{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T23:05:57Z","timestamp":1788822357938,"version":"build-2803163510"},"reference-count":63,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,4,23]],"date-time":"2026-04-23T00:00:00Z","timestamp":1776902400000},"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. Microbiol."],"abstract":"<jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>\n                      Lily bulb rot, which is mainly caused by\n                      <jats:italic>Fusarium oxysporum<\/jats:italic>\n                      (\n                      <jats:italic>F. oxysporum<\/jats:italic>\n                      ), is a destructive soil-borne disease that significantly reduces lily yield and quality. Biocontrol strategies are preferable for counteracting the threats associated with pathogens.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      Confrontation assays were used to screen antagonistic rhizosphere bacteria against\n                      <jats:italic>F. oxysporum<\/jats:italic>\n                      and evaluate their antifungal activity. The most effective isolate,\n                      <jats:italic>Burkholderia pyrrocinia<\/jats:italic>\n                      , was further characterized using a multi-omics approach to investigate its modulation of lily defense responses.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      In this study, the strain YFLYS026, identified as\n                      <jats:italic>B. pyrrocinia<\/jats:italic>\n                      , was isolated from the rhizosphere soil surrounding healthy lily bulbs. It not only exhibited distinct antagonistic activity against six phytopathogens, with inhibition rates on PDA plates ranging from 46.62 to 59.02%, but also showed plant growth-promoting traits, such as nitrogen fixation, phosphorus solubilization, and siderophore production. In pot experiments, strain YFLYS026 effectively controlled bulb rot in lilies, showing a biocontrol efficacy of 61.11%. A total of 1,592 differentially expressed genes (DEGs) were shared in both treatment groups compared with the control; most of these genes were upregulated, and their composition indicated rapid activation of the plant immune network. The DEGs shared between the two treatment groups were significantly enriched in flavonoid, phenylpropanoid, starch\/sucrose and alkaloid metabolic pathways associated with energy production and defense compound biosynthesis. Meanwhile, we found that strain YFLYS026 inoculation upregulated dirigent protein (\n                      <jats:italic>DIR<\/jats:italic>\n                      ) expression, driving pinoresinol accumulation and cell wall lignification to form a physical barrier against pathogen invasion. Integrated multi-omics analysis suggested that phenylpropanoid and flavonoid metabolic pathways were downregulated, potentially indicating carbon metabolic flux redistribution to prioritize lignin synthesis.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Discussion<\/jats:title>\n                    <jats:p>\n                      These results support the potential of\n                      <jats:italic>B. pyrrocinia<\/jats:italic>\n                      YFLYS026 to alleviate lily bulb rot disease and lay a foundation for its application as an effective biocontrol agent.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fmicb.2026.1788193","type":"journal-article","created":{"date-parts":[[2026,4,23]],"date-time":"2026-04-23T05:38:17Z","timestamp":1776922697000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["Characteristics of Burkholderia pyrrocinia and the biocontrol mechanism by which it affects lily bulb rot caused by F. oxysporum"],"prefix":"10.3389","volume":"17","author":[{"given":"Nana","family":"Chang","sequence":"first","affiliation":[{"name":"Jiangxi Province Key Laboratory of Sustainable Utilization of Traditional Chinese Medicine Resources, Institute of Traditional Chinese Medicine Health Industry, China Academy of Chinese Medical Sciences","place":["Nanchang, China"]},{"name":"Jiangxi Health Industry Institute of Traditional Chinese Medicine","place":["Nanchang, 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China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chu","family":"Wang","sequence":"additional","affiliation":[{"name":"Jiangxi Province Key Laboratory of Sustainable Utilization of Traditional Chinese Medicine Resources, Institute of Traditional Chinese Medicine Health Industry, China Academy of Chinese Medical Sciences","place":["Nanchang, China"]},{"name":"Jiangxi Health Industry Institute of Traditional Chinese Medicine","place":["Nanchang, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ye","family":"Cao","sequence":"additional","affiliation":[{"name":"Jiangxi Province Key Laboratory of Sustainable Utilization of Traditional Chinese Medicine Resources, Institute of Traditional Chinese Medicine Health Industry, China Academy of Chinese Medical Sciences","place":["Nanchang, China"]},{"name":"Jiangxi Health Industry Institute of Traditional Chinese Medicine","place":["Nanchang, 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