Isolation of polyethylene‑modifying soil bacteria from Egypt and Genome-based functional characterization of Sphingobacterium spiritivorum ASb3.

Polyethylene (PE) has been widely utilized, resulting in its accumulation in the environment due to its recalcitrant nature. In this study, seven bacterial isolates from garden soil and garbage dumps in Cairo and Giza, Egypt, grew on PE films as the sole carbon source, reduced PE weight, and formed biofilms. Scanning electron microscopy revealed surface perforations, while Fourier transform infrared spectroscopy detected new carbonyl and hydroxyl groups. Based on 16 S rRNA gene sequencing and phylogeny, the isolates exhibited high similarity to Sphingobacterium spiritivorum, Rhodococcus pyridinivorans, Pseudomonas putida, Ectopseudomonas mendocina, Zobellella taiwanensis, Achromobacter mucicolens, and Pseudomonas sp. To the best of our knowledge, S. spiritivorum, E. mendocina, Z. taiwanensis, and A. mucicolens have not previously been reported in PE biodeterioration studies. S. spiritivorum was selected for whole-genome sequencing. Comparative functional genomics revealed variation in enzyme families potentially associated with oxidation, hydrolysis, and β-oxidation. CAZy profiling identified carbohydrate-active enzymes, including proteins carrying predicted signal peptides. KEGG reconstruction supported alcohol- and aldehyde-to-fatty-acid conversion, fatty-acid activation, and β-oxidation-related metabolism. SignalP predicted secretion signals in selected proteins, while local synteny analysis showed conserved organization of these loci in Sphingobacterium strains. Overall, these findings suggest the potential of these isolates for PE biodeterioration.