Abstract
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 NO3− 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.
Highlights
Ammonia oxidation is the rate-limiting step of nitrification, a microbially mediated nutrient transformation that serves as a bottleneck for nitrogen loss in terrestrial ecosystems (Vitousek et al 1979)
Day 0 and day 30 estimates of ammonia-oxidizing archaeon (AOA) and Ammonia-oxidizing bacteria (AOB) ammonia monooxygenase subunit A (amoA)/g dw of soil are presented in Fig. 1a and b, respectively
We suspected that unamended net nitrification incubations would lead to growth of AOA and AOB as well due to the increased ammonium availability to these organisms (Norman and Barrett 2014 showed that this occurred in one soil from a reference watershed at Coweeta)
Summary
Ammonia oxidation is the rate-limiting step of nitrification, a microbially mediated nutrient transformation that serves as a bottleneck for nitrogen loss in terrestrial ecosystems (Vitousek et al 1979). The first ammonia-oxidizing archaeon (AOA) was isolated in 2005 (Konneke et al 2005) and these organisms were soon found to co-occur with AOB in soils from a range of temperate biomes (Leininger et al 2006). Both AOA and AOB use the energy they acquire from ammonia oxidation to fuel chemoautotrophic growth. We sought investigate the explicit links between carbon and nitrogen metabolism in natural temperate forest soil AOA and AOB during in situ net nitrification incubations. Estimating how much carbon each group accumulates from ammonia oxidation in the field allowed us to assess the relative importance of each group to this ecosystem-level process and investigate group-level differences in paired carbon and nitrogen metabolism in temperate forest soils
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