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Animal Pavilion
 Cow Rumen
-Rumen microbes help the cow eat hay, which is made of cellulose and other polymers, which are long molecules that the
animal cannot digest, but microbes can. The microbes break down the cellulose into smaller bits which the cow can take in, or
absorb. The microbes use special proteins called enzymes to break down cellulose into small bits.
-Because there is "room in it"! Actually, the term rumen is Latin for throat or gullet. The rumen is the first of four stomachs.
Ruminant animals have a lot of room in their rumens. The average cow rumen can hold over 160 liters (40 gallons)! The rumen
is the first of four parts of the stomach in ruminant animals. Food is partly digested in the rumen and then spit up (regurgitated)
for further chewing.
- The rumen is home to billions and billions of microbes, including bacteria, protists, fungi, and viruses. These many different
rumen microbes form a complex community of organisms that interact with one another, helping the animal digest its food.
-The rumen stinks. This is because microbes in the rumen produce stinky organic acids. The billions of microbes in the rumen
quickly use up all the oxygen. Because there is no oxygen, the rumen is anaerobic. When oxygen is lacking, microbes must get
their energy from anaerobic respiration or from fermentation. In anaerobic respiration, microbes breathe compounds other than
oxygen for energy. Fermentation is the breaking down of organic molecules into smaller molecules such as organic acids like
butyric acid and valeric acid that stink.
One of the effects of life without oxygen is that methane is produced. Methane is a gas produced by certain microbes called
methanogens. Methanogens are members of the Archaea. The Archaea, also known as Archaebacteria, are a group of bacteria
which look similar to eubacteria, but are remarkably different at the molecular level. Archaea and bacteria are presumed to have
diverged billions of years ago.
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Methane Producer
Kingdom: Archaebacterium
Scientific Name: Methanosarcina
This microbe thrives where there is no oxygen. Places lacking oxygen are called
anaerobic. Methane producers live in swamps, in the guts of cows and deer, in
human bowels, and in sewage. This microbe, known as a methanogen, produces
methane, also known as swampgas. Other microbes that live in anaerobic
environments give off acetate, hydrogen, and carbon dioxide as wastes. Methanosarcina consumes these
biproducts to get energy for itself. It then gives off methane gas.
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Cellulose degrader
Cellulose is the strong material in plant cell walls that makes plant stems stringy
and tough so that they can stand up. Cellulose is difficult to break down, so
animals that eat lots of plants (like cows) have a hard time digesting their food.
Some microbes living in the stomachs of many plant-eating animals can easily
break down cellulose, and in so doing provide the animal with food that it can use.
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Spirochete in Cow Rumen
Kingdom: Eubacteria
Scientific Name: Spirochete
Spirochetes are spiral-shaped bacteria. They swim along by twisting like a
corkscrew. Spirochetes live in many habitats, including cow stomachs, termite
guts and compost heaps. Many types of spirochetes cause diseases in animals,
including humans. Most spirochetes are anaerobic. The spirochete is the
squiggly microbe near the center of this view.
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Rumen protist
Entodinium- This protist lives inside ruminant animals
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Entodinium dividing
This protist is in the process of replication. This microbe is splitting itself in half, a
process known as "binary fission." This protist "Entodinium" lives inside the rumen
of cows.
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Hairy Rumen Protist with bacteria
This protist lives inside the rumen of cows. The hairy stuff on the outside of it
is "cilia." Cilia is Latin for eyelash. These cilia wave back and forth and either
propels the microbe through the water, or they propel food toward it. This
protist has several chains of bacteria that are stuck to it. Protists that are
covered with cilia are members of a group of protists called Ciliophora. This
means eyelash bearer.
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Ophryoscolex
This is one of the biggest rumen protists.
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Cow Rumen Protist and Bacilli
The large creature in this view is a protist that lives in the rumen (one of the
stomachs) of a cow. The protist is covered with many other microbes that look like
strings of beads or sausage links. The smaller microbes are bacilli, a type of
bacterium. Bacilli (the singular form is bacillus) is a term used to refer to any of the
many types of rod-shaped bacteria. Several kinds of plant-eating animals related to
cows, called ruminants, have similar microbe populations in their guts. Goats,
reindeer, camels, giraffes and deer are all ruminants.
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Habitat on Humanity
o Health Promoting Microbes
Teeth
When you eat sugar, you are not only feeding yourself, but you are also feeding the millions of microbes that call your mouth
home. These microbes grow and stick to your teeth, forming plaque which can cause cavities and tooth decay.
Streptococcus
The most predominant microbes in your mouth are these sphere-shaped bacteria. They convert sugars and other
carbohydrates into lactic acid. This acid then dissolves tooth enamel, eventually forming a cavity.
Streptococcus mutans
This bacterium is the major culprit in giving your teeth cavities. If you have ever had a dental cavity, you are not alone:
this is probably the leading cause of infection. Cavities are not only a bummer to have, they are expensive to treat,
costing about $20 billion per year in fillings in the United States!
Cavities
If you don't remove these bacteria, they can produce acids which dissolve the enamel on your teeth and produce
cavities. Normally, the pH of your mouth is neutral, around pH 7. However, after you eat some sugar, bacteria in the
plaque on your teeth produce acid, dropping the pH to about 5.5. People who do not eat sweets have about 90% fewer
cavities.
Gum Disease
When you don't brush the plaque off your teeth, the plaque hardens. This hardened plaque is called "calculus", which
only a dentist can remove. If left untreated the plaque and calculus growing near the gum line irritate the gums. This
irritation causes a redness and soreness (inflammation). This inflammation is called gingivitis. The gum separates
from the teeth and bacteria grow inside this space where they attack the bones. Gingivitis is the leading cause of tooth
loss in older people.
- Eat a piece of candy. After about 5 minutes, notice what happens in your mouth. Do you notice a coating
developing on your teeth? Some people say their mouth feels mossy. This sticky film is slime (dextran, a
polysaccharide) that is produced by the bacterium Streptococcus mutans when sugar (sucrose) is present. This
slime helps the bacteria stick to your teeth and to each other. Eventually, this slime on your teeth sticks to
other bacteria and a plaque begins to form. Perhaps after you have performed this experiment, you would like
to brush these bacteria off your teeth so they can't form a cavity.
Stomach
The stomach has very few microbes in it because of its high acidity (low pH). (The stomach produces acid to digest
food.) The lining of the stomach provides some refuge against the high acidity for some hardy bacteria.
One area of the stomach called the "antrum" produces no acids. In this part of the stomach, some microbes can live
and may be responsible for giving people ulcers. To find out more about these ulcer-causing bacteria see: "Bacteria
blamed for ulcers, cancer" in Microbes in the News.
Helicobacter pylori
This bacterium lives in a portion of the stomach called the "antrum."
Large Intestine
Human guts are hosts to many billions of microbes. Each gram (about a thimble-full) from the large intestine contains
up to ten trillion (10,000,000,000,000) microbes! Microbes provide nutrients to animals.
Microbes in the intestines perform many essential tasks. For example, microbes make several vitamins in the
intestines. One of these is vitamin K, a vitamin that is otherwise lacking from human diets.
Matter passes through intestines in approximately 24 hours.
Some of the different microbes in the intestine are:
Bacteroides
This is one of the most abundant microbes in the intestine, and is found in higher numbers in people who eat
meat than in vegetarians.
Lactobacillus acidophillus
This is a normal, helpful inhabitant of intestines. The billions of Lactobacilli in your intestines crowd out
harmful microbes so they cannot grow. This is why many travelers take capsules filled with Lactobacillus, so
they don't get traveler's diarrhea.
E. coli
This is the most well-studied organism. It is a normal resident of your intestine and provides you with vitamin
K and some of the B vitamins.
Klebsiella
It is speculated that these bacteria can fix nitrogen into protein in the intestines of people who have too little
protein in their diet.
Bifidobacterium
The intestines of newborn, milk-fed infants contain almost a pure culture of this bacterium.
Methanobacterium smithii
This bacterium produces methane in human guts. Normal humans fart about 10 - 15 times per day, passing a
few hundred milliliters of gas per day. Boys and girls fart about the same amount. Though over 50 percent of
this gas is nitrogen, some of the gas is microbially produced, including the gas methane, which is flammable
and is also a powerful greenhouse gas. Carbohydrates that cannot be digested by humans, but can be digested
by microbes, are the leading cause of farts. Methane is an odorless gas: smells come from dimethyl sulfide
and methanethiol. Other gases include oxygen, hydrogen, carbon dioxide, and nitrogen.
Skin
Most skin is a dry, inhospitable place where few microbes like to live. The population of microbes on the back is only
about 100 bacteria per square centimeter. However, on hot humid days sweaty skin becomes a much nicer place for
microbes to live.
Propionibacterium acne
This bacterium is a normal inhabitant of skin. It produces propionic acid which prevents the growth of other,
unwanted microbes.
Staphylococcus epidermidis
This sphere-shaped bacterium is resistant to the dry conditions often found on skin.
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Health promoting intestinal microbe - Lactobacillus acidophillus
This microbe is a bacterium called Lactobacillus acidophillus. It is
special because it can help preserve foods. It does this by making
its environment, our food, acidic. This acid makes food taste sour.
Some of the foods this microbes helps preserve include cabbage to
form sauerkraut, milk to form yoghurt, and flourdough to form
sourdough bread. These microbes make acids as a waste product
(byproduct) of fermentation. This acid makes the environment
toxic to most other microbes which might otherwise ruin the food.
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Gut Bacterium - E. coli
- E. coli is the lab rat of the bacterial world. More details are known about the
molecular biology of this organism that any other, including humans. E. coli is very
popular for use in research because it is so easy to grow, with a fast doubling time of
only 20 minutes.
- E. coli was discovered in 1885 by Theodor Escherich, a German bacteriologist. E.
coli is used in industrial biotechnology to produce enzymes.
- E. coli is a normal resident of the large intestine in healthy people. It is a type of
probiotic organism because it crowds out disease causing bacteria. E. coli also makes
vitamin K which humans require to be healthy.
- Although it is generally a good microbe, some strains make people sick. The toxic strains of this microbe are
responsible for about half of all cases of traveler's diarrhea. One famous strain, O157:H7, has caused disease in
people who eat uncooked hamburger.
- E. coli was the first bacterium to have been observed mating (conjugation in bacteria). Conjugations is transferring
DNA from one cell to another cell.
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Skin Baterium - Stapylococcus epidermidis
Intestinal Dweller - Citrobacter freundii
Intestinal Dweller - Proteus vulgaris
Intestinal Dweller - Alcaligens faecalis
Disease Promoting Microbes
 Tuberculosis microbe
 Tooth Cavity Cause-Streptococcus
 Leptospira interrogans
This spiral-shaped bacterium is a member of the order Spirochaetales, which also
includes the Spirochetes. These microbes have an unusual means of moving around. They
swim by twisting back and forth, propelling themselves like a corkscrew being turned
into the cork of a bottle of wine.
L. interrogans is harmful to humans. Harmful microbes that cause diseases are called
pathogens.
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Food Poisoning microbe - Salmonella typhimurium
This bacterium is causes food poisoning. It can grow on poultry, uncooked eggs, and
various meats. When these foods are eaten by humans, Salmonella grows in the intestine,
producing such symptoms as headaches, chills, vomiting and diarrhea. The long whiplike
hairs projecting from this strain are called "flagella". The flagella move this bacterium. A
closely related species of S. thyphimurium is S. typhi, the cause of typhoid fever.
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Poo Corner
o Nitrogen Recycler - Ammonia Chomper
Nitrosomonas europaea is an "ammonia-powered" microbe that uses ammonia as a fuel to
live and grow. Power generating membranes (long, thin tubes inside the cell) use
electrons from ammonia's nitrogen atom to produce energy. In this image, created with a
transmission electron microscope, we can see the interior of one of this microbe's cells.
The semi-transparent, roughly circular area towards the top of this image (just left of
center) is a cross-section of one of the bacteria. The dark lines circling much of the
interior of the cell are the power generating membranes that process the ammonia. The
cell to the right is more heavily stained, so it appears dark and reveals less internal structure.
Nitrosomonas europaea can obtain the carbon that it needs to grow by getting it from the atmosphere in a process
known as "carbon fixation". Carbon fixation is the process of converting carbon in a gaseous form into carbon bound
up in organic molecules. This bacterium contains "carboxysomes" (dark spots which can be seen scattered throughout
the cell), which store the enzymes used to fix carbon dioxide for cell carbon. You may recall that plants can fix
carbon, that is, they can convert carbon dioxide into sugar, using the energy from photosynthesis. This strange
bacterium can also fix carbon, but instead of photosynthesis for its energy it uses the energy produced by "burning"
ammonia with oxygen. N. europaea must consume large amounts of ammonia before it will divide, and cell division
may take up to several days. This microbe, which does not like being exposed to light, will cover itself in slime and
form clumps with other microbes to avoid it.
Some ammonia-chomping microbes can live in the walls of buildings and on the surfaces of monuments, especially
in polluted areas where air contains high levels of nitrogen compounds. When these microbes use ammonia from the
air, they produce nitric acid. The acid can cause dissolve some stone and other construction materials found on
statues and in buildings.
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Most Studied Microbe - Escherichia coli
Swamp Gas Makers - Biofilm of Methane Makers
- Bacteria, like other organisms in nature, depend on one another for survival, particularly in hostile conditions. The
above image shows various bacteria from an environment where there is no oxygen and where microbes make
methane.
- This particular environment is called a methane-producing biomass digester which scientists have set up in the lab
to study such organisms.
- Some of the microbes in this picture are called methanogens (fancy name for methane makers). Methanogens live
where there is no oxygen. Like other microbes that grow without oxygen, methanogens are called anaerobes.
- The methane produced by this community is used for fuel, a flammable gas known as natural gas used to heat your
home.
- Bacteria often like to live on surfaces. The bacteria and other microbes that live on surfaces make up a slimy surface
people generally refer to as slime. Since this slim consists of live creatures, it is called a biofilm.
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Termite Gut
o Protists
o Spiral Shaped Microbes
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Poo corner
Wild Dung Devourers
Animal manure is easily degraded by microbes. In fact, poop is already being degraded before it ever hits the ground,
since one third of poop by weight is microbes. In nature, millions of different species of protists, fungi and bacteria
recycle poop into carbon dioxide and water. In the past, humans laid their loads upon the roads and walked away
contented. In more modern times in developed countries this practice has given way to more organized forms of
disposal discussed below.
Some Wild Dung Devours include:
Escherichia coli
This most famous bacterium can live inside and outside of humans and other animals.
Pilobolus
This fungus grows on dung and launches its spores in the direction of light toward an open meadow where
grazing animals will eat the spore so that Pilobolus can continue it's life cycle.
Aerobic Sewage Treatment
After sewage is digested anaerobically in septic tank, it is treated with oxygen (aerobically) in a leach field. In the
leach field, any pathogens not killed by the anaerobic treatment in the septic tank are killed by oxygen in the leach
field.
Ammonia Chomper
Community Sewage Treatment
When people live in cities, sewage is collected and treated in municipal sewage reactors. In contrast to septic tanks,
community sewage sludge reactors are aerobic, meaning that oxygen is present. Because they contain oxygen,
aerobic sewage treatment facilities can treat a lot more sewage in a lot less time. The amount of sewage is determined
by the amount of oxygen required by microbes to break down the sewage into carbon dioxide and water. This
measurement of the oxygen required by microbes to degrade wastes is known as the Biological Oxygen Demand
(BOD).
Poopy Problems
If sewage is not disposed of properly it can pose serious health problems. More than 500 disease causing microbes
are carried in poop. Some of human disease organisms (pathogens) carried in poop include the following:
Vibrio cholera
This bacterium is the cause of cholera which causes severe, but treatable diarrhea.
Salmonella typhi murium
This bacterium causes food poisoning. Carriers of this disease may excrete
10,000,000,000 (ten billion) S. typhi bacteria per gram of poop.
This bacterium is causes food poisoning. It can grow on poultry, uncooked eggs, and
various meats. When these foods are eaten by humans, Salmonella grows in the
intestine, producing such symptoms as headaches, chills, vomiting and diarrhea. The
long whiplike hairs projecting from this strain are called "flagella". The flagella move
this bacterium. A closely related species of S. thyphimurium is S. typhi, the cause of
typhoid fever.
Giardia lamblia
This protist is the cause of giardiasis, an disease of the intestines which causes gas, cramps, and diarrhea.
Dirtland
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Ag Acres
Plant Disease
Some nasty microbes kill or damage plants. In fact, of all the crop destruction by insects, drought and microbes,
microbes are responsible for most problems. Microbes cause plants to rot, wilt, spot, lose leaves, pale in color,
become stunted, grow tumors, overgrow and die. Microbes causing plant disease include fungi, viruses, and bacteria.
Fungal Diseases:
Most plant diseases are caused by pathogenic fungi.
Rust Fungi
There are more than 20,000 species of rust fungi. These fungi often create rust-colored patches on plant leaves.
Rhizoctonia
This fungus causes root rot of various plants. Rhizoctonia solani causes root rot in tomatoes.
Viral Diseases:
Some plant diseases, like animal diseases, are caused by viruses.
Tobacco Mosaic Virus
This rod-shaped virus contains RNA as its chemical blueprint for invading tobacco cells.
Bacterial Disease:
Many bacteria cause plant diseases.
Agrobacterium tumefaciens
This bacterium produces tumors called galls (growths) on the stems of plants.
Burkholderia cepacia
This bacterium rots onion roots.
Microbial Fertilizers
Some microbes add nutrients to the soil. Some add nitrogen by fixing it from the atmosphere. These include
Rhizobium and Azotobacter which are discussed in the root cellar. Other microbes, such as Mycorrhizal fungi,
help supply plants with phosphorus. Please visit the Root Cellar to find out more about microbes that help fertilize
the soil.
Insect Killers
Wouldn't it be great if farmers didn't have to spray crops with chemicals (pesticides) to kill unwanted destructive
insects? Well, thanks to microbes, farmers don't need to use as many chemicals. Farmers are now using microbes to
kill unwanted insects. Using organisms such as microbes to kill unwanted pests is called "Biocontrol." Several
different microbes are used to kill insects. These microbes can be either viruses, bacteria, fungi or protists.
Bacillus thuringiensis
This bacterium is the most widely used microbial insecticide. B. thuringiensis contains a poison which looks
like a crystal. This poison (toxin) is called BT toxin. BT toxin kills lepidopterans such as cabbage worms, tent
caterpillars, and gypsy moths; dipterans such as mosquitoes and black flies; and coleopterans such as
Colorado Potato Beetles, Japanese beetles. At least 412 preparations of Bacillus thuringiensis and the BT
toxins are registered for sale in the United States.
Baculovirus
This virus is widely used to combat many caterpillars, moths, and flies. Although there are over 450 viruses
found to kill insects, the most widely studied viruses are the Baculoviruses.
Soil Builders
Soil is not just the stuff that gets your hands dirty when you play on the ground. Soil is a complex, living environment
necessary for the growth of plants. But how is soil formed? By an interaction of five factors including the action of
microbes and other life.
The other factors forming soil are weather, topography, parent material, and time.
When soil is first made, for example after a volcano, some nutrients are missing, including nitrogen and carbon.
Therefore, the first organisms to colonize the soil are generally nitrogen fixers and photosynthesizers that fix carbon.
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Natural Insect Killer - Bacillus thuriengensis
This bacterium is used as a pesticide to kill insects. This is a cross section of several
spores of the bacterium, Bacillus thuringeinsis. The round structures are spores,
which are surrounded by cell wall of the bacterium. The angular dark object at the
lower right corner is the B.t. toxin (short for Bacillus thuringeinsis toxin). This
crystal toxin is poisonous to many different insects that eat them, including moths
and flies and mosquitos.
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Cause of Plant Tumors - Agrobacterium
Mercenary Microbes
The bacterium, Agrobacterium, is like a mercenary commando. It invades a living plant,
commandeers it's genetic machinery, throws the plant's cells into anarchy, and forces the plant to
produce K rations for the invading bacterium and its legions in the soil.
The anarchy that Agrobacterium causes plants is uncontrolled growth of cells into masses of tissue
called tumors. Different species of Agrobacterium form different types of tumors. Agrobacterium tumefaciens causes
a tumor called a crown gall. Agrobacterium rhizogenes, like the name implies, causes the sprouting of root tissue
from an infection site, a condition known as hairy root. Agrobacterium rubi causes cane gall of raspberries.
The weapon Agrobacterium tumefaciens weilds is a circular bit of DNA called the Ti plasmid. Ti is short for tumor
inducing. Part of the DNA from the Ti plasmid (the T-DNA) infiltrates the plant's DNA. Once this bit of DNA from
Agrobacterium's Ti plasmid is integrated into the plant's DNA, it makes a growth hormone which causes the cells to
grow into tumors. The Agrobacterium's DNA takes control of the plant's genetic machinery, forcing the plant to
produce food, called opines, which only Agrobacterium can eat.
Agrobacterium and Genetic Engineering
Sometimes this mercenary microbe works for humans, helping scientists to genetically engineer plants. The ability of
Agrobacterium's Ti plasmid to insert its DNA into that of dicotyledenous plants has been the major tool in genetic
engineering of plants. In the early 1980's scientists discovered that they could cut out the tumor forming part of the Ti
plasmid and insert genes of novel or commercial interest. Over 35 genetically engineered plants created this way are
approved by the United States department of agriculture. Many of these plants, including potatoes, cotton, tomatoes
and corn are in commercial production.
Some of the genes which have been inserted into plants DNA using Agrobacterium's Ti plasmid include:
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Glow in the dark genes - The luciferase gene from a firefly has been successfully introduced into tobacco
plants with glowing results: the plant glows in the dark! Not only do the plants look cool, but this proved to
scientists that the technique worked.
Insect killing genes - An insect toxin from the bacterium Bacillus thuriengensis has been inserted into cotton,
potato and corn plants, making the plants toxic to insect pests.
Pesticide resistance genes - Scientists have engineered plants that can degrade herbicides such as Roundup™.
This means farmers can spray weeds with Roundup™, which contains the active ingredient glyphosate, and it
won't kill the crop. Scientists took a glyphosate resistance gene from the bacterium Salmonella and inserted
this into the Ti plasmid which was then introduced into the plant.
Tomato anti-softening genes - A gene genetically engineered into Flavr Savr tomatoes slows the ripening of
tomatoes, giving them a longer shelf life. These engineered tomatoes lack the ability to degrade pectin, the
stuff that your grandmother uses to make jellies gel and that gives fruit their firmness. The genetically
engineered Flavr Savr tomato produces an "antisense" gene that encodes a strand of RNA that "zips" onto the
complementary strand of RNA from the pectin degrading gene (polygalacturonase). This bound-up RNA
molecule is rendered useless, so the pectin degrading enzymes are not produced and hence the tomato stays
firm.
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Corn Blight Fungus - Dreschlera
Grass Disease - Xanthomonas
Compost Heap
o Wood Eater - Phanerochaete chrysosporium
Phanerochaete chrysosporium is a fungus that degrades wood. Because this microbe looks
like white chalk on rotting wood, it is called a white rot fungus.
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Hot Composter - Bacillus stearothermophilus
These bacteria grow in warm temperatures. For this reason it is called a "thermophile"
which means heat loving. These bacteria are among the most abundant in warm compost
piles. This is a cross section (a view of a slice of the middle) of a spore of Bacillus
stearothermophilus. Spores of bacteria allow the bacteria to survive harsh conditions until
the time when the bacterium can thrive and reproduce.
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Banana Mold
This is a mold that was found growing on a banana peel in a compost pile. The
small round objects on the "branches" of this mold are a type of spore. Spores are
somewhat like seeds. These spores, called conidiospores, are asexual. The
"branches" that the conidiospores are on are called conidiophores ("phore" means to
carry or bear).
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Thermus thermophilus
Deep Underground
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Bacillus infernus
- What lives under several kilometers of dirt and rock, away from oxygen and light? No plant
nor animal can tolerate these conditions. Only microbes, like Bacillus infernus featured here,
can thrive deep underground.
- Deep underground most organisms would choke from lack of oxygen, but not this
bacterium! - It doesn't need to breath oxygen. Instead, it breathes iron or manganese dioxide.
Bacteria that do not breathe oxygen are called anaerobes.
- This particular microbe was found a mile beneathe the surface in Virginia. It was isolated
by Dave Boone and others who discovered it in an NSF sponsored deep drilling project.
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Home Sweet Home
Cutting Board
Microbes in your kitchen! Well maybe not so many if you use a wooden cutting board instead of a plastic cutting
board. A recent study has found that wooden cutting boards harbor far fewer bacteria than do other types of cutting
boards.
Couch
What creatures lurk in your couch?
Mites
Microscopic animals live in couches and on beds, feeding off of flakes of dead skin cells.
Hot Water Heater
Bacteria called thermophiles can live in your hot water heater.
SBS Slayers
Sick Building Syndrome, SBS, is a recently recognized disorder in which fumes from materials in buildings give
people headaches. Microbes growing in the potting soil of plants have been found that degrade some of these fumes,
and in the process eliminate sick building syndrome.
Shower Slimers
Is that dirt that has rinsed off your body on your shower curtain? Or is it microbes that are growing there?
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Shower Curtain Fungus
Coffee Cup Fungus
Hot Springs
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Pyrococcus furiosus
How would you like to swim in boiling water? Although you and all plants and animals would
quickly die in such hot water, the microbe Pyrococcus furiosus thrives in boiling water. This
bacterium not only lives at hot temperatures, but it freezes to death at temperatures below 70
degrees Celsius. Microbes that thrive in boiling hot water are called "hyperthermophiles".
Not only do these exotic microbes live in boiling water, they do not breathe oxygen. In fact,
oxygen kills them. Instead of oxygen, these fiery microbes breathe sulfur and exhale the stuff
that gives rotten-eggs their smell: hydrogen sulfide.
Since these microbes like boiling hot water with no oxygen, they live in the hot water bubbling from undersea hot
vents.
These bacteria are classified as members of the Archeae, one of two major groups of bacteria. Some scientists believe
that the Archeae are the most direct descendants of the oldest life forms to inhabit Earth. Over 3 billion years ago,
ancient Earth was probably steaming hot with little oxygen and plenty of sulfur, a comfy place for Pyrococcus to
swim and enjoy life.
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Thermus thermophilus
House of Horrors
Vampirococcus
This bacterium sucks the life juices (cytoplasm) out of another bacterium called Chromatium. Don't worry, it won't
attack you.
Vampirococcus
This sphere shaped bacterium is much smaller than its prey.
The Invader:Bdellovibrio
An example of a microbe that attacks another microbe is the bacterium Bdellovibrio. This bacterium attacks other
bacteria, such as Escherichia coli (E. coli).
The Strangler Fungus
Some bizarre fungi can strangle worms called Nematodes. These fungi capture the worms for food. These fungi make
ring-like nooses from their hyphae to capture the worms. Once the nematode is trapped, the fungus penetrates it,
eating it
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Redox Mine
All animals, plants, fungi and many microbes breathe oxygen. Some microbes are particularly amazing because they
can breathe a whole range of compounds other than oxygen such as iron, nitric acid, sulfuric acid, and carbon dioxide.
Some of these different oxidizers are found in the Redox Mine.
Microbes that breathe oxygen are called "aerobes." Microbes that cannot breathe oxygen are collectively called
"anaerobes."
Don't let the word oxidizer confuse you, since not all oxidizing agents contain oxygen. To eliminate confusion when
talking about oxidizing agents (which often contain no oxygen) we call them "electron acceptors". Think of oxygen
and other electron acceptors as a greedy elements that love electrons and will gladly accept them at every opportunity.
When electrons are transferred from one molecule to another in a redox reaction, energy is released.
Different electron acceptors yield different amounts of energy. The electron acceptors deeper in this Redox Mine
generally yield less energy. At the surface is oxygen, a powerful oxidizer which provides lots of energy. When
oxygen runs out, organisms that can breathe another available oxidizer such as nitrate, survive.
In rocket ships fuel is burned. This burning is from the combination of fuel with oxygen, which releases chemical
energy and blasts the rocket into space. Like rocket ships, microbes and other living things obtain energy from
chemical energy. In humans, food (the fuel) like potatoes, hamburgers and ice cream, is combined with oxygen to
provide energy. We breathe oxygen for energy to grow, move, talk and think.
Redox reactions involve the oxidation of one molecule and the reduction of another molecule. This is a difficult
concept, but just remember that burning requires a fuel and an oxidizer. When a fuel such as sugar is oxidized, it
loses electrons. Oxidation is the "loss of electrons" = Ole! When an oxidizer has accepted additional electrons, it is
said to be reduced. (Since electrons are negatively charged, an increase in electrons means a reduction in electrical
charge.) Thus, reduction is the addition of electrons.
When a redox reaction involves two different types of molecules and this energy is converted into metabolic energy,
this is called respiration.
Fermentation is a special kind of redox reaction. In fermentation, the fuel and oxidizer are the same compound, such
as sugar. The sugar is simultaneously oxidized and reduced.
Here are some of the compounds and the organisms that breathe them:
Oxygen Breathers
All large organisms must breathe oxygen. Only oxygen is powerful enough to give large organisms enough energy to
function. Many bacteria also breathe oxygen.
Oxygen has not always been present in the atmosphere. Over 2 billion years ago, before the evolution of
photosynthetic microbes that could produce oxygen, the atmosphere contained no oxygen.
Bacillus megaterium
This rod-shaped bacterium grows with oxygen.
Bacillus cereus
This bacterium grows in the presence of oxygen and can form a protective endospore.
Yeast
These fungi can breathe oxygen, or, when oxygen is lacking, they can obtain energy by fermentation.
Halomonas
This salt-loving bacterium requires oxygen to breathe as well as to degrade the herbicide 2,4-D.
Nitric Acid Breathers
Nitric acid breathers, are generally called nitrate reducers. These bacteria convert nitrate to nitrite. Some also convert
nitrite to nitrous oxide and then to nitrogen gas. Many of these bacteria also have the ability to breathe oxygen.
Anaerobic Toluene Degrader
Pseudomonas
Sulfuric Acid Breathers
Many different bacteria breathe sulfuric acid (or sulfate). These bacteria are inhibited by oxygen.
Desulfomonas
Carbon Dioxide Breathers
These organisms can breathe carbon dioxide. They combine carbon dioxide with hydrogen, which produces methane.
Organisms that can breathe carbon dioxide are called methanogens.
Methanogen
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Biofilm of Methane Producers
Biofilm in Swamp Gas Reactor (page 6)
methane - a gas commonly known as natural gas or swamp gas.
scanning electron microscope - an electron microscope that bounces electron off a sample to create a 3-D image.
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Methanogens
This microbe thrives where there is no oxygen. Places lacking oxygen are called
anaerobic. Methane producers live in swamps, in the guts of cows and deer, in
human bowels, and in sewage. This microbe, known as a methanogen, produces
methane, also known as swampgas. Other microbes that live in anaerobic
environments give off acetate, hydrogen, and carbon dioxide as wastes.
Methanosarcina consumes these biproducts to get energy for itself. It then gives
off methane gas.
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Yeast
Yeast are small fungi which are incredibly important in the food and beverage
industries. Yeast ferement the sugars in fruits to make wine, the sugars in grains to
make beers. When grown in the presence of oxygen, yeast give off the gas carbon
dioxide which makes bread rise. Yeast can grow with oxygen, (aerobically) or
without oxygen (anaerobically.) Because it can grow either aerobically or
anaerobically, it is known as a "facultative aerobe."
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Halomonas
These bacteria love high salt concentrations and like to eat the herbicide 2,4-D.
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Bacillus megaterium
This bacterium, like all species of Bacillus, forms spores, like the one shown
here. These spores help the bacteria survive hostile conditions, such as heat and
drying out. The genus Bacillus contains many related species of bacteria.
Because of their spores, many species of Bacillus are found in the desert. This
particular species is relatively big, as bacteria go, and hence the name "mega".
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Bacillus cereus
This cross section of B. cereus (pronounced B. serious) shows a central dark
endospore. Endospores in Bacillus species are produced when the organism slows
down in stationary phase of growth. This microbe produces and enterotoxin which
causes the intestine to secrete fluid into them. This can then lead to diarrhea. B.
cereus grows on rice.
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Anaerobic Toluene Degrader
This bacterium is an anaerobic toluene degrader. It was isolated from a gasolinecontaminated aquifer in Michigan. This organism was isolated and studied by Joanne
Chee-Sanford as part of her doctoral dissertation research. It is being displayed as our
"Microbe of the Week" (during April 1996) in honor of Dr. Chee-Sanford's recent
successful defense of her dissertation project.
Toluene is one of the most toxic components of gasoline. Gasoline sometimes leaks
from storage tanks (particularly older ones), including underground ones found at
many gas stations. Leaking gasoline, and with it toluene, often finds its way into underground water supplies. Wells
that tap into such aquifers can become contaminated with toluene, making them unfit for human use. Bacteria that
degrade (break down) toluene are being studied as a possible way to bioremediate (clean up) such contaminated water
supplies.
Although aerobic toluene-degrading microbes had been isolated previously, this bacterium was one of the first
anaerobic toluene degraders found. Aerobic microbes need oxygen to survive and to produce energy (in a sense, they
"breathe" oxygen, like we do). Anaerobic microbes don't need oxygen; instead they "breathe" other substances to use
for energy processing. Anaerobic microbes can survive in many environments that don't have a ready supply of air,
such as in stagnant water or underground.
Toluene-degrading bacteria that are aerobic cannot thrive in wet, underground environments like many aquifers.
Sometimes bioremediation is accomplished by giving microbes a helping hand. If we could get oxygen to aerobic
toluene degraders in contaminated aquifers, they might clean up our mess for us. Unfortunately, pumping oxygen into
water supplies is not very feasible. Because of this, scientists are interested in finding anaerobic toluene degraders,
such as this one. This bacterium "breathes" nitrate instead of oxygen. Nitrate is soluble in water, so it might be
possible to help it clean up a water supply by dissolving nitrate into the water. Providing these bacteria with an
abundance of nitrate might enable them to create lots of energy in support of a rapid metabolism, thus enabling them
to gobble up lots of toluene. This bacterium can function either as an aerobe or as an anaerobe, breathing either
oxygen or nitrate. Scientists are particularly interested in its anaerobic metabolism because of its implications for
bioremediation.

Root Cellar
A favorite habitat of microbes is near and in the roots of plants. Many microbes live in soil, but even more (up to 100 times
more) live close to the roots of plants. This area near the roots is called the "rhizosphere" which is the thin layer of soil that
sticks to the roots. The rhizosphere is a huge habitat in the soil, because plants have so many root fibers. An individual wheat
plant, for example, may have a root surface area of 6 square meters (yards)!
Some microbes have very close relationships with plants. The plant and the microbes become so close that the microbe actually
lives inside the plant! This association of microbes and roots often benefits both organisms. The plant gives the microbes food,
such as sugars and amino acids, and the microbes give the plants minerals, some vitamins, nitrogen, and some amino acids.
One example of a microbe living inside plant roots is Rhizobium, which lives inside the roots of plants such as peas
and clover. Another group of microbes living inside roots are mycorrhizal fungi. Rhizobia and the mycorrhizal fungi
live with plants in symbiotic relationships. Symbiosis is the living together of two or more organisms. Often, this
association helps both organisms.
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Rhizosphere Microbes
The thin layer of soil next to the roots of plants is called the rhizosphere. The rhizosphere contains many
more microbes than in the surrounding soil. This is because plants "leak" nutrients into the soil, which the
microbes can use
Many microbes live near the roots of plants.

Azospirillum brasilense
Scientific Name: Azospirillum brasilense
Kingdom: Eubacterium
This bacterium lives in soil. It is able to live on its own in soil, or in close associations
with plants in the rhizosphere (the area right next to the roots of plants in soil). A.
brasilense is helpful to plants and important to farmers because it is able to fix
nitrogen - it can convert nitrogen gas in the air into nitrogen bound up in amino acids and proteins

Nitrifying bacterium
This is a cross section of a microbe which is a type of "nitrifier". Nitrifiers convert
ammonia into nitrite and nitrate. Because of this, they are important in wastewater
treatment plants because they get rid of excess ammonia. This organism, Nitrosomonas
converts the ammonia into nitrite which is then converted to nitrate by another group of
bacteria. Nitrosomonas is a problem in agriculture because it turns the ammonia,which
is used as a fertilizer, into nitrite. Nitrite is a problem because it is not as easy for plants
to use as is ammonia, and because nitrite can leach into groundwater where it may be a
pollutant.

Azotobacter Cysts
This is the cross section of a cyst of the bacterium, Azotobacter. Azotobacter is an
organism that lives in soil. It can fix nitrogen. Unlike rhizobium, azotobacter is free-living.
This cyst is a resting stage for this organism that allows it to survive in harsh conditions.
This cyst has the same function as endospores in other bacteria.
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Rhizobium
Rhizobia (singular is rhizobium) are bacteria that form a symbiosis with the roots of certain plants called
legumes.

Rhizobium in Soil
Rhizobium is a type of bacterium that lives in soil and around and inside of the roots of
certain plants (legumes). This is Rhizobium in its free-living state in soil, surrounded by a
halo of protective covering called a capsule. The slimy capsule, made of exopolysaccharide,
protects rhizobium from drying out. It also helps the bacterium stick to root hairs during
other stages of its life cycle, when rhizobium forms a symbiotic partnership with plants like
clover.

Rhizobia on Root Hair Tip
The large object in the center of this view is the tip of a clover root hair. The cylindershaped creatures on the top of the root tip are rhizobia, bacteria that live in a symbiotic
relationship with the clover. The rhizobia shown here are clustered on the surface of the
root. Soon they will start to invade the roots and begin a symbiotic partnership that will
benefit both organisms.

Rhizobia on Clover Root Hair
These rhizobia have attached themselves onto a clover root hair. The sticky, web-like tendrils
extending from the rhizobia across the root surface are called cellulose microfibrils. These
rhizobia (a type of bacteria) are beginning to invade the root, where they will form a
symbiotic relationship with the clover plants.

Aquatic Root Nodules
This view shows microbes inside the root of an aquatic plant. These bacteria form
"symbiosomes" of bacteroids which are inside the root nodules of an aquatic plant,
Neptunia. Root nodules form when a type of bacterium, rhizobium, infects the plant's
roots. This "infection" is not harmful to the plant, and is not the source of a disease.
Once inside the plant, the rhizobia are called bacteroids. The bacteroids establish a
symbiotic partnership with the plant, which is beneficial to the plant and the bacteria.
The plant provides energy-rich food, produced by photosynthesis, to the rhizobia. In return, the
rhizobia "fix" nitrogen for the plant. What does "fixing" nitrogen mean? Nitrogen, an element, is
plentiful in the Earth's atmosphere. It exists there in the form of a gas, with two nitrogen atoms
bound together to form a molecule. Nitrogen is found in all living creatures. It is one of the key
components of proteins, which are the structural building blocks of living cells. The process of
extracting nitrogen from air and combining it with other compounds to form proteins is called
"nitrogen fixation". Since plants cannot fix nitrogen themselves, they are dependent on these
nitrogen fixing bacteria for the proteins that they need to survive and grow.
Nitrogen Fixers Help Make Protein:
Where does our protein come from? It comes from nitrogen in the air which microbes, such
as rhizobia, help turn into protein. Rhizobia live in the roots of plants called legumes such
as peas, clover and peanuts, where they convert nitrogen in the air into a form of nitrogen
called ammonia that the plants can then turn into protein. Rhizobia can live independently
in soil, or in a special association with plants called a symbiosis. When they live with plants,
Rhizobia live in special root tissues called "nodules". When Rhizobia are in root nodules,
they gain a special ability to help fertilize the plants. Rhizobia convert nitrogen in the air
into a form of nitrogen that the plants can use. This conversion of nitrogen is called
"nitrogen fixation." The protein from plants is then used by animals, including humans, that
eat them.
This is a cartoon of rhizobium fixing nitrogen (N2) from the air into ammonia (NH3) a form of nitrogen that plants
can use.
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Mycorrhizal Fungi
Most plants, including more that 90% of all trees, have special fungi associated with their roots. These fungi help
plants absorb nutrients and water. These fungi form a symbiotic association with the roots of nearly all plants to help
them grow. Sometimes these microbes become macrobes, large organisms, that you can see as mushrooms.
Mycorrhizal fungi live with and help the roots of nearly all plants. Mycorrhizae means "fungus root." In this
association, the fungus extends itself into the soil and helps the plant by gathering water and nutrients, such as
phosphorus and nitrogen. In return, the plant helps the fungus by giving it sugar produced by photosynthesis. This
is an example of symbiosis, a win-win association.
Mycorrhizae allow plants to live in desolate areas that are poor in nutrients, such as road-sides, disturbed soil near
mining operations and in tropical rain forests. Surprisingly, rain forests are often depleted of nutrients because there
is so much competition by other plants for nutrients. In these nutrient-poor soils mycorrhizae can help plants to live
where they otherwise might die.
ENDOMYCORRHIZAE
The most common mycorrhizae grow inside the cells of roots. These are called "endomycorrhizae," (Endo means
inside.) Many of these endomycorrhizae form tiny trees and little sacs inside root cells. These tiny trees, called
"arbuscules" (Latin for tree) and tiny sacs, called "vesicles" (little sac) are connected to long threads of the
mycorrhizae that lead out into the soil. These long threads, called hyphae, are analogous to the roots of plants. These
hyphae extend beyond the length of roots, and allow the roots to absorb more nutrients than they would without the
help of the fungus.
ECTOMYCORRHIZAE
Another type of mycorrhizae grows between the cells of roots and on the outside of the root, not inside the cells.
Because these fungi live outside the cells of the plant, they are called ectomycorrhizae (ecto = outside.) These fungi
have a thick network of thin, fungal cells, or hyphae, that cover the roots of the plants. This covering protects the
roots in a sheathe of ectomycorrhizal cells. These fungi are friends mostly with pine trees. Often, deforested lands
are planted with tree seeds, together with mycorrhizal fungi, which help seedlings get a good start in life. Some
ectomycorrhizal fungi associated with trees form mushrooms, such as Boletus, Aminita, and truffles. All conifer trees
have mycorrhizal associations.

Mycorrhizal Spore
The light round object is a spore of a root fungus called Glomus intraradix . This spore
inside the root tissue of Sorghum. These spores are rich in oil droplets. The oil serves as
energy storage for the fungus. This is especially important since the absorbtion of nutrients
from the soil by the fungus consumes a lot of energy.

Giant Spore of endomycorrhizae
Mycorrhhizal fungi reproduce by forming spores, such as this of Gigaspora rosea . From a
microbial perspective, these spores are gigantic. Spores of Gigaspora may measure up to
300 microns, and are visible to the naked eye. These spores are reproductive structures
which serve to propogate the fungus.

Glomus intraradix
Root fungi, also called mycorrhizal fungi, are symbiotic organsims which associate
with the roots of nearly all plants. This is sorghum root infected with the Vesiculararbuscular mycorrhizal (VAM) fungus Glomus intraradix. The image shows hyphal
growth (the thin hairs) and vesicles (little ovals) inside the host's root. Root fungi,
also called mycorrhizal fungi, are symbiotic organsims which associate with the
roots of nearly all plants.

Glomus intraradix spores
This is a dying root of Sorghum with spores of the mycorrhizal fungus Glomus
intraradix. When the root gets old, vesicles of this fungus harden to become spores.

Mycorrhizal "Little Trees"
Kingdom: Fungi
Scientific Name: Gigaspora rosea
These white bushy creatures are mycorrhizal fungi living inside the cells of roots.
Because these mycorrhizae live inside root cells, they are called "Endomycorrhizal
fungi" ("endo" means inside). These fungi form structures inside the cells of plant
roots called "arbuscules" which means "little trees." The branches of these little
trees are the site of interaction between the cell and the fungus.

Vesicular Arbuscular Mycorrhizal Fungi Vescicles
Most all plants have a symbiotic association with fungi called mycorhizal fungi.
This is an image of a root from sorghum with vescicles ("little sacs") of the
mycorhizal fungus called Gigaspora rosea.

Statue
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Lichen

Toxic Waste
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Anaerobic Toluene Degrader
Eater of Weed Killer - Salt-loving, 2,4-D degrader
Kingdom: Eubacteria
Scientific Name: Halomonadaceae
These bacteria degrade 2,4-D, the herbicide found in "Weed Be Gone" that people
spray on their lawns to get rid of dandelions and other weed plants. This bacterium
is unusual among 2,4-D degrading bacteria found so far because it can live in high
concentrations of salt at high pH.
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2,4-D Animation
2,4-D degradation
This animation shows the first couple steps in the degradation of the herbicide 2,4-D. 2,4-D is one of the most well studied
herbicides and scientists understand how some microbes break down this molecule. Microbes use a set of enzymes (proteins
that can transform one molecule into another) to degrade 2,4-D. These enzymes chew off bits of the 2,4-D molecule a bit at
a time in a particular order called a biochemical pathway.
The first step in the pathway is removal of the molecules sticking off from the ring. Just like when you eat the head off a chocolate Easter
bunny, the first 2,4-D degrading enzyme chomps off the "head" of the 2,4-D molecule, leaving a carbon ring "body" called 2,4dichlorophenol.
2,4-Dichlorophenol
The next enzyme in the pathway adds oxygen to the remaining carbon ring to make it easier to break (the extra oxygen
destabilizes the ring). This oxygen makes the ring easier for the next enzyme in the pathway to break. This reaction
then produces the molecule 3,5-dichlorocatechol.
3,5-Dichlorocatechol
After 3,5-dichlorocatechol is formed, the next enzyme breaks open the ring, and in so doing, one of the chlorine
molecules is lost. Other enzymes then chew the straightened carbon molecule into smaller and smaller bits until it is
converted entirely to water (H2O), carbon dioxide (CO2), and hydrochloric acid (HCl).
Glossary:
Amino Acid- a molecule which is the building block of protein. Amino acids contain nitrogen as well as carbon, hydrogen and oxygen, the
basic atoms of life. All organisms contain at least 20 different types of amino acids. Some bacteria are able to make all amino acids, unlike
humans which cannot make about 8 amino acids for which they must rely on other organisms, like microbes and plants, to make for them.
One type of amino acid, glutamate, is made by bacteria which humans then use to make the flavor enhancer, MSG -- monosodium glutamate.
Legume- a flowering plant which bears its seeds in pods. All legumes looked at so far have a symbiotic association with root-colonizing
bacteria called rhizobia. Legumes includes plants such as clover, peas, beans. Legumes contain seeds, such as peas and beans, that are rich in
protein.
Nodule -a special structure of roots of certain plants which contain the symbiotic, nitrogen fixing bacteria Rhizobium.
Nutrients- the necessary components of food that microbes and all life require to exist and grow. Essential elemental nutrients include such
basic molecules as nitrogen, carbon, oxygen, hydrogen, phosphorus, potassium and trace minerals.
Protein- an important molecule that is found in all life. Proteins are polymers, that is, long strings of individual amino acids.
Sugars -a sweet tasting substance produced by many organisms which is used as an energy storage molecule.
- dissimilar organisms living together. A symbiosis is an ecological relationship between two or more
different species living together in direct contact. There are several types of symbiotic relationships, including
parasitism, in which one organism hurts the other; commensalism, in which one organism benefits without hurting
the other; and mutualism, in which both partners gain from the association. In microbial ecology when the term
symbiosis is used, unless stated otherwise, it refers to mutually beneficial relationships.
Symbiosis
Snack Bar


Food Makers
o Yogurt microbe - Lactobacillus
o Bread makers - Yeast
o Blue Cheese Microbe - Penicillium
Food Contaminators
o Blood Colored Microbe - Serratia marcescens
o Good guy gone awry - E. coli
o Bacillus cereus
Space Adventure

Frequent Fliers
o Bacillus megaterium
o Spores and Threads
These are the spores of a slime mold. The somewhat round objects that look like
raisins are the spores. The objects that look like twisted, spiky ropes are very thin
threads, called "elators". The elators act as springy microbial sling shots, hurling
the spores into the air. The spores, which are analogous to the seeds of plants, are
carried by the wind to new locations which the slime mold then colonizes. The
spores are very tough. Some are viable (can grow into new organisms) even after
they have been dormant for as long as century! The spores range in color from
golden yellow to brown or rusty reddish-brown. This slime mold is found in many
places around the world, generally in forests. It lives on dead wood, fallen leaves and other forest litter.
Although it is called a mold, this microbe is not related to fungal molds. Instead, it is a protoctist.
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Slime Mold Spores
Many types of microorganisms produce spores. Spores serve a function for microbes
similar to the role that seeds serve for plants. These spores are the way that this slime
mold reproduces. The spores also help the microbe move around; they blow around on
the winds, just as many types of seeds do, until they land and "take root" in a new
environment.

Mission with Microbes
Biosphere II
- In preparation for extended missions in space, scientists are developing simulations of enclosed space stations.
These enclosed spaces are called Closed Ecological Life Support Systems, or CELSS for short.
-The largest CELSS project yet is Biosphere II in the Sonoran desert of Arizona. Biosphere II contains three acres
sealed from our atmosphere under glass. Biosphere II contains eight different biomes including desert, salt marsh,
ocean, rain forest, tropical savanna, rain forest, agricultural area, and human habitat. Each of these environments has
its own rich communities of microbes.
-In 1991, 8 people were sealed inside Biosphere II for 2 years. Microbes helped maintain life in Biosphere II for all
that time. Microbes recycled wastes, purified the air, and changed the atmosphere.
Microbes used to Recycle Wastes:
About 2000 liters (600 gallons) of waste water were treated per day in Biosphere II using microbes. The
microbes that treated waste water in Biosphere II were similar to those discussed in Poo Corner.
Microbes Used to Purify Air:
Biosphere II has 30,000 tons of soil containing billions and billions of microbes. The microbes recycle dead
plants in the soil and some of these microbes eat pollutants in the air keeping the air safe to breathe.
Microbes Deplete Oxygen in Biosphere II:
Microbes profoundly affected Biosphere II, as they do Biosphere I (the Earth). In Biosphere II, microbes
where found to be responsible for the decreasing levels of oxygen, which dropped from 20 percent to less than
14 percent. Biosphere II had more microbes consuming oxygen than there were plants and photosynthetic,
oxygen producing (oxygenic) bacteria that could recycle oxygen through photosynthesis.

Microbes on Mars?
o Martian Bacillus?
In August of 1996 NASA scientists reported finding what look like fossils of
microbes inside a meteorite (called ALH84001) thought to be from Mars. They
believe the 4.5 billion year old rock was once a part of Mars. It was blasted
from Mars by a huge meteor impact 16 million years ago. It fell to Earth in
Antarctica 13 thousand years ago. A piece of the meteorite was discovered on
an ice field in Antarctica by scientists in 1984. Inside of the meteorite, along
cracks and fissures within the rock, scientists found mineral structures such as
the one shown here. Some scientists believe this may be a fossil of an ancient
Martian microbe, similar to Earthly bacteria. Other scientists are skeptical, and
believe that these deposits are the result of inorganic chemical processes that by chance happen to
resemble terrestrial monerans. The NASA scientists have also found traces of chemicals within the cracks
in the meteorite that they believe came from living organisms. These polycyclic aromatic hydrocarbons
(PAHs) and carbonate globules may be products of microbial metabolisms. Visually, this structure
certainly does resemble rod-shaped bacteria found on Earth. It is, however, quite small compared to
terrestrial monerans; it's size is closer to that of large viruses than to the size of most bacteria. Most
scientists doubt that life currently exists on Mars. However, it is very likely that Mars was much wetter
early in the history of that planet, and water seems to be a critical ingredient for the formation and
continuation of living organisms on Earth. Further studies, including two NASA space missions due to be
launched toward Mars in late 1996, may shed additional light on the question of whether there is life
elsewhere in the universe.
Water World

Deep Thermal Vents
Deep below the ocean suface, where there is no light, whole ecosystems with dense animal life surround
hydrothermal vents. These communities are suppported by bacteria, which create food from chemicals flowing
out of volcanic vents. Some of these bacteria are free living, others live together with animals is a symbiotic
relationship.
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Tube Worm Symbionts
These bacteria feed an animal that cannot eat. The relatives of this microbe make life possible deep beneath the ocean
near volcanic vents. This particular microbe lives inside and feeds tall white worms sporting red, feathery caps, that
live at the dark bottom of the sea.
Endosymbiosis
The microbes and the worm depend upon each other for survival in what is called a
symbiotic relationship. In a symbiotic relationship, two different species live together
and each benefits from the partnership. In this case, the worm gives the bacteria a place
to stay and the bacteria provide food for the worm.
This worm, called Riftia pachyptila, is an unusual animal because it has no mouth or
digestive tract and no apparent way to eat! Instead of eating food like other animals, Riftia allows bacteria to live
inside of it and provide its food. The worms have a special feeding sac, called a trophosome, which provides the
bacteria with shelter and ingredients to make food. In turn, the bacteria use these ingredients to make food for the
worm. The trophosome and the bacteria inside it are so important that they make up over half the weight of this
animal.
Strange Life in the Dark
Dark ocean floors near deep sea vents are home to giant clams, shrimps, tube worms, crabs and other strange
creatures. When these communities were first discovered living deep on the dark ocean floor, no one know how life
could exist there without sunlight. Until recently, people thought that all food ultimately comes from plants and other
photosynthetic creatures like algae and cyanobacteria. These photosynthesizers use energy from sunlight to convert
carbon dioxide into food. Organisms that make food for an entire community are called primary producers. But who
are the primary producers deep under water where there is no light?
Undersea Food Chain Based on Chemicals not Sunlight
The primary producers of deep sea vents are bacteria. These bacteria, like the ones in the picture above, get their
energy from chemicals flowing out of the volcanic vents, not from energy found in sunlight.
Hydrogen sulfide, the stuff that smells like rotting eggs and is toxic to us, is one of the main chemicals used by the
vent bacteria for making food. These bacteria make energy by combining hydrogen sulfide with oxygen (also
supplied by the tube worms) to make sulfur, water and energy. The bacteria then uses this energy to convert carbon
dioxide into food just like plants use energy from the sun to make food. This food in turn feeds the entire community
of worms, clams, crabs and other creatures.
In the case of the tube worm, the bacteria living inside the worm use the hydrogen sulfide supplied by the worm. The
worm collects the hydrogen sulfide with its red feathery cap. This cap is red because it is filled with blood containing
a special hemoglobin that transports the hydrogen sulfide to the bacteria.
The tubeworm also provides the symbionts with oxygen which it needs to combine with the hydrogen sulfide for
energy. This oxygen comes from the ocean surface. The tube worm provides the perfect place for bacteria to get both
oxygen and hydogen sulfide which are often difficult to find in one place.
Microbe with no Name
Bacteria that live inside tube worms have no name yet. Like the majority of all microbes, this one has no name
because it cannot be grown in the lab. Despite the difficulty of growing this microbe by itself, scinetists know a lot
about this microbes physiology, ecology, and some of its DNA sequences.
Soon, this bacterium will be given a name and its relatives will be learned because of a new way to identify microbes.
This technique, called DNA sequencing, allows scientists to take a small bit of DNA from the microbe in question,
sequence it, and compare this sequence to all other known microbes. This microbe may be closely related to a
bacterium we already know or it could be something completely new.
GLOSSARY:
-bacteria - single celled organisms lacking a nucleus during their entire life cycle.
-Calvin cycle - a set of chemical reactions that creates carbohydrates from carbon dioxide.
-DNA sequencing - a technique of determining the sequence of A, T, G, and C from a bit of DNA. In determining a
microbes identity, the section of DNA encodes a gene found in all living organisms, in this case the small subunit of
the ribosome, the organelle used to make proteins.
-carbohydrates - chemicals with the basic structure of CH2O. Sugar is a carbohydrate.
-endosymbiosis - a relationship in which one organism (the symbiont) lives inside another (the host) and in which
both partners benefit.
-hemoglobin - a molecule found in red blood cells of your blood that carries oxygen to your body and is poisoned by
hydrogen sulfide. In tube worms, hemoglobin floats freely in blood and is modified to carry both oxygen and
hydrogen sulfide.
-primary producers - organisms at the base of the food chain
-symbiosis - The term "symbiosis" was originally coined by the German botanist Anton De Bary to mean "the living
together of differently named organisms". A symbiosis can benefit both organisms (called mutualism) or one partner
can hurt the other (parasitism) or the relationship can be anywhere in between. Over the years "symbiosis" has come
to mean mutually beneficial, but biologists define symbiosis as it was originally intended. The Riftia/bacterium
symbiosis would then be refered to as a "mutualistic symbiosis" a relationship in which both partners benefit versus
just symbiosis. To not confuse young readers, the word symbiosis is used in the mutualistic sense.
-symbiont - a partner in a symbiotic relationship
-trophosome - Greek for feeding body, organ of tube worms where symbiotic bacteria live and produce food
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Pyrococcus furiosus
Pond
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Spirogyra
Kingdom: Protist
Scientific Name: SpirogyraThis is the spiral-shaped chloroplast of the algae, Spirogyra. This chloroplast
is green when viewed with traditional light microscopy. Here it is seen as red, since the chloroplast was
fluorescing red.
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Star Filament Algae Fluorescing
This is a type of algae that lives in ponds. Algae are protists that have
chlorophyll, like plants do, and are thus able to make food for themselves
using sunlight via photosynthesis. Many algae, such as this one, grow in
long strands of individual cells strung end to end. This image shows
several cells in a portion of such a strand. This image does not show the
whole algal cells, but instead highlights a part of the internal structure of
the algae, their chloroplasts.
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Methanogens
Gleocapsa
This photosynthetic bacterium belongs to a group of bacteria known as a
cyanobacteria. Many of these organisms live in ponds. Gleocapsa is a genus
name which includes the species gleocapsa and chroococcus. The picture of this
microbe may be misleading to your senses. Although this image looks like
several fried eggs on a griddle, the organism is actually spherical, with six dark
central spheres inside of six additional spheres that cannot be seen. This image,
like others in the Microbe Zoo, must be interpreted by you, the scientist. Many
times, your brain will have to do some mental morphing to make more accurate
models of how microbes actually are in nature. No imaging technique is perfect. Often times, many
different imaging techniques must be used to properly interpret the true structure of a microbe.
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Rhodospirillum rubrum
This microbe likes it in the light and in the dark. It grows anaerobically in the
light when it is undergoing photosynthesis. In the dark, it can grow aerobically
with oxygen. This microbe is purple-red in color because it contains a pigment
called a carotenoid. This carotenoid helps gather light energy for photosynthesis.
Unlike green plants, this organism does not produce oxygen as a by product of
photosynthesis. Also, the chlorophyll of this bacterium differs from that of the
green chlorophyll of plants. This organism contains chlorophyll b, which
absorbs longer wavelength light.
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Hydra with green symbiotic algae
This brilliant green organism is a hydra with green, photosynthetic algae in it. Hydras
are simple animals. This freshwater hydra and the algae live together in a symbiosis.
The hydra protects the bacteria from the environment and the algae provide the hydra
with sugar from symbiosis. The algae also supply oxygen and remove carbon dioxide.
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Algae in symbiotic relationship with hydra
Actinopod-protozoa
Heliozoa are members of group of organims called actinopods. Actinopods are
spherical organisms with many projections - like rays of the sun. These
projecting rays are what give them their name, since actinopod means "ray
foot." Heliozoa are found in freshwater ponds. The rays on this organism help
keep it afloat and help it eat. These organims are heterotrophic meaning that
they eat other organisms.
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Rotifer
This microbe is a tiny, true animal. The name rotifer is from Latin meaning
"Wheel bearer". The two wheels on rotifers are made of cilia that beat and
create a current that draws water containing food into the gut of the rotifer.
These live mainly in freshwater, in bogs, lakes, and rivers, although some
inhabit seas and damp soil. There are about 2000 species of rotifers. Rotifers eat
bacteria, protists and other small animals.
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Diatoms
The large, round object in the center of this view is a diatom. Diatoms are protists that grow a silica shell
around themselves. When diatoms divide, each offspring takes half of the original shell with it, and grows
another matching half to complement the inherited shell portion. Diatoms are
frequently found in wet environments, such as ponds. They also grow on most
soil. Diatoms grow on the surface layer of soil, where they can use sunlight to
produce food via photosynthesis. This species of diatom is yellow-brown in
color when viewed with visible light. There are two basic types of diatoms:
elongate ones and round ones, like this microbe. Elongated diatoms can move
themselves about; round diatoms cannot. There may be as many as 10,000
species of diatoms. Huge accumulations of fossilized diatoms make up
diatomaceous earth, which is used in toothpaste and in filters.
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Mummy-shaped diatoms
= The large creatures in this image that look like mummy cases are diatoms. Diatoms are protists that grow a silica
shell around themselves. When diatoms divide, each offspring takes half of the original shell with it, and grows
another matching half to complement the inherited shell portion.
= These diatoms are shown here growing on duckweed plants found in a pond.
The smaller creatures around the diatoms are various species of bacteria. Diatoms
are frequently found in wet environments.
= Diatoms also grow on most soil. They grow on the surface layer of soil, where
they can use sunlight to produce food via photosynthesis.
= There are two basic types of diatoms: round ones and elongated ones, like these.
Elongated diatoms can move themselves about; round diatoms cannot.
= There may be as many as 10,000 species of diatoms. Huge accumulations of
fossilized diatoms make up diatomaceous earth, which is used in toothpaste and in filters.
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Anabaena
These beautiful strands are not pearls, but rather bacteria that provide us with an
element even more valuable to our survival than pearls - namely nitrogen.
Anabaena fixes nitrogen; it takes nitrogen gas from the air and binds it into protein
molecules. Certain species of bacteria are the only organisms on Earth that are able
to fix nitrogen. Since all living things require proteins to function, and since all
protein molecules include nitrogen atoms, nitrogen-fixing bacteria play a major role
in supporting life on Earth. These bacteria grow in rice paddies on the underside of Azolla ferns. The
nitrogen they fix provides an important source of fertilizer for rice. Anabaena is a multi-talented organism;
it is also able to create sugar that it uses for food via photosynthesis, just as plants do.
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Amoeba
Amoebas are some of the most famous members of the microbial world.
Amoebas have no fixed shape. Instead, these blobs of protoplasm constantly
shift their shape while moving and eating. An amoeba moves by extending part
of its "body", called a psuedopod ("false foot"), and then using the psuedopod to
drag itself to the new location. Amoebas also use their shape-shifting abilities
while feeding; they surround their food with extended psuedopodia, engulfing
their prey.
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Pipe Slimers
o Iron Oxidizer - Leptothrix ochracea
Plankton
o Diatom
o Dinoflagellate
o Coccolithophore
o Picoplankton
Salty Tidal Pool
o Halomonas
Sediment
o Beggiatoa alba
Watery Desert
o Tiny Plankton