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Here, we revealed that bacterial wilt disease (BWD) induced pronounced niche-specific microbiome alterations in tobacco, with the rhizoplane (RP) emerging as a critical hub for beneficial microbial recruitment and defense coordination. Utilizing 16S and ITS amplicon sequencing across 6 distinct plant niches, we observed significantly enhanced bacterial diversity and a striking enrichment of potentially beneficial microbes in the RP under BWD stress. Eight potent antagonistic bacterial strains were isolated from this key niche, with Stenotrophomonas sp. ASV61 and Chryseobacterium sp. ASV172 demonstrating robust in vitro biocontrol potential and confirming in vivo plant resistance and growth promotion. We further elucidated the superior biocontrol mechanisms of Chryseobacterium sp. ASV172, attributing its superior efficacy to enhanced colonization and flexirubin-mediated antagonism. Crucially, plant transcriptomic profiling unveiled that these beneficial microbes engaged in a signaling dialogue with host plants, dynamically modulating defense hormone pathways. While Ralstonia alone manipulated host defenses by sustaining salicylic acid responses, antagonistic strains re-directed the plant toward robust jasmonic acid signaling, thereby restoring a more effective defense posture. Collectively, our findings underscore the disproportionate importance of the RP over the rhizosphere in assembling a resilient microbiome against soil-borne diseases, paving the way for targeted RP microbiome engineering strategies for sustainable disease management.<\/jats:p>","DOI":"10.1093\/plphys\/kiag483","type":"journal-article","created":{"date-parts":[[2026,7,7]],"date-time":"2026-07-07T11:38:50Z","timestamp":1783424330000},"source":"Crossref","is-referenced-by-count":1,"title":["Rhizoplane microbiome: niche-specific recruitment and plant defense priming against bacterial wilt disease"],"prefix":"10.1093","volume":"201","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4998-1279","authenticated-orcid":false,"given":"Jiemeng","family":"Tao","sequence":"first","affiliation":[{"name":"China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC , Zhengzhou 450001 ,","place":["China"]},{"name":"Beijing Life Science Academy , Beijing 102200 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2162-3819","authenticated-orcid":false,"given":"Shizhou","family":"Yu","sequence":"additional","affiliation":[{"name":"Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco , Guiyang 550081 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peng","family":"Lu","sequence":"additional","affiliation":[{"name":"China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC , Zhengzhou 450001 ,","place":["China"]},{"name":"Beijing Life Science Academy , Beijing 102200 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mengli","family":"Gu","sequence":"additional","affiliation":[{"name":"China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC , Zhengzhou 450001 ,","place":["China"]},{"name":"School of Agricultural Sciences, Zhengzhou University , Zhengzhou 450001 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mengmeng","family":"Kong","sequence":"additional","affiliation":[{"name":"China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC , Zhengzhou 450001 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junjia","family":"Guo","sequence":"additional","affiliation":[{"name":"China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC , Zhengzhou 450001 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhe","family":"Zhao","sequence":"additional","affiliation":[{"name":"Technology Center, China Tobacco Shandong Industrial Co., Ltd. , Jinan 250014 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