Johnson, D., Ruan, C., Ramoneda, J., Kan, A., Rudge, T., & Wang, G. (2024). Phage predation accelerates the spread of plasmid-encoded antibiotic resistance. https://doi.org/10.21203/rs.3.rs-3875656/v1

Ramoneda, J., Hoffert, M., Stallard-Olivera, E., Casamayor, E. O., & Fierer, N. (2024). Leveraging genomic information to predict environmental preferences of bacteria. The ISME Journal, 18(1). https://doi.org/10.1093/ismejo/wrae195

Jiang, G., Zhang, Y., Chen, M., Ramoneda, J., Han, L., Shi, Y., Peyraud, R., Wang, Y., Shi, X., Chen, X., Ding, W., Jousset, A., Hikichi, Y., Ohnishi, K., Zhao, F.-J., Xu, Y., Shen, Q., Dini-Andreote, F., Zhang, Y., & Wei, Z. (2024). Effects of plant tissue permeability on invasion and population bottlenecks of a phytopathogen. Nature Communications, 15(1). https://doi.org/10.1038/s41467-023-44234-7

Ramoneda, J., Fan, K., Lucas, J. M., Chu, H., Bissett, A., Strickland, M. S., & Fierer, N. (2024). Ecological relevance of flagellar motility in soil bacterial communities. The ISME Journal, 18(1). https://doi.org/10.1093/ismejo/wrae067

Ma, Y., Ramoneda, J., & Johnson, D. R. (2023). Timing of antibiotic administration determines the spread of plasmid-encoded antibiotic resistance during microbial range expansion. https://doi.org/10.1101/2023.02.01.526709

Ramoneda, J., Jensen, T. B. N., Price, M. N., Casamayor, E. O., & Fierer, N. (2023). Taxonomic and environmental distribution of bacterial amino acid auxotrophies. Nature Communications, 14(1). https://doi.org/10.1038/s41467-023-43435-4

Ramoneda, J., Ma, Y., Schmidt, J., Manhart, M., Angst, D. C., & Johnson, D. R. (2023). Physical contacts between sparse biofilms promote plasmid transfer and generate functional novelty. https://doi.org/10.1101/2023.02.01.526699

Johnson, D., Ruan, C., Borer, B., Ramoneda, J., & Wang, G. (2023). Evaporation-induced hydrodynamics control plasmid transfer during surface-associated microbial growth. https://doi.org/10.21203/rs.3.rs-2864267/v1

Ramoneda, J., Stallard-Olivera, E., Hoffert, M., Winfrey, C. C., Stadler, M., Niño-García, J. P., & Fierer, N. (2023). Building a genome-based understanding of bacterial pH preferences. https://doi.org/10.1101/2023.01.24.524446

Siegenthaler, M. B., Ramoneda, J., Frossard, E., & Mészáros, É. (2022). Microbial community responses to phosphorus and nitrogen inputs in the organic soil horizons of two contrasting temperate beech forests. Applied Soil Ecology, 172, 104357. https://doi.org/10.1016/j.apsoil.2021.104357

Dolinšek, J., Ramoneda, J., & Johnson, D. R. (2022). Initial community composition determines the long-term dynamics of a microbial cross-feeding interaction by modulating niche availability. ISME Communications, 2(1). https://doi.org/10.1038/s43705-022-00160-1

Ruan, C., Ramoneda, J., Gogia, G., Wang, G., & Johnson, D. R. (2022). Fungal hyphae regulate bacterial diversity and plasmid-mediated functional novelty during range expansion. Current Biology, 32(24), 5285-5294.e4. https://doi.org/10.1016/j.cub.2022.11.009

Ramoneda, J., Le Roux, J., Stadelmann, S., Frossard, E., Frey, B., & Gamper, H. A. (2021). Soil microbial community coalescence and fertilization interact to drive the functioning of the legume–rhizobium symbiosis. Journal of Applied Ecology, 58(11), 2590–2602. Portico. https://doi.org/10.1111/1365-2664.13995

Ramoneda, J., Hawes, I., Pascual-García, A., J. Mackey, T., Y. Sumner, D., & D. Jungblut, A. (2021). Importance of environmental factors over habitat connectivity in shaping bacterial communities in microbial mats and bacterioplankton in an Antarctic freshwater system. FEMS Microbiology Ecology, 97(4). https://doi.org/10.1093/femsec/fiab044

Lear, L., Dr Matt Lloyd Jones, Ramoneda, J., & Castledine, M. (2021). A systematic review of diversity-invasibility relationships in experimental microbial communities. OSF Registries. https://doi.org/10.17605/OSF.IO/FZYRX

Ruan, C., Ramoneda, J., Chen, G., Johnson, D. R., & Wang, G. (2021). Evaporation-induced hydrodynamics promote conjugation-mediated plasmid transfer in microbial populations. ISME Communications, 1(1). https://doi.org/10.1038/s43705-021-00057-5

Ramoneda, J., Roux, J. J. L., Frossard, E., Frey, B., & Gamper, H. A. (2020). Geographical patterns of root nodule bacterial diversity in cultivated and wild populations of a woody legume crop. FEMS Microbiology Ecology, 96(10). https://doi.org/10.1093/femsec/fiaa145

Ramoneda, J., Le Roux, J. J., Frossard, E., Frey, B., & Gamper, H. A. (2020). Experimental assembly reveals ecological drift as a major driver of root nodule bacterial diversity in a woody legume crop. FEMS Microbiology Ecology, 96(6). https://doi.org/10.1093/femsec/fiaa083

Ramoneda, J., Hawes, I., Pascual-García, A., Mackey, T. J., Sumner, D. Y., & Jungblut, A. D. (2020). Environmental controls and habitat connectivity of phototrophic microbial mats and bacterioplankton communities in an Antarctic freshwater system. https://doi.org/10.1101/2020.07.13.200626

Ramoneda, J., Le Roux, J., Frossard, E., Frey, B., & Gamper, H. A. (2020). Ecological patterns of root nodule diversity in cultivated and wild rooibos populations: a community prediction approach. https://doi.org/10.1101/2020.01.15.907972

Ramoneda, J., Le Roux, J., Frossard, E., Frey, B., & Gamper, H. A. (2020). Different ecological processes drive the assembly of dominant and rare root-associated bacteria in a promiscuous legume. https://doi.org/10.1101/2020.01.13.900290

Ramoneda, J., Le Roux, J., Stadelmann, S., Frossard, E., Frey, B., & Gamper, H. A. (2020). Coalescence of rhizobial communities in soil interacts with fertilization and determines the assembly of rhizobia in root nodules. https://doi.org/10.1101/2020.01.16.908863

Rivett, D. W., Jones, M. L., Ramoneda, J., Mombrikotb, S. B., Ransome, E., & Bell, T. (2018). Elevated success of multispecies bacterial invasions impacts community composition during ecological succession. Ecology Letters, 21(4), 516–524. Portico. https://doi.org/10.1111/ele.12916

Paschke, Melanie. (2017). Agriculture in Transformation. Concepts for agriculture production systems that are socially fair environmentally safe: Proceedings of the PSC Summer Schools 2014 and 2016. ETH Zurich. https://doi.org/10.3929/ETHZ-B-000218321

Jones, M. L., Ramoneda, J., Rivett, D. W., & Bell, T. (2017). Biotic resistance shapes the influence of propagule pressure on invasion success in bacterial communities. Ecology, 98(7), 1743–1749. Portico. https://doi.org/10.1002/ecy.1852

Muñoz-Muñoz, F., Ramoneda, J., Pagès, N., Pujol, N., & Talavera, S. (2016). Is the morphology of Culicoides intersexes parasitized by mermithid nematodes a parasite adaptation? A morphometric approach to Culicoides circumscriptus (Diptera: Ceratopogonidae). Journal of Invertebrate Pathology, 135, 1–9. https://doi.org/10.1016/j.jip.2016.01.008

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