Andreas Schneider. Photo Laura Hinojosa

How do forest management strategies that aim on improving plant growth influence the fungal community? Andreas Schneider, PhD student in Nathaniel Street´s group at Umeå Plant Science Centre, has contributed to the development of new sequence analysis methods that make it easier to study fungal communities. He will defend his PhD thesis on Wednesday, 1st of June 2022 at Umeå University.

Text: Anne Honsel

Studying fungal communities in the forest soil is very challenging. The mushrooms seen in the forest in autumn are just made by some of the fungi to spread their spores. The most time of their lifecycle fungi are hidden in the soil or inside of the roots of their host plants. Recently developed advanced sequencing techniques offer many new possibilities and Andreas Schneider and his colleagues used these advances to develop automated bioinformatic tools that allow to study the dynamic and diversity of fungal communities in the soil.

“Many of the methods used to study fungi today are indirect. We take a soil sample, extract DNA from it and see to which species this DNA might belong to,” explains Andreas Schneider. “We used these methods in some of our studies, but one problem is that you do not know if the DNA comes from fungi that are dead or from some that are alive and active. That is why we used and further developed another method that is also indirect but that shows how active the fungi are. The great thing is that this can tell us what the fungi are up to, which genes are being expressed.”

To test their method, the researchers analysed how nitrogen addition affects the fungal community. Swedish forests are usually low in nitrogen and conifer trees compensate for this limitation by establishing the symbiosis with mycorrhizal fungi. The trees deliver carbon to the fungi and receive nitrogen in return. For seedlings on reforestation sites, it is crucial to establish the connection with the fungi to improve their chances to survive.

“Nitrogen addition, especially in high doses, is already known to change the fungal community in the soil quite a lot. Our experiments show that small amounts of organic nitrogen fertilization do not affect the fungal community but can improve the survival and growth rates of seedlings,” says Andreas Schneider. “This was true for seedlings coming from nurseries and also for seeds that were directly placed on the field site. We still need to follow up on the seedling growth rates over a longer period of time and for more different local conditions, but the current results are very promising.”

In a different approach, Andreas Schneider and his colleagues analysed why nitrogen addition inhibits the degradation of lignin in forest soils. Lignin is the component in dead plant material that is decomposed the most slowly by white-rot fungi. The researchers could show that nitrogen addition affects chemical processes in the soil and that this can have a negative impact on the efficiency of white-rot fungi.

They could also confirm that the composition of the fungal community associated with tree roots is changed on sites with high nitrogen fertilization favouring nitrogen tolerant fungi species. This can be caused both by soil chemistry changes and by a reprogramming of the mycorrhizal symbiosis from the side of the host tree.

“We could show that our methods are working and are useful to study dynamic changes in the fungal community”, thinks Andreas Schneider. “The biggest limitation now is the lack of genetic information for most fungal species, but we and many others are working on that. I am sure that in the future, this new knowledge and these methods will help us to evaluate even better how different forest management strategies influence fungal activity and biodiversity.”

About the public defence:

Andreas Schneider, Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, will defend his PhD thesis on Wednesday, 1st of June 2022. Faculty opponent will be Colin Averill, Department of Environmental Systems Science, ETH Zurich, Switzerland. The thesis was supervised by Nathaniel Street. Andreas Schneider was part of the PhD Research School in Forest Genetics, Biotechnology and Breeding and collaborated for his PhD project with Holmen Skog.

Title of the thesis: Perturbance and stimulation - using nitrogen addition and high throughput sequencing to study fungal communities in boreal forests

Link to the thesis

Hernán Dario Capador-Barreto. Photo Rob van Wijk

There is a large variation in Norway spruce in resistance to the fungi H. parviporum and H. annosum s.s. This is shown in Hernán Dario Capador-Barreto's new doctoral thesis. The results can be used in the Swedish breeding program to promote spruce genotypes that are more resistant to the fungi and help to control the spread of root rot in future forests.

Text: Malin Elfstrand

Forest products make up around one tenth of Sweden's total exports. A large part of the trees that are felled and processed into forest products in the Swedish forest industry are Norway spruce, Picea abies, which makes up around 40% of the trees in our forests. Norway spruce has basically two major pests in Sweden, the most widely discussed right now is the spruce bark beetle due to the massive attacks we saw after the drought in 2018. The other major pest that may not have been as visible in the debate lately is the root rot fungi of the species complex Heterobasidion annosum s.l. Seen in a longer perspective root and stem rot, is at least as big a problem for forest owners as the bark beetle attacks.

Heterobasidion renders the wood useless for timber

In Sweden there are two species of Heterobasidion, Heterobasidion parviporum and Heterobasidion annosum s.s. Both species can infect spruce and cause root and stem rot. The decay can reach many meters up into the stem and make it useless for saw timber. The spores of the fungi infect fresh stumps after thinning or felling, and the fungus grows down into the root system. From there, it can spread to adjacent, healthy trees via root contacts. The fungus can also stay alive in stumps and root remains for decades after the felling and from there attack and damage the next generation of trees.

To reduce the infestation of Heterobasidion, Swedish forestry has adopted new management regimes and today stump surfaces are treated with biocontrol preparations immediately after felling. Despite this, about 15% of Sweden's spruces have root rot when they are harvested, and the proportion increases by about 3 percent units per decade.

Norway spruce with better resistance

Since it is difficult to target the fungi that has already colonized a site, it would be good if the Norway spruce replantation material held good resistance to Heterobasidion. For this to become a reality, Sweden's forest tree breeders need both more knowledge about what constitutes resistance to Heterobasidion as well as methods for finding the most resistant trees and using them in the breeding of Norway spruce.

The aim of Hernán Dario Capador-Barreto's Ph. D. work at the Department of Forest Mycology and Plant Pathology at SLU was to support Sweden's forest tree breeding by describing and comparing the genetic variation in Norway spruce that controls resistance to H. parviporum and H. annosum s.s.

Rotting logs after harvesting close to Uppsala, resistance testing for spread of fungus in sapwood and testing of resistance in seedlings in a nursery. Photo: Hernán Dario Capador-Barreto.

Markers for resistance to more than one species of Heterobasidion

In his recently published doctoral dissertation, he shows that there is large variation in the levels of resistance to both H. parviporum and H. annosum s.s. among Norway spruces trees in the Swedish breeding program and that the resistance has a high heritability, ie the Norway spruce genotype has a large impact on how resistant it is to root rot. However, the resistance to different species of the fungus is not correlated.

– We found that the offspring from a specific tree could have very good resistance to one species of Heterobasidion but not to the other. We also saw that the environment the spruces grew in affects how much the measured resistance varied, says Hernán.

Hernán and his co-authors then analyzed whether they could identify new genetic markers in Norway spruce that could be used to find trees that have good resistance to H. parviporum and H. annosum s.s. or against both fungi simultaneously.

Genes that help slow down the infecting fungus

Geneticists and breeders call genetic markers associated with more than one trait pleiotrophic markers. The researchers found 20 pleiotrophic markers in this study, most of them were positive pleiotrophic markers, i.e., the same marker was associated with better resistance to both fungal species at the same time.

– An exciting positive pleiotrophic marker is the laccase PaLAC5, the gene is active in the bark right next to the infection with Heterobasidion. Together with results of other researchers, we know that PaLAC5 is activated during stress, and we think it helps to produce defence substances and lignin in the tissue that slow down the infecting fungus, says Hernán.

Spruces in Europe and North America have common markers of resistance

In his third paper, Hernán studied the known resistance marker PaLAR3, which controls how fast H. parviporum can spread in Norway spruce wood. Hernán compared the DNA sequence of PaLAR3 in Norway spruce with the DNA sequences of North American spruce species to understand how it changed during evolution. In Norway spruce, the variation in is likely to have been maintained through what is known as balancing selection. The fact that a gene is under balancing selection means that it has relatively few variants with relatively even (balanced) frequencies, which are also stable for many generations.

– Our results indicate that PaLAR3 was under balancing selection before Norway spruce and the North American white spruce separated from each other and became different species, says Hernán.

Robust gene expression patterns in trees with higher resistance to Heterobasidion

Another method that Hernán has used in his Ph. D. work is gene expression studies. In these studies, he and his colleagues examined which genes are active in Norway spruce and H. annosum s.s. before and after infection, respectively, according to the hypothesis that genes that control resistance or infectivity are turned on or off when the fungus infects spruce tissues. The study used Norway spruces with different levels of resistance and H. annosum s.s. individuals with different virulence. By virulence, researchers mean how far fungal individuals can spread in the tree and how many disease symptoms they cause.

The experiment showed that Norway spruce individuals with relatively high resistance to Heterobasidion reacted in a robust manner. Regardless of which fungal individual they were infected with, approximately the same group of genes were active after the infection.

– Among the active genes, there were several genes involved in recognition of Pathogenic microorganisms. In contrast, the gene expression in the more susceptible Norway spruce individual was more variable. The activity of genes in the susceptible individual depended on the severity of the disease symptoms caused by the fungus, concluced Hernán.

Links:

Hernán Dario Capador-Barreto’s doctoral theses ”Genetics of disease resistance in Norway spruce (Picea abies): a look in the past with an eye to the future”

Hernán Dario Capador-Barreto defends his thesis 22 April 2022, 13.00. Read more about the dissertation here.

Jenny Lundströmer on campus in Umeå in front of Norway spruce trees (photo Sonali Ranade)

How will Norway spruce behave in a changing climate? Jenny Lundströmer, industrial PhD student in Rosario García Gil’s group at UPSC and at former Bergvik Skog, investigated how warmer temperatures, more frequent spring frosts and drought affect Norway spruce from different origins. She recommends breeding not only for better growth but also for drought tolerance and other characteristics that help to adapt to a changing climate. In case of seed shortage from Swedish seed orchards, she advices Norway spruce provenances from Eastern Europe as valuable alternative. Jenny Lundströmer will defend her PhD thesis at SLU on Friday this week, 29th of January. 

Text Anne Honsel

You investigated how Norway spruce can adapt to a changing climate. What aroused your interest into this PhD topic?

I am from a small village just below the arctic circle and grew up with the forest just besides me and have always been interested in how we can use the forest in a sustainable way and still enjoy it. The PhD topic was focussing on where to plant which provenances of Norway spruce to see which ones we should choose today that can survive the next 60 years. The project was part of the industrial graduate school in forest genetics, biotechnology and breeding and was in collaboration with Bergvik Skog that is now part of Stora Enso. For me, that sounded like a great opportunity to work more applied - which I was not doing during my masters - and combine it with my interest in forestry.

How was it to be part of the industrial graduate school that is a collaboration between the UPSC Centre for Forest Biotechnology and its industrial partners?

It was really great because we had regular meetings where we presented our projects and discussed them. I really appreciated this extra training but also the opportunity to follow the projects of the others over the years, see how they develop, discuss problems and exchange tips. Harry Wu also arranged great lectures with top professors in their field and courses that were specifically adjusted to our needs, as well as a trip to the US and Brazil where we saw some breeding institutes and plant nurseries. We also visited each other’s companies and met people there. My industrial partner was Bergvik Skog, where I did a project with seed orchards at their nursery, but I also had collaboration projects with Skogforsk and could get a deeper look into their work. I am really happy that I was part of the graduate school because I learned a lot, got additional experiences and valuable insights into industry and I found new friends through the graduate school.

What are the major threats for Norway spruce due to climate change in Sweden?

One of the biggest problems will be warmer temperatures. You could think that warmer temperatures are good because the trees can grow more as they have a longer vegetation time, but the winters will still be cold with freezing temperatures. This means that the trees have to stop their growth during autumn. There will also be more temperature backlashes in spring increasing the risk for frost damage - especially if bud burst starts earlier due to higher temperatures. In summer, higher temperatures increase the risk for drought. That is why we need trees that set their buds in time despite warmer autumns, that are able to bud burst at the right time in spring to prevent frost damage and that are drought tolerant. Both drought and spring frosts are mostly local problems. The crux will be to choose the right tree for the right place like for example trees with later bud burst on frost prone sites.

Do you think Norway spruce is able to tolerate future climate changes?

It has been growing good here for a long period and I think Norway spruce will survive the near and far future. To predict climate changes in the far future is difficult but the seedlings are the ones that are most sensitive to frost and drought, which make the prediction for the near future more valuable. One of my projects was to test how seeds from Eastern Europe with later bud burst and bud set perform when planted in the South of Sweden. It turned out that the trees are growing good there even though they start the vegetation period later than the Swedish ones. The growth rates are not as good as for trees from Swedish seed orchards but specifically on frost prone sites, the Eastern European provenances with later bud burst are a good alternative. This indicate that in a future with more spring frost events transfer of Norway spruce has to be performed for it to survive.

Which of your results is the most fascinating for you?

We analysed not only the first generation of Eastern European Norway spruce in Sweden but also second-generation material. These are trees that derive from Eastern European stands planted in Sweden that were open pollinated with Swedish populations around and which seeds were then planted out. Normally, we would assume that these trees have about 50% genetic material from the Eastern European material and 50% from the surrounding Swedish ones and that they bud burst after the Swedish material but before the Eastern European material. Astonishingly, we saw that they were closer to the Swedish population in terms of bud burst. Some other studies showed that the climate on the site where you plant a tree is affecting its seeds and we think that this might happen also here. I find it really fascinating to see that Norway spruce has the capacity to adapt this fast to the climate on its local site.

What challenges did you face during your PhD?

Everything took longer than planned but especially the last year was really challenging for me - not only because I wanted to finish my thesis but also because of Corona and all changes connected to this. I used to work from home a lot also before, but I found it strange to not be able to communicate with others in the usual way. The discussions are different if everything is online.

Do you have any recommendations for breeders, forest companies and/or forest owners?

I think that it is important to breed not only for better growth characteristics but also for trees that are able to adapt to a changing climate like for example that are more drought and frost tolerant. By comparing different clones, we saw that there are some that can deal better with drought than others. So, there is the potential. Provenances with later bud burst are better to use on frost prone sites because they are more likely to survive. I can just enhance the recommendation to use also seeds from Eastern Europe, especially as there is a shortage of seeds from Swedish seed orchards due to unregular flowering, insects and pests. Even the second generation of Eastern European trees are a good alternative, but it will be good to think about where to plant them to make sure they are suitable for the respective site.

What are your plans for the future?

First, I would like to take time for myself and my family. Then, I want to finish my papers and do some further analyses that I could not finish before. In parallel, I will look for a job. I would like to work in the forest industry. It does not have to be breeding but should be related to forestry or forest work and it would be nice to do something practical and not only computer work. In one of my projects, I joined the final assessment of the trees at the field sites. The weather was horrible, but I enjoyed doing practical work and see how the trees grow.

About the public defence:

The public defence will take place on Friday, 29th of January 2021 at SLU Umeå. Faculty opponent will be Darius Danusevičius from Vytautas Magnus University, Lithuania. Jenny Lundströmer was first supervised by Bengt Andersson Gull and later by María Rosario García Gil and co-supervised by Anna Maria Jönsson from Lund University. She was member of the industrial graduate school in forest genetics, biotechnology and breeding and worked with Bergvik Skog that is now part of Stora Enso, with Oskar Skogström as co-supervisor. At Skogforsk with which she had collaboration projects, she was co-supervised by Johan Westin and Mats Berlin. The dissertation will be live broadcasted via Zoom.

Title of the thesis: Adaption of Norway spruce (Picea abies (L.) Karst.) to current and future climatic conditions

Link to the thesis: https://pub.epsilon.slu.se/21159/

For more information, please contact:

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

Thesis defense: Jenny Lundströmer

Thesis title: Adaptation of Norway spruce (Picea abies (L.) Karst.) to current and future climatic conditions

Date: 2021-01-29, 9:00, P-O Bäckströms Sal, SLU

Opponent: Darius Danusevičius, Faculty of Forest Science and Ecology,Vytautas Magnus University, Lithuania

This spring, PhD students and two PIs of the UPSC Research School of Forest Genetics, Biotechnology and Breeding visited different forest research organisations and forest companies in New Zealand and Australia. On their two weeks long trip they got an overview over the Australian forestry sector, and insights into national breeding and seed preservation programs. This was the third time the research school was organising an international excursion. Unfortunately, the additional visit to forestry sites in China had to be cancelled due to the start of the Corona pandemic.

”This trip was amazing, inspiring and a once-in-a-life-time-opportunity,” says Bodil Häggström, one of the students that joined the excursion. “One obvious difference when comparing this area to Sweden is of course the very different assemblage of species”, she explains further. But also “the much higher focus on using foreign species for wood production compared to Swedish forestry where native species are the most used”, was new and interesting information for her.

In New Zealand, the members of the research school visited two institutions – Scion and Timberlands limited. The governmental owned institute Scion is a located in Rotorua and is specialised in research, science and technology development for forest industry. Beside breeding programs, the group got insights into other research activities. Some of those clearly remembered of research conducted at UPSC, like whole genome sequencing of radiata pine, research on somatic embryogenesis or forest pathology.

Timberlands Limited, one of the big New Zealand forest companies working with forest management and operations works closely together with Scion but produces their own clones. The students visited a nursery outside of Rotorua that produces about 10 Million seedlings per year.


Participants of the excursion gathering under Redwood trees from the Scion breeding program (left). A Timberland limited nursery outside of Rotorua (Photos: B. Häggström and MR. García-Gil)

The first Australian institution they visited was Tree Breeding Australia (TBA). TBA is the Australian national body that manages tree improvement programs. The original goal of the TBA is to create seed orchards and new breeding values for the Australian forestry industry. In their breeding arboreta, the students saw the production of new genotype seed material for forestry companies. The main species they work with are radiata pine and blue gum eucalyptus. 

Another Australian Institution, the research school group took a closer look at, was the Australian Tree Seed Centre (ATSC). The ATSC belongs to the Commonwealth Scientific and Industrial Research Organisation (CSIRO) and is one of the National Research Collections. ATSC is a collection and research centre for Australian native tree species and has been supplying quality tree seed to customers worldwide. ATSC not only has a big physical collection of seeds but also an extensive database with information about these seeds. The data can be used to track nationally and internationally exported tree material and also in worldwide studies on invasive species.

Eucalyptus clones are planted in straight rows at a TBA plantage (photo left).  Eucalyptus is not only an important Australian tree species for forestry but also serves as habitat for Koalas (photo middle). In ATSC seed storage all seeds are stored in tin cans to keep them dry (photo right; Photos: B Häggström, MR García-Gil).

Thesis defense: Irena Fundova

Thesis Title: Quantitative genetics of wood quality traits in Scots pine

Date: 2020-04-24, 9:00, P-O Bäckström Sal.

Opponent: Philippe Rozenberg, French National Institute for Agriculture, Food, and Environment (INRAE)

The committee:
Ann Christin Rönnberg-Wästljung, Dpt. Plant biology, SLU 
Arne Steffenrem, Norwegian Institute of Bioeconomy Research, NIBIO 
Matti Haapanen, National Resource Insitutet Finland, LUKE

Congratulations to Irena Fundova! She successfully defended her PhD thesis at SLU Umeå. Due to the current situation and following official regulations, the entire thesis defens was broadcasted online. Both the commitee and the opponent joint remotely. The whole defens has been recorded and the video is still openly accessible (link: https://play.slu.se). 


Irena Fundova after successfully defending her PhD. The whole defens was conducted online with the commmitee members joining remotely (Photos: S. Ranade,
R. Garcia-Gil).

On the homepage of UPSC you can read more about Irena and her PhD work. Please follow this link: Fast and non-destructive ways to estimate wood quality in forest trees to optimize breeding strategies for Scots pine

Thesis defense: Alexis SULLIVAN

Thesis title: A Forest Dark: An Evolutionary History of Norway Spruce

Date: 2020-03-11, 13:00, Kempe salen KBC.

Opponent: Prof. Bengt Oxelman, Department of Biological & Environmental Sciences, University of Gothenburg.

The committee:
Professor Martin Lascoux, Evolutionary Biology Centre, Uppsala University
Docent Folmer Bokma, Centre for Ecological and Evolutionary Synthesis, University of Oslo
Docent Benedicte Albrectsen, Department of Plant Physiology, UPSC, Umeå University

Thesis defense: Ainhoa Calleja-Rodriguez 

Thesis title: Quantitative Genetics and Genomic Selection of Scots Pine

Date: 2019-05-29, 09:00, P-O Bäckströms sal (SLU Umeå)

Opponent: Dr Heidi Dungey, Senior Scientist and Science Leader of Forest Genetics, Scion (New Zealand Forest Research Institute

Thesis defense: Julia Christa Haas
 Thesis title: Abiotic stress and plant microbe interaction in Norway spruce.
Swedish title: Abiotisk stress och interaktioner mellan växter och mikroorganismer i gran.

Date: 2018-12-14, 10:00 AM, KBC-huset, Stora hörsalen KB.E3.03 

Opponent:
Jennifer Baltzer, Associate Professor and Canada Research Chair in Forest and Global Change Department of Biology, Wilfrid Laurier University, Waterloo, Canada.