17Ammonia oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA) co-exist in soil, 18 but their relative distribution may vary depending on the environmental conditions. Effects of 19 changes in soil organic matter and nutrient content on the AOB and AOA are poorly 20 understood. Our aim was to compare effects of long-term soil organic matter depletion and 21 amendments with labile (straw) and more recalcitrant (peat) organic matter, with and without 22 easily plant-available nitrogen, on the activities, abundances and community structures of 23 AOB and AOA. Soil was sampled from a long-term field site in Sweden that was established 24 in 1956. The potential ammonia oxidation rates, the AOB and AOA amoA gene abundances 25 and the community structures of both groups based on T-RFLP of amoA genes were 26 determined. Straw amendment during 50 years had not altered any of the measured soil 27 parameters, while the addition of peat resulted in a significant increase of soil organic carbon 28 as well as a decrease in pH. Nitrogen fertilization alone resulted in a small decrease in soil 29 pH, organic carbon and total nitrogen, but an increase in primary production. Type and 30 amount of organic matter had an impact on the AOB and AOA community structures and the 31 AOA abundance. Our findings confirmed that AOA are abundant in soil, but showed that 32 under certain conditions the AOB dominate, suggesting niche differentiation between the two 33 groups at the field site. The large differences in potential rates between treatments correlated 34 to the AOA community size, indicating that they were functionally more important in the 35 nitrification process than the AOB. The AOA abundance was positively related to addition of 36 labile organic carbon, which supports the idea that AOA could have alternative growth 37 strategies using organic carbon. The AOB community size varied little in contrast to that of 38 the AOA. This indicates that the bacterial ammonia oxidizers as a group have a greater 39 ecophysiological diversity and potentially cover a broader range of habitats. 40

Characterization of spatial patterns of functional microbial communities could facilitate the understanding of the relationships between the ecology of microbial communities, the biogeochemical processes they perform and the corresponding ecosystem functions. Because of the important role the ammonia-oxidizing bacteria (AOB) and archaea (AOA) have in nitrogen cycling and nitrate leaching, we explored the spatial distribution of their activity, abundance and community composition across a 44-ha large farm divided into an organic and an integrated farming system. The spatial patterns were mapped by geostatistical modeling and correlations to soil properties and ecosystem functioning in terms of nitrate leaching were determined. All measured community components for both AOB and AOA exhibited spatial patterns at the hectare scale. The patchy patterns of community structures did not reflect the farming systems, but the AOB community was weakly related to differences in soil pH and moisture, whereas the AOA community to differences in soil pH and clay content. Soil properties related differently to the size of the communities, with soil organic carbon and total nitrogen correlating positively to AOB abundance, while clay content and pH showed a negative correlation to AOA abundance. Contrasting spatial patterns were observed for the abundance distributions of the two groups indicating that the AOB and AOA may occupy different niches in agro-ecosystems. In addition, the two communities correlated differently to community and ecosystem functions. Our results suggest that the AOA, not the AOB, were contributing to nitrate leaching at the site by providing substrate for the nitrite oxidizers.

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