The present invention relates to the continuous process of sequestration of nutrients from waste effluents released from gas fermentation plants or green-house gases emission managing plants by novel Thraustochytrids. Particularly this invention relates to the methods and systems to enhance sequestration rate and productivity of the process. This invention also relates to rapid biotransformation of nutrients present in waste effluents into high value omega-3 fatty acids like Docosahexaenoic acid (DHA), Docosapentaenoic acid (DPA), Eicosapentaenoic acid (EPA) and lipids for biodiesel. This disclosure is about means of processing of waste streams and producing value added products out of it.