The phylogenetic and global distribution of bacterial polyhydroxyalkanoate bioplastic degrading genes

Abstract

Polyhydroxyalkanoates (PHAs) are a family of microbially-made polyesters that have been commercialized as biodegradable plastics. PHA production rates are predicted to increase rapidly as global concerns around environmental plastic contamination and limited fossil fuel resources have increased the importance of bio-based plastic alternatives. PHAs are meant to quickly degrade in the environment, but this degradation is reliant on microbially-secreted PHA depolymerases, whose taxonomic and environmental distribution have not been well-defined. As a result, the impact of increased PHA production and disposal on global environments is unknown. Here we used 3,842 metagenomes to analyze the distribution of PHA depolymerase genes in microbial communities from diverse aquatic, terrestrial and waste management systems. Our results indicate that extracellular PHA depolymerases are globally widespread but unevenly distributed, with certain environments showing little to no evidence for this activity. In tandem, we screened 5,290 metagenome-assembled genomes to describe the phylogenetic distribution of this trait, which is substantially broader compared to current cultured representatives. We identified members of the Proteobacteria and Bacteroidetes as key lineages with PHA biodegradation potential and predict this activity in members of the Actinobacteria, the Candidate phylum Rokubacteria, Firmicutes, Planctomycetes and Spirochaetes.ImportanceEnvironmental concerns alongside legislation banning single-use petroleum-based plastics are expected to promote the production of bio-based plastics, including PHAs. PHAs represent a novel and emerging waste stream. If PHA disposal follows the precedent set by conventional plastics, a significant portion will be littered into the environment, or improperly discarded into landfills instead of composting facilities. Traditionally, the identification of bioplastic degrading enzymes and organisms has relied on culture-dependent assays. As a result, the PHA degradation capabilities of the “unculturable” fraction of microorganisms remain largely unexplored. Here, we leverage large amounts of environmental sequence data to assess which environments harbor PHA-degrading organisms and to determine the taxonomic affiliations of bioplastic degraders. Our analyses inform our understanding of the biodegradation potential in the environment, with implications for the impact of bioplastic pollution. We identify enzymes and organisms that may be suitable for future bioremediation, chemical processing or biotechnological applications.

Comparative Genomics of Marine Bacteria from a Historically Defined Plastic Biodegradation Consortium with the Capacity to Biodegrade Polyhydroxyalkanoates

“…Vibrios multiply rapidly under favorable conditions and can dominate conventional plastic surfaces [ 102 , 103 , 105 , 106 ]. A recent meta-analysis of metagenomes by Viljakainen and Hug [ 107 ] analyzed the distribution of PHA depolymerases in microbial communities from diverse aquatic, terrestrial, and waste management systems. Putative PHA depolymerases were predicted in Firmicutes, which includes the genus Bacillus , Gammaproteobacteria, that includes the genus Vibrio , and in the order Rhodobacterales, among others.…”