‘Bloggers’ and ‘spies’ will clarify marine processes

Rice researchers turn attention to gas sensors, microbial ‘memory’ for marine environments

Rice University researchers who have developed sophisticated gas-sensing microbes to report on conditions within soil are making tools for similar tasks in marine environments.

Rice biogeochemist Caroline Masiello, synthetic biologist Jonathan Silberg and microbiologist George Bennett are leading the development of tools to extend the soil technologies they’ve established in recent years.

The work backed by the Gordon and Betty Moore Foundation could lead to living sensors, modified bacteria that remember and report on what they see in fluids. They may be used, for example, to monitor how the environment affects rapid evolution among marine lifeforms through horizontal gene transfer or details about the iron, nitrogen and sulfur cycles essential to life at the cellular level.

Rice University researchers who have developed sophisticated gas-sensing microbes to report on conditions within soil are making tools for similar tasks in marine environments. Working on an experiment are, clockwise from left, professors Caroline Masiello and Jonathan Silberg and graduate students Emily Fulk and Ilenne Del Valle.

The ocean and its sediments present a far more challenging sensing problem than soil because the ecosystem changes dramatically with depth and evolution happens at a faster rate, said Masiello, a professor of Earth, environmental and planetary sciences.

“Our goal is to build synthetic microbes that tell us how their behavior changes as environmental conditions change,” she said. “We will do those experiments in the laboratory so we can control the variables and learn how microbial behavior responds to different environmental conditions.”

The team plans to construct two classes of genetically modified microbes to capture and deliver information: “bloggers” that report on their own behaviors and “spies” that report on their local environments.

Most biological sensing relies on fluorescent proteins that light up when triggered, but that doesn’t work in environments like soil where the light can’t be seen. The Rice labs’ solution was to program E. coli bacteria to emit a detectable gas instead.

E. coli’s limited lifespans and capabilities are inadequate for marine experiments, Masiello said. In the new study, the researchers plan to modify strains of Roseobacter, significant and plentiful bacteria in marine environments.

“One of the things we care about is detecting steps in the nitrogen cycle,” she said. “The advantage of a chassis organism like Roseobacter that participates in the nitrogen cycle is that you can ask it to report on those different behaviors.”

The lab is also interested in using microbes as “scribes” that record activities for later retrieval. Silberg said recent advances show it’s possible to use integrase enzymes programmed to sense activities and rewrite short segments of the microbe’s DNA to preserve a record of the event.

“It’s a kind of DNA barcode,” said Silberg, an associate professor of biochemistry and cell biology. “Now we can ask, ‘Have I seen iron at some threshold?’ ‘Have I seen some nitrate?’ And have every microbe write it down. As one thinks about long-term incubation, this is a really powerful tool, because even six months later we can pull out the DNA and see what happened.”

That will help scale synthetic biology experiments up to a level that’s more useful for environmental testing, he said. “In my lab, three or four days is a long time for a lab experiment. But for an ecologist, three or four days is silly. Processes sometimes take months. But with scalability comes longevity of measurements, and that’s where memory comes in. It’s complementary to gas sensing because it gives us a longer time scale.”