Bioremediation of Chlorpyrifos Contaminated Soil: Microcosm Investigation and 16S rRNA Gene Amplicon Sequencing

ABSTRACT This study describes the isolation and characterization of two biofilm‐forming bacterial strains, Pseudomonas aeruginosa MD3 and Bacillus toyonensis LD07, capable of degrading chlorpyrifos. These isolates demonstrated remarkable phenotypic plasticity, maintaining biofilm formation across varying pH, temperature and salinity levels. To maximize microbial stability and metabolic efficiency, sugarcane bagasse was utilized as a support matrix. Analytical characterization (EDX, BET and XRD) confirmed that the bagasse possesses a highly porous architecture, serving as a protective scaffold and an auxiliary carbon source for synergistic co‐metabolism. A bio‐product formulated via solid‐state fermentation on this matrix exhibited exceptional bioremediation efficacy, eliminating 99% of chlorpyrifos at an extreme concentration of 4500 ppm within 35 days. Furthermore, 16S rRNA gene amplicon sequencing of coffee‐growing soils across different treatments (natural control, pesticide‐stressed and 10% bio‐product amended) with accession numbers PRJNA1529359 revealed distinct shifts in microbial community dynamics. While the taxonomic landscape was broadly dominated by Bacillota, Pseudomonadota and Actinomycetota, the bio‐product amendment caused P. aeruginosa and B. toyonensis to become the dominant taxa. Ultimately, these insights underscore the viability of cost‐effective agricultural by‐products for cell immobilization and highlight metagenomics as a powerful predictive framework for monitoring the remediation of anthropogenically stressed ecosystems.