Cool Job: One green chemist is mining zoo dung for biological helpers | Science News for Students

Cool Job: One green chemist is mining zoo dung for biological helpers

Her goal is to convert farm-field wastes into useful fuels and chemicals
Oct 11, 2019 — 6:50 am EST
a photo of Michelle O’Malley

Michelle O’Malley, 37, is a chemical and biological engineer at the University of California, Santa Barbara. Her team is looking to mine microbes from animal wastes in a search for making “greener” products.

UC Santa Barbara

You might call this group of lab members a poop patrol. Sometimes, they hang out at the Santa Barbara Zoo waiting for certain goats and sheep to do their business. But they’re not there just as a cleanup crew. To them, these droppings are more than waste. They’re the source of microbes that might one day become the route to greener fuels and chemicals.

Michelle O’Malley, 37, leads this group. She’s a chemical and biological engineer at the University of California campus across town. Her team is hunting for fungi that live in the digestive tract of plant-eating animals, such as sheep, goats, cows, giraffes and elephants. As anaerobes (AN-uh-roabs), those fungi can only live in the absence of oxygen. Together with some anaerobic bacteria, these fungi can break down grass and other plants. Along the way, they release sugars and other nutrients.

These particular microbial helpers do not usually show up in the human gut. That’s why much of the fibrous parts of plants that we eat goes undigested. It passes through our guts, largely unaltered, exiting as wastes out the other end.

Here at the zoo, the researchers are focusing on San Clemente Island goats and Navajo-Churro sheep. “It can be hard to tell the difference between goat and sheep poop,” notes O’Malley. So it helps to “watch the donation take place.”

San Clemente goats; Navajo-Churro sheep
O’Malley’s team collects samples of poop from San Clemente Island goats and Navajo-Churro sheep (both pictured here) at the Santa Barbara Zoo.
Xuefeng (Nick) Peng

Once collected, their pellets go to the lab. There, team members coax out the fungi that enable these animals to digest certain plants.

O’Malley had to learn what she calls “very old-school technology” to grow the finicky fungi in her lab. Then she turned to tracking down the distinctive plant-degrading enzymes that these fungi make. Her big-picture plan is to help society move away from fossil fuels, such as petroleum. In their place, she hopes to find more sustainable ways to make chemicals and fuels. Her raw materials could be agricultural leftovers — such as corn stover and wheat straw, for example. In the past, such leftover plant materials have often been viewed as waste because people can’t eat them.

Fungi point to helpful enzymes

The fibrous parts of plants are made of lignocellulose (Lig-no-SEL-yu-loas). That chemical, in turn, is made from smaller compounds. Among them are two sugars: cellulose and hemicellulose. And those sugars are rich in carbon. Carbon is also a major ingredient in most fuels and many other chemicals and drugs.

O’Malley’s team would like to mine lignocellulose for its carbon. The problem is that the fibrous parts of plants also contain lignin. It’s a structural material that serves “to keep microbes and their enzymes out” of plant cell walls, O’Malley explains. So lignin makes it difficult to get to the sugars in lignocellulose.

Industrial chemists have found ways to chemically or physically remove lignin. But those processes often are costly, toxic and wasteful (as lignin itself contains valuable chemicals).

Some fungi have a better approach. And that’s what drew O’Malley’s attention to plant-eating animals and their poop. It turns out, O’Malley says, that certain anaerobic fungi found in the guts of these animals could give industry a greener way to break down cellulose, hemicellulose — and even lignin.

After a goat’s grassy lunch, certain anaerobic fungi burrow into the plant cell walls. There they release enzymes that break down lignocellulose — lignin and all. These challenging fungi have a 10-syllable name: Neocallimastigomycota.

O’Malley studied under chemical engineer Anne Robinson. That was back when she was in graduate school at Carnegie Mellon University in Pittsburgh, Pa. Robinson isn’t surprised her former student is working with such a challenging microbe. She recalls her student as being “very unafraid to tackle problems” and “able to recognize the interesting or unusual result.”

One fungus: Many, many digestive enzymes

After graduate school, O’Malley contacted scientists who had worked with anaerobic fungi. Most had abandoned those studies. The microbes just proved too difficult to work with. Then Michael Theodorou invited her to work with him. He had pioneered research on such microbes. Today he works at Harper Adams University in Newport, England. Back then, though, Theodorou was in Wales. And there he taught O’Malley how to isolate and grow these fungi.

Their challenge was feeding the fungi what they needed to grow, all the while keeping oxygen out.

Her team now begins with roll tubes. Think of them as 3-D petri dishes that can support growth across their inner walls, all in an oxygen-free environment. Carbon dioxide and a food source with digestive fluids are added to the closed tubes. Next, her team rolls the tubes to get an even coat on the internal walls. After adding a fungi-rich poop slurry, they roll the tubes again. If the process works, fungal colonies grow.

“All of this requires a lot of careful, coordinated, quick movements,” O’Malley says. It’s “a lost art.”

In her UC Santa Barbara lab, O’Malley has been isolating fungi from zoo samples and studying their enzymes. Until now, “nobody really knew their true power,” she says. Those fungi (with a mouthful of a name) turn out to have genes to make the largest number of biomass-degrading enzymes known. That’s something her team reported in Science three years ago.

The researchers have now partnered these anaerobic fungi with brewers’ yeast (Saccharomyces cerevisiae). That yeast is a mainstay of the biochemical industry.

O’Malley’s group showed that the fungi efficiently broke down lignocellulose in reed canary grass. That freed the sugars to be converted to other products by the yeast. O’Malley and colleagues shared their findings, last year, in Biotechnology and Bioengineering.

With the goal of unleashing these powers for the biotechnology industry, O’Malley and her group are exploring whether it makes sense to harvest the enzymes from the fungi. Maybe they should just insert fungal DNA into yeast and bacteria. That could turn them into enzyme-making machines.

Figuring out the ideal way to break down lignocellulose “has been a really [unsolveable] problem for a long time,” says Michael Betenbaugh. This biochemical engineer works at Johns Hopkins University in Baltimore, Md. O’Malley “kind of forged out on her own,” he says. Her trick, he adds, was “looking for these unusual microbes that have been doing [it] for millennia.”

Power Words

(more about Power Words)

3-D     Short for three-dimensional. This term is an adjective for something that has features that can be described in three dimensions — height, width and length. 

anaerobe     An organism able to live in the absence of oxygen.

anaerobic     Occurring in the absence of oxygen. Anaerobic reactions take place in oxygen-free locations.

bacteria     (singular: bacterium) Single-celled organisms. These dwell nearly everywhere on Earth, from the bottom of the sea to inside other living organisms (such as plants and animals). Bacteria are one of the three domains of life on Earth.

biochemical     (adj.) Referring to something made and used within living things.

bioengineering     The application of technology for the beneficial manipulation of living things. Researchers in this field use the principles of biology and the techniques of engineering to design organisms or products that can mimic, replace or augment the chemical or physical processes present in existing organisms. This field includes researchers who genetically modify organisms, including microbes. It also includes researchers who design medical devices such as artificial hearts and artificial limbs. Someone who works in this field is known as a bioengineer.

biomass     Matter that contains carbon and can be used as a fuel, especially in a power station for the generation of electricity. Plants are a kind of biomass.

carbon     The chemical element having the atomic number 6. It is the physical basis of all life on Earth. Carbon exists freely as graphite and diamond. It is an important part of coal, limestone and petroleum, and is capable of self-bonding, chemically, to form an enormous number of chemically, biologically and commercially important molecules.

carbon dioxide (or CO2)     A colorless, odorless gas produced by all animals when the oxygen they inhale reacts with the carbon-rich foods that they’ve eaten. Carbon dioxide also is released when organic matter burns (including fossil fuels like oil or gas). Carbon dioxide acts as a greenhouse gas, trapping heat in Earth’s atmosphere. Plants convert carbon dioxide into oxygen during photosynthesis, the process they use to make their own food.

cell     The smallest structural and functional unit of an organism. Typically too small to see with the unaided eye, it consists of a watery fluid surrounded by a membrane or wall. Depending on their size, animals are made of anywhere from thousands to trillions of cells. Most organisms, such as yeasts, molds, bacteria and some algae, are composed of only one cell.

cellulose     A type of fiber found in plant cell walls. It is formed by chains of glucose molecules.

cereals     Plants in the grass family that provides an edible seed, which serves as a food staple (such as wheat, barley, corn, oats and rice).

chemical     A substance formed from two or more atoms that unite (bond) in a fixed proportion and structure. For example, water is a chemical made when two hydrogen atoms bond to one oxygen atom. Its chemical formula is H2O. Chemical also can be an adjective to describe properties of materials that are the result of various reactions between different compounds.

chemical engineer     A researcher who uses chemistry to solve problems related to the production of food, fuel, medicines and many other products.

colleague     Someone who works with another; a co-worker or team member.

compound     (often used as a synonym for chemical) A compound is a substance formed when two or more chemical elements unite (bond) in fixed proportions. For example, water is a compound made of two hydrogen atoms bonded to one oxygen atom. Its chemical symbol is H2O.

defecate     To discharge solid waste from the body.

digest     (noun: digestion) To break down food into simple compounds that the body can absorb and use for growth. Some sewage-treatment plants harness microbes to digest — or degrade — wastes so that the breakdown products can be recycled for use elsewhere in the environment.

digestive tract     The tissues and organs through which foods enter and move through the body. In people, these organs include the esophagus, stomach, intestines, rectum and anus. Foods are digested — broken down — and absorbed along the way. Any materials not used will exit as wastes (feces and urine).

DNA     (short for deoxyribonucleic acid) A long, double-stranded and spiral-shaped molecule inside most living cells that carries genetic instructions. It is built on a backbone of phosphorus, oxygen, and carbon atoms. In all living things, from plants and animals to microbes, these instructions tell cells which molecules to make.

dung     The feces of animals, also known as manure.

environment     The sum of all of the things that exist around some organism or the process and the condition those things create. Environment may refer to the weather and ecosystem in which some animal lives, or, perhaps, the temperature and humidity (or even the placement of things in the vicinity of an item of interest).

enzymes     Molecules made by living things to speed up chemical reactions.

fiber     Something whose shape resembles a thread or filament. (in nutrition) Components of many fibrous plant-based foods. These so-called non-digestible fibers tend to come from cellulose, lignin, and pectin — all plant constituents that resist breakdown by the body’s digestive enzymes.

fossil fuel     Any fuel — such as coal, petroleum (crude oil) or natural gas — that has developed within the Earth over millions of years from the decayed remains of bacteria, plants or animals.

fuel     Any material that will release energy during a controlled chemical or nuclear reaction. Fossil fuels (coal, natural gas and petroleum) are a common type that liberate their energy through chemical reactions that take place when heated (usually to the point of burning).

fungus     (plural: fungi) One of a group of single- or multiple-celled organisms that reproduce via spores and feed on living or decaying organic matter. Examples include mold, yeasts and mushrooms.

gene     (adj. genetic) A segment of DNA that codes, or holds instructions, for a cell’s production of a protein. Offspring inherit genes from their parents. Genes influence how an organism looks and behaves.

graduate school     A university program that offers advanced degrees, such as a Master’s or PhD degree. It’s called graduate school because it is started only after someone has already graduated from college (usually with a four-year degree).

gut     An informal term for the gastrointestinal tract, especially the intestines.

hemicellulose     A comparatively soft fiber found in a plant’s cell walls.

lignin     A natural substance that helps strengthen the cell walls of plants. Although lignin is made from a large number of sugar molecules, which should provide energy, livestock can’t digest this material because of the way its sugars are chemically bonded together.

microbe     Short for microorganism. A living thing that is too small to see with the unaided eye, including bacteria, some fungi and many other organisms such as amoebas. Most consist of a single cell.

millennia     (singular: millennium) Thousands of years.

nutrient     A vitamin, mineral, fat, carbohydrate or protein that a plant, animal or other organism requires as part of its food in order to survive.

oxygen     A gas that makes up about 21 percent of Earth's atmosphere. All animals and many microorganisms need oxygen to fuel their growth (and metabolism).

petroleum     A thick flammable liquid mixture of hydrocarbons. Petroleum is a fossil fuel mainly found beneath the Earth’s surface. It is the source of the chemicals used to make gasoline, lubricating oils, plastics and many other products.

stover     Corn stalks, once the ears have been harvested. This fibrous material is used to feed livestock.

sustainable     An adjective to describe the use of resources in a such a way that they will continue to be available long into the future.

technology     The application of scientific knowledge for practical purposes, especially in industry — or the devices, processes and systems that result from those efforts.

toxic     Poisonous or able to harm or kill cells, tissues or whole organisms. The measure of risk posed by such a poison is its toxicity.

tract     A particular, well-defined area. It can be a patch of land, such as the area on which a house is located. Or it can be a bit of real estate in the body. For instance, important parts of an animal’s body will include its respiratory tract (lungs and airways), reproductive tract (gonads and hormone systems important to reproduction) and gastro-intestinal tract (the stomach and intestines — or organs responsible for moving food, digesting it, absorbing it and eliminating wastes).

Wales     One of the three components of Great Britain (the other two being England and Scotland. It’s also part of the United Kingdom (whose other members include England, Scotland and Northern Ireland).

waste     Any materials that are left over from biological or other systems that have no value, so they can be disposed of as trash or recycled for some new use.

yeast     One-celled fungi that can ferment carbohydrates (like sugars), producing carbon dioxide and alcohol. They also play a pivotal role in making many baked products rise.


Journal:​ J. K. Henske et al. Metabolic characterization of anaerobic fungi provides a path forward for bioprocessing of crude lignocelluloseBiotechnology and Bioengineering. Vol. 115, April 2018, p. 874. doi: 10.1002/bit.26515.

Journal:​ ​ K. V. Solomon et al. Early-branching gut fungi possess a large,comprehensive array of biomass-degrading enzymesScience. Vol. 351, March 11, 2016, p. 1192. doi: 10.1126/science.aad1431.