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by Carrie Holl, Ph.D., OI Shrimp Department


“Why would you want to study microbes?”

“ How long did you have to live on that ship in the middle of nowhere?”

“ Eeew, you study what?” (My personal favorite, and one that I have been asked a lot, lately.)

The short answer to why I do this is that microbes rule our planet, so somebody had better try and understand what is going on.

Secretly, the real answer is that I am continually intrigued—and sometimes frustrated—by the myriad intricate details and intertwined processes of biology.

My career has led me from studying what limits the biological input of nitrogen into nutrient-poor regions of the world’s oceans, to understanding how the microbial community is responsible for the detoxification and recycling of nitrogenous compounds in shrimp aquaculture.

These two marine systems cannot be more different, yet they share many of the biological processes responsible for nitrogen and carbon cycling. The field and players are different, but the game remains the same.

The development of recirculating closed aquaculture is necessary in order to produce marine protein, at Oceanic Institute, in an environmentally sound manner. And it is a highly functional microbial nitrogen cycle that makes this technology possible.

To understand the microbial ecology in high-intensity shrimp aquaculture, we are using two cutting-edge research tools: stable isotope geochemistry and molecular probing. By measuring the natural abundance of the stable isotopes of nitrogen and carbon, 15N and 13C, we can explore sources of supplementary nutrition to the shrimp and define and quantify microbial processes such as photosynthesis, nitrification, and denitrification. Our samples are analyzed by the brilliant folks at the isotope ratio mass spectrometry lab at the University of Hawai‘i. Data stemming from these analyses have shown, among other things, that the microbial response to increased nitrogen loading increases linearly with time, and that phytoplankton are necessary for the retention of expensive nitrogen feed inputs as well as for the removal of nitrogenous compounds from the water column.

My lab also has begun to use molecular tools to determine who the key bacterial players are in our microbial soup. We have begun to use Fluorescent In Situ Hybridization to “fish” for specific nitrifying bacteria based on their 16s gene sequences and to quantify their abundance with direct counts of the fluorescently tagged cells. Concurrent nutrient enrichment incubations will allow us to define cell-specific ammonium or nitrite oxidation rates at a given concentration and help us to define environmental factors that could affect these rates such as pH, temperature, and ambient light.

Due to very high concentrations of both organics and the organisms that thrive on those organics, microbial ecology in recirculating aquaculture can be a confusing puzzle. Conflicting processes such as the production of nitrate (nitrification) and the removal of nitrate (denitrification) take place simultaneously in the water column. Controlling for environmental variation and inhibiting conflicting processes in such a way that one or the other process can be measured are intriguing elements of this unraveling puzzle that often keep me awake at night.

You don’t have to stay awake all night to work in my lab, but if you are intrigued, information about internships can be obtained from Gary Karr, Oceanic Institute’s director of communication and education at 259-3146 or via e-mail at gkarr@oceanicinstitute.org.



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