{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T12:11:18Z","timestamp":1789992678961,"version":"4.0.1"},"reference-count":111,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T00:00:00Z","timestamp":1789948800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Heilongjiang Plant Protection Society of China","award":["HT-2026-01-003"],"award-info":[{"award-number":["HT-2026-01-003"]}]},{"name":"Talent Introduction Project of Heilongjiang Bayi Agricultural University","award":["XYB202010"],"award-info":[{"award-number":["XYB202010"]}],"id":[{"id":"https:\/\/ror.org\/030jxf285","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Talent Introduction Project of Heilongjiang Bayi Agricultural University","award":["XYB202005"],"award-info":[{"award-number":["XYB202005"]}],"id":[{"id":"https:\/\/ror.org\/030jxf285","id-type":"ROR","asserted-by":"crossref"}]},{"award":["XYB202010"],"award-info":[{"award-number":["XYB202010"]}],"id":[{"id":"https:\/\/ror.org\/030jxf285","id-type":"ROR","asserted-by":"publisher"}]},{"award":["XYB202005"],"award-info":[{"award-number":["XYB202005"]}],"id":[{"id":"https:\/\/ror.org\/030jxf285","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Research Project on Ecological Environment Protection in Heilongjiang Province","award":["HST2025TR008"],"award-info":[{"award-number":["HST2025TR008"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Healthy host plants harbor taxonomically structured and diverse endophytic microbial communities that establish sophisticated symbiotic crosstalk with their hosts. These endophytic microbiomes confer multiple beneficial traits, including growth promotion, nutrient acquisition, and enhanced resistance to biotic and abiotic stresses, and are increasingly recognized as key modulators of plant fitness. The assembly of endophytic communities is not random but shaped by combined effects of environmental cues, host filtering, and microbial\u2013microbial interactions, among which plant immunity constitutes an important host-selection dimension. Beneficial endophytes deploy diverse molecular tactics, such as masking microbe-associated molecular patterns (MAMPs) and secreting immune-suppressive compounds, to evade host PAMP-triggered immunity and effector-triggered immunity (PTI-ETI) surveillance for persistent internal colonization. In this review, based on the literature retrieved from Web of Science Core Collection and Scopus (2010\u20132026), we systematically summarize the colonization process, dynamic assembly rules, and driving factors of plant endophytic microbiomes. We further elaborate their multifaceted physiological functions in regulating plant growth, nutrient utilization, and stress adaptation. Deciphering such multilayered plant\u2013endophyte interactions provides important insights for harnessing beneficial endophytes to advance sustainable agricultural development.<\/jats:p>","DOI":"10.3390\/microorganisms14092118","type":"journal-article","created":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T11:05:53Z","timestamp":1789988753000},"page":"2118","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Dynamic Assembly and Multifunctional Roles of Plant Endophytic Microbiomes"],"prefix":"10.3390","volume":"14","author":[{"given":"Jie","family":"Song","sequence":"first","affiliation":[{"name":"College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China"},{"name":"Heilongjiang Provincial Key Laboratory Crop Pest Interaction Biology and Ecological Control, Daqing 163319, China"},{"name":"National Coarse Cereals Engineering Research Center, Daqing 163319, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenhui","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan","family":"Sun","sequence":"additional","affiliation":[{"name":"School of Resources and Environment, Northeast Agricultural University, Harbin 150030, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinfeng","family":"Shi","sequence":"additional","affiliation":[{"name":"College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-9682-8552","authenticated-orcid":false,"given":"Meiqi","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuting","family":"Dai","sequence":"additional","affiliation":[{"name":"College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuhu","family":"Zuo","sequence":"additional","affiliation":[{"name":"College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China"},{"name":"Heilongjiang Provincial Key Laboratory Crop Pest Interaction Biology and Ecological Control, Daqing 163319, China"},{"name":"National Coarse Cereals Engineering Research Center, Daqing 163319, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qin","family":"Yao","sequence":"additional","affiliation":[{"name":"College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China"},{"name":"Engineering Research Center of Crop Straw Utilization, Heilongjiang Province, Daqing 163319, China"},{"name":"Key Laboratory of Low-Carbon Green Agriculture in Northeastern China, Ministry of Agriculture and Rural Affairs P.R., Daqing 163319, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,21]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"E9403","DOI":"10.1073\/pnas.1710455114","article-title":"Root-associated fungal microbiota of nonmycorrhizal Arabis alpina and its contribution to plant phosphorus nutrition","volume":"114","author":"Almario","year":"2017","journal-title":"Proc. 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