| description |
The agricultural application of nitrogen fertilizer has profoundly altered the terrestrial nitrogen system, with high economic and environmental costs. Ammonia not assimilated by plants or soil biota is nitrified by the combined activities of ammonia- and nitrite-oxidizing microorganisms, converting relatively immobile ammonia to highly mobile nitrate. This contributes to the loss of nitrogen and other soil nutrients, and the production of atmospherically active nitrogen oxides. Thus, mitigating these costs through better management of nitrogen is of critical importance to a growing bioenergy industry. To better resolve the impact of agricultural management on nitrifying populations, amplicon sequencing (“tag sequencing”) of genetic markers associated with ammonia- and nitrite-oxidizing taxa (ammonia monooxygenase-amoA, nitrite oxidoreductase-nxrB, respectively) was conducted on samples from long-term managed and nearby native soils in Eastern Washington, USA. Native nitrifier population structure was altered profoundly by management. The native ammonia-oxidizing archaeal (AOA) community (comprised primarily of Nitrososphaera subcluster 2.1, Nitrososphaera sister subclusters 1.1 and 2) was displaced in managed soils by populations of Nitrosopumilus, Nitrosotalea, and different assemblages of Nitrososphaera (subcluster 1.1, and un-associated lineages of Nitrososphaera). A similar displacement of major ammonia-oxidizing bacterial (AOB) taxa was also associated with management, with native groups of Nitrosospira (cluster 2 related, cluster 3A.2) displaced by Nitrosospira clusters 8B and 3A.1. Although a shift in nitrite-oxidizing bacteria (NOB) was also correlated with management, altered distribution patterns could not be linked exclusively to management. Additionally, nxrB sequences observed in native soils displayed only distant relationships to other NOB, indicating significant unrecognized breadth of phylogenetic diversity within this group. |