Paired carbon and nitrogen metabolism by ammonia‐oxidizing bacteria and archaea in temperate forest soils

Nitrification is a biologically mediated nutrient transformation, which influences the availability of inorganic nitrogen to other microorganisms and plants and mediates mobility of nitrogen in the environment. Ammonia oxidation, the rate‐limiting step of nitrification, is performed by two groups of microbes: ammonia‐oxidizing archaea (AOA) and bacteria (AOB) that couple this process with the chemoautotrophic fixation of carbon. Due to the energetic constraints on these organisms, both AOA and AOB likely oxidize large amounts of ammonia to fix relatively small amounts of carbon in natural environments. Here we sought to investigate paired carbon and nitrogen metabolism by AOA and AOB in forest soils. To accomplish this objective, we used quantitative polymerase chain reaction (qPCR) to quantify changes in AOA and AOB ammonia monooxygenase subunit A ( amoA ) genes during in situ incubations. We then used qPCR data alongside AOA and AOB community profiles at each site to convert changes in amoA gene copy number to carbon accumulation by each group. Finally, we regressed group‐specific carbon accumulation values against observed values of NO 3 − accumulation to establish cross‐site relationships between ammonia oxidation and carbon accumulation by each group. By this procedure we estimated that forest soil AOA oxidized 59.8 μg of ammonia‐N to add 1 μg of carbon to biomass, while forest soil AOB oxidized 58.2 μg of ammonia‐N to add 1 μg of carbon to biomass. These findings represent the first field‐based estimates of paired carbon and nitrogen metabolism by these organisms, and could be used to inform microbially explicit models of nitrification in forest soils.