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Vegetation communities with high soil carbon (C) inputs, e.g. grassland ecosystems, promote N protection via microbial communities in the soil whereas communities with low soil C inputs, e.g. desert scrub ecosystems, promote nitrification and are therefore susceptible to N loss. This study examines this relationship more closely by assessing the effects of two vegetation-soil systems on soil N transformation, in a grassland-desert scrub in Cuatro Cienegas Basin, Mexico. Metrics used in our study include: the belowground biomass of C, N and phosphorus (P) in both vegetation types; the availability of C, N and P in the soil; and the potential transformation of these nutrients by the microbial community which was characterized by 16S rRNA clone libraries. We found: (1) a higher NI4+ and microbial N concentration in the grassland soil than in the desert scrub soil, and (2) a different bacterial soil communities between both vegetation-soil systems. These findings suggest an interrelationship between nutrients in the belowground biomass, soil nutrient dynamics, and the soil bacterial community whereby grasslands promote a closed system that conserves N, whereas desert scrub vegetation exhibits an open system that sheds N. (C) 2014 Elsevier Ltd. All rights reserved.