Genome mining and characterisation of biosynthetic clusters in Aspergillus japonicus isolated from the Amazon rainforest

BACKGROUND In light of the biotechnological potential demonstrated by Aspergillus species and, considering the great need for further research into the search for new sources of active molecules and the biodiversity of these microorganisms occurring in the Amazon region. OBJECTIVES This research aimed to investigate the biotechnological potential of the fungus Aspergillus japonicus Amazon Fungi Collection (CFAM) 0234, a fungal strain isolated from Amazonian soil and stored in the CFAM. METHODS For this purpose, the Aspergillus species was investigated through comparative genomic analysis and antimicrobial activity assays. FINDINGS Genome sequencing revealed a fragmented assembly (72.67 Mbp, N50 = 152 kbp) containing 106 biosynthetic clusters (BGCs), surpassing the reference strain CBS 114.51 (57 BGCs). Among the clusters identified, NRPS, PKS type I and hybrid NRPS-PKS systems stood out, including clusters exclusive to betalactones and isocyanides, potentially involved in the synthesis of β-lactam antibiotics and innovative metabolites. BiG-SCAPE analysis identified 63 BGC families unique to CFAM 0234, suggesting evolutionary adaptations to the competitive environment of the Amazon. Biological assays demonstrated selective antimicrobial activity of the ethyl acetate extract against Escherichia coli, Shigella sonnei and Sthapylococcus aureus (MRSA), with inhibition halos ranging from 8 mm to 6 mm in diameter, pathogens classified as priorities for research into new antibiotics. The correlation between predicted BGCs and antimicrobial activity reinforces the strain’s biotechnological potential. Despite the fragmentation of the genome, the high completeness assessed by BUSCO (98.5%) confirms the quality of the assembly, while the detection of single nucleotide polymorphisms (SNPs) in regulatory regions and rearrangements close to BGCs suggests evolutionary pressure for metabolic diversification. The lack of correspondence with the minimum information about a biosynthetic gene cluster (MIBiG) bank and the limitations of crude extracts highlight the need for complementary techniques, such as long-read sequencing (Oxford Nanopore) and metabolomic analysis [liquid chromatography-mass espectrometry (LC-MS)], to link clusters to active metabolites. MAIN CONCLUSIONS Aspergillus japonicus CFAM 0234 represents a promising microbial resource for bioprospecting in the Amazon, offering relevant genomic and chemical insights for the development of new antimicrobial agents. Future studies will focus on the purification of compounds and activation of silent BGCs, aiming at sustainable pharmaceutical applications.