There are more microbes than meet the eye: exploring the genomic diversity in an aquifer

First: it’s Tuesday, November 8th, 2016 – before you even think about putting your feet up and reading this post, I hope you’ve managed to wrangle yourself one of those highly prized “I voted” stickers.

Now, on to more microbial matters! Under all the dirt we build our houses on, is a whole lot of carbon. This carbon is involved in a variety of biogeochemical cycles, e.g. cycles that involve important elements (like carbon, nitrogen, sulfur and hydrogen), that are driven by biological, geological, and chemical forces. Studies exploring the terrestrial subsurface, not to mention those attempting to take a crack at what’s going on in the oceanic deep subsurface, have just begun to get a glimpse at the diversity of the microbes involved in the bio portion of those cycles. 

Anantharaman et al., (2016). Figure 2. Phylogeny of sequenced genomes.

“Thus, it appears that organisms often work in cohorts to turn biogeochemical cycles. Further, the organisms that mediate individual reaction steps display a multitude of combinations of metabolic traits, and different organisms proliferate as conditions change..”

Anantharaman et al., (2016). Figure 3. Rank abundance plots.

In a recent paper by Anantharaman and colleagues, the authors point out that only a tiny fraction (less than 8%) of the 16S rRNA sequence data publicly available represents microbes living in the subsurface. There are very few isolates in culture from this habitat, even though the microbial communities in the subsurface are thought to have essential roles in all this biogeochemical cycling business.

Anantharaman et al. sequenced a TON of DNA from 33 sediment and groundwater samples from an aquifer next to the Colorado River. The main goal was to use the sequence data they obtained to figure out what microbes are doing there. They were able to put together 2,516 bacterial genomes (21 of which are complete) as well as 24 archael genomes. The article isn’t just a survey of diversity, they also attempt to couple the functional genes identified from the aquifer microbial communities to roles in the ecosystem. One of the key findings of the paper is that interactions between different microbes are key in driving biogeochemical cycles, turns out going it alone isn’t in the game plan for these guys.

“Given the novel phylogenetic diversity of the studied organisms, the genomes reported here represent a vast treasure-trove that could be mined for biotechnological applications and for potential strategies for genome-enabled cultivation of novel organisms.”

Anantharaman et al., (2016). Biogeochemical cycling in microbial communities.

Overall, they found a vast amount of diversity that was previously overlooked, including many lineages that fall in the Candidate Phyla Radiation (CPR) described recently. There’s a lot of data packed into this article as well as supplemental files to keep you busy if you need a break from election coverage.

I’m constantly amazed by the incredible level of improved resolution that continually advancing methods in sequencing and data analysis bring to the molecular aspect of microbial ecology. It’s exciting that there’s plenty still to learn about the microbes that drive global cycles, you might even say, we’ve only just scratched the surface.




Anantharaman, K., Brown, C.T., Hug, L.A., Sharon, I., Castelle, C.J., Probst, A.J., Thomas, B.C., Singh, A., Wilkins, M.J., Karaoz, U. and Brodie, E.L., 2016. Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nature Communications, 7, p.13219. doi:10.1038/ncomms13219

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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