Sequestering carbon in soils may be one method to reduce the concentration of carbon dioxide in the atmosphere. We measured inorganic and organic carbon, bacterial biomass and structural community diversity in southern Idaho soils having long term land use histories that supported native sagebrush vegetation (NSB), irrigated moldboard plowed crops (IMP), irrigated conservation (chisel) tilled crops (ICT) and irrigated pasture systems (IP). Organic carbon in soil decreased in the order IP>ICT>NSB>IMP. We use our findings to estimate the organic carbon, potentially sequestered if the use of irrigated agriculture were increased. We also use our findings to estimate inorganic and total carbon, potentially sequestered if the use of irrigated agriculture were increased. If irrigated agricultural land was expanded by10 percent worldwide and NSB were converted to IMP, a possible 2.78 percent of the total carbon, emitted in the next 30 years could potentially be sequestered in soil. If irrigated agricultural land was expanded by 10% worldwide and NSB were converted to ICT, a possible 1.87 percent of the total C emitted in the next 30 years could be sequestered in soil. We used molecular methods to determine the bacterial diversity in all soils. Bacterial diversity was the greatest in the NSB 5-15 cm soil and lowest in the IMP soil. ICT and IP increased soil C and to some extent increased bacterial diversity relative to IMP. Irrigated agricultural systems can produce twice the yield compared to non-irrigated land. Irrigation also favors economic sustainability and increasing soil C relative to native semi arid or arid sites, but decreases bacterial diversity compared to native sagebrush soils. Irrigation decreased soil bacterial diversity compared to native sagebrush soils, but because irrigated agriculture produces higher yields, less land needs to be put into production relative to rain-fed agriculture. Altering land use practice to produce crops on high output irrigated agriculture, while returning less-productive rain-fed agricultural land to temperate forest or native grassland, could reduce atmospheric carbon dioxide.