Though the presence and location of the systems which fix and assimilate nitrogen within cyanobacteria are fairly well known, ammonium metabolism and transport within cyanobionts of cycads has been somewhat of a puzzle, and the exact details of how and in what form nitrogen is transferred from symbiont to host still remains a question for investigation. A few studies have been conducted, however, that may help to solve the puzzle. Both cycad roots and their symbiotic cyanobacteria contain functional GS/GOGAT systems for the assimilation of ammonia into amino acids. In research by Pate et al. (1988) translocation of nitrogen within the xylem of cycad coralloids was found to be in the form of glutamine, glutamic acid or citrulline, depending on the species, whereas ammonium was never shown to be transported from the coralloids. Their findings indicate that the process of ammonium metabolism may be shared by the cycad and it's symbiont. They concluded that the primary route for ammonium assimilation is most likely via glutamine synthetase, and that if the GOGAT system is operational, it is probably compartmentalized away from glutamine synthetase. Rai et al. (2000) provide evidence that cycad symbionts were incapable of metabolizing ammonia because of the absence of one of the ammonium transport systems responsible for the uptake of ammonium for assimilation via glutamine synthetase. Microaerobiosis may be responsible for repression of the transport system. More work needs to be done to identify the nitrogen solutes leaving the cyanobacteria, and at what stages and locations ammonia and it's primary products of assimilation are involved.

Operation of the GS/GOGAT sytem requires an expenditure of energy. One ATP and two reducing equivalents are required for the net formation of one glutamate unit. Fixed carbon is required as an energy source for the production of ATP. In addition, the GS/GOGAT system of ammonia assimilation is dependant on a supply of carbon skeletons, or reducing equivalents, especially alpha-ketoacids. These are the compounds onto which the fixed nitrogen is placed, forming the amino acid glutamate, which is a precursor to synthesis of other amino acids (Guerrero and Lara, 1987). These are most likely provided by the cycad host. The coralloid roots inhabited by cyanobacteria are filled with mucilage consisting of mixed polysaccharides of host origin. This may be the source of the nutrients and reducing equivalents required by cyanobacteria for nitrogen assimilation (Rai et al., 2000)