Category Archives: Microbiology

Swimming with Salmon(ids)

Dams, bears, and anglers aren’t the only challenges that salmon face as they undergo their journeys from their mountain river birthplaces to the Pacific Ocean and back again. Timber harvests, dam-induced streamflow changes, and climate change have increased stream temperatures throughout the Pacific Northwest. Native cold-water-loving species like salmon and trout struggle in warm water, while certain parasitic microbes flourish.

The confluence of the Deschutes and Columbia Rivers. Illustration by Daniel Watkins.

Sofiya Yusova, a master’s degree candidate in the Department of Microbiology at Oregon State University, researches the microbe Ceratonova shasta. Her work aims to understand how C. shasta adapts to climate change in river ecosystems in the Pacific Northwest. Her advisor, Dr. Jerri Bartholomew, runs a long-term monitoring project in the Klamath River, and recently began applying the same methods to the Deschutes and Willamette Rivers. Dr. Bartholomew and her lab identified the complex lifecycle of the parasite, recognizing that C. shasta requires an intermediate host (the polychaete worm) in order to infect fish. Understanding the lifecycle is critical for understanding how to intervene when fish populations are struggling, as well as for anticipating the effects of climate change. As stated on Dr. Bartholomew’s website, “Climate change is expected to have profound effects on host-pathogen interactions. We are examining how this might affect myxozoan disease by developing predictions for how the phenology of parasite life cycles will change under future climates, how changing flow dynamics will alter disease, and to identify river habitats that should be protected as refugia.”

Lifecycle of ceratanova shasta. Illustration by Daniel Watkins.

Having a healthy population of salmon is important for many groups, including tribal communities, commercial and recreational anglers. Salmonids (a family of fish including salmon, trout, whitefish, and char) are particularly susceptible to infection when water temperature is warmer than usual, stream flow is low, or the number of C. shasta spores is high. Collaborative monitoring projects on the Klamath River and the Deschutes River have shown that the danger of deadly infections varies along the course of the river. This knowledge has allowed river managers to focus their efforts. For example, if the number of infectious spores is especially high, dam flowthrough rates can be increased to “flush out” the pathogens.

Tune in Sunday, February 2nd at 7pm on 88.7 FM or online to learn more about Sofiya’s research and her personal journey.

The bacteria living inside us and what they have to say about autism

Trillions of bacterial cells are living within us and they’re controlling your brain activity.

Grace Deitzler is a 2nd year PhD student in microbiology working in Dr. Maude David’s lab on the gut-microbiome and its relation to autism spectrum disorder.

The gut-microbiome is the total population of bacteria living within our digestive tract. These bacteria are critical for digestive health, but also for our immune system and mental health. For example, we harbor bacteria capable of digesting plant fibres we otherwise could not digest. And if you’ve been told that probiotics are good for you, that’s because probiotics can change the gut microbiome in a positive way, allowing for increased bacterial diversity associate with improved health. These bacteria communicate with each other through chemical signaling but also communicate with us. Tryptophan, for example, is an amino acid produced through bacteria metabolism and is a precursor for serotonin, a brain-signaling chemical which causes feelings of happiness.

When the gut communicates with the brain, we call this, the “gut-brain axis”. Grace’s work narrows in on the gut-brain axis and more specifically, how one bacterial species in particular impacts autism spectrum disorder. To further complicate things, the gut-microbiome helps to regulate estrogen levels, and we also know that autism is a disorder found primarily in biological males. Which leads Grace to one of her biggest questions: are the bacteria involved in endocrine system regulation in women, also that responsible for this variation we see. Grace uses a mouse model to elucidate underlying mechanisms at play.

Step one is to feed the mice bacteria that have been found in elevated amounts in people with autism spectrum disorder than in neurotypical peers. These bacteria will colonize in the gut, and mice will go through several behavioral tests to determine if they are exhibiting more behaviors associated with autism. Grace performs three types of tests with the mice: one to test inclination to form repetitive behaviors, one to test anxiety, and one to test social behaviors. One test is a marble-burying test, in which a mouse more inclined to form repetitive behaviors will bury more marbles.

After behavioral testing is complete, the mice are sacrificed and different regions of the gut are taken to look for presence of bacterium. Tissues taken from the mice are used to look for transcriptional markers. The transcriptome is collected for both the mouse and the bacteria present, or the sum total of all genes that are read and converted to RNA. RNA are able to be isolated and sequenced using distinctive markers such as a “poly-A tail”. After this data is collected, Grace can finally move to the computational side of her work which involves combining biological and biochemical data with her behavioral studies.

In addition to her work on autism spectrum disorder, Grace also has a side project working in a honey bee lab, looking at the gut microbiome of honey bees in response to probiotics on the market for beekeepers. But Grace is one very busy bee herself because in addition to her lab work, she’s also involved with an art-science club called “seminarium”. The club is filled with scientists interested in art and artists interested in science. Grace is a painter primarily but is also working on ink illustration. The focus of this group is that art and science are complimentary, not at odds. The group has produced some collaborative projects, including a performance for a lab studying a parasite that effects salmon. The group put together a collage of interpretations of the parasites and had a performance in which one member played piano while someone else drew the parasite live.

Grace moved to Oregon from St. Louis Missouri. She completed her undergraduate degree in biological sciences with minors in chemistry and psychology at a small engineering college, Missouri University of Science and Technology, where she was a radio DJ! Grace first became involved in research during a summer internship in a microbiology lab at Washington University. There she studied the vaginal microbiome and how it effects pregnancy outcomes. Grace went back to this lab for the next couple summers and produced 4 publications! Ultimately, Grace graduated college early after they offered her a full time research position where she worked for a year and a half as a research tech. Through this experience, Grace came to realize that medical school was not her path, canceled her scheduled MCAT and signed up for GRE. Grace looked for schools in the PNW because she knew she wanted to live there, got an interview at OSU, loved it, and here we are!

Join us at 7 pm on Sunday, August 11th, 2019, to hear more about Grace’s research and her journey to OSU. Stream the show live on KBVR Corvallis 88.7FM or check out the episode as a podcast after a few weeks.

When Fungus is Puzzling: A Glimpse into Natural Products Research

Ninety years ago, a fungal natural product was discovered that rocked the world of medicine: penicillin. Penicillin is still used today, but in the past ninety years, drug and chemical resistance have become a hot topic of concern not only in medicine, but also in agriculture. We are in desperate need of new chemical motifs for use in a wide range of biological applications. One way to find these new compounds is through natural products chemistry. Over 50% of drugs approved in the last ~30 years have been impacted by natural products research, being directly sourced from natural products or inspired by them.

Picture a flask full of microbe juice containing a complex mixture of hundreds or thousands of chemical compounds. Most of these chemicals are not useful to humans – in fact, useful compounds are exceedingly rare. Discovering new natural products, identifying their function, and isolating them from a complex mixture of other chemicals is like solving a puzzle. Donovon Adpressa, a 5th year PhD candidate in Chemistry working in the Sandra Loesgen lab, fortunately loves to solve puzzles.

Nuclear Magnetic Resonance (NMR): an instrument used to elucidate the structure of compounds.

Donovon’s thesis research involves isolating novel compounds from fungi. Novel compounds are identified using a combination of separation and analytical chemistry techniques. Experimentally, fungi can be manipulated into producing compounds they wouldn’t normally produce by altering what they’re fed. Fungi exposed to different treatments are split into groups and compared, to assess what kind of differences are occurring. By knocking out certain genes and analyzing their expression, it’s possible to determine how the compound was made. Once a new structure has been identified and isolated, Donovon moves on to another puzzle: does the structure have bioactivity, and in what setting would it be useful?

Donovon’s interest in chemistry sparked in community college. While planning to study Anthropology, he took a required chemistry course. Not only did he ace it, but he loved the material. The class featured a one-week lecture on organic chemistry and he thought, ‘I’m going to be an organic chemist.’ However, there were no research opportunities at the community college level, and he knew he would need research experience to continue in chemistry.

At Eastern Washington University, Donovon delved into undergraduate research, and got to work on a few different projects combining elements of medicinal and materials chemistry. While still an undergrad, Donovon had the opportunity to present his research at OSU, which provided an opportunity to meet faculty and see Corvallis. It all felt right and fell into place here at OSU.

As a lover of nature and hiking in the pacific northwest, Donovon has always had a soft spot for mycology. It was serendipitous that he ended up in a natural products lab doing exactly what interested him. Donovon’s next step is to work in the pharmaceutical industry, where he will get to solve puzzles for a living!

Tune in at 7pm on Sunday, March 18th to hear more about Donovon’s research and journey through graduate school. Not a local listener? Stream the show live.

Hungry, Hungry Microbes!

Today ocean acidification is one of the most significant threats to marine biodiversity in recorded human history. Caused primarily by excess carbon dioxide in the atmosphere, the decreasing pH of the world’s oceans is projected to reach a level at which a majority of coral reefs will die off by 2050. This would have global impacts on marine life; when it comes to maintaining total worldwide biodiversity, coral reefs are the most diverse and valuable ecosystems on the planet.

Unfortunately, there is reason to believe that ocean acidification might proceed at levels even faster than those predicted. Large resevoirs methane hydrates locked away in deep sea ice deposits under the ocean floor appear to be melting and releasing methane into the ocean and surrounding sediments due to the increasing temperature of the world’s oceans. If this process accelerates as waters continue to warm, then the gas escaping into the ocean and air might accelerate ocean acidification and other aspects of global climate change. That is, unless something– or someone– can stop it.

The area of the seafloor Scott studies lies several hundred to a few thousand meters below the surface–much too deep (and cold!) to dive down. Scott gets on a ship and works with a team of experienced technicians who use a crane to lift a device called a gravity corer off the ship deck and into the water, lowering it until it reaches the bottom, capturing and retrieving sediment.

The area of the seafloor Scott studies lies several hundred to a few thousand meters below the surface–much too deep (and cold!) to dive down. Scott gets on a ship and works with a team of experienced technicians who use a crane to lift a device called a gravity corer off the ship deck and into the water, lowering it until it reaches the bottom, capturing and retrieving sediment.

This is where methanotrophs and Scott Klasek come in. A 3rd year PhD student in Microbiology at Oregon State University, Scott works with his advisor in CEOAS Rick Colwell and with Marta Torres to study the single celled creatures that live in the deep sea floor and consume excess methane. Because of their importance in the carbon cycle, and their potential value in mitigating the negative effects of deep sea methane hydrate melting, these methanotrophs have become a valuable subject of study in the fight to manage the changes in our environment occurring that have been associated with anthropogenic climate change.

 

Here Scott is opening a pressure reactor to sample the sediment inside. Sediment cores retrieved form the ocean floor can be used for microbial DNA extraction and other geochemical measurements. Scott places sediment samples in these reactors and incubates them at the pressure and temperature they were collected at, adding different amounts of methane to them to see how the microbial communities and methane consumption change over weeks and months.

Here Scott is opening a pressure reactor to sample the sediment inside. Sediment cores retrieved form the ocean floor can be used for microbial DNA extraction and other geochemical measurements. Scott places sediment samples in these reactors and incubates them at the pressure and temperature they were collected at, adding different amounts of methane to them to see how the microbial communities and methane consumption change over weeks and months.

Most people don’t wake up one morning as a kid and say to themselves, “You know what I want to be when I grow up? Someone who studies methanotrophs and the threat of warming arctic waters.” Scott Klasek is no exception, in fact, he went into his undergraduate career at University of Wisconsin, Madison expecting to pursue an academic career path in pre med. To learn all about Scott’s research, and the twists and turns that led him to it, tune in this Sunday, April 10th, at 7pm to 88.7 KBVR FM or stream the show live!