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Bacillus amyloliquefaciens: A Versatile bacterium in Food Preservation, Agriculture, and Beyond

In the drive toward sustainable, residue-free solutions across food, agriculture, and biotechnology, Bacillus amyloliquefaciens emerges as a true microbial multi-tool.


This Gram-positive, spore-forming bacterium thrives in diverse environments—from soil and plant rhizospheres to fermented foods—offering antimicrobial, antifungal, probiotic, and enzymatic functions that address pressing industry needs.


Its remarkable versatility stems from robust stress tolerance, prolific secondary-metabolite production, and safe-use status (GRAS by FDA; QPS by EFSA).


This comprehensive overview delves into the organism’s biology, mechanisms of action, and applications spanning food spoilage prevention, biological fungicide, fermentation technology, environmental remediation, and high-value bioproduct synthesis.


1. Biology and Safety Profile of Bacillus amyloliquefaciens


1.1 Taxonomy and Physiology


Originally misclassified as Bacillus subtilis until the 1980s, B. amyloliquefaciens is a rod-shaped, endospore-forming bacterium in the Bacillaceae family. Spores confer exceptional heat, desiccation, and pH tolerance, enabling survival during industrial processing and in harsh soils. Genomic analyses reveal diverse gene clusters encoding nonribosomal peptide synthetases (NRPS) and polyketide synthases (PKS) for antimicrobials (pmc.ncbi.nlm.nih)


1.2 Safety and Regulatory Recognition


Multiple strains are non-toxigenic and lack virulence factors.


The U.S. FDA has affirmed GRAS status for B. amyloliquefaciens–derived carbohydrases and proteases in food, and EFSA includes it on the Qualified Presumption of Safety (QPS) list.


Its long history in traditional fermented foods and probiotic preparations further attests to its safety.


2. Mechanisms Underpinning Versatility


  1. Spore Formation

    • Ensures product shelf stability and field survival.


  2. Secondary Metabolite Production

    • Lipopeptides (iturins, fengycins, surfactins) disrupt membranes of bacteria and fungi.

    • Polyketides (macrolactins, difficidins) inhibit diverse pathogens.


  3. Hydrolytic Enzymes

    • Extracellular proteases, amylases, cellulases, xylanases degrade complex substrates.


  4. Biofilm Formation

    • Benign colonization on produce or root surfaces excludes competitors.


  5. Induced Systemic Resistance (ISR)

    • Root association triggers plant immune pathways for long-term disease suppression.



      Bacillus amyloliquefaciens - PGPR mechanisms
      PGPR (Plant growth-promoting rhizobacteria) mechanisms of action. Plant growth-promoting rhizobacteria are microbes associated with plant roots that promote plant growth, supplying improved mineral nutrition, creating hormones or other molecules that stimulate plant growth and strengthen the plant defenses against biotic and abiotic stresses, or defending plants from pathogens by reducing the survival of pathogenic microorganisms. ISR: Induced Systemic Resistance ( source)

3. Food Preservation and Functional Fermentation


3.1 Slowing and Preventing Spoilage


Competitive Exclusion: Rapid colonization of fresh produce surfaces consumes nutrients, inhibiting spoilage microbes. Antimicrobial Lipopeptides: Surfactin and fengycin permeabilize bacterial and fungal cell membranes, extending shelf life of berries, cut fruits, and leafy greens by days to weeks. Biofilm Barriers: Protective biofilms on dairy and meat surfaces block pathogen attachment, enabling “clean-label” preservation.


3.2 Fermentation Starter Cultures


  • Dairy: Transglutaminase from strain DSM7 improves cheese texture and yield.


  • Beverages: Strain JP21 reduces ethyl carbamate precursors in Chinese baijiu without flavor loss.


  • Cereals & Legumes: Koji fermentation with B. amyloliquefaciens yields bioactive peptides, vitamins, and aromatic compounds in miso, tempeh, and dosa.


  • Fruit & Vegetable Ferments: Mango pickle and kimchi preparations incorporate probiotic strains to enhance flavor, safety, and health benefits.


3.3 Functional Food Ingredients


  • Exopolysaccharides (EPS) like γ-polyglutamic acid (γ-PGA) deliver prebiotic benefits and modulate glycemic response.


  • Bioactive Peptides from fermentation exhibit antioxidant, anti-inflammatory, anticancer, and antidiabetic activities—e.g., fengycin and bacillomycin Lb target cancer cell lines.


4. Biological Fungicide in Sustainable Agriculture


4.1 Broad-Spectrum Disease Control


B. amyloliquefaciens effectively suppresses soil-borne and foliar pathogens including Fusarium, Rhizoctonia, Botrytis, and Pythium.


B. amyloliquefaciens effectively suppresses soil-borne and foliar pathogens including Fusarium, Rhizoctonia, Botrytis, and Pythium.
A clear inhibition zone indicating growth suppression of the fungal pathogen is visible on agar plates simultaneously inoculated with both microbes. Bacillomycin D was detected as the only prominent compound by Matrix-Assisted Laser Desorption/Ionization coupled to time of flight (MALDI TOF) mass spectrometry of samples taken from the surface of the agar plate within the inhibition zone (compiled from data obtained by J. Vater, TUB and K. Dietel, ABiTEP GmbH).(source)

4.2 Modes of Action

Mode of Action

Mechanism

Antibiosis

Lipopeptides prevent spore germination and hyphal extension

Enzymatic degradation

Chitinases and glucanases degrade fungal cell walls

Nutrient competition

Iron-chelating siderophores starve pathogens of essential micronutrients

ISR activation

Root colonization triggers plant defense hormone pathways (salicylic acid, jasmonic acid)


Root colonization triggers plant defense hormone pathways (salicylic acid, jasmonic acid)
Biological control exerted by the plant-beneficial bacterium FZB42. The cartoon illustrates our present picture about the complex interactions between a beneficial Gram-positive bacterium (FZB42, light green), a plant pathogen (R. solani, symbolized by red filled circles) and plant (lettuce, Lactuca sativa). FZB42 colonizes the root surface and is able to produce non-ribosomally cyclic lipopeptides, mainly surfactin and bacillomycin D and to a minor extent fengycin as indicated by the green circles (Chowdhury et al., 2015). It is very likely, but not shown until now, that VOCs (e.g., acetoin, 2,3-butandiol), and small peptides (e.g., plantazolicin, amylocyclicin) are also produced in vicinity of plant roots. Direct antibiosis and competition for nutrients (e.g., iron) suppresses growth of bacterial and fungal plant pathogens in the rhizosphere. However, these effects seem to be of minor importance, since the composition of the root microbiome is not markedly affected by inoculation with FZB42 (Erlacher et al., 2014), and the number of vegetative B. amyloliquefaciens cells on root surfaces is steadily decreasing (Kröber et al., 2014). Due to production of Bacillus signaling molecules (cLPs and VOCs) and in simultaneous presence of R. solani, the plant defensing factor 1.2 (PDF1.2) as indicated by the green-filled red circles is dramatically enhanced and mediates defense response against plant pathogens (Chowdhury et al., 2015). The picture of the lettuce plant (Lactuca crispa) was taken from Bock, 1552, p. 258).








4.3 Field Performance


  • Tomato: 60% reduction in root-rot incidence.


  • Strawberry: 40–70% gray mold suppression.


  • Cucumber & Watermelon: Control of Fusarium wilt with yield boosts of 10–15%.



4.4 Application Guidelines


  1. Timing: Seed treatment or transplant dip delivers root protection; foliar spray at first disease detection.


  2. Formulation: Spore-based powders or wettable granules ensure shelf life and viable cell delivery.


  3. Compatibility: Co-formulants with fertilizers and biostimulants; avoid tank-mix with copper or broad-spectrum fungicides.


  4. Environmental Conditions: Optimal root colonization at 20–30 °C; well-drained soils.


5. Industrial Bioproduct Synthesis


5.1 Enzymes for Bioprocessing


  • Amylases & Cellulases for bioethanol and brewing industry.


  • Pectinases for fruit juice clarification and textile processing, produced cost-effectively from banana peel substrates.


  • Proteases for detergent and leather industries, with robust activity across pH and temperature ranges.


5.2 Biopolymers and Specialty Chemicals


  • γ-PGA for biodegradable plastics, cosmetics, and wastewater treatment—yields improved via metabolic engineering of LL3 strain to 7.5 g/L.


  • Surfactants: Iturins and fengycins serve in bioremediation and enhanced oil recovery by reducing surface tension.




Application of B. amyloliquefaciens for genetic engineering, production of industrial chemicals or enzymes, agriculture, medicine, and biomaterials.
Application of B. amyloliquefaciens for genetic engineering, production of industrial chemicals or enzymes, agriculture, medicine, and biomaterials. (source)


6. Probiotic and Prebiotic Potentials


6.1 Human and Animal Probiotics


Spore resilience enables B. amyloliquefaciens to survive gastric transit, colonize the gut, and modulate microbiota. Clinical trials in mice demonstrate reduced obesity, enhanced insulin sensitivity, and anti-inflammatory effects in high-fat diet models. Poultry studies show suppression

of Clostridium perfringens and improved weight gain.


6.2 Prebiotic Fiber Production


Enzymatic hydrolysis of inulin by strain NX-2S generates low-DP fructooligosaccharides with barrier-enhancing properties on intestinal epithelium. Pectin lyases yield rhamnogalacturonan oligomers that promote tight-junction integrity and wound healing in vitro.


7. Environmental and Bioremediation Applications


7.1 Soil Health and Phytoremediation


Inoculation of degraded or saline soils with plant-growth-promoting B. amyloliquefaciens enhances nutrient cycling, soil enzyme activities, and crop salt tolerance by reducing reactive oxygen species and sodium uptake.


7.2 Wastewater and Plastics Treatment


Xenobiotic degradation: Extracellular enzymes break down lignocellulosic agro-wastes into fermentable sugars. Microplastic resilience studies reveal spores endure polylactic acid microparticle toxicity, suggesting robustness in polluted environments.


8. Antimicrobial and Antiviral Biocontrol


8.1 Bacterial Pathogen Suppression


  • Circular bacteriocins (amylocyclicin, subtilosin) inhibit Listeria, Staphylococcus, and Gardnerella.


  • ChbB chitin-binding protein synergizes with chitinases against Valsa mali in orchards.


8.2 Viral Interference


Subtilosin-loaded nanofibers exhibit virucidal action against Herpes simplex virus-1 by blocking viral egress and enhancing cellular autophagy. Other lipopeptides show antiviral activity in aquaculture and against plant viruses (tobacco streak, potato virus Y) by inducing host defense signals.


9. Genetic and Metabolic Engineering Toolkits


CRISPR-Cas9n and base-editing systems now enable >90% gene knockout efficiency in B. amyloliquefaciens. Synthetic promoter and RBS libraries optimize secretion of heterologous proteins. Overexpression of competence regulator ComK facilitates marker-free genome editing.


10. Challenges and Future Directions


While B. amyloliquefaciens has demonstrated broad utility, barriers remain:


  • Regulatory approval for novel field and food uses, particularly residue and allergenicity assessments.


  • Strain consistency: Ensuring stable metabolite profiles across production batches.


  • Mechanistic gaps: Molecular understanding of ISR induction, biofilm dynamics, and probiotic-host interactions.


  • Scale-up: Optimizing fermentation parameters for high-value metabolite production without compromising spore viability.


    Leveraging its robust metabolic versatility and proven safety profile, Bacillus amyloliquefaciens stands at the forefront of biotechnological innovation, offering residue-free solutions across the entire value chain—from sustainable crop protection and natural food preservation to high-value biochemical synthesis—driving the transition toward greener industrial processes.






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