Analysis of PLA-degrading enzyme from metagenome-assembled genomes and single-cell amplified genomes using TreeSAPP
Abstract
Since the global production of polyester microplastics is expected to grow, there is an urgent need to understand its fate in the ultimate sink: the marine environment. Global temperature rise and temporal oxygen minimum zone spread will likely influence the community composition of marine prokaryotes which adhere to microplastic polyester particles and which carry genes for polyester degradation. Polylactic acid (PLA), a biodegradable polyester derived from renewable resources, is a leading candidate for the replacement of traditional petroleum-based polyesters, with a simple structure to represent degradation capacity for polyesters as a class. To decipher the microbial community capable of polyester degradation in a future ocean scenario, a phylogenetic reference package for PLA-degrading enzymatic activity (PLAase), with sequences for an enzyme known for PLA degradation and promiscuous activity for multiple polyesters, was developed using the Tree-based Sensitive and Accurate Phylogenetic Profiler (TreeSAPP). Metagenome-assembled genomes (MAGs) and single-cell amplified genomes (SAGs) for a seasonally anoxic fjord, Saanich Inlet, were then screened for phyla containing PLAase genes, using the PLAase reference package, at different depths and correlated against oxygen. Overall, our results revealed a widespread phylogenetic distribution of PLAase genes and transcripts. Additionally, total abundance of PLAase-containing phyla was found to vary with depth in the water column, displaying a general decrease in abundance with increasing depth. Certain phyla, most notably Proteobacteria, were higher in relative abundance, and this pattern was consistent throughout the length of the water column, suggesting that these phyla may have more active PLA-degrading roles. Analysis of geochemical data from the Saanich Inlet showed fluctuations in O2, CH4, H2S, NH4, NO2, and NO3 levels with respect to depth. Although no clear trends were noted between these variables and abundance of PLAase-containing bacterial phyla, specific phyla were identified within a seasonally anoxic depth profile, indicating a possible link between PLAase activity and oxic environments.
