In the southern Great Plains (USA), the encroachment of grassland ecosystems by Prosopis glandulosa (honey mesquite), a nitrogen-fixing tree, is widespread and has contributed to altered states of ecosystem structure and function. Mesquite encroachment often leads to increased above- and belowground plant biomass and enhanced stores of C and N in plants and soil. We hypothesized that changes in aboveground community composition and organic matter inputs would be reflected in the structure and functional capacity of the soil microbial community. Soil bacterial and fungal communities occurring beneath four dominant plant functional groups in a mesquite-encroached savanna (C₃ perennial grasses, C₄ midgrasses, C₄ shortgrasses, and mesquite) were characterized using a direct cloning and sequencing approach, and the functional gene capacity of these same communities was evaluated using the GeoChip functional gene microarray. 
Results/Conclusions

Similarity of operational taxonomic unit composition among vegetation-based clone libraries was low to moderate, ranging, on a scale of 0 to 1, from 0.034 to 0.276 among bacterial libraries and 0.399 to 0.620 among fungal libraries. The bacterial clone libraries were largely composed of Proteobacteria, Actinobacteria, Firmicutes, and Acidobacteria, and no significant differences were found with respect to their community structure using the parsimony test. Significant differences were detected, however, with respect to fungal community structure. The fungal community associated with mesquite was significantly different from those associated with all other vegetation types, harboring increased abundances of Zygomycota and uncharacterized fungi. Despite the substantial variation in productivity rates, growth form, phenology, and tissue chemistry known to exist among the four plant types, as well as the differences that were found with respect to fungal community composition, few significant differences in functional gene capacity were detected using the GeoChip. Gene probes were detected in similar numbers across all samples, their relative intensity occurred at similar levels, and they shared a common distribution across all gene types, suggesting that a high level of functional redundancy may occur among the portion of the soil communities examined. In combination, the results of the clone library characterizations and microarray analysis demonstrate that a substantial degree of overlap occurs with respect to the composition and functional capacity of the soil bacterial communities in this ecosystem; however, detectable differences do occur among the fungi. Such differences could be important in shaping the interactions of plant species with their biological and physical environments as well as the biogeochemical cycling of nutrients, successional processes, and other ecosystem attributes.