Pangenome analysis of Aquipseudomonas alcaligenes 67P: insights into ecological distribution, environmental adaptation, and metabolic versatility

• Whole-genome sequencing and comparative genomics revealed that Aquipseudomonas alcaligenes 67P harbors genetic adaptations for biofilm formation, oxidative stress resistance, and heavy metal detoxification, supporting its survival in diverse environments. • Biosynthetic gene cluster (BGC) analysis identified siderophores, arylpolyenes, and polyketides, suggesting roles in iron acquisition, antimicrobial defense, and oxidative stress protection, highlighting its metabolic adaptability. • The presence of antibiotic resistance genes (mexB, acrB, ampC) and virulence-associated factors, along with metagenomic evidence of its occurrence in aquatic and gut-associated environments. Aquipseudomonas alcaligenes 67P (formerly known as Pseudomonas alcaligenes ), isolated from a diseased goldfish, exhibits genetic features linked to environmental resilience, metabolic versatility, and potential opportunistic traits. Whole-genome sequencing was performed on the Illumina NovaSeq 6000 platform. Reads were processed with Trim Galore, assembled using BV-BRC and refined with Pilon. Pangenome analysis with Roary (via Galaxy) and OrthoVenn3 identified core, accessory, and unique genes, while CAFE5 assessed gene family expansions/contractions. Secondary metabolite biosynthetic gene clusters (BGCs) were predicted with antiSMASH, Virulence-associated genes were identified using the Virulence Factor Database (VFDB), and antibiotic-resistance genes were screened using CARD. IMNGS metagenomic analysis determined environmental distribution, and phylogenomic analysis was performed using BV-BRC Phylogenetic Tree Service. Pangenome analysis with Aquipseudomonas strains ( A. alcaligenes NCTC10367, A. campi S1-A32-2, A. guryensis SR9, A. ullengensis UL070) identified a core genome of 2,800 clusters and 209 unique genes in strain 67P, linked to biofilm formation, oxidative stress resistance, and heavy metal detoxification. BGCs, including siderophores (amphibactin), arylpolyenes, and polyketides, suggest roles in iron acquisition, antimicrobial defense, and oxidative stress protection. Antibiotic resistance determinants highlight potential opportunistic infectivity. Ecological analysis confirmed the presence in aquatic and gut-associated environments. These findings emphasize the bioremediation potential, metabolic adaptability, and dual environmental-pathogenic nature of A. alcaligenes 67P, warranting further studies on host-pathogen interactions and ecological impact.