Researchers Squash Fungal Processing Time to Accelerate Biofuels Development

May 20, 2024 by Dan McCue
Researchers Squash Fungal Processing Time to Accelerate Biofuels Development
Guoliang Yuan was manually squashing the spores of Aspergillus niger using a specially designed 96-well plate for mutant screening. (Photo: Jasmin Alvarez)

RICHLAND, Colo. — Researchers at the Pacific Northwest National Laboratory found a way to significantly speed up biofuel and biochemical production.

The breakthrough, published in the journal Fungal Biology and Biotechnology, involves microorganisms, such as fungi, which are used in the DNA analysis that is a critical step in converting renewable feedstock materials into useful biochemical products.  

The challenge has always been that the process known as polymerase chain reaction, which amplifies the fungi DNA for analysis, has always been inordinately time consuming.

Led by Guoliang Yuan, a research team at the national laboratory has found that simply squashing the fungal spores — rather than the fungal biomass — reliably yields high-quality DNA samples suitable for use in the polymerase chain reaction.

While it may seem straightforward, squashing the spores is counterintuitive for a couple reasons. 

The spores are small, tough to break open, and don’t respond well to the same extraction chemicals used on fungal biomass. 

In order to circumvent these obstacles, the researchers needed to go shockingly low-tech, mechanically squashing the spores in a buffer on a microscope slide with their thumbs. 

After squashing, the DNA is released into the buffer, which can then be used for polymerase chain reaction. 

Yuan, who is first author of their research paper, said that this took the DNA extraction process from “at least three days to maximum three minutes.” 

This thousand-fold speed-up in the time it takes to extract DNA from fungal samples will help researchers at the national lab and across the bioproducts community iterate and analyze mutated fungi much more quickly, accelerating biofuels development.

The technique is remarkably effective, with only a minor downside: squashing lots of samples by hand can be tiring and time-consuming. 

To address this, the team created a specialized plastic plate with 96 wells and a corresponding cover with pins to more efficiently squash large volumes of samples. Further refinements to the process are ongoing.

The team’s work was supported by the U.S. Department of Energy’s Bioenergy Technologies Office, and the Agile BioFoundry consortium.

Dan can be reached at [email protected] and @DanMcCue

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