The local environment of a microbe can make the difference between life and death

The microbial world shapes essentially every aspect of our lives. Whether they are in the soil where our food is grown, or in the lungs of a person with an infection, or at the bottom of the ocean, microbes live in diverse communities made up of multiple species, all working together and influencing each other . Just as in our own neighborhoods, how a microbial community is structured, geography affects how those microbes live and function together.

Now, Caltech researchers have discovered that changes in local oxygen concentration have drastic effects on whether microbial neighbors live or die in the presence of a common microbial byproduct, nitric oxide (NO). The results suggest that large-scale global models such as the nitrogen cycle should work towards representing the fact that microscale chemical environments affect microbial behavior.

An article describing the research appears in the journal Current Biology on October 27th. The study was led by graduate student Steven Wilbert and conducted in the laboratory of Dianne Newman, Gordon M. Binder/Amgen Professor of Biology and Geobiology and Executive Officer of Biology and Bioengineering.

Nitrogen oxide is formed as an intermediate product in the multi-stage process of converting nitrate (NO₃^–) in nitrogen gas (N₂). This entire process, called denitrification, is a crucial part of biological processes around the world. Recent research has shown that different steps in this pathway can be performed by different members of different microbial communities.

To study how a microbe’s local environment affects its ability to carry out the denitrification process, Wilbert used Pseudomonas aeruginosa, a bacterium that has been extensively studied in the Newman lab, as a model organism. Using genetic engineering techniques, Wilbert produced a strain that only performed the first half of the denitrification pathway and another strain that only performed the second half of the pathway.

Wilbert then studied how these two genetically engineered bacterial strains interact under different oxygen environments. The idea was that the ‘first half’ strain produced NO as a by-product, and the team wanted to find out how the ‘second half’ strain would deal with NO under different local oxygen concentrations and how this in turn would affect the entire community.

The study showed that in the absence of oxygen, the second genetically engineered Pseudomonas strain was able to take up the NO produced by the first and chemically alter or reduce this chemical as part of the normal denitrification process. In addition, the bacteria could use NO as a substrate on which to grow. However, in an environment with higher oxygen concentrations, NO became toxic, killing strains of Pseudomonas that could not reduce the molecule.

“Oxygen dramatically alters these microbial interactions: they can either live or die,” says Newman. “This in turn affects the entire denitrification process. Models attempting to account for how microorganisms contribute to the nitrogen cycle must therefore account for the microscopic spatial environment. That is a really important variable.”

While the study revealed the specifics of how oxygen mediates cellular interactions with NO, the research also points to more general principles across a broad class of microbial byproducts. NO is an example of a “redox-active metabolite” or RAM. This study offers a new avenue to study how the effects of RAMs on microbes are influenced by their local microenvironment, which can be highly variable in space and time.

“Microbial metabolism is like a race to gain and lose electrons,” explains Wilbert. “Essentially all life revolves around this transmission of energy. With their ability to donate or receive electrons, RAMs serve as an important currency between microbial neighbors. While this can facilitate energy transfer, RAMs are sensitive to changes in local oxygen concentrations that vary in space and time. Based on our results with NO, we are convinced that oxygen holds the key to a clearer picture of what’s in the unseen soils, the oceans, and happens anywhere microbial interactions can take place, if we understand how oxygen is changing in the microscale environment, we can make better predictions about how microbial communities survive in the lungs or in agricultural systems.”

The paper is titled “The opposing roles of nitric oxide drive microbial community organization as a function of oxygen presence”.