Archaea predominate among ammonia-oxidizing prokaryotes in soils

  title={Archaea predominate among ammonia-oxidizing prokaryotes in soils},
  author={Sven Leininger and Tim Urich and Michael Schloter and Lorenz Schwark and Jie Qi and Graeme W. Nicol and James I. Prosser and Stephan C. Schuster and Christa Schleper},
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 activity. 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… 
Autotrophic ammonia oxidation by soil thaumarchaea
Nitrification plays a central role in the global nitrogen cycle and is responsible for significant losses of nitrogen fertilizer, atmospheric pollution by the greenhouse gas nitrous oxide, and
Growth, activity and temperature responses of ammonia-oxidizing archaea and bacteria in soil microcosms.
Community structure changes were similar during incubation at different temperatures and much of the activity was due to a group of non-thermophile crenarchaea associated with subsurface and marine environments, rather than soil.
Drivers of archaeal ammonia-oxidizing communities in soil
Soil ammonia-oxidizing archaea (AOA) are highly abundant and play an important role in the nitrogen cycle, but soils can vary greatly in the relative abundance of AOA.
Bacteria rather than Archaea dominate microbial ammonia oxidation in an agricultural soil.
It is shown that Bacteria rather than Archaea functionally dominate ammonia oxidation in an agricultural soil, despite the fact that archaeal versus bacterial amoA genes are numerically more dominant.
Distribution and Activity of Ammonia-Oxidizing Archaea in Natural Environments
The complete genome sequence of C. symbiosum was determined from a metagenomic library providing further insights into the potential physiological properties of uncultured ammonia-oxidizing archaea (AOA), and there is now unambiguous evidence for the occurrence of AOA in environments of elevated temperature.
Ammonia oxidation coupled to CO2 fixation by archaea and bacteria in an agricultural soil
The results demonstrate a diverse and dynamic contribution of ammonia-oxidizing archaea in soil to nitrification and CO2 assimilation and that their importance to the overall archaeal community might be larger than previously thought.
Nitrification driven by bacteria and not archaea in nitrogen-rich grassland soils
It is suggested that nitrification is driven by bacteria rather than archaea in these nitrogen-rich grassland soils in New Zealand, with a significant relationship between the abundance of ammonia-oxidizing bacteria and the rate of nitrification.
Cultivation of a highly enriched ammonia-oxidizing archaeon of thaumarchaeotal group I.1b from an agricultural soil.
Nitrification of excess ammonia in soil causes eutrophication of water resources and emission of atmospheric N(2) O gas. The first step of nitrification, ammonia oxidation, is mediated by Archaea as
Ammonia-Oxidizing Archaea Dominate Ammonia-Oxidizing Communities within Alkaline Cave Sediments
The results showed that AOA outnumber ammonia-oxidizing bacteria (AOB) by up to four orders of magnitude in cave sediments, and data suggest that despite the alkaline conditions within the cave, the low NH3 concentrations measured continue to favor growth of AOA over AOB populations.
Quantitative analyses of ammonia-oxidizing Archaea and bacteria in the sediments of four nitrogen-rich wetlands in China
The results indicated that AOA distributed widely in wetland sediments, and the phylogenetic tree revealed that archaeal amoA functional gene sequences from wetlands sediments cluster as two major evolutionary branches: soil/sediment and sediment/water.


Isolation of an autotrophic ammonia-oxidizing marine archaeon
The isolation of a marine crenarchaeote that grows chemolithoautotrophically by aerobically oxidizing ammonia to nitrite—the first observation of nitrification in the Archaea is reported, suggesting that nitrifying marine Cren archaeota may be important to global carbon and nitrogen cycles.
The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations
The data suggest that amoA represents a very powerful molecular tool for analyzing indigenous ammonia-oxidizing communities due to (i) its specificity, (ii) its fine-scale resolution of closely related populations, and (iii) the fact that a functional trait rather than a phylogenetic trait is detected.
Ammonia-oxidizing bacteria: a model for molecular microbial ecology.
This chapter reviews recent progress in knowledge of Chemolitho-autotrophic ammonia-oxidizing bacteria of the beta-subclass Proteobacteria, and examines their distribution, diversity, and ecology.
Quantitative analysis of ammonia oxidising bacteria using competitive PCR.
A competitive PCR (cPCR)-based method based on the amplification of 16S rRNA genes specific for the beta-subgroup proteobacterial ammonia oxidising bacteria for enumeration of these organisms is developed.
Use of Molecular and Isotopic Techniques To Monitor the Response of Autotrophic Ammonia-Oxidizing Populations of the β Subdivision of the Class Proteobacteria in Arable Soils to Nitrogen Fertilizer
The rapidity of the rise in nitrification rates observed after 3 days suggests that it results from phenotypic changes in the ammonia-oxidizing bacterial population, similar to those prevalent in other soils.
Cultivation-based and molecular approaches to characterisation of terrestrial and aquatic nitrifiers
There is increasing evidence for physiological properties driving the environmental distribution of particular groups of ammonia oxidisers and for associations between nitrification process rates and ammonia oxidiser community structure.
Quantification of Ammonia-Oxidizing Bacteria in Arable Soil by Real-Time PCR
Real-time PCR was used to quantify populations of ammonia-oxidizing bacteria representing the β subdivision of the classProteobacteria in samples of arable soil, both nitrogen fertilized and unfertilized from Mellby, Sweden, and showed that the concentration of template DNA released at various times remained constant after 10 to 100 s of bead beating.
Application of Real-Time PCR To Study Effects of Ammonium on Population Size of Ammonia-Oxidizing Bacteria in Soil
A quantitative real-time PCR assay targeting part of the ammonia-monooxygenase gene (amoA) was developed to estimate AOB population size in soil and found that the population size was significantly greater in annually fertilized versus unfertilized soil, suggesting a long-term effect of ammonium fertilization on AOBpopulation size.
Analysis of β-Subgroup Proteobacterial Ammonia Oxidizer Populations in Soil by Denaturing Gradient Gel Electrophoresis Analysis and Hierarchical Phylogenetic Probing
The present study demonstrates the value of DGGE and probing for rapid analysis of natural soil communities of β-subgroup proteobacterial ammonia oxidizers, indicates significant pH-associated differences in Nitrosospira populations, and suggests that NitrosOSPira cluster 2 may be of significance for ammonia-oxidizing activity in acid soils.