Journal Club: Alternative Lifestyles

We know that all bacteria in lakes don’t all perform the same functions, so it makes sense that different bacterial groups may have different lifestyles. You could also think of these as survival strategies. In the paper we read for journal club (see below!), several freshwater isolates were classified into four lifestyles based on their genome content – specifically codon usage, an indicator of growth rate, and carbon substrate utilization pathways. These categories were:

– Passive + streamlined (slow growth, few carbon pathways)

– Slow + augmented (slow growth, many carbon pathways)

– Fast + reduced (fast growth, few carbon pathways)

– Vagabonds (fast growth, many carbon pathways)

The passive category includes some of our favorites, acI and Pnec, two groups that are almost always present in relatively high numbers. The slow and augmented group likely never reach quite as high of an abundance, but could survive in more conditions because of their many potential substrates. The fast and reduced group has the opposite strategy – although they can only use a few carbon substrates, they can reach high abundances when those substrates are available. And finally, the vagabonds are hypothesized to be bacteria that are just passing through. Perhaps they use freshwater as a vector, or are better adapted to a different environment.

This train of thought led to a discussion of a prevalent issue in microbiology – culture bias. Growing microbes in pure cultures is by far the simplest way to characterize a species. It’s a lot easier to study an organism in the lab than in nature. However, the methods used to isolate bacteria could select for only some of the categories. Culturing techniques often favor the fastest growing microbes, or require that a microbe be able to grow on a certain carbon substrate. This means that it would be more difficult to isolate slow or picky microbes, and that cultured organisms may not accurately represent what is found in nature.

Thanks to Sarah for organizing our inaugural journal club and for choosing the following paper!

Livermore, Joshua A., Scott J. Emrich, John Tan, and Stuart E. Jones. “Freshwater bacterial lifestyles inferred from comparative genomics.” Environmental microbiology 16, no. 3 (2014): 746-758.

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