Popular Science in Microbiology

Collected here are popular science-type articles written by undergraduate members of the Microbiology Club about research being conducted by faculty of the Department of Microbiology.

Light as an Advantageous Ally in the Fight Against Antimicrobial Resistant Pathogens

Dr. Actis’ research concerning the effects of light and temperature on Acinetobacter baumannii

Dr. Luis Actis
Braelyn Binkowski

Oftentimes, it is assumed that the sole purpose of research is to immediately solve the problem at hand and find a solution. In reality, it is used to better understand the topic to more effectively find potential solutions in the future. As Dr. Actis says, “How does the toaster toast the toast?” He follows this exact philosophy in his lab while researching the photoreception and regulation in Acinetobacter baumannii: an antibiotic-resistant, opportunistic pathogen that has become a growing concern, especially in hospital environments. This bacterium takes full advantage of immunocompromised patients, often leaving them greatly debilitated or worse. This pathogen’s virulence, or harmfulness, depends greatly on its ability to produce its own biofilms to live on, allowing it to survive on most surfaces found in medical environments, including polystyrene, which is often what medical devices or implants are composed of. Dr. Actis has studied this pathogen since the mid-1980s, but it wasn't until 2010 that his laboratory observed that the expression of specific virulence factors was dependent on the presence of light (Mussi 2010).

Dr. Actis has two major focuses in his lab: the effects of temperature and light on the gene regulation and behavior of A. baumannii and how these components are related. By growing samples of A. baumannii in varying environments, Dr. Actis has found that this pathogen responds to light in a temperature-dependent manner. Exploring this unique trait and gaining a deeper understanding of it presents a novel avenue for treatment.

Light: quite a curious variable to test considering that A. baumannii does not perform photosynthesis. Typically, the protein in charge of regulating specific virulence factors such as biofilm formation or motility in response to illumination, BlsA, functions effectively within a specific temperature range. But, if the environment exceeds 30°C, this protein is rendered dysfunctional. Interestingly, Actis and his team have found that something is functioning at +30°C that is allowing this pathogen to express virulence-associated functions on a phenotypic, or physical, level; but only under light regulation! This phenomenon is shown in Figure 1. Through the use of lightboxes and strict temperature control, he has found direct correlations between light and the behavior of the pathogen at a temperature that renders BlsA inactive. His studies are currently aimed toward further characterizing this light-based regulation at 37ºC.

A simplified diagram of Dr. Actis' findings
Figure 1. A simplified diagram of Dr. Actis findings, showing a cause and effect cycle of Acinetobacter baumannii under varying conditions. Observing A. baumannii under different conditions has opened up new questions about the bacteria.

Notably, as mentioned above, temperature has also been found to greatly affect the function of A. baumannii. By strictly controlling the temperature of the A. baumannii samples and using genetic analysis and manipulation, Actis has found that BlsA, which regulates biofilm, motility, and virulence, effectively functions at 24°C, which is approximately room temperature (Wood 2019). Once the environment exceeds 30°C, the protein changes shape and is no longer active concerning the function of the protein at a lower temperature. A lack of this functioning protein affects the virulence of A. baumannii, which is crucial to its ability to interact with human target cells. Better understanding the mechanisms through which A. baumannii regulates its virulence factors under conditions that are closer to those encountered in the human host will help us further understand how this bacterium works and can help in providing treatment and prevention of A. baumannii infections caused by multi-drug resistant isolates in the near future.

Literature Cited

Mussi, A, J. A. Gaddy, M. Cabruja, B. A. Arivett, A. Viale, R. Rasia, and L. A. Actis. The opportunistic human pathogen Acinetobacter baumannii senses and responds to light. J. Bacteriol., 192, 6336-6345, 2010.

Wood, C. R., M. S. Squire, N. L. Finley, R. C. Page, and L. A. Actis. Structural and functional analysis of the Acinetobacter baumannii BlsA photoreceptor and regulatory protein. PLoS ONE, 14, e0220918, 2019.

Opportunities for Combating an Opportunistic Pathogen

Dr. Actis’ research regarding the therapeutic strategies against Acinetobacter baumannii

Dr. Luis Actis
Benjamin Nagle

Hospital visits can be a cause for worry, especially when surgery is involved. However, it may be the subsequent bacterial infections that are the real cause for concern. Dr. Actis’s research goal is to better understand Acinetobacter baumannii. A. baumannii is an opportunistic pathogenic bacteria, which means that it is most successful when infecting a weakened host. Moreover, it is most infectious when it has a direct entrance into the host’s body, such as severe burns, open wounds, or recent surgeries. While A. baumannii may not seem to be particularly hazardous to healthy individuals, it poses a serious risk to public health when there are outbreaks in hospitals. Not only are hospitals laden with weakened individuals, but the rugged A. baumannii also thrives in the nutrient-devoid environment created there and is highly resistant to antibiotics and other cleaning methods (Ramirez et al., 2019). One particularly effective strategy A. baumanniiuses to survive these inhospitable environments is to form biofilms. Biofilms are essentially a large number of bacterial cells in extremely close proximity encased in a protective structure made of secreted macromolecules like carbohydrates, proteins, and DNA, also known as exopolymers. Interestingly, A. baumannii is particularly good at forming these structures on polystyrene, a plastic material that is commonly used in hospital equipment (Wood et al. 2018).

One of Dr. Actis’ primary research questions is focused on how A. baumannii uses biofilms to survive in hospital settings. Thus his research not only relates to immunology and microbial ecology but also to medicine. Another question addressed by Dr. Actis’s research relates to how A. baumannii obtain the necessary nutrients such as iron in nutrient-poor environments.

To gain a better understanding of A. baumannii, Dr. Actis performs various experiments with the organisms and runs analyses of their genetic material. By exposing samples of A. baumannii to different environmental conditions, including varying temperatures, light, and low iron conditions, he simulates bacterial infections in different parts of the body or areas of a hospital. This helps Dr. Actis and his peers to understand the behavior of this pathogen, when it exchanges or uptakes genetic material, and when it reproduces. Additionally, he has examined the genetics of A. baumannii using DNA and RNA sequencing, as well as proteomics, a method of protein sequencing and analysis, to assess the genes and proteins, respectively, which could play a role in the virulence of this pathogen. By comparing the genetics of A. baumannii to the genetics of similar bacterial strains, Dr. Actis was able to gain a better understanding of how the various bacterial genes lead to their unique functions. He has used the information from observation of bacterial activity and genetic analysis in various environments to assess the systems behind this unique and hardy bacteria.

Diagram depicting the use of gallium to inhibit cellular respiration in A. baumannii
Figure 1. Panel A: A. baumanii in its natural state, using iron in cytochromes to transfer high energy electrons between proton pumps. Cellular respiration progresses normally. Panel B: A. baumanii treated with gallium which replaces iron in cytochromes. Cytochromes can no longer transfer electrons. Cellular respiration is interrupted. This cell will die over time.

Through his research, Dr. Actis hopes to provide the knowledge needed to develop treatments for this resilient pathogen that expresses resistance to a large number of antibiotics used in human medicine. Additionally, Dr. Actis’s more recent research has led to a possible method of eradicating the bacteria by targeting its iron-reliant functions. If it is possible to shut down or block these essential functions, the bacteria will die due to missing key nutrients (Arivett et al., 2015). Early trials using gallium to block iron utilization functions are quite promising, but they lack an easy delivery method in patients (Figure 1). Despite this, Dr. Actis’s research will be invaluable in future endeavors to treat this difficult pathogen.

Literature Cited

Arivett, B. A., S. E. Fiester, E. J. Ohneck, W. F. Penwell, C. M. Kaufman, R. F. Relich and L. A. Actis. Antimicrobial activity of gallium protoporphyrin IX against Acinetobacter baumannii strains displaying different antibiotic resistance phenotypes. Antimicrobial Agent and Chemotherapy, 59, 7657-7665, 2015.

Ramirez MS, Penwell WF, Traglia GM, Zimbler DL, Gaddy JA, Nikolaidis N, Arivett BA, Adams MD, Bonomo RA, Actis LA, Tolmasky ME. Identification of Potential Virulence Factors in the Model Strain Acinetobacter baumannii A118. Front Microbiol. 2019 Jul 23;10:1599. doi: 10.3389/fmicb.2019.01599. PMID: 31396168; PMCID: PMC6663985.

Wood CR, Ohneck EJ, Edelmann RE, Actis LA. A Light-Regulated Type I Pilus Contributes to Acinetobacter baumanniiBiofilm, Motility, and Virulence Functions. Infect Immun. 2018 Aug 22;86(9):e00442-18. doi: 10.1128/IAI.00442-18. PMID: 29891547; PMCID: PMC6105899.

These Bacteria May Be Small, but They Pack a Good Punch!

Dr. Balish’s research on Mycoplasma bacteria virulence factors

Dr. Mitchell Balish
Alex Chapman

Everyone has faced disease in their life, and many pathogens – disease-causing organisms – are well-known. Even people without scientific backgrounds can recognize infamous pathogens like influenza and E. coli. One pathogen, however, is not as well-known. Mycoplasma, a small bacterium with a small genome and no cell wall, is the focus of the lab of Dr. Mitchell Balish, a Miami University professor. Dr. Balish’s lab focuses on three Mycoplasma species: the pneumonia-causing Mycoplasma pneumoniae, the poultry pathogen M. iowae, and M. penetrans, an opportunistic species (i.e., one that only causes infection in certain conditions) that affects immunocompromised individuals, such as those who have HIV.

There is no better way to understand how a pathogen causes disease than to understand its structures and its life processes. That is why Dr. Balish’s lab studies the structures and processes that constitute the Mycoplasma’s virulence factors, which help it cause disease. One such factor, the attachment organelle, allows for initial attachment to host cells through a process called cytoadherence. Understanding this process allows Dr. Balish to study how the bacteria make biofilms, structures in which groups of bacteria form a sticky micro-community for enhanced survival. Most importantly, Dr. Balish studies what happens after the bacteria’s initial attachment. This includes biofilm contribution to virulence factors like antibiotic resistance (Daubenspeck et al., 2020) and the effect of oxygen concentration in the environment on virulence factor production (Pritchard and Balish, 2015).

Studying these structures is pointless if they cannot be seen. To study the Mycoplasma attachment organelles in more detail, Dr. Balish views them under an electron microscope, which uses electrons to illuminate the specimen rather than light (University of Massachusetts Medical School, n.d). To watch how the organisms move or divide, he uses time-lapse microcinematography, in which multiple pictures are taken at specific time intervals and subsequently merged together to map one continuous movement (Hatchel et. al, 2006). It’s like a tiny movie, except the frames are layered rather than being in a sequence.

Dr. Balish also studies Mycoplasma’s genes and proteins to determine how they make their attachment organelles, and how gene expression changes under certain conditions. This requires two processes. The first is PCR, in which a single gene can be copied multiple times without copying the entire DNA sequence (See Figure 1)(NCBI, n.d.). The other is RT-PCR, which amplifies messenger RNA (mRNA, the RNA transcribed from a gene) by transcribing it into complementary DNA (cDNA), which can then be amplified by PCR (MedicineNet, n.d.). These processes are extremely important; in order to study genes, and thus to study how they change, a lot of DNA or RNA must be acquired.

balish.png
Figure 1. Depiction of the basic mechanisms involved in PCR. Heat seperates the double-stranded DNA into two single strands. RNA primers (pink) attach to the strands, and TaqDNA polymerase enzymes (purple) replicate the strands, starting at the primer and moving in the opposite direction. The process is repeated multiple times to achieve a large quantity of a specific gene. Illustration: Alex Chapman

Don’t think that working in the lab is boring. Dr. Balish and his students always try to keep things light-hearted and fun. Before the COVID-19 pandemic, they presented their findings at scientific meetings. Although the meetings had small audiences (Mycoplasma aren’t the most popular organisms), they allowed Dr. Balish and his students to visit new places, like Italy, China, and Australia.

The lab has also had many noteworthy achievements. Two of Dr. Balish’s research publications have been singled out as “Paper of the Month” in science journals, a huge honor considering how little Mycoplasma is talked about compared to more popular bacterial species. Dr. Balish and the students in his lab were also the first people to look at the biofilms of Mycoplasma that infect humans, and they have been able to view structures that were previously unseen. Mycoplasma may be less popular than other bacteria, but they are certainly not less important.

Literature Cited

Daubenspeck, J. M., Totten, A. H., Needham, J., Feng, M., Balish, M. F., Atkinson, T. P., & Dybvig, K. (2020). Mycoplasma genitalium Biofilms Contain Ply-GlcNAc and Contribute to Antibiotic Resistance. Frontiers in microbiology, 11, 585524. https://doi.org/10.3389/fmicb.2020.585524

Hatchel, J. M., Balish, R. S., Duley, M. L., Balish, M. F. (2006). Ultrastructure and gliding motility of Mycoplasma amphoriforme, a possible human respiratory pathogen. Microbiology (Reading, England) 152(Pt 7), 2181-2189. https://doi.org/10.1099/mic.0.28905-0

MedicineNet. (n.d.). Medical Definition of RT-PCR. https://www.medicinenet.com/rt-pcr/definition.htm

National Center for Biotechnology Information. (n.d.). Polymerase Chain Reaction (PCR). https://www.ncbi.nlm.nih.gov/probe/docs/techpcr/

Pritchard, R. E. & Balish, M. F. (2015). Mycoplasma iowae: relationships among oxygen, virulence, and protection from oxidative stress. Veterinary research, 46(1), 36. https://doi.org/10.1186/s13567-015-0170-7

University of Massachusetts Medical School (n.d.). What is Electron Microscopy. UMASS Medical School, https://www.umassmed.edu/cemf/whatisem/

The Amazing Relationships of Ammonia Oxidizers

Dr. Bollmann’s investigation into microbial interactions between ammonia oxidizers

Dr. Annette Bollmann
Camber Hayes

Nitrogen is a key component in proteins and DNA, so it is important for organisms to get adequate amounts of nitrogen to function properly. However, atmospheric nitrogen cannot be readily used by most organisms. Certain microbes are needed to change nitrogen into forms that can be absorbed. Through a series of steps, bacteria and archaea are able to convert atmospheric nitrogen into ammonium and further into nitrate. Dr. Annette Bollmann at Miami University focuses her research on one of the intermediate steps, nitrification. Nitrification is the oxidation of ammonia to form nitrate via nitrite (figure 1). Although ammonium is more energy efficient to assimilate, most plants prefer to use nitrate as the main source of nitrogen (Killpack & Buchholz, 1993). Ammonia oxidizing bacteria (AOB), ammonia oxidizing archaea (AOA), and nitrite oxidizing bacteria (NOB) facilitate nitrification. Currently, Dr. Bollmann’s lab is studying the microbial interactions between AOB and AOA to better understand nitrification.

Nitrification diagram
Figure 1. Nitrification is a two-step process that ultimately converts ammonia into nitrate. Illustration: Camber Hayes

Microbial interactions are the relationships between microbes and the environment. These interactions between microbes include positive relations, like mutualism, and negative relations, like competition, while interactions with the environment could be behavior in certain concentrations of a chemical. Dr. Bollmann’s lab quantifies microbial interactions by measuring the growth rate of AOB and AOA cultures. To test the microbial interactions, AOB and AOA cultures are placed in varying conditions, such as different pH levels, oxygen concentrations, and microorganisms present, to observe the effect on microbial interactions and ultimately the nitrification process. Perhaps the most surprising finding so far is that AOB grew better in the presence of heterotrophic bacteria, which are bacteria that consume organic carbon as their source of energy, than by themselves in pure cultures (Sedlacek et al., 2016). These findings help clarify how the interactions of ammonia oxidizers and other microorganisms affect microbial activity and therefore the process of nitrification.

The results of Dr. Bollmann’s research on microbial interactions of ammonia oxidizers have many implications. Depending on circumstances, higher or lower levels of nitrification are beneficial. For example, higher levels of nitrification are beneficial for wastewater treatment. AOB is the dominant nitrifier to remove ammoniacal nitrogen, a toxin produced by humans, from wastewater (Bai et al., 2012). Although nitrification is important for the growth and development of plants, too much nitrogen has a detrimental effect on the environment. Nitrate, which is a frequent ingredient in fertilizers, can runoff into bodies of water and allow algae to rapidly multiply, which results in algae blooms. Algae blooms reduce the oxygen in water and block sunlight, and subsequently kill aquatic life. Therefore, it is necessary to determine the optimal levels of nitration and conditions for these systems. The efforts of Dr. Bollmann’s lab to understand the behaviors and interactions of ammonia oxidizers provide insights to the conditions needed to raise or lower the rate of nitrification.

Literature Cited

Bai, Y., Sun, Q., Wen, D., & Tang, X. (2012, May 01). Abundance of ammonia-oxidizing bacteria and archaea in industrial and domestic wastewater treatment systems. FEMS Microbiology Ecology. https://doi.org/10.1111/j.1574-6941.2012.01296.x

Killpack, S, and Buchholz, D. (1993, October). Nitrogen in the Environment: Nitrogen's Most Common Forms. University of Missouri Extension. https://extension.missouri.edu/publications/wq253.

Sedlacek CJ, Nielsen S, Greis KD, Haffey WD, Revsbech NP, Ticak T, Laanbroek HJ, Bollmann A. (2016). Effects of bacterial community members on the proteome of the ammonia-oxidizing bacterium Nitrosomonas sp. strain Is79. Appl Environ Microbiol 82:4776 –4788. doi:10.1128/AEM.01171-16.

The “Unculturables”: Unmasking a Hidden World

Designing novel methods for culturing microorganisms in the Bollmann Lab

Dr. Annette Bollmann
Daria Perminova

If every human on Earth disappeared, other life would still go on. Take away all the bacteria, however, and virtually all life as we know it could not exist. From our gut to the roots of plants, microorganisms make our world possible (Sirisinha, 2016). The study of how microbes interact with one another and their environment to fulfill important roles is known as microbial ecology. This topic is a major interest for Dr. Bollmann’s lab at Miami University, and has led to many fascinating projects. One student, for example, tested how well bacteria adapt to stressors such as extreme acidity and uranium levels (Brzoska and Bollmann, 2016). With new developments in technology, microbial ecology may be more important than ever before. One reason is that scientists have discovered that the diversity of bacteria is larger than we had previously imagined. They were able to quantify and identify species using ribosomal ribonucleic acid (rRNA) (Hurek et al., 1993). This molecule has a structure that is unique for each species -- like a fingerprint for bacteria!

Diagram of cultured vs. suspected bacterial diversity
Figure 1. A graphical comparison of cultures vs. suspected bacterial diversity. While most cultures archael and bacterial species come from only three phyla (left), rRNA sequencing revealed that most species come from other phyla (right). The species of the other phyla are mostly "unculturables." This brings to light the need for new culturing methods to understand the true archael/bacterial diversity.

It is difficult, however, to study most species because they cannot be cultured using traditional laboratory methods. These species are called “unculturables.” In fact, more than 99% of microorganisms have never been cultured (Kaeberlein et al., 2002) (Figure 1). Without cultivation, it is difficult to study microbial behavior and cellular structures. Consequently, designing more efficient methods for culturing became a goal for a few of Dr. Bollmann’s lab members in the past.

A significant obstacle in culturing the “unculturables” is that they require certain nutrients or relationships from their natural environment to survive. These necessities are hard to predict or reproduce in the laboratory. One way to culture bacteria with unknown requirements involves using a diffusion chamber (Figures 2 and 3). In this method, the bacteria are separated from a sample of their natural environment by a membrane with pores only big enough for nutrients to pass through (Kaeberlein et al., 2002). In this setting, colonies are separated from the surrounding environment, but still able to obtain nutrients as they normally would.

Diagram of a difusion chamber
Figure 2. Diagram of a diffusion chamber. A membrane separates the bacterial culture from a sample of its natural environment. The membrane allows nutrients from the surrounding environment to diffuse and nourish the culture, while keeping the bacteria isolated for ease of study.
Examples of diffusion chambers
Figure 3. Examples of diffusion chambers. While some diffusion chambers (left) can have more components and seem more complicated than others (right), their main purpose is to separate a bacterial colony from the surrounding environment. At the same time, however, nutrients can diffuse in through a porous membrane. This is important when a scientist cannot predict the exact factors that a certain bacterial species may require for survival.

While culturing the “unculturables” is not currently the focus of Dr. Bollmann’s lab, the subject may still provide an avenue for future projects. It may even assist in her lab’s main focus on nitrifying bacteria, which are important in the nitrogen cycle. In a broader sense, however, unculturable work will provide access to organisms that have never been studied before. As a result, researchers can gain a better understanding of the interactions that these microbes have with one another and their environment. How bacteria sustain global cycling of common elements (i.e. carbon, nitrogen, etc.), for instance, may be further elucidated through this research. On another note, we may even discover microbes that produce new antibiotics or help break down toxic material. These are just a few examples of how growing new bacteria species opens the door for many other research paths and benefits to humanity. They are also reasons that we should really appreciate microbes because, at the end of the day, these ‘little guys’ reign supreme!

Literature Cited

Brzoska, R. M., & Bollmann, A. (2015). The long-term effect of uranium and ph on the community composition of an artificial consortium. FEMS Microbiology Ecology, 92(1). doi:10.1093/femsec/fiv158

Hurek, T., Burggraf, S., Woese, C. R., & Reinhold-Hurek, B. (1993). 16S rRNA-targeted polymerase chain reaction AND Oligonucleotide hybridization to screen FOR Azoarcus spp., Grass-associated diazotrophs. Applied and Environmental Microbiology, 59(11), 3816-3824. doi:10.1128/aem.59.11.3816-3824

Kaeberlein, T., Lewis, K., & Epstein, S. S. (2002). Isolating "uncultivable" microorganisms in pure culture in a simulated natural environment. Science, 296(5570), 1127-1129. doi:10.1126/science.1070633

Lewis, W. H., Tahon, G., Geesink, P., Sousa, D. Z., & Ettema, T. J. (2020). Innovations to culturing the uncultured microbial majority. Nature Reviews Microbiology. doi:10.1038/s41579-020-00458-8

Sirisinha, S. (2016). The potential impact of gut on your health: Current status and future challenges. Asian Pacific Journal of Allergy and Immunology, 34(4), 249-264. doi:10.12932/ap0803

Vasconcelos, G. J., & Swartz, R. G. (1976). Survival of bacteria in seawater using a diffusion chamber apparatus in situ. Applied and Environmental Microbiology, 31(6), 913-920. doi:10.1128/aem.31.6.913-920

The Difficulties of Studying Chlamydia trachomatis

Dr. Carlin’s research on the interaction between the immune system and Chlamydia trachomatis

Dr. Joseph Carlin
Mackenzie Britton

Dr. Joseph Carlin is currently studying the bacterium Chlamydia trachomatis in his research lab here at Miami University (Carlin, 2021). C. trachomatis is a sexually transmitted infection that affects millions of people every year. Often it remains undetected and therefore goes untreated, leading to complications such as infertility and, in extreme cases, blindness. There is currently no vaccine available due to the fact that the interaction between the immune system of humans and Chlamydia is not well-defined. Discovering how the immune system reacts to the presence of Chlamydia is the main goal of Dr. Carlin's research.

When Chlamydia trachomatis infects the human body, the immune system produces cytokines which are many different types of molecules that fight infections in our bodies. These molecules signal an enzyme called indoleamine dioxygenase to break down the amino acid tryptophan, which Chlamydia is dependent on. Once tryptophan is broken down, the lack of tryptophan should cause the cells to starve and kill the Chlamydia present. Yet Chlamydia trachomatis is still a widespread infection, the Chlamydia must somehow be evading the immune system. This unknown relationship is one of the main topics being researched by Dr. Carlin (Carlin, 2021).

Typically, a lab will conduct experiments with model organisms such as mice to simulate the effect of an infection on the human body, but, unfortunately, mice do not react the same way to a Chlamydia trachomatis infection as humans do. The only organism close to resembling this interaction is monkeys, which are not able to be used as a test subject in labs for established ethical reasons. Since there is no animal that can be used effectively in a lab to study the effect of C. trachomatis, the bacterial cells themselves are used instead. To understand the interaction between C. trachomatis and the immune system, Dr. Carlin is studying how indoleamine dioxygenase is produced in cells. By better understanding how it is produced, a greater understanding of how Chlamydia evades the immune system can be gained. To achieve this, Dr. Carlin is analyzing how the expression of the gene that codes for indoleamine dioxygenase is affected when a Chlamydia infection occurs. He uses a fluorescent lipid that is incorporated into a specific part of the cell so that it will give off a green fluorescent color. In the case of studying Chlamydia, the green fluorescent lipid is incorporated into the Chlamydia (Figure 1). This will allow him to isolate Chlamydia-infected cells using flow cytometry to follow the production and regulation pathway of indoleamine dioxygenase and therefore gain a better understanding of how Chlamydia affects the pathway.

Fluorescent lipid trafficking in Chlamydia-infected cells
Figure 1. Using green fluorescent lipids to study Chlamydia trachomatis by incorporating the lipid into the cell. Lipids are initially trafficked to the Golgi, and from there they are incorporated into the chlamydial inclusion.

Another aspect being investigated is how the cells respond to the infection signal. C. trachomatis is blocking a signaling molecule that has been shown to play a role in programmed cell death called apoptosis that occurs when a cell is damaged or infected, thus allowing the Chlamydia infection to prevail. By learning more about the interaction between Chlamydia and the immune system, this infection could become less widespread or eradicated altogether.

Literature Cited

Carlin, J. M. (2021). Carlin | Microbiology | CAS - Miami University. Retrieved March 21, 2021, from https://www.miamioh.edu/cas/academics/departments/microbiology/research/ faculty/carlinjm/index.html.

Baculovirus as a pesticide? That might be a thing in 2040

Dr. Cheng’s research on the mechanisms of baculovirus use in agricultural insect control

Dr. Xiao-Wen Cheng
Charlotte Siu

Pesticides are currently the most prominent chemicals used to curb the spread of insects in agriculture. However, research has shown that long term pesticide exposure is related to a range of diseases like cancer, autism, and diabetes. The aim of Dr. Cheng’s research is to study how the reproduction/replication mechanism of baculovirus could help reduce chemical dependence in agriculture. In simpler words, this lab studies whether the use of baculovirus is a “suitable alternative” to insect control for current farming practices.

Diagram of baculovirus structure
Figure 1. The general structure of a baculovirus.

A virus generally has an envelope surrounding its genetic material (Figure 1). The baculovirus is enclosed in a polyhedra, a three-dimensional shape with flat polygonal faces, straight edges and sharp corners or vertices.

The polyhedra gene is highly expressed and crystalized to enclose viral protein and protect the viral genome from UV light and viral proteins from desiccation (Figure 2).

SEM of baculovirus structures
Figure 2. Electron photomicrograph of a group of baculoviruses and their polyhedra enclosures.

When caterpillars eat cabbages that contain this “polyhedra enclosed virus”, it will enter their guts. The gut pH of caterpillars is around 9 to 11, giving the polyhedra ability to mix into the gut’s liquid and the virus to hijack the host’s cells for replication. The polyhedra binds to the receptors in the cell membranes of the epithelial cells that line the midgut. This binding allows the virus entry into the host cells where it can use host cell machinery to make copies of itself. This replication will eventually kill the caterpillar and the newly assembled viruses will leave to infect other tissues (Garretson, 2017)(Figure 3).

Baculovirus Life Cycle
Figure 3. The baculovirus replication process in the insect body. Illustration:Tyler Garretson

From what we now understand, this will not work on humans because the pH of the human digestive system is much lower than the proper range for polyhedra dissolution . In addition to this, the machinery in humans that would be used by the baculovirus is different from that of insects, and therefore is incompatible towards the replication of the baculovirus.

The findings of this research can help reduce chemicals present in the environment as it could be possible that polyhedra baculovirus can act as a “natural alternative to pesticides” someday. This can also promote better safety and health, as long-term effects of chemicals like pesticides on our bodies are not clear.

Literature Cited

Garretson, T. A., McCoy, J. C., & Cheng, X.-W. (2016). Baculovirus FP25K Localization: Role of the Coiled-Coil Domain. Journal of Virology, 90(21), 9582–9597. https://doi.org/10.1128/jvi.01241-16.

How do Microorganisms survive in the freezing depths of Antarctic Lakes?

Dr. Rachael Morgan-Kiss’s research on Antarctic algae adaptations needed for survival in extreme environments

Dr. Rachael Morgan-Kiss
Connor Wasmund

Microorganisms are everywhere and have adapted to survive under the most extreme conditions. Dr. Morgan-Kiss studies microscopic Antarctic algae that are capable of performing photosynthesis, despite being located under six meters of ice. Photosynthesis is a process by which certain organisms convert the light rays from the sun into usable energy for producing food, such as sugar. This process is important to all creatures who breathe oxygen because photosynthetic organisms create oxygen as an end product. Dr. Morgan-Kiss’s main goal is to discover what mechanisms allow Antarctic algal survival and use this knowledge to develop synthetic photosynthesis. Dr. Morgan-Kiss specializes in microbial ecology and conducts her field research in the McMurdo Dry Valleys of Antarctica. She studies the diversity and function of microorganisms in permanently ice-covered lakes, focusing on the physiological adaptations of autotrophic organisms. Autotrophic organisms are able to produce their own nutrients using various sources of energy such as light energy and chemical compounds. By drilling through the ice, Dr. Morgan-Kiss and her team are able to collect and analyze samples at various water depths.

Effect of ice binding protein on freezing of different algal species
Figure 1. Two different species of algae (green) are shown, the alga on the left hasnIBP (red) and keeps ice crystals (blue) from combining and solidifying. On the righgt, the alga has no IBPs and thus freezes over which stops regular functions.

Dr. Morgan-Kiss has discovered several adaptations that allow for the organism Chlamydomonas raudensis to survive in the harsh Antarctic environment. This organism can survive in freezing temperatures due to a special protein it secretes called an ice-binding protein (IBP) (Raymond and Morgan-Kiss, 2013). IBPs act like antifreeze by preserving a liquid environment in cells at low temperatures that would normally cause them to freeze (figure 1). This protein exemplifies how specifically C. raudensis has evolved and adapted to its extreme environment.

Another adaptation that allows C. raudensis to survive in freezing water is the configuration of polyunsaturated fatty acids in the cell membrane. The cell membrane is a layer of lipids surrounding the cellular environment that functions to moderate movement in and out of the cell. The special membrane lipids are comprised of a head and fatty acid tail. Due to the configuration in C. raudensis, there was an increase in membrane fluidity (Dolhi, et al., 2013). This configuration can be seen in many organisms that live in cold environments. This is because freezing temperatures can freeze the membrane, but with the correct configuration of the membrane, the membrane can remain in a liquid state. In addition, C. raudensis is a phototroph synthetic organism and is surrounded by low light deep in Antarctic lakes; this is not ideal for an organism that converts light energy from the sun into energy. However, it was found that C. raudensis has an increased amount of Light-Harvesting Complex (LHC), LHC are complexes of proteins that are able to obtain light energy and transfer it to different areas to complete photosynthesis (Liu et al., 2004). With this known, it is inferred that C. raudensis is well adapted for growth under low light and can acclimate to changes in light intensity (Dolhi, et al., 2013).

Dr. Morgan-Kiss hopes to predict how cold-dwelling photosynthetic communities will respond to climate change and adapt to increasing temperatures. In the future, she plans to sequence a protein super complex, an advanced complex housing different proteins that work together, within C. raudensis to explore synthetic photosynthesis. Synthetic photosynthesis is a process that mimics actual photosynthesis by converting light energy, water, and CO2 into usable energy. Similar to solar energy, it is a renewable energy source that can out compete harmful fuels such as coal and oil that negatively impact the environment. However, unlike solar panels, Dr. Morgan-Kiss has the vision of using organic mattel and harvesting the energy from the protein super complexes within the cells, thus continuing to benefit the environment and create a “green” energy source.

Literature Cited

Dolhi, J. M., Maxwell, D. P., & Morgan-Kiss, R. M. (2013, August 1). Review: the Antarctic Chlamydomonas raudensis: an emerging model for cold adaptation of photosynthesis. Extremophiles. https://link.springer.com/article/10.1007/s00792-013-0571-3?error=cookies_not_supported&code=0e14cc2c-2aae-4171-8106-cdfe383a7a8c

Kong, W. K., Li, W. L., Romancova, I. R., Prasil, O. P., & Morgan-Kiss, R. M. K. (2014, March 3). An integrated study of photochemical function and expression of a key photochemical gene (psbA) in photosynthetic communities of Lake Bonney (McMurdo Dry Valleys, Antarctica). FEMS MICROBIOLOGY ECOLOGY. https://academic.oup.com/femsec/article/89/2/293/2680449

Liu, Z., Yan, H., Wang, K., Kuang, T., Zhang, J., Gui, L., An, X., & Chang, W. (2004, March 18). Crystal structure of spinach major light-harvesting complex at 2.72 Å resolution. Nature. https://www.nature.com/articles/nature02373

Raymond, J. A., & Morgan-Kiss, R. M. K. (2013, March 11). Separate Origins of Ice-Binding Proteins in Antarctic Chlamydomonas Species. PLOS ONE. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0059186

 

Cold and Salty Neighbors? Antarctic Microbes Know All About That!

Dr. Morgan-Kiss’s research on the biodiversity in Antarctic lakes

Dr. Rachael Morgan-Kiss
Amber Blevins

While many professors at Miami are involved in research, how many can say that their work is funded by NASA, involves ATV races during downtime, and takes place under the glare of 24-hours of daylight? Dr. Rachael Morgan-Kiss can, and she can also tell you about the microbes she studies in Antarctica’s Lake Bonney! She didn’t always study these organisms, though. During her undergraduate years, she worked in a laboratory focused on plants’ reactions to stress. Dr. Morgan-Kiss then took a graduate opportunity and began her study of microbes that survive especially well in stressful environments that are very cold or have a high salinity. The microbial research for her PhD led her to the McMurdo Dry Valleys in Antarctica and to Lake Bonney, a salty, ice-coated lake.

Diagram of conditions within Lake Bonney
Figure 1. A diagram of conditions within Lake Bonney as seen by depth.

A big focus of her research is to understand the types of life that are able to survive the lake’s harsh conditions. Through her research, Dr. Morgan-Kiss discovered many surprisingly diverse lifeforms were able to survive the stressful environment (Bielewicz et al. 2011). The diverse organisms in the lake are stratified because the water conditions vary by depth (Figure 1). The bottom of the lake has little access to light, but a greater availability of nutrients. Salinity also increases the further down you sample. This means the lake has many different environmental conditions that organisms must adapt to or evolve to survive under (Kong et al. 2012, Kong et al. 2014).

Lake Bonney food web
Figure 2. A simplified version of the food web found in Lake Bonney, showing the diverse forms of life found under its surface (Priscu et al., 1999) The poionts of the arrows show the flow of energy within the ecosystem; for example, bacteria are consumed by and provide energy to phytoplankron, viruses, nanoflagellates, and ciliates.

As Dr. Morgan-Kiss has discovered, many have. Their diversity allows these organisms to develop complex relationships and contribute to the ecosystem's food web (Figure 2). In the lake’s food web, some microbes are producers who gain energy from the sun, while others are consumers who survive through carnivorous behavior (Priscu et al. 1999).

This vast array of organisms was discovered mostly using fluorescence microscopy and flow cytometric analysis (Kong et al. 2014). Fluorescence microscopy quickly estimates the amount of photosynthesizers in a sample using the microbes’ chlorophyll, which absorbs the sun’s rays and releases a specific wavelength of light. The fluorometer measures this released wavelength. The amount of fluorescent radiation in a given sample size correlates directly to the size of the producer population found within it. Flow cytometry is another method used to rapidly measure fluorescence. Fluorescent dyes are used to mark the food vacuoles of predators and find the ratio of predators to prey within samples. Another instrument the team uses, a diving fluorometer, measures the fluorescence around it while it is lowered into the lake. Different organisms release different levels of fluorescent radiation, allowing for evaluation of the microbe populations under the surface not only in number, but also in type by depth.

Dr. Morgan-Kiss’s research has become increasingly important as the climate has evolved and will continue to change. This diverse ecosystem may eventually be lost to the warming planet, but Dr. Morgan-Kiss’s research will ensure that the ways in which the organisms within it have adapted to survive in such a hostile environment are documented and understood. These lakes have been described by NASA as the closest habitat on Earth to the conditions found in space, so the wealth of information that they contain about stress adaptation has very real applications. As the planet continues to warm and humans put more and more stress on the organisms in all environments, understanding stress adaptations will likely become more important as we strive to understand and prevent the extinction of species and the destruction of habitats.

Literature Cited

Bielewicz, S., Bell, E., Kong, W., Friedberg, I., Priscu, J. C., Morgan-Kiss, R. M. (2011). Protist diversity in a permanently ice-covered Antarctic Lake during the polar night transition. The ISME Journal, 5(9), 1559–1564. https://doi.org/10.1038/ismej.2011.23

Kong, W., Dolhi, J. M., Chiuchiolo, A., Priscu, J., Morgan-Kiss, R. M. (2012). Evidence of form II RubisCO (cbbM) in a perennially ice-covered Antarctic lake. FEMS Microbiology Ecology, 82(2), 491–500. https://doi.org/10.1111/j.1574-6941.2012.01431.x

Kong, W., Li, W., Romancova, I., Prášil, O., Morgan-Kiss, R. M. (2014). An integrated study of photochemical function and expression of a key photochemical gene (psbA) in photosynthetic communities of Lake Bonney (McMurdo Dry Valleys, Antarctica). FEMS Microbiology Ecology, 89(2), 293–302. https://doi.org/10.1111/1574-6941.12296

Priscu, J. C., Wolf, C. F., Takacs, C. D., Fritsen, C. H., Laybourn-Parry, J., Roberts, E. C., Sattler, B., Lyons, W. B. (1999). Carbon Transformations in a Perennially Ice-Covered Antarctic Lake. BioScience, 49(12), 997–1008. https://doi.org/10.1525/bisi.1999.49.12.997

Celebrating Cyanobacteria: Microbes that Pave the Way for a Cleaner Future

Dr. Wang’s exploration of cyanobacteria and their contribution to biofuels and food

Dr. Xin Wang
Maddy Zimmerer

There are many professors at Miami University that study various fascinating microbes. A good example is Dr. Wang, an Assistant Professor in the Microbiology department. Dr. Wang has always been inspired and intrigued by the potential and breadth of microbiology, leading him to pursue several facets of it throughout his academic and professional career. Dr. Wang received his B.S. degree in Biology from Xiamen University in China and his Ph.D. in Microbiology from University of Hawaii at Manoa.

Dr. Wang has studied many different topics concerning microbiology, such as the diversity of marine fungi, symbiosis of marine algae, and deep-sea tubeworms. Currently, he focuses on cyanobacteria. Cyanobacteria are photosynthetic bacteria found in both freshwater and saltwater. Although microscopic, they have the ability to form cyanobacterial blooms, an exponential growth of cells that appear similar to algal blooms and are visible to the naked eye (Percival et al, 2014). Similar to plants, cyanobacteria are able to use light as an energy source to convert carbon dioxide into organic carbon, a process known as photosynthesis. Dr. Wang mainly focuses on cyanobacteria’s potential in the production of biofuel (fuel made from living matter) and food.

Cyanobacteria are used as a model organism for photosynthesis research. They are inexpensive and ethical to manipulate in a lab setting while also having anatomical and metabolic parallels to larger organisms of interest. For example, both cyanobacteria and plants have the potential to produce biological molecules called terpenes. In one particular study, Dr. Wang and his colleagues found a potential correlation that connects terpene production to biofuel production by manipulating the molecule limonene, which is commonly found in citrus (Xin Wang et al, 2016).

Effect of limonene on biofuel production
Figure 1. The graph showcases how an increase of limonene ultimately leads to an increase in biofuel production.

Cyanobacteria were engineered to produce more limonene by manipulation of a cellular function called transcription. Transcription is the process of cellular machinery reading a DNA sequence encoding one or more genes, collectively referred to as an operon, and transcribing the operon’s message into RNA. RNA can then be translated into a protein. In this case, the manipulated operon encodes the protein responsible for creating limonene. A variety of operon promoters (DNA sequences that signal the start of transcription) were added to the cyanobacterial limonene operon, and subsequent limonene production was measured. This process of trial and error was used to determine the promoters allowing maximum limonene production. Elevated limonene production increased terpene production as shown in Figure 1. The perfection of cyanobacterial engineering may lead to a sizable increase in efficient biofuel production (Xin Wang et al, 2016). More recently, it has been found that using ATP (a molecule of energy used to propel biological processes) can provide another solution for successful terpene engineering in eukaryotic organisms. Through a mechanism that utilizes sodium, a marine microeukaryote can become motivated to increase ATP production and consequently fuel terpene synthesis (Aiqing Zhang et al, 2020).

The abundance and low cost of cyanobacteria provide a better alternative to current biofuel and food sources. The ability to use cyanobacteria to cater to greener ways of life is a promising first step towards a future where green power is dominant. Not only do cyanobacteria offer a sustainable future, they offer a healthier one too. A primarily plant-based diet can significantly lower one’s risk for heart disease (Harvard Health Publishing). Research on cyanobacteria could pave the way for more efficient protein production in the application of the impossible burger, a plant-based burger found in stores today. Using cyanobacteria to produce plant-based foods will make a healthier diet more widely accessible to people across the globe.

Literature Cited

Percival, S. (2014). Cyanobacteria. Cyanobacteria - an overview | ScienceDirect Topics.
https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/cyanobacteria

Wang, X. (2016). Enhanced limonene production in cyanobacteria reveals photosynthesis limitations. Proceedings of the National Academy of Sciences of the United States of America. https://pubmed.ncbi.nlm.nih.gov/27911807/

Zhang, A. (2020, January 1). ATP drives efficient terpene biosynthesis in marine thraustochytrids. bioRxiv. https://www.biorxiv.org/content/10.1101/2020.11.20.391870v2

Publishing, H. H. (2020). The Right Plant-Based Diet for You. Harvard Health.
https://www.health.harvard.edu/staying-healthy/the-right-plant-based-diet-for-you.