Response of archaeal communities in the rhizosphere of maize and soybean to elevated atmospheric CO₂ concentrations

Background: Archaea are important to the carbon and nitrogen cycles, but it remains uncertain how rising atmospheric carbon dioxide concentrations ([CO₂]) will influence the structure and function of soil archaeal communities. Methodology/Principal Findings: We measured abundances of archaeal and bacterial 16S rRNA and amoA genes, phylogenies of archaeal 16S rRNA and amoA genes, concentrations of KCl-extractable soil ammonium and nitrite, and potential ammonia oxidation rates in rhizosphere soil samples from maize and soybean exposed to ambient (~385 ppm) and elevated (550 ppm) [CO₂] in a replicated and field-based study. There was no influence of elevated [CO₂] on copy numbers of archaeal or bacterial 16S rRNA or amoA genes, archaeal community composition, KCl-extractable soil ammonium or nitrite, or potential ammonia oxidation rates for samples from maize, a model C₄ plant. Phylogenetic evidence indicated decreased relative abundance of crenarchaeal sequences in the rhizosphere of soybean, a model leguminous-C3 plant, at elevated [CO₂], whereas quantitative PCR data indicated no changes in the absolute abundance of archaea. There were no changes in potential ammonia oxidation rates at elevated [CO₂] for soybean. Ammonia oxidation rates were lower in the rhizosphere of maize than soybean, likely because of lower soil pH and/or abundance of archaea. KCl-extractable ammonium and nitrite concentrations were lower at elevated than ambient [CO₂] for soybean. Conclusion: Plant-driven shifts in soil biogeochemical processes in response to elevated [CO₂] affected archaeal community composition, but not copy numbers of archaeal genes, in the rhizosphere of soybean. The lack of a treatment effect for maize is consistent with the fact that the photosynthesis and productivity of maize are not stimulated by elevated [CO₂] in the absence of drought.