A metagenomic catalog for exploring the plastizymes landscape covering taxa, genes, and proteins

Abstract

There are significant environmental and health concerns associated with the current inefficient plastic recycling process. This study presents the first integrated reference catalog of plastic-contaminated environments obtained using an insilico workflow that could play a significant role in discovering new plastizymes. Here, we combined 66 whole metagenomic data from plastic-contaminated environment samples from four previously collected metagenome data with our new sample. In this study, an integrated plastic-contaminated environment gene, protein, taxa, and plastic degrading enzyme catalog (PDEC) was constructed. These catalogs contain 53,300,583 non-redundant genes and proteins, 691 metagenome-assembled genomes, and 136,654 plastizymes. Based on KEGG and eggNOG annotations, 42% of recognized genes lack annotations, indicating their functions remain elusive and warrant further investigation. Additionally, the PDEC catalog highlights hydrolases, peroxidases, and cutinases as the prevailing plastizymes. Ultimately, following multiple validation procedures, our effort focused on pinpointing enzymes that exhibited the highest similarity to the introduced plastizymes in terms of both sequence and three-dimensional structural aspects. This encompassed evaluating the linear composition of constituent units as well as the complex spatial conformation of the molecule. The resulting catalog is expected to improve the resolution of future multi-omics studies, providing new insights into plastic-pollution related research.

Toward a Circular Bioeconomy: Designing Microbes and Polymers for Biodegradation

“…16S rRNA gene amplicon sequencing and metagenomics enable the identification of polymer-degrading microbes in an environmental sample. − When a microbial community is exposed to a polymer, increases in the relative abundance of specific taxa can indicate their capability to utilize the polymer as a carbon source. These omics tools were employed to study the PET-degrading capabilities of microbial communities isolated from marine plastic debris in Wales, UK, and to investigate the degradation of biodegradable polymers by microbiomes isolated from the Tsurumi River in Japan .…”

Potential routes of plastics biotransformation involving novel plastizymes revealed by global multi-omic analysis of plastic associated microbes

“…These data can enable a better understanding of microbial interactions with these pollutants, yet there is a significant gap in terms of meta-analyses exploring the broader relationship between plastics and the functional response of their associated microbial communities (i.e., the plastisphere). Recent efforts have been made towards this aim with a portion of the available metagenomic data 24 , however these lack most of the available oceanic and river plastic-associated metagenomes; these locations are a primary destination for mismanaged plastic waste 25 . Additionally, these studies do not consider the available plastic degrading isolate genomes or other forms of ‘omic data such as transcripts or proteins, which are crucial to understanding how laboratory-based bioremediation efforts compare to the microbial communities in situ.…”