Archaea predominate among ammonia-oxidizing prokaryotes in soils

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Abstract
Nitrification, the microbial conversion of ammonia to nitrate, is a key process in the global nitrogen cycle. It has been generally assumed that specialist bacteria are the main aerobic ammonia oxidizers on the soil. An analysis of the abundance of the amoA gene encoding a subunit of the key enzyme ammonia monooxygenase shows that in twelve different soil types from three different climatic zones, amoA gene copies from archaea of the kingdom Crenarchaeota were up to 3,000-fold more abundant than bacterial amoA. So in both pristine and agricultural soils, it seems that archaea are by far the dominant ammonia oxidizers. Nitrification, the microbial conversion of ammonia to nitrate, is a key process in the global nitrogen cycle. This reaction is predominately carried out by archaeal and not bacterial ammonia oxidizer, as the archaeal ammonia oxidizers are more abundant in soils than their well-known bacterial counterparts. Ammonia oxidation is the first step in nitrification, a key process in the global nitrogen cycle that results in the formation of nitrate through microbial activity1,2. The increase in nitrate availability in soils is important for plant nutrition, but it also has considerable impact on groundwater pollution owing to leaching. Here we show that archaeal ammonia oxidizers are more abundant in soils than their well-known bacterial counterparts. We investigated the abundance of the gene encoding a subunit of the key enzyme ammonia monooxygenase (amoA) in 12 pristine and agricultural soils of three climatic zones. amoA gene copies of Crenarchaeota (Archaea) were up to 3,000-fold more abundant than bacterial amoA genes. High amounts of crenarchaeota-specific lipids, including crenarchaeol, correlated with the abundance of archaeal amoA gene copies. Furthermore, reverse transcription quantitative PCR studies and complementary DNA analysis using novel cloning-independent pyrosequencing technology demonstrated the activity of the archaea in situ and supported the numerical dominance of archaeal over bacterial ammonia oxidizers. Our results indicate that crenarchaeota may be the most abundant ammonia-oxidizing organisms in soil ecosystems on Earth.