Microbes Coming into Focus - The Biotechnology Institute

Volume 11, Issue No. 2
About This Issue...
They outnumber and surround you. You
can’t hide from them. Some are deadly,
but most are harmless or even friendly.
Microbial Genomics
• Most microbes are one-celled
organisms visible only under a
microscope, which explains
the name “microorganism.”
Anton van Leeuwenhoeck
called them “wee animacules”
in the mid-1700s.
You need them to survive. Indeed, they
make Earth a livable planet.
They are microbes, tiny organisms that come in
an amazing variety of shapes and sizes. Microbes
include bacteria, viruses, fungi, protista, and
• Microbes are the smallest
organisms on the planet, but
archaea. They were the first life forms, appearing 3.8
they influence some of the
billion years ago in the boiling ocean. Earth
biggest events.
was hot and the atmosphere was
• They are valued partners in
saturated with the heat-trapping gas,
maintaining our bodies and our
carbon dioxide. Gradually, microbes
environment.
changed the face of the planet. They
• The genomic revolution is giving
produced the atmosphere’s first
us a fundamental knowledge of
oxygen, which paved the way for
biology and a new view of the
more complex organisms and
relationships among species.
ecosystems. Today, microbes exist in
• Microbial genomics broadens
every nook and cranny, under every
our ability to use microbes to
benefit our health, economy,
condition imaginable. They are the
and ecosystem.
ultimate adapters.
Although individual microbes are
tiny, they are massive as a group.
They account for almost two
thirds of the Earth’s biomass
(living material). They recycle
the Earth’s oxygen, carbon,
nitrogen, and sulfur through
the air, water, soil, and
rock. Their collective
“breathing” creates our
atmosphere and
controls our climate.
Making bread or
They decay our waste
and return nutrients to
yogurt requires growing a
microbial culture. Find a recipe the soil. They help us
digest our food. One
microbe was so essential to us that it became our cell’s
energy producer: the mitochondria. (Similar bacteria
became chloroplasts in plants.)
While some microbes can make you sick, others can
make you well: They produce antibiotics that treat
infections. Microbes are important to both old and new
biotechnologies. We harness them to make our bread
rise and to turn milk into cheese. We use them as “minifactories” for drugs like insulin (which treats diabetes).
In spite of their importance, we know very little
about microbes. We’ve probably only studied about
one percent of them: those that either cause disease
(called pathogens), or that we can use for our benefit.
and practice classical
microbial biotechnology.
2
Microbes Coming into Focus
These people are testing water quality, and microorganisms have an important
impact on water quality. (Photo courtesy of Visuals Unlimited, Inc.)
Contents...
What about the other ninety-nine percent of the microbes?
What do they do on the planet? What can they tell us about the
origins of life? How can they live in seemingly deadly conditions?
How do they adapt to radical changes in their environment? How
can we foil their attacks on humans, animals, and plants? Can we
use some of their strange characteristics to solve such problems as
pollution and global warming?
Unfortunately, most microbes don’t grow well in the laboratory,
so they are hard to study. The science of genomics, however,
provides new techniques. Genomics allows scientists to analyze
the complete set of an organism’s genes (called a genome).
Microbial genomics has changed the way we think about these
small but mighty
creatures. It is also
revealing exciting
insights into the
biology of every life
form. This issue of
Your World looks at how
microbial genomics
boosts our ability to use
biotechnology to
improve our own
health and that of the
world around us.
Revealing the Microbial World: Inside Gene Discovery ................ 4
Biofilms and Quorum Sensing: The Gang’s All Here ................... 6
Anthrax: The Sleeper Cell ......................................................... 8
Bioremediation: Microbes That Like it Hot! ............................... 10
Ecosystem in the Abyss: Black Smokers and “Umbs” ................. 12
Profile: Karen Nelson, Genome Researcher ............................... 14
Something You Can Try: Growing Biofilms ................................ 15
Resources ................................................................................ 16
Dear Readers,
The Biotechnology Institute (BI) is pleased to
present this spring 2002 issue of Your World:
“Microbes Coming into Focus,” which
explores the amazing universe of microbial
genomics. I hope that it sparks your interest
in biotechnology and its on-going impact.
The bioterrorism threat has made us all
keenly aware that scientific discoveries can
be used in destructive ways. As this issue of
Your World makes clear, however,
manipulating microbes also can make life
better - helping to cure disease and clean up
the environment. Scientists may one day help
combat cystic fibrosis based on an
understanding of how Australian long-leaf
seaweed protects itself from biofilm
formation by bacteria. Other scientists may
reduce water pollution using microbes that
break up waste materials. These
accomplishments can be starting points for
the next generation of scientists - your
generation, the readers of Your World - for
rewarding careers in biotechnology.
I hope that you become engaged and
excited about biotechnology and its
enormous potential as you explore
“Microbes Coming into Focus.” I welcome
your comments about this issue of Your
World and about the Institute.
BI is especially grateful to the American
Society for Microbiology and the U.S.
Department of Energy for their support of this
issue of Your World. The Institute also thanks
Kim Finer, Ph.D., Associate Professor,
Biological Sciences, Kent State University for
serving as the scientific advisor for “Microbes
Coming into Focus.”
Bacteria
A typical bacterium has one
chromosome that forms a loop
(rather than a strand like in our DNA)
and has no nucleus. Many bacteria
have extra genes on plasmids, which
are circular pieces of DNA separate
from the chromosome.
Biotechnology & You
Volume 11, Issue No. 2
Published by:
Jeff Alan Davidson Writing by:
The Writing Company,
Cathryn M. Delude and
Kenneth W. Mirvis, Ed.D.
Design by:
Snavely Associates, Ltd.
Illustrations by:
Science Advisor:
Kim Finer, Ph.D.,
Kent State University
Reviewers:
Daniel Drell, Ph.D.,
Office of Biological and Environmental
Research, US Department of Energy
Lynn Jablonski, Ph.D.,
GeneData
Geoff McMullan, Ph.D.,
University of Ulster
Marissa Mills,
Oak Ridge National Laboratory
William C. Nierman, Ph.D.,
The Institute for Genomic Research
Sincerely,
Special Appreciation
Bill Costerton, Ph.D.,
Montana State University
Paul Hanle, President
Michael Daly, Ph.D.,
Uniformed Services University
of the Health Sciences
The Biotechnology Institute (BI) is a national
non-profit entity based in Arlington, VA,
and dedicated to education and research
about biotechnology. Our mission is to
engage, excite, and educate people about
biotechnology’s potential to solve human
health and environmental problems. Your
World focuses on biotechnology issues and
brings scientific discoveries to life for 7th to
12th grade students. We publish issues on
different topics each fall and spring. Please
contact Jeff Alan Davidson, Publisher, for
information on subscriptions (individual,
teacher, or library sets). Some back issues
are available.
For more information:
Jeff Alan Davidson, Publisher
1524 W. College Avenue, Suite 206
State College, PA 16801
800-796-5806
[email protected]
www.BiotechInstitute.org
Copyright 2002, BI. All rights reserved.
Jim Frederickson, Ph.D.,
and Roy Gephart, M.S.,
Pacific Northwest National Laboratories
John Lennox, Ph.D.,
Pennsylvania State University, Altoona
Tim Read, Ph.D.,
The Institute for Genomic Research
The Biotechnology Institute acknowledges
with deep gratitude the financial support
of the DOE and ASM in
producing this issue.
The Biotechnology Institute would
like to thank the Pennsylvania
Biotechnology Association, which
originally developed Your World.
Your World
3
Genomics has “popped the hood” off of microbes,
allowing us to peek at the genetic sequences inside
their “engines.” This is NOT your parents’ biology!
Detective Work
When spores for anthrax were sent through the mail in late
2001, investigators searched for clues: Who sent this bacterium?
Where did they get it? They turned to genomics, the study of an
organism’s DNA. Genomics provides a kind of fingerprint for a
microbe. This fingerprint can help investigate crimes – and such
questions as “How did life on Earth begin? What does the tree of
life look like? How does a microbe cause disease? How can we
prevent disease? How can we use microbes for food, industry,
space research, and the environment?”
Before genomics, scientists studied microbes by collecting
samples from nature. They grew them in a nutrient-rich culture in
the laboratory and studied their
reaction to different substances and
conditions. With DNA technology,
however, scientists encountered an
undiscovered microbial world.
Uncultured Bugs
In one study, scientists wanted to
see how many microbial species were
actually in a sample of ocean water
from the Sargasso Sea. They counted
the variations in a gene found in all
known organisms. (This universal
gene builds part of the
ribosome, the cell’s protein
factory.) They found the
genetic traces of many
more organisms than
would grow in the laboratory. One species, which
scientists named Sar 11,
made up a quarter of the
sample, yet it had not been
identified in the lab. It
4 Microbes Coming into Focus
thrived in water with extremely few nutrients and was killed by
the richness of the laboratory culture. It was unculturable.
That study opened the eyes of microbiologists! Microscopes
had made microbes visible. Now DNA technology unveiled a
more populated microbial community. Unculturable microbes
make up the bulk of species from both strange and familiar
places. They are in your backyard soil, on your skin, and in your
cheese. One scientist commented that it’s like being in a dark
room without a flashlight, surrounded by mysterious creatures.
You don’t know what they look like, how they live, or if they hide
treasures, such as a new
antibiotic or cancer
treatment.
The Big Picture
Genomics provides a flashlight for that roomful of microbes.
Getting the information about an entire genome is like having the
recipe for a pastry. It doesn’t show what the pastry will look like,
but it tells a lot about its ingredients and assembly.
Genomic recipes reveal how biology works at the most basic
level, and microbes are a great study group. Scientists can control
everything in a microbe’s environment, so they can test how cells
respond genetically to changes around them. It’s easier to study
how genes behave in a single cell that reproduces rapidly than in a
complex, slow-developing human being, or even a mouse. They
can analyze genes one at a time, or as a whole, integrated genome.
You may wonder what this has to do with you. A lot! We share
a surprising number of genes with microbes. Many of the similar
genes control basic functions, such as how you extract energy
from your food (metabolism) and copy chromosomes for growth
and reproduction. Scientists often identify a gene in a microbe and
Gene Swapping
Tracing microbial evolution on the family tree has
one problem: It doesn’t make sense! Comparing
genomes should tell us which microbe is older
and place it on the correct twig of the tree. That’s
because organisms inherit genes vertically, from
one generation to the next. Yet microbes also
inherit genes horizontally, passing a section of
DNA to other microbes in the same generation. Microbes even “swap genes” with
microbes on completely unrelated
branches of the tree. Their family tree
of life looks more like a web!
Gene swapping is like passing on
a “shareware” package with programs you don’t use but your friend
might. That helps explain how
microbes can develop resistance to
antibiotics so cleverly – or adapt to
polluted environments. Exposure to
an oil spill puts the same kind of
selective pressure on microbes that
antibiotics do. The microbial shareware
probably includes programs to help
them adapt to changing food supplies
and temperatures, too. (Of course,
microbes also adapt to new environmental pressures the old fashioned, vertical
inheritance way: mutations.)
then find a similar one in humans. For example, studying gene
mutations in yeast is teaching scientists a great deal about cancer
genes in humans. Thus, microbial genomes are a sort “Cliff’s
Notes®” for interpreting our own, more complicated genome.
Once scientists have a microbe’s genetic recipe, they can
manipulate its genes. They can mutate (change) or knock out
(delete) a gene to see the effect on the microbe. They can insert an
unknown gene into a well-known microbe to discover its
function. In this way, they can study uncultured microbes or even
unidentified genes from human beings. Similar techniques show
how diseases and drugs work, and they allow scientists to
“customize” microbes to do specific jobs for us.
What is Life?
How many genes are required for life? The smallest known
genome belongs to Mycoplasma genitalium, which has only 517
genes compared to our 30,000 or so. By knocking out its genes one
at a time, researchers identified up to 350 genes that it needs to live
(in the laboratory). These core genes might provide a short cut to
the essential genes of higher organisms. They might also reveal how
primitive organisms functioned. Currently, researchers figure out
how life evolved by tracing genes from different species backwards
to the oldest common ancestors. Genomics may help us start
reading the story of life at the beginning.
Three Methods of Gene Transfer
Horizontal Gene Transfer:
Microbes can receive genes
on a DNA plasmid from
another living microbe, and
they scavenge bits of free
DNA from dead bacteria. A
bacteriophage (bacterial
virus) can also transfer genes
to bacteria.
Career Center: Laboratory Researcher: Get
microbes to grow in the laboratory by recreating the
right mix of nutrients and temperature.
Your World
5
have varying “climates.” Thus, even genetically identical
microbes may look or act quite differently. In some biofilms,
like the plaque on your teeth, many species live together in an
integrated community.
We all have everyday experiences with biofilms, such as when
you wake up with morning breath. They’re on your retainer or
headgear. They cause you to slip on rocks in a stream. They build
up inside water mains and oil pipelines. They contaminate tubes
and tanks in factories. Some are beneficial. Cows couldn’t digest
hay without a biofilm in their stomachs. Others form stubborn
infections on heart valve implants, catheters, and contact lenses.
You may have suffered from a biofilm: a middle ear infection
caused by Haemophilus influenzae and Streptococcus pneumoniae.
Inside your ear, the biofilm acts like a gated community, protecting the bacteria from antibiotics. If drugs do get in, they may not
reach the biofilm’s interior caves where hibernating microbes will
eventually awaken and revive the infection. It may take several
rounds of antibiotics to get rid of your earache.
Calling the Meeting to Order
Luminescent squid provided the first clues that microbes are not
just simple, solitary creatures. Why do these squid glow at only
certain times? Bacteria that colonize the squid produce the glowing
substance, but only when there are enough of them to make the
light visible. How do they know when there are
Outsmarting
Resistance
Antibiotics are in a losing battle with
microbes. An antibiotic is a chemical that interferes with an organism’s
essential life processes. If a drug
fails to kill all the bacteria, however,
the ones that survive may be more
resistant. Microbes can develop
defenses faster than we can make new
antibiotics. Now we’ve learned that in
addition to these biological defenses, many
microbes also build physical barriers: biofilms.
Genomics may help us overcome these microbial defenses. It gives us a root understanding of
potential targets in the microbe’s cell so we can
develop new compounds and new strategies. This
understanding may lead to molecules that inactivate
microbial genes, garble the genetic instructions, or
disrupt quorum sensing. All in all, though, microbial
resistance is a moving target, and it is an ongoing
challenge to keep one step ahead.
enough? They “listen” for their neighbors’ signals. When they pick
up enough signals, they turn on the light. It is like when your
student council must have a quorum (enough members present) to
call a meeting to order. Many microbes also wait for a “quorum”
before they activate certain genes. Thus, scientists call this behavior
quorum sensing.
Disease-causing microbes may use quorum sensing in their
attack strategy. A lone bacterium enters your ear and “listens” for
comrades. If it doesn’t sense enough signals, it keeps its “weapon”
genes inactive. Otherwise, it would alert your immune cells,
which could easily destroy it. The microbe multiplies. When the
concentration of signals reaches a certain level, the bacterial
crowd is large enough to overpower the immune cells. They
turn on the disease-causing genes and
attack your tender ear cells.
Counter-Intelligence
Think
about it
!
As biofilm guru Bill Costerton
explains, the key to battle is
intelligence. If you destroy the
Quorum sensing signals
enemies’ communication network,
are like the hormones that
they can’t coordinate an attack. A
turn on a new set of genes
form of counter-intelligence may
at puberty. They are also
help defeat some diseases by
like an animal’s pherojamming the signals and stopping
mones, which are
the microbial conversations.
chemicals that drive
Such a counter-intelligence ploy
complex behaviors such
actually exists in nature. A long-leaf
as mating.
seaweed in Australia never gets
biofilms. It emits a chemical
called furanone that silences
the signal genes. Bacteria “think” they are still alone
and free-floating, so they don’t coordinate the
biofilm construction project.
Could the Australian seaweed’s furanones
be used in human medicine? Researchers are
experimenting on the genetic disease cystic
fibrosis (CF). Children with CF often die from a
lung infection caused by Pseudomonas
aeruginosa. This bacterium coats the lungs with a
thick biofilm that protects the bacteria from
antibiotics. When researchers gave mice with CF
some furanone, the signals fell silent. The bacteria
left the biofilm, became free-floating, and were
killed by antibiotics. The infection was cured. If
this approach works in humans, it may provide
new ways to subdue infections. It may also lead
to new techniques for dissolving troublesome
biofilms insides pipes, on boat bottoms, and
other places.
To see animations of antibiotic resistance, go to:
Career Center: Genomics Researcher: Discover
• http://www.usatoday.com/graphics/news/gra/antibiotics/frame.htm
the genes involved in the microbial communication
network and develop new drugs to jam the signals.
• http://www.pbs.org/wgbh/evolution/library/10/4/l_104-03.html
Your World
7
Microbes have killed more people throughout history than wars have. It’s not surprising, then, that
some people have used germs as weapons. Now
we’re turning to biotechnology to protect us from
bioweapons.
When a photo editor in Florida got what seemed like a bad
flu, his doctor ran a blood test. Dr . Lar ry Bush saw r od-shaped
bacteria called bacilli and thought, “Hmm. I better make sur e
this isn’ t anthrax.” (Anthrax is a disease caused by
Bacillus
anthracis.) Although anthrax is a natural disease in cattle and
sheep, it has never occur red naturally in Florida. However , the
spores have been pr ocessed for use as a militar y weapon. Dr .
Bush pr obably wouldn’ t have checked for anthrax befor e the
September 11 ter rorist attacks. Now , bioter rorism was on
people’s minds, and doctors wer e on the watch. Dr . Bush’s
suspicion tur ned out to be right. Although it was too late to save
his patient, his quick thinking alerted doctors to watch for
anthrax elsewher e, in time to save others.
The Florida man had the deadliest kind of anthrax: inhalation.
He had br eathed in spor es, a kind of sleeper cell for m. Bacillus
bacteria for m spores when they ar e star ved for nutrients. Spor es can
lie dor mant for a hundr ed years, thr ough heat, cold, and dr ought.
Once inside the lungs, scavenger immune cells ( macrophages or
“big eaters”) gobble up the spor es. Macr ophages usually pr otect us
from bacteria, but in this disease they unwit tingly
become the bacteria’ s hosts.
The spor es somehow sense
they ar e inside the cell
and “wake up.” They
turn on genes, transfor m
into bacteria and multiply
rapidly. They burst out of the
cell and flood into the
bloodstr eam. Ther e, they
produce a thr ee-part toxin
(poison) that invades mor e
cells. Even though antibiotics
may kill the bacteria, the toxins may still kill the
patient. Scientists have r ecently lear ned how these
toxins work. (See illustration on page 9.)
Detection and
Diagnosis
Much of the “terror” in
bioterrorism results from
not knowing if or when it
will strike. Detecting bacteria
in the air is key to limiting the damage. The earlier we know about
an attack, the quicker patients can get antibiotics and vaccines.
However, detection is har d because ther e are so many bacteria
similar to B. anthracis in the envir onment. Also, a typical air sample
might have such a tiny number of anthrax spor es that they ar e hard
to detect. Tnvir onment. 8J/00 1.-*-0l(bacteria367dif spo1-0.ficj-0eger ihave r)-7(d)]
Can microbes help us solve
environmental problems?
A million-gallon tank of radioactive waste
at the Hanford site: The crystallized ring
shows the original level of the waste,
which has begun to leak. (Photo courtesy
of the U.S. Department of Energy)
Hanford National Monument in Washington state: This scenic region of the Columbia River lies not far from the
largest radioactive waste cleanup project in the nation. (Photo courtesy of the U.S. Department of Energy)
In the 20th century, we created a new, long-lasting,
and lethal material: radioactive nuclear waste.
Microbes, the planet’s oldest residents, might be
harnessed to convert this waste into less
dangerous forms.
Wild River in a Pristine Wilderness
When Lewis and Clark made their way to the Pacific Ocean in
1805, they followed the Snake River out of the Bitter root Mountains
to the Columbia River – a tumbling rush of rapids filled with
leaping salmon. Not far upstr eam lies one of the few str etches of the
Columbia that still runs wild. Most of the river has been dammed
for hydr opower, endangering the salmon r uns. This still-wild
section was r ecently pr otected as Hanfor d National Monument.
A Lasting Legacy of War
Within this wilderness lies a former U.S. military site. This site
produced plutonium for nuclear weapons from the1940s through
the end of the Cold War in the 1980s. That production created a
nasty stew of radioactive waste, heavy metals, and chemical
10 Microbes Coming into Focus
solvents. The waste was stored in million-gallon tanks, and now
some of it has leaked into the soil.
These contaminants would be bad enough if they stayed in the
soil near the tanks. Some of them, however, are soluble. They
dissolve in water and “travel.” Their molecules have a negative
electrical charge that keeps them from sticking to soil particles.
They stay dissolved in groundwater (the water that
travels underground) and flow in the same direction as
groundwater. At Hanford, groundwater flows into the
Columbia River, potentially carrying these contaminants with it.
Cleanup Project
Hanford is now the largest
environmental cleanup project
in the nation. It could cost
$100 billion to clean up or
remediate this 600-squaremile site. Now, tiny microbes might help out with
this big task. That effort is
called bioremediation:
using biology to fix
contamination.
Use microbes to recycle
your own garbage. Collect
some vegetable scraps from
your cafeteria and start a
compost heap. In time, you
can fertilize a garden with
the compost.
(Link: http://ohioline.osu.edu/hyg-fact/1000/1189.html)
Global Warming
Sixty-five million years ago the dust from an asteroid
How do microbes pave the
way for other life forms?
How does a bacterium “live forever”? (So to speak.) It starves.
Into the Abyss
We often picture the ocean as teaming with life, but much of
it is as barren as a desert. It has scarce nutrients and very few
life forms per unit of seawater. Oceanographers call such waters
the “abyssal” area. (In Greek mythology, life sprang out of the
chaos in the abyss, which is a deep chasm.)
Indeed, life can grow in the abyss given the right conditions,
such as the opening of a deep-sea vent. Vents can occur at
geological faults (divides) on the ocean floor. A crack opens,
and hot gases, black smoke, and molten lava spurt forth,
creating a “black smoker.” The gases contain methane and
hydrogen sulfide – smelly compounds that are deadly for most
organisms. These regions are in areas too deep for sunlight to
penetrate, and sun provides the basic energy for life. Thus, a
black smoker seems like the last place on Earth where organisms would gather. On the contrary!
Um… What’s an Umb?
This deep-sea vent or “black
smoker” emits gases and smoke
from deep within the Earth.
Extremophile bacteria use these
gases as their energy source and
form the basis of a complex
ecosystem. (Photo courtesy of
Visuals Unlimited, Inc.)
12 Microbes Coming into Focus
Floating through the abyssal area are sprinklings of tiny
microbes. To live there, they adopt a trick that microbes
sometimes use on land, too. When there is no food, they
divide and become smaller. After three or four divisions, they
are so tiny they have room for just their DNA. They shrink
from about one micron in diameter (one one-thousandth of a
millimeter) to just 0.3 microns. Microbiologists call them
ultramicrobacteria (“umb”). These umbs can remain dormant
for decades, and probably for centuries.
A black smoker is a great thing for these umbs. Unlike us,
ultramicrobacteria thrive on methane and hydrogen sulfide
gases. Both of these gases are chemical compounds that contain
the element hydrogen (H). Anything with hydrogen contains a
lot of energy. The umbs use the hydrogen from the gases and get
a sudden surge of energy, like eating a bowl full of jellybeans. (A
sugar molecule is ringed with hydrogen atoms, which is why
candy gives you a burst of energy.) The umbs revive and grow.
An Ecosystem Grows
The revived bacteria stay close to their energy supply. They
form biofilms on the cones and towers that build up around the
vent. Soon, they cover these surfaces with a jelly-like mass.
Some of these bacteria die and become food for other kinds of
bacteria. Predator bacteria arrive, gobbling up some of the
microbes. Eventually, there is a diverse community of microbes,
with one member depending on another. Such is the beginning
of a micro-ecosystem.
Before long, the larvae of clams and worms float by. They
find fertile ground for settling down. In time, this deep-sea vent
might sprout a waving forest of brilliant red tubeworms that
may reach the height of six feet. The abundance of bacteria,
worms, clams, and even plants attracts various strange fish and
shrimp that are adapted to live in the pitch dark. Thus, an
increasingly complex ecosystem spreads out from the vent – all
nourished by the energy that microbes extract from gases
instead of from sunlight.
Scientists compare the diversity of life at a deep-sea vent to that
in a tropical rain forest or coral reef. At the vent, we can see clearly
how this vast diversity is based on an under-layer of microbes
This may be how all life began on Earth, at a time of boiling
waters, oxygen-less atmosphere, and an utter lack of what most
organisms today use as food. A similar process probably happens
P
R
O
F
I
L
E
Karen Nelson wanted to be a
veterinarian. Now she reads the
genetic codes of microbial life.
K
aren Nelson grew up in Jamaica,
surrounded by pets and nature. Her
love of animals drew her to science.
“Back then, I thought going into science meant
either becoming a vet or a doctor,” Karen
recalls. She went to the University of the West
Indies in Trinidad and Tobago and then got a
Master’s degree in Animal Science from the
University of Florida, intending to become a
veterinarian. Along the way, however, she took
a course in ruminant microbiology that changed her
life. (Ruminants are cows or animals that “chew their
cud” to digest grasses.) “I had not realized how
dependent animals – and people – are on microbes in
the gut to extract nutrients from their food,” Karen
explains. While working on her Ph.D. at Cornell
University in microbial physiology, she identified
bacteria in the digestive tracks of tropical animals that
can degrade toxins. These toxins exist naturally in
many plants that tropical animals eat, so the animals
have developed cooperative “friendships” (symbiotic
relationships) with microbes that detoxify the food.
Such microbes might be helpful in detoxifying
human-made compounds.
Karen’s career took her away from animals and
towards genomics. Her first assignment at The
Institute for Genomic Research (TIGR) was to
sequence the genome of the bacterium Thermotoga
maritima, discovered in a thermal vent in Italy.
Scientists were interested in this bacterium because it
could survive high temperatures and might have uses
in industry and in bioremediation. “Almost a quarter
of the genes in Thermotoga are not found in any other
bacterium,” Karen explains. “At first we thought it was
one of the oldest bacterial species. But by doing
evolutionary analyses, we realized that it had a mosaic
(mix) of genes from bacteria and from a completely
different branch of life: the archaea. Its genetic
14 Microbes Coming into Focus
Dr. Karen Nelso
n
Dr. Karen Nelso
n is
in Rockville, MD Assistant Investigator at The Ins
titute for Genomi
.(Photo courtesy
of The Institute
for Genomic Resea c Research (TIGR)
rch)
composition was not
a sign of its age, but showed that, in addition to having
unique genes, the bacterium had borrowed DNA
from archaea.” Archaea probably developed these
genes back when most life existed in boiling hot
waters. The more modern Thermotoga borrowed
some of these genes to help it survive in similar
conditions at the sea vent. Thus, Karen’s work led to
a breakthrough in the scientific understanding of
evolution and horizontal gene transfer. Karen is also
studying Pseudomonas putida, a bacterium that can
degrade benzene and other compounds that are often
found as contaminants in the environment. “It is also
very willing to accept genes from other species,”
Karen adds, so it might be customized to clean up oil
and chemical spills.
Lately, Karen’s genomic research is taking her back
to animals. Under a grant from the U.S. Department of
Agriculture, she is sequencing the genomes of
ruminant bacteria in hopes of improving the way
bacteria extract nutrients from food. If these bacteria
were more efficient in cows, the animals would need
less food to produce milk and beef. That would save
on the cost of grain, and it would reduce the need to
cut down forests to graze cattle.
Karen encourages young people to “Follow your
dreams, be curious, and always ask questions.”
something
can
YouTry
Growing Biofilms
Grow some biofilms and then take a peak at them
Part 3: Observe the biofilms
under the microscope.
1) Remove the rack from the water, inspect the slides, and record
your observations.
Part 1: Create a biofilm haven
Put some organic material (such as hay, dried leaves, or
peppercorns) in a glass beaker, weight it down with a glass rod,
and fill the beaker with water. In a few days you will see a slime
form. This solution is called an infusion. Use this infusion for
Part 2. Your class could compare several different infusions. You
could create a “control” without organic material and another
with a bit of anti-microbial chlorine. Be creative!
2) Place the slides one at a time under a microscope. Can you see
bacteria? Adjust the focus so you can see the bacteria living at
different levels in the film. Record your observations.
3) If your teacher has methylene blue or crystal violet dyes, you
can stain the slides to get a more dramatic view of the biofilms.
To see colored photos of biofilms, visit http://www.itqb.unl.
pt:1111/~jxavier/clsmip/clsm_stack.php?stack_ref=1.
Discussion
Part 2: Build a biofilm rack
1) Why did slime appear on the glass?
1) Prepare five microscope slides per infusion. Keep one slide
clean as a control. Treat the top of the other slides with
different materials to see their effect on biofilm growth. (Try
petroleum jelly, ointments, or paint. Would mixing in chili
pepper or detergent kill biofilms?)
2) Was there an observable difference among the biofilms growing
on the five microscope slides?
2) Take the plastic spine from a report folder and cut it in half
lengthwise. Cut the edges diagonally to make it easier to insert
the microscope slides. The spines will act like a two-sided
frame for the slides. Hold them together with rubber bands.
3) If so, describe the difference and develop a hypothesis to explain them.
4) What can you conclude about biofilm growth?
5) If your classroom used different infusions and
treatments, compare the results and conclusions.
6) How might you treat a boat bottom
or water main to prevent
biofilm formation?
! Caution:
3) Place the rack in a glass container and fill it with an infusion
from Part 1. Wait a week or so.
Bacteria at work! Wear
gloves, and don’t taste or
touch the infusion or
biofilm. When you’re
finished, wash your
hands. Your teacher will
disinfect the equipment.
Adapted from activities developed by John Lennox, Pennsylvania State
University, Altoona. Additional activities are available at his web site
(www.personal.psu.edu/faculty/j/e/jel5/Biofilms.) This activity can also
be downloaded at www.microbeworld.org/mlc/pages/activities.asp
Your World
15
Living in a Microbial World
The Biotechnology Institute is a
not-for-profit organization
dedicated to education and
research about the present and
future impact of biotechnology.
Its mission is to engage, excite,
and educate as many people as
possible, especially young
people, about biotechnology
and its immense potential for
solving human health and
environmental problems. The
Institute thanks the following
sponsors for financial support
of its activities for 2001-2002.
Abgenix, Inc.
Aventis
Biogen, Inc.
BIO
• Follow the instructions exactly when
you are taking antibiotics. Overuse
and misuse of antibiotics lead to more
virulent microbes.
• Don’t take antibiotics for a viral infection.
• Use antibiotic detergents only when
someone in your household is taking
cancer treatments or has a form of
immune deficiency.
• Wash your hands thoroughly and
regularly. It’s the best way to
prevent disease.
Keep an eye out for news related
to microbial genomics and how it
affects your life.
Online Teacher’s Guide
Visit the Biotechnology Institute on-line at
www.BiotechInstitute.org for:
•
•
•
•
•
Teacher’s Guide.
Activity Supplement: Student and Teacher Procedures.
Overheads, links, and survey.
Information on subscriptions and previous issues.
Downloadable Teacher’s Guides from previous issues.
Connetics Corporation
Ernst & Young
Genencor
Genentech, Inc.
Genzyme Corporation
Inspire Pharmaceuticals
InterMune, Inc.
Johnson & Johnson
Edward Lanphier
The following issues of Your World are
available for free downloading:
• Exploring the Human Genome (5:2)
• Gene Therapy (4:2)
• Environmental Biotechnology (4:1)
• Industrial Biotechnology (3:1)
• Plant Biotechnology (2:2)
• Molecular Diagnostics (2:1)
• Heath Care, Agriculture, and the Environment (1:1)
MdBio, Inc.
Merck and Co., Inc.
Monsanto Fund
Microbial Resources
Neose Technologies, Inc.
A Ballad about Bacteria by Bill Harley, http://www.npr.org
American Society for Microbiology http://www.asm.org
Attacking Anthrax by John A.T. Young and R. John Collier, Scientific American, March 2002
Battling Biofilms by J.W. Costerton and Phillip S. Stewart, Scientific American, July 2001
Biofilms Basics http://www.erc.montana.edu/Cbessentials-SW/bf-basics-99/
Bioterror (NOVA) http://www.pbs.org/wgbh/nova/bioterror
Biotoons http://www.mbl.edu/baypaul/microscope/general/page_01.htm
Genomics Timeline http://gnn.tigr.org/timeline/timeline_frames.shtml
Intimate Strangers: Unseen Life of Earth, book and video
(http://www.pbs.org/opb/intimatestrangers/)
MicrobeWorld http://www.microbeworld.org
Microbe Zoo http://commtechlab.msu.edu/sites/dlc-me/zoo/index.html
Microbial Solutions to Energy, Environmental, and Biothreats Challenges
http://DOEGenomesToLife.org/payoffs.html
Primer: What’s a Genome?
http://gnn.tigr.org/whats_a_genome/Chp1_1_1.shtml
Stalking the Mysterious Microbe http://www.microbe.org
The Genes We Share With Yeast, Flies, Worms, and Mice by the
Howard Hughes Medical Institute
U.S. DOE Microbial Genomics Gateway http://microbialgenome.org/
Pfizer Inc
Syngenta Biotechnology, Inc.
U.S. Dept. of Commerce
U.S. Dept. of Energy
Thomas G. Wiggans
Wyeth
This issue sponsored by: