Note
The objective of this chapter is to detail two strategies important in order to overcome constraints inherent in flow cytometric analysis of marine microalgae and sponge cells. The two strategies are: (I) selective cell enrichment, employing physical separation techniques, and (2) selective signal enhancement, optimizing the optics. Specifically, we detail cell dissociation and density gradient separation of sponge cells, concentration of microalgae from seawater samples, determination of absolute (vs relative) abundance of microalgal subpopulations, and a metabolic index protocol that can be used for both microalgae and sponge cells.