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Background  The utilization of  Chlorella  for the dual goals of biofuel production and wastewater nutrient removal is highly attractive. Moreover, this technology combined with flue gas (rich in CO 2 ) cleaning is considered to be an effective way of improving biofuel production. However, the sterilization of wastewater is an energy-consuming step. This study aimed to comprehensively evaluate a cost-effective method of culturing  Chlorella pyrenoidosa  in unsterilized piggery wastewater for biofuel production by sparging air or simulated flue gas, including algal biomass production, lipid production, nutrient removal rate and the mutual effects between algae and other microbes.    Results  The average biomass productivity of  C. pyrenoidosa  reached 0.11 g L −1  day −1 /0.15 g L −1  day −1  and the average lipid productivity reached 19.3 mg L −1  day −1 /30.0 mg L −1  day −1  when sparging air or simulated flue gas, respectively. This method achieved fairish nutrient removal efficiency with respect to chemical oxygen demand (43.9%/55.1% when sparging air and simulated flue gas, respectively), ammonia (98.7%/100% when sparging air and simulated flue gas, respectively), total nitrogen (38.6%/51.9% when sparging air or simulated flue gas, respectively) and total phosphorus (42.8%/60.5% when sparging air or simulated flue gas, respectively). Culturing  C. pyrenoidosa  strongly influenced the microbial community in piggery wastewater. In particular, culturing  C. pyrenoidosa  enriched the abundance of the obligate parasite Vampirovibrionales, which can result in the death of  Chlorella .    Conclusion  The study provided a comprehensive evaluation of culturing  C. pyrenoidosa  in unsterilized piggery wastewater for biofuel production. The results indicated that this cost-effective method is feasible but has considerable room for improving. More importantly, this study elucidated the mutual effects between algae and other microbes. In particular, a detrimental effect of the obligate parasite Vampirovibrionales on algal biomass and lipid production was found.    Electronic supplementary material  The online version of this article (10.1186/s13068-019-1407-x) contains supplementary material, which is available to authorized users.

Comprehensive evaluation of a cost-effective method of culturing Chlorella pyrenoidosa with unsterilized piggery wastewater for biofuel production