Metagenomic mining of microorganisms for polyhydroxyalkanoate (PHA) biosynthetic genes from marine sample of the Western Pacific Ocean

Polyhydroxyalkanoates (PHAs) are biodegradable and biocompatible polyesters produced by various microorganisms as intracellular carbon and energy storage compounds. Marine environments, remain underexplored in the context of microbial PHA metabolism due to logistical and technical challenges associated with sampling and cultivation. In this study, a publicly available shotgun metagenomic dataset from the Western Pacific Ocean (SRA: SRR31715427) was analyzed to investigate the taxonomic and functional potential of marine organisms for PHA biosynthesis and degradation. Quality-filtered sequencing reads were assembled using MEGAHIT and binned into metagenome-assembled genomes (MAGs) with MaxBin2. Functional and structural annotations were performed using Prokka, RASTtk, and DRAM, while taxonomic classification was conducted using GTDB-Tk. A total of 34 putative PHA-related genes, including Class I–III synthases, depolymerases (phaZ), and accessory proteins (phaP, phaJ), were identified across 29 high-quality MAGs. Taxonomic profiling revealed that the majority of bacterial PHA-producing lineages belonged to Pseudomonadota, whereas archaeal PHA genes were predominantly found within the Thermoplasmatota phylum, suggesting a broader phylogenetic distribution of PHA biosynthetic potential than previously recognized. The co-occurrence of biosynthesis and degradation genes in several MAGs indicates that these microbes are capable of dynamic PHA metabolism, possibly linked to survival strategies in nutrient-limited conditions. These findings provide new insights into the metabolic diversity of unexplored marine microbial communities and highlight the biotechnological relevance of sea environments for the discovery of novel biopolymer-producing organisms.