Scientists track ocean microbe populations in their natural habitat to create a ‘day in the life’ montage

January 22, 2013

Denise Brehm
Civil & Environmental Engineering 

Microbiologists who study wild marine microbes, as opposed to the lab-grown variety, face enormous challenges in getting a clear picture of the daily activities of their subjects. But a team of scientists from MIT and the Monterey Bay Aquarium Research Institute recently figured out how to make the equivalent of a nature film, showing the simultaneous activities of many coexisting species in their native habitat over time.

Instead of making a movie, the scientists used a robotic device that dangled below the surface of the ocean, drifting in the water with a neighborhood of microbial populations and gathering samples of one billion microbes every four hours. Similar to fast photography that stops action, the robotic device “fixed” each sample so that whatever genes the microbes were expressing at the moment of capture were preserved for later study in the lab, where the scientists used whole-genome gene-expression analysis to create a time-lapse montage of the daily labors of multiple microbial species over a two-day period. 

“A naturalist like Sir David Attenborough can follow a herd of elk and see how the elk’s behavior changes hour to hour, day to day and week to week. But we haven’t been able to observe naturally occurring microbes with that kind of resolution until now,” says Edward DeLong, the Morton and Claire Goulder Family Professor in Environmental Systems in the MIT Department of Civil and Environmental Engineering and Department of Biological Engineering. 

DeLong is senior author of a paper on the study appearing online the week of Jan. 21 in the Proceedings of the National Academy of Sciences. Co-authors on the paper are Elizabeth Ottesen, a former MIT postdoc who is now an assistant professor at the University of Georgia; MIT postdoc Curtis Young and research engineer John Eppley; and senior research specialist John Ryan, senior scientist Francisco Chavez and president Christopher Scholin of the Monterey Bay Aquarium Research Institute.

“We’ve essentially captured a day in the life of these microbes,” DeLong says. “As little as three years ago, I wouldn’t have even have considered it possible to get such a high resolution picture of microbial population dynamics and activity in the ‘real world.’”

Because microbes are extraordinarily sensitive to slight environmental changes and alter their gene expression rapidly in response to fluctuations in temperature, light, nutrient availability and other environmental variables, the genes they express tell a story about their habitat and their interactions with it: In essence, changes in their gene expression provide information on the good times and the bad times they experience. In a sense, each naturally occurring microbe is a living sensor; the researchers read the sensors’ outputs by studying their gene express