Sebastian Silva

I obtained my Bachelor’s degree in Marine Biology from the Pontificia Universidad Católica de Chile, where I carried out two research projects. The first was about developing a method to detect Prochlorococcus peaks in CTD data from the Oxygen Minimum Zones off the Chile–Peru coast. The second focused on the application of machine learning to identify toxic dinoflagellates in flow cytometry data. After completing my undergraduate studies, I completed a diploma in Artificial Intelligence at the Universidad de Chile. My final project focused on using convolutional neural networks to detect toxic dinoflagellates in low-cost microscopy images. Following this, I worked for a year analysing data for two research projects, one under the supervision of Pablo Marquet, and another under Miriam Fernandez.

In 2021, I joined the MarMic program. I did three lab rotations: one with Margot Bligh, where we worked on a glycan de novo annotation pipeline that resulted in a methodological manuscript and an R package, GlycoAnnotateR. Another was with Daniel Schurholz, where I learned how to implement deep learning pipelines for large datasets of coral images using Snakemake. The third took me on an expedition to Svalbard as part of a project that intends to understand seasonal effects on the microbial community and carbon cycling in Arctic sediments. This project later became my Master’s thesis under the supervision of Katrin Knittel, where I characterized the family Ilumatobacteraceae, a prevalent bacterial group in coastal sediments from Isfjorden, Svalbard. I designed FISH probes for their identification and analysed their phylogeny based on 16S rRNA amplicon sequences and metagenomes. This work led to a manuscript on the taxonomy of Acidimicrobiia and to the description of a new bacterial order, Benthobacterales.

The main project of my PhD research focuses on the assembly and succession of bacteria on sand grains. Beyond the specifics of my project, I am drawn to theoretical ecology—the idea that the same fundamental “laws” may govern ecological dynamics across different scales thrills me.

In parallel, I have also worked together with Dirk de Beer on describing the microbial community of manganese-rich, fine-grained sediments in the Red Sea, combining detailed microsensor biogeochemical measurements with centimetre-resolution 16S rRNA amplicon sequencing. This study revealed stratified profiles in both chemistry and community structure, with distinct microbial groups dominating different sediment layers.

Although the future is uncertain, I would very much like to continue in academia. The unique combination of intensity, freedom, and international collaboration makes me feel very comfortable. I believe that big things are coming for environmental biology, and I would love to be in the front row to contribute and witness them.

Publications

Silva-Solar, S., Amann, R., Viver, T., Rosselló-Móra, R., Santibáñez-Molina, J., Rodriguez, L. M., & Konstantinidis, K. (2026). A simple mathematical model for the discontinuity in average nucleotide identity distributions in prokaryotes. biorxiv.

Silva-Solar, S., van Erk, M. R., Antler, G., Knittel, K., Basu, S., & de Beer, D. (2025). Microbial diversity, autotrophic- and heterotrophic processes in Mn-rich marine sediments. Frontiers in Marine Science, 12, 1639181.

Bligh, M., Silva-Solar, S., Biehler, L., Fitzgerald, C. C. J., Crawford, C. J., Schultz-Johansen, M., Niggemeier, S., Seeberger, P. H., Liebeke, M., & Hehemann, J.-H. (2025). De novo glycan annotation of mass spectrometry data. Journal of the American Society for Mass Spectrometry, 36(8), 1686–1695.

Silva-Solar, S., Viver, T., Wang, Y., Orellana, L. H., Knittel, K., & Amann, R. (2024). Acidimicrobiia, the Actinomycetota of coastal marine sediments: Abundance, taxonomy and genomic potential. Systematic and Applied Microbiology, 47(6), 126555.

Knittel, K., Miksch, S., Moncada, C., Silva-Solar, S., Moye, J., Amann, R., & Arnosti, C. (2024). Distinct actors drive different mechanisms of biopolymer processing in polar marine coastal sediments. Environmental Microbiology, 26(8), e16687.

Wong, J. C. Y., Raven, J. A., Aldunate, M., Silva, S., Gaitán-Espitia, J. D., Vargas, C. A., Ulloa, O., & von Dassow, P. (2023). Do phytoplankton require oxygen to survive? A hypothesis and model synthesis from oxygen minimum zones. Limnology and Oceanography, 68(7), 1417–1437.

Mardones, J. I., Krock, B., Marcus, L., Alves-de-Souza, C., Nagai, S., Yarimizu, K., Clément, A., Correa, N., Silva, S., Paredes-Mella, J., et al. (2022). From molecules to ecosystem functioning: Insight into new approaches to taxonomy to monitor harmful algae diversity in Chile. In Advances in Phytoplankton Ecology (pp. 119–154). Elsevier.