Nature Journal Club

David Kirchman

University of Delaware, Lewes

A microbial ecologist learns something new from an old-fashioned study.

What could be easier than learning about an organism simply by watching how it varies over time in its natural habitat? You’d think this would have been done long ago for marine bacteria, which are important in many biogeochemical processes, including the carbon cycle; in fact, they’re the organisms running the biosphere. But it’s not easy to follow microbes in the open ocean, far from the lab and beyond the reach of standard techniques.

Craig Carlson at the University of California, Santa Barbara, and his colleagues took on this challenge for the most abundant group of marine bacteria: SAR11. They examined variations in SAR11 over several years in the Sargasso Sea, where the group was first discovered nearly 20 years ago (C. A. Carlson et al. ISME J. 3, 283–295; 2009). Sequencing and other data had previously revealed that SAR11 bacteria are diverse and can account for almost 50% of microbes in a given marine environment; however, we still knew little about their natural history.

So Carlson’s group looked to address a basic question: how do different members of SAR11 vary with depth and over time? They examined 13 years’ worth of DNA samples, viewed 3 years’ worth of preserved cells under the microscope, and then analysed the microbial data in light of what is known about SAR11’s environment. Three SAR11 ‘ecotypes’, they say, flourish differently at various depths and over a yearly cycle, which starts in spring, when deep mixing stops and photosynthesis speeds up.

The authors make good use of new genomic data from a lab-grown representative of SAR11 (Pelagibacter ubique) to understand Sargasso Sea populations, but the study’s insight comes from the old approach of patiently watching organisms over time in their natural habitat.

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