Niche differentiation of ammonia oxidizing bacteria and archaea in managed soils

Soils offer humanity a multitude of ecosystem services, including production of food and clean drinking water, and many such services are driven by soil microbial communities. However, human activities are constantly affecting soil ecosystems through altered land use or various management strategies, and thereby influence microbial communities and their functions. Human activities also result in increasing amounts of nitrogen entering terrestrial ecosystems, which modifies the global nitrogen cycle. This can lead to a number of negative environmental effects such as increased amounts of nitrous oxide (N2O) being emitted to the atmosphere or nitrate (NO3-) being leached from soils to surrounding water bodies, causing eutrophication. This thesis explores how indigenous soil bacterial and archaeal communities are affected in managed soils, with emphasis on ammonia oxidizing bacteria (AOB) and archaea (AOA). The objectives were to identify specific environmental drivers for AOB and AOA and to evaluate how potential changes might affect their activity. Long-term application of various fertilizer regimes on an agricultural soil was found to alter the total abundance of targeted bacterial and archaeal phyla and classes in similar ways, although different taxa-specific responses were observed for the relative abundance of certain phyla/classes. Long-term organic and fertilizer amendments also affected the ammonia-oxidizing community. The AOA appeared to be functionally more important in the nitrification process than the AOB at the studied field site. Also, the AOA dominated in abundance except under certain conditions, when the AOB dominated, suggesting niche differentiation between the two groups. Studies on a drained forested peat soil revealed that the AOB were numerically superior to the AOA, and that AOB and AOA community structures and AOB abundance exhibited temporal variation. Furthermore, a spatially focused study on an agricultural soil revealed contrasting spatial patterns between the AOB and AOA with regard to both abundance and structure, which correlated differently to soil properties. This too indicates niche differentiation between the two ammonia oxidizing groups and there were also indications that the AOA were the drivers of nitrate leaching from the studied agro-ecosystem. In conclusion, the AOB and AOA communities clearly respond to different management strategies. Based on current knowledge, it is suggested that the size of the AOB and AOA communities could serve as a good bioindicator when monitoring soil status