Sofia Gomes

Assistant Professor in Urban Ecology

I am fascinated by the hidden world of soil biodiversity and its vital role in supporting trees and ecosystems, especially in the face of global change. My research focuses on understanding how soil microbial communities interact with trees across different landscapes, from forests to cities. These belowground interactions are essential for plant health, resilience, and ecosystem functioning, yet they’re often overlooked. My vision is to help bring this invisible biodiversity into focus, both in science and in practice, especially where ecosystems are under pressure from urbanization, climate change, and land-use legacies.

Key Research Lines:

A. Monitoring Urban Soil Biodiversity
Urban green spaces depend on healthy soils, but we still know very little about the biodiversity that supports them. Together with Naturalis Biodiversity Center and through hands-on teaching, I investigate how soil microbial communities respond to urbanization. By mapping environmental and spatial patterns in microbial diversity across cities, we gain insights into how to manage urban ecosystems more sustainably. This work also connects students directly to active research, reinforcing a research-led education approach.

B. Understanding Tree–Microbiome Interactions Across Landscapes
As part of the Silva Nova consortium, I study how tree–microbiome relationships change across land-use gradients, from agricultural fields to restored and natural forests. Trees carry the imprint of past land use through their microbial associations. By exploring these legacy effects, we can improve our understanding of how land-use history shapes tree performance, soil biodiversity, and restoration success. This work is highly interdisciplinary, bridging ecology, microbiology, and restoration science.

C. Enhancing Tree Resilience through Soil Biodiversity in Cities
I focus on drought: one of the most urgent stressors for urban trees. My research investigates how microbial communities, especially mycorrhizal fungi, can help trees tolerate drought stress and how this knowledge can inform climate-adaptive urban planning. The NWA (NWO) funded project Thirsty Cities project is a collaboration with TU Delft, Rotterdam University of Applied Sciences and others, where we aim to make urban green spaces more resilient and future-proof by improving the urban water balance, providing direct links between ecology and policy.

Get in Touch

Urban Ecology

Thirsty Cities

Publications

Georgopoulos K, TM Bezemer, Vesterdal L, Li K, de Nobel L, Kasal N, Gomes SIF. 2025. Soil microbes and nutrient inputs influence root nodulation and tree performance in Alnus glutinosa. Applied Soil Ecology, 215, 106466. https://doi.org/10.1016/j.apsoil.2025.106466

Wang D, Merckx VSFT, Jacquemyn H, Gomes SIF. 2025. Mycorrhizal communities in Orchidaceae are likely shaped by plant trophic mode and biogeography but not phylogeny. Plant Diversity, in press. https://doi.org/10.1016/j.pld.2025.08.002

Cambon MC, Xu X, Kovács ÁT, Gomes SIF*, McDonald JE*. 2025. Synthetic microbial communities for studying and engineering the tree microbiome: challenges and opportunities. Current Opinion in Microbiology, 87, 102636.

https://doi.org/10.1016/j.mib.2025.102636; *corresponding authors

·Aslani F, Tedersoo L, Gomes SIF, Põlme S, Anslan S, Bezemer TM. 2025. Shifting community assembly mechanisms in soil eukaryotes over successional time and their implications for restoration. Scientific Reports, 15, 25804.

https://doi.org/10.1038/s41598-025-11507-8

Georgopoulos K, Bezemer TM, Vesterdal L, Li K, de Nobel L, Gomes SIF. 2025. Nondestructive detection of Frankia in Alnus glutinosa with NIR spectroscopy. Plant-Environment Interactions, 6: e70066. https://doi.org/10.1002/pei3.70066

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. Global Change Biology, 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