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Illuminating the dark corners of nature’s nitrogen cycle by mimicking rocket-fuel-producing bacteria

Genetically modified E. coli to be used to mimic - and therefore finally understand - a mysterious kind of rocket-fuel-producing bacteria that plays a critical role in the nitrogen cycle

By Kat J. McAlpine

In areas known as the ocean’s shadow zones, where oxygen is as its lowest saturation in seawater, certain bacteria have the metabolic ability to form nitrogen gas by combining ammonia and nitrite. These bacteria, known as anaerobic ammonia oxidation (anammox) bacteria, play a critical role in the biosphere’s hugely important nitrogen cycle and the substantial nitrogen losses observed in marine environments.

Yet in their metabolic activity, anammox bacteria also generate an energy-rich, yet highly toxic compound, called hydrazine, which is used in rocket fuel. How anammox bacteria manage to contain and make use of hydrazine – without self combusting, so to speak – has so far been a mystery to scientists. Until now, it has been very difficult to culture and study anammox bacteria and their oxygen-deprived microenvironment inside a conventional laboratory.

Kateryna Kon/

But a trio of researchers including Wyss Institute Core Faculty member and Harvard Medical School (HMS) professor Pam Silver, Wyss and HMS postdoctoral fellow Tobias Giessen, and Princeton University professor Bess Ward believe that specialized protein nanocompartments inside these bacteria could be essential to the anammox process, and could act as firewalls blocking hydrazine from damaging the bacteria themselves.

By unlocking the secrets of how these nanocompartments work, anammox bacterial metabolic processes could potentially be leveraged for the removal of nitrogen from wastewater. That’s why with the support of a grant from the Gordon and Betty Moore Foundation, which funds path-breaking scientific discovery and environmental conservation efforts, the team is seeking creative routes to understanding the functions of anammox bacteria and how they play a role in nature’s nitrogen cycle. The Moore Foundation’s support is through its Marine Microbiology Initiative.

The team will explore which anammox bacterial species are present in shadow zones and use genomics, transcriptomics and bioinformatics to determine their metabolic mechanisms. The team will then use that information to establish heterologous hosts using engineered E. coli that can make these processes observable in the lab.

“The ultimate example of systems biology is the interactions that happen between the earth and atmosphere that fuel our entire biosphere and world,” said Silver. “We hope to illuminate an until-now dark corner of the nitrogen cycle that could have broad implications for the earth as a whole.”

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