Soil Nitrification Properties and Bacterial and Archaeal Nitrifier Communities Vary by Land Management.

Ammonia oxidation is the first step in nitrification, the microbially mediated biogeochemical process that determines the balance between soil nitrate and ammonium.  Both bacterial and archaeal organisms are capable of oxidizing ammonia, but the archaeal contribution to soil nitrification is unclear.  We examined the abundance (using quantitative PCR) and composition (using terminal restriction fragment length polymorphism (T-RFLP)) of amoA genes in ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), and soil nitrification potential (NP) in the presence of a variety of nitrification inhibitors in soils from a range of land uses and contrasting N input levels (Douglas-fir or red alder forest, heavily or lightly grazed pasture, actively cropped and fallow cultivated soils).  Pasture soils had low ambient NP and AOB abundance (respectively, 2.4±0.7 μg NO₂^-+NO₃^--N g^-1 dry soil d^-1, 2.2±1.6 x 10⁵ copies g^-1 dry soil) in comparison to cultivated (17.5±6.4, 8.9±1.9 x 10⁵) and forest soils (6.4±1.3, 1.3±0.5 x 10⁶).  However, pasture soils were the least sensitive to NP inhibition.  In the presence of the copper chelator allylthiourea (ATU, 100μM), NP was reduced by 95% in forest soils, by 92-95% in cropped and fallowed soils and by 47% in pasture soils.  NP was completely inhibited by acetylene in all soils; however, cropped, fallowed and pasture soils recovered NP activity upon the removal of acetylene.  In the presence of bacterial protein synthesis inhibitors kanamycin + gentamycin, NP recovery from acetylene inhibition was reduced by 100% in cropped soils, 70% in fallowed soils, and by 0% in pasture soils.  NP of forest soils did not always recover after acetylene removal, even with no antibiotics present.  AOA population size did not vary significantly, but AOA community composition was distinct in the forest, pasture and cultivated soils.  AOB communities were distinct in forest and cropped soils, but were similar in fallow and pasture soils.  In sum, NP inhibition susceptibility and amoA gene community composition varied significantly among the different soils, with contrasting patterns in bacterial and archaeal diversity and in total and non-bacterial NP.  At a landscape scale, management conditions and unique niche preferences of AOA and AOB may influence the relative importance of each group’s contribution to soil nitrification activity.