Soil bacteria curb Fusarium wilt in tomato, but silicon backfires

Two soil bacteria isolated from Taiwanese farm fields can sharply reduce Fusarium wilt in greenhouse-grown tomatoes, according to a new study published in Botanical Studies. The strains, designated NRBC and NRBA, belong to the genus Burkholderia and were selected from a collection of silicate-solubilizing rhizobacteria for their ability to inhibit the wilt pathogen Fusarium oxysporum f. sp. lycopersici, or FOL, in laboratory assays. When applied to the soil of tomato seedlings, the bacteria significantly lowered disease incidence, slowed symptom development, and reduced the recovery of the pathogen from infected stem tissue. Unexpectedly, adding silicon to the soil, the very trait the bacteria were originally screened for, did not improve disease control and in some cases appeared to weaken it.

Fusarium wilt is one of the most destructive diseases of tomato worldwide, with the cited literature attributing yield losses of approximately 80 percent to the disease. The pathogen attacks the xylem vessels, the water-conducting tissue of the plant, and most conventional fungicides fail to reach the site of blockage. Its chlamydospores, thick-walled resting spores, can survive in harsh soil conditions for several years, so crop rotation and soil solarization reduce pathogen density but cannot eradicate the fungus. Host resistance bred into commercial cultivars provides efficient control, but the authors note that resistance can be eroded by the diversity and dynamic co-evolution of pathogen populations. Growers therefore rely heavily on fungicides, which raise production costs and carry environmental and health concerns, motivating the search for biological alternatives.

The research team, led by Sunil Khayamali with colleagues including Tao-Ho Chang, Jenn-Wen Huang and Pi-Fang Linda Chang, isolated 68 rhizobacteria with plant growth-promoting abilities from soil samples collected in four organic fields in Pingtung County, Taiwan. Many of the strains came from the rhizosphere of rice, a crop that the authors describe as an ideal habitat for silicate-solubilizing bacteria because rice is a high silicon accumulator. After morphological and functional screening, 18 strains were identified by 16S rDNA sequencing, revealing membership in six genera including Acinetobacter, Burkholderia, Klebsiella, Pseudomonas, Ralstonia and Serratia, with Pseudomonas the most dominant. Thirteen unique strains were carried forward for detailed characterization.

In vitro assays showed that all 13 strains solubilized both silicate and phosphate, produced the plant hormone indole-3-acetic acid at concentrations ranging from 6.50 to 48.72 micrograms per milliliter, and, in seven cases, produced siderophores, iron-scavenging compounds that can starve fungal pathogens of this essential nutrient. The highest silicate-solubilizing index, 4.10, belonged to an Acinetobacter baumannii isolate, while the remaining strains ranged from 2.03 to 3.66. In dual culture assays on potato dextrose agar, eight of the 13 strains inhibited at least one of five tested phytopathogenic fungi. Three strains, NRBC, NRBA and a Pseudomonas aeruginosa isolate called LCPA, antagonized all five pathogens, including two FOL isolates, a watermelon Fusarium isolate, a Colletotrichum gloeosporioides strain and the rice blast fungus Magnaporthe oryzae. LCPA was excluded from further work because its sequence matched P. aeruginosa, a well-known opportunistic human pathogen, at 100 percent similarity.

Because 16S rRNA gene sequences generally lack the resolution needed to distinguish species within the Burkholderia cepacia complex, the team performed multilocus sequence analysis using seven housekeeping genes, producing a 2760-base-pair concatenated sequence. This analysis confirmed that NRBC clusters with the type strain of Burkholderia contaminans with strong bootstrap support and 99 percent identity to B. contaminans MS14, a strain previously reported to have biocontrol activity. NRBA, however, did not group with B. aenigmatica as the 16S analysis had suggested; instead it fell within the B. cepacia lineage with moderate support and 97 percent sequence similarity. Given a 3 percent divergence from closely related species, the authors conservatively designated it Burkholderia sp. NRBA, leaving its exact taxonomic position unresolved.

The greenhouse experiments used the tomato cultivar Farmers 301, which is susceptible to FOL race 2. Ten-day-old seedlings were transplanted and either supplemented with 2 millimolar silicon as potassium silicate or given potassium chloride to balance potassium. Two days later, the soil was drenched with bacterial suspension, reapplied at nine days, and the plants were then inoculated with a conidial suspension of the Foly4 isolate or mock-inoculated, producing twelve treatment groups in a completely randomized design with at least five replicate plants per group. Disease incidence was recorded at 14 and 21 days post-pathogen inoculation, severity was rated on a 0 to 4 scale at five time points, and the area under the disease progress curve was calculated by trapezoidal integration.

Under normal conditions without pathogen challenge, the combination of NRBC and silicon significantly increased shoot dry weight by 22.86 percent compared with the silicon-only control, while other growth parameters rose slightly but not significantly. Under FOL stress at 21 days post-inoculation, all bacteria-treated plants were significantly taller, by roughly 10 centimeters, than the water-treated controls. NRBA treatment reduced disease incidence by 65.02 percent and NRBC by 34.98 percent relative to the control at 21 days. Disease severity in the control groups reached 66.7 percent with silicon supplementation and 67.9 percent without, whereas all bacteria-treated groups ranged from 16.7 to 40.5 percent, a reduction of at least 39 percent. The lowest severity, 16.7 percent under NRBA alone, represented a reduction of more than 74 percent, and NRBA also produced the lowest AUDPC value, 99.40, approximately 76 percent below the control values of 423.81 and 416.67.

A pathogen recovery assay reinforced these results. Hypocotyl segments from infected plants were surface-sterilized and placed on a selective medium for Fusarium, and re-isolation of the fungus confirmed that bacterial treatments reduced pathogen colonization. Control plants yielded FOL from 95.24 percent of samples, while NRBA-treated plants yielded only 33.33 percent, a reduction of roughly two-thirds. NRBC-treated plants showed recovery rates of 61.90 percent without silicon and 66.67 percent with it. Notably, adding silicon to NRBA raised pathogen recovery to 71.43 percent, and disease incidence under the combined bacteria-plus-silicon treatments was higher than under the bacteria alone, indicating that silicon co-application lessened the protective ability of the bacteria rather than enhancing it.

Quantitative reverse-transcription PCR of six defense-related genes in hypocotyl tissue at 0, 4 and 8 days post-inoculation suggested that the bacteria influenced plant hormonal signaling. The salicylic acid marker genes WRKY70 and PR1 were strongly upregulated at 4 days in plants treated with NRBA plus silicon, while NRBC-treated groups showed higher expression of these genes at 8 days. ACS2, a marker of ethylene signaling, was upregulated under NRBA at 4 days and NRBC at 8 days, and ERF1 and AOS, markers of jasmonic acid and ethylene pathways, showed moderate changes. The authors caution that these transcriptional patterns are consistent with SA and JA/ET involvement but do not provide direct in planta validation of the pathways, and that the study cannot fully distinguish whether disease suppression came from direct antifungal activity of the bacteria or from host-mediated induced resistance.

The authors conclude that NRBA and NRBC are effective standalone biocontrol candidates against FOL race 2, while silicon supplementation failed to deliver the anticipated growth promotion or disease suppression in this susceptible cultivar. They emphasize that both strains belong to the Burkholderia cepacia complex, a group containing opportunistic human pathogens as well as beneficial members, so whole-genome sequencing, average nucleotide identity analysis and biosafety assessments are essential before any agricultural application. Future work, they suggest, should identify the antifungal compounds produced by the strains, quantify FOL biomass by qPCR, measure silicon in plant and soil samples, analyze defense-related enzymes, and sample additional tissues and time points to clarify the mechanisms underlying the observed disease suppression.

Subject of Research: Biological control of tomato Fusarium wilt using silicate-solubilizing Burkholderia bacteria isolated from Taiwanese rhizosphere soils

Article Title: Biocontrol potential of Burkholderia spp. against Fusarium oxysporum f. sp. lycopersici infecting tomato

Article References: Khayamali, S., Chang, T.-H., Mushyakhwo, K., Huang, J.-W., & Chang, P.-F. L. (2026). Biocontrol potential of Burkholderia spp. against Fusarium oxysporum f. sp. lycopersici infecting tomato. Botanical Studies, 67(1), Article 10. https://doi.org/10.1186/s40529-026-00497-z

Image Credits: AI Generated

DOI: 10.1186/s40529-026-00497-z

Keywords: Fusarium wilt, tomato, Burkholderia, biological control, silicate-solubilizing bacteria, plant growth-promoting rhizobacteria, greenhouse experiment, defense gene expression, silicon supplementation, Burkholderia cepacia complex, plant pathology, sustainable agriculture