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JGI at 25: Following Fungi that Pry Apart Plant Polymers

2022 marks the JGI’s 25th anniversary. Over the last year, we’ve been revisiting a number of notable achievements that showcase our collaborations and capabilities to enable great science that will help solve energy and environmental challenges.

A brown goat with small white horns stands on top of a wooden platform.

Elway, a San Clemente Island Goat at the Santa Barbara Zoo, contributed fecal matter to support O’Malley’s work on biomass-busting microbes. (Courtesy Photo)

Usually, plants have the upper hand against any kind of biomass breakdown. They’ve spent millions of years evolving tactics against potential threats. 

“Because plants can’t run away, they’ve evolved these really tough cell wall materials that keep microbes — and the enzymes that would be produced by microorganisms — out,” said JGI user/collaborator Michelle O’Malley, a chemical and biological engineer at the University of California Santa Barbara.

So plants don’t break down without a fight, but it’s an important battle to fine-tune. Plant biomass harbors all kinds of organic material and stores quite a bit of energy. Eventually, that biomass could serve as the starting material for a wide range of fuels and chemicals. To get to that point, industrial facilities will need large-scale approaches to processing plant biomass.

Here, cud-chewers like goats, sheep and cows share an important talent. In their herbivorous lives, they all process loads of tough plants. Thanks to gut microbes — namely, anaerobic fungi — these animals are able to pry apart plant polymers and efficiently harvest the energy they store. 

Since 2012, O’Malley has worked with the JGI to understand the enzymes these organisms use to bust biomass apart. She and her team find these fungi, and their enzymes, primarily in animal poop. 

“As an engineer, I think of poop as a biotech resource,” O’Malley said as she opened her talk at the 2022 JGI Annual Meeting. In an herbivore’s poop sample, there’s a whole heap of microbes, each potentially contributing to powerful biomass processing. “So if you peer inside a poop sample, or a rumen sample, you’re going to find beautiful diversity.”

Within that diversity of bacteria and fungi, O’Malley and her team are amassing all kinds of supplies in the quest to break down plants. In 2016, her team leveraged transcriptomics and other assays to identify and test carbohydrate-active enzymes. They found many enzymes that outperformed industry standards. A year later, her team used proteomics, genomics and transcriptomics to discover another advantage these fungi wield: the capacity to form enzyme complexes that work like assembly lines for efficiency. In 2021, her team saw that four strains of anaerobic fungi also, unexpectedly, secrete natural products. Those results showed that these fungi may be able to provide tools beyond biomass breakdown, extending into biochemical production. 

Over time, as these projects have delivered results, they have also snowballed into more collaborations. One of O’Malley’s former postdocs, Kevin Solomon — now an assistant professor at the University of Delaware — is building on this work to explore an enzymatic ‘toolbox’ of biomass-degrading capabilities for anaerobic fungi.

Eventually, it’s possible that fungal communities — or enzymes from fungal communities — could pave the way for many different kinds of plant-derived production. 

“Sculpting those communities is really a hard problem,” O’Malley noted. “There’s a lot that we and others have to do to tackle that. But there’s opportunities for borrowing and porting parts from nature — enzymes, transporters, pathways — into microbes that we do know, to advance our biotech goals.”

 

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