A robust two-stage microbial sensor developed at Rice
University will help researchers observe gene expression and the
bioavailability of nutrients in environments like soil and sediments without
disturbing them. Rather than fluoresce, like current biosensors, these release
gas to report on their host microbes’ presence and activity. (Image credit:
Illustration by Ilenne Del Valle)
The gas is generated by using microbes
genetically engineered to give an account of their environment as well as
activity and combined into soil samples in restrained laboratory experiments. A
gas that oozes out informs scientists about the number of target microbes that
exist, and another gas informs the activities of the microbes. Ultimately, the
Rice researchers will expect the programmed microbes to disclose whether and
how they communicate with one another.
The sensor has been described in the ACS
Synthetic Biology journal published by the American Chemical
Society.
The study in progress started in 2015 with the
help of a grant of $1 million from the W.M. Keck Foundation and has been headed
by Jonathan Silberg, a Rice synthetic biologist; Caroline Masiello, a
biogeochemist; and Hsiao-Ying (Shelly) Cheng, a graduate student and lead
author of the study. Their aim is to evaluate bioactivity in opaque
environments, specifically those in which modifying the environment will change
the outcomes.
According to Silberg, the new gas-emitting
microbes function on the same principle that governs those that include two
fluorescent proteins; for instance, a green-fluorescing protein will tag all
the cells in a dish, and a red protein will get illuminated when triggered by
microbial activity, such as proximity of a specific molecule or protein
expression.
“In those systems, you can check the ratio of
green to red and know, on average, what the cells are doing,” he
stated. “But that
doesn’t work in soils.”
At present, scientists evaluate microbial
activity in soil by crushing samples and adopting processes such as
high-performance liquid chromatography to quantify their constituents. This
removes the chances of analyzing the same sample over time, and also restricts
the scope of the data.
“Our system answers the right question,”
stated Masiello. “Do microbes know these compounds are present,
and what are they doing in response to them?”
In the ratio-metric system developed at Rice
lab, gases discharged from modified Escherichia coli or other
microbes can assist researchers in evaluating soil development. The term
ratio-metric indicates that the gas output is directly proportional to the
input, which is the level of activity sensed by the microbe here.
In one of the tests, E. coli was
transformed to expel enzymes that produce bromomethane and ethylene. The
microbe continuously produced ethylene, thereby enabling the researchers to
observe the microbe population size; however, it produced only bromomethane
when triggered by, here, bioavailability of acylhomoserine lactones (AHL),
molecules enabling signaling between bacteria.
Once Cheng placed the E. coli in
agricultural soil and fixed the temperature to increase gas signals, she
discovered that the addition of short- and long-chain AHL did not have an
impact on ethylene output but drastically impacted bromomethane. The highest
concentration of short-chain AHL elevated the bromomethane signal by over an
order of magnitude, and that of long-chain AHL elevated it by nearly two orders
of magnitude.
Investigations with a different bacterium,
Shewanella, with sediment as a native habitat, revealed similarly robust
outcomes.
“The dynamic range for sensing chemicals with
what Shelly’s built is very good,” stated Silberg. “It will
vary with the organism, but synthetic biology is really about tuning all of
that.”
The particularly useful aspect of this work is
the potential to distinguish between what’s chemically extractable in a marine
or soil environment and what a microbe perceives is there. Just because we
can grind up a soil and measure something doesn’t mean that plants or microbes
know what’s there. These tools are what we need to be able to, for the first
time, measure microbial perception of their environment.
Caroline Masiello, Biogeochemist
The transformed microbes are meant to be
applied for lab investigation, as opposite to in the open. But tests would be
much faster than current processes and allow labs to monitor a sample
continuously over time. The researchers anticipate applications not only in
synthetic biology and environmental science but also for tracking the
environmental fate of gut bacteria being developed for diagnostics and
therapeutics.
In the future, the Rice lab aims to focus its
attempts on the conditional output portion of the sensor.
As we’ve been building this, people like (Rice
bioscientist) Jeff Tabor and others are standardizing the sensing
modules. We’re building new output modules that you could then couple to
the great diversity of sensors they are building.
Shelly’s really led the way to prove that we
can do gas reporting, and she was the first to do it in soils. She then
showed we could do it with horizontal gene transfer as part of our proof of
concept, and now this. The tools are just getting there, and I think
applications will be next.
Jonathan Silberg, Rice Synthetic Biologist
Graduate student Ilenne Del Valle in the
Systems, Synthetic and Physical Biology graduate program, research scientist
Xiaodong Gao, and George Bennett, the E. Dell Butcher Professor of Biochemistry
and Cell Biology, all from Rice University, are the co-authors of the paper.
Silberg is an associate professor of biochemistry and cell biology. Masiello is
a professor of Earth, environmental and planetary sciences.
The W.M. Keck Foundation, Rice University, a
Taiwan Ministry of Education Scholarship, the National Science Foundation
Long-term Ecological Research Program, Michigan State University AgBioResearch,
and the Department of Energy, Offices of Science and Energy Efficiency and
Renewable Energy supported the study.
No comments:
Post a Comment