Science on Display | Bellevue University 
Dr. John Kyndt, Professor of Microbiology and Sustainability is one of this year’s recipients of the Nebraska EPSCoR grants for Undergraduate Research Experience in Small Colleges and Universities.
His proposal entitled: ‘Nebraska Salt Marsh Microbiome: an exploration of spatial and temporal microbial diversity’, will allow BU students to delve deeper into the largely unexplored world of microbes in these distinctive environments. The Nebraska Salt Marsh areas are a relic of ancient oceans that once covered the middle of North America. This project is focused on the conservation of this unique area, and aimed to identify the presence of any potentially harmful viral contaminants that might impact plant, animal, and human disease development.
“With our preliminary studies we had already shown that the microbial composition of the Nebraska Salt Marshes is quite unique and contains some potentially very interesting new species” says Dr. Kyndt. That study was published in 2021: https://doi.org/10.3390/life11050446. “Now, thanks to the EPSCoR funding, we can explore this further and study the spatial and temporal variations of these environments over an entire year”
Not only will this project address broader questions about long-term habitat and groundwater conservation, and potential disease prevention from environmental pathogens, but it is also an excellent opportunity for undergraduate students to gain real-life field sampling experience and learn specialized lab techniques like genome sequencing and metagenomic data analysis.
The Undergraduate Research Experience grant program was established by EPSCoR to provide research experience for selected students interested in research projects, and the program is funded by an NSF infrastructure grant to Nebraska EPSCoR. If you are a student interesting in working on this project, feel free to contact Dr Kyndt at jkyndt@bellevue.edu.
This week our senior science student Kaziah Terrell is in the spotlight. Kaziah is graduating this Spring with her Biology bachelor’s degree with a minor in Chemistry!
Kaziah is originally from Atlanta and joined Bellevue University four years ago to study Biology and play for the BU Bruins basketball team. She is currently completing her senior thesis with research on the resilience and diversity of the human skin microbiome.
Not often do students have a chance to combine their science and sports the way Kaziah did. She took her science to the next level when she recruited six of her basketball teammates as participants to test the skin microbiome of their hands and their basketballs over several weeks (shoutout to the Sensational Six!).
As part of the study, participants applied several cleaning methods to the skin to test their effectiveness in altering the skin microbiome, and tested the transmissibility of the microbiome to the basketball during practice. She collected about a hundred samples and sequenced them with our in-house Illumina genome sequencer. As it turns out, the skin microbiome is very resilient and very specific for each individual, even over longer periods of time!
The results of this study provide further insight into the ability to alter or manipulate one’s skin microbiome and has potential applications in clinical and forensic microbiome studies. If you want to find out more about these exciting results: Kaziah will be presenting the results of her research at the American Society of Microbiology (ASM) meeting in Atlanta in June!
Besides her thesis project, Kaziah has also been working the past two years as a lab research assistant on various sequencing projects in the BU Science Labs. She has spent many long evenings extracting DNA from soil samples or analyzing plant phylogeny plots. Even though she’s in the lab often, you probably have seen her around campus as she has helped with organizing and planning many of the residential on campus student activities during the past four years. As if that’s not enough, she is also the Vice President of BOSA (Board of Student Athletes) for the NSAA conference.
In addition to her academic efforts, Kaziah also has had 4 successful years playing for the BU Women’s basketball team! Kaziah is a busy bee, but she has done a fantastic job of achieving success in both her academic, social, and athletic life!
Kaziah is planning to continuing her education and her basketball passion in grad school and will be pursuing a Masters in forensics and criminal justice.
We wish you the best of luck Kaziah, keep making the BRUINs proud and keep exploring in science!
This week we highlight our senior science student Emma Stock, who’s about to graduate this Spring with her Biology bachelor’s degree with a minor in chemistry!
Emma is currently finishing up her thesis with research on the genetics and genomics of endangered Shoal Chub (Macrhybopsis). She has been sequencing DNA from environmentally collected fish samples that have been preserved, with the purpose of performing a detailed phylogenetic and ecological study of these species. Since these samples have been preserved for several years, it is certainly a challenging task to obtain sufficient intact genomic DNA for Illumina high-throughput sequencing, but according to Emma, taking on these challenging subjects “helps build character”.
After many lengthy hours of DNA extraction from preserved native fish samples and library preps for genome sequencing, she successfully sequenced the complete mitochondrial genomes for three endangered Nebraska fish species. This will help with further preservation efforts and provide a better understanding of the evolution of these species. Besides her thesis project, Emma has also been working this past year as a lab research assistant on various soil and plant sequencing projects in the BU Science Labs. Emma is planning to present the results from her research at the Nebraska Academy of Sciences conference in April.
In addition to her academic efforts, Emma also has had 4 successful years playing for the BU Women’s soccer team, where she functioned as team captain for the last year two years. Balancing academics and athletics can be challenging, but Emma has done a fantastic job of excelling in both!
Emma is continuing her education and passion for environmental science and has been accepted to the Master program in Environmental Studies at Evergreen State College. Good luck Emma, we know you will go on to do great things!
It’s never too late to be a continuous learner, especially when it comes to sustainable development which is concerned with providing present solutions, but taking into account the needs of future generations.
No one knows that better than Dr. Lance Stokes, who is in his 80s, and came to Bellevue University for another degree, this time in sustainability studies. With multiple degrees from other institutions already, he’s driven by a passion for lifelong learning and believes education is key to unlocking greatness.
Dr. Stokes graduated with his new degree in Sustainability Management (SUST) and reflects on his learning experiences and the program:
The Kaizen-based process of continuous improvement is also a concept that we teach in the SUST program in the broader concept of sustainable long-term improvement of processes and projects, but as indicated by Dr. Stokes testimonial, this is certainly also relatable on a personal level.
If you want to learn more about the Sustainability program, or other science opportunities at BU, feel free to contact the Program Director, Dr. John Kyndt: jkyndt@bellevue.edu.
Bellevue University professor John Kyndt, will be one of nine speakers to take the stage and present his ideas that push the boundaries of the unknown at the TEDx Omaha event, “EDGE,” set for Saturday, Nov. 18 at Creighton University.
Dr. Kyndt, who is a Professor of Microbiology and Sustainability at Bellevue University, will talk about his focused research on the genomics and biochemistry of bacteria and viruses from extreme environments, to better understand life’s adaptations to extreme conditions.
“These explorations and discoveries at the extreme edges of life teach us more about the diversity of life and how cells can adapt, and possibly even how there can be life on other planets with extremely different environments,” said Kyndt.
Dr. Kyndt specializes in microbial genomics, metabolomics and bacterial photosynthesis.
TEDx Omaha is an independently organized TED event. As part of the global TED community, TEDx Omaha connects locally to explore ideas and situations that affect our culture, our environment and our minds.
Tickets for TEDx Omaha are available now and can be purchased online.
Don’t Miss Out on the Annual Event Taking Place on Saturday, Nov. 18
Repost from BU Newsroom https://news.bellevue.edu/bellevue-universitys-john-kyndt-will-discuss-work-in-genomics–biochemistry-at-tedx-omaha/
Chances are you’ve heard that native plant gardens help the environment because they require less watering and provide habitats for pollinator insects like bees and butterflies.
But thanks to a Bellevue University natural sciences research team composed of faculty and students, we now know there’s another reason – native plant gardens support more microbial diversity and beneficial bacteria in the soil in which they’re planted.
In a paper recently published in the scientific journal Urban Ecosystems, the research team found that converting turf grass, what’s traditionally found on lawns and in many community settings, to native gardens could improve the microbial diversity of soil.
Microbial diversity, for the uninitiated, is simply the existence of difference kinds of one-cell organisms, including bacteria. All kinds of different microbes surround us, but they’re too small to be seen by the human eye.
“We live in a microbial world,” commented Dr. John Kyndt, Associate Professor of Microbiology, Nutrition and Sustainability. “Microbes capture carbon from greenhouse gasses, but also produce important gases, like our oxygen. They cycle nutrients.” Bottom line, microbes are important because they create the conditions conducive for human survival and evolution of other living creatures.
Dr. Kyndt and Dr. Tyler Moore, Associate Professor of Biology, along with Bellevue University student Danielle Baldi and Rice University student Christine Humphrey worked from the premise that as native plant gardens enhance the wildlife habitat, they were possibly having an impact on the underlying soil.
“People can see that insects and pollination increase with native gardens,” said Dr. Kyndt. “But changing the soil microbiome might have a more profound impact on sustainability”. Dr. Moore agreed, adding that “even a small native plant garden area,” noted Dr. Moore, “can make a rather large difference on the microbial community. And people really hadn’t been looking at that.”
To test their hypothesis, the small but mighty research team first collected small samples of soil from native plant gardens and turf grass areas in two nearby Nebraska communities.
Benjamin Vogt, founder of Monarch Gardens and a well known landscape designer, was one the homeowners whose soil was sampled. “I live on a quarter acre suburban lot right on the edge of Lincoln,” Vogt said, noting that when he moved into the newly constructed home, the builders installed sod. Today, nearly a decade later, Vogt has replaced that sod, mostly with native plants, and has minimal lawn/turf areas.
“Then we had to get the DNA out of the soil,” explained Dr. Moore. “Basically, you take the soil and you get rid of all the non-living material and you blow up the bacteria. Inside of the bacterial cells is where the DNA is.”
The lab work, which was primarily handled by Dr. Kyndt and the students, then commenced. “All three of us did some DNA extraction, some library prep, and some data analysis,” Dr. Kyndt said. The DNA was sequenced in the Bellevue University science labs. The facilities are up to date and equipped with a MiniSeq for Next Generation sequencing, as well as equipment for amplifying and visualizing DNA and the labs have the systems and experience to perform genomic and metagenomic data analysis.
From there, the DNA samples from the native plant areas were compared with the samples from the turf areas. Specifically, the research team looked at the bacterial structure and diversity, and the individual bacterial taxa differences between native plant gardens and adjacent turf grass. Bacterial taxa is a large group of microorganisms organized based on their similarity or relatedness.
The team found several potentially beneficial bacterial taxa, including Kofleria and Gemmatimonas, to be more abundant in native garden soil than in nearby turf. Both of these, the research team said, are key for helping fix and sequester atmospheric carbon that is involved in climate change, into soil. In soil, carbon is critical because it provides nutrient to plants, helps soil store water and provide it to plants, and helps give soil structure so it doesn’t erode.
Gemmatimonas, in particular, the research team found, also acts as a potential “sink,” metabolizing the greenhouse gas nitrous oxide into a form where it can’t escape into the atmosphere or into water.
Both scientists encourage people and communities to explore the impact of native plant gardens rather than simply installing turf as a default landscape choice. “Native plant gardens can make things more interesting in the areas that you see, like birds and insects, but also in the areas that you can’t see,” said Dr. Moore.
Vogt, the homeowner, author of Prairie Up: An Introduction to Natural Garden Design and native plant landscaper, is one of those on board. “When you just have a lawn, a monoculture, there’s only so much biologic activity that’s going to happen in the soil,” he said. “And every plant makes a difference.”
Ultimately, as the team’s study found, the microbiome from the native garden soil is changed significantly and “by changing the microbiome (of soil), you’re creating a longer-term impact,” said Dr. Kyndt.
And that invisible benefit may be key, because “the smaller the organism gets,” said Dr. Moore. “The more important it is.”
Reproduced from the BU Newsroom story with permission: https://news.bellevue.edu/bellevue-university-professors-and-students-study-unseen-impact-of-native-plant-gardens/
BU faculty Drs. Sarah Gaughan and John Kyndt recently published a new publication on a study that compares the gut microbiome of hatchery-raised and wild Pallid Sturgeon fishes.
https://www.mdpi.com/2075-1729/13/2/309
You may wonder why anyone wants to look at a fish gut microbiome (fish poop essentially). Well, the bacterial community in an organism’s intestine is called the bacterial gut microbiome and this bacterial community plays an essential role in nutrient supply, immunity and overall health of the host. In this study they described the Pallid Sturgeon’s bacterial community.
Why study this fish species? The Pallid Sturgeon, Scaphirhynchus albus, (Figure 1) is an endangered species that is native species to the Mississippi and Missouri Rivers. Because it is endangered, it has been actively managed to prevent population declines, including stocking of hatchery-raised fish. Since the gut microbiome plays an innate role in an organism’s absorption of nutrients and health, it can provide new insights for Pallid Sturgeon management. By comparing hatchery-raised to wild specimen, one can see how well, or badly the restocked fish adapt to the environment.
In the study, the Pallid Sturgeon’s microbiome is dominated by the phyla Proteobacteria, Firmicutes, Actinobacteria and Fusobacteria. It was also determined that the gut bacterial diversity in hatchery-raised Pallid Sturgeon was not significantly different from wild Pallid Sturgeon, supporting that hatchery-raised Pallid Sturgeon are transitioning effectively to wild diets.
The study was performed in collaboration with researchers from the Nebraska Game and Parks Commission and the U.S. Geological Survey. The sequencing was done with Illumina next gen sequencing and data analysis was done by Bellevue University.
This study demonstrated that genetic markers may be used to effectively describe the dietary requirements for wild Pallid Sturgeon and provides the first genetic evidence that Pallid Sturgeons are effectively transitioning from hatchery-raised environments to the wild. It is another example of how new developments in genomic research can help with conservation efforts of endangered species.
Reducing waste and upscaling waste products is one of the key components of sustainable development. As part of the BU sustainability lab, we are constantly exploring new ways or testing new technologies to make our labs and campus more sustainable and energy efficient.
One component of the outdoor sustainability lab is a 40-gallon biodiesel reactor that was purchased to produce biodiesel from a variety of oil sources. “The lab has done small-scale experiments with biodiesel production from algal oils (produced in-house), but until that technology is ready to scale up, we were looking to supplement with other oils, and used frying oil seems readily available from our own student cafeteria”- says Dr. John Kyndt.
The BU campus cafeteria crew was immediately excited to help out. “Aladdin Campus Dining is excited to be a part of research involving sustainability. Being able to collaborate with departments within Bellevue University is an excellent opportunity for dining services to contribute in additional ways to the campus” – says Heather Summers DeBlanche from Aladdin Campus Dining.
The technology to convert waste frying oil into biodiesel has been around for some time now, and although this involves relatively straightforward chemical reactions, this process had to be optimized for this specific waste oil.
That is where students from our SUST310 (Energy, Environment and Sustainability) and BI 205 (Biological Investigation ll Laboratory) classes came in. Students Sierra, Anna, and Kaziah, worked on optimizing the catalyst and reaction conditions on a small scale. Students set up reactions (up to 1 liter) in the lab and tested and compared the biodiesel production under several conditions.
The final biodiesel is on the top right image.
These reaction conditions can now be scaled up for the larger 40-gallon reactor (some time in the coming weeks). The small-scale process already generated purified biodiesel that can be ignited by compression (as in a regular diesel engine).
The plan is to produce enough biodiesel in the coming weeks to run a small diesel generator or possibly power some of the lawn care equipment around the campus in the future.
This project is a great example of how local community resources can be used to generate valuable products and how basic principles in chemistry and sustainability can be taught using real-world applications.
So the next time you order your delicious fried food from the cafeteria, you can feel good about the fact that you are supporting science at BU!
The evolution of phototrophic bacteria and photosynthesis in general is certainly an interesting but complex topic. It is commonly well accepted that anoxygenic phototrophy evolved well before the gradual oxygenation of the Earth. This means that the photosynthetic machinery of anaerobic phototrophic bacteria (like purple and green bacteria) evolved well before the existence of oxygenic photosynthesis of algae and plants.
One of the best studied model organisms for studying photosynthesis in purple non-sulfur bacteria is Rhodobacter. Members of the genus Rhodobacter all perform anoxygenic photosynthesis, but can also grow aerobic (but when doing so repress the synthesis of photosynthetic pigments). They also fix nitrogen and thereby play key roles in biogeochemical cycles.
A novel Rhodobacter species, designated strain M37P, was isolated a couple of years ago by Dr. Robert Ramaley (a collaborator from UNMC on this project) from the Mushroom hot spring runoff within the Lower Geyser Basin of Yellowstone National Park.
“When we first tried to grow and characterize this new Rhodobacter species from Yellowstone National Park, we were quite surprised and puzzled that this species could not be grown anaerobically.” says Dr. Kyndt, who was one of the leads on the study. Up until that point, all Rhodobacter species were easily grown under anaerobic photosynthetic conditions. “It’s easier to show that something can be done in science, than proving that something cannot be done. The latter takes a lot more experiments, replications, and time.”- Dr. John Kyndt.
After several cultivation attempts from both the BU team and the collaborating lab from Dr. Ramaley at UNMC, the team had to conclude that this new species was a so-called aerobic, anoxygenic phototroph (AAP). The unique physiology, whereby the cells make a red-pink pigment in the dark, but loose the pigment in the light, was consistent with the species being an AAP. This was the first AAP identified in the large Rhodobacter genus.
Genome sequencing by BU biology student Sydney Robertson, and further genomic analysis by a visiting biochemistry student from New Mexico State University, Isabella Shoffstall, revealed some clues from the genome that relate to those unique features. This new strain does not contain the RuBisCo gene for fixation of CO2, which is typical for AAP’s. RuBisCO is an essential protein in the Calvin-Benson-Bassham cycle that catalyzes the addition of carbon dioxide to ribulose-1,5-bisphosphate. The new genome also lacks the genes for the Light Harvesting complex II, which is typically an important photosystem component in Rhodobacter (and other photosynthetic bacteria) and augments the collection of solar energy.
The student research also led to the discovery that this new strain contains a unique xanthorhodopsin protein, which likely contributes to the cells red-pink color. Xanthorhodopsins (XR) are light-harvesting proton pumps with a dual chromophore. They have one retinal molecule, similar to archaeal bacteriorhodopsin and the rhodopsin in your eyes that allow you to read this text, but in addition, XR also contains an additional carotenoid antenna chromophore which allows the cells to utilize a wider range of light for energy conversion. No other Rhodobacter species contains rhodopsin.
However, a clue for this uniqueness might come from the environmental conditions where this new strain was isolated. An earlier metagenomics study of the Mushroom Hot Spring had shown an unexpected diversity of potential retinal-based phototrophy in this area (although only partial genomes were found, and it was uncertain whether these were producing functional rhodopsins). This new xanthorhodopsin-containing Rhodobacter was isolated from the same area (albeit it at a lower temperature point) and possibly obtained the rhodopsin gene through horizontal gene transfer from nearby organisms. Blue-green light (450-550 nm) is not absorbed very well by the chlorophyll a, phycocyanin and carotenoids of cyanobacteria and algae in that area, and the presence of an antenna chromophore in xanthorhodopsin certainly provides a selective advantage in the complex microbial community of the Mushroom Spring runoff area.
“It is fascinating to see how diverse and adaptable bacterial species are, and how, with the power of genome sequencing we can find new clues about this diversity and adaptability of life in general.” says Dr. Kyndt.
The findings and a full detailed description were recently published in the journal Microorganisms and can be accessed here:
https://www.mdpi.com/2076-2607/10/6/1169
This collaborative project has provided some additional insight in the possible evolution of bacterial anoxygenic photosynthesis and the adaptation of bacterial species to varying environmental conditions, but (as often in science) also raised more questions about the complexity of this evolution. The team is planning to continue this research and more detailed studies on the Rhodobacter xanthorhodopsin and this new clade of species are already underway.
Repost from BU Newsroom story by Cris Hay-Merchant
Bellevue University Associate Professor John Kyndt collaborated with researchers at the University of Arizona and at GEOMAR Helmholtz Centre for Ocean Research in Kiel, Germany, and the team recently published a paper in Microorganisms defining the Halorhodospiraceae bacterial family.
“Being able to define a new bacterial family is like discovering a new breed of animal,” explained Dr. Kyndt, an Associate Professor of Microbiology, Nutrition and Sustainability. “It doesn’t happen a lot,” he said. The bacterial family the team classified – extremely halophilic, purple sulfur bacteria, to be specific – was first discovered in a sample of water from Summer Lake in Oregon state, but many members are found in African and Mongolian soda lakes.
The new bacterial family has potential use in industrial applications, Dr. Kyndt said. Enzymes from extremophilic bacteria play an important role in industrial processes, because they are stable at high temperature or extreme conditions that are used to produce and purify materials. For example, extremophilic enzymes are used in the synthesis of pharmaceuticals and cosmetics, or textile or paper processing.
“Being able to define a new bacterial family is like discovering a new breed of animal.”
Dr. John Kyndt, Associate Professor
Dr. Kyndt’s primary role in the research involved mapping and sequencing the genomes of the bacterial family. Sequencing the genomes is an essential part of building the bacterial family’s taxonomy. Bacterial taxonomy is used to classify different types of bacteria on the basis of their mutual similarity or evolutionary relatedness.
The research team was able to distinguish the new bacterial family from other bacterial families. According to Dr. Kyndt, the team’s work sets an important foundation for future research related to sustainable industrial processes.
Recent Comments