bacteria

#IAmScience George Stewart

February 21, 2020 By Becca Wolf in #IAmScience Tags: bacteria

By Becca Wolf | Bond LSC

Medical bacteriologist, George Stewart has had a few stops along the way before he got to Bond LSC in 2004. Having done schooling and research at universities from the midwest to the east coast, it has been a long journey filled with many ups and downs, but a rewarding one at that.

Stewart hadn’t always wanted to be a medical bacteriologist though, “When I was going to college, I actually wanted to be a marine biologist,” he says, “And then my sophomore year in college, I took a microbiology course. And that changed that.”

This microbiology course at the University of North Texas was the first course where he was able to do hands on work in a laboratory and he found that, “culturing organisms and identifying organisms was very appealing.”

“The technological advancements are so fast in this discipline that you just have to change and there are easier ways to do things and better ways to do things now,” he states.

But these changes help Stewart delve deeper in understanding his passion for an organism best known for the white powder derived from its spores and sometimes used in terror attacks. Technically called Bacillus anthracis, the organism causes the disease anthrax. Stewart focuses on the outer spore of the bacteria which first comes in contact with the infected host and is responsible for protein production. He looks at how the spore contributes to anthrax’s ability to persist in soil and how it contributes to resistance properties.

Unfortunately for Stewart, funding for anthrax research has declined over the years, “It’s not considered a high priority organism,” he explains, however, “it still is an organism of concern for bio-threats.” To work around the lack of funding, Stewart has turned in other directions.

“Part of that has actually been the biggest success stories of recent times in my lab,” he said.

The direction? Using Bacillus thuringiensis, a bacterium similar to anthrax, to do research on. One problem Stewart approached using this bacterium was cleaning up Atrazine, a herbicide used by farmers to kill weeds. This herbicide, while helpful to farmers, can contaminate groundwater, potentially causing diseases in humans.

To find a solution, Stewart and Brian Thompson, a postdoc student in his lab, collaborated with Chung-ho Lin, a research associate professor in the MU Center for Agroforestry, “looking at could we possibly have come up with approaches using this basic technology to improve agriculture from a number of different ways to make plants grow faster, better, that sort of thing.”

They found that they could display proteins on Bacillus thuringiensis spore that would break down Atrazine. Farmers would only have to spray their fields with this organism and the soil would be clean of Atrazine.

Taking this a step further, Thompson created the company, Elemental Enzymes, to sell products like this to farmers in order to clean the environment. Located in St. Louis, Elemental Enzymes currently has 11 products in use today on more than 11% of corn acres in the United States in 2019, and that number seems to be increasing.

“It’s kind of interesting in the sense that we started off trying to answer a very basic biological question related to spore biology and involving a significant high consequence pathogen, and we ended up discovering something which has huge benefits for agriculture. So you never know what direction it’s going to take you in these things,” says Stewart.

Stewart hasn’t stopped there. In fact, he was one of the driving forces behind starting a Bachelor of Science degree program in microbiology here at MU. After a microbiology degree program here was discontinued in the early 2000s, Stewart has since found evidence that the degree would be successful here at the university and it was approved by the board of curators and the Missouri Department of Higher Education in 2018. The first students in this program began this past semester and Stewart says, “we’re getting underway.”

Despite these accomplishments, Stewart is getting ready to retire this year, explaining, “part of the reason that I stayed on this year was to make sure this program gets off the ground and help out with that.” While his career is winding down here at MU, he is still keeping busy, “I’m actually teaching two undergraduate courses in microbiology, once called fundamentals of microbiology, it’s an introductory microbiology course. And the other one is public health microbiology, which is more of a junior level type course.”

He also continues to do some work in his lab as he has two graduate students finishing up their degrees this year and recently stepped down as the Department of Veterinary Pathobiology chair in January.

What does Stewart have planned for when he retires? He is not slowing down, that is for sure. Stewart and his wife already have a vacation planned for New Zealand within the next few months, and he plans on spending quality time with his children and grandchildren.

“I won’t have accomplished all the things I wanted to,” he says, “but I think we’ll have gotten the major things done. So that’s satisfying.”

Planting a seed for sciences

March 17, 2017 By Jinghong Chen in Research Tags: bacteria, plant sciences

Rhizobia bacteria — Plants on the left grow with rhizobia bacteria, one type of fixing nitrogen bacteria, in the greenhouse, while the plants on the right grow without the bacteria. | photo by Jinghong Chen, Bond LSC

Jinghong Chen | Bond Life Sciences Center

Since eight years old, Beverly Agtuca knew she wanted to be a scientist.

A trip to Philippines changed Agtuca, an American-born Filipino, and inspired her passion on plants.

“My grandma always told me to work in the field all day so that they can have enough food for us to eat,” Agtuca said. “The life [in Philippines] is so different from here…I want to not just provide food but be that scientist trying to figuring something out, and hopefully saving the world.”

Agtuca is on her way to her dream. She is now a third year doctoral student in Gary Stacey’s lab at Bond Life Sciences Center with a focus on nitrogen-fixing bacteria.

Although she has been involved in research since high school, Agtuca recently faced a new challenge of telling people about her work. The Preparing Tomorrow’s Leaders of Science class tasked her with making a 90-second video to explain her two-year study to the general public.

Her team, “The A Team,” chose to go with the benefits of having nitrogen-fixing bacteria.

For decades, people have been adding nitrogen fertilizers to plants to improve yields, but this can lead to pollution in water systems and ecosystems. Scientists need to enhance plant productivity to meet a huge food demand by the year of 2050.

One little bacteria might make this possible and save the world. Rhizobia, a type of natural bacteria in soil, are able to fix nitrogen via biological nitrogen fixation. These bacteria can convert nitrogen gas into ammonia as a plant nutrient source, while the plants give all the carbon sources back to the bacteria.

“It is like a walky-talky,” Agtuca said. “They are communicating with each other.”

Yet before speaking to the public, Agtuca needs to explain the plant-bacteria interaction to her teammates. Students less well versed in science like Jessica Kaiser, a strategic communication student, thinks of science differently.

“The biggest issue we ran into is jargon, like basic science words that [my teammates] are so comfortable with,” Kaiser said. “We need to focus on what people care about instead of the technical sides, to focus on why it matters to anybody rather than just to a science person.”

Within two weeks, they produced the video “Good Microbes: reducing pollution one farm at a time.” Along with two other teams, their videos will be commented and judged by representatives from Monsanto.

"The A Team" — “The A Team” stands together at Bond Life Sciences Center. From left to right: Jessica Kaiser, Sven Nelson, Anna Glowinski, Eleni Galata and Beverly Agtuca. | photo by Jinghong Chen, Bond LSC

The 90-second video is just a glimpse of Agtuca’s study. In the last two years she has been focusing on the use of a new technique — laser ablation electrospray ionization mass spectrometry (LAESI-MS) — that does in situ metabolic profiling of tissues. The lab is using LAESI-MS to investigate the metabolites in a well-characterized model plant-rhizobium system, specifically nitrogen-fixing soybean nodules resulting from root infection by the symbiotic bacterium Bradyrhizobium japonicum.

This work includes a huge collaboration that was developed through a Department of Energy (DOE) grant involving the George Washington University, Washington D.C. and the Environmental Molecular Science Laboratory (EMSL), Pacific Northwest National Laboratory, Richland, WA.

LAESI-MS works like a superhero’s laser-like beams. You first aim the laser on the sample, which then heats it and causes neutral particles to be released into the air. This plume of neutrals is then captured and ionized by the electrospray, and finally analyzed by the spectrometer to figure out the exactly what metabolites in nodules are involved in biological nitrogen fixation.

“It takes about three seconds to analyze one sample using this LAESI-MS technique,” Agtuca said. Other metabolic techniques require extensive pre-treatment of the sample before analysis.

By analyzing the data collected via LAESI-MS, the lab is able to confirm that future plant studies could apply this new approach to understand the interactions between plant and bacteria.

Agtuca’s research is a long way from her first experiences with plants. She still remembers the moment she found her plants in her own garden died. She was less than 10 years old, yet devoted to taking care of her plants with water and fertilizers.

“I was really sad. I could not get my tomatoes, peppers and eggplants to live.…That makes me think that I want to answer why they didn’t grow,” Agtuca said.

More than ever, her future is helping her answer those question for herself.

Gary Stacey is a Bond LSC investigator and MU curators’ professor of plant science and MSMC endowed professor of soybean biotechnology. Read more here about Stacey lab.

Sven Nelson is a USDA/ARS postdoctoral research scientist at the University of Missouri. Anna Glowinski is a Ph.D. student in the USDA/ARS lab. Jessica Kaiser is a graduate student in strategic communication. Eleni Galata works as the team mentor and she is a Ph.D. student in agricultural and applied economics at MU.

Seminal work

March 15, 2016 By Roger Meissen in Research Tags: bacteria, big data, Cheryl Rosenfeld, epigenetics, mice, seminal fluid

How unruly data led MU scientists to discover a new microbiome
By Roger Meissen | MU Bond Life Sciences Center

seminal vesicles 3_11_16.jpg — This seminal vesicle contains a newly-discovered microbiome in mice. Some of its bacteria, like *P. acnes*, could lead to higher occurrences of prostate cancer. | contributed by Cheryl Rosenfeld

It’s a strange place to call home, but seminal fluid offers the perfect environment for particular types of bacteria.

Researchers at MU’s Bond Life Sciences Center recently identified new bacteria that thrive here.

“It’s a new microbiome that hasn’t been looked at before,” said Cheryl Rosenfeld, a Bond LSC investigator and corresponding author on the study. “Resident bacteria can help us or be harmful, but one we found called P. acnes is a very important from the standpoint of men. It can cause chronic prostatitis that results in prostate cancer. We’re speculating that the seminal vesicles could be a reservoir for this bacteria and when it spreads it can cause disease.”

Experiments published in Scientific Reports — a journal published by Nature — indicate these bacteria may start disease leading to prostate cancer in mice and could pass from father to offspring.

A place to call home

From the gut to the skin and everywhere in between, bacterial colonies can both help and hurt the animals or humans they live in.

Seminal fluid offers an attractive microbiome — a niche environment where specific bacteria flourish and impact their hosts. Not only is this component of semen chockfull of sugars that bacteria eat, it offers a warm, protected atmosphere.

“Imagine a pond where bacteria live — it’s wet it’s warm and there’s food there — that’s what this is, except it’s inside your body,” said Rosenfeld. “Depending on where they live, these bacteria can influence our cells, produce hormones that replicate our own hormones, but can also consume our sugars and metabolize them or even cause disease.”

Rosenfeld’s team wasn’t trying to find the perfect vacation spot for a family of bacteria. They initially wanted to know what bacteria in seminal fluid might mean for offspring of the mice they studied.

“We were looking at the epigenetic effects — the impact the father has on the offspring’s disease risk — but what we saw in the data led us to focus more on the effects this bacterium, P. acnes, has on the male itself,” Rosenfeld said. “We were thinking more about effect on offspring and female reproduction — we weren’t even considering the effect the bacteria that live in this fluid could have on the male — but this could be one of the more fascinating findings.”

But, how do you figure out what might live in this unique ecosystem and whether it’s harmful?

First, her team found a way to extract seminal fluid without contamination from potential bacteria in the urinary tract.

“We gowned up just like for surgery and we had to extract the fluid directly from the seminal vesicles to avoid contamination,” said Angela Javurek, primary author on the study and recent MU graduate. “You only have a certain amount of time to collect the fluid because it hardens like glue.”

Once they obtained these samples, they turned to a DNA approach, sequencing it using MU’s Genomics Technology Core.

They compared it to bacteria in fecal samples of the same mice to see if bacteria in seminal fluid were unique. They also compared samples from normal mice and ones where estrogen receptor genes were removed.

The difference in the data

It sounds daunting to sort and compare millions of DNA sequences, right? But, the right approach can make all the difference.

“A lot of it looks pretty boring, but bioinformatics allow us to decipher large amounts of data that can otherwise be almost incomprehensible,” said Scott Givan, the associate director of the Informatics Research Core Facility (IRCF) that specializes in complicated analysis of data. “Here we compared seminal fluid bacterial DNA samples to publicly available databases that come from other large experiments and found a few sequences that no one else has discovered or at least characterized, so we’re in completely new territory.”

The seminal microbiome continued to stand out when compared to mouse poop, revealing 593 unique bacteria.

One of the most important was P. acnes, a bacteria known to cause chronic prostatitis that can lead to prostate cancer in man and mouse. It was abundant in the seminal fluid, and even more so when estrogen receptor genes were present.

“We’re essentially doing a lot of counting, especially across treatments to see if particular bacteria species are more common than others,” said Bill Spollen, a lead bioinformatics analyst at the IRCF. “The premise is that the more abundant a species is, the more often we’ll see its DNA sequence and we can start making some inferences to how it could be influencing its environment.”

Although this discovery excites Rosenfeld, much is unknown about how this new microbiome might affect males and their offspring.

“We do have this bacteria that can affect the male mouse’s health, that of his partner and his offspring,” Rosenfeld said. “But we’ve been studying microbiology for a long time and we still find bacteria within our own bodies that nobody has seen before. That blows my mind.”

The study, “Discovery of a Novel Seminal Fluid Microbiome and Influence of Estrogen Receptor Alpha Genetic Status,” recently was published in Scientific Reports, a journal published by Nature.

Chemical beacons: LSC scientist discovers how plants beckon bacteria to attack

April 24, 2014 By Roger Meissen in Research Tags: Arabidopsis, bacteria, Bond Life Sciences Center, chemical signals, Scott Peck

Scott Peck studies Arabidopsis and how bacteria perceive it before initiating an infection. Roger Meissen/ Bond LSC — Scott Peck, Bond LSC scientist and associate professor of biochemistry, studies Arabidopsis and how bacteria perceive it before initiating an infection. Roger Meissen/ Bond LSC

Sometimes plants inadvertently roll out the red carpet for bacteria.

Researchers at the University of Missouri Bond Life Sciences Center recently discovered how a plant’s own chemicals act as a beacon to bacteria, triggering an infection. Proceedings of the National Academy of Sciences published their study April 21.

“When bacteria recognize these plant chemicals it builds a needle-like syringe that injects 20-30 proteins into its host, shutting down the plant’s immune system,” said Scott Peck, Bond LSC plant scientist and lead investigator on the study. “Without a proper defense response, bacteria can grow and continue to infect the plant. It looks like these chemical signals play a very large role in mediating these initial steps of infection.”

The question of how bacteria actually know they are in the presence of a plant has puzzled scientists for years. Being able to identify the difference between a plant cell and, say, a rock or a piece of dirt, means the bacteria saves energy by only turning on its infection machinery when near a plant cell.

“Our results show the bacteria needs to see both a sugar – which plants produce quite a bit of from photosynthesis – and five particular acids at the same time,” Peck said. “It’s sort of a fail-safe mechanism to be sure it’s around a host before it turns on this infection apparatus.”

Peck’s work started with one mutant plant called Arabidopsis mkp1.

Discovered several years ago by Peck’s lab, this little mustard plant acts differently than others by rebuffing the advances of bacteria. Lab tests confirmed that this mutant didn’t get infected by Pseudomonas syringae pv. tomato DC3000, a bacterial pathogen that causes brown spots on tomatoes and hurts the model plant Arabidopsis. Along with MU biochemistry research scientist Jeffrey Anderson and post doc Ying Wan, they showed that this mutant didn’t trigger the bacteria’s Type III Secretion System, the needle-like syringe and associated proteins that lead to infection.

Pacific Northwest National Laboratory (PNNL) worked with Peck’s team to compare levels of metabolites between the mutant Arabidopsis and normal plants. This comparison helped Peck identify a few of these chemicals – created from regular plant processes – that existed in much lower levels in their special little mutant.

Using the PNNL work as a guide, the team found five acids collectively had the biggest effect in turning on a bacteria’s infection: aspartic, citric, pyroglutamic, 4-hydrobenzoic and shikimic acid.

“The key experiment involved us simply adding these acids back into the mutant,” Peck said. “Suddenly we saw the mutant plant wasn’t resistant anymore and the bacteria were once again capable of injecting proteins to turn off the plant’s immune system.”

First contact and recognition means all the difference, whether bacteria or plant. Just a slight jump out of the starting blocks by one or the other could change who will win a battle of health or infection.

While low concentrations of these five acids trigger the bacteria’s attack, high levels blind it to the plant’s presence, leading Peck to believe it could be used to hinder bacterial growth. If this actually thwarts the bacteria’s head start, it could mean stopping disease in crops and could lead to a different approach in the field.

“A lot of the winning and losing occurs within the first 2-6 hours and it seems to be that if the microbe is too slow to turn off the immune system, the plant can actually fight off the infection,” Peck said. “In the future we could possibly make a new generation of anti-microbial compounds that don’t try to kill the bacteria, but rather just make them no longer virulent by blocking these chemical signals so the natural plant immune system can basically take over.”

Peck’s team believes at least some other bacteria will respond to these chemical signals, and he plans to test other bacterial pathogens to make certain. They also want to test bacteria to see if they are more virulent in humans once primed for attack by these plant chemical signals.

“In the long run the question is how far this extends. A lot of people get salmonella or listeria infections through a food source,” Peck said. “The question is do other bacteria that come in through plant food sources have similar perception systems and end up being more infectious in humans because they are already primed for infection.”

A $500,000 grant from the National Science Foundation supported this research.