Friends and Foes: The Double Role of Microbes in Postharvest Quality

Fresh fruits and vegetables carry a diverse microscopic community on their surfaces: the phyllosphere (leaves, stems and flowers) and carposphere (fruit surfaces).

Tal Shalev, PhD | Head of Microbiology Department

These microbiomes include bacteria, fungi, yeasts and viruses, and they act as a double-edged sword: while some microbes drive spoilage and safety concerns, others serve as natural allies that can protect produce and extend shelf life.

The “foes”: how the microbiome drives spoilage

Postharvest spoilage stems from the interplay between natural tissue physiology and microbial activity. After harvest, fruits and vegetables continue to respire, and ripening or senescence processes (ethylene production, cell-wall-modifying enzymes, membrane changes) weaken tissues and increase susceptibility to microbial attack. 

Microorganisms exploit this vulnerability. Bacteria such as Pseudomonas and Erwinia secrete pectinases, cellulases and xylanases which degrade the cell wall, causing soft rot, water-soaking and tissue collapse. Fungal pathogens including Botrytis, Penicillium and Alternaria quickly colonise wounds or humid surfaces, producing metabolites and mycotoxins that drive off-odours and quality loss. 

Intrinsic fruit traits (high water activity, near-neutral pH, rich nutrient content) and extrinsic factors (temperature, humidity, handling damage) further accelerate spoilage. In bruised berries, for example, both plant enzymes and microbial pectinases degrade the cell wall, while elevated humidity and respiration create an ideal niche for bacterial and fungal colonisers.

These processes occur throughout the supply chain, making microbial spoilage a major contributor to food waste.

Estimates suggest that up to 30% of postharvest losses in perishable crops at the last mile are driven by microbial decay. Reducing this burden is essential for extending shelf life, improving quality and cutting waste. 

The Microbial Battle for the Strawberry

The “friends”: beneficial microbes and their mechanisms

Not all microbes are harmful.  Many naturally occurring species help protect fresh produce from spoilage. Beneficial lactic acid bacteria (LAB), Bacillus spp., certain yeasts and fungal antagonists inhibit pathogens through multiple mechanisms: competing for nutrients and space, secretion of antimicrobial metabolites, pH modification and even activation of plant defence responses. 

Bacillus subtilis and related species, naturally present on fresh produce and recognized as safe for food use (GRAS, EFSA QPS-listed), exhibit strong inhibitory activity against common postharvest pathogens like Botrytis cinerea, Alternaria spp., and Colletotrichum spp. LAB also have a well-established track record of antimicrobial activity and long-standing use in food preservation. 

Beyond their activity as live competitors on the fruit surface, beneficial microbes are also inspiring new preservation strategies.

Microbial metabolites, especially those produced by LAB, can be incorporated into edible coatings to deliver antimicrobial and pH-modifying effects without relying on live cells. For example, alginate films enriched with LAB-derived compounds have been shown to reduce weight loss and delay softening in passion fruit.

Turning ecology into technology

Modern preservation approaches increasingly aim to work with the microbiome rather than against it. Beneficial microbes - along with the metabolites they produce - are applied through technologies such as microbial coatings, biofilms, spray treatments and biological control agents. Commercial examples include Serenade®, Aspire®, YieldPlus, BioSave-110, SMARTBLOCK, T-22, BioProtect and BioTelo. These solutions supress pathogens, stabilize the fruit surface, and can even prime the plant’s own defence pathways. 

When paired with modified-atmosphere packaging or edible coatings, they offer synergistic benefits in slowing spoilage. While performance can vary across crops and environments, advances in metagenomics and metabolomics are helping researchers design more targeted, stable and crop-specific microbiome-based solutions.

Challenges and the path ahead

Real-world implementation still faces hurdles: ensuring strain safety and consistency, navigating regulatory approval, maintaining stability in formulation and storage, and dealing with the complexity and variability of crop-dependent microbiomes. Yet the evidence is clear — the future of postharvest protection is shifting from blanket disinfection toward microbiome-aware, ecology-based approaches.

By leveraging beneficial microbes rather than eliminating all microbial life, the fresh-produce industry can reduce waste, lower chemical inputs and preserve the sensory and nutritional quality of fruits and vegetables. As tools for understanding plant–microbe interactions continue to advance, microbiome-guided preservation will play an increasingly central role in building a more sustainable and resilient food system.

References

1. Zaman, W., Amin, A., Khalil, A. A. K., Akhtar, M. S., & Ali, S. (2025). Plant–Microbe Interactions for Improving Postharvest Shelf Life and Quality of Fresh Produce Through Protective Mechanisms. Horticulturae, 11(7), 732. https://doi.org/10.3390/horticulturae11070732 

2. Muñoz-Martinez, T. I., Rodríguez-Hernández, B., Rodríguez-Montaño, M., Alfau, J., Reyes, C., Fernandez, Y., Ramos, R. T., De Los Santos, E. F. F., & Maroto-Martín, L. O. (2025). Unlocking the Hidden Microbiome of Food: The Role of Metagenomics in Analyzing Fresh Produce, Poultry, and Meat. Applied Microbiology, 5(1), 26. https://doi.org/10.3390/applmicrobiol5010026 

3. Fenta, L., Mekonnen, H., & Kabtimer, N. (2023). The Exploitation of Microbial Antagonists against Postharvest Plant Pathogens. Microorganisms, 11(4), 1044. https://doi.org/10.3390/microorganisms11041044 

4. Karanth, S., Feng, S., Patra, D., & Pradhan, A. K. (2023). Linking microbial contamination to food spoilage and food waste: The role of smart packaging, spoilage risk assessments and date labeling. Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2023.1198124 

5. Sohrabi, R., Paasch, B. C., & Liber, J. A. (2023). Phyllosphere Microbiome. Annual Review of Plant Biology, 74, 539-568. https://doi.org/10.1146/annurev-arplant-102820-032704