Why is the Department of Energy interested in genomics and metabolomics? How do we eventually create sustainable fuels from biomass in a “one pot solution”?
Metabolomics and carbon cycling
Tools of Science visited the Joint Genome Institute (run by the DOE) in Walnut Creek, California to find out how the study of metagenomics can help create better models for carbon cycling (which affects climate) and discover more efficient processes for turning biomass into sugar and eventually fuels or other useful materials.
Trent Northen is the Metabolomics lead at JGI and a Director at both the Joint Bio Energy Institute (JBEI) and the Lawrence Berkeley Laboratory. He is developing a suite of technologies that complement the DOE’s DNA sequencing efforts both at JGI and as part of other DOE programs.
He uses high resolution/accurate mass LC-MS to understand how different organisms work together to cycle nutrients and at the Joint BioEnergy Institute his group has pioneered high throughput technologies for discovering enzymes that break down lignocellulose.
It’s a pretty sweet gig. The government pays Trent to make cocktails at work. High performance enzyme cocktails. You can’t drink them, but someday they might help power your hovercar.
Here are a couple of things Trent is trying to do:
- Discover all the exogenous metabolites in a sample
- Find out why is there so much diversity in a small sample of soil and how each organism works with the others in that ecosystem
- Understand how is biomass is cycled and carbon returned back into the atmosphere
Improving models of carbon cycling in soil
As a result, we’re not sure what will happen in the soil as atmospheric CO2 continues to increase. Trent is working to improve those models.
One way is through metagenomics and metatranscriptomics. Changes in transcription can be correlated with metabolism of substrates to identify which organisms are contributing to certain steps in a pathway.
The goal is to build model communities to see what metabolites they produce and how they work together. Can scientists reproduce the processes observed in environmental samples to discover what the role of a particular gene is in a relationship between organisms?
Match.com for microbes
By understanding what some microbes produce and what others are looking for in a relationship, Trent can help them hook up in a test tube to create completely new pathways. Those pathways could be assembled either within a new host or even a cell free system to turn biomass into sugar.
Synthetic ecology is just getting started.
The ideal case is the one-pot approach where all the enzymes needed are present to take pretreated biomass and convert it to fuel or even precursors for synthesizing new materials.
How do they do that?
That’s what Tools of Science is all about. Fasten your geekbelts, Scotty, we’re going in.
Trent looks to see how combinations of 3 organisms at a time in a controlled environment affect what metabolites are found (or consumed) in the growth media. Liquid chromatography is used to separate compounds and mass spec provides a snapshot profile of what’s in the soup.
Fragmenting ions in the Thermo Q Exactive allows Trent to identify and quantify metabolites that are appearing or disappearing.
For high throughput screening, Nanostructure Initiator Mass Spectrometry (NIMS) takes advantage of the MALDI LTQ Orbitrap mass spectrometer.
It allows Trent to look across lots of combinations of organisms to quickly see what their combined activity is and the kinetics of those activities so he can identify the high performers. (Remember the cocktail?)
NIMS is a direct infusion technique. It starts with about 10000 tiny spots of media (containing metabolites) in 10-nanometer pores on a plate. We’ll explain how the spots are arrayed in a minute. The MALDI laser heats up oil (the initiator) on the plate and it vaporizes (explodes) whatever is on the surface into the air where it is pulled by vacuum into the LTQ Orbitrap Mass Spectrometer and analyzed to see which metabolites are present.
10,000 spots (samples) can be analyzed in about 12 hours.
How do you get all those spots on the plate? Acoustic printing.
Imagine a 384 well plate with liquid in each well. Focused acoustic energy is used to “flick” each well and shoot a 1 nanoliter drop onto the NIMS plate hovering above it. Repeat that for thirty-six 384 well plates in a defined pattern and you have your array.
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