Alignment-Free Identification of Microplastic Bioremediation Potential Using K-mer Frequency Patterns

Abstract

To address the critical global challenge of microplastic pollution and the limitations of alignment-dependent genomic tools in analyzing fragmented environmental data, this study introduces an alignment-free computational framework for identifying microbial bioremediation potential. We established a standardized, multi-domain dataset encompassing Bacteria, Protists, Archaea, and Fungi, integrating metadata on polymer interactions to fill existing data gaps. Utilizing tetranucleotide frequency patterns (k=4), we developed a novel analysis method to isolate predictive genomic signatures, identifying C-rich motifs such as ‘CCCC’ as primary indicators of degradation capability.A statistical scoring model was subsequently implemented to rank candidate taxa, effectively prioritizing high-value organisms from complex metagenomes derived from plastic-associated microbial assemblages. Our approach demonstrates significantly reduced computational time and more sensitive than the older methods, identifying potential degraders that alignment techniques often miss. It connects the theoretical side of detecting functional genes with real-world environmental checks, creating a flexible tool to speed up finding new microbes for tackling plastic waste and restoring ecosystems.