Science on Display | Bellevue University 
It is not every day that an entire bacterial genus is discovered and reclassified. We are lucky when occasionally we find a new species, but that alone certainly does not redefine an entire genus. It took the sequencing and comparative analysis of eight new genomes, in addition to the three known genomes of heliobacteria, to come to this discovery.
Dayana Montano Salama, an undergraduate research student at BU, sequenced the Heliomicrobium genomes using the in-house Illumina MiniSeq.
The family of heliobacteria are a small group of phototropic bacteria that were serendipitously found while Dr. Howard Gest was teaching a lab class in microbiology some 38 years ago. It is therefore suiting that an undergraduate student, Dayana Montano Salama, was a key player in this new research that led to new genus of Heliomicrobium.
“A combination of genome sequencing, whole genome comparison and detailed genetic analysis of the 11 species was performed to reclassify them into the Heliobacterium and Heliomicrobium genera.” says Dr. John Kyndt, who was the lead on this research project. “In the end, the new genus Heliomicrobium includes four unique species, although more will undoubtedly be discovered in the future with growing metagenomic efforts.”
The new genus name comes from the Greek words helios sun; micros small; bios life, so Heliomicrobium literally means ‘sun microbe’. Heliobacteria have been recognized as the ancestors of photosynthesis in the evolution of photosynthetic bacteria. All heliobacteria are strictly anaerobic, endospore-forming bacteria, and the ability to form endospores is unlike all other phototrophic bacteria, but similar to species of Clostridium and Bacillus. An improved understanding of the taxonomic classification of these bacteria will ultimately lead to a better understanding of the evolution of photosynthesis in bacteria in general.
The research was an international collaboration with Dr. Johannes Imhoff from the GEOMAR institute in Germany, and was recently published in the International Journal of Systematic and Evolutionary Microbiology, which is the flagship scientific journal for bacterial taxonomy.
A link to the publication can be found here: https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.004729
Mutualistic relationships that involve close cell–cell interactions are most studied between bacterial and eukaryotic interactions, for example between pathogens and eukaryotic hosts (plant or animal). However symbiotic relationships between bacteria themselves have only been studied more recently. They can be found amongst archaea and bacteria in microbial mats where nutrient exchange and waste removal roles are crucial, in anaerobic methane-oxidizing communities of marine environments, or even in human digestive systems.
Microbial mats contain many bacterial species living in close interactions.
Although these syntrophic cocultures appear to be more widespread than commonly expected, very little is known about the physical interaction that are formed in the cell–cell interactions and the specific chemistry involved to establish a mutually beneficial relationship.
The clue is in the genomes…
By sequencing the genomes of two different species of a symbiotic mixture, and comparing the unique features of these genomes to other free living species, we were able to identify specific, unique interactions that can be formed within this syntrophy. The study showed several types of pili (hair-like appendages found on the surface of many bacteria) and so-called close-adhesion proteins present in one of the partners, while unique e-pili (electron-transporting pili) are formed by the other partner. The details of this are described in a publication by Kyndt et. al., just released this month in Microorganisms: https://www.mdpi.com/2076-2607/8/12/1939
One interesting technical aspect of the study was that the sequencing of both species in the symbiosis was performed simultaneously (without separating the species). However, we were able to separate and assemble the genomes by a process called metagenomic binning. This was made possible by our in-house Illumina sequencing and the publicly available PATRIC bioinformatics platform.
One cell’s trash is another cell’s treasure.
You may wonder what the benefit is for each of these cells to form this symbiosis. In the studied model, the green sulfur bacteria (Prosthecochloris) grow by photosynthesis. This is similar to the photosynthesis you may know from plants and algae, however it occurs anaerobic (without oxygen) and uses hydrogen sulfide (H2S) instead of H2O, and deposits elemental sulfur globules (S0) outside the cells, as a waste product. The partner bacteria in the mixture (Desulfuromonas) loves this, and uses this sulfur as an electron acceptor, converting it to sulfide. This sulfide in turn is used by the green sulfur bacteria to performs its photosynthesis, thereby completing the cycle.
Overview of interactions between Prosthecochloris ethyilca (green) and Desulfuromonas acetoxidans (brown/red). Image created in BioRender.com
Close interactions are preferred.
Thanks to the recent study, we now have a model by which so-called ‘tight adhesion’ (Tad) pili and large agglutination proteins from the green sulfur Prosthecochloris are key elements in the formation of the syntrophic complex. Once close cell–cell interactions are formed, the closed sulfur cycle can be established by electron transfer through specialized e-pili and several cytochromes produced by the Desulfuromonas component.
In addition to the sulfur cycling, another benefit of this relationship is that the colorless bacterium has flagella. This gives the entire complex the advantage of mobility and allows it to swim towards light and nutrients.
It is interesting that both the Tad pili and the adhesion proteins are best known from studies of bacterial virulence factors. However, based on their presence in other nonpathogenic species, they seem to be more widespread amongst bacteria and are likely involved in many environmentally important symbiotic interactions between bacteria.
What do you get when you put a project manager with an electrical & electronics engineering degree, and a biochemist together in a lab? It sounds like the beginning of a bad joke, but nothing is further from the truth. Sometimes unusual interdisciplinary collaborations can turn out to be very productive.
Shivangi Dubey – Manager, Project Management Office and Software Development at Bellevue University
This is exactly what happened when Shivangi Dubey, a BU employee in the IT Department, reached out to Dr. John Kyndt at the Science Department, and expressed that she had an interest in working on some real-life science projects. Together they started working on some of the ongoing project of bacterial genome sequencing at the BU Science Labs.
The collaboration turned out to be fruitful very fast. “Shivangi showed an honest interest and curiosity in the project and was very driven to accomplish results” says Dr. Kyndt. “From the start she described herself as a science enthusiast and a constant leaner. That made it real easy to teach her basic lab and bioinformatic skills”.
In less than two months after the start of the project, the team was able to publish a new article on the genome analysis of an unusual bacterial species. The publication was just released online in Microbiology Resource Announcements this week: Genome Sequence of the Unusual Purple Photosynthetic Bacterium Phaeovibrio sulfidiphilus, Only Distantly Related to Rhodospirillaceae, Reveals Unique Genes for Respiratory Nitrate Reduction and Glycerol Metabolism
Not only did they complete the genome of this species, the genomic analysis and comparisons also revealed the genetic reason behind the strict anaerobic nature of this bacteria and revealed unique metabolic pathways that will be the basis for further physiological studies.
“It all started when a research article on “Photoactive Proteins” by Dr. Kyndt caught my attention and out of curiosity I reached out to Dr. Kyndt to learn more about his research. He not only addressed my curiosity but also provided me an opportunity to learn from him and partner with him in his next research project. Dr. Kyndt has been very supportive and provided guidance throughout this research. I look forward to many more such opportunities to learn from him” Shivangi.
In an effort of continuous education, both Shivangi and Dr. Kyndt are currently taken an online course in Bacterial Bioinformatics, and are hoping to complete their Certificate in Bioinformatics from the University of Virginia in a couple of weeks.
The giant phototrophic bacterium Thiospirillum jenense was first discovered in 1838. Its large size (up to 100μm), spiral shape, orange-brown color, and formation of sulfur globules visible under the light microscope, made it an interesting study object for several renowned microbiologists throughout the 20th century.
Microscopic image of Thiospirillum jenense.
Although a very intriguing organism, it was proven to be extremely difficult to cultivate in the lab and even to date, no pure culture has been obtained. For a long time, the only source of this bacterium was a pond in former East Germany where it grew April to July, and bacterial cultures had to be smuggled across the then closed borders to West Germany. For more than five decades, the problems in cultivation of Tsp. jenense and later also the missing availability of cultures, have disabled further detailed studies.
Even though the growth and phototactic behavior was studied, nothing was known about the molecular genetics of this intriguing species, not even 16S rRNA sequences, so no complete taxonomic classification could be performed. Up until now.
Illumina-based sequencing was performed at Bellevue University on an enriched sample of Thiospirillum jenense, obtained from Dr. Johannes Imhoff from the GEOMAR Ocean Research Center in Kiel (Germany). Genome sequencing and metagenomic binning analysis now provided the full genome of Thiospirillum jenense which was published just this week in Archives of Microbiology. It showed the unique placement of this species amongst the purple sulfur bacteria and, in addition, potentially resolved some of the genetic reasons behind the challenges of cultivating Tsp. jenense that have been limiting further experiments in the past.
One key component appears to be lack of a high-affinity oxidase (FixNOP), which presumably renders the cells highly sensitive to oxygen damage. In addition, the two sequenced contaminant species, Rhodopseudomonas palustris and a new species Rhodoferax jenense, might help with removal of oxygen in the cultures. These results likely explain the difficulties with obtaining pure cultures of Tsp. jenense as described in the paper, and opens up the doors for new cultivation methods.
Having genomic and genetic data available for Tsp. jenense has widened our understanding of the microbial diversity and will undoubtedly help to further identify similarly unique species in environmental samples, where they play an important role in the sulfur cycle and other nutrient recycling in the environment.
With the recent growth in Natural Science courses and rapid development of the sustainability outdoor lab, the time was ripe to expand on the biology instructors for the science department.
Dr. Sarah Gaughan has a Ph.D. in Natural Resources (from UNL) and a background in aquatic ecology, fishes and genome sequencing. Her research has been focused on applying novel techniques to facilitate conservation of native species. She also focuses on population management and finding new ways to control invasive species.
Dr. Sarah Gaughan and Justin Haas with Nebraska Game and Parks doing Pallid Sturgeon gut microbiome research.
This provides a perfect fit for the growing science program and at the same time expands the experience and knowledge of the overall science faculty at BU. Having someone with a diverse ecology background will not only be beneficial for the outdoor lab projects, but also opens up the possibility for students that have an interest in environmental biology and ecology research projects or careers.
Dr. Gaughan will be teaching a variety of natural science courses for the general education but will also be available to mentor students in various research projects in the Biology or Sustainability program throughout the year.
To find out more about Dr. Gaughan’s research projects please check out our Faculty and Staff page, or feel free to contact her directly (sgaughan@bellevue.edu) if you have any environmental or ecology questions or project suggestions.
Welcome to the science team Sarah!
During the entire month of May the BU Library has their display around the theme of Sustainability and featuring the development of the new Sustainability Learning lab.
While the library is practicing social distancing, the library is open and provides a great opportunity to refresh your knowledge on native gardens, greenhouses, biofuels and solar and wind energy. Besides a large selection of books on these topics, the display also highlights some tips on how to set up a native garden and provides some more background on the use of algal ponds for biofuels. You might even come away with some ideas and inspiration to set up some renewable energy yourself or start some small-scale sustainable farming at home!
The main inspiration for this display comes from the new outdoor Sustainability Learning lab that is currently being constructed behind the Joe Dennis Learning Center. This lab will be a 7000 square foot indoor/outdoor educational and research area, consisting of a greenhouse (1,600 square foot), algae pond, wind and solar energy generating stations, and a native plants garden. The lab will give students a unique hands-on opportunity to study various aspects of biology, environmental science and sustainability. The garden of native Nebraska plants was already started last October and some blooms are already sprouting up! (check out our @scienceondisplay on Instagram for updates). This is just the beginning of a three year innovative project. Most of the construction will be occurring in the Summer and Fall of 2020 when the greenhouse is built. In the second phase, the algae pond and the solar and wind generation stations will be installed.
If you can’t make it to the BU Library but still would like more information and resources on the various aspects of sustainability and on the outdoor learning lab, you can also visit the virtual Library Libguide page, where you can find lots of links to library books and ebooks on native plant gardens, net-zero greenhouses (including an interesting historical overview), and renewable energy from solar, wind or biofuels.
Both the library display and Libguide were created and are maintained by Margie McCandless, Reference Support Specialist at the Freeman Lozier Library at Bellevue University.
The COVID-19 pandemic has disrupted everyday lives globally and many scientific research labs have halted or shifted their research efforts. Student research at Bellevue University has also been impacted by this, and students are only allowed to continue working in the labs under restricted circumstances, following social distancing and with additional PPE requirements in place.
Senior Biology student Fabiola Aviles inspecting her bacterial cultures.
On the other hand, this change has allowed for some students to finish writing up and publish some of the interesting research projects that they had been working on. Many of them have been doing genome sequencing projects, that started in the months before the COVID-19 pandemic, and are now taking time to complete the analysis of the data. This doesn’t require as much, or any, wet lab benchwork and can often be done from their own computer thanks to bioinformatic platforms like BaseSpace (by Illumina) or PATRIC (by Argonne National Labs).
Fabiola Aviles collected water samples from Puerto Rico for metagenomics earlier this year.
Fabiola Aviles, one of our senior Biology majors, recently published her first article in Microbiology Resource Announcements (MRA) entitled: Draft Genome Sequences of Thiorhodococcus mannitoliphagus and Thiorhodococcus minor, Purple Sulfur Photosynthetic Bacteria in the Gammaproteobacterial Family Chromatiaceae.
Fabiola is also continuing her thesis work where she is sequencing metagenomes from water samples collected in her home state of Puerto Rico. She hopes to finish that study by the end of the spring term.
Dayana Montano Salama a junior in the BU biology program recently co-authored two publications.
Earlier this year, Dayana Montano Salama, who is a junior in our Biology program, was the lead author on a publication entitled: Genome Sequence of the Acidophilic Nonsulfur Purple Photosynthetic Alphaproteobacterium Rhodovastum atsumiense, a Divergent Member of the Acetobacteraceae Family
And just last week, a second paper where Dayana is co-author was also accepted for publication in the journal MRA. This second paper, ‘Genome sequence of the alphaproteobacterium, Blastochloris sulfoviridis DSM 729, which requires reduced sulfur as growth supplement and contains bacteriochlorophyll b’, will be available online in a few weeks.
Although our traditional pizza and cake party to celebrate these achievements will have to wait until later, it is great to see that our students are adaptable in these challenging times and continuously committed to their projects and studies.
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