Eco-evolutionary adaptations of plastic-degrading microbes

Abstract

the enduring nature, widespread dispersion, small particle size, often challenging to detect and characterize for further remediation approaches. Its potential toxicity, as well as adverse effects on our ecosystems, biodiversity, and human health makes it a global crisis and calls for robust bioremediation approaches. Although physical and chemical degradation processes contribute to plastic breakdown in natural settings, microbial biodegradation has emerged as a promising and eco-friendly strategy for managing plastic waste, leveraging plastic-degrading proteins (PDPs) encoded in microbial genomes that enable the utilization of plastic as a carbon source. Despite growing recognition of microbial biodegradation’s capabilities, which offers a sustainable remediation paradigm, a comprehensive understanding of plastic-degrading proteins across microbial taxa and their eco-evolutionary dynamics is still lacking. Moreover, a comprehensive understanding of the distribution and functional diversity of PDPs across varied environmental niches remains elusive, largely due to limitations in comparative genomic analyses. Studies have revealed the presence of plastic-degrading genes in diverse microbial species, yet the resolution of these genomic studies are often constrained by incomplete reference databases and the complexity of microbial consortia. This limitation necessitates advanced bioinformatic approaches to map the global prevalence and efficiency of PDPs, thereby addressing the current knowledge deficit. Here, we present the Plastic-Degrading Clusters of Orthologous Groups (PDCOGs) database (https://phylobone.com/microworld/PDCOG), comprising 625,616 potential plastic-degrading proteins (PPDPs) from free-living prokaryotes, organized into 51 orthologous groups. The extensive database of PDCOGs enable the systematic analysis of microbial plastic-degrading capacity across ecosystems and phylogenetic lineages, along with a reliable predictive tool to identify potential degraders. Remarkably, PPDPs constitute ~3.5% of all prokaryotic proteins, with over 95% of species carrying the potential to biodegrade at least one polymer type. This resource provides a genomic tool for exploring the ecological and evolutionary significance of PDPs, while mitigating extensive enzyme testing in controlled conditions and supports future efforts of synthetic biology applications to mitigate the global MNPP crisis.