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Rapid urbanisation and increasing industrial activities generates large volumes of wastewater which requires treatment prior to being released back into the environment. Conventional treatments require heavy energy consumption and produce carbon dioxide. Valorisation of wastewater effluents using microalgal treatments has been receiving attention for the past decades. Wastewater represents an alternative source of nutrients to grow microalgae which provides a solution for wastewater treatment. Nevertheless, microalgal cultures are still challenged by high cost and low productivity. In the present study, a novel approach was incorporated by integrating microalgal wastewater treatment with carrier systems to favour the growth of both attached and suspended cells of T. obliquus. This study has found that T. obliquus was able to uptake nutrients from municipal wastewater while the addition of 12.5% fill ratio carrier systems produced higher microalgal cell productivity (1.2. 106 cells ml-¹ d-¹). Besides, MinION nanopore sequencing was conducted to assess the impact of microalgal and carriers treatment on wastewater bacterial communities. It was found that treating wastewater with microalgae had changed bacterial communities when compared to the ones found in the original wastewater. The microbiome of the biofilms and suspended cultures was also studied. Interestingly, it was found that attached microbial communities differed to the ones growing suspended within the same cultures. In short, the addition of 12.5% fill carrier ratio increased microalgal productivity while stimulating changes in the algal microbiome.