Unveiling plastic biodegradation pathways through ¹³C-DNA stable isotope probing and metagenomics

Area of Science:

• Microbiology
• Environmental Science
• Biotechnology

Background:

• Polyhydroxyalkanoates (PHAs) are biodegradable plastics with potential environmental benefits.
• Marine PHA degradation pathways and microbial players are not well understood.

Purpose of the Study:

• To identify and functionally characterize bacteria actively degrading poly(3-hydroxybutyrate) (PHB) in marine environments.
• To investigate the genomic basis for PHB biodegradation in marine bacteria.

Main Methods:

• Utilized 13C-labeled PHB and DNA-stable isotope probing (DNA-SIP) combined with metagenomics.
• Performed comparative genomic and structural analyses of identified depolymerase genes.
• Conducted 3D structural modeling of fusion proteins.

Main Results:

• Identified three metagenome-assembled genomes (MAGs) of the genus Agarilytica actively degrading PHB.
• Discovered an exceptional expansion of extracellular PHA depolymerase genes (ephaZ_scl) with up to 14 copies per genome.
• Revealed gene duplication and fusion events leading to diverse depolymerase variants with potential for enhanced activity.

Conclusions:

• Genomic redundancy and structural diversification of PHA depolymerases provide an adaptive advantage for marine biodegradation.
• Findings offer new insights into marine microbial ecology and evolution of plastic degraders.
• Demonstrated the efficacy of DNA-SIP metagenomics for studying active biodegradation pathways in situ.