Sofia Gomes


Research interest

My research interests focus on the interactions between plants and mycorrhizal fungi, in particular on the evolution of the mycorrhizal specialization of mycoheterotrophic plants. These non-green plants cheat the belowground interaction between green plants and mycorrhizal fungi, from which they obtain their carbon.

I am currently a postdoc at the University of Bayreuth (Germany) in the group of Prof. Gerhard Gebauer. My goal is to obtain stable isotope natural abundances of mycorrhizal fungi that do not form fruiting bodies.

The aim of my PhD project was to study the diversity, ecology and evolution of the interaction between mycoheterotrophic plants and their mycorrhizal partners. I used high throughput sequencing to characterize the fungal communities in the roots of these plants, combined with phylogenetic reconstruction methods trying to detect common mycorrhizal specialization patterns among the evolutionary independent lineages of mycoheterotrophs. Also, I studied the ecological drivers of mycoheterotrophy at global and local scale. The advisors of my thesis were Dr. Nadia Soudzilovskaia and Prof. Peter van Bodegom.



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 PEichenberg DStöckel 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 plantsFunctional Ecology, 342453– 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 SIFMerckx VSFTSaavedra S. 2017. Fungal-host diversity among mycoheterotrophic plants increases proportionally to their fungal-host overlapEcol Evol7: 36233630

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. J. 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.


I am assistant in the MSc. field course ‘Tropical Biodiversity’ taking part in Leiden University (2 weeks) and Danau Girang Field Station, Sabah, Malaysia (2 weeks) organized by Prof. Menno Schilthuizen and Dr. Vincent Merckx.

Students from Leiden University

  • Petros Dimitriadis in the MSc project “Ribosomal secondary structure models for Glomeromycotina fungi” in collaboration with Dr. Alexandre Gultiaev (LIACS).
  • Janna Horjus in the MSc project “Plant – fungus interactions of the Berkheide dune area” (successfully finished in October 2017)
  • Annisa Ratna in the MSc project “Performance of ITS and SSU markers in arbuscular mycorrhizal fungi species delimitation” (successfully finished in August 2017)


Prof. Serguei Saavedra (Massachusetts Institute of Technology. USA)

Dr. Nicole Hynson (University of Hawaii, Manoa. USA)

Dr. Martin Bidartondo (Imperial College. UK)

Dr. Jesús Aguirre-Gutiérrez (Naturalis Biodiversity Center. The Netherlands / University of Oxford. UK)

Dr. Alexandre Gultiaev (Leiden Institute of Advanced Computer Science, Leiden University. The Netherlands)


Leiden University, Institute of Environmental Sciences, Einsteinweg 2, 2333 CC Leiden, The Netherlands

Naturalis Biodiversity Center, Vondellaan 55, 2332 AA Leiden, The Netherlands