Understanding belowground biogeochemical C and N processes in different ecosystems is important to predict C storage potential. A field project was initiated in 2004 with three treatments: big blue stem (BB) (Andropogon gerardii), tilled (CT) grain sorghum (Sorghum bicolor), and no-till (NT) grain sorghum. The objectives were to (1) evaluate changes in belowground C pools; (2) evaluate differences in soil microbial communities; and (3) measure differences in plant and microbial grazing nematodes in each of the three ecosystems. Soil samples were taken at the beginning and end of each growing season in 2004-2005. Microbial biomass C was not different after the first growing season, with values of 282 mg C kg-1 soil. Soil disturbance resulted in significant changes (CT>NT>BB) in the level of gram(+) bacteria phospholipid fatty acid (PLFA) i16:0 with values of 5.8, 5.3, and 4.8 mole% for CT, NT, and BB, respectively. The CT ecosystem also had higher levels of gram(+) bacteria and actinomycetes PLFA a17:0, i17:0, 10Me17:0, and 10Me18:0 than NT or BB. There was no difference between NT and BB. After the first growing season, there was double the amount of herbivorous nematodes in NT and CT as compared to BB, while microbial grazing nematodes were twice as abundant in BB as compared to NT or CT. We were also able to detect 13C signature differences in nematodes, with some types having a transitional C4 to C3 signal, indicating a more direct role in C cycling; others, however, were shown to show a C3 signal, indicating a more indirect role in C cycling. For example, Filenchus taxa had a significantly more enriched 13C signature than Aphelenchus or Cephalobidae taxa with values of -15, -25, and -27‰ δ13CVPDB. Data show that ecosystem disturbance and plant composition play an important role in determining belowground biology.