Diversity of ammonia-oxidizing archaea in soils under managed and native conditions

Abstract

Ammonia oxidizing archaea (AOA) contribute to a significant portion of ammonia oxidation in soil. These organisms have significant impacts on plant proliferation, as well as production of fugitive gases. AOA community distribution patterns are influenced by multiple factors, of which, biogeography has emerged as an important variable. Developing an understanding of community differences in AOA amid differing land management types may provide tools to understand differences in N use efficiency and other, broader impacts of AOA on soil and atmospheric biogeochemistry. The goal of this study was to assess whether agriculturally cropped (managed) soils displayed shifts in AOA community diversity in contrast to native (non-managed) soils located in close proximity. Soil was collected from two sites in eastern Washington with similar climate and precipitation patterns, but representing two different soil series. At both sites soil was collected from the surface horizon (0-15 cm) of the adjacent native shrub-steppe (dominated by sagebrush and bunchgrass) and from plots cultivated in switchgrass. AOA communities were evaluated by terminal restriction fragment length polymorphism (TRFLP) targeting subunit A of the Archaeal ammonia monooxygenase and analyzed using multivariate statistical approaches. The AOA communities were also evaluated via sequenced clone libraries where similarity was compared using chi-squared statistical tests. At both the slightly alkalkine (Prosser) and slightly acidic (Paterson) agricultural sites, significant differences in AOA community diversity were observed based on the contribution of differing terminal restriction fragments (TRFs) to managed and native soils based on analysis of similarity (ANOSIM, R value greater than 0.6, p value less than 0.05). In contrast, native soils displayed higher similarity to one-another, despite significant spatial separation, than either agriculturally influenced site. In addition, a higher number of TRFs were observed in the non-managed areas, indicative of a more diverse AOA community. The sequences clone libraries targeting the AOA amoA gene clarified the TRFLP findings and indicated a much greater diversity of Nitrososphaera clades in the native site, but an absence of the genera Nitrosopumilus and Nitrosotalea, which were both observed in the cultivated site. At the slightly alkaline site, similar differences between native and cultivated AOA communities were also observed. At the slightly alkaline site the most abundant TRFs in the native soils were non-detectable in the cultivated areas, suggesting a complete replacement of native ecotypes. Sequenced clone libraries from the slightly alkaline site confirmed that there was greater diversity of Nitrososphaera clades in the native soil and an, again, an absence of Nitrosopumilus which was detected in great abundance in the cultivated soil and effectively replaced many of the Nitrososphaera clades that were observed in the adjacent native soil. These results suggest that agricultural land-management significantly alters AOA community diversity patterns and relative abundance for the soils examined. These results can inform future research to assess whether these soils are also attributed with differing rates of nitrogen usage and production of fugitive gases, parameters that would be useful for modeling the impacts of switchgrass cultivation on nitrogen cycling soil ecosystems.