The Global Ocean Microbiome: Studying Microbes in Southern California

The human microbiome is described as the collection of all the microorganisms in and on our bodies that contribute to our health and wellness. The ocean has a similar collection of plankton, bacteria, fungi, and viruses that play a major role in the health of the largest biome on Earth. All of these microscopic organisms are collectively termed the marine microbial community, and are integral in cycling nutrients that sustain ecosystem functions we rely on. I observe these microbes in their natural habitat and study how changing environmental conditions–both natural and anthropogenic–affect their wellbeing. 

I work under one of the Marine and Environmental Biology Program’s newest professors, Dr. Noelle Held in the Proteocean Lab. We study proteins, complex molecules that are cells’ “tools” to interact with their environment. In our research, proteins can tell us which organisms are present, what they are doing in the environment, and how they are doing it. For example, during a harmful algal bloom, we may see proteins that help produce toxins, or those that promote the collection of resources giving the species in possession a competitive advantage. Availability of important nutrients, like carbon, nitrogen, phosphorus, and iron, have a large influence on these microbial proteins.

This summer I am conducting experiments and observational studies on how changes in nutrient availability affect the whole microbial community. Each month, I continue my involvement in the San Pedro Ocean Time Series cruise, a long-term time series has been tracking oceanography characteristics like community composition and nutrient availability since its founding in 1998.

The deep water channel is a fascinating field site due to its similarities with the open ocean and proximity to the urban Los Angeles area. Halfway between the Port of L.A. and Two Harbors on Santa Catalina Island, our boat stops and I collect water samples from multiple depths to analyze for microbial proteins. These samples will be used as an indicator of the current ecological baseline of the system. Our future research will then be used to identify deviations from this baseline, indicating responses from abnormal climate or chemical conditions. 

Recently, I also began running experiments to test nutrient limitation at this location. This refers to any nutrient that is relatively scarce compared to other important nutrients, and therefore the main limiter of microbial community growth. In human microbiome terms, this is the same as not getting enough calcium in your diet. Since we can not produce it ourselves, the deficit would limit our bone growth and decrease our overall health.

I can determine how limited a marine system is by adding more of my target nutrient, currently nitrogen, to collected seawater and quantifying the change in microbial community growth compared to if I do not provide any additional nitrogen. These lab incubation experiments are helping me to determine which nutrients are the most important for us to study in Southern California in order to fully understand the ecosystem. 

This summer, I am running my largest experiment yet at the Wrigley Marine Science Center. Similar to my experiments described above, I start with adding nitrogen to stimulate microbial growth. Then I introduce an added layer of variable light availability to determine how this factor interacts with nitrogen to influence growth characteristics. This interaction of two limiting factors is termed co-limitation and is an increasingly important area of study in oceanography. I hope these experiments will continue to help us unravel the complexities of the marine environment. 

While I’m not in the lab, on Catalina Island, or in the channel, I can be found at Santa Monica Pier studying the impact of wildfires on the marine ecosystem. This past January, Los Angeles was subject to the large Eaton and Palisades wildfires that wrecked havoc on our communities and the environment. These fires produced debris that was carried by wind or rain into the Santa Monica Bay. In addition to unknown natural and human made debris, the fire retardant, Phos-Chek, which contains a compound high in both nitrogen and phosphorus, important macronutrients, was likely blown into the bay. To understand the wildfires’ impact on the coastal marine system, I began a time series at the pier on January 25th, the day before the first rainfall of the year. Together with our collaborators at USC and UC Riverside, my lab takes samples for nutrient availability, microbial DNA and proteins, organic molecules (like pollutants, or microbial toxins), and trace metals. We plan to take samples biweekly for the next year to track the influence of runoff and determine the lasting effects of the Palisades fire. This summer, you might catch me at the end of Santa Monica Pier with the other fishermen, throwing my bucket to haul up some seawater! 

The integral topic that ties all my projects together is studying marine microbes, the ocean’s microbiome. We study the human microbiome because it is integral to understanding our health, and the marine microbial community is no different. It is integral to Earth’s functioning. However, just as we can impact our microbiome, the Earth, and what humans do to it, can impact the wellbeing of the microbial community. I am working to untangle this complex relationship so we can ensure the future stability of our community. 

Mia Franks is supported by USC Dornsife Wrigley Institute Graduate Fellowship.