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To achieve strong, successful and commercial aqua-biotechnological microalgae applications, screening, isolation, molecular identification, and physiological characterizations are needed. In the current study, a native cyanobacteria strain Arthrospira platensis NIOF17/003 was isolated from the surface water of El-Khadra Lake, a saline-alkaline lake located in Wadi El-Natrun, Egypt. The cyanobacterium was phylogenetically identified by 16S rRNA molecular marker and deposited in the GenBank database (accession number MW396472). The late exponential phase of A. platensis NIOF17/003 was reached at the 8th day of growth using Zarrouk medium, with a recorded dry weight (DW) of 0.845 g L−1. The isolated strain showed 52% of protein, 14% of carbohydrate, biomass productivity of 143.83 mg L−1 day−1, 8.5% of lipid, and lipid productivity of 14.37 mg L−1 day−1. In general, the values of cetane number, iodine value, cold filter plugging point (52.9, 85.5 g I2/100 g oil, and −2.2 °C, respectively) of the isolated fatty acid methyl esters are in accordance with those suggested by international standards. Besides, applying algal-free lipid (FL) as biodiesel byproduct in the production of rotifer (Brachionus plicatilis) revealed that a 0.6 g L−1 FL significantly increased the rotifer population females carrying eggs, confirming that FL can be used efficiently for B. plicatilis production. The current study concluded that the new isolate A. platensis NIOF17/003 is a promising strain for double sustainable use in biodiesel production and aquaculture feed.

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