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The microbiological diversity of cultivable bacteria was analyzed in an aerated facultative lagoon. The removal of specific compounds and measures of pollutant load was evaluated with isolated native bacteria, selected and identified in kraft cellulose effluent. The system was operated with an organic loading rate of 0.2 kgCODm-3d-1 for 60 days. Analyses of the fluorescence excitation-emission matrix, acute ecotoxicity, and microbiology were performed. Bioaugmentation tests were done to emphasize the removal of color, using promising species. The removals of biochemical oxygen demand, chemical oxygen demand, and total organic carbon in AFL were 94%, 51%, and 41%, respectively. Regarding color, removal was up to 4%, and the total phenolic compounds were not removed through biological treatment. The treatment also decreased turbidity by 94% and lignin derivatives by 12%. The bacteria identified through NCBI-BLAST and statistical similarity totaled 9 species in the cellulose effluent, three of which have the potential for color treatment: Bacillus cereus, Bacillus thuringiensis, and Paenibacillus sp. The Bacillus cereus combined with biomass removed color (69%), total phenolic compounds (37%), and compounds derived from lignin (53%). These species are promising for removing specific parameters combined with biomass from biological AFL treatment systems.