Ella Thoen

• Fonseca, Jose Mauricio Salamanca; Sanchez, Adriana; Corrales, Adriana; Kauserud, Håvard; Thoen, Ella & Krabberød, Anders K. [Show all 7 contributors for this article] (2025). Beyond seasonal and host factors: ecosystem dynamics drive palm-associated root fungal communities at a local scale. Plant and Soil. ISSN 0032-079X. 514, p. 1027–1041. doi: 10.1007/s11104-025-07438-y. Full text in Research Archive Show summary

  Background and Aims The increase of extreme weather events due to climate change may alter ecosystem dynamics. In the tropics, little is known about how ecosystems and species will respond to droughts or floods. Identifying the most important biotic and abiotic factors in ecosystems at the local level is key to developing better forest management practices and understanding the effects of climate change on the fungal community. Methods We conducted a random sampling of adult individuals from several palm species across three adjacent ecosystems with different hydrological conditions, during rainy and dry seasons. Using next-generation sequencing, we identified fungal communities and determined the influence of soil physicochemical properties, as well as host and seasonal variables, on the relative abundance of the root- and rhizosphere-associated fungal communities. Results The composition of the fungal communities was similar between the seasonally flooded forest and the terra-firme forest, while the palm swamp diverged due to differences in soil physicochemical properties. Seasonal analyses revealed significant differences in the relative abundance of several taxa, mainly associated with the seasonally flooded forest. However, no influence of palm species on fungal abundance was detected at any taxonomic level. Conclusion This study highlights the importance of studying ecosystems at the local scale and considering ecosystem dynamics into the study of fungal communities and other microorganisms. Such an approach is crucial for improving predictions under climate change scenarios and understanding the consequences of altering these dynamics in vulnerable, often understudied ecosystems.

• Thoen, Ella; Krabberød, Anders K.; Nogerius, Veera Tuovinen; Skrede, Inger; Rosling, Anna & Kauserud, Håvard (2025). Short‐ and long‐read metabarcoding of Archaeorhizomycetes reveals high phylogenetic diversity structured by vegetation and climate. New Phytologist. ISSN 0028-646X. 249 (2026)(1), p. 418–432. doi: 10.1111/nph.70682. Full text in Research Archive Show summary

  Summary Archaeorhizomycetes is a class of globally widespread soil‐dwelling fungi, originally proposed to be associated with plant roots, but their ecology and nutritional mode are not clearly defined. To increase the knowledge about Archaeorhizomycetes' ecology and biogeography, we investigate how they are distributed along major environmental gradients, as well as different soil compartments. To assess their abundance and diversity, we use both short‐ and long‐read metabarcoding with class‐specific primers for the long reads. The short‐read sequences revealed that Archaeorhizomycetes is proportionally abundant and a dominant fungal class in alpine vegetation types, as well as boreal spruce and pine forests. The long‐read sequences revealed high phylogenetic diversity of Archaeorhizomycetes, with 120 OTUs grouping into 13 clades with potentially differing ecologies and biogeographic distributions. Vegetation types and climate primarily structure the Archaeorhizomycetes community, while community composition was similar in litter, soil, and roots. However, Archaeorhizomycetes were significantly more abundant in soil and plant roots than litter, supporting the idea that Archaeorhizomycetes depend on the presence of plant roots. Our study illustrates that targeted group‐specific amplification coupled with long‐read sequencing is a powerful approach for exploring the diversity and ecology of specific fungal groups.

• Ronold, Eivind Kverme; Vik, Unni; Vandvik, Vigdis; Kauserud, Håvard & Thoen, Ella (2025). Elevational range expansion of Betula pubescens may be slowed by lack of suitable mycorrhizal symbionts in alpine soils. Fungal ecology. ISSN 1754-5048. 77. doi: 10.1016/j.funeco.2025.101454. Full text in Research Archive Show summary

  The elevational limit for trees is increasing worldwide due to global warming. The elevational range expansion of obligate ectomycorrhizal trees, such as Betula pubescens, may however be limited by lack of fungal symbionts above the treeline since the vegetation here is often dominated by plants forming other mycorrhizal types. We set up a cross-factorial experiment cultivating Betula pubescens seedlings in alpine and lowland soils, at simulated alpine and lowland temperatures, to test whether the fungal community may limit seedling establishment. We found that alpine soils contained fewer ectomycorrhizal fungi in general and that seedlings cultivated in alpine soil were smaller and recruited fewer ectomycorrhizal fungi compared to seedlings cultivated in lowland soil. Our results indicate a link between seedling success, soil fungal community and mycorrhizal colonization. We suggest that unsuccessful mycorrhization of seedlings above the treeline may be limiting for treeline expansion under increased alpine temperatures.

• Barbi, Florian; Martinović, Tijana; Odriozola, Iñaki; Machac, Antonin; Moravcová, Andrea & Algora, Camelia [Show all 22 contributors for this article] (2025). Disentangling drivers behind fungal diversity gradients along altitude and latitude. New Phytologist. ISSN 0028-646X. 247(1), p. 295–308. doi: 10.1111/nph.70012. Full text in Research Archive
• Harder, Christoffer Bugge; Miyuachi, Shingo; Virágh, Máté; Kuo, Alan; Thoen, Ella & Andreopoulos, Bill [Show all 28 contributors for this article] (2024). Extreme overall mushroom genome expansion in Mycena s.s. irrespective of plant hosts or substrate specializations. Cell Genomics. 4(7), p. 1–16. doi: 10.1016/j.xgen.2024.100586. Full text in Research Archive Show summary

  Mycena s.s. is a ubiquitous mushroom genus whose members degrade multiple dead plant substrates and opportunistically invade living plant roots. Having sequenced the nuclear genomes of 24 Mycena species, we find them to defy the expected patterns for fungi based on both their traditionally perceived saprotrophic ecology and substrate specializations. Mycena displayed massive genome expansions overall affecting all gene families, driven by novel gene family emergence, gene duplications, enlarged secretomes encoding polysaccharide degradation enzymes, transposable element (TE) proliferation, and horizontal gene transfers. Mainly due to TE proliferation, Arctic Mycena species display genomes of up to 502 Mbp (2–8× the temperate Mycena), the largest among mushroom-forming Agaricomycetes, indicating a possible evolutionary convergence to genomic expansions sometimes seen in Arctic plants. Overall, Mycena show highly unusual, varied mosaic-like genomic structures adaptable to multiple lifestyles, providing genomic illustration for the growing realization that fungal niche adaptations can be far more fluid than traditionally believed.

• Krabberød, Anders Kristian; Stokke, Embla Elen; Thoen, Ella; Skrede, Inger & Kauserud, Håvard (2024). The Ribosomal Operon Database: A Full-Length rDNA Operon Database Derived From Genome Assemblies. Molecular Ecology Resources. ISSN 1755-098X. doi: 10.1111/1755-0998.14031. Full text in Research Archive Show summary

  Current rDNA reference sequence databases are tailored towards shorter DNA markers, such as parts of the 16/18S marker or the internally transcribed spacer (ITS) region. However, due to advances in long-read DNA sequencing technologies, longer stretches of the rDNA operon are increasingly used in environmental sequencing studies to increase the phylogenetic resolution. There is, therefore, a growing need for longer rDNA reference sequences. Here, we present the ribosomal operon database (ROD), which includes eukaryotic full-length rDNA operons fished from publicly available genome assemblies. Full-length operons were detected in 34.1% of the 34,701 examined eukaryotic genome assemblies from NCBI. In most cases (53.1%), more than one operon variant was detected, which can be due to intragenomic operon copy variability, allelic variation in non-haploid genomes, or technical errors from the sequencing and assembly process. The highest copy number found was 5947 in Zea mays. In total, 453,697 unique operons were detected, with 69,480 operon variant clusters remaining after intragenomic clustering at 99% sequence identity. The operon length varied extensively across eukaryotes, ranging from 4136 to 16,463 bp, which will lead to considerable polymerase chain reaction (PCR) bias during amplification of the entire operon. Clustering the full-length operons revealed that the different parts (i.e., 18S, 28S, and the hypervariable regions V4 and V9 of 18S) provide divergent taxonomic resolution, with 18S, the V4 and V9 regions being the most conserved. The ROD will be updated regularly to provide an increasing number of full-length rDNA operons to the scientific community.

• Tonjer, Lea-Rebekka; Thoen, Ella; N, Luis Morgado; Botnen, Synnøve; Mundra, Sunil & Nybakken, Line [Show all 8 contributors for this article] (2021). Fungal community dynamics across a forest–alpine ecotone. Molecular Ecology. ISSN 0962-1083. 30(19), p. 4926–4938. doi: 10.1111/mec.16095. Full text in Research Archive Show summary

  Climate change is causing upward shift of forest lines worldwide, with consequences for soil biota and carbon (C) sequestration. We here analyse compositional changes in the soil biota across the forest line ecotone, an important transition zone between different ecosystems. We collected soil samples along transects stretching from subalpine mountain birch forests to alpine heath. Soil fungi and micro-eukaryotes were surveyed using DNA metabarcoding of the ITS2 and 18S markers, while ergosterol was used to quantify fungal biomass. We observed a strong shift in the soil biota across the forest line ecotone: Below the forest line, there were higher proportions of basidiomycetes and mucoromycetes, including ectomycorrhizal and saprotrophic fungi. Above it, we observed relatively more root-associated ascomycetes, including Archaeorhizomycetes, ericoid mycorrhizal fungi and dark septate endophytes. Ergosterol and percentage C content in soil correlated strongly and positively with the abundance of root-associated ascomycetes. The predominance of ectomycorrhizal and saprotrophic fungi below the forest line probably promote high C turnover, while root-associated ascomycetes above the forest line may enhance C sequestration. With further rise in forest lines, there will be a corresponding shift in the below-ground biota, probably leading to enhanced release of soil C.

• Botnen, Synnøve Smebye; Thoen, Ella; Eidesen, Pernille Bronken; Krabberød, Anders Kristian & Kauserud, Håvard (2020). Community composition of arctic root-associated fungi mirrors host plant phylogeny. FEMS Microbiology Ecology. ISSN 0168-6496. 96. doi: 10.1093/femsec/fiaa185. Full text in Research Archive Show summary

  The number of plant species regarded as non-mycorrhizal increases at higher latitudes, and several plant species in the High-Arctic Archipelago Svalbard have been reported as non-mycorrhizal. We used the rRNA ITS2 and 18S gene markers to survey which fungi, as well as other micro-eukaryotes, were associated with roots of 31 arctic plant species not usually regarded as mycorrhizal in Svalbard. We assessed to what degree the root-associated fungi showed any host preference and whether the phylogeny of the plant hosts may mirror the composition of root-associated fungi. Fungal communities were largely structured according to host plant identity and to a less extent by environmental factors. We observed a positive relationship between the phylogenetic distance of host plants and the distance of fungal community composition between samples, indicating that the evolutionary history of the host plants plays a major role for which fungi colonize the plant roots. In contrast to the ITS2 marker, the 18S rRNA gene marker showed that chytrid fungi were prevalently associated with plant roots, together with a wide spectrum of amoeba-like protists and nematodes. Our study confirms that arbuscular mycorrhizal (AM) fungi are present also in arctic environments in low abundance.

• Thoen, Ella; Harder, Christoffer Bugge; Kauserud, Håvard; Botnen, Synnøve Smebye; Vik, Unni & Taylor, Andy F.S. [Show all 8 contributors for this article] (2020). In vitro evidence of root colonization suggests ecological versatility in the genus Mycena. New Phytologist. ISSN 0028-646X. 227, p. 601–612. doi: 10.1111/nph.16545. Full text in Research Archive Show summary

  - The root‐associated habit has evolved on numerous occasions in different fungal lineages, suggesting a strong evolutionary pressure for saprotrophic fungi to switch to symbiotic associations with plants. Species within the ubiquitous, saprotrophic genus Mycena are frequently major components in molecular studies of root‐associated fungal communities, suggesting that an evaluation of their trophic status is warranted. Here, we report on interactions between a range of Mycena species and the plant Betula pendula. - In all, 17 Mycena species were inoculated onto B. pendula seedlings. Physical interactions between hyphae and fine roots were examined using differential staining and fluorescence microscopy. Physiological interactions were investigated using 14C and 32P to show potential transfer between symbionts. - All Mycena species associated closely with fine roots, showing hyphal penetration into the roots, which in some cases were intracellular. Seven species formed mantle‐like structures around root tips, but none formed a Hartig net. Mycena pura and Mycena galopus both enhanced seedling growth, with M. pura showing significant transfer of 32P to the seedlings. - Our results support the view that several Mycena species can associate closely with plant roots and some may potentially occupy a transitional state between saprotrophy and biotrophy.

• Botnen, Synnøve Smebye; Davey, Marie Louise; Aas, Anders Bjørnsgard; Carlsen, Tor; Thoen, Ella & Heegaard, Einar [Show all 12 contributors for this article] (2019). Biogeography of plant root-associated fungal communities in the North Atlantic region mirrors climatic variability. Journal of Biogeography. ISSN 0305-0270. 46(7), p. 1532–1546. doi: 10.1111/jbi.13613. Full text in Research Archive Show summary

  Aim Polar and alpine ecosystems appear to be particularly sensitive to increasing temperatures and the altered precipitation patterns linked to climate change. However, little is currently known about how these environmental drivers may affect edaphic organisms within these ecosystems. In this study, we examined communities of plant root‐associated fungi (RAF) over large biogeographical scales and along climatic gradients in the North Atlantic region in order to gain insights into the potential effects of climate variability on these communities. We also investigated whether selected fungal traits were associated with particular climates. Locations Austria, Scotland, Mainland Norway, Iceland, Jan Mayen and Svalbard. Taxa Root fungi associated with the ectomycorrhizal and herbaceous plant Bistorta vivipara. Methods DNA metabarcoding of the ITS1 region was used to characterize the RAF of 302 whole plant root systems, which were analysed by means of ordination methods and linear modelling. Fungal spore length, width, volume and shape, as well as mycelial exploration type (ET) of ectomycorrhizal (ECM) basidiomycetes were summarized at a community level. Results The RAF communities exhibited strong biogeographical structuring, and both compositional variation as well as fungal species richness correlated with annual temperature and precipitation. In accordance with general island biogeography theory, the least species‐rich RAF communities were found on Jan Mayen, a remote and small island in the North Atlantic Ocean. Fungal spores tended to be more elongated with increasing latitude. We also observed a climate effect on which mycelial ET was dominating among the ectomycorrhizal fungi. Main conclusions Both geographical and environmental variables were important for shaping root‐associated fungal communities at a North Atlantic scale, including the High Arctic. Fungal OTU richness followed general biogeographical patterns and decreased with decreasing size and/or increasing isolation of the host plant population. The probability of possessing more elongated spores increases with latitude, which may be explained by a selection for greater dispersal capacity among more isolated host plant populations in the Arctic.

• Thoen, Ella; Aas, Anders Bjørnsgard; Vik, Unni; Brysting, Anne Krag; Skrede, Inger & Carlsen, Tor [Show all 7 contributors for this article] (2019). A single ectomycorrhizal plant root system includes a diverse and spatially structured fungal community. Mycorrhiza. ISSN 0940-6360. 29(3), p. 167–180. doi: 10.1007/s00572-019-00889-z. Full text in Research Archive Show summary

  Although only a relatively small proportion of plant species form ectomycorrhizae with fungi, it is crucial for growth and survival for a number of widespread woody plant species. Few studies have attempted to investigate the fine scale spatial structure of entire root systems of adult ectomycorrhizal (EcM) plants. Here, we use the herbaceous perennial Bistorta vivipara to map the entire root system of an adult EcM plant and investigate the spatial structure of its root-associated fungi. All EcM root tips were sampled, mapped and identified using a direct PCR approach and Sanger sequencing of the internal transcribed spacer region. A total of 32.1% of all sampled root tips (739 of 2302) were successfully sequenced and clustered into 41 operational taxonomic units (OTUs). We observed a clear spatial structuring of the root-associated fungi within the root system. Clusters of individual OTUs were observed in the younger parts of the root system, consistent with observations of priority effects in previous studies, but were absent from the older parts of the root system. This may suggest a succession and fragmentation of the root-associated fungi even at a very fine scale, where competition likely comes into play at different successional stages within the root system.

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• Kirkhus, Mika Helene; Thoen, Ella; Vandvik, Vigdis & Kauserud, Håvard (2026). Root-associated fungal diversity in ericaceous roots across a precipitation and temperature gradient in Norway. Full text in Research Archive
• Kirkhus, Mika Helene; Thoen, Ella; Kauserud, Håvard; Haugum, Siri Vatsø & Vandvik, Vigdis (2025). Drought response of fungi in ericaceous roots and heathland soil vary across post‑fire succession. Full text in Research Archive
• Samuelsson, Sofia Irene; Jepsen, Jane Uhd; Thoen, Ella; Kauserud, Håvard; Vindstad, Ole Petter Laksforsmo & Ims, Rolf Anker (2025). Do root-associated fungi influence birch sapling growth across forest recovery states and grazing regimes? doi: https:/nordicsocietyoikos.glueup.com/event/oikos-norway-2025-120232/home.html. Full text in Research Archive Show summary

  Moth outbreaks in mountain birch forests have the potential to reshape the forest tundra ecotone. With warmer climate, the defoliation events have escalated both in severity and coverage, to the extent where the mountain birch forest may no longer recover. Forest recovery is further hindered by grazing. However, we still lack a comprehensive understanding of which mechanisms are involved in successful birch tree establishment, following pest outbreaks. In this study, we investigate if the root-associated fungal communities have an impact on sapling establishment and growth. We harvested birch saplings with intact root systems at the northern Norwegian-Finnish border. The growth of the saplings was analyzed with dendroecological methods, while the rootassociated fungal communities were assessed using DNA metabarcoding. We will present results on the relationship between symbiotic fungi and birch sapling growth across varying forest recovery states and grazing regimes.

• Halbritter, Aud Helen; Althuizen, Inge; Demenaux, Morgane; Farsund, Peter Groth; Geange, Sonya Rita & Goldberg, Deborah E. [Show all 15 contributors for this article] (2024). Climate change impacts on biodiversity and multifunctionality across a boreal landscape. Full text in Research Archive
• Kirkhus, Mika Helene; Kauserud, Håvard; Vandvik, Vigdis; Thoen, Ella; Vollsnes, Ane Victoria & Rechsteiner, Aud Helen Halbritter (2024). The effect of drought on ericoid mycorrhizal fungal communities. Full text in Research Archive Show summary

  The boreal, alpine, and arctic heaths and forests are dominated by dwarf-shrubs along with their symbionts, ericoid mycorrhizal fungi. Dwarf-shrubs are sensitive to climate change and are already affected in large-scale diebacks. It remains to explore how their mycorrhizal symbionts mitigate damages, since little is known about these plant-fungal interactions. Ericoid mycorrhizal fungi are known to aid the host plant with nutrient uptake, but little research exists on their dealings with drought, suggesting a major knowledge gap. A better overview of belowground ericoid fungi at different drought levels might help predict future climate-change induced damage. In our study we aim to find out if and how drought affects ericoid mycorrhizal fungal communities, and pinpoint key species related to drought mitigation.

• Ronold, Eivind Kverme; Vik, Unni; Kauserud, Håvard & Thoen, Ella (2024). Elevational range expansion of Betula pubescens may be slowed by lack of suitable mycorrhizal symbionts in alpine soils. Full text in Research Archive
• Ronold, Eivind Kverme; Maurice, Sundy; Torp, Vilde Åvesland; Kostich-Nilsen, Celina Alexandria; Methlie, Ine-Susanne Hopland & Schmidt, Frida [Show all 17 contributors for this article] (2024). USING eDNA TO ASSESS THE EFFECTS OF CLEAR-CUTTING FORESTRY ON FUNGAL DIVERSITY IN BOREAL SPRUCE FORESTS. Full text in Research Archive
• Kirkhus, Mika Helene; Kauserud, Håvard; Vandvik, Vigdis; Thoen, Ella; Vollsnes, Ane Victoria & Rechsteiner, Aud Helen Halbritter (2024). The effect of drought on ericoid mycorrhizal fungal communities. Full text in Research Archive Show summary

  The boreal, alpine, and arctic heaths and forests are dominated by dwarf-shrubs along with their symbionts, ericoid mycorrhizal fungi. Dwarf-shrubs are sensitive to climate change and are already affected in large-scale diebacks. It remains to explore how their mycorrhizal symbionts mitigate damages, since little is known about these plant-fungal interactions. Ericoid mycorrhizal fungi are known to aid the host plant with nutrient uptake, but little research exists on their dealings with drought, suggesting a major knowledge gap. A better overview of belowground ericoid fungi at different drought levels might help predict future climate-change induced damage. In our study we aim to find out if and how drought affects ericoid mycorrhizal fungal communities, and pinpoint key species related to drought mitigation.

• Ronold, Eivind Kverme; Kauserud, Håvard; Thoen, Ella & Vik, Unni (2022). Unsuccessful mycorrhization of seedlings slow the advance of the tree- and forest line in alpine ecosystems. Full text in Research Archive
• Vik, Unni; Pérez-Izquierdo, Leticia; Thoen, Ella & Clemmensen, Karina E. (2018). Fungal communities in a changing climate. Full text in Research Archive
• Tonjer, Lea-Rebekka; Thoen, Ella & Bryn, Anders (2018). Uten soppen når ikke skogen toppen. p. 12–13. Full text in Research Archive
• Tonjer, Lea-Rebekka; Thoen, Ella; Morgado, Luis Neves; Mundra, Sunil; Nybakken, Line & Bryn, Anders [Show all 7 contributors for this article] (2018). Changes in the soil fungal community across the mountain birch tree line ecotone. Full text in Research Archive
• Brandrud, Tor Erik; Bendiksen, Egil; Bredin, Yennie Katarina; Dima, Bálint; Eng, Sondre & Kauserud, Håvard [Show all 7 contributors for this article] (2022). Nasjonal overvåking av kalklindeskog og kalklindeskogsopper. Aktiviteter i 2021, samt sammenstilling av basisdata fra 1. og 2. overvåkingsomløp 2013-2021. Norsk institutt for naturforskning (NINA). ISSN 9788242649584. Full text in Research Archive Show summary

  - Overvåking - kalklindeskogsopper - truete arter - fruktlegeme-registrering - miljø-DNA fra jord - Oslofjordsområdet

• Thoen, Ella (2019). Functional versatility and diversity in the plan root mycobiome. Faculty of Mathematics and Natural Sciences, UiO. Full text in Research Archive
• Hansen, Simen Hyll; Kauserud, Håvard; Davey, Marie Louise; Thoen, Ella; Vik, Unni & Brysting, Anne Krag (2018). Climate and host identity structure fungal endophyte communities. Universitetet i Oslo. Full text in Research Archive

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