Searies on Scientific Mobility in Microbiology. J. Almario. Trends in Microbiology 2025. https://www.cell.com/trends/microbiology/abstract/S0966-842X(25)00183-0
Kemen, E., Mahmoudi, M., Hu, Y., Almario, J., Lyon, U., Stincone, P., Tenzer, L.-M., & Chaudhry, V. (2025). Machine Learning Reveals Biocontrol Agents Shaping Disease Protection in Natural Arabidopsis Populations and Synthetic Communities https://doi.org/10.21203/RS.3.RS-6130404/V1
Almario, J. 2025. Blurred lines in the mycorrhiza world. Nature Reviews Microbiology https://rdcu.be/exbZY (Highlight article)
Guigard, L., Nazaret, F., Almario, J., Bertolla, F., Boubakri, H., Cantarel, A. A. M., Cournoyer, B., Favre-Bonté, S., Florio, A., Galia, W., Hazard, C., Henry, G., Belaroussi, A. H., Chong, S. K. T. F., Lavire, C., Lobreau, C., Luis, P., Maréchal, M., Meyer, T., … Shade, A. (2025). The connections of climate change with microbial ecology and their consequences for ecosystem, human, and plant health. Journal of Applied Microbiology https://doi.org/10.1093/JAMBIO/LXAF168
Bruyant, P., Doré, J., Vallon, L., Moënne-Loccoz, Y., Almario, J*. 2025. Needle in a Haystack: Culturing Plant-Beneficial Helotiales Lineages From Plant Roots. Environmental Microbiology 27: e70082 https://doi.org/10.1111/1462-2920.70082
Mahmoudi, M., Almario, J., Lutap, K., Nieselt, K., Kemen, E. 2024. Microbial communities living inside plant leaves or on the leaf surface are differently shaped by environmental cues. ISME Communications 4:ycae103 https://doi.org/10.1093/ismeco/ycae103
Bruyant, P., Moënne-Loccoz, Y., Almario, J*. 2024. Root-associated Helotiales fungi: Overlooked players in plant nutrition. Soil Biology and Biochemistry https://www.sciencedirect.com/science/article/pii/S003807172400052X
Almario, J.*, Fabiańska, I., Saridis, G., Bucher, M*. 2022. Unearthing the plant-microbe quid pro quo in root associations with beneficial fungi. New Phytologist https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.18061
Almario, J.*, Mahmoudi, M.*, Kroll, S.*, Agler, M., Placzek, A., Mari, A., Kemen, E. 2022. The leaf microbiome of Arabidopsis displays reproducible dynamics and patterns throughout the growing season. Mbio https://journals.asm.org/doi/full/10.1128/mbio.02825-21
Mayer, T., Mari, A., Almario, J., Murillo-Roos, M., Abdullah, H.S.M. Dombrowski, N., Hacquard, S., and Kemen, E.M., Agler, M.T. 2021. Obtaining deeper insights into microbiome diversity using a simple method to block host and non-targets in amplicon sequencing. Molecular ecology resources doi.org/10.1111/1755-0998.13408.
Xue, L.* , Almario, J.* , Fabiańska, I., Saridis, G. and Bucher, M. 2019. Dysfunction in the arbuscular mycorrhizal symbiosis has consistent but small effects on the establishment of the fungal microbiota in Lotus japonicus. New Phytologist doi:10.1111/nph.15958.
Fabiańska, I., Gerlach, N., Almario, J.*, Bucher, M*. 2018. Plant-mediated effects of soil phosphorus on the root-associated fungal microbiota in Arabidopsis thaliana. New Phytologist doi:/10.1111/nph.15538.
Karasov, T., Almario, J., Friedeman, C., Ding, W., Giolai, M., Heavens, D., Kersten, S., Lundberg, D., Neuman, M., Regalado, J., Neher, R.A., Kemen, E., Weigel, D. 2018. Arabidopsis thaliana and Pseudomonaspathogens exhibit stable associations over evolutionary timescales. Cell Host & Microbe 24:168-179.
Almario, J., Jeena, G., Wunder, J., Langen, G., Zuccaro, A., Coupland, G., Bucher, M. 2017. The root fungal microbiota of non-mycorrhizal Arabis alpina and its contribution to plant P acquisition. PNAS 114:E9403-E9412.
Almario, J., Bruto, M., Vacheron, J., Prigent-Combaret, C., Moënne-Loccoz, Y., Muller, D. 2017. Distribution of 2,4-Diacetylphloroglucinol biosynthetic genes among the Pseudomonas spp. reveals unexpected polyphyletism. Frontiers in Microbiology 8:1218.
Almario, J., Muller, D., Défago, G., Moënne-Loccoz, Y. 2014. Rhizosphere ecology and phytoprotection in soils naturally suppressive to Thielaviopsis black root rot of tobacco. Environmental Microbiology16:1949-1960.
Almario, J., Gobbin, D., Muller, D., Défago, G., Moënne-Loccoz, Y., Rezonico, F. 2014. Prevalence of type III secretion system in effective biocontrol pseudomonads. Research in Microbiology 165:300-304.
Donn, S., Almario, J., Muller, D., Moënne-Loccoz, Y., Gupta V.V.S.R., Kirkegaard, J.A., Richardson, A.E. 2014. Rhizosphere microbial communities associated with Rhizoctonia damage at the field and disease patch scale. Applied Soil Ecology 78:37-47.
Kyselková, M., Almario, J., Kopecký, J., Ságová-Marečková, M., Haurat, J., Muller, D., Grundmann, G. L. and Moënne-Loccoz, Y. 2014. Evaluation of rhizobacterial indicators of tobacco black root rot suppressiveness in farmers' fields. Environmental Microbiology Reports 6:346-353.
Almario, J., Prigent-Combaret, C., Muller, D., Moënne-Loccoz, Y. 2013. Effect of clay mineralogy on iron bioavailability and rhizosphere expression of 2,4‑diacetylphloroglucinol biosynthetic genes in biocontrol Pseudomonas protegens. Molecular Plant-Microbe Interactions 26:566-574.
Almario, J., Moënne-Loccoz, Y., Muller, D. 2013. Monitoring of the relation between 2,4‑diacetylphloroglucinol-producing Pseudomonas and Thielaviopsis basicola populations by real-time PCR in tobacco black root-rot suppressive and conducive soils. Soil Biology and Biochemistry 57:144-155.
Almario, J.*, Kyselková, M.*, Kopecký, J., Ságová-Marečková, M., Muller, D., Grundmann, G. L., Moënne-Loccoz, Y. 2013. Assessment of the relationship between geologic origin of soil, rhizobacterial community composition and tobacco black root rot suppressiveness in Savoie region (France). Plant and Soil 371:397-408.