Deep Sequencing the English Channel, Or How You Can Find Any Microbe If You Look Hard Enough


If you took a random sample of seawater from the ocean, how many species of microbes do you think you would find? A dozen? 500? Sean Gibbons, a student in the graduate program in biophysical sciences, repeatedly sequenced the DNA of bacteria living in a 2-liter sample of water from the English Channel to identify what species were living there. When he compared it to a global database of microbes, he found 44 percent of the world’s microbes—from the kind that normally live in the open ocean to ones that usually thrive in brackish mangrove swamps—all in that tiny sample. What’s more, he and his colleagues said that if you looked long enough, you could eventually find all species of the ocean’s microbes in any given sample.

Ed Yong from National Geographic wrote about the study, and explained how this concept of “deep sequencing” works:

Here’s the problem: If you collect a sample of seawater, you can sequence the genetic material of whatever’s living in it and work out their identities. But you can’t sequence everything in one go. On your first pass, you’d only spot the most common residents. Try it again, and you’d pick up a few more. To get everything, including the really rare species, you need to do this millions, perhaps billions, of times. That’s called deep sequencing. It’s extremely deep sequencing. It’s like trying to track a city’s people using a few security cameras. Look at a day’s worth of footage and you’d spot the regular commuters. Give it a week, and new people would show up. Give it a decade, and even agoraphobes would turn up.

Gibbons worked with microbiologist Jack Gilbert from the department of ecology and evolution and Argonne National Laboratory, who is also working on a project to track the evolution of the bacterial community in our new hospital, the Center for Care and Discovery. They sequenced the sample of channel water 10 million times for this study. Gilbert told Yong that he estimated it would take 200 billion passes to find 100 percent overlap between their sample and the global database of species.

When I spoke to Gibbons about the study, he said that doesn’t necessarily mean they’re all thriving though.

“Obviously some organisms are just transients. They’ve come from somewhere else, they’re passing through the system and maybe they’ve gone dormant and they’re very rare. They’re not actively growing,” he said. “When you move into a particular environment, you get a very distinct fingerprint of who is abundant and who is actively doing something. So in a mangrove swamp there’s a very different mix of active organisms than in the surface ocean in the middle of the Atlantic.”

Still, he said given the implication that everything is everywhere in the ocean, at least in very tiny amounts, there’s potential for any biochemical process to occur too.

“From a biogeochemical standpoint, the implication is that any biogeochemical process that can occur in the ocean, does occur in the ocean. If the physical properties arise for nitrogen fixation or inorganic phosphate uptake, these things are going to happen, because the organisms are always there and they will rise in abundance,” he said. “Anything that can happen, does happen.”

Gibbons, S., Caporaso, J., Pirrung, M., Field, D., Knight, R., & Gilbert, J. (2013). Evidence for a persistent microbial seed bank throughout the global ocean Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1217767110

About Matt Wood (531 Articles)
Matt Wood is a senior science writer and manager of communications at the University of Chicago Medicine & Biological Sciences Division.
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