Do Archaea dominate nitrification in acid soils?

Lead Research Organisation: University of Aberdeen
Department Name: Inst of Biological and Environmental Sci


Which organisms are responsible for nitrogen cycling in acid soils? Nitrification is essential to the cycling of nitrogen throughout the environment. It involves the conversion of ammonia to nitrate by two groups of microorganisms. Ammonia oxidisers convert ammonia to nitrite, which is subsequently converted to nitrite by nitrite oxidisers. Although an essential process, nitrification can also have deleterious consequences. Ammonium can be retained in soil, but after conversion to nitrate, it can be readily leached resulting in the pollution of groundwaters that may be used to supply drinking water. In addition, ammonia oxidation is accompanied by the production of nitrous oxide, a potent greenhouse gas which is also involved in destroying stratospheric ozone in the atmosphere. Approximately 30% of the world's soil can be considered acid (with a pH less than 5.5) and represent a wide range of natural and managed habitats including forestry, agriculture and grasslands. They are therefore of great environmental and economic importance. In contrast to other soils (such as managed arable land), the processes and organisms responsible for nitrification in acid soils are not fully understood, as typical ammonia oxidisers that were thought to be primarily responsible for ammonia oxidation are unable to grow in laboratory media at acidic pH. Until recently it was believed that the most important soil ammonia oxidisers were bacteria. However, this view has changed with the recent discovery of another group of abundant group of organisms that possess the ability to oxidise ammonia, the Crenarchaea. These organisms belong to another domain of microbial life, the archaea. Although they resemble bacteria in many ways, they are evolutionary distinct. These organisms were once thought to be restricted to hyperthermophilic environments such as deep-sea vents or terrestrial thermal springs. However, with the use of molecular techniques, these organisms have been demonstrated to be ubiquitous in the environment. We have recently obtained evidence that in one experimental field site, ammonia oxidising Crenarchaea show greatest activity in acidic soils, in direct contrast to ammonia oxidising bacteria which show greatest activity in neutral soils. This therefore indicates that there are fundamental ecological and physiological differences between these two groups. This research programme aims to determine whether soil crenarchaea, rather than bacteria, are primarily responsible for ammonia oxidation in acid soils from a range of different habitats. Their abundance will be measured in acidic soils and neighbouring neutral pH soils from four sites from within the UK, and their relative abundance will also be determined in forest and pasture soils from three other countries (Finland, Canada and Australia). The findings will benefit those in agriculture, forestry and industry by increasing our knowledge of the organisms responsible for nitrogen cycling in natural and managed acidic soil systems. The findings will also be important to researchers trying to understand the links between biodiversity and ecosystem function, including the mechanisms and organisms potentially responsible for the emission of nitrous oxide from soil.


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Description The overall aim of this project was to determine which organisms are responsible for nitrification in acid soils. Acid soils (pH =5.5) represent 30% of the earth's land surface and are therefore of significant economic and environment importance. Nitrification is a central component of the nitrogen cycle and there was considerable uncertainty regarding which organisms are responsible for nitrification in acid soils. The aim of this research programme is to test the hypothesis that ammonia oxidising archaea (AOA) rather than ammonia oxidising bacteria (AOB) are primarily responsible for ammonia oxidation in acidic soils.

All objectives outlined in the grant proposal were met, and the major findings were the following:
1. We provided unequivocal evidence that AOA, and not AOB, are primarily responsible for ammonia oxidation in acidic soils globally.
2. We demonstrated that it is specific evolutionary lineages of AOA that are found exclusively in acidic soils, while other lineages are found in near-neutral or neutral soils.
3. Soil pH is the major driver for evolutionarily adaptation of AOA in soil
4. This use of urea is not the primary mechanism enabling adaptation to low pH.
Exploitation Route The nitrogen cycle is an essential biogeochemical cycle required for sustaining all life on the planet. The major findings of this research programme are largely of academic benefit, with the ultimate aim to increase understanding of the mechanisms contributing to an essential ecosystem process, the oxidation of ammonia in soil. In the future, this information (on which microbes are converting ammonia in soils (including acidic soils)) may improve strategies for fertiliser application, and allow increased mitigation of fertiliser loss and nitrous oxide gas emissions by understanding the mechanisms and organisms responsible for these processes.
Sectors Agriculture, Food and Drink,Environment

Description At this moment in time, this research is largely of academic benefit. The research will add significantly to basic science understanding of how ammonia is transformed in the soil environment (by identifying the key organisms responsible), and will be of interest to governmental environmental agencies concerned with pollution associated with nitrogen fertiliser loss and atmospheric pollution associated with ammonia oxidation in soil.
Sector Agriculture, Food and Drink,Environment
Impact Types Policy & public services