While often overlooked in photosynthetic organisms, the mitochondria also play critical roles in energy balance. Two nitrogen-related pathways are relevant and they may also change under ammonium () nutrition compared with nitrate () nutrition. First, in diatoms, and likely some other algae, there is a urea cycle. The long-known function of the urea cycle in animals is to excrete excess nitrogen produced by amino acid catabolism; like photorespiration, the urea cycle had long been considered a waste pathway. However, in diatoms the urea cycle appears to play a role in exchange of nutrients between the mitochondria and the cytoplasm, and potentially the plastid and may help to regulate ammonium metabolism. Because of this cycle, marine diatoms, in contrast to chlorophytes, also have acquired a mitochondrial urea transporter and, in fact, based on bioinformatics, a complete mitochondrial GS-GOGAT cycle has been hypothesised.
