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Fungal ecology in a broad sense
Fungal ecology in a broad sense
Our research pursues diverse, question-driven and exploratory investigations into fungal ecology that can be broadly grouped into four research themes. Most of our work focuses on fungal biodiversity, ecosystem function, and responses to global change. An overview of our research and curation of select peer-reviewed publications from our group are highlighted below. To learn more about how we address these themes in our current research, see our other website pages, follow us on social media, and send us a message to learn more, collaborate, and chat all about fungi.
Theme 1: Soil biodiversity & ecosystem functioning
Theme 1: Soil biodiversity & ecosystem functioning
Forests are a massive carbon sink and home to hyper-diverse microbial communities. Each year, forests absorb 1/9th of all the carbon dioxide emissions released by humans. We rely on forests for carbon storage, but also timber, biomass, biodiversity, and cultural and artistic connection. Yet global forests are vulnerable to climate change, deforestation, and invasive species, and these pressures are only exacerbating over time. This is why a major focus of our research agenda focuses on the links between soil microbiomes and emergent forest system functioning, especially forest growth, death, and carbon cycling. See recent coverage of this work in BBC Earth [scan QR code or click here].
Research snapshot 1: ectomycorrhizal fungi are unique bio-indicators of forest productivity.
Research snapshot 1: ectomycorrhizal fungi are unique bio-indicators of forest productivity.
Our recent research shows that ectomycorrhizal fungal biodiversity is linked to a three-fold variation in forest tree growth, with unique fungi "bio-indicative" of specific tree species, tree growth rates, and soil functions.
Read the entire publication in ISME.
Research snapshot 2: fungal, not bacterial, communities predicts forest carbon storage.
Research snapshot 2: fungal, not bacterial, communities predicts forest carbon storage.
Our recent research suggests that fungi, and in particular, tree-associted symbiotic guilds of ectomycorrhizal and endophytic taxa are strong predictors of variation in tree growth across Europe. Read the entire publication in Nature Communications.
Research snapshot 3. Soil is home to approximately 59% of species.
Research snapshot 3. Soil is home to approximately 59% of species.
Our recent work published in PNAS shows that soil is the singular most biodiverse ecosystem on Earth.
We reviewed the literature and analyzed global datasets of species biodiversity from the simplest (viruses) to most complex organisms (mammals) to report the total biodiversity of most groups of life on Earth and what proportion lives in soil.
Read the entire paper in PNAS: Enumerating soil biodiversity
Learn more about our soil biodiversity research in the media
Learn more about our soil biodiversity research in the media
More than half of Earth's species live underground - Scientific American
Theme 2: Microbiomes and global change biology
Theme 2: Microbiomes and global change biology
Microbes are drivers of terrestrial biogeochemistry. How they will respond to global change will feedback to shape earth system functioning. Our research explores how biotic invasions, climate change, nitrogen pollution, and other aspects of global change affect forest fungi and the ecosystem processes they mediate.
This research spans scales from the individual site to global level. Our ultimate goal is to better predict how fungi will respond to global change and in turn whole forest functioning.
Explore our publications on fungal responses to global change below and see our global collaboration page.
Photo taken by: A. Barker-Plotkin
Our drought experiment plots in Switzerland.
Research snapshot 4: Invasive species
Impacts of Alliaria petiolata invasion on soil fungi and edaphics across the northeastern USA
Recovery of soil fungi and edaphics after Alliaria petiolata management
Response of non-native earthworms to invasive plant eradication
Research snapshot 5: Climate change
Impacts of soil warming and crossed N additions on soil fungal communities and functional genes
Changes in forest soil organic matter chemistry in response to warming and nitrogen additions
Research snapshot 6: Atmospheric pollution
Research snapshot 7: Multiple elements of global change
Typical forest soils where we expect ca. 25% of the carbon in the soil to come from fungal necromass. Ectomycorrhizal fungi are a major fraction of this biomass in temperate and boreal forests, so we are trying to link their growth, turnover, and death to soil carbon storage and plant productivity.
Theme 3: Microbial mediated soil carbon cycling
Theme 3: Microbial mediated soil carbon cycling
Microbial growth and death can build soil carbon stocks while decomposition can release carbon. Microbial inputs constitute a major fraction of the total soil carbon and nitrogen pool. While the exact proportion of microbial versus plant derived soil carbon is unclear, current estimates suggest ca. 50%. How microbial community variation contributes to soil carbon formation, stabilization, and loss is a key area of investigation fundamental to understanding soil biogeochemistry, informing carbon cycling models, and sustainably managing our ecosystems.
Alliaria petiolata plants inoculated with arbuscular mycorrhizal fungi
Alliaria petiolata plants inoculated with arbuscular mycorrhizal fungi
Theme 4. Evolution & structure of mycorrhizae
Theme 4. Evolution & structure of mycorrhizae
Mycorrhizae are nearly everywhere plants grow. What sustains the symbiosis and what evolutionary and ecological factors contribute to variation in mycorrhizal fungal outcomes?
The loss of mycorrhizae: Some plants have escaped this symbiosis. What are the ecological implications of this and how did it occur?
In some mustard plants, arbuscular mycorrhizal fungi (AMF) can actually enhance plant growth! See our recent work on Alliaria petiolata invasions in Plant, Cell and Environment where we show that there may be an entirely new type of mycorrhizal symbioses which we call "adjacent mycorrhizal symbiosis".
Common mycorrhizal fungal networks have been proposed as beneficial counter explanations to a competition-focused understanding of plant co-existence. While there is much discussion around these networks - which interconnect different plants through fungal mycelium - our recent research suggests that these networks have much more complicated effects on plant growth than once thought. Check out our new publication in Physiologica Plantarum where we demonstrate that the benefits of clonal plant reproduction are reduced by common mycorrhizal networks.
Growth of mycorrhizal fungal mycelium in soil with interconnecting rhizomorphs
Growth of mycorrhizal fungal mycelium in soil with interconnecting rhizomorphs
Review our publications
Review our publications
Below is a list of the currently published papers by FEL members. If you are interested in a particular person, please check out our Teams page and explore their biography.
1. T. Benocci, C. Fiorenzani, A. Menicucci, S. Lacono, M. Anthony, F. Baltar,R. Baroncelli. Draft genome sequence of recently described Trichoderma sinokoningii strain CBS 124367. J. of Plant Pathology. https://doi.org/10.1007/s42161-026-02284-y
2. T. Zhuo….M.A. Anthony… et al. Stratification enhances yet self-limits carbon sequestration through microbial necromass accumulation at reservoir sediment–water interfaces. J. of Cleaner Production. https://doi.org/10.1016/j.jclepro.2026.148911
3. J.D. Edwards, J. van den Hoogen, C.V. Hawkes, M. A. Anthony….et al. Stephanie N. Kivlin. Niche constraints drive differences between mycorrhizal fungal guilds in future range shifts. PNAS (in revision). Preprint available: https://doi.org/10.64898/2026.05.18.725971
4. Waschk P…et al…M.A. Anthony. Evidence for resource transfer via common endophyte networks. Scientific Reports. https://doi.org/10.1038/s41598-026-56653-9
5. Mansfield, T….et al….M.A. Anthony. Ecological and genomic variation in ectomycorrhizal fungal exploration types. New Phytologist. (2026) https://doi.org/10.1111/nph.71157
6. M.A. Anthony et al. Soil microbial community differences drive variation in Pinus sylvestris physiology, productivity, and responses to elevated CO2. Environmental Microbiome; https://doi.org/10.1186/s40793-025-00828-w
7. Laura van Galen…M.A. Anthony, et al. A global database of soil microbial phospholipid fatty acids (PLFAs) and enzyme activity. Scientific Data. https://doi.org/10.1038/s41597-025-05759-2
8. Y. Qingshui, M.A. Anthony…J. Fang. Decadal nutrient addition reveals phosphorus limitation and its adaptive mechanisms in tropical rainforests. (2025). Soil Biology and Biochemistry. https://doi.org/10.1016/j.soilbio.2025.109976
9. T. Kaiser, M.A. Anthony. The role of ectomycorrhizal functional diversity in mediating soil C cycling under global change. (2025). New Phytologist. https://doi.org/10.1111/nph.70559
10. N. Keller, M.A. Anthony, T.S. van der Voort, K.N. Binte, M. Ramdzan, M.B. Mills, N.C. Raczka, L.P. Koh. The Blind Spot in active tropical forest restoration: unknown impacts on soil carbon. (2025). Current Biology. https://doi.org/10.1016/j.cub.2025.05.060
11. Z. Xu, Z. Hu, T.Qiu, W. Li, L. Jiang, M.A. Anthony. Contrasting wood carbon quality of angiosperms and gymnosperms drives fungal-mediated decomposition responses to nutrient enrichment. (2025). Forest Ecology and Management https://doi.org/10.1016/j.foreco.2025.122910
12. J.Trombely, J.L. Celenza, S.D. Frey, M.A. Anthony. ‘Adjacent Mycorrhizal Symbiosis’ boosts invasive Alliaria petiolata (garlic mustard). (2025). Plant, Cell & Environment. https://doi.org/10.1111/pce.15508
13. Y. Zhang, M.A. Anthony, Q. Yuan, Y. Wang, P. Zhao, E. Chen, S. Peng. Capacity to form common mycorrhizal networks reduces the positive impact of clonal integration between plants. (2025) Physiologia Plantarum https://doi.org/10.1111/ppl.70149
14. M.A. Anthony. Does ectomycorrhizal fungal biodiversity affect tree growth? (2025). Fungal Ecology. https://doi.org/10.1016/j.funeco.2025.101413
15. Y. Qingshui, H. Chenqi, M.A. Anthony…J. Fang. Decoupled responses of aboveground plants and soil biota to global change across the world’s land ecosystems. (2024). Nature Communications. https://doi.org/10.1038/s41467-024-54304-z
16. Lopez, M.A. Anthony…A.L. Romero-Olivares. Dryland fungi are spatially heterogenous and resistant to global change drivers in the northern Chihuahuan Desert. (2024). Ecosphere. https://doi.org/10.1002/ecs2.70031
17. M.A. Knorr, A.R. Contosta, E.W. Morrison, T.J. Muratore, M.A. Anthony, Stoica, K.M. Geyer, M.J. Simpson, S.D. Frey. Unexpected soil carbon response to simultaneous warming and nitrogen enrichment. (2024). Nature Ecology and Evolution. https://doi.org/10.1038/s41559-024-02546-x.
18. M.A. Anthony, L. Tedersoo….C. Averill. Fungal community composition predicts forest carbon storage at a continental scale. (2024). Nature Communications. https://doi.org/10.1038/s41467-024-46792-w.
19. J. Stewart, T.E. Kiers, M.A. Anthony, A.H. Kiers. (2024). Supporting urban greenspace with microbial symbiosis. Plants People Planet. https://doi.org/10.1002/ppp3.10403.
20. M.A. Anthony, F.S. Bender, M. van der Heijden (2023). Enumerating soil biodiverstiy. PNAS. https://doi.org/10.1073/pnas.2304663120.
21. B.W. Borgmann-Winter, R. Stephens, M.A. Anthony, S.D. Frey, R.J. Rowe. (2023). Wind and small mammals are complementary fungal dispersers. Ecology. https://doi.org/10.1002/ecy.4039.
22. H. Iven, T. Walker, M.A. Anthony. (2023). Biotic interactions are underestimated drivers of microbial carbon use efficiency. Current Microbiology. https://doi.org/10.1007/s00284-022-02979-2.
23. M.A. Anthony, A. Gessler. (2022). A call to characterize functional mycobiome responses to experimental climate change. Soil Organisms. https://doi.org/10.25674/so94iss3id300
24. C. Averill, M.A. Anthony, P. Baldrian, F. Finkbeiner, J.V.D. Hoogen, T. Kiers, P. Kohout, E. Hirt, G.R. Smith. (2022). Defending Earth’s terrestrial microbiome. Nature Microbiology. https://doi.org/10.1038/s41564-022-01228-3.
25. M.A. Anthony, I. Hordijk, N. Nakatsuka. (2022). Justice, Equity, Diversity, and Inclusion Seminars: What They Do and Do Not Do. ETH Learning and Teaching Journal. https://www.learningteaching.ethz.ch/index.php/lt-eth/article/download/199/176.
26. M.A. Anthony, et. al. C. Averill. (2022). Forest tree growth is linked to mycorrhizal fungal composition and function across Europe. The ISME Journal*. https://doi.org/10.1038/s41396-021-01159-7. *ISME Journal 2022 Best Paper award: https://www.nature.com/collections/aedhjihhgh
27. A.N. Trautwig, M.A. Anthony, S.D. Frey, K.A. Stinson. (2021). Introduced mustard, Thlaspi arvense, reduces mycorrhizal fungal phylogenetic diversity in subalpine meadows. Fungal Ecology, https://doi.org/10.1016/j.funeco.2021.101135
28. M.A. Anthony, M. Knorr, J. Moore, M. Simpson, S.D. Frey. (2021). Fungal community and functional responses to soil warming are greater than for soil nitrogen enrichment. Elementa. https://doi.org/10.1525/elementa.2021.000059
29. E.D. Whalen, N. Lounsbury, K. Geyer, M.A. Anthony, E. Morrison, L.T.A. van Diepen, J.L. Moine, K. Nadelhoffer, L. Van den Enden, M.J. Simpson, S.D Frey. (2021). Root control of fungal communities and soil carbon in a temperate forest. Soil Biology and Biochemistry. https://doi.org/10.1016/j.soilbio.2021.108390
30. L. Van den Enden, M.A. Anthony, S.D. Frey, M. Simpson. (2021). Biogeochemical evolution of soil organic matter composition after a decade of warming and nitrogen addition. Biogeochemistry. https://doi.org/10.1007/s10533-021-00837-0
31. J.A. Moore, M.A. Anthony, G.J. Pec, L.K., Trocha, A. Trzebny, K.M. Geyer, S.D. Frey. (2021). Fungal community structure and function shifts with atmospheric nitrogen deposition. Global Change Biology. https://doi.org/10.1111/gcb.15444.
32. M.A. Anthony, K.A. Stinson, J.A. Moore, S.D. Frey. (2020). Fungal responses to plant invasion depend on soil warming and nitrogen deposition. Oecologia. https://doi.org/10.1007/s00442-020-04797-4.
33. M.A. Anthony, J.L. Celenza, A. Armstrong, S.D. Frey. (2020). Indolic glucosinolates provide resistance to mycorrhizal fungal colonization in a non-host Brassicaceae. Ecosphere. https://doi.org/10.1002/ecs2.3100.
34. M.A. Anthony, D.S. Maynard, J. van der Hoogen, C. Averill. (2020). Distinct assembly processes and microbial communities constrain soil organic carbon formation. One Earth. https://doi.org/10.1016/j.oneear.2020.03.006.
35. M.A. Anthony, K.A. Stinson, A,N. Trautwig, E. Coates-Connor, Frey, S.D. (2019). Fungal communities do recover to garlic mustard (Alliaria petiolata) eradication. Biological Invasions. https://doi.org/10.1007/s10530-019-02031-8.
36. K.A. Stinson, S.D. Frey, M.R. Jackson, E. Coates-Connor, M.A. Anthony, K. Martinez. (2019). Responses of non-native earthworms to experimental eradication of garlic mustard and implications for native vegetation. Ecosphere. https://doi.org/10.1002/ecs2.2353.
37. M.A. Anthony, Frey, S.D., Stinson, K.S., (2017). Fungal community homogenization, shift in dominant trophic guild, and appearance of novel taxa with biotic invasion, Ecosphere. https://doi.org/10.1002/ecs2.1951.
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