, John Lawton´s view from the park about community ecology (the whole series of these papers are now in Oikos´s virtual issue nr 8!).

But the top-down approach still looms large. Taxon grops, diversities, traits, trait groups etc are plotted against different diversities, environmental factors, indices etc. And there is hope. The hope will not go away, that´s for sure.

The other side, however, almost like wants to go back in time. When ecological publications were still so through that you could get sufficient information for each location, species and trait studied. It´s difficult to do it, when the sites are all across the globe and you have trait data for 10 000 species or sth. Big data can only take us to a point. Like self-help books would say: “What Got You Here Won’t Get You There”. Instead of self-help books I cite here a recent essay review by Angela Moles about this exact thing: “Being John Harper: Using evolutionary ideas to improve understanding of global patterns in plant traits“.

A recent global modelling paper (that includes Ülo Niinemets as a coauthor) in PNAS, based on big data on SLA and leaf nitrogen and phosporous content (from TRY database) is, at least in my mind, trying to take both paths in this crossroads. Whether they succeed or not, take a look!

Check also out this blog post that describes the same PNAS paper in a way that makes much more sense…

Citation: Butler, E. E., Datta, A., Flores-Moreno, H., Chen, M., Wythers, K. R., Fazayeli, F., … Niinemets, Ü., … & Blonder, B. (2017). Mapping local and global variability in plant trait distributions. Proceedings of the National Academy of Sciences, 201708984, (link to full text)


Global crossroads (pic from here)


Currently, Earth system models (ESMs) represent variation in plant life through the presence of a small set of plant functional types (PFTs), each of which accounts for hundreds or thousands of species across thousands of vegetated grid cells on land. By expanding plant traits from a single mean value per PFT to a full distribution per PFT that varies among grid cells, the trait variation present in nature is restored and may be propagated to estimates of ecosystem processes. Indeed, critical ecosystem processes tend to depend on the full trait distribution, which therefore needs to be represented accurately. These maps reintroduce substantial local variation and will allow for a more accurate representation of the land surface in ESMs.


Our ability to understand and predict the response of ecosystems to a changing environment depends on quantifying vegetation functional diversity. However, representing this diversity at the global scale is challenging. Typically, in Earth system models, characterization of plant diversity has been limited to grouping related species into plant functional types (PFTs), with all trait variation in a PFT collapsed into a single mean value that is applied globally. Using the largest global plant trait database and state of the art Bayesian modeling, we created fine-grained global maps of plant trait distributions that can be applied to Earth system models. Focusing on a set of plant traits closely coupled to photosynthesis and foliar respiration—specific leaf area (SLA) and dry mass-based concentrations of leaf nitrogen (Nm) and phosphorus (Pm), we characterize how traits vary within and among over 50,000 50×50-km cells across the entire vegetated land surface. We do this in several ways—without defining the PFT of each grid cell and using 4 or 14 PFTs; each model’s predictions are evaluated against out-of-sample data. This endeavor advances prior trait mapping by generating global maps that preserve variability across scales by using modern Bayesian spatial statistical modeling in combination with a database over three times larger than that in previous analyses. Our maps reveal that the most diverse grid cells possess trait variability close to the range of global PFT means.


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New publication – A major trade-off between structural and photosynthetic investments operative across plant and needle ages in three Mediterranean pines

Text by Vivian Kuusk

Lots of species grow different looking leaves when they are young and adult. For example young conifers look more like little soft brushes rather than the forest giants, and lots of common houseplants look totally different in their natural habitat, because on our windowsills they produce only juvenile leaves (good example is devil`s ivy – Epipremnum aureum). The phenomena of juvenility has been a question for quite some time and we wanted to understand which morphological, anatomical and chemical changes occur in the needles upon juvenile-to-adult transition. As Mediterranean pines tend to keep juvenile needles longer than pines in temperate zone, stone pine (Pinus pinea), Aleppo pine (Pinus halepensis) and black pine (Pinus nigra) were chosen for the investigation. We found that juvenile needles are narrower, contain less dry mass per area and have thinner cell walls. Nitrogen content per dry mass was similar in all plant ages, but the photosynthetic tissue and size of chloroplasts was bigger in juvenile leaves. So we suggest that the ecological advantage of having juvenile leaves is of maximum carbon gain and establishing the saplings. The role of mature type leaves is to be more durable against various stress conditions, like for example mechanical stress from wind. I´d like to draw a parallel with human homes here – if you are young and don´t have lots of money, you live in a cheap condo, but when you have a bit more, you start thinking of building a house that would last a lifetime or more. Therefore plants invest more into growing durable leaves when they are older and have established their above- and underground parts well enough.

Citation: Kuusk, V., Niinemets, Ü., & Valladares, F. (2017). A major trade-off between structural and photosynthetic investments operative across plant and needle ages in three Mediterranean pines. Tree physiology, (link to full text)


Juvenile (left) and adult (right) foliage of Stone Pine (Pinus pinea) – (Pic from here)


Pine (Pinus) species exhibit extensive variation in needle shape and size between juvenile (primary) and adult (secondary) needles (heteroblasty), but few studies have quantified the changes in needle morphological, anatomical and chemical traits upon juvenile-to-adult transition. Mediterranean pines keep juvenile needles longer than most other pines, implying that juvenile needles play a particularly significant role in seedling and sapling establishment in this environment. We studied needle anatomical, morphological and chemical characteristics in juvenile and different-aged adult needles in Mediterranean pines Pinus halepensis Mill., Pinus pinea L. and Pinus nigra J. F. Arnold subsp. salzmannii (Dunal) Franco hypothesizing that needle anatomical modifications upon juvenile-to-adult transition lead to a trade-off between investments in support and photosynthetic tissues, and that analogous changes occur with needle aging albeit to a lower degree. Compared with adult needles, juvenile needles of all species were narrower with 1.6- to 2.4-fold lower leaf dry mass per unit area, and had ~1.4-fold thinner cell walls, but needle nitrogen content per dry mass was similar among plant ages. Juvenile needles also had ~1.5-fold greater mesophyll volume fraction, ~3-fold greater chloroplast volume fraction and ~1.7-fold greater chloroplast exposed to mesophyll exposed surface area ratio, suggesting overall greater photosynthetic activity. Changes in needle traits were similar in aging adult needles, but the magnitude was generally less than the changes upon juvenile to adult transition. In adult needles, the fraction in support tissues scaled positively with known ranking of species tolerance of drought (P. halepensis > P. pinea > P. nigra). Across all species, and needle and plant ages, a negative correlation between volume fractions of mesophyll and structural tissues was observed, manifesting a trade-off between biomass investments in different needle functions. These results demonstrate that within the broad trade-off, juvenile and adult needle morphophysiotypes are separated by varying investments in support and photosynthetic functions. We suggest that the ecological advantage of the juvenile morphophysiotype is maximization of carbon gain of establishing saplings, while adult needle physiognomy enhances environmental stress tolerance of established plants.

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