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The study evaluated the effects of the probiotic BioPlus® PS on shrimp-tilapia polyculture pond soil using an integrated approach of physical-chemical analysis, metagenomics, and Pfeiffer circular chromatography. Soil was collected from a shrimp farm immediately after harvest and distributed in 75 plastic boxes with a useful volume of 1 L. The probiotic was applied once at the following doses in triplicate: 0, 150, 300, 1000 and 2000 g ha−1. After fifteen days, we verified a significant reduction in the content of organic matter, oxidizable carbon and potential acidity. Metagenomics demonstrated that the probiotic increased α diversity, while decreasing the relative abundance of Vibrio parahaemolyticus. Pfeiffer chromatography showed that the two samples that received higher doses showed characteristics associated with higher quality soils and higher enzymatic activity. Our results suggest that the application of the probiotic BioPlus® PS in shrimp pond soils has bioremediation potential and can positively modulate the soil microbiome. [ABSTRACT FROM AUTHOR]