Research report: Leveraging pineapple-derived eco-enzyme for sustainable microbiome modulation to manage tomato leaf spot disease

A spray made from fermented pineapple peel and core waste cut the leaf spot damage on diseased tomato plants by 74.6% in a 30-day field experiment at a Hong Kong farm, according to a study published in the Journal of Agriculture and Food Research. The treatment, a pineapple-derived eco-enzyme brewed from fruit-juice processing residues, did more than suppress the visible disease: it rebuilt the microbial communities living on the leaves and in the surrounding soil, shifting them toward a composition associated with healthy plants.

Tomatoes are the world’s second most produced vegetable, and fungal leaf spots caused by members of the Mycosphaerellaceae family, such as Cercospora and Septoria species, can cause defoliation, reduced photosynthetic capacity, and yield losses of up to 50% in humid conditions. Globally, crop diseases cause an estimated 20 to 40% of annual yield losses, with economic damages exceeding 220 billion US dollars. Conventional control relies on synthetic fungicides, but their overuse is linked to pathogen resistance, human health risks, and disruption of beneficial microbial communities; the fungicide tebuconazole, for example, can reduce soil microbial diversity by up to 20%.

The research team, led by scientists at Lingnan University, produced the eco-enzyme at Hung Yat Farm in Yuen Long District by grinding fresh pineapple waste, mixing it with water at a 1:3 ratio, and fermenting it in sealed containers for 30 days at room temperature, with a tiny amount of previously fermented enzyme as a starter. Over the fermentation period the pH dropped from 4.3 to an average of 3.1, and dissolved oxygen fell sharply, indicating active aerobic fermentation. By day 30, the bacterial community was dominated by Lactobacillus at 50.0% and Acetobacter at 37.1%, while the fungal community was led by the yeast genus Candida at 96.2%. Metabolomic analysis identified 38,445 metabolites, of which 7,700 were annotated, with 41.7% classified as carboxylic acids, organooxygen compounds, and prenol lipids. Compounds with known antimicrobial and plant growth-promoting properties, including the flavonoid isorhamnetin, succinic acid, and pinolenic acid, increased significantly after fermentation, and Lactobacillus showed strong correlations with these metabolites.

To test the enzyme against real disease, the researchers ran a plot experiment from winter 2024 to spring 2025 using tomato plants about three months old that had naturally acquired leaf spot symptoms from pathogens resident in the local farm soil; no artificial inoculation was performed. Three groups of three plants each were compared: healthy plants, diseased plants, and diseased plants treated with a 2% solution of the enzyme, applied daily as a foliar spray and soil drench at 50 milliliters per plant for 30 days. The healthy and diseased control groups received the same volume of water. At the start, both diseased groups showed early symptoms of small pale-yellow lesions with central brown necrosis.

By day 30, the untreated diseased group had developed severe leaf wilting and fruit damage with extensive lesion expansion, while the enzyme-treated group showed partial recovery with markedly reduced symptoms. Quantitative image analysis showed the treatment reduced lesion area by 74.6% relative to the diseased group, a difference that was statistically significant. Photosynthetic measurements told a similar story. Leaf spot disease lowered photosynthetic efficiency and chlorophyll content compared with healthy plants, although those differences were not statistically significant. The treated group, however, had significantly higher chlorophyll a and chlorophyll b contents than both other groups, and its photosystem II efficiency ratio of 0.77 exceeded the diseased group’s 0.72 and was comparable to healthy tomatoes.

Sequencing of the leaf microbiomes revealed what the enzyme was doing beneath the symptom relief. Amplicon sequencing generated 2.48 million bacterial and 3.19 million fungal reads from tomato leaves, identifying 16,835 bacterial and 1,730 fungal sequence variants. Community structure showed no significant shifts within the first week but clear separation by day 30, indicating that treatment effects developed progressively. Permanova analysis found the treatment had a stronger impact on fungal communities in leaves, with a test statistic of 7.42 and an effect size explaining 71% of the variation, than on bacterial communities, where the effect was not statistically significant. The dominant fungal groups in diseased leaves included the Mycosphaerellaceae family and the genus Cladosporium, and both were significantly more abundant in untreated diseased plants. Genetic matching confirmed a major Cercospora sequence variant representing 75.5% of that family’s abundance, while fungal isolation from lesion margins confirmed Cladosporium tenuissimum, indicating a mixed natural infection. In contrast, the beneficial bacterial genus Pseudomonas was significantly enriched in the enzyme-treated group.

The soil microbiome responded as well. Both bacterial and fungal soil communities differed significantly among the three groups by day 30, and diversity indices showed that leaf spot disease had reduced soil microbial diversity compared with healthy plants, while the Shannon index indicated a recovery of diversity following treatment. Treated soils showed notable enrichment of beneficial bacterial genera including Bacillus, Paenibacillus, and Chitinophaga, alongside a lower prevalence of pathogens such as Fusarium and the Mycosphaerellaceae family.

Metagenomic sequencing of day-30 leaf samples added a functional dimension to these findings. The analysis showed that pathogen infection induced a kind of functional dysbiosis in the leaf microbiome, activating stress-related pathways such as lipopolysaccharide biosynthesis and antibiotic biosynthesis while suppressing essential functions including immune responses, growth regulation, signal transduction, and carbohydrate and lipid metabolism. Treatment with the enzyme reversed this dysbiosis, restoring key defense pathways such as cationic antimicrobial peptide resistance and beta-lactam resistance, although the restored functional profile remained closer to the diseased state than to that of healthy plants. Co-occurrence network analysis reinforced the picture of ecological disruption and partial repair: the healthy group’s cross-kingdom network was the most complex, with 1.3-fold more nodes and twice as many edges as the diseased group, and the enzyme treatment increased network nodes and edges relative to the diseased state, though not to healthy levels. Cross-kingdom interactions in these networks were exclusively negative, with bacteria making up 80% of the top ten hub nodes.

The study also carries practical significance for waste reduction, since pineapple processing generates peel and core residues that typically account for 50 to 60% of the fruit mass and are largely underutilized, making the enzyme a low-cost feedstock for circular bioeconomy approaches.

The researchers are careful to note the limitations of the work. The experiment used only three biological replicate plots per group, a sample size they acknowledge is relatively low for multivariate analyses, and there was no healthy group treated with the enzyme, no commercial fungicide positive control, and no molecular quantification of initial pathogen load. Future studies, they write, should include fungicide benchmarking, in vitro inhibition assays against isolated pathogens, increased replication, and quantitative pathogen monitoring.

Subject of Research: Fermented pineapple waste as a microbiome-modulating biocontrol for tomato fungal leaf spot disease.

Article Title: Leveraging pineapple-derived eco-enzyme for sustainable microbiome modulation to manage tomato leaf spot disease

Article References: Ip, J. C.-H., Cui, D., Li, Y., Zhao, H., Mo, J., Tan, A. L. S., Li, R., Yang, Q., & Wong, C. M. (2026). Leveraging pineapple-derived eco-enzyme for sustainable microbiome modulation to manage tomato leaf spot disease. Journal of Agriculture and Food Research, 32, Article 103403. https://doi.org/10.1016/j.jafr.2026.103403

Image Credits: AI Generated

DOI: 10.1016/j.jafr.2026.103403

Keywords: pineapple eco-enzyme, tomato leaf spot, Mycosphaerellaceae, Cercospora, phyllosphere microbiome, metagenomics, biopesticide, circular agriculture, Lactobacillus, Pseudomonas, foliar spray, soil microbiome