Serendipitous history in the microbial making

It’s been over 100 years since the Dutch Microbiologist Martinus Willem Beijerinck theorized that microbes could oxidize manganese to generate energy for growth. Last week, the first evidence for this theory was published, and you might be surprised about from where these fascinating microbes hail.

Microbes do all sorts of metabolic magic, growing across incredibly diverse environments from the deepest ocean to glaciers. The stars of the show in this study are chemolithoautotrophs, explained here as “microbes that utilize chemicals (chemo) from the bedrock (litho) as an energy source for making their own (auto) food (troph)”.

In the article by Hang Yu and Jared Leadbetter, a co-culture made up of two bacterial species oxidized manganese to grow and fix carbon, generating manganese oxide nodules. These wacky microbes were isolated from a glass jar left over from a previous experiment that happened to be coated with a slurry of Mn(II)CO3 (manganese carbonate), which was filled by chance with something quite exotic…tap water from Pasadena, California. It turns out that this was an accidental experiment, as the jar was then left to *ahem* incubate, on the side of a sink for a few months. When Leadbetter returned to his office after working off campus he realized that the creamy carbonate on the interior of the glass turned into a dark manganese oxide.  

After the party started in that glass jar, Yu and Leadbetter took a bit of whatever was growing and did what all biologists love: transferred liquid A (the culture) into liquid B (fresh media), then waited some more and then did it all over again (see Tweet below for methods). The goal was to get a stable and consistently growing culture, which they accomplished quite well. They analyzed a sample of the very first culture and found it was made up of a diverse community of ~70 species. After multiple rounds of liquid A into liquid B, they managed to reduce the block party to an intimate dinner for two, with the main course being MnCO3.

This co-culture was dominated by the microbe the authors termed ‘Candidatus Manganitrophus noduliformans’ (whew, that is a mouthful). The secondary “minority” member was designated Ramlibacter lithotrophicus. Only R. lithotrophicus was successfully isolated all by its lonesome, but it did not oxidize manganese when isolated.

Even without isolating each individual member, they were able to sequence the full genomes for both, which was helpful to guide experiments in the lab and can now be used to understand the distribution of these organisms in the environment.

Yu and Leadbetter also sequenced the transcriptomes of the co-culture, to understand what genes were being used during growth. Compared to the genomes, they could tell what capabilities each microbe had and what wasn’t expressed. To further delve into the metabolism of the co-culture, they grew it with two labeled isotopes and observed that both of the microbes identified incorporated the isotopes. Although from the data, C. M. noduliformans looked to be the main player in manganese dependent CO2 fixation.

Original caption from Figure 4 included.

This study has broad reaching implications, that will allow us to better understand the web of biogeochemical cycles that drive life on this planet. It’s also is a lesson in recognizing that you never know when an opportunity to transfer a new exciting liquid A into liquid B might be waiting in your office.


Yu, H. and Leadbetter, J.R., 2020. Bacterial chemolithoautotrophy via manganese oxidation. Nature583(7816), pp.453-458.

Bacteria with Metal Diet Discovered in Dirty Glassware. Whitney Clavin. July 15, 2020.

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