Making ecology “count”: a review of the why and how of molecular ecology  

It’s likely that everyone has been asked by either a friend or family member “What do you do?” Which, depending on what level of detail you shoot for, might be relatively straight forward. The follow-up question, however, can be a little trixie: “Why??”

A recent review by Creer and colleagues gives a nice broad overview of molecular ecology, defines key terms, and highlights the main advances that new technology has afforded the field. From sampling to sequencing, this article briefly covers landmark moments that have laid the foundation for the advancement of molecular ecology and emphasizes the future potential of continuing to link traditional ecological approaches with sequence-based techniques.

Figure 1. Creer et al., 2016.

We often find the inevitable: “thanks to recent advances in next generation sequencing technology…” somewhere nestled in the introduction of recent articles that include some type of –omics approach.  Creer et al., focus on how these new technologies have been a game changer, and highlight that this revolution has led to the identification of the uncultivable majority of microbes, and also moved us closer to understanding entire communities. This formidable challenge is complicated by the fact that it is difficult to identify all members, let alone figure out their individual roles.

“…we are gaining previously impossible insights into alpha and beta diversity from all domains of life, irrespective of body size.”

Figure 2. Creer et al., 2016.Whether you’re new to the field or just generally interested in how ecologists get at big questions, this review is a good place to start. Not only are a list of essential terms included, different –omic based approaches to sequence various types of samples are also summarized.

Figure 3. Creer et al., 2016.For a primer introduction to key tools for the bioinformatics side of things, the supplementary files are helpful. While not an exhaustive list of what is available (let’s be real, that’s really hard to curate, although they’re trying it here, although there are constantly new options to keep up with, such as CLARK-S, DESMAN, Taxonomer, and anvi’o).

 

“In conclusion, the standardized format and open source nature of sequencing data, accompanied by radical shifts in sequencing technology, mean that we can catalogue the spatial and temporal distribution of species from all domains of life and from all habitats.”

Creer et al., point out the end goals of studying ecology, emphasizing the importance of providing tools to assess invasive species, to ultimately understanding how environmental stress affects biodiversity and the functioning of our planet. If you’re interested in a nice succinct read on the current state of the art in molecular ecology, this review has you covered.

References

Creer, S., Deiner, K., Frey, S., Porazinska, D., Taberlet, P., Thomas, W.K., Potter, C. and Bik, H.M., 2016. The ecologist’s field guide to sequence‐based identification of biodiversity. Methods in Ecology and Evolution. doi:10.1111/2041-210X.12574

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About Kelle Freel

I’m currently a postdoc working at the Hawai’i Institute of Marine Biology with Dr. Mike Rappé. I’m interested in the biogeography and ecology of microbes, especially of the marine variety. After studying a unique genus of marine bacteria at Scripps Oceanography in grad school, I moved to France, where I worked with a group studying yeast population genomics. In my free time, I like to do outdoorsy stuff, travel, and cook.

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