Abstract
Soil ammonia-oxidizing archaea (AOA) are highly abundant and play an important role in the nitrogen cycle. In addition, AOA have a significant impact on soil quality. Nitrite produced by AOA and further oxidized to nitrate can cause nitrogen loss from soils, surface and groundwater contamination, and water eutrophication. The AOA discovered to date are classified in the phylum Thaumarchaeota. Only a few archaeal genomes are available in databases. As a result, AOA genes are not well annotated, and it is difficult to mine and identify archaeal genes within metagenomic libraries. Nevertheless, 16S rRNA and comparative analysis of ammonia monooxygenase sequences show that soils can vary greatly in the relative abundance of AOA. In some soils, AOA can comprise more than 10% of the total prokaryotic community. In other soils, AOA comprise less than 0.5% of the community. Many approaches have been used to measure the abundance and diversity of this group including DGGE, T-RFLP, q-PCR, and DNA sequencing. AOA have been studied across different soil types and various ecosystems from the Antarctic dry valleys to the tropical forests of South America to the soils near Mount Everest. Different studies have identified multiple soil factors that trigger the abundance of AOA. These factors include pH, concentration of available ammonia, organic matter content, moisture content, nitrogen content, clay content, as well as other triggers. Land use management appears to have a major effect on the abundance of AOA in soil, which may be the result of nitrogen fertilizer used in agricultural soils. This review summarizes the published results on this topic and suggests future work that will increase our understanding of how soil management and edaphoclimatic factors influence AOA.
Highlights
FIRST DISCOVERIES OF NOVEL GROUP Chemolithotrophic nitrification is a two-step process
First step includes oxidation of ammonia to nitrite conducted by ammoniaoxidizing bacteria (AOB) and second step is conversion of nitrite to nitrate by nitrite-oxidizing bacteria (NOB; Hastings et al, 2000; Hermansson and Lindgren, 2001; Kowalchuk and Stephen, 2001)
Ammonia-oxidizing archaea are more tolerant to low pH than AOB, and ammonia-oxidizing archaea (AOA) are mainly responsible for nitrification in acidic soils (Leininger et al, 2006; Gubry-Rangin et al, 2010; Yao et al, 2011; Zhang et al, 2011; Isobe et al, 2012)
Summary
FIRST DISCOVERIES OF NOVEL GROUP Chemolithotrophic nitrification is a two-step process. Genetics, physiology, and culturing happened in the field of AOA, such as sequencing of first genome of non-symbiotic marine AOA (Walker et al, 2010), obtaining pure cultures, and high enrichments of Nitrososphaera viennensis (Tourna et al, 2011), Ca. Nitrosoarchaeum koreensis, Ca. Nitrosoarchaeum limina, Ca. Nitrosotalea devanaterra and sequencing of their genome; discovery of AOA ecotypes in soils based on different pH levels (Gubry-Rangin et al, 2011) and another evidences of organic carbon utilization provided more information about physiology and metabolism of this group.
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