Microbes and Nitrogen

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Estimates of the abundance of Archaea (Marine Group 1 Crenarchaeota) in the Duplin River at the GCE-LTER site, showing a peak in August. Inset shows the abundance of ammonia oxidizing genes in relation to the abundance of Archaea (regression line slope= 0.51, r2=0.99). The presence of both the Archaea and the ammonia oxidizing genes were detected using molecular techniques (quantitative PCR) targeted towards Crenarchaea 16S rRNA and amoA, respectively.
Adapted from Hollibaugh et al. in press.

Modern molecular techniques have vastly increased our ability to catalogue molecular diversity, but do not reveal how this diversity affects ecological processes. GCE-LTER researchers (in collaboration with researchers funded by the NSF-funded Sapelo Island Microbial Observatory and the Moore Foundation) have combined state of the art molecular methods with ecological studies to explore both microbial diversity and how this diversity affects nitrogen cycling.

The nitrogen cycle is the process by which nitrogen cycles between inorganic forms such as the nitrates and ammonia found in fertilizer to organic forms such as proteins and enzymes found in cells. One step in this process, called nitrification, involves converting ammonium first into nitrite (a step called ammonia oxidation) and then into nitrate. Nitrification is carried out by specialized groups of bacteria and the more recently discovered Archaea. It is possible to use genetic techniques to determine whether there are organisms in the water capable of carrying out this process. It is also possible to measure rates of nitrification in water samples to determine how fast the process is occurring. However, it is rare to combine these two approaches.

In a series of studies performed in the GCE domain, these researchers have combined these two approaches. In one study, they found that high rates of potential nitrification (the rate of nitrification that occurs when there is plenty of ammonia around) corresponded to high abundances of a particular type of Archaea (marine group 1 Crenarchaeota). This relationship suggested that the Archaea were potentially important in nitrogen cycling.

Next, they performed a detailed molecular analysis on samples collected when there was a high abundance of these organisms. The metabolic pathway by which this important group of microorganisms convert ammonia to nitrite is not well-understood, and this study allowed the researchers to exclude one of the pathways that had been proposed. Other important findings were that the ammonia oxidizing Archaea (AOA) abundance varied considerably over the course of a year, that they were not active at the same time as ammonia oxidizing bacteria (AOB), that the AOA population has low diversity, and that a population of AOA is present (genes are found) that does not seem to be growing (they are not expressing those genes).

This research is important from several perspectives. Archaea are just being described so any information builds on our knowledge of their presence and diversity. Very little is known about the relationship between the presence of particular organisms (Archaea or bacteria) and their ecological function(s), so the linkage to nitrification discovered here is of keen interest. Nitrification is a critical step in the nitrogen cycle, and these results suggest that these Archaea are potentially major agents on N transformation in both terrestrial and aquatic systems. This understanding will be broadly useful for both understanding the nitrogen cycle and controlling nitrogen pollution.

For further reading: 
Caffrey, J.M., Bano, N., Kalanetra, K. and Hollibaugh, J.T. 2007. Ammonia oxidation and ammonia-oxidizing Bacteria and Archaea populations from estuaries with differing histories of hypoxia. ISME Journal. 1:660-662. (DOI: http://dx.doi.org/10.1038/ismej.2007.79)
Hollibaugh, J.T., Gifford, S., Sharma, S., Bano, N. and Moran, M. 2010. Metatranscriptomic analysis of ammonia-oxidizing organisms in an estuarine bacterioplankton assemblage. ISME Journal. (in press)
For further information: 
James T. Hollibaugh
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