A Scientist's Life: Jeff Bowman

Biological oceanographer studies how microbes, plankton interact with their habitats

Jeff Bowman is a biological oceanographer who joined Scripps Institution of Oceanography at the University of California San Diego in 2017. He received his PhD in 2014 from the University of Washington as one of the first students to take part in a joint degree program between astrobiology and oceanography. He received a bachelor’s degree in biological oceanography from the University of Washington in 2008 and previously served as an Army Airborne Ranger from 1999 to 2003.
 

explorations now: What do you do for a living?

Jeff Bowman: I study the diversity and function of marine microbial communities. Marine microbes are the bacteria and the single celled phytoplankton that exist out in the ocean. My lab conducts field work, laboratory studies and modeling studies. Our primary method is to go into the field and use microscopy and other techniques and sequencing to digitize data out in the field. We bring that digitized data into our laboratory, where we can analyze and model it with computers.

Because of the tremendous number of marine bacteria and phytoplankton out there, they have an enormous influence on the carbon, nitrogen and the other elemental cycles that facilitate all life here on Earth. All of the diversity represented by these groups gives rise to many ecological functions that we are now just beginning to understand. I was one of the first students to go through the joint degree program between oceanography and astrobiology at the University of Washington, and I'm also continuing some of that work here. I am particularly interested in how Europa and other icy moons in our solar system might be viable microbial habitats and how we might use different marine environments on Earth to understand how life might exist on Europa.

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en: What are some of the main questions in your field?

JB: One of the big questions in my field is how does this massive amount of diversity that we observe among marine microbes give rise to the actual ecological functions that we see. There's a tremendous diversity of organic compounds that are present within the marine system. There's this huge genetic diversity of what we call heterotrophic bacteria that consume those compounds and turn them back into CO2. But trying to understand which groups of marine microbes are interacting with which groups of compounds and how fast those reactions occur is a major limiting factor in our understanding of how carbon cycles through the marine system.

There are two main field sites where my lab is working at this time. We've had the opportunity to work with the Palmer Long-Term Ecological Research project along the western Antarctic Peninsula. There we've worked from both ship and land to collect samples of the polar marine environment.

We know that there has been a long-term decline in sea ice along the western Antarctic Peninsula, but more recently, that decline has rapidly reversed, and there's been an actual increase in the amount of sea ice in that region. The specific dynamics of how that sea ice occurs is really complicated, however, and up against the shorelines where the environment is most productive and most of the phytoplankton biomass is found, the ice is constantly drifting in and out throughout the winter season. So the phytoplankton—which are photosynthetic, meaning they’re dependent on light to create food during the spring and summer—are exposed to these rapidly changing light conditions. We're using powerful gene expression techniques to try to understand the response of marine phytoplankton in the coastal Antarctic to the presence or absence of sea ice.

In addition, we started some new work in a tropical environment in Ecuador. We are now working in the Cayapas Mataje Ecological Reserve, one of the largest mangrove reserve systems left in the world. This site is special because mangrove forests are being heavily deforested worldwide. Because this reserve is largely intact, it gives us an opportunity to understand how that ecosystem functions in comparison with ecosystems that have been deforested. However, this is an incredibly difficult place to work in. It's in a very rural part of Ecuador right on the Colombian border. It was too dangerous to travel to up until a few years ago, and we've recently been able to leverage some collaborations with colleagues in Ecuador to start to do some initial field studies at that site.

Mangroves and the microbes are equally dependent on each other for survival in this environment. The mangrove trees are providing carbon and nitrogen for the microbes that are living in the water, and the microbes are providing micronutrients and certain protections back to that mangrove forest system. We look along stress gradients within the mangrove forest, for example, changes in sewage runoff or salinity. We're really interested in the health of the microbial communities along that gradient and how that might be impacting the health of the mangrove forest itself.

en: What tools do you use in your research?

JB: There are a couple of main things that we do with most of the samples that we collect. One thing we're really interested in knowing is what the abundance of the microbes are in those samples. There are a couple ways that we can get at that. One is to use traditional microscopy techniques, which we do in our lab, but microscopy is slow and it's somewhat subjective. It's prone to error based on the individual user who is using the microscope to observe the cells that we see in the environment.

So we use some newer techniques including flow cytometry, which is a really powerful technique to actually count and optically characterize the cells that we observe out in the environment in an objective fashion. Once we have approximated the abundance of the microbes that are in the environment, we are very interested in who those microbes are and what their metabolic capabilities might be.

The way that we get at who's actually there is to collect the cells onto a filter. We then extract the DNA from it and use genome sequencing techniques to sequence particular genes, or in some cases, whole genomes from those samples. We can then analyze that digital data by matching it to databases. We can develop a profile of who's present in the community. We then build models that predict the metabolic function of those microbes based on their taxonomic composition.

We do occasionally use small boats to sample here in the California coastal environment. One of our projects is to look at the role of seagrass in maintaining the microbial communities here in the coastal California environment. Studies in other parts of the world have shown that seagrass can reduce the load of pathogens such as the fecal bacteria that are present within coastal waters. We're very interested in whether similar processes are taking place here in California. Seagrasses are easily threatened by urbanization along the coastline, so we can understand fully the ecological role of those seagrass meadows. We can understand how important it is to preserve them.

en: Why did you come to Scripps?

JB: There are three reasons that I was really excited to come to Scripps. First is its proximity to the ocean. We can use ships to go out and do our oceanographic research, but here at Scripps, we're almost unique in having a truly oceanic environment immediately adjacent to the institution. My lab can go right out on Scripps Pier, collect samples, and bring them back into our lab within just a few moments. And this is something that we do on an almost daily basis, because we have immediate access to oceanic samples.

Second would be the breadth of knowledge that we have here at Scripps. This institution has a huge range of investigators covering almost all aspects of oceanography, earth science and planetary science. Being here at the same institution allows me to interact with those people and take my research in completely different directions that you wouldn't normally expect to be able to take it.

Third would be the relationship between Scripps Institution of Oceanography and UC San Diego. Scripps is almost unique among earth science institutions in being a quasi-independent research institution as well as a department of UC San Diego. And this gives us access to a whole range of resources and a huge range of colleagues on the main UC San Diego campus to interact with.

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