“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 email@example.com.