Ammonia oxidation in soil: how to rewrite a textbook

This week's article was:
Leininger S, Urich T, Schloter M, Schwark L, Qi J, Nicol GW, Prosser JI, Schuster SC, Schleper C 2006. Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442:806-809.

The title was initially a bit jargony for most of us, without the presence of a soil (or any type of) biologist in this week's gathering. Essentially we worked out that prokaryotes are single-celled organisms lacking nuclei, and prokaryotes are split into 2 major domains: the Archaea and the Bacteria.

Commonly it's thought that the Archaea are extremophiles, preferring environments hostile to many other organisms - very high temperatures (like hydrothermal vents), very high salinity, or very low pH. Not all extremophiles are Archaea; many are bacteria, but many soil biology textbooks (even quite recent ones; late 1990s) restrict discussion of Archaea to extremophile roles and leave it there.

The other main issue is that for a very long time it has been assumed that bacteria, and very specific genera of bacteria, are responsible for oxidation of ammonia/ammonium in soils. The process of ammonia oxidation is central to soil and ecosystem nitrogen cycling, being the first step in nitrification. Textbooks identify bacterial genera such as Nitrosomonas, Nitrosococcus, Nitrosospira and Nitrosolobus as the predominant groups of ammonium oxidising bacteria in soils.

So, the discovery that Archaea are responsible for ammonia oxidation is ground-breaking. Not only will future textbooks need to revise the importance of the Archaea in soils, they will also need to identify Archaean organisms as intimately involved in nitrification.

Did the authors get it right (Leininger et al., including one or two "big names" in soil biology)? They examined soils from a wide range of climatic zones ... but only in Europe. Time and further research will tell whether the Archaea are equally significant in Australia, Africa, Asia, or the Americas, for example.

Another interesting issue is whether soil, or more specifically metabolism of ammonia in soil, represents an "extreme" environment which allows Archaean organisms to predominate over the Bacteria. We didn't know the answer to that one.

Image from http://news.softpedia.com/news/Ammonia-Loving-Archaea-Win-Landslide-Majority-33081.shtml