Fungi and Viruses

Once upon a time, there was a disease. This disease was first identified in a different country overseas, but recently identified in the U.S. Not much was known about the pathogen, how it infected the hosts, or treatment options. But it caused problems. And plenty of debates sprung up about how it spread, how infectious it was, and if it really was a cause for concern. Sound familiar? Huh, I guess more people read my Masters thesis than the required four people.

At Michigan State, I studied a disease that was recently identified in the U.S. It was known to have been in Brazil and South Africa, but in 2014 through 2017, we identified it in eight counties in Michigan. Oh, and the disease I studied only affected beans. 

Often times, I feel that my grad school work in plant diseases doesn’t have any benefits beyond the agricultural world. But I’ve realized that my two and half years studying plant diseases have given me a basic understanding of our current pandemic. One of the main duties of a scientist is to share findings and information. I decided (while waiting for my own subsequently negative COVID-19 test) to share what I’ve learned about plant diseases and how it relates to our current situation.

A little bean plant with Fusarium root rot (distinguished by the red discoloration on the root).

I studied a fungal disease that caused a disease on dry beans and soy beans called Fusarium root rot. The first confusing aspect of diseases is the naming system (or one of my favorite words: nomenclature). Diseases are caused by pathogens such as bacteria, fungi, or viruses. The common cold is a virus, E. coli is a bacterial disease, and yeast infections are caused by fungi. However, the actual organisms that cause these diseases are called by different names. For example, the fungus that causes a yeast infection is Candida. The disease I studied is called Fusarium root rot. It is caused by several species of fungi known by names like: Fusarium phaseoli, Fusarium cuneirostrum, and Fusarium brasilience. The disease we call COVID-19 or coronavirus is caused by a virus that has been named SARS-CoV-2 (a note, in scientific nomenclature, species names are italicized so if SARS-CoV is written out “Severe acute respiratory syndrome – related coronavirus” then it would be italicized). The naming rules for microbes are strange. They follow taxonomy rules – how organisms are genetically related – and often named for where they’re found or by whom. The fungus I studied, Fusarium brasilience, was first identified in Brazil – hence the “brasilience”. The CoV-2 part of the virus’ name comes from its designation of being a coronavirus, a category of viruses based on their physical structures. Coronaviruses as a whole can infect humans or animals. 

My cute, little fungus, Fusarium brasiliense

Diving into any research may leave you frustrated because scientific language is confusing. It’s like its own language. Scientists are very careful not to use absolute language like “this is a newly discovered disease.” Instead, we say, “this is a recently identified disease” or “a novel disease”. But the word choice is intentional and important. A newly “discovered” disease conjures up the idea that the disease has never been known whereas the word “identified” means that it was the first time in scientific record that this disease has been known. Novel is also an intentional choice. When “novel” is used, it also means that it hasn’t previously been reported on in scientific records or literature. It’s not “new” because that is a judgment on the age or recency of the pathogen. For all we know, SARS-CoV-2 has been around for many years, it just hasn’t been around humans. The fungus I studied in Michigan often presented this challenge to me. To us, it was a novel pathogen in Michigan but not new because we didn’t know how long it had been in Michigan. The fungus may have been there for years and our tools unable to detect it or it could have been recently introduced. But it wasn’t for me to make the a judgment about its introduction.  My evidence wasn’t focused on when the fungus arrived or why, it just supported that the fungus was now present. 

This may seem like scientists are leaving the back door open for themselves. We often are. The very nature of science is that we learn something new and something contradictory everyday. Scientists don’t want to use absolute language because the next day new information may come along that changes our understanding. It should be comforting that scientists don’t use absolute statements, especially when describing something recently identified. It means we are open to new information.

Different levels of disease on bean roots, from least virulent to most.

Perhaps the most challenging part of COVID-19 is understanding the pathogenicity versus virulence. Pathogenicity and virulence are foundational principles in the study of diseases. We’ll start with pathogenicity.  Pathogenicity is a yes or no question. Is this fungus or virus a pathogen? In grad school, when Fusarium brasilience was identified in Michigan, we had to first figure out if it was a fungus that was actually causing disease or if it was essentially a fungus along for the ride. To answer this question, we grew Fusarium brasilience in the lab on petri dishes that had a food source, a starch. Then we would allow a single spore of Fusarium brasiliense to colonize sorghum grains. After several weeks, the fungus would have grown all over the grains, using them as an all-you-can-eat feast. These grains were added to a soilless growing medium (so there were no other microorganisms to muddy the results) with bean seeds. The beans were monitored over a several week growing period, with careful observance for disease symptoms such as stunting, yellowing of the leaves, and discoloration or rotting of the roots. Finally, the bean roots were washed, dried, and DNA was extracted. We ran tests to see if the Fusarium brasiliense DNA was found in the bean roots. If we found Fusarium brasiliense DNA in multiple tests, it would confirm that the fungus was indeed a pathogen.

A seedling pathogenicity assay – how we tested the pathogenicity of different pathogens

With the identification of COVID-19 (the disease), scientists had to first confirm the virus in question and whether it was causing disease or not. Confirming the pathogenicity of SARS-CoV-2 (the virus) was different from how I confirmed pathogenicity in grad school. The biggest challenge with viruses is they only live and reproduce on living hosts. Fungi can live on alive (like bean plants) or dead hosts (like downed trees in the forest) and this characteristic makes it much easier to study fungi. Some of the first tests to study the pathogenicity of SARs-CoV-2 were done on lab mice (Bao et al 2020). The lab mice in the study confirmed that the virus was a pathogen specifically of the respiratory system. 

After confirming pathogenicity, scientists can then describe the virulence of a pathogen, or the severity of the infection. This is where debates start springing up in our national discourse. How serious is COVID-19? Why does it cause some people to be asymptomatic and send others to the hospital? First, we often forget that diseases like COVID-19 are caused by living organisms that respond and react to conditions. 

My first classes in grad school taught about the disease triangle. The disease triangle shows an interaction between the pathogen, the host, and environment. Fusarium brasiliense thrives in cool, wet soil where there is compaction or little oxygen. So it will thrive more in a year where there is flooding as opposed to a drought year. The main interaction of the host is its resistance to a pathogen and how it fights back. Resistance in plants is similar to how a mammal’s immune system. I tested two types of beans that came from two different genetic “families” and had different levels of resistance. In my study, black beans had more inherent resistance to Fusarium root rot than kidney beans. And finally, the pathogen. Understanding the pathogen is the most complicated part of the disease triangle, mostly because of the microscopic nature of pathogens. However, we’re living in a microbiology information revolution. While humans have known about microbes for hundreds of years, we’ve lacked the tools to study them in depth. Fortunately, since science is always progressing, we are gaining better tools and understanding every day. 

Without microscopes, I wouldn’t have been able to creep on the reproductive lives of fungi

Preliminary information about SARS-CoV-2 suggests that the virus “tricks” the host’s immune system, causing the immune system to initially downplay its response rather than attack steadily and immediately (Kumar et al 2020). Studies also show that the virus is easily transferred from cell to cell in the vascular system, which can explain its spread into other areas of the body and a larger array of symptoms. The immune system is the most important part of our bodies’ defense system but everyone has a different immune system. Our immune system is both due to our genetics and what we’ve been exposed to throughout our lifetime. This is why public health officials have been calling for people who have chronic illnesses, are older, or have otherwise compromised immune systems to be careful. But none of us know what our immune system is truly like. We can’t have our immune system revealed to us like our blood type. And what makes COVID-19 unnerving is that our immune systems haven’t fought against a virus like this before. The spike we’re seeing now are due to the disease triangle creating an ideal situation – we’re spending more time indoors and near people. Since the virus survives on living hosts, it transfers from person to person. 

Learning about the pathogen, environment, and hosts and how they all interact are crucial. But they’re crucial because they can reveal a game plan for treatment. My work in grad school was spent studying Fusarium brasiliense, but also looking at fungicide treatments to offer farmers a way of combating Fusarium root rot. What surprises me most about plant diseases versus human diseases is the treatment. It often seems we are much more willing to put effort into figuring out treatment for crop diseases than human diseases. One aspect of treating crop diseases is the cultural control. Fusarium root rot had higher rates of disease in compacted soil so farmers were encouraged to use deep tillage to break up compaction as the first step of defense. If they routinely struggled with Fusarium root rot, then a fungicide was suggested. 

Humans struggle with the cultural treatments as well. We don’t like staying home or keeping our distance from people. But this disease is real. It affects people in ways we don’t fully understand. And the way we address it matters. Because the lives of human beings are far more important than human’s beans. 

(If you want to know more about my research (ya nerd), you can watch a short video I made for a communications class here, but you can’t read my thesis because that’s just too much)

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