Although microalgal-bacterial co-cultures have been largely investigated for nutrient removal, their application in treating real wastewaters is still debatable because effluent systems contain complex bacterial communities that might influence the overall bioremediation. We, therefore, verified the interaction effects of Tetradesmus obliquus IS2-Variovorax paradoxus IS1 co-culture and the native bacterial communities in wastewaters, collected from dairy farm and poultry slaughterhouse, during effluent bioremediation. Co-culturing of the two microbial strains in non-sterile wastewaters alone resulted in significant removal of total N (>92%), PO43--P (>89%) and COD (>84%) as well as increased production of ROS and neutral lipids, indicating their significant mutualistic interactions with the native bacterial communities for efficient bioremediation of wastewaters. Analysis of 16S rRNA gene-based community data in wastewaters revealed selective enrichment of Firmicutes and Actinobacteria, resulting in enhanced microalgal growth and nutrient removal. The findings of this novel study suggest that microalgal-bacterial co-cultures mediate interspecies interactions for a shift in population dynamics of the indigenous bacteria in wastewaters to facilitate enhanced bioremediation of effluents with sustainable production of biomass and biodiesel. All rights reserved, Elsevier.