PhD 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: