Fieldwork report – Kaia and Astrid in Australia

Text by Kaia Kask

In front of EucFACE Experiment site (Photo by M. K)

From 28th of March to 13 of April senior scientist Astrid Kännaste and PhD student Kaia Kask were visiting professor David Ellsworth in the Western Sydney University in Hawkesbury, Australia. The purpose of the visit was to measure VOC-s and photosynthesis of 16 different species. Plant VOC-s were collected on multibed cartridges and photosynthesis was measured with Li-Cor 6400. Measured species were located in the EucFACE experimental site and in Davies park, Springwood.


Kaia measuring photosynthesis with Li-Cor 6400 (photo by Astrid)

Most of the time we were lucky to measure the whole day as there was no rain, but during hot and sunny days, especially after midday, we had to pause photosynthesis measurements as plants were not “collaborative” with us. Stomata closure and reduced net assimilation rate would give wrong numbers on measured species. Therewhile we continued work inside the station, weighted leaves and measured leaf area; or collected extra samples from each species for later analyses in Estonia.


Astrid in Davies park (photo by Kaia)

For measuring in the EucFACE site, long trousers, closed shoes and walkie-talkies were obligatory equipment for everyday measurements, as the most venomous black and brown snakes could be on the site territory. Actually we could not even distinguish snakes from the fallen branches and Eucalyptus bark, as these seemed also like snakes. Sometimes we used bigger branched to make some noise or check the area around us. Astrid was the lucky one to see a juvenile brown snake on the pathway in front of the station house. Also while looking for species for measurements we saw kangaroos. Hat and a water bottle were in our ever day equipment as well, because temperatures were mostly up to 35°C.


Equipment – hats and machine (photo by Kaia)

We also managed to visit some botanical gardens, like Blue Mountains Botanic Garden and the Royal Botanic Garden in Sydney. We were amazed from what we saw. Similarly, a visit to the Chinese Garden of Friendship was impressive.


With David (photo by M. K.)

We would like to thank David for his valuable time and suggestions and all his team members who helped us.


Hey, snake! (photo by Kaia)

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Workgroup and EcolChange seminar – Tom Sharkey about the Auxiliary pathways of the Calvin-Benson cycle

Seminar of Chair of Crop Science and Plant Biology and Centre of Excellence EcolChange, Estonian Univ of Life Sciences .

Thomas D. Sharkey is University Distinguished Professor in Michigan State University, and fellow of the AAAS. (Link to his homepage; link to his Wiki page); currently visiting our lab.

Title of the talk: Auxiliary pathways of the Calvin-Benson cycle

Time: Monday, 24. September 2018 at 10.15

Place: Tartu, Kreutzwaldi 5 – 2A41 (Metsamaja)

calvin ja benson

The Calvin-Benson cycle and auxiliary pathways


Tom Sharkey will give a lecture on carbon metabolism of photosynthesis. Tom has studied this topic for over 40 years and has recently written a review on the original discovery by Calvin and Benson of the pathway that converts carbon dioxide to sugars. Recent data from his laboratory indicate that there may be other pathways that work with the Calvin-Benson cycle. In addition to work on carbon metabolism of photosynthesis Tom studies the biochemistry of isoprene emission from trees and is currently visiting Crop Science and Plant Ecology at the Estonian University of Life Science to carry out experiments on isoprene emission.

Tom got his PhD at Michigan State University and returned there in 2008 to become chair of the Biochemistry Department. In between he worked as a post-doc with Graham Farquhar in Australia, then at the Desert Research Institute in Reno Nevada, then as a professor at the University of Wisconsin-Madison. He retired from UW-Madison (he is now emeritus professor of Botany) to return to Michigan.

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New member – welcome Yusuph!

Text and pic Yusuph Olawale Abiola

I would like to use this medium to introduce myself as the recipient of the DoRa+ Scholarship Programme and to also express my profound gratitude to the donor. I finished my master’s degree in Agricultural Sciences in June 2018 from Szent Istvan University, Godollo, Hungary with the support from joint scholarship programme sponsored by the Food and Agricultural Organization of United Nations (FAO) and the Ministry of Agriculture of Hungary. My master’s thesis focused on “Effect of abiotic stress on germination of rice (Orzya sativa L) varieties”.


I’m very excited to be here at Ülo Niinemets’ Lab and I couldn’t be happier than where I am now as it’s a perfect match that will allow me to continue my quest in the field of Agriculture and environmental sciences. In view of the prevailing global challenges of food insecurity and climate change, I really believe that I am at the perfect place with the group of scientists focusing on the alleviating those challenges under the esteemed leadership of Prof. Ülo Niinemets and I am also willing and ready to contribute my own quota. My PhD research will focus on “Comparative study of stress resistance of novel crops; Sweet potato and its resistance strategy to drought and pathogen stress”.

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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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Harvest campaign in August, 2018

Text and video by Bin Liu, pics by Samuel Liga

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



A “frightened” Spider found on our plants.

Summer 2018 is definitely one of the hottest summers in the history of “cold” Estonia. Of course we wouldn’t miss this opportunity to do some cool things in the lab and in the field. Last year we completed some good work with galled oak leaves (Jiang et al. 2018). This time around, we moved to Cirsium arvense, which is one well-known plant species attracting varieties of gall-inducing parasites. In the field next to the forest, the blooming Cirsium arvense plants seemed all identical owing to their beautiful purple flowers. On coming close to them, it is fascinating to find out that some of them have big galls formed on their stems! Our purpose would be to measure the possible volatiles emitted from those galled plants. In the last three weeks, we have accomplished an intensive measurement and harvest campaign in our lab. During this period, nearly one hundred plants were collected in the field and sent to the lab for further analysis. An interesting part of it is that we named each working day and the respective plants collected with a team member’s name, e.g. Hasan_Plant_No. 1; Eve_Plant_No. 5; Sam_Plant_No. 8.  At last, we have collected up to 100 fresh samples and 500 dry samples. All I can say here and now is, we expect exciting results!


A snail came back with us from the field

Last but not the least thing, we give credits to all our team members: Samuel, Hassan, Chika, Eve, Sandra, Anna, Tiina, Ülo and other colleagues that are not mentioned here but in one way or the other contributed to the success of this round of experiment. Thanks a lot for the great effort you put in making this work a productive one.

Please, watch a self-made video of one of the harvest sessions we had in the lab. It is truly a hard work!


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New publication – Global database of plants with root‐symbiotic nitrogen fixation: Nod DB

Text by Lauri Laanisto

It´s really a very simple paper! A (relatively little) database containing information about all the plants (on genus level) that fix nitrogen from the soil. Somehow this information has not been available so far in a comparable and trustworthy way. Plus, it´s readily accessible – in a form or Excel table. Together with some additional taxonomic information for both plant and bacterial taxa, estimation of consensus, comparison with other sources that have tackled the same topic. To an ecologist, especially macroecologist, this dataset is a great source for easily getting potentially crucial trait added to your dataset. Because, as you can see from the GBIF-data based analysis (see the graph below), the proportion of N-fixing plants can differ quite a lot on global scale.

Citation: Tedersoo, L., Laanisto, L., Rahimlou, S., Toussaint, A., Hallikma, T., & Pärtel, M. (2018). Global database of plants with root‐symbiotic nitrogen fixation: Nod DB. Journal of Vegetation Science, (link to full text)

nod db

Figure 2 from the paper: Species richness of N-fixing vascular plants relative to total species richness as based on all GBIF vascular plant records with coordinates. Relative richness is calculated per equal area polygons (ISEA3H) with size ca 7,000 km2. Colours show quantiles. Only terrestrial polygons hosting more than 50 records are shown.


Plants associated with symbiotic N‐fixing bacteria play important roles in early successional, riparian and semi‐dry ecosystems. These so‐called N‐fixing plants are widely used for reclamation of disturbed vegetation and improvement of soil fertility in agroforestry. Yet, available information about plants that are capable of establishing nodulation is fragmented and somewhat outdated. This article introduces the NodDB database of N‐fixing plants based on morphological and phylogenetic evidence (available at and discusses plant groups with conflicting reports and interpretation, such as certain legume clades and the Zygophyllaceae family. During angiosperm evolution, N‐fixing plants became common in the fabid rather than in the ‘nitrogen‐fixing’ clade. The global GBIF plant species distribution data indicated that N‐fixing plants tend to be relatively more diverse in savanna and semi‐desert biomes. The compiled and re‐interpreted information about N‐fixing plants enables accurate analyses of biogeography and community ecology of biological N fixation.

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Workgroup and EcolChange seminar – Kaia Kask about why Australia matters

Seminar of Chair of Crop Science and Plant Biology and Centre of Excellence EcolChange, Estonian Univ of Life Sciences .

Kaia Kask is a junior researcher and PhD-student in the Estonian University of Life Sciences.

Title of the talk: Measurements in Australia: what and why?

Time: Monday, 21. May 2018 at 10.15

Place: Tartu, Kreutzwaldi 5 – D-143 (Metsamaja, Aquarium-room)

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