What are the pros and cons of traditional enrichment culture techniques? What advances in the last decade are improving enrichment culture techniques to aid the cultivation of uncultured microorganisms?

Question

What will be an ideal response?

Answer 1

Answer: The pros of traditional enrichment culture techniques are that enrichment culture can select for organisms with very specific physiologies for generating energy and/or for tolerating specific growth conditions. For instance, someone interested in anoxic photosynthesis in arctic environments would incubate samples under specific wavelengths of light in a minimal media at a very low temperature. The cons of enrichment culture are that fast-growing microbes ("weeds") often out-compete other microbes in the sample, thus underestimating diversity. In addition, it is often the slow growing microbes that are most prevalent in the environment and those organisms may be more difficult to culture through traditional enrichment techniques. Another con of traditional enrichment culture is that laboratory conditions may actually kill the most prevalent microbes (for instance, if growth conditions are not correct) or we may not be supplying the correct carbon, energy, nutrient, or cofactors for growth of the most prevalent microbes.

The first major change in the last decade is our ability to detect and sequence microorganisms in environments with cultivation-independent techniques. This has allowed us to avoid the bias of enrichment cultures and more accurately assess and catalogue the microorganisms present in a sample. Metagenomic techniques have been particularly helpful because the genetic content of a population can be analyzed to gain clues as to what growth conditions, nutrients, cofactors, and energy sources a microorganism may require for growth. Other advances that have improved enrichment culture techniques include high-throughput screening in 96 well plates that allows us to test hundreds of combinations of growth substrates, nutrients, and cofactors. Methods of diluting or separating single cells or populations of similar cells into test plates will also aid in cultivation of the specific microorganisms we would like to study. Lastly, using nucleic acid based techniques (FISH, T-RFLP, etc.), we can monitor enrichment cultures quickly and accurately to determine which growth conditions encourage the growth of the microorganisms we wish to study.