Bacillus amyloliquefaciens is a species gram-positive, rod-shaped bacterium in the genus Bacillus. B. amyloliquefaciens is the source of the BamHI restriction enzyme. The species also synthesizes the enzyme barnase, a widely studied ribonuclease that forms a famously tight complex with an intracellular inhibitor known as barstar, and plantazolicin, an antibiotic with selective activity against Bacillus anthracis.

Cultures of the organism are used in agriculture, aquaculture, and hydroponics to fight pathogens such as Ralstonia solanacearum, Pythium, Rhizoctonia solani, Alternaria tenuissima and Fusarium as well improve root tolerance to salt stress. They are considered a growth-promoting rhizobacteria and have the ability to quickly colonize roots.

Certain strains of Bacillus amyloliquefaciens have been found to be capable of producing a biofilm on plant roots. This enables enhanced nutrient exchange, fostering a stable environment for long-term colonization. Isolates of Bacillus amyloliquefaciens have been found to have a strong biocontrol potential. This allows for plant growth while suppressing disease. In addition, many Bacillus strains, including B. amyloliquefaciens, have been shown to produce many lipopeptide compounds, such as surfactins, iturin, and fengycins, which will change composition depending on the cultural medium and temperature. These compounds have been shown to inhibit certain pathogens such as Ralstonia solanacearum. Beyond direct pathogen inhibition, lipopeptides have also been shown to activate immune responses within a plant. Recent studies have shown that surfactins and fengycins function as key signaling molecules in the induced systemic resistance process. In bean and tomato plants, these two lipopeptides provide defense protection that is often triggered by live Bacillus cells.

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