Title: Understanding and engineering polymer biodegradation processes in microbial isolates and communities

The accumulation of plastic waste in the environment has motivated the search for and design of biological systems capable of converting recalcitrant polymers into useful products. Next-generation sequencing has driven rapid growth in omics technologies, enabling researchers to characterize the enzymatic and metabolic machinery of microorganisms at unprecedented resolution. We applied several omics technologies, including transcriptomics, metatranscriptomics, metabolomics, and 16S rRNA gene amplicon sequencing, to resolve interactions between microbial systems and polymer designs.

White-rot fungi, found in forests, are powerful aerobic fungi that efficiently degrade lignocellulose, a complex structural component of plant biomass composed of natural biopolymers. We demonstrated that the white-rot fungus Phanerochaete chrysosporium could metabolize both cellulose and a lowly-acetylated cellulose acetate plastic. Transcriptomic analysis revealed that P. chrysosporium deployed cellulolytic machinery to metabolize both cellulose acetate and cellulose, alongside distinct substrate-specific responses. Untargeted metabolomic analysis further identified two putative substrate-specific metabolites previously uncharacterized in this fungus, highlighting its potential for converting polymer waste into useful chemicals.

Anaerobic gut fungi, found in ruminant digestive tracts, are also strong lignocellulose degraders. We found that Neocallimastix californiae and Neocallimastix lanati could serve as biological pretreatments to enhance the biodegradability of a polyhydroxyalkanoate straw and a cellulose acetate film within an anaerobic digester sludge microbiome. Transcriptomic and metatranscriptomic analyses revealed that these fungi and the sludge microbiome deployed distinct enzymatic and taxonomic responses depending on the polymer substrate, reflecting different degradation strategies for carbohydrate- and lipid-like polymers.

Researchers can also approach biodegradability from the perspective of polymer design, by engineering chemical triggers into a material to promote its breakdown under specific environmental conditions. We evaluated the anaerobic biodegradability of, and microbial community response to, two polymers engineered for triggered degradation under reducing conditions. A dithiol monomer containing hydrolyzable in-chain ester linkages modestly but significantly biodegraded, while a reduced copolymer lacking such linkages did not. This study identified key taxa uniquely enriched by the dithiol monomer, establishing a link between polymer backbone architecture and microbial community response.

Together, these findings show that microbial biodegradation of synthetic polymers is governed by the interaction between substrate chemistry and the degradative machinery available within a given biological system. This work contributes mechanistic hypotheses toward engineering sustainable biological systems for converting diverse polymer waste into useful bioenergy and biochemical products.