Revealing marine plastic degraders using stable isotope tracers

Plastic biodegradation in natural environment is performed by the microbial biofilm living on its surface (so-called “plastisphere”), whose molecular mechanisms remain a black box. Here, we present the DNA-stable isotope probing (DNA-SIP) coupled with -OMICs techniques as a powerful tool to describe the microorganisms actively involved in plastic biodegradation. We produced two types of ¹³C-labeled polyhydroxyalcanoates with short chain length (¹³C-scl-PHA) and medium chain length (¹³C-mcl-PHA), which were incubated as sole carbon source with natural marine plastispheres. Rapid biodegradation into carbon dioxide (CO₂) was found for scl-PHA, where much longer biodegradation rates were observed in the case of mcl-PHA. DNA-SIP coupled with 16S rRNA metabarcoding identified different active biodegraders according to the polymer types (mainly Marinobacter sp., Cellvibrionaceae and Alteromonas sp. for scl-PHA and Rasiella rasia and Leptonema sp. for mcl-PHA). Another study showed that metagenomics coupled with DNA-SIP identified several PHA-dehydrogenase systems according to the reconstruction of ¹³C-labeled metagenome-assembled genomes (MAGs). Finally, genomic and transcriptomic analysis of a novel bacterium Alteromonas plasticoclasticus isolated from the marine plastisphere confirmed the expression of PHA-dehydrogenase and revealed an example of entire metabolic pathways of scl-PHA biodegradation (Barbe et al. 2024). Overall, these results illustrate the potential of the stable isotope tracers to explore the functional reservoir of the plastisphere for discovering new processes involved in the plastic end-of-life in the marine environment.

Barbe et al. (2022) https://doi.org/10.1016/j.jhazmat.2024.133573