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Sofia Gomes

Assistant Professor in Urban Ecology

My main research interest is to understand how species interactions influence the structure and functioning of plant-microbial communities. I got my PhD from Leiden University in the Institute of Environmental Sciences. 


My previous work has focused on symbiosis between plants and mycorrhizal fungi, but is increasingly expanding to include other groups of organisms that are part of the soil foodweb in forest ecosystems. In my research I work across multiple scales from microcosm assays to field experiments.

I am the scientific coordinator of the Silva Nova project at the Leiden University branch, and I am co-leading the of Trees Future Proof initiative. I am also starting up with my research in Urban Ecology.


Liu H, Banfield C, Gomes SIF, Gube M, Weig A, Pausch J. 2023. Vegetation transition from meadow to forest reduces priming effect on SOM decomposition. Soil Biology and Biochemistry, 184: 109123

Gomes SIF, Giesemann P, Klink S, Hunt C, Suetsugu K, Gebauer G. 2023. Stable isotope natural abundances of fungal hyphae extracted from the roots of arbuscular mycorrhizal mycoheterotrophs and rhizoctonia-associated orchids. New Phytologist

Zahn FE, Söll E, Chapin TK, Wang D,  Gomes SIF, Hynson NA, Pausch J, Gebauer G. 2023, Novel insights into orchid mycorrhiza functioning from stable isotope signatures of fungal pelotons. New Phytologist

Merckx VSFT, Gomes SIF. 2023. Quick guide: Mycoheterotrophy. Current Biology33: R453–R518

Wang D, Gebauer G, Jacquemyn H, Zahn FE, Gomes SIF, Lorenz J, van der Hagen H, Schilthuizen M, Merckx VSFT. 2023. Variation in mycorrhizal communities and the level of mycoheterotrophy in grassland and forest populations of Neottia ovata (Orchidaceae). Functional Ecology 

Gomes SIF, Fortuna MA, Bascompte J, Merckx VSFT. 2022. Mycoheterotrophic plants preferentially target arbuscular mycorrhizal fungi that are highly connected to autotrophic plants. New Phytologist, 235: 2034-2045

Ampt EA, Francioli D, van Ruijven J, Gomes SIF, Maciá-Vicente J, Termorshuizen AJ, Bakker LM, Mommer L. 2022. Deciphering the interactions between plant species and their main fungal root pathogens in mixed grassland communities. Journal of Ecology 110: 3039-3052

Gomes SIF, Kikuchi IABS, Lachenaud O, Perdomo J, Léotard G, Maas PJM, van de Kamer HM, Merckx VSFT. 2022. Unravelling the species diversity, phylogeny and biogeography of the mycoheterotrophic Voyrieae (Gentianaceae) and the description of a new species. Taxon, 71: 1013-1024

Thi LL, Mertens A, Vu DT, Vu TD, Minh PLA, Duc HN, Backer S, Swennen R, Vandelook F, Panis B, Amalfi M, Decock C, Gomes SIF, Merckx VST, Janssens S. 2022. Diversity of Fusarium associated banana wilt in northern Viet Nam. MycoKeys, 87: 53-76.

Wang D, Jacquemyn H, Gomes SIF, Vos RA, Merckx VSFT. 2021. Symbiont switching and trophic mode shifts in Orchidaceae. New Phytologist, 231: 791-800.

Pecoraro L, Rasmussen HN, Gomes SIF, Wang X, Merckx VSFT, Cai L, Rasmussen FN. 2021. Fungal diversity driven by bark features affects phorophyte preference in epiphytic orchids from southern China. Scientific Reports, 11: 11287.

Gomes SIF, Kielak AM, Hannula SE, Heinen R, Jongen R, Keesmaat I, Jonathan R, Bezemer TM. 2020. Microbiomes of a specialist caterpillar are consistent across different habitats but also resemble the local soil microbial communities. Animal Microbiome, 2: 37.

Soudzilovskaia NA, Vaessen S, Barcelo M, He J, Rahimlou S, Abarenkov K, Brundrett MC, Gomes SIF, Merckx VSFT, Tedersoo L. 2020. FungalRoot: global online database of plant mycorrhizal associations. New Phytologist, 227: 955-966.

Gomes SIF, van Bodegom PM, van Agtmaal M, Soudzilovskaia NA, Bestman M, Duijm E, Speksnijder A, van Eekeren N. 2020. Microbiota in dung and milk differ between organic and conventional dairy farms. Frontiers in Microbiology, 11: 1746.

Martorelli I, Helwerda LS, Kerkvliet J, Gomes SIF, Nuytinck J, van der Werff CRA, Ramackers GJ, Gultyaev  AP, Merckx VSFT, Verbeek FJ. 2020. Fungal metabarcoding data integration framework for the MycoDiversity DataBase (MDDB). Journal of Integrative Bioinformatics, 17: 1.

Giesemann P, Eichenberg D, Stöckel M, Seifert LF, Gomes SIF, Merckx VSFT, Gebauer G. 2020. Dark septate endophytes and arbuscular mycorrhizal fungi (Paris-morphotype) affect the stable isotope composition of ‘classically’ non‐mycorrhizal plants. Functional Ecology, 34: 2453– 2466.

Gomes SIF, Merckx VSFT. 2020. Symbiosis: herbivory alters mycorrhizal nutrient exchange. Current Biology, 30: PR437-R439.

Gomes SIF, Merckx VSFT, Kehl J, Gebauer G. 2020. Mycoheterotrophic plants living on arbuscular mycorrhizal fungi are generally enriched in 13C, 15N, and 2H isotopes. Journal of Ecology, 108: 1250-1261.

Gomes SIF, van Bodegom P, Merckx VSFT, Soudzilovskaia N. 2019. Environmental drivers for cheaters of arbuscular mycorrhizal symbiosis in tropical rainforests. New Phytologist, 223: 1575-1583.

Gomes SIF, van Bodegom P, Merckx VSFT, Soudzilovskaia N. 2019. Global distribution of mycoheterotrophic plants. Global Ecology and Biogeography, 28: 1133-1145.

Gomes SIF, Merckx VSFT, Hynson NA. 2018. Biological invasions increase the richness of arbuscular mycorrhizal fungi from a Hawaiian subtropical ecosystem. Biological Invasions, 20: 2421-2437.

Gomes SIF, Merckx VSFT, Saavedra S. 2017. Fungal-host diversity among mycoheterotrophic plants increases proportionally to their fungal-host overlap. Ecology and Evolution, 7: 3623–3630.

Merckx VSFT, Gomes SIF, Wapstra M, Hunt C, Steenbeeke G, Mennes CB, Walsh N, Smissen R, Hsieh T-H, Smets EF, Bidartondo MI. 2017. The biogeographical history of the interaction between mycoheterotrophic Thismia 

(Thismiaceae) plants and mycorrhizal Rhizophagus (Glomeraceae) fungi. Journal of Biogeography, 44: 1869-1879.

Gomes SIF, Aguirre-Gutiérrez J, Bidartondo M, Merckx VSFT. 2017. Arbuscular mycorrhizal interactions of mycoheterotrophic plants are more specialized than in surrounding green plants. New Phytologist, 213: 1418-1427.

Carvalheiro LG, Biesmeijer JC, Benadi G, Fründ J, Stang M, I Bartomeus, Kaiser-Bunbury CN, Baude M, Gomes SIF, Merckx VSFT, Baldock KCR, Bennett ATD, Boada R, Bommarco R, Cartar R, Chacoff N, Dänhardt J, Dicks LV, Dormann CF, Ekroos J, Henson KSE, Holzschuh A, Junker RR, Lopezaraiza-Mikel M, Memmott J, Montero-Castaño A, Nelson IL, Petanidou T, Power EF, Rundlöf M, Smith HG, Stout JC, Temitope K, Tscharntke T, Tscheulin T, Vilà M, Kunin WE. 2014. The potential for indirect effects between co-flowering plants via shared pollinators depends on resource abundance, accessibility and relatedness. Ecology Letters, 17: 1389– 1399.

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