Researchers in Focus: Karin Holmfeldt

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Dr. Karin Holmfeldt, holding a T4 phage 

This week on Researchers in Focus, we sat down with Assistant Professor Karin Holmfeldt, whose work explores the intricate world of marine viruses, and their potential impact in the broader spectrum of marine ecology. With ten million viruses contained in a single milliliter of seawater, Karin has her work cut out for her! Here, Karin discusses her background, and where she derives her interests in the subject…

 

 

 

 

 

CAL: Can you tell us a bit about your background?

KH: I started at Linnaeus University back when it was called University of Kalmar. When I set out to get my Bachelor degree, I was interested in working with the big things, the things you can see – animals. But in my second year here, one of the PhD students told me about microbial ecology, and convinced me and a few other students to join a course called molecular microbial ecology. It was the best course I’ve ever taken.

Since I finished my degree project early during my studies, I discovered that I could pick and choose courses that interested me. During the year that I was working and studying, I realized how much I enjoyed molecular biology, and signed up for a course at Norrgård called Genetics, and I found it incredibly valuable. My undergraduate studies involved a lot of hands-on work and applied knowledge, and I am really grateful for that.

After finishing my Bachelor and Magister degrees, I was looking for a PhD position, and I really wanted to stay in Kalmar. It just so happened that one of my assistant professors, Lasse Riemann, was looking for a PhD student to study viruses. I wasn’t particularly interested in viruses at the time, but I wanted to work with Lasse, so I applied. Since then, I’ve absolutely loved my work with viruses!

After my PhD, I went on a post-doc with research grant from VR and the Sweden-America Foundation to the University of Arizona in the US, studying with Professor Matthew Sullivan. It was quite interesting to do marine microbiology in the desert! I had brought my samples with me and did quite a bit of lab work. It was important to me that I owned my own research. When I came back, I eventually got a VR grant and was employed as an assistant professor.

My research involves a lot of collecting DNA from the LMO sampling station and viral isolation. I’m also involved in a mesocosm experiment, as well as have a post-doctoral student, Sigitas Šulčius, who is working with viruses that affect filamentous cyanobacteria.

 

CAL: Tell me a bit about your work with viruses – why are they interesting to study?

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Six of the 12 phages featured in the work of Holmfedlt et al, Twelve previously unknown phage genera are ubiquitous in global oceans (2013).

KH: One of the things that makes viruses so interesting to study is that so little is known about them. They are extremely diverse biological entities that have enormous potential impact on their environments. When a single-celled organism is infected by a virus, its metabolic potential changes. That means that viruses can actually change the potential of their hosts.

Plus, the viruses that I work with are wholly unique in that there is not an individual gene that all of them share. I mean, some viruses aren’t even DNA-based. The influenza virus, for example, has RNA as its genetic material. They can have single strand or double strand, DNA or RNA… the genetic diversity is enormous. Classification is extremely difficult and we have only scratched the surface of the known universe, and when we come in contact with a new virus, we basically have to re-do the taxonomy. There is an International Committee of Taxonomy of Viruses and they are working to do this, but some viruses are better classified than others.

 

For me, when I was younger, I was always watching those science-themed shows, and was so excited at the idea of researchers going into the jungle and discovering a new species of frog, or something. Now, I myself have discovered more then 15 species of viruses!

 

CAL: What do you hope to achieve with your research?

KH: A lot of the research is still very descriptive – to define new viruses. For instance, we’ve found recently that the majority marine viruses either lack tails or have very short tails, which is different from viruses that you would find elsewhere, like soil, where you would find viruses with long tails. It seems that environment plays a big role in the type of virus you’re going to find.

I’m working with PhD student Emelie Nilsson on metagenomes – we currently have 25 metagenomes from the Linnaeus University Microbial Observatory (LMO) in which we look at temporal patterns and see how different viral types go up and down in abundance and how that is connected to their hosts.

Of course, I’m also interested in the bigger questions, like what is the ecological impact of marine viruses? How do the viruses change their hosts’ metabolic potential and interact with carbon sources? Bacteria are the main circulators of organic carbon, so how does it look when up to 50% of the marine bacterial community is infected by viruses?

Another interesting question to look at is how viruses are changing over time in regard to their relationship with their hosts. There are evolving relationships between viruses and bacteria. That type of issue spurs research into areas like viral phage therapy, which has been shown to be enormously beneficial in treating pathogenic bacterial infections – something to keep in mind when antibiotic resistance is becoming a greater problem today.

-Caroline A. Littlefield

Thanks, Karin!

Read more about Karin’s work and the work of her colleagues with the Linnaeus University Centre for Ecology and Evolution in Microbial model Systems (EEMiS).

 Stay tuned for more Researchers in Focus!

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