Harnessing Microbes for Better Health

Harnessing Microbes for Better Health

UMN researchers study how bacteria can contribute to safer drinking water

By Shayna Korol and Charlie Kidder

Clean water doesn’t happen by accident. Before it is ready to drink, water must be purified of microbes and other pollutants that are harmful to human health. Most drinking water in the United States is treated through biofiltration, a process that uses filter media, such as sand, anthracite coal, or granular activated carbon (GAC), with attached communities of bacteria to remove harmful microorganisms as well as dissolved contaminants. It seems counterintuitive to cultivate bacteria in a drinking water treatment facility, but it is important to realize that not all bacteria are harmful. In fact, many bacteria are beneficial and can be utilized to improve water quality. 

Biofilters use a granular filter medium such as sand, which is covered with a thin bacterial layer known as a biofilm. As untreated water passes through the biofilter, the grains of filter medium collect the microorganisms and other particles from the incoming water while the biofilm “catches” dissolved pollutants, including nutrients and organic contaminants like pesticides. While water treatment never completely eliminates microbes, biofiltration aims to keep the concentration of harmful pathogens low enough to prevent people from getting sick. 

Not all biofilters are created equal. Some biofilters that use sand as a filter medium are known as slow sand filters. As the name suggests, these filters work relatively slowly, making it difficult for an urban water treatment facility (like the city of Saint Paul’s) to process 50 million gallons a day. Tim LaPara and Ray Hozalski, University of Minnesota professors in the department of Civil, Environmental, and Geo-Engineering and the BioTechnology Institute, study differences between biofilters that can impact water quality. “The slow sand filters don’t work well [for large metropolitan areas like the Twin Cities],” says LaPara. Water treatment plants for large cities typically employ “rapid filters”, which process water at a rate that is more than 10 times greater than slow sand filters. Hence, the number of filters needed is much more manageable, and the plant size is reasonable.

In the early 2000s, Saint Paul had a water quality issue because of a substance called geosmin. Although it is not harmful to human health, geosmin has an unpleasant taste and odor. In order to mitigate geosmin’s effects on the water supply – and cut down on hundreds of yearly complaints from Saint Paul residents – the city installed granular activated carbon (GAC) filters. “The idea was the geosmin would stick to those filters, and water would taste better,” says LaPara. 

In Saint Paul, water quality complaints plummeted by about 90 percent after the GAC filters were put in place. “They went from 250 to 300 complaints down to 15 to 30 complaints per year,” says LaPara, a tremendously low number for a city as big as Saint Paul. 

Like Brita water filters in kitchens across the world, the thought was that the GAC filters would eventually have to be replaced. Implementing the filters cost $5 million, and removing and replacing them would cost the city another $5 million each time. Hozalski estimated that the filters would work for at least five years. Surprisingly, the filters kept working well even after five years. Instead of simply accumulating on the GAC filters as the researchers assumed would eventually happen, the geosmin also was being consumed by the bacterial communities on the biofilm as it passed through the filter. The GAC “takes up all the geosmin during the summer and then slowly dissolves it out the rest of the year, and it dissolves it so slow[ly] that the microbes eat it and nobody ever taste[s it],” explains LaPara. Ten years passed, and the researchers found that the filters worked as well as they did the day they were installed. Thus, the GAC filter media was being bioregenerated, allowing for a sustainable treatment process.

“If the bacteria can biodegrade the compounds [that need to be removed], then you don’t have to replace the media because they can basically take care of it naturally,” says Hozaski. The work by the bacteria on the filters provided millions of dollars in savings. 

As an outgrowth of the GAC filter research that began in the early 2000s, the scientists attempted to understand how the microbial communities in these biofilters evolve and function. In a 2018 journal article, Ph.D. student Ben Ma, together with Hozalski and Prof. Bill Arnold, demonstrated that biofilters can remove a wide variety of trace organic contaminants, including pesticides and pharmaceuticals. Hozalski also lead a study by a research team, which included Ma, LaPara, and Ashley N. Evans from the consulting firm Arcadis, in which samples of filter media were collected from biofilters throughout North America. The researchers found that the microbiome of drinking water biofilters is affected by both environmental factors and filter design. 

They published the basic science study in FEMS Microbiology Ecology. “We were trying to understand how different these biofilters are from location to location,” LaPara says. While Minneapolis filters are very similar to Saint Paul filters, they are different from filters in California. 

“Geographic location seems to have some bearing on the [microbial] communities that evolve, and so the closer that water plants are together, the more similar the communities are; the further they are apart, the more different,” Hozalski explains.  

In 2020, the researchers published a paper in Environmental Science & Technology investigating the effects of biofilter design on both the microbiome of the filter media and filtered water itself. This study, also an extension of the earlier GAC filter research, used GAC-sand and anthracite-sand biofilters. Hozalski also served as lead researcher.

While the biofilters reduced bacterial abundance in the water by about 70 percent, they did not significantly affect the microbial composition that remained in the filtered water. These results suggest the biofilms mostly affect water quality by removing pollutants and nutrients rather than changing the microbial composition of the filtered water. “The biofilter does a lot, but it doesn’t add different microbes to our water,” LaPara says.

By shedding further light on how biofilters function, the researchers are setting the groundwork for better filters – and cleaner water. Hozalski said, “I have been working on biofilters since my Ph.D. studies in the early 1990s, and I still have a lot to learn! They are both simple in design yet decidedly complex when you dig into them.”

Tapping the Talents of Enzymes

Tapping the Talents of Enzymes

BTI researchers are working to discover, understand, and improve our ability to enlist the help of molecules that catalyze life.

by Mary Hoff

Enzymes are the movers and shakers of the biomolecular world. A class of proteins found in every cell of every living thing, they bring together molecules that would otherwise be reluctant to interact so they can combine, exchange parts, or otherwise alter each other.

In nature, enzymes facilitate thousands of processes from photosynthesis to decomposition. Enzymes speed up chemical reactions thousands of times faster than the reactions would occur on their own. Over the millennia, humans have found ways apply this superpower to accomplish a variety of useful goals from making beer and cheese, to making our laundry whiter and brighter, to cranking out millions of copies of a sample of DNA to solve crimes or find long-lost relatives.

“And that’s just the beginning,” says Romas Kazlauskas, professor in the department of Biochemistry, Molecular Biology, and Biophysics. “Enzymes can also learn how to do different things. We’re trying to figure out which parts are important and why they’re important, then design something different to do a reaction that doesn’t occur naturally.” By identifying enzymes, improving understanding of how they work, and applying them to new tasks, Kazlauskas and BTI colleagues are taking advantage of the billions of years of evolution that produced these molecules to make medicines, degrade pollutants, speed industrial processes, and more.

 

Trash to Treasure Kazlauskas is working with an enzyme found in nature that degrades PET plastic. First synthesized in the 1940s, PET (a form of polyethylene) is widely used for beverage and food containers with some 70 million tons generated every year—and much of that ending up in landfills and the ocean. Current efforts to recycle the material can only produce lower-quality plastics.

“One idea is to break down to component parts and resynthesize fresh plastic that would be just as good as what you started with,” he says.

Sound like a job for an enzyme? Kazlauskas thought so, too. But the likelihood of finding a suitable one in nature was slim because PET didn’t exist for most of evolutionary history. Nevertheless, in a compost heap in Japan, researchers recently found an enzyme that bacteria use to break down the waxy part of plants that could also break down PET.

Kazlauskas, along with graduate student Colin Pierce and colleagues, is working on modifying that enzyme known as cutinase, to improve its ability to degrade PET. The goal, ultimately, is to be able to develop a commercially viable way to turn old PET into new plastics without experiencing the loss of quality. This would not only reduce the load of plastic waste, it would also reduce pressure to produce more plastic, often from fossil fuels.

Kazlauskas sees huge opportunities beyond PET for efforts to extend nature’s ability to degrade compounds. “There are a lot of cases where we start making stuff and putting it out in nature, and people say it doesn’t degrade,” he says. “We’re finding bugs that can degrade these forever chemicals.” he says. By advancing the ability to modify such natural enzymes to make them do the job even better, the hope is to avoid the buildup of undesirable, manufactured compounds in the environment and reduce the need to make more from raw materials.

 

Life on the Edge

Turning somersaults in a sulfurous hot spring or clinging tenaciously to life on a glacier, the organisms studied by McKnight Presidential Fellow Trinity Hamilton, associate professor in the department of Plant and Microbial Biology, are the stars in microscopic world’s version of “Survivor.” Having evolved within living things, most enzymes work best under fairly mild conditions with respect to things like temperature and acidity. But not all. In the hot springs of Yellowstone National Park, Hamilton is studying how microbes—and the enzymes they use to carry out the activities of daily life—can survive regular temperature fluctuations of 40 degrees Celsius (104 degrees Fahrenheit) or more. And, on the other end of the spectrum, she’s also looking at how other microorganisms that live on ice maintain their function at low temperatures in the absence of liquid water.

Hamilton studies, among other things, enzymes that facilitate photosynthesis and function well up to 72 degrees Celsius, and then suddenly quit. “We have no idea why,” she says. “It’s really hard to perform autopsies on microbes.”

The ability of bacterial enzymes to function at various temperatures is behind the process that makes it possible to sequence DNA using what is called the polymerase chain reaction (PCR) technique. The enzyme used for this was isolated from bacteria in a hot spring in Yellowstone National Park. A better understanding of how bacteria keep these proteins active under extreme conditions could open the door to advancing our ability to solve other human challenges like preserving food or thriving in the face of climate change.

Molecular Assembly Line 

For Michael Smanski, a McKnight land grant professor in the department of Biochemistry, Molecular Biology, and Biophysics, the focus is on bringing together enzymes from different sources to create an efficient work team that can produce a specific molecule.

Most recently he’s been focusing on serofendic acid, a molecule found in the blood of fetal calves. In the early 2000s, researchers in Japan discovered that serofendic acid could prevent the untimely death of neurons and potentially serve as a therapy for minimizing damage from Parkinson’s disease, strokes, and other neurological trauma. The problem? It occurs in such small quantities that it would take 1,000 calves to make a minute 3 milligrams of active substance—providing dismal prospects for practical use.

Biosynthesis and enzymes to the rescue. Using databases describing enzymes from different organisms and the type of work each does, Smanski and colleagues designed a molecular assembly line that could make serofendic acid from readily available feedstock chemicals. Then they introduced the corresponding genes into a bacterium, enabling it to make the desired product.

As any industrial engineer would know, populating an assembly line with ready workers is only part of the solution, however. For efficiency’s sake, it’s also important to have the right capacity at every step of an assembly process to ensure that partially made products don’t pile up, or a slow step doesn’t drag down everything else. To optimize production of serofendic acid, Smanski has been tweaking the activity levels of the various enzymes relative to each other.

Even as he’s working on a strategy to improve outcomes for individuals with brain disorders, Smanski is also discovering principles that can be applied more broadly to optimizing artificial biosynthetic processes.

Optimizing a process means testing multiple levels of expression for the specific gene that’s coding for each enzyme along the way. If the assembly line consists of 15 enzymes, and researchers want to test five levels of expression for each, that would require 5 15 power—more than 30 billion—individual trials. Using combinatorial mathematics, Smanski is devising a strategy for selecting from those millions of possibilities, a mere 100 or so that are most likely to succeed, making the optimization process far more manageable.

“As improvements in the technical aspects of genetic engineering make it easier to rewrite the genetic blueprints of living organisms, learning how to efficiently sift through all of the possibilities of what-to-write is becoming more important,” Smanski says. “We think that our work at the interface of combinatorial mathematics and genetic engineering will benefit any application that requires more than one or a few genes working together.”

 

Self-Assembling Scaffold

Bringing multiple enzymes together in an assembly line is far more easily said than done. The molecules involved in sequential steps must be physically located close enough to each other to be able to pass a product-in-the-making down the line. They also must be positioned correctly at their stations so they can accomplish their task.

Distinguished McKnight University Professor Claudia Schmidt-Dannert is on it. Rather than identifying enzymes to string together to accomplish a molecule-making task, she is working on the assembly line itself.

Her goal is to not only design a stable assembly line of enzymes able to make a useful product but to genetically modify a microorganism—say, the bacterium E. coli—so that it can produce it on its own. Such a self-assembling scaffold, she believes, could dramatically improve the function of molecular assembly lines, reducing the cost of producing pharmaceuticals and other useful products.

“If we stabilize enzymes, we can make reactions more efficient,” she says.

Schmidt-Dannert and colleagues recently received a patent for a self-assembling, modular scaffold that co-locates enzymes in a way that enhances their ability to efficiently produce desired molecules. Her current focus is on developing scaffolds as materials that can correctly self-assemble into 3-dimensional architectures to organize and support enzyme functions. This would allow the manufacture of a broad range of chemicals including pharmaceutically active molecules—a process that can be extremely difficult using conventional chemical synthesis methods. 

She’s also applying her strategy to making molecular assembly lines more economical by including enzymes that recycle required co-factors, which are molecules or metals that assist enzymes in assembling a molecular product.

“You need to recycle the [co-factors]. Otherwise, the process is too expensive,” she says. “A scaffold helps make that possible.”

 

Byproduct

Byproduct

Byproduct

Byproduct

Art installation at the Fulton brewery taproom sheds light on MnDRIVE sponsored sustainable wastewater treatment research.

Byproduct, a new site-specific installation by artist Aaron Dysart, opens at the Fulton Brewery Taproom on September 23 and runs through October 23, 2021. Byproduct will carbonate the façade of the taproom with shifting colors generated from an enormous mirror ball. The colors display data from a sustainable wastewater research project conducted by Paige Novak and her team at the University of Minnesota.

We often overlook the carbon dioxide bubbles drifting up the sides of a pint glass gathering to head. On the one hand, they are just a byproduct of a yeast cell. On the other hand, they are a refreshing grounding in the present moment— and the beer just doesn’t taste right without them. In Byproduct, Dysart uses this visual language of carbonation to speak to innovative research underway at Fulton’s brewery. The installation, which displays some of the team’s data as colorful ‘bubbles’ on the taproom facade, celebrates the continuing push to make the world a better place.

Manufacturing creates waste, and brewing beer is no different. Not only does brewing generate a high volume of wastewater, but this wastewater is also full of carbon-containing compounds that require a lot of energy to treat using standard technology. However, other treatment options operate differently, using bacteria to make energy instead of using energy during wastewater treatment.  

Novak and her team are working on a treatment technology for small to mid-size industries that generates energy (in the form of methane gas) and removes carbon-containing compounds. The collaboration with Dysart allowed the team to share their research with the public as they test their scalable process that treats wastewater onsite while making energy for use at the brewery.

Dysart’s installation presents two colorful light shows comparing the two treatment methods set up side-by-side, treating wastewater at the Fulton Brewery. The first compares the amount of usable energy produced by the Novak lab’s experimental technology with the existing system, which works well but is high-maintenance, energy-intensive, and expensive to use. The second explores the reduction of carbon-containing waste compounds realized through the pilot at Fulton’s brewery. 


 

Aaron Dysart is a sculptor who is interested in using visual language and spectacle to give hidden stories a broader audience. His environmental interventions showcase his love of light shows, fog machines, and data, while his objects showcase his love of a material’s ability to carry content. He has received awards from Franconia Sculpture Park, Forecast Public Art, The Knight Foundation, and The Minnesota State Arts Board, and his work has been in Art in America Magazine, Hyperallergic, Berlin Art Link, and other publications. He has shown nationally and partnered with local and national organizations including the National Park Service, Army Corp of Engineers, NorthernLights.mn, and Mississippi Park Connection. Aaron is currently a City Artist through Public Art Saint Paul. He is embedded in the city of St. Paul, and operates his studio in northeast Minneapolis.

Paige Novak is a professor and the Joseph T. and Rose S. Ling Chair in Environmental Engineering in the Department of Civil, Environmental, and Geo- Engineering at the University of Minnesota. Among other projects, Novak and her team are working on the development of a new type of treatment technology that relies on the encapsulation of bacteria into small, gel-like beads that can be easily deployed and retained—perfect for use at small industries such as craft breweries. This technology treats the waste, and in the process, generates energy in the form of methane gas that can be used on-site. For Dysart and Novak’s collaborative project, funded by the MnDRIVE: Environment Initiative at the University of Minnesota, Novak deployed a small pilot-scale system using these encapsulated bacteria at the Fulton brewery to treat their wastewater in real time, comparing it to a much more operationally and energy-intensive treatment technology. 

Bill Arnold and Natasha Wright were collaborators in the research. Kuang Zhu, Siming Chen, and Olutooni Ajayi also worked on the project

Byproduct is funded by a McKnight Project Grant through Forecast Public Art, and a MnDRIVE: Environment Demonstration Grant through the University of Minnesota.

Photo: Aaron Dysaart © 2021

 

 

The National Microbiome Data Collaborative

The National Microbiome Data Collaborative (NMDC) team is building an integrated data science ecosystem that leverages existing data standards, data resources, and infrastructure in the microbiome research space. The NMDC is launching the NMDC Ambassador program to provide training and support for early career researchers who are motivated to engage with their respective research communities to lower barriers to adoption of metadata standards.

We invite applications from early career leaders who are:

  • Familiar with the challenges of discovering, accessing, and reusing microbiome data

  • Committed to working with the NMDC to make microbiome data findable, accessible, interoperable, and reusable (FAIR)

  • Motivated to engage with researchers in their community

  • Committed to inclusion, diversity, equity, and accountability (IDEA)

Please encourage qualified early career researchers to apply by May 21, 2021. For more details about the program, visit: microbiomedata.org/community/ambassadors or email us at support@microbiomedata.org.

Is PFAS a Problem in Municipal Compost?

Is PFAS a Problem in Municipal Compost?

MnDRIVE brings industry and regulators together to weigh costs, benefits, solutions

by Mary Hoff 

What should researchers be researching? With many needs and finite resources, that’s an important question for MnDRIVE Environment, a partnership between the University of Minnesota and the State of Minnesota that brings the power of University inquiry and innovation to bear on challenges industries face related to clean air, water, and land.

In early 2020, the initiative invited private sector and state agency representatives to discuss issues in need of attention related to per- and polyfluoroalkyl substances or PFAS. This class of chemicals historically has been used in a wide spectrum of consumer goods and has since been implicated as a land and water contaminant linked to a range of health risks. Of particular concern is the fact that PFAS chemicals have started cropping up at municipal compost facilities that turn materials such as grass clippings and food waste into a nutrient-filled substance that is used to enrich soil.  

One of the businesses represented at the meeting was the Shakopee Mdewakanton Sioux Community (SMSC) Organics Recycling Facility. The facility takes in 70,000 tons of materials every year to make compost, compost blends, and landscaping mulch. It has tested its products and found PFAS levels to be well below those that the Minnesota Pollution Control Agency (MPCA) considers a health concern in residential soils. PFAS has shown up in water that drains off piles of materials that are in the process of breaking down, says MPCA composting and recycling specialist Kayla Walsh (as it has for other composting facilities around the state). The test results have facility managers looking for ways to continue to do good while preventing future problems.

The topic is a particularly hot one for SMSC because it would like to open a larger facility to meet increasing demand from community composting.

“We know composting is good. We’re amending the soil,” says SMSC biomass processing assistant manager Dustin Montey. At the same time, he adds, “we don’t want to be introducing a harmful substance back into society” by producing soil amendments containing PFAS.

Erin Skelly, environmental and compliance technician for the facility, notes that SMSC is grounded in the Native American principle of caring for the Earth with the next seven generations in mind. A participant in the 2020 MnDRIVE-hosted meeting, Skelly sees a need for research to find the source of the PFAS and how to get it out of the waste stream so it doesn’t end up in compost.

“There’s a lot that’s unknown about PFAS,” she says. “If it’s in compost and in soil, does it leach out? Does it get into groundwater? Do plants absorb that? There’s a lot of opportunity for research.”

MnDRIVE Environment funding is earmarked specifically for remediation. However, it also works upstream to stimulate discussion and connect stakeholders to collaborate on identifying and characterizing problems that remediation can help solve.

“Once we know where PFAS is and where it is coming from, then these issues can be put forward to remediate. That’s sort of the sweet spot where MnDRIVE funding programs come into play,” says MnDRIVE Environment industry and government liaison Jeff Standish.

For example, University of Minnesota environmental health researcher Matt Simcik and environmental engineering researcher William Arnold have been developing technology to keep PFAS from moving from landfills into groundwater. MnDRIVE Environment funding is supporting this work which, upon completion, might be used to protect water at compost sites.

MnDRIVE Environment will be continuing conversations this spring around strategies for addressing PFAS contamination in the environment. Between entities like SMSC that are seeking to protect the planet, and MnDRIVE, which stands ready to bring the power of University research to the task, the hope is that society can continue to reap the benefits of composting without exacerbating the PFAS problem, and perhaps proactively solving it.