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Publications

2024
​​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), wrae067. https://academic.oup.com/ismej/article/18/1/wrae067/7655987.

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


Ruan, C., Ramoneda, J., Kan, A., Rudge, T.J., Wang, G., & Johnson, DR. (2024) Phage predation accelerates the spread of plasmid-encoded antibiotic resistance. Nature Communications, 15(1):5397. https://www.nature.com/articles/s41467-024-49840-7.

Jiang, G., Zhang, Y., Chen, M., Ramoneda, J., Han, L., Shi, Y., Peyraud, R., Wang, Y., Shi, X., Chen, X., et al. (2024). Effects of plant tissue permeability on invasion permeability and population bottlenecks of a phytopathogen. Nature Communications, 15(62), https://doi.org/10.1038/s41467-023-44234-7.

2023

​Ramoneda, J., Jensen, T.B., Price, M.N., Casamayor, E.O., & Fierer, N. (2023) Taxonomic and environmental distribution of bacterial amino acid auxotrophies. Nature Communications, 14, 7608. https://doi.org/10.1038/s41467-023-43435-4

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Ruan, C., Borer, B., Ramoneda, J., Wang, G., & Johnson, D.R. (2023) Evaporation-induced hydrodynamics control plasmid transfer during surface-associated microbial growth. npj Biofilms and Microbiomes, 9 (1), 58. https://www.nature.com/articles/s41522-023-00428-x

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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. Science Advances, 9, eadf8998. https://www.science.org/doi/full/10.1126/sciadv.adf8998

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Ma, Y., Ramoneda, J., & Johnson, D. R. (2023). Timing of antibiotic administration determines the spread of plasmid-encoded antibiotic resistance during microbial range expansion. Nature Communications, 14 (1), 3530. https://www.nature.com/articles/s41467-023-39354-z

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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, bioRxiv, https://doi.org/10.1101/2023.02.01.526699

2022

​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. https://doi.org/10.1016/j.cub.2022.11.009

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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, 77. https://doi.org/10.1038/s43705-022-00160-1

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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/https://doi.org/10.1016/j.apsoil.2021.104357

2021

​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), 54. https://doi.org/10.1038/s43705-021-00057-5

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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), fiab044. https://doi.org/10.1093/femsec/fiab044

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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. https://doi.org/https://doi.org/10.1111/1365-2664.13995

2020​

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. https://doi.org/10.1093/femsec/fiaa083


Ramoneda, J., Roux, J. J. Le, 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

2019

Ramoneda, J., Le Roux, J., Frossard, E., Bester, C., Oettlé, N., Frey, B., & Gamper, H. A. (2019). Insights from invasion ecology: Can consideration of eco-evolutionary experience promote benefits from root mutualisms in plant production? AoB PLANTS, 11(6), 1–9. https://doi.org/10.1093/aobpla/plz060

2018

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. https://doi.org/10.1111/ele.12916

2017

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. https://doi.org/10.1002/ecy.1852

2016

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/https://doi.org/10.1016/j.jip.2016.01.008

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