The role of bacteria versus archaea in ammonia oxidation in European lakes (Alleen Engelse tekst)

For a long time archaea were supposed to inhabit only extreme environments. However, since a few years crenarchaea that belong to the archaeal kingdom, are found in more moderate habitats such as the ocean, where they are assumed to be involved in the oxidation of ammonium. They are able to change their lipids in the cell membrane in reaction to changes in temperature. It has been established that the lipid composition of crenarchaea can be used as a proxy for paleotemperatures.

In a collaborative project with the Utrecht University the application of crenarchaeal lipids as temperature proxy in deeper lakes is investigated. As part of this project the ecology and ecophysiology of freshwater crenarchaea is studied at the NIOO Centre for Limnology. Since these microorganisms are assumed to be involved in the oxidation of ammonium it is tempting to compare their distribution in time and space with the well known bacterial ammonia-oxidising microorganisms.

Objectives
To determine the distribution of ammonia-oxidising bacteria in deep European lakes and to compare it with the distribution of crenarchaea. The study will be done on a series of sediment and water samples collected on a north-south transect by DNA analysis.

FISH-microscopic image of bacteria (green) and archaea (red)

Techniques
DNA will be isolated from lake water and sediments. A part of the 16S rRNA gene present in the natural DNA will be amplified by PCR using primer sets specific for ammonia-oxidising bacteria. The PCR products will be separated by Denaturing Gradient Gel Electrophoresis and the banding pattern will be compared with known sequences present in a database. Fluorescent In Situ Hybridisation or Quantitative PCR will be used to quantify the size of the ammonia-oxidising bacterial community in the different lakes.

Duration
4 - 6 Months.

Contact
Liesbeth Vissers, e-mail: l.vissers@nioo.knaw.nl