{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T09:43:07Z","timestamp":1785404587462,"version":"3.56.0"},"reference-count":40,"publisher":"MDPI AG","issue":"15","license":[{"start":{"date-parts":[[2026,7,27]],"date-time":"2026-07-27T00:00:00Z","timestamp":1785110400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Survey of Agricultural Biological Species Resources in the Ili River Basin","award":["2022xjkk0503"],"award-info":[{"award-number":["2022xjkk0503"]}]},{"name":"Development Fund for Xinjiang Talents XL","award":["XL202401"],"award-info":[{"award-number":["XL202401"]}]},{"award":["XL202401"],"award-info":[{"award-number":["XL202401"]}],"id":[{"id":"https:\/\/ror.org\/01rkhv978","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Major Science and Technology Special Project of China","award":["2022A02007-4-1"],"award-info":[{"award-number":["2022A02007-4-1"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Plants"],"abstract":"<jats:p>Cotton damping-off caused by Rhizoctonia solani restricts seedling establishment, and locally adapted biocontrol isolates are potential components of sustainable disease management. This study evaluated Pseudomonas chlororaphis-like isolate M6 and tested whether molecular profiles in M6-protected plants differed from those in Pathogen-infected plants in directions that moved toward Healthy Control levels. Culturable bacteria from root-associated soils were screened against R. solani by dual-culture assays, and M6 was evaluated in a greenhouse cotton damping-off assay. RNA sequencing (RNA-seq) and untargeted liquid chromatography\u2013mass spectrometry (LC\u2013MS) data from Healthy Control, Pathogen-infected, and M6-protected plants at 0 and 7 d were analyzed using the Pathogen-infected versus Healthy Control and M6-protected versus Pathogen-infected contrasts. M6 produced the highest inhibition among the candidate isolates (81.9%). Under greenhouse conditions, the M6-protected treatment had lower disease incidence (22.2% versus 88.9%) and disease index (16.4 versus 76.8) than the Pathogen-infected treatment. At 7 d, the primary false-discovery-rate-controlled analysis identified 4457 transcripts and 1620 LC\u2013MS features for which the change between M6-protected and Pathogen-infected plants was opposite to the pathogen-associated change and the M6-protected group mean was closer to the Healthy Control mean. Additional nominal-p-value-only results were retained as exploratory. The two contrasts involved redox regulation, phenylpropanoid\/benzenoid-related metabolism, hormone\/defense signaling, protein synthesis and central metabolism. Antioxidant enzyme and quantitative reverse transcription PCR (qRT-PCR) data provided independent support for selected redox- and defense-associated differences. Because pathogen biomass, bacterial colonization and antagonism-deficient mutants were not assessed, the molecular profiles are interpreted as association-based features of the protected state rather than evidence that host recovery caused disease reduction. Most LC\u2013MS annotations are putative and were not confirmed with authentic standards.<\/jats:p>","DOI":"10.3390\/plants15152305","type":"journal-article","created":{"date-parts":[[2026,7,27]],"date-time":"2026-07-27T14:08:14Z","timestamp":1785161294000},"page":"2305","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["An Indigenous Pseudomonas chlororaphis-like Isolate M6 Is Associated with Reduced Cotton Damping-Off and Partial Redox\u2013Phenylpropanoid Molecular Profiles"],"prefix":"10.3390","volume":"15","author":[{"given":"Yingming","family":"Wei","sequence":"first","affiliation":[{"name":"Key Laboratory at the Universities of Xinjiang Uygur Autonomous Region for Oasis Agricultural Pest Management and Plant Protection Resource Utilization, Agriculture College, Shihezi University, Shihezi 832003, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiuyue","family":"Zhao","sequence":"additional","affiliation":[{"name":"Key Laboratory at the Universities of Xinjiang Uygur Autonomous Region for Oasis Agricultural Pest Management and Plant Protection Resource Utilization, Agriculture College, Shihezi University, Shihezi 832003, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaolei","family":"Cao","sequence":"additional","affiliation":[{"name":"Key Laboratory at the Universities of Xinjiang Uygur Autonomous Region for Oasis Agricultural Pest Management and Plant Protection Resource Utilization, Agriculture College, Shihezi University, Shihezi 832003, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Quanling","family":"Zhang","sequence":"additional","affiliation":[{"name":"Key Laboratory at the Universities of Xinjiang Uygur Autonomous Region for Oasis Agricultural Pest Management and Plant Protection Resource Utilization, Agriculture College, Shihezi University, Shihezi 832003, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Danni","family":"Gu","sequence":"additional","affiliation":[{"name":"Key Laboratory at the Universities of Xinjiang Uygur Autonomous Region for Oasis Agricultural Pest Management and Plant Protection Resource Utilization, Agriculture College, Shihezi University, Shihezi 832003, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nan","family":"Qi","sequence":"additional","affiliation":[{"name":"Key Laboratory at the Universities of Xinjiang Uygur Autonomous Region for Oasis Agricultural Pest Management and Plant Protection Resource Utilization, Agriculture College, Shihezi University, Shihezi 832003, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8638-3158","authenticated-orcid":false,"given":"Zhaoqun","family":"Yao","sequence":"additional","affiliation":[{"name":"Key Laboratory at the Universities of Xinjiang Uygur Autonomous Region for Oasis Agricultural Pest Management and Plant Protection Resource Utilization, Agriculture College, Shihezi University, Shihezi 832003, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1134-9358","authenticated-orcid":false,"given":"Sifeng","family":"Zhao","sequence":"additional","affiliation":[{"name":"Key Laboratory at the Universities of Xinjiang Uygur Autonomous Region for Oasis Agricultural Pest Management and Plant Protection Resource Utilization, Agriculture College, Shihezi University, Shihezi 832003, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,7,27]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Sun, S., Li, Y., Wang, J., Zhang, X., and Li, B. 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