Linking phylotype & phenotype: Identifying the environmental contribution of an uncultivated specie

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Microbial ecologists have the tools to quantitatively decipher the processes taking place in microbial communities. They can follow nitrogen, sulfur, carbon, phosphorous, reducing equivalents, energy, &c, &c, as they are transformed from one form to another. For example, it is reasonable to measure the steady-state levels of all of the forms of nitrogen in a system, determine the inputs and outputs, and the flux rates between all of the forms in a nitrogen-cycling ecological community.

Nitrogen cycle

The limiting factor in microbial ecology these days is that essentially all we know about the organisms that make up these communities comes from the study of the less than 1% of microbes that are readily cultivated. I hope it is clear at this point that even taking a basic quantitative census of a microbial population is not straightforward, but it is possible, with much work, to get a semi-quantitative assessment of the makeup of the population, especially those organisms that are abundant in the population. The next task, then, is to link these bits of information together; to identify the organism(s) responsible for specific steps of an ecological transformation.

For example, suppose you have an environment in which a certain process is taking place, and you have a phylogenetic census of the organisms in a sample from this environment, how would you determine which organisms in your census are the ones that carry out the process you're interested in? Or, coming from the other direction, suppose you know an organism is abundant in an environment, how do you determine what it's doing there, i.e. what it's ecological niche is? The trick is to find or make a connection betwen the metabolic process and phylogentic information. In this Chapter we'll be discussing two approaches to this problem: genomics, and stable-isotope probing (SIP).