Sonja Viljamaa in front of a bush covered slightly with snow
Sonja Viljamaa in front of a bush covered slightly with snowPhD student Sonja Viljamaa (photo: Sonali Ranade)

Trees are key players for carbon removal from the atmosphere. But what is happening with the carbon once it enters the trees? Sonja Viljamaa, PhD student in Totte Niittylä’s group at UPSC and SLU, headed off to track carbon in aspen trees, focusing especially on carbon allocation to wood formation. Together with bioinformaticians, she identified new gene regulatory networks in developing wood and showed that aspen trees save carbon passively under optimal conditions.

What motivated you to do your PhD in Totte Niittylä’s group at UPSC?

Sonja Viljamaa: I wanted to continue studying trees. During my master’s at the University of Oulu I had been working on conifers, more specifically on cryopreservation of a spruce cell culture that produced extracellular lignin. So, I had already a connection to research on trees as well as cell wall and wood development. I had visited UPSC in 2013 for a short internship in Stefan Jansson’s group and had gotten a taste on how it is to work with aspen, and how the institute was as a working place.

When I saw the position in Totte Niittylä’s group combining research on wood development in aspen and Arabidopsis, a classical model species which I had actually never worked with before, I was very interested. Moving from Finland to Sweden sounded both familiar and exotic at the same time, and I thought it was also an advantage that my supervisor is Finnish like me - even though he unexpectedly did not know quite some Finnish research and plant biology vocabulary as he has studied mainly in English.

You analysed in your thesis how carbon that is assimilated during photosynthesis is allocated in aspen trees during growth. Why is it important to know this?

Sonja Viljamaa: All main processes in plants are depending on carbon which is used to deliver energy to the cells and is the main component of cell walls and wood. Many studies related to carbon allocation in plants are and have been performed on Arabidopsis, but it is difficult to transfer this knowledge to trees. Arabidopsis is a small annual plant and most of its carbon-storing parts like the stem and the leaves are photosynthetically active and green.

In trees, a major part of the assimilated carbon ends up in the wood which is mostly dead and not photosynthetically active. Trees are also much larger, long-lived and modular, meaning that for example one branch can be self-sufficient in carbon. All this adds additional complexity which is difficult to study in Arabidopsis and makes studies on trees, especially on carbon allocation to wood, necessary. Knowing more about the mechanisms behind and how they are regulated will hopefully have a practical use in tree breeding in the future.

What do you consider as the major outcome from your studies?

Sonja Viljamaa: Our results fill knowledge gaps related to carbon allocation in trees, and the data that we generated can serve as starting point for many new studies benefiting the scientific community in general. In one of the projects, we produced novel gene network information for developing wood of aspen and added this information to a publicly available database.

In another project, we characterised the first starch-less mutant in trees and showed that starch seemed to be stored passively in aspen trees. This contrasts with previous findings in Arabidopsis, in which carbon storage as starch has been described as an active process.

How can information about gene networks regulating wood development help to study carbon allocation?

Sonja Viljamaa: As wood is a major storage for carbon in trees, our goal was to identify gene networks that are involved in the process of wood formation. For this, we planned a large study to identify possible target genes of 660 transcription factor proteins that bind to the DNA and regulate the expression of genes. Quite many of the transcription factors included in the study were not well described yet. We wanted to find both new target genes of known transcription factors as well as completely new interactions between less known transcription factors and genes. For this, we used two different analysis methods and developed a bioinformatics analysis pipeline with the help of bioinformaticians.

This was the first aspen study with these techniques in this scale and as a result we produced a vast amount of data that is now integrated in the publicly available PopGenIE database. Any researcher interested in studying wood development can now access the data and use it for their research.

Unfortunately, we could not dive deeper into biological questions ourselves and study some of the transcription factors and their identified targets in the context of carbon allocation to wood development. There was just no time for this in the end, but I am happy for the people who will continue working on this project after me and who can start with this nice resource.

What was the most unexpected result you got during your PhD?

Sonja Viljamaa: I was really astonished and surprised to see that the starch-less aspen mutant trees generated in one of the projects looked so similar to the non-mutant trees. The only visible difference compared to the control plants was that the leaves were slightly more hanging down so that canopy area was slightly smaller, but otherwise they looked normal.

As there is such a complex machinery to produce starch and break it down, I was expecting that starch would be essential for tree growth and that the starch-less mutant trees would be sicker, but at least in our greenhouse experiments the young trees were growing without problems.

What was the biggest challenge you faced during your PhD?

Sonja Viljamaa: I have not worked a lot with bioinformatics before and there was quite a learning curve in getting started with that. It was interesting to learn to speak “the computer language” and to work in the command line, but this took some time and effort.

There were also some hiccups in finalising the pipeline for the bioinformatics analysis which took longer than I expected. Thanks to the help from the UPSC bioinformatics platform and from Nathaniel Street’s group, especially from Teitur Ahlgren Kalman, we managed to get everything running.

Additionally, the uncertainty caused by the global pandemic didn’t help with the practical experiments and it extended the delivery times for some of the reagents. Luckily, we got everything to work out in the end.

What are you planning to do now?

I will stay at UPSC until December and try to publish the results of at least one of my manuscripts. I also plan to finish the work on some samples I have collected but that I did not have the time yet to analyse. Then, I will assist a PhD student from Nathaniel Street’s group who is planning to use the same analysis methods as I used. After that I will see.

It would be nice if I could continue doing research, preferably with a focus on trees, or maybe even to go back to plant tissue culture work. I would really like to stay somewhere in the North with its snow and the changing seasons, which would of course be a bit of a limitation when looking for positions. It will be interesting to see where life leads me!

About the public defence:

Sonja Viljamaa, Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, defended her PhD thesis on Monday, 21st of November 2022. Faculty opponent was Andrew D. Friend, Department of Geography, University of Cambridge, Cambridge, UK. The thesis was supervised by Totte Niittylä.

Title of the thesis: Carbon allocation in aspen trees

Link to the thesis: https://pub.epsilon.slu.se/29010/


News about Sonja Viljamaa’s research on carbon storage in aspen trees

Link to PopGenIE - The Populus Genome Integrative Explorer - the database where Sonja Viljamaa’s data is included

For more information, please contact:

Sonja Viljamaa
Umeå Plant Science Centre
Department of Forest Genetics and Plant Physiology
Swedish University of Agricultural Sciences
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.

Building of the Royal Swedish Academy of Agriculture and Forestry in Stockholm
Building of the Royal Swedish Academy of Agriculture and Forestry in StockholmThe Royal Swedish Academy of Agriculture and Forestry in Stockholm (Photo: Johan Fredriksson published under CC BY-SA 3.0 license)

Last week on November 10, the Royal Swedish Academy of Agriculture and Forestry has elected 23 new fellows. Among them are Stefan Jansson and Olivier Keech, both group leaders at UPSC and Umeå University, and Isabella Hallberg Sramek, who is PhD student in Annika Nordin’s group at SLU. Both Stefan Jansson and Olivier Keech will join the General Section of the academy while Isabella Hallberg Sramek will be part of the Forestry Section.

The Royal Swedish Academy of Agriculture and Forestry is an independent organisation that works with questions regarding agriculture, horticulture, food, forest and forest products, fishing and aquaculture, the environment and natural resources. Its mission is to promote these fields and also activities associated with them through support from science and practical experience and to the benefit of society. They emphasise the importance of green industries and aim to highlight all aspects related to it.

Academy fellows are chosen because of their outstanding knowledge and experience in their respective field of work bringing in different professional backgrounds and competences. The General Section, that Stefan Jansson and Olivier Keech will join, deals with cross cutting questions of all fields the academy is working with. The forestry section, to which Isabella Hallberg Sramek is elected, focusses on questions related to management and usage of forests as natural resource. Since before, Stefan Jansson is fellow of the Royal Swedish Academy of Sciences and of the Royal Swedish Academy of Engineering Sciences.

More information:

Links to the announcements of the Royal Swedish Academy of Agriculture and Forestry (in Swedish):
https://www.ksla.se/2022/11/10/nya-ledamoter-i-kslas-allmanna-avdelning/
(General Section)
https://www.ksla.se/2022/11/10/nya-ledamoter-i-kslas-skogsavdelning/ (Forestry Section)

Information about the Royal Swedish Academy of Agriculture and Forestry

Eight thale cress seedlings with adventitious and primary roots in front of a black background
Eight thale cress seedlings with adventitious and primary roots in front of black backgroundThale cress seedlings with adventitous (indicated by the arrow) and primary roots (below the dotted line)

Plants can regenerate new roots on stem cuttings, a characteristic that is widely used in agriculture and forestry to propagate plants. What are the underlying molecular processes controlling the formation of such adventitious roots? Catherine Bellini, group leader at UPSC and professor at Umeå University, will investigate this question in her new project that got this week granted by the Swedish Research Council. Her focus will be on how light together with plant hormones interact to regulate gene expression during the initiation of adventitious roots.

Understanding which factors control the initiation of adventitious roots is one of Catherine Bellini’s main research areas. She and her group have looked deep into the molecular regulation of this process and added a lot of details to the complex regulation puzzle. They identified several genes as well as transcription factors, proteins that activate genes, that are regulating the formation of adventitious roots and figured out which and how different plant hormones cooperate with each other in this process.

Recently, Catherine Bellini’s group confirmed that the transcription factors regulating adventitious root development in thale cress perform a similar role in poplar and probably in Norway spruce. While exploring how light regulates gene activity during adventitious root formation, they could show that red light promotes adventitious root initiation in Norway spruce by inhibiting stress induced plant hormones.

“The results from the tree model species reassured us that we are on the right track with our basic research in thale cress,” says Catherine Bellini. “Thanks to the funding from the Swedish Research Council, we can now continue to research in this direction and investigate the role of the identified candidate genes further. Our results will hopefully help in the future to improve vegetative propagation in horticulture and forest species.”

Focussing on thale cress, Catherine and her group do not only want to understand better how gene activity is regulated during adventitious root formation. They also plan to follow up on their previous findings that certain subunits of the multi-protein complex COP9 signalosome play a significant role in this process. This complex exists not only in plants but also in many other organisms like fungi and human and controls which proteins are labelled for degradation. The molecular details of this regulation on the protein level are not well understood yet and that is what Catherine Bellini wants to investigate further.

Link to the announcement from the Swedish Research Council

More information:

Catherine Bellini
Umeå Plant Science Centre
Department of Plant Physiology
Umeå University
Phone: +46 (0)90 786 9624
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
https://www.upsc.se/catherine_bellini

Portrait photo of Stéphane Verger (left), Stéphanie Robert (middle) and Peter Marhavý (right) in front of a wooden red wall
Portrait photo of Stéphane Verger (left), Stéphanie Robert (middle) and Peter Marhavý (right) standing in fron of a wooden red wallStéphanie Robert (middle) and her co-applicants from UPSC Stéphane Verger (left) and Peter Marhavý (right) (photo: Sara Raggi)

Professor Stéphanie Robert from UPSC and SLU will lead a research project awarded over SEK 32 million by the Knut and Alice Wallenberg Foundation. The aim is to explore how plant cells get their "identity", how different types of cells emerge in the right place and at the right time during plant development. Although carefully studied in animals, this mechanism is still poorly understood in plants.

Knut and Alice Wallenberg Foundation has awarded a total of SEK 700 million to 23 research projects, in medicine, natural science and technology, that are judged to have such a high scientific potential that they have the possibility of leading to future scientific breakthroughs.

One of the awarded projects has the title Decoding cell fate with positional information and is awarded SEK 32,200,000 over five years. The principal investigator is Professor Stéphanie Robert, Professor of Plant Physiology at the Swedish University of Agricultural Sciences (SLU). Co-researchers are her colleagues Peter Marhavý and Stéphane Verger from the Department of Forest Genetics and Plant Physiology, which is part of Umeå Plant Science Centre, and also Eleni Stavrinidou from Linköping University and Maria Tenje from Uppsala University.

How do different cell types emerge at the right time and place in plants?

Animals and plants grow and develop as a result of controlled cellular processes such as division, elongation, and differentiation, where cell differentiation is defined as the acquisition of identity for a specific cell. Although carefully studied in animals, this mechanism is still poorly understood in plants. While a number of genes are known to control the acquisition of identity in plants, we still do not know how these genes are activated.

Positional information is regarded to be a crucial component of this regulatory process: we know that cell identity or cell fate acquisition is dependent on a cell's relative position within the complex organism. However, it remains unknown which signals govern cell destiny determination and how.

The goal of the project that Stéphanie Robert will lead is to contribute to the basic understanding of cell identity determination processes by working on root hair cells in the outer cell layer of the root. Root hairs are epidermal outgrowths present along the root and help the plant to absorb nutrients and water. The researchers will identify the components of positional information and unravel how they transform cell identity in epidermal root hair and non-hair cells.

“Non-hair cells alternate with hair cells along the root and their position in relation to the cell layer below is very predictable, giving us the fantastic opportunity to study cell identity determination”, says Stéphanie Robert. “Better knowledge about these particular cells is very important, and can in the long run help us develop more tolerant crops and trees that can cope with climate change”.

The hypothesis of the project is that positional information not only consists of chemical signals, but also of physical signals such as geometric, mechanical and electrical contacts between cells. To investigate this, the researchers will follow the development of identity when cells are exposed to different stimuli. By systematically changing various physical parameters in root tissue samples from the model plant Arabidopsis thaliana, they will be able to rule out or confirm that these control the cells' properties and development, both individually and in unison.

In addition, the researchers plan to develop for the first time an artificial model of an Arabidopsis thaliana root – a “plant-on-chip” – inspired by a new method where models of human organs are assembled and studied on a microchip.

“Such a method, where plant cells are positioned in specific structures on a surface using advanced micro-manufacturing methods and bioprinting, will revolutionise plant biology. It will enable us to combine genetically modified cells and thereby elucidate how physical stimuli are translated into molecular changes and how these together control the development of different cell types”, says Stéphanie Robert.

Behind this project is an interdisciplinary research group with experts in plant biology, genetics, microfluidics and electronics, who, through their location at three universities in Sweden, have access to the state-of-the-art facilities and instruments that are required to achieve the objective.

“Our project will give us basic knowledge about how cells, both in plants and in other organisms, obtain their identity. This is one of the most central questions in developmental biology that has not yet been answered”, summarises Stéphanie Robert.

Link to press release from KAW
Link to the Swedish news on the SLU homepage

For questions regarding the project, please contact:

Stephanie Robert
Professor at the Department of Forest Genetics and Plant Physiology
Swedish University of Agricultural Sciences, Umeå
Telephone: +46907868609, +46767674595
E-mail: This email address is being protected from spambots. You need JavaScript enabled to view it.
http://www.upsc.se/stephanie_robert
http://srobertgroup.com/

Text: David Stephansson

Close-up of hands doing together a jigsaw puzzle, photo taken at the UPSC PhD and Postdoc Retreat 2022
Close-up of hands doing together a jigsaw puzzleDoing together a jigsaw puzzle during the UPSC PhD and Postdoc Retreat in Skeppsvik (photo: Anne Honsel)

Alumni, team building, grant writing - about 40 PhD students and postdocs from UPSC spent two days at Skeppsvik Herrgård around thirty kilometres outside of Umeå. After two years of distancing, the interest was high to join this years’ UPSC PhD and Postdoc retreat on September 28 and 29. The general feedback afterwards was very positive.

In autumnal weather, the PhD students and postdocs started very early on Wednesday morning with a joint bus drive to Skeppsvik. After a welcoming coffee to get everyone weaken up, the programme started with an alumni session. Four UPSC alumni working now in different professions were invited and shared their experiences. It was an extensive session lasting the full morning and it was highly appreciated by the participants.

"It was motivating to hear what is possible"

“The alumni session was very enlightening. There was one person that moved to industry, one who went into publishing, one became a teacher, and one recently started his own research group”, said Sanchali Nanda, one of the participants. “It was interesting to hear how it went for them, to get to know which steps they took in their career and which role UPSC played for them. The alumni did not hesitate to talk about their struggles and emphasized how networking was a big part of their career progression. All of them were not so long ago in the same career stage as we are now. It is motivating to hear what is possible but also what to think on when choosing a certain career path.”

After the lunch break, the programme went on with team building activities. The participants were split up into smaller groups and the groups had to perform different tasks like for example doing together a jigsaw puzzle, sorting themselves according to different categories like shoe size or age without talking to each other or play the Helium Stick game. Standing in two opposite rows and holding a stick horizontally on their index fingers, they had to lower the stick to the ground without anyone losing the contact with the stick which astonishingly tends to move upwards instead of downwards.

"It is much easier to ask someone for help when you have spent time together"

“Our goal was to bring people together. These games were not necessarily related to research, but people needed to work together and like this got to know each other better,” explains Clément Boussardon, one of the organisers of the retreat and postdoc representatives at UPSC. “It is much easier to ask someone for help in the lab when you have spent time together and laughed together. That is why we think that such activities also profit our work as researcher at UPSC, and we are very grateful for the support from UPSC that allowed us to organise this retreat.”

The second day of the retreat was focussed on funding possibilities for young researchers in Sweden. Caroline Grabbe from the SLU Grants Office presented possible grants for young researchers and gave very useful advice on grant writing. Even though it was disillusioning for several participants to hear that there are not many grants for PhD students and postdocs available in Sweden, they appreciated a lot to receive this information together with the tips on grant writing as this allows them to plan their career accordingly.

The two days were rounded up with an afternoon session focussing on discussions and planning of future activities. This was a follow-up on discussions that were started during the UPSC DAYS 2022 focussing on improving UPSC, but the goal now was to go more into detail and find possible solutions for identified problems. The retreat was organised by the UPSC PhD students and postdocs themselves. It was organised before in 2016 and 2018 and was planned to take place in 2020 but was postponed two times because of the Covid-19 pandemic.

Helium stick - close up of five pair of hands holding a stick on their index fingers and trying to lower it simultaneously down towards the groundThe Helium stick game: the group tries to simultaneously lower the stick to the ground as fast as possible without anyone losing the contact with the stick (photo: Anne Honsel)

Link to the programme of the retreat


For questions regarding the UPSC PhD and Postdoc Retreat 2022, please contact a member of the organising committee:

Clément Boussardon (This email address is being protected from spambots. You need JavaScript enabled to view it.)
Thomas Dobrenel (This email address is being protected from spambots. You need JavaScript enabled to view it.)
Sara Raggi (This email address is being protected from spambots. You need JavaScript enabled to view it.)
Sara Westman (This email address is being protected from spambots. You need JavaScript enabled to view it.)

Portrait photo of Rosario García-Gil
Portrait photo of Rosario García-gilPhoto: Juha Niemi

SLU is awarding Rosario García-Gil with the Gold Medal for Distinguished Service. The announcement of this years’ Medal recipients came out this week. The two other recipients are Harry Blokhuis who is awarded with the Great Medal and Michael Bertram who will receive the Silver Medal. All three medals honour meritorious contributions for SLU and the sector in which SLU works. They will be officially handed over on the 8th of October during this years’ doctoral degree award ceremony at SLU in Uppsala.

Rosario García-Gil, associate professor at the SLU and group leader at UPSC, started to work at UPSC and SLU in 2005 focussing in her research on applied forest genetics and breeding mainly working with Norway spruce and Scots pine. Since 2019, Rosario García-Gil is also Vice-Dean for internationalisation at the Faculty of Forestry at SLU and member of the Faculty board. The Gold Medal for Distinguished Service rewards “exemplary, exceptional efforts of lasting value” that “benefit SLU or the sector in which the university is active”.

In her research, Rosario García-Gil uses advanced genetic methods to improve and fasten the breeding process. She was recently granted a large research project by the Swedish Foundation for Strategic Research (SSF) in which she aims to develop digital breeding tools to speed up the breeding cycle for Norway spruce and in parallel preserves biodiversity. The ecological sustainability perspective as well as the practical use of the research data and scientific innovations are important aspects of her work.

Rosario García Gil has built a wide collaboration network with other universities, companies and organisations, both within and outside the country which allowed her to receive extensive external research funding. It has also led to the wide dissemination of new results in the scientific community. Moreover, Rosario García-Gil has been involved in popular science activities such as Soapbox science and the Fascination of Plants Day.

According to the nomination letter, Rosario García-Gil’s ambition is to build a better society. She is keen on helping others to grow and progress in their careers. In her role as Vice-Dean for internationalisation, her goals are to increase the impact of the faculty’s science on global issues to develop sustainable models and to integrate the faculty’s international community in faculty-relevant matters and support their career development.

Rosario Garcia-Gil started her education as biologist at the University of Valencia in her home country Spain. After finishing her PhD on molecular plant breeding of fruit trees in 1999, she worked for four years as Marie Curie Postdoctoral researcher at the Department of Biology at Oulu University in Finland. She has been administrator of the second and third Research Schools in Forest Biotechnology and Genetics at SLU, is since 2015 member of the UPSC board and since 2019 member of The Barents Forest Sector Network and of the board of Föreningen Skogträdförädling.

Announcement of this years’ Medal recipients on the SLU homepage (only in Swedish)

General information about SLU’s Medals of Distinguished Service

More information about Rosario García-Gil’s research

Jingfang Hao and Alizee Malnoe standing with labcoats and mouth protection in a laboratory cold room.
Jingfang Hao and Alizee Malnoe standing with labcoats and mouth protection in a laboratory cold room.Jingfang Hao and Alizée Malnoë are isolating the lumen of chloroplats, an important technique used in the recently published article, in the cold room (photo: Robert Calderon).

Plants need light but too much of it can be harmful. A recent study, led by Alizée Malnoë from UPSC and Umeå University and by Mei Li from the Chinese Academy of Sciences, sheds light into the mechanism on how plants protect themselves from excess of light.

Jingfang Hao, postdoc at UPSC and shared first author of the study, says that the photoprotection they studied here is a biological process named non-photochemical quenching (NPQ), which plants carry out to dissipate the excess absorbed light as heat under strong illumination.

"The negative regulation of this photoprotection is mediated by a chloroplast membrane-anchored protein, SUPPRESSOR OF QUENCHING 1 (SOQ1). SOQ1 consists of a stromal domain, transmembrane domain and lumenal domain containing thioredoxin-like (Trx-like), NHL domain and C-terminal domain (CTD)", says Jingfang Hao and continues:

"The previous study determined that Trx-like domain is essential for SOQ1 suppression function on photoprotection. We discovered that besides Trx-like domain, CTD is indispensable for the negative regulation of photoprotection. The mechanism is that CTD can accept the electron from Trx-like domain and donate the electron to inhibit the target protein required for NPQ".

Why is this an important finding?

"Because this is the first study to report the crystal structure of SOQ1 lumenal domain and determine the function of the C-terminal domain of SOQ1 protein. Our findings uncover a new mechanism that how plants protect themselves from strong illumination".

Jingfang Hao tells further that investigating the localization of SOQ1, she isolated the chloroplast sub-fractions such as intact thylakoids, thylakoid membranes and lumen.

"I was surprised to find SOQ1 can be cleaved as several truncated forms in the lumenal fraction. Our Chinese colleagues also found these truncated forms when they purified the SOQ1 lumenal domains from bacteria. These findings suggest that the truncated forms could play some physiological functions".

What use will your findings have?

"The structure of the SOQ1 lumenal domain can provide a reference for the researchers to study similar proteins or proteins containing similar domains in other species. Moreover, our findings give a contribution to understanding how plants adapt the stressful environments".White cake with the SOQ1 and a very simplified form of the model described in the paper on it in colourTo celebrate the article, Jingfang got a cake from her colleagues illustrating their new findings (photo: Robert Calderon).

The article

Yu G#, Hao J#, Pan X#, Shi L, Zhang Y, Wang J, Fan H, Xiao Y, Yang F, Lou J, Chang W, Malnoë A*, Li M*. Structure of Arabidopsis SOQ1 lumenal region unveils C-terminal domain essential for negative regulation of photoprotective qH. Nat. Plants. 2022 Jul;8(7):840-855. https://doi.org/10.1038/s41477-022-01177-z


More about SOQ1
Alizée Malnoë and her group are working on photoprotection in plants. To know how plants get rid of excess light energy so that they do not get sunburned is interesting for biological research in general. It is particularly important to know because the amount of light absorbed by plants depends on the amount of CO2 fixed by photosynthesis and therefore determines how much biomass is produced.
SOQ1 is a protein in the leaves that manages the amount of light absorbed. Previously, only the part T and N of this molecular machine were known. In the study, the researchers identified the new part C of this machine and now they are able to understand how it works. SOQ1 has been found to have similarities to a bacterial protein which is known to transfer electrons between the different parts and thus changes the activity of other proteins. The researchers hypothesize that the same thing is happening in the leaf of plants and they are now working on finding the target protein of SOQ1 and how it modifies it exactly.
Not only bacteria and plants but also humans and animals have a version of SOQ1 which when mutated reduces the lifespan to only two short years. The researchers hope that their plant biology research can help to understand the function of SOQ1 in humans and tell more about the neurodegenerative disease in which it is implicated. It is a rare disease whose English acronym is FINCA, or syndrome of fibrosis-neurodegeneration-cerebral angiomatosis. Thanks to plant research, it is also known that SOQ1 acts on a protein, whose human counterpart is involved in Alzheimer's disease. However, the researchers think that it will take them much longer to determine if SOQ1 plays a role in Alzheimer's disease, too.

For questions, please contact:

Alizée Malnoë
Umeå Plant Science Centre
Department of Plant Physiology
Umeå University
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
https://www.upsc.se/alizee_malnoe
https://malnoelab.com/

Jingfang Hao
Umeå Plant Science Centre
Department of Plant Physiology
Umeå University
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.

Text: Per Melander, Jingfang Hao

Group picture of Alizée Malnoe's group in front of the sea
Group picture of Alizée Malnoe's group in front of the seaGroup picture of Alizée Malnoë's group with (from left to right) Aurélie Crepin, Alizée Malnoë, Pierrick Bru, Paola Puggioni, Fadime Demirel & Jingfang Hao (taken in May 2022 by Robert Calderon)

She could have been on Svalbard today, presenting her research and receiving the Early Career Prize from the Scandinavian Plant Physiology Society (SPPS) during the SPPS Congress 2022. Instead, she is taking on a different challenge. Alizée Malnoë, Associate Professor at Umeå University and group leader at UPSC, is currently on maternity leave and raising a baby. Read more about her research, why she became a group leader and joined UPSC in the interview below!

You were supposed to personally receive the SPPS Early Career Prize today on Svalbard during the SPPS Congress 2022. Do you regret that you could not go there and join the conference this week?

Alizée Malnoë: No, I do not regret it! I have attended and presented at many conferences since I started my PhD in 2007, and I am in the process of a challenging time-course experiment: breastfeeding a 4-month-old baby!

The SPPS Early Career Prize is - according to the SPPS homepage - given to “young, highly talented scientist, who has shown good progress and made significant, independent contributions to plant biology”. How does it feel to be awarded?

Alizée Malnoë: It feels really nice. I am grateful to have been nominated and awarded this prize by my colleagues since hard work does not always pay off! I am also very thankful to my mentors, collaborators and past and current group members.

You are awarded for your work on photoprotection in plants. What fascinates you about this topic?

Alizée Malnoë: I am fascinated by plants who can just stand there in the bright sun and not get sunburnt. It is amazing that they have evolved both the capacity to use the energy from sunlight for photosynthesis and the ability to dissipate the excess energy that would otherwise be harmful. A good example of the Swedish philosophy “lagom”: not too little, not too much light.

Did you always want to become a scientist?

Alizée Malnoë: I liked biology from childhood and had a kids laboratory kit! But I had no idea that I would pursue a PhD because I had thought it would be way too difficult.

Do you remember a key moment that influenced your decision to go on in academia and start your own group?

Alizée Malnoë: While mentoring students during my postdoctoral training, and sharing the fun of doing science, they told me “You’d be a great PI” which was a big confidence booster!

Why did you choose UPSC to start up your group?

Alizée Malnoë: Joining UPSC solved my family’s so-called “two-body problem” by giving work opportunities for both me and my husband, who himself is a plant scientist. With an ongoing tradition of photosynthesis research and possibilities for collaboration, plus the overall strong scientific environment of UPSC and its balanced and kind work-culture, it was an easy decision.

The SPPS prize is a monetary award. Do you have already an idea what you will do with it?

Alizée Malnoë: I will celebrate with my group and we will go eat something very nice.

Alizée Malnoë started her research group at UPSC in January 2018 after a Postdoc in Krishna K. Niyogi’s group at the University of California, Berkeley. She and her group study the molecular mechanisms that plants use to prevent damage by excess sunlight, a process called photoprotection. The SPPS Early Career Prize is acknowledging her (and her co-workers) research achievements in this field. It is given to young, talented scientists, who independently made important contributions to plant biology and who received their PhD less than 10 years before the SPPS Congress.

During the SPPS Congress in Svalbard, another scientist from UPSC, Kristoffer Jonsson, will also receive a prize, the SPPS PhD Prize. He was awarded already in 2021 but could not officially receive the prize because the SPPS Congress was postponed to 2022. Have a look here in case you would like to read more about Kristoffer Jonsson’s research and his prize

More information about the SPPS Prizes


For questions, please contact:

Alizée Malnoë
Umeå Plant Science Centre
Department of Plant Physiology
Umeå University
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
https://www.upsc.se/alizee_malnoe
https://malnoelab.com/

Three young aspen trees standing next to each other in front of a black background; left control, middle and right pgm mutant trees
Three young aspen trees standing next to each other in front of a black background; left control, middle and right pgm mutant treesYoung aspen trees lacking starch reserves (middle and right) grow as well as trees with starch (left). The starchless pgm mutant trees were created using the gene editing tool CRISPR-Cas9 which works as a pair of high-precision genetic scissors (pgm: PHOSPHOGLUCOMUTASE gene; photo: Wei Wang).

Aspen trees are not relying on their starch reserves when grown under benign conditions. This is shown in a new study with modified aspen defective in starch synthesis. The starch-lacking trees were also absorbing less carbon dioxide compared to non-modified trees, but their growth and performance was not affected. The study done by Totte Niittylä’s group from Umeå Plant Science Centre and SLU was published today in Current Biology.

About one third of the annual human-made carbon emissions are removed from the atmosphere by terrestrial photosynthesis and trees play a crucial role in this process. Like all plants, trees invest the carbon-containing sugars produced during photosynthesis either directly into growth, or they save them for future use - mainly in the form of starch. Increased atmospheric carbon dioxide levels stimulate photosynthesis, but its effect on trees is uncertain. How is the carbon used in trees? Totte Niittylä and his group set out to tackle this question from the opposite direction, by disrupting starch synthesis.

A lack of starch does not affect tree growth and biomass production

“We used the CRISPR-Cas9 technology, the genetic scissor, to introduce mutations in two genes that are essential for starch synthesis in aspen,” explains Wei Wang, postdoc in Totte Niittylä’s group and the first author of the study. “The modified trees contained no starch and assimilated up to 30 percent less carbon dioxide, but the growth and biomass production were not impacted – at least under the benign conditions that the trees experienced in the greenhouse.”

The researchers used different light conditions such as shorter days or low light levels to see how the modified trees deal with a shortage of carbon supply resulting from reduced photosynthesis. However, the modified trees did not show any sign of performance loss when compared to non-modified trees. The researchers concluded that aspen trees passively save carbon in the form of starch, contrasting the annual model plant Arabidopsis that depends on its starch reserves for normal growth.

Seasonal growth of aspen trees does not depend on starch reserves

To test if the perennial growth style of aspen trees requires starch reserves, the researchers simulated seasonal growing conditions in the greenhouse. Previous publications have indicated that starch is important for bud flush in the spring when photosynthesis is limiting. Surprisingly, the starch-lacking aspen trees set and flushed their buds in the same way and at the same time as non-modified trees.

“It was striking for us to see that aspen trees cope so well with the lack of starch and do not need it for the seasonal growth-dormancy cycle,” states Totte Niittylä, senior lecturer at SLU and group leader at Umeå Plant Science Centre. “The results also suggest that the needs of the growing tissues largely determine how much carbon dioxide is assimilated by the trees. This is important knowledge when estimating the capacity of trees to take up carbon dioxide from the atmosphere.”

The article

Wei Wang, Loïc Talide, Sonja Viljamaa and Totte Niittylä (2022) Aspen growth is not limited by starch reserves. Current Biology, https://doi.org/10.1016/j.cub.2022.06.056

Link to the article in Current Biology


For more information please contact:

Totte Niittylä
Umeå Plant Science Centre
Department of Forest Genetics and Plant Physiology
Swedish University of Agricultural Sciences
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
https://www.upsc.se/totte_niittyla

Close-up of a mushroom in a conifer forest
Close up of a mushroom in a conifer forestFertilisation promotes plant growth but changes the plant’s interaction with their mycorrhizal fungal partners (Photo by Dalibor Perina on Unsplash)

How do nutritional changes affect the interaction between trees and soil microorganisms? This has long remained a black box but a new study has shed light onto this cryptic association. It shows that increased soil nutrition changes the communication between trees and their associated fungi, restructuring the root-associated fungal community with major implications for carbon cycling in the forest.

The study was published today in Proceedings of the National Academy of Sciences. Researchers from Umeå Plant Science Centre, a collaboration between Swedish University of Agricultural Sciences and Umeå University, were leading the study and were supported by Science for Life Laboratory researchers from Stockholm University and Uppsala University.

Advances in sequencing techniques have made it possible to capture the dynamics of how tree roots and their fungal partners interact with each other. The researchers from Swedish University of Agricultural Sciences, Umeå University and Science for Life Laboratory compared a forest that was fertilised continuously over 25 years with a non-fertilised forest. They analysed the gene activity in tree roots and in over 350 fungal species over the course of a growing season and revealed that the fertilised trees changed their communication strategy and became more hostile to their fungal partners. As a result, the fungal community shifted from being dominated by specialist to more versatile species.

“In nutrient-poor boreal forests, trees are reliant on root-associated myccorhyzal fungi for their nutrient supply and maintain this partnership through the exchange of valuable sugars”, says Simon Law, first author of the study and former postdoc in Vaughan Hurry’s group at Umeå Plant Science Centre. “Soil fertilisation disrupts this sensitive trading relationship, causing trees to divert these sugars to their own growth and defence, with profound implications for the fungal community.”

Stress tolerant fungi are promoted in fertilised soils

The researchers showed that fertilised trees reduced the activity of genes that encode the information for sugar exporting proteins, while bolstering defence processes. The specialist myccorhyzal fungal species that are highly dependent on the carbon-containing sugars from the trees were the hardest hit. By ramping up their defence processes, the plants made root colonisation by these specialist fungi even more difficult and they became less abundant.

In contrast, metabolically versatile fungal species with less reliance on the trees flourished in the fertilised forests. These myccorhyzal fungi are characterised by dark coloured, resilient, cell walls that make the fungi more resistant to stress but also make the cell walls slower to decompose. This shift in the fungal community also influences the carbon cycling in the soil because the specialist fungi play an important role in decomposing plant litter. It has been shown in other studies that fertilisation of the northern conifer forests increases carbon storage both in the above ground plant tissues and in the soil. This new study provides insights into the underlying mechanisms of the soil storage processes. 

“It is well known that fertilisation leads to an increase in carbon storage in the above ground tissues of the trees at the expense of the below ground root and fungal network”, explains Vaughan Hurry, professor at the Swedish University of Agricultural Sciences. “But what this study shows is the complexity of the communication between the tree and the associated fungal community – and it highlights the importance of the tree’s voice in that communication.”

Nutritional changes affect carbon cycling in boreal forests

The conifer-dominated boreal forest circles the Northern Hemisphere and contains the largest terrestrial carbon store on Earth, potentially playing a vital role in mitigating climate change. Warming temperatures will increase the decomposition of dead material in the soil and thus increase nutrient cycling. This will affect the nutrient status of the trees and their associated fungal partners.

The researchers show that the complex relationship between trees and their associated microorganisms needs to be better understood to improve predictive models of how changing environmental conditions affect carbon and nutrient cycling in boreal forests.

Starting point for many more studies

“The relationship between the different organisms in the soil is hugely complex and has been largely inaccessible. The sequencing approach we have used allows us to probe these complex interactions at a molecular level, telling us who is there and what are they doing”, says Nathaniel Street, second corresponding author of the study and associate professor at Umeå University. “The approach we used in this study offers many new possibilities and we think that, in the long run, this will enable us to better understand the functional mechanisms driving ecosystem dynamics.”

The massive amount of data that the researchers have collected in their study on plant roots and soil microorganisms is made publicly available via an online tool, the Boreal Rhizospheric Atlas, that is hosted by the Science for Life Laboratory. Researchers can access this tool freely and explore the data further. The future plan is to include data from additional studies in the tool to shine further light on the complex relationship between plants and soil microorganisms.

The article

Simon R. Law, Alonso R. Serrano, Yohann Daguerre, John Sundh, Andreas N. Schneider, Zsofia R. Stangl, David Castro, Manfred Grabherr, Torgny Näsholm, Nathaniel R. Street, Vaughan Hurry (2022) Metatranscriptomics captures dynamic shifts in mycorrhizal coordination in boreal forests. Proceedings of the National Academy of Sciences (PNAS), 119 (26) e2118852119; doi.org/10.1073/pnas.2118852119

Link to the article in PNAS

For more information please contact:

Vaughan Hurry
Umeå Plant Science Centre
Department of Forest Genetics and Plant Physiology
Swedish University of Agricultural Sciences
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
https://www.upsc.se/vaughan_hurry

Nathaniel Street
Umeå Plant Science Centre
Department of Plant Physiology
Umeå University
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
https://www.upsc.se/nathaniel_street