The Haber-Bosch process creates ammonia (a solution that can then be oxidized to create nitrates and nitrites) by passing nitrogen from the air and hydrogen, currently stripped from hydrocarbons, over an iron catalyst. If a "hydrogen economy" were to actually appear this same H2 would be used to produce ammonia (and you could actually cut out several steps in the current process that are necessary to eliminate any trace of carbon monoxide during the conversion of methane into H2, CO2, and water.) If alternative energy can be used to create hydrogen in a cost-effective manner then you are golden as far as fertilizer is concerned.