How do RNA and protein abundances relate to microbial activity in a microbial community?
THANKFULLY not every microbe is E. coli (the best studied gut microbe that is occasionally a pathogen). This means, however, that we cannot apply the same principle we have learned in E. coli to every environmental microbe. From just a basic look at the biological molecules that make up cells, there is a lot of variation. For example, there is a wide disparity in the number of ribosomes different organisms have. In the environment not every organism invests as much energy in the regulation of transcription and translation, or even just that the concentration of RNA can have a huge difference in terms of the rates of protein synthesis and protein abundance across these organisms. If you are a slow growing organism, how do you control what genes you turn on and when, and does the magnitude of the change matter very much? These questions are important when we think about the context of transcriptome studies and interpreting what relative amounts of different RNAs mean in environmental systems. In conjunction with the biomarker RNA work done for my PhD, I looked at delving into some of these questions by comparing biomarker abundance in the two anaerobes I studied; asking what this relationship might mean for the amount of proteins you can generate from RNAs in different organisms. Ultimately, being able to understand and quantify microbial activity is essential to understanding their ecology, community dynamics and interactions. But it is important to keep in mind that not every microbe behaves the same.
Rowe et al. Applied Microbiology and Biotechnology, 2015
That being said, we can’t study every microbe on the planet in the lab! This makes modeling an important part of what we do as microbial ecologists. Picking the right representatives to tell us something about the environment and then testing them to make sure our assumptions are informative are our main objectives.