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.

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Urban Ecology

Publications

Gomes SIF, Gundersen P, Bezemer TM, Barsotti D, D'Imperio L, Georgopoulos K, Justesen MJ, Rheault K, Rosas YM, Schmidt IK, Tedersoo L, Vesterdal L, Yu M, Anslan S, Aslani F, Byriel DB, Christiansen J, Hansen SH, Kasal N, Kosawang C, Larsen H, Larsen KS, Lees J, van Dijke ACP, Kepfer-Rojas, S. 2025. Soil Microbiome Inoculation for Resilient and Multifunctional New Forests in Post-Agricultural Landscapes. Glob Change Biol, 31: e70031. https://doi.org/10.1111/gcb.70031

Verbeek TC, Gomes SIF, Merckx VSFT. 2025. Arbuscular mycorrhiza in the urban jungle: Glomeromycotina communities of the dominant city tree across Amsterdam. Plants, people, planet, 1-17. https://doi.org/10.1002/ppp3.10634

Georgopoulos K, Bezemer TM, Christiansen JR, Larsen KS, Moerman G, Vermeulen R, Anslan S, Tedersoo L, Gomes, SIF. 2025. Reduction of forest soil biota impacts tree performance but not greenhouse gas fluxes. Soil Biology and Biochemistry, 200: 109643. https://doi.org/10.1016/j.soilbio.2024.109643

Georgopoulos K, Bezemer TM, Neeft L, Camargo AM, Anslan S, Tedersoo L, Gomes SIF. 2024. Effects of soil biotic and abiotic characteristics on tree growth and aboveground herbivory during early afforestation. Applied Soil Ecology, 202: 105579. https://doi.org/10.1016/j.apsoil.2024.105579

Merckx VSFT, Gomes SIF, Wang D, Verbeek C, Jacquemyn H, Zahn FE, Gebauer G, Bidartondo MI. 2024. Mycoheterotrophy in the wood-wide web. Nature Plants, 1-9.
https://doi.org/10.1038/s41477-024-01677-0

Wang D, Trimbos KB, Gomes SIF, Jacquemyn H, Merckx VSFT. 2024. Metabarcoding read abundances of orchid mycorrhizal fungi are correlated to copy numbers estimated using ddPCR. New Phytologist, 242(4): 1825-1834. https://doi.org/10.1111/nph.19385

Liu X, Vrieling K, Gomes SIF, Ossowicki A, Lommen STE, van der Drift MCH, Zwart FA, Ekas LS, de Sousa TXM, Erol Ö, Bezemer TM. 2024. Exploring the potential of root-associated bacteria to control an outbreak weed. Plant and Soil. https://doi/10.1007/s11104-024-06726-3

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, 239(4): 1166-1172. https://doi/10.1111/nph.18990

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, 239(4): 1449-1463 https://doi/10.1111/nph.18991

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. https://doi.org/10.1016/j.soilbio.2023.109123

Merckx VSFT, Gomes SIF. 2023. Quick guide: Mycoheterotrophy. Current Biology, 33: R453–R518. https://doi.org/10.1016/j.cub.2023.02.009

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, 37(7): 1948-1961. https://doi-org/10.1111/1365-2435.14354

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. https://doi.org/10.1111/nph.18310

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. https://doi.org/10.1111/1365-2745.14012

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. https://doi.org/10.1002/tax.12765

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. https://dx.doi.org/10.3897/mycokeys.87.72941

Wang D, Jacquemyn H, Gomes SIF, Vos RA, Merckx VSFT. 2021. Symbiont switching and trophic mode shifts in Orchidaceae. New Phytologist, 231: 791-800. https://doi.org/10.1111/nph.17414

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. https://doi.org/10.1038/s41598-021-90877-1

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. https://doi.org/10.1186/s42523-020-00055-3

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. https://doi.org/10.1111/nph.16569

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. https://doi.org/10.3389/fmicb.2020.01746

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. https://doi.org/10.1515/jib-2019-0046

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. https://doi.org/10.1111/1365-2435.13673

Gomes SIF, Merckx VSFT. 2020. Symbiosis: herbivory alters mycorrhizal nutrient exchange. Current Biology, 30: PR437-R439. https://doi.org/10.1016/j.cub.2020.04.016

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. https://doi.org/10.1111/1365-2745.13381

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. https://doi.org/10.1111/nph.15876

Gomes SIF, van Bodegom P, Merckx VSFT, Soudzilovskaia N. 2019. Global distribution of mycoheterotrophic plants. Global Ecology and Biogeography, 28: 1133-1145. https://doi.org/10.1111/geb.12920

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. https://doi.org/10.1007/s10530-018-1710-7

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. https://doi.org/10.1002/ece3.2974

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. https://doi.org/10.1111/jbi.12994

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. https://doi.org/10.1111/nph.14249

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. https://doi.org/10.1111/ele.12342