{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T14:36:04Z","timestamp":1791297364016,"version":"4.1.0"},"reference-count":225,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2026,2,2]],"date-time":"2026-02-02T00:00:00Z","timestamp":1769990400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000780","name":"European Union","doi-asserted-by":"crossref","award":["862555"],"award-info":[{"award-number":["862555"]}],"id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000780","name":"European Union","doi-asserted-by":"crossref","award":["2131"],"award-info":[{"award-number":["2131"]}],"id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Microbiomes play a pivotal role in sustaining plant function and broader ecosystem processes. Leguminous plants host vast populations of intracellular bacteria within specialized root organs known as nodules. The intricate mutualism between legumes and rhizobia ensures a stable supply of biologically fixed nitrogen (N) essential for plant growth. While rhizobia remain the central actors in this symbiosis, recent discoveries reveal the presence of non-rhizobial endophytes within nodules, suggesting a complex interplay shaped by host selection and compatibility with rhizobial partners. Understanding the structure and dynamics of crop nodule-associated microbial communities is thus critical for optimizing host responses to rhizobia and for leveraging beneficial plant\u2013microbe interactions. This review explores the dualistic nature\u2014both facilitative and inhibitory\u2014of the nodule microbiome in relation to nodulation. We examine the diversity of soil bacteria that stimulate nodulation and those that ultimately colonize nodule tissues, questioning whether these functional groups overlap. Furthermore, we discuss the molecular dialogs and counter-signaling mechanisms that regulate endophyte ingress into nodules, and evaluate how nodule endophytes contribute to plant performance and soil fertility.<\/jats:p>","DOI":"10.3390\/ijms27031487","type":"journal-article","created":{"date-parts":[[2026,2,3]],"date-time":"2026-02-03T09:00:58Z","timestamp":1770109258000},"page":"1487","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["Nodule\u2013Microbiome Dynamics: Deciphering the Complexities of Nodule Symbiosis and the Root Microbiome"],"prefix":"10.3390","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1656-0462","authenticated-orcid":false,"given":"Raja","family":"Ben-Laouane","sequence":"first","affiliation":[{"name":"FSTE-FSM Joint Laboratory \u201cNatural Resources, Health, and Environment\u201d-UMI, Bioresources, Environment and Health Research Team, Faculty of Science and Technology of Errachidia, Moulay Ismail University of Meknes, Marjane 2, BP 298, Meknes 50050, Morocco"},{"name":"Center of Agrobiotechnology and Bioengineering, Research Unit Labelled CNRST (Centre AgroBiotech-URL-7 CNRST-05), Cadi Ayyad University, Marrakesh 40000, Morocco"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8096-9927","authenticated-orcid":false,"given":"Mohamed","family":"Ait-El-Mokhtar","sequence":"additional","affiliation":[{"name":"Laboratory of Biotechnology, Agri-Food, Materials, and Environment (LBAME), Department of Biology, Faculty of Science and Technology Mohammedia, Hassan II University of Casablanca, Mohammedia 28800, Morocco"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9590-4405","authenticated-orcid":false,"given":"Abdelilah","family":"Meddich","sequence":"additional","affiliation":[{"name":"Center of Agrobiotechnology and Bioengineering, Research Unit Labelled CNRST (Centre AgroBiotech-URL-7 CNRST-05), Cadi Ayyad University, Marrakesh 40000, Morocco"},{"name":"African Sustainable Agriculture Research Institute (ASARI), University Mohammed VI Polytechnic (UM6P), Laayoune 70000, Morocco"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3598-7565","authenticated-orcid":false,"given":"Marouane","family":"Baslam","sequence":"additional","affiliation":[{"name":"Center of Agrobiotechnology and Bioengineering, Research Unit Labelled CNRST (Centre AgroBiotech-URL-7 CNRST-05), Cadi Ayyad University, Marrakesh 40000, Morocco"},{"name":"GrowSmart, Paul van Vlissingenstraat 10 F, 1096BK Amsterdam, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,2,2]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1314","DOI":"10.1111\/1751-7915.13517","article-title":"Minireview Effectiveness of nitrogen fi xation in rhizobia","volume":"13","author":"Lindstrom","year":"2020","journal-title":"Microb. 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