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Fermentation & the microbial highway

Earth is littered with molecules that contain many, excited electrons. They are often found next to other molecules or solid minerals that want those electrons. However, moving electrons can be an impossible task... without microorganisms. Microbes act as a highway on which electrons can travel. But the microbial highway isn't free. It has a tollbooth with a small energetic cost. Electrons arrive at their destination with slightly less energy than when they started, and microbes use that energy deficit to create life. 


"Life is nothing but an
electron looking for a place to rest."

- Albert Szent-Györgyi

Here's where my research comes in: Many of those juicy, electron-rich molecules have a hard time getting on the microbial highway. They are too big or too hydrophobic. They just can't pick up speed. Fortunately, there is a type of microbe, called a fermenter, that helps clunky molecules. Fermenters also run a tollbooth. This time at the entrance ramp of the electron highway. Clunky molecules gain speed and fermenters are rewarded with energy. Without fermentation, the microbial highway would be a lot less trafficked and those bigger tollbooths would have few customers to charge.


Microbes act as the engine for global elemental cycles that keep our planet habitable. There is so much still to learn about how they survive and interact, but we should pay special attention to the ever-important, often-unsung fermenters. That's what my research is all about. I try to use light stable isotopes to track the number of transactions at the fermenters' tollbooth. When current techniques aren't useful for this purpose, I develop new ones. Okay, you're ready to read below!


Carbon isotope signatures of fermentation

Fermentation is an important part of the microbial electron highway or as we call it, biogeochemical cycling. Yet microbial ecologists still lack tools to quantify fermentation in the environment. We are working to fill this gap by identifying unique carbon isotopic signatures of biomolecules created during fermentation. We use model organisms with known pathways to approximate natural communities. These signatures may lead to an in situ carbon isotope measurement to identify fermentation in the environment.


Orbitrap mass spectrometry of hydrogen isotopes

Sometimes carbon isotopes just aren't enough to answer questions about fermenters in the environment, so we moved to hydrogen isotopes. Unfortunately, high-sensitivity techniques for measuring the hydrogen isotope composition of fermentation products are rare, so we had to design our own technique.


Orbitrap isotope measurements takes advantage of the mass spectrometer's exceptionally high mass resolution. It measures the exact mass of every molecule in a sample, resolving isotopologues with very similar masses. It then reports the amount of each isotopologue and converts those to isotope ratios. 

Hydrogen isotope ratios are particularly difficult to measure because the rare isotope, deuterium ( H), constitutes <0.015% of hydrogen atoms. We pushed the limits of Orbitrap technology and demonstrated that quantified the δ H of acetate's methyl-site with precision and accuracy that rivals current techniques while using 50-1000x less sample.


Here's the paper.




Isotopologue modelling tools

To contextualize the carbon and hydrogen isotope signatures in metabolisms like fermentation, we realized that there should be a computational tool that can generalizably tracks isotope compositions of molecules in metabolic networks. Instead of treating isotopic compositions as a property of an atomic-site or of a molecule, we modelled individual isotopologues of molecules as different species in a box model. A number of isotope compositions (e.g. site-specific, compound-specific, clumped, etc.) can then be calculated from the distribution of a molecule's isotopologues. This treatment is generalizable to any isotope system (e.g. S, C, N, etc.) and can be used on reaction networks of any complexity. 

We call this modelling tool Quantifying Isotopologue Reaction Networks (QIRN, "churn"). We've used it to model prebiotic chemistry reactions, sulfur metabolism, photosynthesis and other important processes. QIRN is available in this Github repository with instructions on how to install and run models:

Here's the paper.

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Isotope-exchange 'clocks'

We've recently developed a method that gleans information about a molecule's in situ turnover mechanism and rate based on its hydrogen isotope composition.

Using the Orbitrap, we discovered that hydrogen from water abiotically exchanges with acetate at a predictable, temperature-dependent rate. This reaction pushes acetate toward an isotopic-equilibrium with water. It's an "expiration date" on acetate in the environment: If acetate is found at the equilibrium isotope effect with the ambient water, it has been around for longer than this expiration date. Otherwise, it must be created and consumed at a rate that is faster than the abiotic exchange reaction. This means we can go to the environment and set minimum in situ turnover times for acetate - and possible other biomolecules.

Stay tuned for some collaborative work using an isotope-exchange clock in one of the most isolated environments on Earth, the deep continental subsurface!



Isotope: An atom with the same number of protons, but different number of neutrons. For example, carbon-12 has 6 protons and 6 neutrons.  Carbon-13 has 6 protons and 7 neutrons. For more information on how we use isotopes, check out this article in Chembites!

Isotopologues: Molecules with the same chemical structures and formulas but with one or more of the atoms being a different isotope (i.e. H H  O and H H  O)

Delta Notation: To quantify the isotope composition of samples, we assign it as a per-thousand or "permil" change from an international standard. Where "R" is the ratio of the rare isotope to the abundant isotope.

Equilibrium Isotope Effect (EIE): The offset between the isotope ratios of two molecules if their atoms are freely exchanging with one another. This offset is driven by the heavier isotope's preference for a chemical bond where its presence lowers the energy of the bond. For example, given a choice at low temperatures, deuterium would rather be substituted into water than acetate's methyl-group and this is reflected in the EIE between these molecules.







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