{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T12:45:30Z","timestamp":1790858730507,"version":"4.1.0"},"reference-count":213,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T00:00:00Z","timestamp":1785196800000},"content-version":"vor","delay-in-days":208,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100012352","name":"Universit\u00e0 degli Studi di Milano","doi-asserted-by":"publisher","award":["60770"],"award-info":[{"award-number":["60770"]}],"id":[{"id":"10.13039\/100012352","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,7,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The microbiome is fundamental to plant performance in agroecosystems, influencing primary productivity and climate resilience. Microbiome modulation refers to the targeted manipulation (or steering) and optimization of microbiota features, including taxonomic structure, diversity, composition, assembly dynamics, stability, functional capacity, interactions, and network architecture. Here, we review the current state-of-the-art knowledge and strategies used for microbiome modulation, encompassing biological interventions such as bacteria, fungi, protists, nematodes, and phages, as well metabolites, compounds, and nutrients derived from plants. We further discuss emerging tools and strategies for next-generation microbiome modulation, including function-oriented, multitrophic defined microbial communities assembled based on ecological traits and interactions across multiple trophic levels to enable their establishment and function within the phytobiome; temperate phages; microbiome transplantation and breeding; and functional synbiotics, defined as combinations of beneficial microorganisms and compounds that improve microbiome health and function. In addition, we highlight key knowledge gaps and research priorities for advancing precision microbiome modulation. Addressing current challenges will require integrated frameworks combining experimental validation in planta and reductionist approaches with in silico modeling and multiomics analyses to better predict, design, and sustain beneficial plant-microbiome outcomes. Overall, microbiome modulation represents a paradigm shift in advancing sustainable and climate-resilient agri-food systems.<\/jats:p>","DOI":"10.1093\/sumbio\/qvag032","type":"journal-article","created":{"date-parts":[[2026,7,27]],"date-time":"2026-07-27T11:22:38Z","timestamp":1785151358000},"source":"Crossref","is-referenced-by-count":2,"title":["Microbiome modulation for sustainable crop production and climate resilience"],"prefix":"10.1093","volume":"3","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6945-2732","authenticated-orcid":false,"given":"Malek","family":"Marian","sequence":"first","affiliation":[{"name":"AIT Austrian Institute of Technology , Bioresources Unit, Konrad Lorenz Strasse 24, 3430 Tulln an der Donau ,","place":["Austria"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7128-597X","authenticated-orcid":false,"given":"Ioannis","family":"Stringlis","sequence":"additional","affiliation":[{"name":"Laboratory of Plant Pathology, Agricultural University of Athens , 75 Iera Odos st., 11855 Athens ,","place":["Greece"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5814-9735","authenticated-orcid":false,"given":"Eleonora","family":"Rolli","sequence":"additional","affiliation":[{"name":"Department of Food, Environmental and Nutritional Sciences, University of Milan , via Celoria 2, 20133 Milan ,","place":["Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6800-4233","authenticated-orcid":false,"given":"Christopher James","family":"Barnes","sequence":"additional","affiliation":[{"name":"Department of Agroecology, Faculty of Technical Sciences, Aarhus University , Forsoegsvej 1, Slagelse, 4200 ,","place":["Denmark"]},{"name":"Centre for Evolutionary Hologenomics, The Globe Institute, Faculty of Health, University of Copenhagen , Oester Farimagsgade 5, Copenhagen 1014 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