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Unit 21 Notes
Terrestrial Microbiology
Since the resources on our earth are finite and scarce, all of its life must share – and cycle – those resources in
order to survive. Much of the cycling depends on earth’s tiniest inhabitants, our friends the microbes! We tend
to view each of earth’s cycles as a separate, individual process, but what we must realize is that what changes
one cycle will change all cycles. In these notes, we will examine each of these intricate cycles.
Carbon Cycle
Carbon is an element in nature that makes up all living things, and thus must be recycled constantly so that
living things can synthesize organic compounds (carbon compounds). The carbon cycle is a process by which
carbon is cycled between the atmosphere, land, water, and living organisms. Photosynthetic organisms take in
carbon in the form of CO2, and form carbohydrates using the sun’s energy and chlorophyll pigments.
Photosynthetic organisms, in turn, are consumed by animals, fish, and humans; these creatures use some of the
carbohydrates as energy sources and convert the remainder to cell parts. Although some carbon is released by
respiration and returns to the atmosphere as carbon dioxide, the major portion of the carbon is returned to the
soil when an organism dies.
In the soil, microbes (bacteria, fungi, and other microbes) are the primary decomposers of organic matter and
release CO2 for use by plants. In marine environments, cyanobacteria and zooplankton do the same thing. But
not all of the broken-down organic matter is used, and what is left is a combination of mineral particles and
organic matter called humus. Similarly, a compost pile is simply a product of microbes breaking down manure
and other organic materials to form a produce called compost. Microbes can also perform one other useful
task: they can break down the carbon-based chemicals produced by industrial processes, such as herbicides,
pesticides and plastics (called bioremediation).
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The Nitrogen Cycle
All organisms need nitrogen to build proteins, which are used to build new cells. Nitrogen makes up 78% of the
gases in the atmosphere. However, most organisms cannot use atmospheric nitrogen – it must be put into
another form before it is usable. The only organisms that can “fix”, or change, atmospheric nitrogen into
chemical compounds are the nitrogen-fixing bacteria that live in the soil. The nitrogen cycle is the process in
which nitrogen circulates among the air, soil, water, plants, and animals in an ecosystem. As shown in the
figure below, bacteria take nitrogen gas from the air and transform it into molecules that living things can use.
Nitrogen fixing bacteria live within the nodules on the roots of plants called legumes, which include beans,
peas, and clover. The bacteria use sugars provided by the legumes to produce nitrogen-containing compounds
such as nitrates. The excess nitrogen fixed by the bacteria is released into the soil. In addition, some nitrogenfixing bacteria live in the soil rather than inside the roots of legumes. Plants that do not have nitrogen-fixing
bacteria in their roots get nitrogen from the soil. Animals get nitrogen by eating plants or other animals, both of
which are sources of usable nitrogen.
After nitrogen cycles from the atmosphere to living things, nitrogen is again returned to the atmosphere with the
help of bacteria. These decomposers are essential to the nitrogen cycle because they break down wastes, such
as urine, dung, leaves, and other decaying plants and animals and return the nitrogen that these wastes and dead
organisms contain to the soil. And the cycle begins again!
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The Phosphorus Cycle
Phosphorus is an element that is a part of many molecules that make up the cells of living organisms. For
example, phosphorus is an essential material needed to form bones and teeth in animals. Plants get the
phosphorus they need from soil and water, while animals get their phosphorus by eating plants or other animals
that have eaten plants. The phosphorus cycle is the movement of phosphorus from the environment to
organisms and then back to the environment. This cycle is slow and does not normally occur in the atmosphere
because phosphorus rarely occurs as a gas.
Phosphorus may enter soil and water in a few ways. When rocks erode, small amounts of phosphorus dissolve
as phosphate in soil and water. Plants absorb phosphates in the soil through their roots. In addition, phosphorus
is added to soil and water when excess phosphorus is excreted in waste from organisms and when organisms die
and decompose. Some phosphorus also washes off the land and eventually ends up in the ocean. Many
phosphate salts are not soluble in water, so they sink to the bottom of the ocean and accumulate as sediment.
It is important to note that excess phosphorus and nitrogen in an aquatic ecosystem can cause rapid and
overabundant growth of algae, which results in an algal bloom. These can deplete an aquatic ecosystem of
important nutrients such as oxygen.
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The Sulfur Cycle
Sulfur is one of the components that make up proteins and vitamins. Proteins consist of amino acids that contain
sulfur atoms. Sulfur is important for the functioning of proteins and enzymes in plants, and in animals that
depend upon plants for sulfur. Plants absorb sulfur when it is dissolved in water. Animals consume these plants,
so that they take up enough sulfur to maintain their health.
Most of the earth's sulfur is tied up in rocks and salts or buried deep in the ocean in oceanic sediments. Sulfur
can also be found in the atmosphere. It enters the atmosphere through both natural and human sources. Natural
resources can be for instance volcanic eruptions, bacterial processes, evaporation from water, or decaying
organisms. When sulfur enters the atmosphere through human activity, this is mainly a consequence of
industrial processes where sulfur dioxide (SO2) and hydrogen sulfide (H2S) gases are emitted on a wide scale.
When sulfur dioxide enters the atmosphere it will react with oxygen to produce sulfur trioxide gas (SO3), or
with other chemicals in the atmosphere, to produce sulfur salts. Sulfur dioxide may also react with water to
produce sulfuric acid (H2SO4). Sulfuric acid may also be produced from dimethylsulfide (DMS), which is
emitted into the atmosphere by plankton species. All these particles will settle back onto earth, or react with
rain and fall back onto earth as acid rain. The particles will than be absorbed by plants again and are released
back into the atmosphere, so that the sulfur cycle will start over again.
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The Oxygen Cycle
The cyanobacteria are the prime bacteria that recycle oxygen (O). They absorb water molecules during
photosynthesis, and break them down to use the hydrogen atoms, thus releasing the oxygen into the atmosphere
as a gas. MOST of our atmospheric oxygen is given off by bacteria, not plants.
Symbiosis - A Universal Principal of Life
Symbiosis is the term that scientists use to describe the relationship between two or more species living in close
association with one another. Many of these interactions involve one species living on or within another
species. In this way, most, if not all, larger organisms are actually composite organisms: multiple organisms
living symbiotically with one another. Consider, for a moment, the fact that the bacterial cells on and within
your body outnumber your own cells 10:1! In some species, such as termites and cockroaches, symbiotic
microorganisms make up 30-50% of their body weight. In many cases, symbioses between species have
evolved to the point that each species is critically dependent on the other: eliminate one partner and the other
will be eliminated also.
We live in a magnificently diverse world. In the 14 mile thick blanket of life that covers the Earth's surface
reside an estimated 100 million species. Regardless of where we look, from the driest deserts to the deepest
depths, we find an incredibly diverse assemblage of living things, and across all geographical boundaries and
taxonomic categories we find symbiosis. Of course, the vast majority of life on Earth is microscopic: virtually
unnoticed until the mid-17th century, and arguably under appreciated even today. But, the truth is, it is upon
this microscopic world and its symbiotic relationships that the diversity of life depends.
Symbioses are generally described as falling into one of three categories: parasitism, commensalism and
mutualism:
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Commensalism – this is a symbiosis in which one partner benefits and the other neither benefits nor is
harmed. An example of this is our normal flora microbes that live in our bodies all the time. The
microbe benefits because it is housed in our bodies and fed. We are unaffected.
o At least two species of mites live commensalistically on the foreheads of humans. Demodex
folliculorum lives in hair follicles, whereas Demodex brevis inhabits the sebaceous glands. The
mites spend the day in the protected confines of their respective hiding places, but at night they
typically will move from one place to another, all the while going unnoticed by their host!
o Bacteria that live commensalistically within our digestive system, when displaced, can cause
disease. How many people haven't had strep throat? Strep throat is a disease caused by
Streptococcus pyogenes, which lives commensalistically in our own digestive tract. However,
when these bacteria find their way into one's throat or onto one's skin, they typically behave as
parasites.
Mutualism - mutualism is a symbiotic relationship from which both organisms derive benefit.
o Most of the shallow coral species form mutualistic symbioses with dinoflagellate algal species.
The coral receives nutrition from the the photosynthesis of the algae and the algae receives a
protected environment and nutrients obtained by the coral. This interaction has enabled coral
reefs to be among the most productive of Earth's ecosystems. These ecosystems have a
profound impact globally as sites of carbon dioxide absorption, energy production for larger
oceanic ecosystems and as nurseries for many fish species.
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o Most animals have a diverse microbial flora within their digestive tracts. Humans, for example,
have many mutually beneficial relationships with some of our intestinal microbiota. For
instance, several species of Bacterioides and Escherichia are our principle source of vitamin K
which is an essential factor involved in blood clotting. Other species have been shown to be
important sources of some B vitamins, and recently one species of Bacterioides has been
determined to be an essential component in the development of blood vessels of the small
intestine.
o Another example is in the gut of the termite. In some termite species, the microbial flora
(bacteria and protists) of their digestive tract amounts to as much as 50% of the individual's
weight. Within the digestive tract of these termites is a diverse microbial world that has evolved
along with the termites' ecologic role in the environment. Termites, like most animals, lack the
enzymes necessary to break down the principle components of plant tissues: cellulose and
lignin. Bacteria and protists release energy from the food that it absorbs while other bacteria
produce the enzymes necessary for digestion of the cellulose and lignin fibers that are the main
components of wood. Some bacteria within a termite's digestive tract are involved in recycling
the termite's wastes. Like all insects, termites eliminate toxic nitrogen containing wastes in the
form of uric acid. Some of these bacteria actually breakdown the uric acid wastes and release
the nitrogen back into the termite's "blood" in the form of readily usable amino acids.
Parasitism - Parasitism is a symbiotic relationship in which one organism benefits (the parasite) and
the other organism is harmed (the host).
o For instance, the fungi, Tinea pedis, causes the symptoms of athlete's foot in humans because it
is actually consuming the tissue around the foot. However, parasitism does not always involve
one organism directly consuming the other. In many cases, such as with tapeworms, the parasite
simply "steals" some of the food that is being digested by the host, and, among parasitic plant
species, the strangler fig of the tropical rainforest doesn't consume any nutrition obtained by its
host: it simply out-competes its host for light.
o Malaria is a wonderful example of the incredibly complex and specific nature of many hostparasite relationships. While there are similar diseases that affecting other species, the cause of
the disease in humans, several species of protists from the genus Plasmodium, are, with perhaps
one exception, entirely specific to their human and the Anopheles mosquito hosts.
Microbes in the Rainforest
The tropical rainforests are the richest places in the world in terms of biodiversity. A larger variety of animals
and plants live here than anywhere else. The same is true in microbiological terms as well. As with the
animals and plants of the rainforest, most have never been studied scientifically. They do not even have
scientific names! Discoveries of new living species are being made all the time by rainforest researchers.
Many of the new creatures and plants look interesting and their behavior and lifestyles are fascinating, so they
deserve to be preserved and cared for if only for this reason. But rainforest organisms have also been found to
possess other amazing properties that are of potential benefit to mankind. Rubber, medical products and
treatments, food-stuffs such as potatoes, chocolate and spices all originate from the rainforests. New
discoveries are being made regularly. The microorganisms are at the bottom of the food chain. So what types
of microbes inhabit the rainforest?
The rainforests are home to an enormous range of fungi, protists, algae and bacteria. Many diseases also
originate in the rainforests, caused not only by bacteria and viruses, but also by protists. These include some of
the most dangerous and frightening - malaria, yellow fever, ebola and HIV, for instance.
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Where Are Microbes Found in the Rainforest?
Generally, microbes are found in the lower levels of the rainforest near the ground. The moss layer that grows
in trees and exposed rocks, shade-tolerant mosses, lichens and fungi. Below this is the litter layer which
consists of dead vegetation (leaves, branches, twigs), dead animals (mostly insects) and feces, though this is in
small quantities compared with the other matter. Under this is a humus layer, where worms and other
invertebrate animals feed and turn over the matter. Also here are billions of bacteria and micro fungi that
decompose the litter (detritus) and recycle its nutrients for the community. This layer blends into the soil layer,
which consists of inorganic clays, sand, or rock. Overall the organically active humus layer is just a few
centimeters at most. Rainforest bacteria and fungi are extremely efficient workers! Here’s a summary:
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bacteria and viruses live in the humus and soil
bacteria live in water - ponds, streams and rivers
fungi and molds live on dead matter - animals, wood and other plant remains - and underground
protists live in water, on plants and animals and in the soil
bacteria and viruses live in animals and plants
Interactions of Microbes and the Rainforest
1. Mycorrhizae – Fungi play a significant role in keeping the mineral and nutrient cycles going in all
terrestrial ecosystems, but they are particularly important members of the web of life in the rainforests.
Without fungi, the lush tropical rainforests would become barren wastelands. One might assume that
the soil in the rainforest is very rich and lush, but this is not true – the soil is actually nutrient-depleted
due to the high rate of decomposition by microbes (due to increased temperatures and high moisture).
But even though nutrients are released faster, the rain quickly washes them away. The reason such lush
plant life can be supported in nutrient-deficient soil is because of the microbes! One secret rests in the
key partnerships between the plants and a group of fungi called mycorrhizae, which are a symbiotic
relationship between a fungus and the roots of a plant. These partnerships are so intimate that the fungi
actually become a part of the physical structure of the plant root. The plant and the mycorrhizae each
clearly benefit from their partnership. The fungus roots serve as nutrient scavengers. As dead material
falls to the forest floor, many different kinds of fungi and bacteria participate in its decomposition,
breaking the organic material into smaller and smaller pieces for reuse. Mycorrhizae help both to
decompose material and to quickly sequester key elements like phosphorus and nitrogen inside their
own cells. This rapid “snatching” of nutrients keeps the rain from leaching them from the soil, and the
fungus then transfer the nutrients directly to the plant root. In exchange, the plant provides a safe haven
from the mycorrhizae’s fungal and bacterial predators, as well as additional nutrients, such as glucose
and vitamins, that the fungus needs to grow. Today, 98% of all plants have some sort of mycorrhizal
partnership.
2. Decay - In a "forest system" nothing is wasted. Plants are constantly shedding leaves and bark which
then mix with the excreta of living forest animals and the carcasses of dead ones to form a rich layer of
humus on the forest floor. Micro-organisms, insects and fungi break down this humus and convert it into
nutrients for the soil. Through the soil, with the help of water, these nutrients are taken up, absorbed
through the roots of the trees and plants, nourishing them, which in turn provides food and shelter for
birds and animals. So the process of decay, recycling and renewal goes on.
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3. Symbioses – there are many partnerships in the rainforest that are important in the transfer of energy
and nutrients in the web of life. In a mature forest, almost all photosynthesis is conducted high in the
treetops, in the canopy. This is because sunlight can’t penetrate much below the dense topmost layers of
leaves. Since the majority of the energy stores are overhead, it is important for the forest’s diverse
populations of living creatures to find a way to reach this resource. One significant way in which this
vast biologic storehouse of energy is transferred to other living creatures is through some important
partnerships between microbes and insects. Below are a few:
a. Leaf-Cutter Ants – these ants are responsible for transferring as much as 1/3 of the carbonbased energy stored by the leaves in the canopy to the forest floor. This happens due to a fungus
that the ants cultivate underground. The ants bring the leaves from the canopy to the fungus in
their underground nests, and the fungus decomposes the leaves and makes the nutrients and
energy available to the ants. The fungus in return depends on the ants to keep predators at bay
and the food supply steady. The ants even carry a special kind of bacteria, Streptomyces, on their
chest, which produces a natural antibiotic that will kill fungal predators!
b. Caterpillars – caterpillars are also important in transferring stored energy from the treetops to
the rainforest floor! Called “cows of the canopies”, they feast on leaves from the canopy of the
rainforest. Just like cows eating grass, the caterpillars cannot digest the leaves without help from
a fungus. The fungi live in the caterpillar gut and convert the energy into a form usable for the
caterpillar and the fungus.
c. Termites - In civilization, termites are one of the worst pests that we can imagine. However, in
nature they play an important role in the decomposition of plant material. Termites have bacteria
in their gut that allow them to digest cellulose and thereby recycling plant material. In additional
because of their large biomass, they also serve as a food source for a number of other species of
animals in the rainforest.
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