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PDG_DB: A comprehensive database unveils environmental distribution patterns of plastic-degrading genes via large-scale multi-omic data analysis.
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Researchers built PDG_DB, a curated database of 341 experimentally validated plastic-degrading gene sequences, then mined 5,466 environmental metagenomic datasets to identify over 7,000 field-distributed genes—finding unexpectedly high abundance in drinking water systems and highest transcriptional activity in marine environments, with PHA-degrading genes dominating globally.
Plastic pollution has become a global environmental crisis, driving urgent research into plastic-degrading enzymes for achieving efficient green transformation and recycling of plastic waste. However, current plastic-degrading gene (PDG) databases remain fragmented and incomplete. Simultaneously, research has predominantly focused on laboratory-isolated strains with the limited exploration of the vast reservoir of PDGs in environmental metagenomes. To address these limitations, we employed large-scale environmental multi-omics analysis to systematically mine and characterize PDGs across diverse ecosystems. We constructed PDG_DB (https://github.com/Z-bioinfo/PDG_DB), a comprehensive PDG database containing 341 experimentally validated sequences categorized by substrate specificity. Large-scale multi-omics analysis across environmental samples identified 7,111 PDGs (3,612 non-redundant), with polyhydroxyalkanoate (PHAs) degrading genes predominating. Molecular docking revealed that novel putative PDGs for PHA degradation exhibited stronger binding affinity compared to known PDGs, demonstrating the necessity of mining novel enzymes from environmental sources. Most PDGs were bacterial, primarily from Pseudomonadota, with the genus Pseudomonas showing the broadest degradation range. Our global analysis of 5,466 datasets revealed high PDG abundance in East Asia, North Europe, America, and the oceans. Unexpectedly, drinking water systems harbored the highest PDG abundance, challenging assumptions about plastic contamination in potable water. PDG distribution varied by environment: soil favored genes for non-biodegradable plastics, while wastewater systems preferred those for biodegradable plastics. Metatranscriptomic analysis showed the highest PDG activity in marine environments. This work provides a comprehensive resource for PDGs, revealing distinctive global distribution patterns with drinking water systems as an unexpected reservoir. PDG_DB serves as a foundational database for identifying PDGs, facilitating future environmental monitoring and biotechnology applications.
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