We examined the relationship between the decomposition of seven litter and root substrates, soil N availability, and populations of soil biota in field microcosm for 13 months. Most of the variation of N loss from the substrates was a function of initial substrate N concentration. Small portions of the variation of substrate mass loss and soil inorganic N were explained by initial substrate N concentration. Most of the variation of substrate mass losss, soil inorganic N, and soil biota populations was explained by differences between the decomposition of roots vs litter and of annual roots vs perennial roots. N loss from roots was more rapid than from litter. Mass of bacteria plus yeast in root microcosms was lower, nematode populations were higher, and the potential N mineralization rate at 9 months was higher than in litter microcosms. These results suggest that organic matter turnover in root microcosms was more rapid than in litter microcosms. Mass loss from annual roots was higher but N loss was lower than from perennial roots. Bacteria plus yeast mass in annual-root microcosms was lower, nematode populations were higher, and soil inorganic N was less than in perennial-root microcosms. The addition of annual roots reduced inorganic N concentrations below that of the unamended controls and the other substrate treatment on month 6 and 9 samples indicating that annual-root decomposition led to N immobiliaztion or dentrification. The addition of litter or perennial-roots increased soil inorganic N concentrations above the unamended control in the month 9 samples. The decomposition of N-poor annual plant roots may significantly reduce N availability in desert ecosystems.