Michelle O’Malley: Biomaterials and Fluoride Antibiotics


Biofuels and the Global Energy Transition

Recent years have seen an increase in the call for the “energy transition.” This implies the global energy sector’s shift from fossil-based systems of energy production to renewable energy sources like wind and solar, and lithium-ion batteries. Switching from non-renewable energy sources like oil, natural gas and coal to renewable energy is made possible by technological advancements and a societal push toward sustainability [1]. 

Among these newer and more sustainable sources of energy, biofuels are emerging as an increasingly potent option. Biofuels are liquid fuels derived from biomass (plant or algae material or animal waste). It is commonly advocated as a cost-effective and environmentally benign alternative to petroleum and other fossil fuels. Particularly, this is within the context of rising petroleum prices and increased concern over the contributions made by fossil fuels to global warming [2]. The two most common types of biofuels in use today are ethanol and biodiesel.

Fungi, bacteria, and yeast are emerging microbes that have potential to fulfil the current demand of feedstock needed for biodiesel production. They could easily utilise waste materials for producing biodiesel. In fact, this method might even prove to be more cost-effective as compared to conventional means of biodiesel production. Dr. Michelle O’Malley, professor of Chemistry at the University of California, Santa Barbara, explores this emerging possibility in her research endeavours. 

Fungi and the Breakdown of Lignin

A major difficulty faced by the bioenergy industry, as Dr. Michelle O’Malley highlights, is the breakdown of lignin (Figure 1). Lignin is a type of organic polymer found in the cell walls of trees and responsible for many biological functions like water transport and mechanical support. Lignin holds up trees and helps in preventing them from rotting, and is needed to transform non-food plants into biofuels. However, the strong molecular architecture of the polymer makes breaking it down into simple sugars a very difficult process. Most current industrial processes burn the lignin or treat it with expensive and inefficient chemicals. But the development of newer and more efficient methods for lignin breakdown for the bioenergy industry remains a pressing need. 

Figure 1: Molecular structure of lignin

By co-evolving with trees, fungi have managed to get around the difficulty presented by lignin decomposition. Fungi are, in fact, the only major organism that can break down or significantly modify lignin, even better than the machines we have developed so far. Learning how these organisms break down lignin and cellulose could make our existing industrial processes more affordable and sustainable, suited for a modern future. 

Dr. Michelle O’Malley: Using Fungi for Biofuel Production

Dr. O’Malley has discovered novel strains of fungi in the intestinal tracts of goats, sheep and other herbivorous animals from samples collected from the Santa Barbara Zoo. These fungi develop structures called ‘tendrils.’ These invade the digesting material of the animal and secrete enzymes which help in the breakdown of plant matter into sugars [3]. The enzymes work by splitting many of lignin’s chemical bonds, turning it into simple sugars and releasing carbon dioxide into the air. Dr. O’Malley has devised means to identify their enzymes using genetics and enabled the development of new bioengineering approaches to biofuels. 

Most of her early work focused on identifying specific microbes and deconstructing biomass materials to sugars. Recently, she has begun to investigate methods of creating new chemicals. Her research explores the possibility of upgrading lignin and sugars into volatile fatty acids or aviation fuels, useful in various fields. She has also begun synthesizing bio-derived monomers* that can potentially be transformed into novel materials [4].  

*A monomer is a molecule of any class of compounds, mostly organic, that can react with other molecules to form very large molecules called polymers.

Fungi and Fluorides in Biotechnology

Scientists have long been aware of the dangerous overuse of antibiotics and the increasing number of antibiotic-resistant microbes that have resulted. Over-prescription of antibiotics for medicinal use has adverse implications for human health. But so too does the increasing presence of antibiotics in the natural environment. A large part of this accumulation stems from the biotechnology field, which has depended on antibiotics as a selection device in the lab [5]. 

Researchers use these antibiotics to kill cells that they don’t want to grow. Within a population of cells, a certain genetically engineered cell is given an antibiotic resistance gene. The rest are killed using antibiotics. The problem that arises, however, is that many of these organisms have developed resistance to the antibiotics used. This has resulted in their unwanted proliferation in the wrong ecosystems. 

The use of fluoride in place of antibiotics provides a potent solution to this problem. Anaerobic fungi discovered in Dr. O’Malley’s lab consisted of fluoride exporters in their cells. These exporters are a kind of protective mechanism against the potentially fatal accumulation of fluoride. Through a process developed by Justin Yoo, a former graduate student researcher in Dr. O’Malley’s lab, the working of these exporters is rendered non-functional. Essentially, what this implies is that the cell would still thrive in the lab, where fluoride-free distilled water is normally used. But if it escaped into the natural environment, it would die as soon as it encountered fluoride, thus preventing propagation [4]. 

Learn More

If you’d like to hear more about Dr. Michelle O’Malley’s life as a professor of chemistry, visit us on Spotify to listen to our ChemTalk podcast! Learn more about her meeting with President Obama, her path to researching biomaterials, and what her favourite honour is that she’s received. 

Find the ChemTalk podcast here.

Works Cited

[1] “What is Energy Transition?” S&P Global. 24 February 2020. 

[2] Lehman, C. and Selin, . Noelle Eckley (2022, December 16). biofuel. Encyclopedia Britannica.

[3] Manke, Kristin. “What Biofuel Production Can Learn from the Zoo: Michelle A. O’Malley.” Office of Science. 11 May 2016. 

[4] O’Malley, Michelle. Personal Interview. Conducted by Scott Gietler, Lawton Long and Rylie Maziek. 20 May 2021. 

[5] Badham, James. “Fluoride to the Rescue?” The Current. 22 December 2020.