This article is part of the Research Topic Nitrogen cycling in terrestrial ecosystems


Front. Microbiol., 15 June 2012 | doi: 10.3389/fmicb.2012.00210

Drivers of archaeal ammonia-oxidizing communities in soil

Kateryna Zhalnina1, Patrícia Dörr de Quadros2, Flavio A. O. Camargo2 and Eric W. Triplett1*
  • 1 Microbiology and Cell Science Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
  • 2 Soil Science Department, Federal University of Rio Grande do Sul, Porto Alegre, Brazil

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.

Keywords: ammonia-oxidizing archaea, ammonia monooxygenase, soil

Citation: Zhalnina K, Dörr de Quadros P, Camargo FAO and Triplett EW (2012) Drivers of archaeal ammonia-oxidizing communities in soil. Front. Microbio. 3:210. doi: 10.3389/fmicb.2012.00210

Received: 15 March 2012; Paper pending published: 05 May 2012;
Accepted: 22 May 2012; Published online: 15 June 2012.

Edited by:

Rich Boden, University of Plymouth, USA

Reviewed by:

Jennifer F. Biddle, University of Delaware, USA
J. Michael Beman, University of California, Merced, USA
Nathan Basiliko, University of Toronto, Canada

Copyright: © 2012 Zhalnina, Dörr de Quadros, Camargo and Triplett. This is an open-access article distributed under the terms of the Creative Commons Attribution Non Commercial License, which permits non-commercial use, distribution, and reproduction in other forums, provided the original authors and source are credited.

*Correspondence: Eric W. Triplett, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 1052 Museum Road, Gainesville, FL 32611-0700, USA. e-mail:

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