Environmental Proteomics of Microbial Plankton In Upwelling Waters:

Metaproteomics is an up and coming development within the microbe studying community. What it is in layman's terms is the study of proteins within this community to see whether there is a distinct common group of proteins (clade), and from this a rough conclusion can be made as different proteins will be present depending on which resource is the main limiting factor. Proteins also as they are the final product of gene expression show/indicate cellular priorities, so help to back up conclusions that might have been made from the general clade discoveries.

This study performed in 2006 looked at the proteomic composition of the microbial community at a depth of less than 1.2 micrometres, just off the coast of Newport,Oregon during the Summer of 2006.

The method started with the collection of these microbial cells as mentioned above 5 miles off the coast of Newport, when it was seen that the waters were in a halocline mode, which essentially means that there is a strong vertical salinity gradient within the selected body of water, this had to be the case as this is related to upwelling waters and as the study wanted to look at the results during this time they had to be sure.

Essentially the cells were filtered, then the still concentrated cells were sedimented for centrifugation. Then after this the cell pellet was resuspended and then from what was left, 500 micrograms of digested proteins were loaded into the 2-D high performance liquid chromatography column for analysis. As well as this to determine the type of proteins present, mass spectrometry was performed afterwards with the results being compared to an already present protein database so that they knew exactly what was present.

The results showed that of all of the bacteria isolated, a significant amount of them were matched to the SAR11 clade, with other clades also present but in a smaller percent with 17% belonging to the roseobacter, and 6 belonging to the oligotrophic marine gammobacteria group. From all of these detected what was seen was that they were mostly related to ones involved in protein folding, biosynthesis, transport and viral capsid structure.

In contrast to oligotrophic environments, phosphate transporters were not detected in a high number in this nutrient rich system so these could be developed or be activated when nutrient stresses occur. However transporters for amino acids etc were among the most highly deteced proteins possibly suggesting/predicting that carbon and nitrogen are more limiting than phosphates within this environment.

Finally, one of the highly detected proteins was methanol dehydrogenase originating from the OM43 clade, providing further support for recent reports that the metabolism of one-carbon compounds by these streamlined methylotrophs might be an important feature of coastal ocean biogeochemistry.

This study is one of only a few around at the moment but it does show what advances in protein analysis can provide that other methods perhaps couldnt and is a good starting point for future studies.

The paper is available at: 

http://www.nature.com/ismej/journal/v5/n5/full/ismej2010168a.html

Reference:

Sowell S., Abraham P., Shah M., Verberkmoes N., Smith P., Barofsky D., Giovannoni S. Environmental proteomics of microbial plankton in a highly productive coastal upwelling system. The ISME Journal (2011) 5, 856-865