Nitrification in acid soils: solving the paradox, possibly

Ammonia oxidation in soil was, until recently, thought to be dominated by autotrophic, chemolithotrophic proteobacteria. These organisms gain energy from oxidation of ammonia to nitrite and perform the first step in nitrification. All cultivated ammonia oxidising bacteria show no or very poor growth in liquid batch culture below pH 7. Paradoxically, nitrification occurs in acid soils at rates that are often faster than those in apparently more favourable neutral and alkaline soils.

Understanding acidophilic ammonia oxidation is important globally and economically. Approximately 30% of the world’s soils are acidic (pH<5), including 50% of arable soils, and up to 70% of ammonia-based nitrogen fertiliser is lost through nitrification and leaching or denitrification of nitrate.

Potential mechanisms for acidophilic ammonia oxidation include urea hydrolysis, protection in biofilms and aggregates and heterotrophic nitrification, but could also be due to acidophilic or acidotolerant ammonia oxidisers. Assessment of selection for such groups in acid soils was impossible using traditional techniques and acidophilic ammonia oxidising bacteria have never been isolated. Molecular techniques enable cultivation-independent analysis of ammonia oxidisers and recently led to the discovery that archaea can also oxidise ammonia.

This talk will describe how a combination of molecular and cultivation-based techniques have identified a novel ammonia oxidiser that provides a solution to the paradox of nitrification in acid soils that applies at local, regional and global scales. It will also consider the degree to which niche specialisation, exemplified in these studies, can explain soil microbial community composition.