Science on Display | Bellevue University 
New evolutionary study shows evidence for LUPA (Last Universal Photosynthetic Ancestor)
Life on Earth as we know it essentially depends on photosynthesis. The process of photosynthesis is arguably the most important biochemical process on the planet because it captures the energy from the sun and produces biomass to support nearly all life on Earth.
You may associate photosynthesis mainly with plants or algae, which are important contributors to this process, however there are far more photosynthetic bacteria than plants and algae combined in terms of sheer numbers and individual organism count on the planet. While plants and algae hold a larger total biomass, photosynthetic marine bacteria and phytoplankton are vastly more numerous, dominating photosynthesis in the oceans.
Furthermore, just like multicellular life originated from ancestral single cell organisms, so does the origin of the photosynthetic machinery in all plants and algae. There is much similarity between the bacterial photosynthetic systems and the algal and plant systems, and it is generally accepted that oxygenic photosynthesis (that produces oxygen, like in plants and algae) originated from ancient bacterial photosynthetic organisms (that did not produce oxygen).
However, there are still several uncertainties and controversies about the order of events on how photosynthesis has evolved. One fundamental question is whether photosynthesis was established only once in these ancient photosynthetic bacteria or whether there were multiple points of origin that led to the different types of photosynthesis that we observe today.
The recent paper by Drs. Imhoff and Kyndt takes a multilayered phylogenetic approach to answer this fundamental question. Previous studies have focused on individual sets of evidence, however, unlike those previous studies, the recent paper used a comprehensive approach that studies three independent lines of evidence: phylogenetic analysis of the reaction centers, and the key enzymes of bacteriochlorophyll biosynthesis, BchN and AcsF, as well as gene synteny of the photosynthetic gene clusters. The convergence of the findings across these different sets provides a compelling and resilient argument for a single origin of photosynthesis, more robust than previously achieved.
The study was entitled “Photosynthesis Has Been Established Only Once—Evolution of Photosynthetic Reaction Center Proteins and Bacteriochlorophyll Biosynthesis” and published in the journal ‘Current Issues in Molecular Biology: https://www.mdpi.com/3783556
The paper describes that there was likely an ancient bacterial-like species that can be considered ‘the last universal photosynthesis ancestor (LUPA)’. This species had a homodimeric Type I photosynthetic reaction center, most similar to the systems we observe in Heliobacteria, Chlorobi, and Chloracidobacteria today. This system was likely present in very special ecological niches as long as 3.5 billion years ago. For comparison, algae have ‘only’ been around for an estimated 1-1.5 billion years and land plants only a mere 500 million years on the planet! So the bacterial origin of photosynthesis far outdates the presence of these organisms.
The authors do caution that with studying evolution over such long time scales, one must consider that most of the intermediate forms of photosynthetic systems that existed are now extinct. Nevertheless, the occurrence of photosynthesis was a process of major significance for early life on Earth and very likely considerably promoted early bacterial life on the planet.
Although this study shows the single establishment of photosynthesis in ancient photosynthetic anoxygenic bacteria, there are many undiscovered bacterial species on the planet and possibly yet-to-be-discovered bacterial species in special ecological niches that could be impacting this evolutionary puzzle in the future.
Have you ever tried growing native plants or setting up a native garden and found that some plants grow slow or not at all? The issue may not be your lack of a green thumb, but rather that the microbes and fungi in the soil may not have been established well.
In a recent publication, the BU science team found that the establishment of a healthy soil microbiome and mycobiome in the first 4-7 weeks after planting seeds is important for the initial germination and growth of the native grass Bouteloua (commonly known as sideoats grama). If there is an early disruption of the microbiome (called dysbiosis), this will lead to slower growth of the grass and allows for potential plant pathogens to establish themselves. This is similar to your need for a healthy gut or skin microbiome to keep you healthy. The study was just published this week in PLOS One:
Both bacteria and fungi are important in setting up the right plant environment, but it appears from the study that bacteria are involved in the initial establishment of beneficial conditions, which sets the stage for a robust fungal and plant seedling development. The study compared both planted and not planted soil and sterile (autoclaved) versus non-sterile soil and their impact on the growth of the native grass. The soil metagenome and its impact on the Bouteluoa growth was monitored for 7 weeks under controlled greenhouse conditions.
The impact of soil bacteria and fungi on agricultural crop plants is currently of great research interest, as soil quality is critical to food production for a growing global population. An estimated one-third of the world’s topsoil is already gone, and the rest could erode away within 60 years, according to a 2014 report by the United Nations. Reversing this trend is a daunting task, which will take a significant amount of time, so sustainable soil practices to maintain good soil health is imperative.
Microorganisms play a crucial role in the soil nutrient cycling process, and the loss of a diverse microbiome leads to problems with soil depletion and nutrient loss. Sustainable, natural soil management needs to include a better understanding and management of the soil microbes that help to improve the soil chemistry. A growing amount of research is becoming available on the soil microbiome impact on crops, however very little has been studied on native plants and non-food crops. Nevertheless, native plant areas provide important ecosystem services and biodiversity.
Our newest publication in PLOS One presents the work of BU science graduates Alisiara Hobbs and Daisy Ochoa-Rojas, together with Christine E. Humphrey who was a visiting summer student, under the guidance of Drs. John Kyndt and Tyler Moore.
Obtaining and analyzing a large amount of sequencing data and performing comparative analysis of the hundreds of bacterial and fungal species can be a tedious and challenging endeavor. The students spend many hours of their student research work optimizing the DNA extraction and analyzing sequencing data. In the end, understanding these microbiome-plant relationships in native Bouteluoa curtipentula opens up possibilities for incorporating target strains that help the colonization and growth of this native grass in restored native habitats. Soil microbial health is important for native plant establishment in urban or prairie settings, and microbial optimization in the case of Bouteloua or other native plants could help their long-term establishment.
The sequencing of microbiomes of native plants and fungi is an ongoing project and there are more student opportunities to join in this research. For more information contact Dr. John Kyndt (jkyndt@bellevue.edu).
The Nebraska salt marshes are a very unique ecosystem and one of the few places in the US where the ground water is naturally salty. They are a relic of ancient oceans that once covered central North America. Conservation of natural areas has historically typically emphasized plant and insect ecology, however it is important to start at the basis, by looking at the microbial changes that often show signs of distress, or start the recovery, months or years before changes become evident in the larger ecosystem. To provide a better understanding of the Nebraska salt marsh micro-ecosystem, we performed a 16-month study to analyze and compare the salt marsh microbiome throughout different seasons.
The research team that performed this study was composed of a group of dedicated Bellevue University and international visiting students that performed different parts of this study over a two-year time period. The team found that the salt marsh microbiome is resilient, but also shows both temporal and spatial variations that are concurrent with seasonal variations in salinity, temperature, and vegetation growth. The study also identified several new species for which the whole genomes were determined. Surprising was the discovery of several antibiotic resistance markers (AMR) and human pathogenic strains of Vibrio cholerae and Pseudomonas in these somewhat secluded marsh ecosystems.
In the end the study was able to determine which species are critical for the health of the salt marsh microbiome, and this could help in future conservation and microbial stewardship efforts to preserve the marshes from further degradation and loss. The result were published this week in the journal ‘Microorganisms’: https://www.mdpi.com/2076-2607/13/10/2369
This is not only a great scientific achievement, but also a great illustration of the collaborative science research success at BU. The research was partially sponsored by the 2024-25 EPSCoR NE grant (to Dr. John Kyndt) and the Wilson Undergraduate Research Enhancement fund at BU. Two of the co-authors are BU students that were sponsored by the EPSCoR grant, one student was from the Delphin summer research program, and two other ones were from the Erasmus research student exchange program between BU and Erasmus University in Belgium.
This research was a collaboration between Bellevue Biology students: Emma Stock, Ketlyn Rota, Brandi Dunn, and Maddy Vasquez, a student from our Delfin summer research program (summer 2024) Daniela Hernandez-Velazquez from the Universidad Veracruzana (Mexico), visiting students Alyssia Lespes and Solenn Bosmans (spring 2025) from the Erasmus University Brussels (Belgium), and Jace Smith who provided additional bioinformatics support, all under the guidance of Dr. John Kyndt.
The results provide a baseline understanding of the microbial processes that support these important ecosystems, and can be used to monitor the future health of the marshes. With increasing urban development near the Nebraska salt marshes there are increasing challenges with effluent contamination of the marshes and, alternatively, potential transfer of these pathogenic and AMR containing species to neighboring developments. Preserving these wetlands is not only important for the ecosystem of the marsh and the health of the environment, but also allows us to get a historical glimpse of the evolution and adaptation of species to more extreme environments.
If you are interested in joining projects like these, there are more student opportunities to join in this type of research. For more information contact Dr. John Kyndt (jkyndt@bellevue.edu).
This week we have a special edition of our senior science student spotlight, highlighting our visiting international student, Rana Petre from Erasmus University College (EhB) in Brussels (Belgium).
Thanks to a recent student exchange program between their college and Bellevue University, Rana worked at Bellevue University as Science Lab Assistants for 12 weeks and gained practical experience aligned with her Erasmus studies in the area of biomedical and pharmaceutical lab technology.
EhB each year has ‘international days’ and for the past three years Dr. John Kyndt yearly gives a presentation to the second-year students about the ongoing research at BU, as an invitation for students from EhB to join for an internship. Dr. Kyndt is originally from Belgium and earned his Ph.D. in Biochemistry at the University of Ghent and build the connections with EhB through former colleagues that are Faculty at that University.
Rana is graduating this Spring with her Bachelor’s degree in Pharmaceutical Biological Lab Technologies!
Rana has been involved in several projects during her research stay at BU and spent countless hours performing DNA extractions and completed over a hundred library preparations for Illumina and Oxford Nanopore sequencing. In particular, she has played a crucial role in helping complete the skin microbiome sequencing project with one of our senior students Kaziah Terrell (featured last week!).
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. Rana will be presenting her final thesis on this topic in Belgium in June this year!
Rana is continuing her education in the next two months with an additional internship at AB InBev, which is global brewing company with approximately 400 beer brands produced and sold throughout the world. Their flagship brands are Stella Artois, Brahma, Beck’s, Corona, and Leffe. Rana is looking to continue her career with a position in a chemical or pharmaceutical company after graduation.
We wish you the best of luck Rana, we are thankful for all the hard work you put in and for the scientific and culinary knowledge you shared with our local students!
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/
Six junior- and senior-level college students from Latin American countries spent time at Bellevue University this summer participating in research projects with University students and faculty, and experiencing life in the United States.
It was all possible thanks to Bellevue University’s participation in DELFIN, a network of academic institutions in five Latin American countries that is designed to enhance undergraduate research, expand students’ international perspectives and open the door to faculty collaborations.
The students and their research projects included:
- Delgado Ortega Jazmín Azucena – “Unveiling the secrets of Mono Lake’s extreme environment through characterization and genomic analysis of extremophilic bacterial species”
- Ibarra Zamudio Jose Saul – “Metagenomic analysis of soil microbial health after glyphosate (Roundup) treatment”
- Martinez Yesenia – “Genomic analysis of new bacterial species from extreme environments”
- Peña Durán Emiliano – “Poly I:C-induced cell death following CRISPR Cas9 knockout of IRF3 in B16 melanoma cells”
- Ramirez Oxte Hannia Nahomi
- Vieyra Vega Montserrat – “Unveiling the secrets of Mono Lake’s extreme environment through characterization and genomic analysis of extremophilic bacterial species.
Bellevue University is one of just a handful of American universities that is a member of DELFIN, which stands for the Inter-Institutional Program for Strengthening of Research and Graduate Studies in the Pacific. The University of Nebraska at Kearney was the first U.S. member of the DELFIN program and houses the United States DELFIN chapter.
DELFIN includes more than 200 academic institutions and research centers across Mexico, has been established with chapters in Colombia, Costa Rica, Nicaragua, and Peru, and students travel to countries such as Germany, Argentina, Canada, Chile, Colombia, South Korea, Costa Rica, Cuba, Spain, United States, England, Peru, Puerto Rico, and Uruguay. Since DELFIN began in 1995, more than 55,000 students have participated alongside faculty in research projects.
“We’re energized by the opportunities that DELFIN represents,” said Julie Verebely, Director, Global Partnerships at Bellevue University. “We have strong relationships with educational partners in a variety of different countries and our joining DELFIN builds on those connections and creates even more opportunities for our students and our faculty to have wonderful experiences.”
This story was adapted from the BU Newsroom post: https://news.bellevue.edu/delfin-students-do-research-at-bellevue-university/
Native plants don’t get nearly enough research attention and the representation of genome information for native plants is substantially lower than the database information available for crop plants or popular ornamental plants.
The new student-led research at Bellevue University is trying to change some of that paradigm, and students from our research classes, visiting student programs and student worker positions have been sequencing a variety of plants from our native plant garden on campus to gain more insight into the genetic wonders these plants might contain.
Our newest publication in the International Journal of Plant Biology, presents the work of BU students Maddy Vasquez, Emma Stock and Kaziah Terrell, together with our greenhouse manager Julian Ramirez and Professor John Kyndt. The work was focused on sequencing the chloroplast genome of the native plant Cleomella serrulata (also known as Rocky Mountain bee plant or stinking clover). The chloroplast was sequenced in house and the genome was analyzed to determine the evolutionary origin of this plant and compare its genetic differences with other plant families. This is a first step to determine how native plants have evolved and adapted to certain environments over many years.
Cleomella has the ability to adapt to harsh environmental conditions and is of ecological importance in maintaining biodiversity within arid ecosystem. Historically, Native American tribes utilized various parts of the plant for medicinal purposes, from treating skin ailments to alleviating respiratory issues. Here is the link to the full publication:
https://www.mdpi.com/2037-0164/15/3/65
Obtaining plant genomic data is still a challenging endeavor. Both Emma and Kaziah spend many hours of their student research work trying to optimize the DNA extraction and sequencing methods for Cleomella and other plants. Maddy took the lead on the write up of the publication as part of her BI 305 Biological Investigations class. Under the guidance of Dr. John Kyndt and Julian Ramirez, the team was able to uncover some interesting features of the evolution of this native plant within its family. This now opens the doors for future evolutionary studies of these plant families.
Cleomella serrulata was also one of the plants that was highlighted last year in our Art + Science presentation at the Benson Theatre for its unique color pigmentation. More information and a link to that presentation can be found here:
The sequencing of native plants, soil and mushrooms is an ongoing project and there are more student opportunities to join in this research. For more information contact Dr. John Kyndt (jkyndt@bellevue.edu).
| Join us for TEDxOMAHA Salon: Your microbes and you! |
| 5 September 2024 at 6:00 PM. Fun facts. Did you know that the microbes that live in you, on you, and around you have a large impact on your health and the health of the environment? A healthy gut microbiome is important to help prevent conditions like obesity, diabetes, heart health and even mental health conditions like depression and anxiety. The microbes that live on your skin are as unique to you as your fingerprints, and they closely work with your immune system to keep you healthy. Just like the microbes living on you and in you, the ones living in your garden soil can help create a healthier environment for the plants to grow and insects to thrive. Dr. John Kyndt is inviting you to come explore the wonderful world of microbes and see some of the research he and the team have done on skin microbiomes and soil microbiomes, and learn to appreciate the importance of the microbial world that we all live in. TEDxOmaha Salon Thursday September 5th starting at 6.00 p.m. at Kaneko, located at 1111 Jones Street, Omaha, NE 68102 – please enter via the library entrance door, which is on 12th St Street Register soon because space is limited.  Thursday, 5 September 2024 18:00TEDxOMAHA Salon: Your microbes and you! Register here We hope you’re able to join us! |
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