Edward DeLong - Small RNAs yield great amounts of data from ocean microbe samples
Denise Brehm, Civil and Environmental Engineering
May 14, 2009
An ingenious new method of obtaining marine microbe samples while
preserving the microbes' natural gene expression has yielded an
unexpected boon: the presence of many varieties of small RNAs -- snippets
of RNA that act as switches to regulate gene expression in these singlecelled
creatures. Before now, small RNA could only be studied in
lab-cultured microorganisms; the discovery of its presence in a natural
setting may make it possible finally to learn on a broad scale how microbial
communities living at different ocean depths and regions respond to
"Microbes are exquisite biosensors," said Edward Delong, a professor of
civil and environmental engineering (CEE) and biological engineering. "We
had developed this methodology to look at protein-encoding genes,
because if we know which proteins the microbes are expressing under what
conditions, we can learn about the environmental conditions and how these
microbes influence those. The unexpected presence and abundance of
these small RNAs, which can act as switches to regulate gene expression,
will allow us to get an even deeper view of gene expression and microbial
response to environmental changes.
DeLong and co-authors Yanmei Shi, a graduate student in CEE, and
postdoctoral associate Gene Tyson describe this work in the May 14 issue
of Nature. The team used a technique called metatranscriptomics, which
allows them to analyze the RNA molecules of wild microbes, something that
previously could be done only with lab-cultured microbes.
Microbes are ultra-sensitive environmental sensors that respond in the
blink of an eye to minute changes in light, temperature, chemicals or
pressure and modify their protein expression accordingly. But that
sensitivity creates a quandary for the scientists who study them. Sort of like
the observer effect in quantum physics, by entering the environment or
removing the microbes from it, the observer causes the microbes to change their protein expression. That same sensitivity makes some of these
creatures exceedingly difficult to grow in lab cultures.
To overcome the hurdle of quickly collecting and filtering microbial samples
in seawater before the microbes change their protein expression, the
research team -- collaboratively with CEE Professor Sallie (Penny)
Chisholm and her research team, which has successfully grown and
studied the photosynthetic microbe, Prochlorococcus, in the lab -- created a
method for amplifying the RNA extracted from small amounts of seawater
by modifying a eukaryotic RNA amplification technique.
When Shi began lab studies of the RNA in their samples, she found that
much of the novel RNA they expected to be protein-coding was actually
small RNA (or sRNA), which can serve as a catalyst or regulator for
metabolic pathways in microbes.
"What's surprising to me is the abundance of novel sRNA candidates in our
data sets," said Shi. "When I looked into the sequences that cannot be
confidently assigned as protein-coding, I found that a big percentage of
those sequences are non-coding sequences derived from yet-to-be-cultivated microorganisms in the ocean. This was very exciting to us
because this metatranscriptomic approach -- using a data set of sequences
of transcripts from a natural microbial community as opposed to a single
cultured microbial strain -- opens up a new window of discovering naturally
occurring sRNAs, which may further provide ecologically relevant
"We've found an incredibly diverse set of molecules and each one is
potentially regulating a different protein encoding gene," said DeLong. "We
will now be able to track the protein expression and the sRNA expression
over time to learn the relevance of these little switches."
If we think of marine bacteria and their proteins as tiny factories performing
essential biogeochemical activities -- such as harvesting sunlight to create
oxygen and synthesize sugar from carbon dioxide -- then the sRNAs are the
internal switches that turn on and off the factories' production line. Their
discovery in the ocean samples opens the way to learning even more
detailed information in the lab: the researchers can now conduct lab
experiments to look at the effects of environmental perturbation on
microbial communities. These new sRNAs also expand our general
knowledge of the nature and diversity of these recently recognized
"Being able to track the dynamics of small RNA expression in situ provides
insight into how microbes respond to environmental changes such as
nutrient concentration and physical properties like light and pressure," said Shi. "A very interesting question to follow up in the lab is how much fitness
advantage a small RNA confers to microbes. Can the microbes with a
specific small RNA perform better in competing for nutrients in a tough
situation, for instance? The discovery of naturally occurring small RNAs is a
first step towards addressing such questions."
This work was supported by the Gordon and Betty Moore Foundation, the
National Science Foundation and the U.S. Department of Energy.
A version of this article appeared in MIT Tech Talk on May 20, 2009. MIT News article.