{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,5]],"date-time":"2026-08-05T05:52:29Z","timestamp":1785909149695,"version":"3.56.0"},"reference-count":107,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,8,5]],"date-time":"2026-08-05T00:00:00Z","timestamp":1785888000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Plant Sci."],"abstract":"\n Introduction<\/jats:title>\n \n Cassava stem and root rot caused by\n Fusarium falciforme<\/jats:italic>\n (\n Fusarium solani<\/jats:italic>\n species complex) constrains production in waterlogged tropical systems. In Kerala, India, disease endemicity differs markedly between wetlands and uplands, yet the ecological basis of this variation remains unresolved. We tested whether rhizoplane mycobiome structure and functional stability govern pathogen suppression across these habitats.\n <\/jats:p>\n <\/jats:sec>\n \n Methods<\/jats:title>\n \n Rhizoplane fungal communities from healthy and diseased plants in endemic wetlands and non-endemic uplands were profiled using Internal Transcribed Spacer amplicon sequencing, complemented by culture-dependent isolation and soil physicochemical analyses. Core taxa were identified through microbiome modeling and validated by ITS sequencing of isolates. Antagonistic activity against\n F. falciforme<\/jats:italic>\n was assessed using dual-culture assays and greenhouse validation.\n <\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n \n Quality filtering retained 847,760, 1,037,834, and 539,722 high-quality paired-end reads from the upland, wetland diseased, and wetland healthy rhizoplane samples, respectively. Healthy wetland rhizoplanes exhibited higher diversity and stability than diseased counterparts (Shannon +20%; inverse Simpson +60%). Disease was associated with diversity collapse and enrichment of opportunistic taxa, whereas upland communities remained distinct and stable. A conserved core mycobiome dominated by the members of\n Pichia<\/jats:italic>\n ,\n Aspergillus<\/jats:italic>\n ,\n Sugiyamaella<\/jats:italic>\n , and\n Fusarium<\/jats:italic>\n was identified, with\n Penicillium<\/jats:italic>\n and\n Talaromyces<\/jats:italic>\n forming an extended functional core. Isolates of\n Penicillium oxalicum<\/jats:italic>\n and\n Talaromyces pinophilus<\/jats:italic>\n inhibited\n F. falciforme<\/jats:italic>\n by &gt;90%\n in vitro<\/jats:italic>\n and reduced disease incidence to 0% in greenhouse assays, matching chemical control. Soil acidity and nutrient imbalance were strongly associated with mycobiome disruption and disease.\n <\/jats:p>\n <\/jats:sec>\n \n Discussion<\/jats:title>\n \n Disease emergence coincided with loss of rhizoplane diversity and depletion of key antagonists, indicating failure of microbial resistance under edaphic stress. The consistent identification and validation of\n P. oxalicum<\/jats:italic>\n and\n T. pinophilus<\/jats:italic>\n as keystone antagonists support their functional role in pathogen suppression. Integrating microbiome conservation with soil health restoration offers a robust, climate-resilient strategy for managing cassava stem and root rot in tropical agroecosystems.\n <\/jats:p>\n <\/jats:sec>","DOI":"10.3389\/fpls.2026.1782244","type":"journal-article","created":{"date-parts":[[2026,8,5]],"date-time":"2026-08-05T05:40:04Z","timestamp":1785908404000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Integrated metabarcoding and culturomics reveal the rot-suppressive rhizoplane mycobiome of cassava across contrasting agroecological habitats"],"prefix":"10.3389","volume":"17","author":[{"given":"Santha","family":"Divya","sequence":"first","affiliation":[{"name":"Division of Plant Pathology, Indian Council of Agricultural Research (ICAR)\u2013Indian Agricultural Research Institute","place":["New Delhi, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tusar Kanti","family":"Bag","sequence":"additional","affiliation":[{"name":"Division of Plant Pathology, Indian Council of Agricultural Research (ICAR)\u2013Indian Agricultural Research Institute","place":["New Delhi, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muthulakshmi Lajapathy","family":"Jeeva","sequence":"additional","affiliation":[{"name":"Division of Crop Protection, Indian Council of Agricultural Research (ICAR)\u2013Central Tuber Crops Research Institute","place":["Thiruvananthapuram, Kerala, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thangaraj","family":"Makeshkumar","sequence":"additional","affiliation":[{"name":"Division of Crop Protection, Indian Council of Agricultural Research (ICAR)\u2013Central Tuber Crops Research Institute","place":["Thiruvananthapuram, Kerala, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Binoy","family":"Ambika Manirajan","sequence":"additional","affiliation":[{"name":"School of Biosciences, Mahatma Gandhi University","place":["Kottayam, Kerala, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vinod","family":"Chouhan","sequence":"additional","affiliation":[{"name":"Division of Plant Pathology, Indian Council of Agricultural Research (ICAR)\u2013Indian Agricultural Research Institute","place":["New Delhi, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Syamala Swayamvaran","family":"Veena","sequence":"additional","affiliation":[{"name":"Division of Crop Protection, Indian Council of Agricultural Research (ICAR)\u2013Central Tuber Crops Research Institute","place":["Thiruvananthapuram, Kerala, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aundy","family":"Kumar","sequence":"additional","affiliation":[{"name":"Division of Plant Pathology, Indian Council of Agricultural Research (ICAR)\u2013Indian Agricultural Research Institute","place":["New Delhi, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,8,5]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"325","DOI":"10.1007\/s11103-021-01170-8","article-title":"Modelling cassava production and pest management under biotic and abiotic constraints","volume":"109","author":"Alonso Chavez","year":"2022","journal-title":"Plant Mol. 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