Publications

ZORA Publication List

Publications

• 2026

  • Serra Moncadas, L., Shakurova, A., Hofer, C., & Andrei, A.-S. (2026). Deep-branching Chloroflexota lineages illuminate the eco-evolutionary foundation of cross-ecosystem colonization Nature Communications, Epub ahead of print. https://doi.org/10.1038/s41467-026-71228-y

• 2025

  • Hug, L. A., Hatzenpichler, R., Moraru, C., Soares, A. R., Meyer, F., Heyder, A., The Data Reuse Consortium, Abdallah, R. Z., Abdalrahem, A., Abdulkadir, N., Adesiyan, I. M., Alteio, L., Anantharaman, K., Anderson, R., Andrei, A.-S., Baeza, J. A., Bak, F., Baker, B., Bartholomäus, A., … et al. (2025). A roadmap for equitable reuse of public microbiome data Nature Microbiology, 10, 2384–2395. https://doi.org/10.1038/s41564-025-02116-2
  • Andrei, A.-S., Grossart, H.-P., & Pernthaler, J. (2025). Europe’s water law needs genomic resolution Nature Water, 3, 963–964. https://doi.org/10.1038/s44221-025-00488-7
  • Hager, K., Luo, Z.-H., Montserrat-Diez, M., Ponce-Toledo, R. I., Baur, P., Dahlke, S., Andrei, A.-S., Bulzu, P.-A., Ghai, R., Urich, T., Glatzel, S., Schleper, C., & Rodrigues-Oliveira, T. (2025). Diversity and environmental distribution of Asgard archaea in shallow saline sediments Frontiers in Microbiology, 16, 1549128. https://doi.org/10.3389/fmicb.2025.1549128

• 2024

  • Schalch-Schuler, M., Bassin, B., Dirren, G., Waller, K., Hofer, C., Pernthaler, J., Andrei, A.-S., & Posch, T. (2024). The planktonic freshwater ciliate Balanion planctonicum (Ciliophora, Prostomatea): A cryptic species complex or a “complex species”? Journal of Eukaryotic Microbiology, 72, e13084. https://doi.org/10.1111/jeu.13084
  • Serra Moncadas, L., Hofer, C., Bulzu, P.-A., Pernthaler, J., & Andrei, A.-S. (2024). Freshwater genome-reduced bacteria exhibit pervasive episodes of adaptive stasis Nature Communications, 15, 3421. https://doi.org/10.1038/s41467-024-47767-7
  • Villena-Alemany, C., Mujakić, I., Fecskeová, L. K., Woodhouse, J., Auladell, A., Dean, J., Hanusová, M., Socha, M., Gazulla, C. R., Ruscheweyh, H.-J., Sunagawa, S., Silva Kavagutti, V., Andrei, A.-S., Grossart, H.-P., Ghai, R., Koblížek, M., & Piwosz, K. (2024). Phenology and ecological role of aerobic anoxygenic phototrophs in freshwaters Microbiome, 12, 65. https://doi.org/10.1186/s40168-024-01786-0
  • Zhu, B., Chen, Z., Hu, H., Andrei, A.-S., & Li, Y. (2024). Greenhouse gas emissions and mitigation: microbes, mechanisms and modeling Frontiers in Microbiology, 15, 1363814. https://doi.org/10.3389/fmicb.2024.1363814
  • Hofer, C., Wälchli, D., Moncadas, L. S., Rain-Franco, A., & Andrei, A.-S. (2024). A high-quality genome of an undescribed Flavobacterium species uncovered using Q20+ Nanopore chemistry Microbiology Resource Announcements, 13, online. https://doi.org/10.1128/mra.00716-23
  • Serra Moncadas, L., Schnellmann, V., Hofer, C., Rain-Franco, A., & Andrei, A.-S. (2024). Complete genome of Flavobacterium pectinovorum str. ZE23VCel01 obtained through Nanopore Q20+ chemistry Microbiology Resource Announcements, 13, online. https://doi.org/10.1128/mra.00715-23
  • Boukheloua, R., Mukherjee, I., Park, H., Šimek, K., Kasalický, V., Ngochera, M., Grossart, H.-P., Picazo-Mozo, A., Camacho, A., Cabello-Yeves, P. J., Rodriguez-Valera, F., Callieri, C., Andrei, A.-S., Pernthaler, J., Posch, T., Alfreider, A., Sommaruga, R., Hahn, M. W., Sonntag, B., … et al. (2024). Global freshwater distribution of Telonemia protists The ISME Journal, 18, wrae177. https://doi.org/10.1093/ismejo/wrae177
  • Rain-Franco, A., Le Moigne, A., Serra Moncadas, L., Silva, M. O. D., Andrei, A.-S., & Pernthaler, J. (2024). Dispersal shapes compositional and functional diversity in aquatic microbial communities MSystems, 9, e0140324. https://doi.org/10.1128/msystems.01403-24

• 2023

  • Hofer, C., Lingenhag, S., Serra Moncadas, L., Rain-Franco, A., & Andrei, A.-S. (2023). Q20+ Nanopore sequencing data recover a high-quality Asticcacaulis sp. genome Microbiology Resource Announcements, 12, online. https://doi.org/10.1128/MRA.00717-23
  • Serra Moncadas, L., Rogenmoser, J., Hofer, C., Rain-Franco, A., & Andrei, A.-S. (2023). Pseudomonas kielensis str. Ze23jcel16 complete genome obtained through R10.4.1 Nanopore Flow cell chemistry Microbiology Resource Announcements, online. https://doi.org/10.1128/MRA.00714-23
  • Ngugi, D. K., Salcher, M. M., Andrei, A.-S., Ghai, R., Klotz, F., Chiriac, M.-C., Ionescu, D., Büsing, P., Grossart, H.-P., Xing, P., Priscu, J. C., Alymkulov, S., & Pester, M. (2023). Postglacial adaptations enabled colonization and quasi-clonal dispersal of ammonia-oxidizing archaea in modern European large lakes Science Advances, 9, eadc9392. https://doi.org/10.1126/sciadv.adc9392
  • Kavagutti, V. S., Bulzu, P.-A., Chiriac, C. M., Salcher, M. M., Mukherjee, I., Shabarova, T., Grujčić, V., Mehrshad, M., Kasalický, V., Andrei, A.-S., Jezberová, J., Seďa, J., Rychtecký, P., Znachor, P., Šimek, K., & Ghai, R. (2023). High-resolution metagenomic reconstruction of the freshwater spring bloom Microbiome, 11, 15. https://doi.org/10.1186/s40168-022-01451-4

• 2022

  • Bulzu, P.-A., Kavagutti, V. S., Andrei, A.-S., & Ghai, R. (2022). The Evolutionary Kaleidoscope of Rhodopsins MSystems, 7, e0040522. https://doi.org/10.1128/msystems.00405-22
  • Mauch, E., Serra Moncadas, L., & Andrei, A.-S. (2022). Complete Genome Sequence of an Uncultivated Freshwater Bacteroidota Lineage Microbiology Resource Announcements, 11, e0076622. https://doi.org/10.1128/mra.00766-22
  • Ajvazi, X., Serra Moncadas, L., & Andrei, A.-S. (2022). Study of Complete Genome Sequence of Uncultivated Hyphomonadaceae sp. Microbiology Resource Announcements, 11, e0076522. https://doi.org/10.1128/mra.00765-22
  • Bernet, J., Serra Moncadas, L., & Andrei, A.-S. (2022). Complete Genome Sequence of an Uncultivated Freshwater Flavobacterium sp. Strain Microbiology Resource Announcements, 11, e0065922. https://doi.org/10.1128/mra.00659-22
  • Cremer, F., Serra Moncadas, L., & Andrei, A.-S. (2022). Complete Genome Sequence from an Uncultivated Freshwater Elusimicrobiota Lineage Microbiology Resource Announcements, 11, e0042622. https://doi.org/10.1128/mra.00426-22
  • Zhu, B., Karwautz, C., Andrei, A.-S., Klingl, A., Pernthaler, J., & Lueders, T. (2022). A novel Methylomirabilota methanotroph potentially couples methane oxidation to iodate reduction MLife, 1, 323–328. https://doi.org/10.1002/mlf2.12033
  • Chiriac, M.-C., Bulzu, P.-A., Andrei, A.-S., Okazaki, Y., Nakano, S., Haber, M., Kavagutti, V. S., Layoun, P., Ghai, R., & Salcher, M. M. (2022). Ecogenomics sheds light on diverse lifestyle strategies in freshwater CPR Microbiome, 10, 84. https://doi.org/10.1186/s40168-022-01274-3
  • Hofer, C. (2022). Long-Read MinION data for microbial community analysis (Master’s thesis, University of Zurich) https://doi.org/10.5167/uzh-255853

• 2021

  • Baricz, A., Chiriac, C. M., Andrei, A.-S., Bulzu, P., Levei, E. A., Cadar, O., Battes, K. P., Cîmpean, M., Șenilă, M., Cristea, A., Muntean, V., Alexe, M., Coman, C., Szekeres, E. K., Sicora, C. I., Ionescu, A., Blain, D., O’Neill, W. K., Edwards, J., … Banciu, H. L. (2021). Spatio-temporal insights into microbiology of the freshwater-to-hypersaline, oxic-hypoxic-euxinic waters of Ursu Lake Environmental Microbiology, 23, 3523–3540. https://doi.org/10.1111/1462-2920.14909
  • Mujakić, I., Andrei, A.-S., Shabarova, T., Fecskeová, L. K., Salcher, M. M., Piwosz, K., Ghai, R., & Koblížek, M. (2021). Common Presence of Phototrophic Gemmatimonadota in Temperate Freshwater Lakes MSystems, 6, 01241–20. https://doi.org/10.1128/mSystems.01241-20
  • Bulzu, P.-A., Kavagutti, V. S., Chiriac, M.-C., Vavourakis, C. D., Inoue, K., Kandori, H., Andrei, A.-S., & Ghai, R. (2021). Heliorhodopsin Evolution Is Driven by Photosensory Promiscuity in Monoderms MSphere, 6, e00661-21. https://doi.org/10.1128/msphere.00661-21
  • Durán‐Viseras, A., Andrei, A.-S., Vera‐Gargallo, B., Ghai, R., Sánchez‐Porro, C., & Ventosa, A. (2021). Culturomics-based genomics sheds light on the ecology of the new haloarchaeal genus Halosegnis Environmental Microbiology, 23, 3418–3434. https://doi.org/10.1111/1462-2920.15082

• 2020

  • Mukherjee, I., Salcher, M. M., Andrei, A.-S., Kavagutti, V. S., Shabarova, T., Grujčić, V., Haber, M., Layoun, P., Hodoki, Y., Nakano, S., Šimek, K., & Ghai, R. (2020). A freshwater radiation of diplonemids (No. 15209; ArXiv.Org). https://doi.org/10.1101/2020.05.14.095992
  • Andrei, A.-S., Bulzu, P., & Banciu, H. L. (2020). Blossoms of Rot: Microbial Life in Saline Organic-Rich Sediments In J. Seckbach & H. Stan-Lotter (Eds.), Extremophiles as Astrobiological Models (pp. 45–82). Wiley-Blackwell Publishing, Inc. https://doi.org/10.1002/9781119593096.ch3

• 2019

  • Kavagutti, V. S., Andrei, A.-S., Mehrshad, M., Salcher, M. M., & Ghai, R. (2019). Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics Microbiome, 7, 135. https://doi.org/10.1186/s40168-019-0752-0
  • Bulzu, P.-A., Andrei, A.-S., Salcher, M. M., Mehrshad, M., Inoue, K., Kandori, H., Beja, O., Ghai, R., & Banciu, H. L. (2019). Casting light on Asgardarchaeota metabolism in a sunlit microoxic niche Nature Microbiology, 4, 1129–1137. https://doi.org/10.1038/s41564-019-0404-y
  • Andrei, A.-S., Salcher, M. M., Mehrshad, M., Rychtecký, P., Znachor, P., & Ghai, R. (2019). Niche-directed evolution modulates genome architecture in freshwater Planctomycetes The ISME Journal, 13, 1056–1071. https://doi.org/10.1038/s41396-018-0332-5

• 2018

  • Mehrshad, M., Salcher, M. M., Okazaki, Y., Nakano, S., Šimek, K., Andrei, A.-S., & Ghai, R. (2018). Hidden in plain sight—highly abundant and diverse planktonic freshwater Chloroflexi Microbiome, 6, 176. https://doi.org/10.1186/s40168-018-0563-8