Genome mining reveals an architecturally expanded pyoluteorin-associated biosynthetic gene cluster and a divergent flavin-dependent halogenase-like sequence in deep-sea Pseudomonas Aeruginosa from the Gulf of Guinea.

backgroundMarine deep-sea environments harbour microorganisms with extraordinary biosynthetic potential, yet their secondary metabolite repertoires remain largely uncharacterised.

resultsThis study reports the isolation, phenotypic characterisation, and whole-genome analysis of Pseudomonas aeruginosa strain E1, recovered from deep Atlantic seawater (Gulf of Guinea, ~2500 m depth), which exhibits antifungal activity against multidrug-resistant Candida parapsilosis. Three presumptive P. aeruginosa isolates (E1, E17, and E44) showed > 99% 16S rRNA gene sequence identity to P. aeruginosa reference sequences, while whole-genome dDDH analysis of strain E1 yielded 95.2% (95% CI: 93.6-96.4%; formula d4) relative to the P. aeruginosa type strain DSM 50071ᵀ (= ATCC 10145ᵀ), supporting its species-level assignment. Antifungal screening and PCR-based detection of flavin-dependent halogenase genes identified strain E1 as the primary candidate for genomic investigation. Illumina whole-genome sequencing produced a 6.33 Mb draft genome assembly (113 contigs, 5862 protein-coding genes, 66.4% GC content). Genome mining with antiSMASH 8.0 identified 27 biosynthetic gene clusters (BGCs) spanning nonribosomal peptide synthetase (NRPS), polyketide synthase (PKS), phenazine, terpene, and metallophore pathways. Region 7.1 of strain E1 harbours a predicted 50.8 kb pyoluteorin-associated BGC, comprising 34 genes, substantially larger than its terrestrial counterpart (~ 22 kb, ~ 17 genes), and featuring nine transport genes and three regulatory elements. Phylogenetic analysis resolved three halogenase genes: ctg7_146 showed 98.7% amino acid identity to PltA, and ctg7_149 showed 99.2% amino acid identity to PltM, supporting their annotation as PltA-like and PltM-like components of the predicted pyoluteorin biosynthetic pathway. Among the characterised reference enzymes included in this analysis, ctg7_143 showed the highest amino acid identity to PltM from P. fluorescens Pf-5. However, the identity remained low at approximately 30.4%, supporting its placement as a divergent FDH-like sequence rather than a close PltM orthologue.

conclusionThis study provides the first comprehensive genomic characterisation of a pyoluteorin-BGC-harbouring marine P. aeruginosa strain, demonstrating conservation of the core biosynthetic machinery alongside an expanded transport architecture and a divergent FDH-like sequence that may represent a candidate for future biochemical investigation. These findings expand current knowledge of FDH-like sequence diversity in deep-sea bacteria and support further investigation of Gulf of Guinea microorganisms as a potential source of biosynthetic and enzymatic diversity.