The root-soil interface (i.e. rhizosphere) is zone of key nutrient transformation and intense biological activity. Recent studies suggest that root-microbe interactions may have an important influence on ecosystem responses to environmental changes, such as rising atmospheric CO₂ concentrations ([CO₂]). Projecting how these interactions and thus soil processes may respond to environmental change requires an understanding of the composition and function of rhizosphere microbial communities. However, our understanding of factors influencing spatial and temporal variation in soil microbial communities remains limited, partly because most molecular tools are not well-suited for comparing multiple samples and for sequencing at great depth, which are critical when studying potentially heterogeneous soils and microbial communities characterized by low evenness and high richness. Here we use quantitative PCR (qPCR) and pyrosequencing of two genes (the V3 region of 16S rDNA and the amoA gene), along with biogeochemical assays, to assess the influence of plant type (maize vs. soybean) and [CO₂] (~380 vs. ~550 ppm) on the abundance, composition, and function of soil microbial communities involved with nitrification using FACE (free-air concentration enrichment) technology in a replicated experiment in central Illinois during the 2006 and 2008 growing seasons.  

Results/Conclusions

Significantly greater copy numbers of the archaeal 16S rDNA gene were found in the rhizosphere of soybean than maize during both years. In contrast, no difference in copy number of bacterial 16S rDNA was found between plants, and there was no influence of [CO₂] on 16S rDNA copy number for either microbial domain or plant. Significant positive correlations were obtained between copies of archaeal 16S rDNA and soil nitrite concentrations and potential nitrification rates with antibiotics incorporated. Ratios of archaeal/bacterial amoA copies were ~10:1. These results suggest that archaea are important ammonia oxidizers in this agroecosystem, and we thus focused our sequencing efforts on archaeal genes. Nearly all recovered sequences were members of the phylum Crenarchaeota. PCA indicated archaeal community composition differed significantly between [CO₂] treatments beneath soybean, although this difference was less than between maize and soybean. We hypothesize that greater net mineralization and/or release of fixed nitrogen from roots and nodules in the rhizosphere of soybean leads to greater soil ammonium availability and increased nitrification rates by unique archaeal communities. These results suggest that the influence of changes in [CO₂] on the structure and function of rhizosphere communities will be mediated by aboveground community composition.