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Genome mining and metabolomics of Burkholderia highlight secondary

metabolites with biocontrol potential against banana Fusarium Wilt

,3
1,2
Tung-Han Lin, #,1.2,3 Bo-Wei Wang, Wen-Chieh Tsai,* Y u -Liang Yang* ,1,2,3

1 Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115201, Taiwan
2 Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 711010, Taiwan

3 Institute of Tropical Plant Science and Microbiology, National Cheng Kung University, Tainan
704016, Taiwan
* E-mail: tsaiwc@mail.ncku.edu.tw, ylyang@gate.sinica.edu.tw

Abstract
Microbial natural products remained a rich source of bioactive compounds for agriculture
and medicine. This study investigated Burkholderia isolates from disease-suppressive soils to
identify secondary metabolites with antifungal activity against Fusarium oxysporum f. sp.
cubense tropical race 4 (Foc TR4). Fifteen Burkholderia strains were screened, and
metabolomic profiling using LC-MS/MS combined with Feature-Based Molecular Networking
(FBMN) revealed a diverse spectrum of secondary metabolites. Among them, pyrrolnitrin, a
well-known antifungal compound, was consistently detected in multiple strains, while
siderophore-associated metabolites indicated strong iron-chelating potential. Genome mining
of six representative strains confirmed biosynthetic gene clusters (BGCs) corresponding to
these metabolites, underscoring their biosynthetic capacity. Greenhouse assays further
demonstrated that strain HP2-1-A significantly reduced disease severity in banana plants. Soil
metabolomic profiling after greenhouse experiments indicated compositional differences
between treated and control groups, suggesting that Burkholderia inoculation influenced the
soil metabolite landscape. These findings demonstrated that Burkholderia species represented
a valuable microbial reservoir of antifungal natural products, offering both established and
potentially novel compounds for sustainable crop protection and natural product discovery.

Keywords: Burkholderia; Foc TR4; Antifungal secondary metabolites