Bacillus amyloliquefaciens: A Multifunctional Biocontrol and Biofertiliser Powerhouse

Overview of the Microbe#

B. amyloliquefaciens belongs to the Bacillus subtilis species complex and was first described by Priest et al. in 1987 based on 16S rRNA and DNA–DNA hybridisation analyses. It is a rod‑shaped, motile bacterium that forms resistant endospores, enabling survival under adverse environmental conditions[1]. Genomic analyses reveal a ~3.9 Mb genome with a GC content around 46.5 % and harbouring genes for diverse metabolic pathways, including carbohydrate metabolism, secondary metabolite biosynthesis, and stress response[4].Phylogenetically, it clusters with B. velezensis and B. siamensis, forming a distinct lineage within the B. amyloliquefaciens group. Pan‑genome studies highlight a core genome enriched in energy‑metabolism genes and an accessory genome carrying strain‑specific clusters for antimicrobial compound synthesis[4]. These genomic features underpin its ecological adaptability and multifunctional applications.

Plant Growth Promotion and Disease Suppression#

Phytohormone Production and Nutrient Mobilisation#

Certain strains synthesise indole‑3‑acetic acid (IAA), enhancing root development and nutrient uptake under both normal and stress conditions[3]. They also solubilise phosphate via organic acid secretion, increasing phosphorus availability and promoting plant biomass accumulation[2].

Antimicrobial Compound Synthesis#

B. amyloliquefaciens produces lipopeptide antibiotics such as iturins, fengycins, and surfactins, which disrupt fungal cell membranes and inhibit phytopathogens including Rhizoctonia, Fusarium, and Pythium species[7]. In trials, strain DB2 showed >75 % control efficacy against Bipolaris sorokiniana in wheat[3].

Induced Systemic Resistance#

Beyond direct antagonism, inoculation can induce systemic defence responses in plants, elevating expression of pathogenesis‑related proteins and antioxidant enzymes, thus priming plants for enhanced pathogen resistance[6].

Industrial Enzymes and Bioprocessing Applications#

B. amyloliquefaciens is exploited as a production host for industrial enzymes thanks to its high secretion capacity and GRAS status. α‑Amylases from this species hydrolyse starch in food, textile, and paper industries[1]. It also produces subtilisin‑type proteases used in detergents and leather processing[1].

Recombinant protein expression platforms in B. amyloliquefaciens leverage strong promoters and secretion signals, facilitating high yields of heterologous enzymes such as cellulases and keratinases for biomass conversion and waste valorisation.

Volatile Organic Compounds in Biocontrol#

Spectrum of VOCs#

Strains emit VOCs including acetoin, 2,3‑butanediol, and various ketones that exhibit broad‑spectrum antimicrobial activity. These compounds inhibit spore germination and mycelial growth of soil‑borne and postharvest pathogens.

Mechanisms and Applications#

VOCs penetrate fungal cell walls, triggering reactive oxygen species accumulation and membrane disruption. In storage trials, VOC application reduced rot incidence in cherry and apple fruits[5]. Development of VOC‑based biopackaging is underway to leverage these fumigant‑like properties.

Abiotic Stress Alleviation and Bioremediation#

Salt and Drought Tolerance#

Inoculation enhances plant tolerance to salinity by modulating ion homeostasis and osmolyte accumulation, as seen in maize under salt stress. Drought‑stress mitigation involves elevated antioxidant enzyme activities and osmoprotectant synthesis.

Heavy Metal Resistance and Bioremediation#

Certain isolates (e.g., Bam1) exhibit high heavy‑metal tolerance, carrying genes for efflux pumps and metal‑binding proteins. Genome sequencing of Bam1 identified nine unique heavy‑metal resistance genes compared to reference strains[8]. These capabilities enable bioremediation of contaminated soils.

Challenges and Future Potential#

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Field translation faces challenges including formulation stability, strain survival, and regulatory hurdles. Variability in soil microbiomes and environmental conditions affects efficacy, necessitating tailor‑made consortia and carrier materials.

Advances in metabolic engineering and CRISPR‑based genome editing promise to enhance metabolite yields and stress tolerance traits. Synthetic biology approaches aim to design chassis strains with defined functionalities, while omics‑guided screening will accelerate discovery of novel bioactive compounds.

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Spotlight on Research: Pan‑Genome Analysis of the B. amyloliquefaciens Group#

Brief Overview#

A pan‑genome study by Chun et al. analysed genomes of B. amyloliquefaciens, B. velezensis, and B. siamensis, revealing core and accessory genome traits [4].

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Key Insights#

• Core genes enriched in aerobic and anaerobic energy‑metabolism pathways.
• B. velezensis genomes harboured more antimicrobial biosynthesis genes.
• All species carried xanthine oxidase clusters implicated in nitrogen cycling.

Why This Matters#

Understanding pan‑genome architecture guides strain selection for targeted applications, enabling exploitation of species‑specific traits and ensuring robust biocontrol and biofertiliser performance.

Summary Table: Spotlight Study#

Category	Details
Lead Researchers	Byung Hee Chun, Kyung Hyun Kim, Sang E. Jeong, Che Ok Jeon
Affiliations	Chung‑Ang University, Seoul, Republic of Korea
Research Focus	Pan‑genome analysis of B. amyloliquefaciens group
Key Breakthroughs	Identification of core vs accessory genes; species‑specific metabolic clusters
Collaborative Efforts	University‑based genomic research collaboration
Published Work	Genomic insights for industrial and agricultural biotechnology
Publication Date	Feb 2019
Location	Seoul, Korea
Key Findings	Core energy‑metabolism genes abundant; accessory antimicrobial clusters enriched in B. velezensis[4]

Conclusion#

B. amyloliquefaciens stands out as a multifunctional microbial resource, offering sustainable solutions in agriculture, industry, and environmental remediation. Its diverse metabolite repertoire, genomic plasticity, and safety profile make it a cornerstone of next‑generation bio‑inputs. Continued integration of omics, synthetic biology, and field‑scale validation will unlock its full potential, driving innovation in eco‑friendly technologies.

References#

Zalila‑Kolsi, I., Ben‑Mahmoud, A., & Al‑Barazie, R. (2023). Bacillus amyloliquefaciens: Harnessing its potential for industrial, medical, and agricultural applications—A comprehensive review. Microorganisms, 11(9), Article 2215. https://doi.org/10.3390/microorganisms11092215

Vasques, N. C., Nogueira, M. A., & Hungria, M. (2024). Increasing application of multifunctional Bacillus for biocontrol of pests and diseases and plant growth promotion: Lessons from Brazil. Agronomy, 14(8), Article 1654. https://doi.org/10.3390/agronomy14081654

Lu X, Wang Y, Sun X, et al. Biocontrol potential and action mechanism of B. amyloliquefaciens DB2 against Bipolaris sorokiniana. Front. Microbiol. 2021;12:1149363. doi:10.3389/fmicb.2021.1149363.

Ngalimat MS, Radin Yahaya RS, Baharudin MM, et al. Genomic and metabolic features of the B. amyloliquefaciens group revealed by pan‑genome analysis. Food Microbiol. 2019;77:146‑157. doi:10.1016/j.fm.2018.09.001.

Grahovac, J., Pajčin, I., & Vlajkov, V. (2023). Bacillus VOCs in the context of biological control. Antibiotics, 12(3), 581. https://doi.org/10.3390/antibiotics12030581

Silva, F. A., Pereira, G. H., & Souza, L. M. (2024). Bacillus amyloliquefaciens in agriculture: Systematic literature review. RGSA, 19(7), Article 013. https://doi.org/10.24857/rgsa.v19n7‑013

Zouari I, Jlaiel L, Tounsi S, Trigui M. Biocontrol activity of B. amyloliquefaciens CEIZ‑11 against Pythium aphanidermatum. Biol. Control. 2016;96:74‑83.

Luo Y, Chen Y, Zhang W, et al. Genome sequencing of biocontrol strain B. amyloliquefaciens Bam1 and heavy‑metal resistance mechanisms. Bioresour. Bioprocess. 2022;9:18.