Chapter 2
Chapter 2The Microbial World
Some Basic Biological Principles
Cell TheoryRobert Hooke coined the term cell in 1665, based on
his initial microscopic observations of cork. These observations
ultimately gave rise to the cell theory, as postulated by
Schleiden, Schwann, and Virchow, about two centuries later. The
major points of the cell theory are as follows:1. All organisms are
composed of a fundamental unit, the cell.
2. All organisms are unicellular or multicellular.
3. All cells are fundamentally alike regarding their structure
and metabolism.
4. Cells only arise from preexisting cells (life begets
life).
Life begets life is a refutation of the once popular idea of
spontaneous generation, a doctrine that proposed life could arise
from non-living components (which was disproved in the late 1800s).
Viruses and prions are not composed of cells; they are acellular or
subcellular infectious agents. Neither of these two agents is
considered to be alive by most biologists.Metabolic DiversityLiving
things possess several attributes commonly associated with life, as
summarized in Table 2.1. The attributes common to life include the
following: being composed of one or more cells, requiring energy,
being able to reproduce, being able to respond to stimuli, and
having the ability to grow.Most cells obtain energy through a
complex series of biochemical reactions termed metabolism. Cells
metabolize organic compounds (proteins, fats, and carbohydrates) in
food and capture the energy stored in chemical bonds by forming
high-energy bonds in adenosine triphosphate (ATP). Most microbes
are heterotrophs, which require an organic source of energy. Some
microbes and plants, the autotrophs, do not need to extract energy
from organic compounds. Photosynthetic autotrophs obtain energy
directly from the sun, while chemosynthetic autotrophs obtain their
energy from inorganic compounds. Autotrophs manufacture organic
compounds, and some photosynthetic autotrophs produce oxygen (O2),
thus, heterotrophs depend upon autotrophs for their energy needs
and as a source of carbon (Figure 2.1).Requirement for
OxygenMicrobes have diverse requirements for O2. Aerobes require O2
for metabolism, while anaerobes do not. Many anaerobic microbes are
killed by O2. Bacterial facultative anaerobes actually grow better
in the presence of O2, but they can grow in its absence. In
clinical microbiology, knowledge of the O2 requirements of bacteria
is required, as any bacteria suspected of being anaerobes must be
transported and cultured under anaerobic conditions (Figure
2.2).Genetic Information The genetic information of all cells is
stored in molecules of deoxyribonucleic acid (DNA). Genes are
segments of the DNA molecule. Each type of organism has its genetic
characteristics encoded in DNA molecules that confer its species
identity. Thus, DNA acts as the hereditary material for cellular
organisms (and DNA viruses).What Makes a Microbe?
Algae and some fungi are macroscopic; hence, microscopic is not
an absolute characteristic of microbes. Similarly, the term
unicellular does not apply to those algae and fungi that are
macroscopic and clearly must be multicellular. There are even
macroscopic bacteria, like the recently discovered monster bacteria
Epulopiscium shelsoni and Thiomargarita namibiensis (Box 2.1).
Microbes are sometimes described as simple because many consist of
only a single cell or are less than a cell (viruses and prions).
Consider, however, that this single cell must fulll all the
functions of life. Hence, single-celled organisms, and even those
multicellular organisms without specialized cells, are simple only
in the sense of numbers and not in a physiological sense.Microbe,
or microorganism, is a term of convenience used to describe
biological agents that are generally too small to be seen without
using a microscope. Some consider microbes to be organisms that are
at a level of organization below tissues (Figure 2.4). This
organizational hierarchy is summarized as follows: subcellular
cells tissues organs organ systems.
All microbes are unicellular or multicellular, but devoid of
tissues. Prions and viruses can be properly placed at the acellular
or subcellular level and are at the threshold of life.
Procaryotic and Eucaryotic Cells
Biologists divide all life into two distinct types of cells,
procaryotic and eucaryotic. Procaryotes have a simpler structure
than eucaryotic cells and are primarily distinguished by lack of a
true membrane-bound nucleus. Instead, bacteria possess a DNA-rich
region in the cytoplasmthe nucleoid. Further, in procaryotic cells
there are no membrane-bound organelles at all, in contrast to the
cellular anatomy of eucaryotic cells (Table 2.2 and Figure 2.5).
Bacteria are procaryotic microorganisms; protozoans, algae, fungi,
and all other forms of life (except viruses and prions) are
composed of eucaryotic cells.Microbial Evolution and DiversityIn
the 1700s, the botanist Carolus Linnaeus classied all life into
either the plant or the animal kingdom. When bacteria were
discovered they were placed with plants (probably because they had
a cell wall). Taxonomy, the science of classication, has become
more and more complex over the intervening years. Ernst Haeckel
(1866) proposed a three- kingdom systemanimals, plants, and
Protista (which included some microbes). In 1969 a ve-kingdom
system was proposed by Robert Whittaker, which became accepted by
most biologists. The five kingdoms were Monera (bacteria), Protista
(protozoans and unicellular algae), Fungi, Animalia, and Plantae
(Figure 2.6). In 1990 Carl Woese, along with Otto Kandler and Mark
L. Wheelis, proposed a novel classification scheme (based on rRNA
analysis) that placed all life into three super kingdoms or
domainsBacteria, Archaea and Eucarya (Figure 2.7). All three arose
from a single common ancestor, from which the prokaryotic Bacteria
and Archaea first diverged, followed by the eucaryotes (Eucarya).
These domains all differ significantly from each other in chemical
composition and other characteristics (Table 2.3). No matter the
classication scheme, bacteria were the rst forms of life on Earth.
Fossilized bacteria have been discovered in stromatolites (stratied
rocks dating back 3.5 billion to 3.8 billion years, in Earths 4.6
billion year history). Earths ancient atmosphere is thought to have
been devoid of oxygen and would not have supported many familiar
life forms. However, about 2 billion years ago, photosynthetic
microbes evolved to use sunlight, water and carbon dioxide to
produce oxygen and carbohydrates.
Bacteria are biochemically diverse and have lled every known
ecological niche. Some estimate that fewer than 2% of bacterial
species have been identified and even fewer have been cultured.
Archaea continue to be found in environments once considered too
extreme or too harsh for life at any level. Some of these bacterial
extremophiles cannot be cultured with existing techniques; evidence
of their existence is deduced from their RNA found in environmental
samples. Hyperthermophiles (heat lovers), have been discovered
which grow best at temperatures above 100C. Pyrococcus furiosus
lives in boiling water bubbling from undersea hot vents and cant
grow in temperatures below 70C (Figure 2.8a). Other extremophiles,
the psychrophiles, may grow at temperatures below 20C and thrive in
Arctic and Antarctic environments (Figure 2.8b). Some extreme
halophiles (salt lovers) can only grow in high salinity, as found
in the Dead Sea (Figure 2.9). Archaea have even been found, which,
as a byproduct of their metabolism, produce methane (natural gas).
Given their unusual growth requirements, no Archaea have been found
to cause disease in humans.
A comprehensive survey of microbial life on Earth is underway.
Microbes were the first life forms on this planet, and how they
arose is of great interest to science. A bacterium arising from a
primordial soup is one common suggestion for lifes origin, and a
few hypothesize that Earth was seeded by microbes from Mars (an
explanation that is intriguing, but lacks hard evidence at this
point).Introducing the MicrobesAlthough there is no universally
accepted definition for microbes, much is known about their biology
and biochemical composition, as summarized in Table 2.4. Acellular
and unicellular microbes extend over a range of sizes from
nanometers (billionths of a meter) to micrometers (millionths of a
meter), as depicted in Figure 2.11.
PrionsPrions are infectious protein particles, and like viruses
they are acellular. However, unlike viruses, they lack nucleic acid
(i.e., a DNA or RNA genome). Prions reproduce in a unique way from
a normal protein commonly found in the brainan infectious prion
molecule physically interacts with the normal protein, converting
it to the infectious form. This cycle continues, amplifying the
infectious prion particles until a neurological disease process
results in humans and other mammals (e.g., BSE or mad cow
disease).VirusesViruses are acellular infectious agents containing
genomic RNA or DNA, never both. They are obligate intracellular
parasitesrequiring a living cell for their own replication. Viruses
must co-op the molecular machinery of the host cell for their own
synthesis and frequently kill the cell they infect. Viruses are
submicroscopic, thus requiring an electron microscope for their
visualization (Figure 2.12).BacteriaBacteria are the best-known
microbes (Figure 2.13). They are unicellular, procaryotic cells;
most possess a cell wall (except for the mycoplasmas). Bacteria can
be seen with a light microscope, and they replicate asexually, by
binary fission. Metabolically, many bacteria are heterotrophs
(using organic compounds as an energy source). Other bacteria are
autotrophs, using the sun or inorganic molecules, as a source of
energy. Because of this metabolic flexibility, bacteria are found
ubiquitously in nature. Although a few bacterial species are
pathogenic for humans, the vast majority are harmless. Moreover,
all other life depends upon bacteria for its
existence.Protozoans
Protozoans are unicellular, heterotrophic, eukaryotes, and they
are traditionally classified by their means of locomotion. Most are
harmless microbes; however, some of the best-known and most
significant human diseases are caused by protozoans (e.g., malaria,
sleeping sickness, amebic dysentery, etc.).AlgaeAlgae are
eukaryotic autotrophs that generate oxygen during photosynthesis.
Dinoflagellates and diatoms are two types of unicellular algae
(plankton), which are a primary source of food for larger
heterotrophic organisms in the worlds oceans and lakes. Algae are
important to the planets ecology. While none infect humans, some
marine algae (like the dinoflagellate Gymnodinium breve) produce
neurotoxins that are capable of harming marine life and any humans
who consume algae-contaminated fish and shellfish. Red tide is the
name for a bloom of toxic marine dinoflagellates (the
dinoflagellates in a bloom grow to such high density, that they
literally turn the tide red).FungiFungi are non-motile,
heterotrophic eucaryotes, possessing a cell wall and may reproduce
sexually or asexually (Figure 2.16). They are commonly subdivided
into the groups yeasts or molds. Yeasts are unicellular cells, much
larger than bacteria. Molds are the more common type; they are
multicellular and form a tangled mass of long, branched filaments,
termed hyphae. A mass of hyphae is visible to the unaided eye. Like
other microbes, fungi are usually harmless or even beneficial, but
a relative few are pathogenic for humans. Some fungi are
opportunistic pathogens, only causing disease in those with a
depressed immune system, as in the case of AIDS.
Viruses fascinate me. How is that they are not living organisms?
Do you have an idea how did they evolve from other organisms? I was
thinking that they probably evolved from the mitochondria, is it
possible?Answer 1:Viruses are not classified as being alive because
they dont have their own machinery for reproducing. They can only
take over the machinery of cells, turning them into virus
factories. But not everyone agrees with this system. Someone might
say, Hey, parasites need to reproduce inside other organisms, but
theyre alive. That would be a reasonable argument for saying that
viruses are a form of life. I tell my students that people like to
make nice neat categories, but the natural world almost never fits
into them. Putting things into categories can be helpful, but we
have to remember that the categories are usually artificial and
should not get in the way of understanding all of the amazing
diversity of the world.
Im really impressed that you thought about the mitochondria as a
possible ancestor for viruses. They best story we have today is
that mitochondria were once free-living bacteria. Did viruses
evolve from bacteria? Maybe. It is difficult to say because it may
have happened 3 billion years ago, and DNA just doesnt last that
long. Viruses dont seem to fossilize well, either. Since bacteria
were around before the cells that we call eukaryotic (plant,
animal, fungal, and protist cells), that may be what happened. Some
scientists think that different groups of viruses evolved
independently, maybe some even came from eukaryotic cells, and some
from bacterial cells.
If viruses are basically parasites that evolved from living
bacteria, would that be another argument for saying that they are a
type of life?
We still know very little about viruses and bacteria, compared
to what we know about multicellular organisms. You may want to
consider a career in microbiology if you want to explore them.
Thanks for asking,
Answer 2:Viruses fascinate me too, so I actually wrote an
article all about them. Feel free to check it out here:
viruses originsI think it will answer your questions (and maybe
raise some more!). There's actually a lot of debate over whether
they are "alive" or not, and some scientists think that we might
have evolved from viruses, or something like them! Viruses have
definitely been around for a very long time. See the article for
more details.
Answer 3:Viruses are not considered "alive" because they lack
many of the properties that scientists associate with living
organisms. Primarily, they lack the ability to reproduce without
the aid of a host cell, and don't use the typical cell- division
approach to replication. Essentially, however, this is just how
scientists have defined the word. If viruses were classified as
living, other types of self-replicating genes, proteins, and
molecules would make the list as well.
There are a few theories on the origin of viruses. Since there
is no historical record of the earliest viruses, the only evidence
available is from current species. Indeed, one theory suggests that
viruses may have arisen from parasitic cells which lost their
cellular structure through evolution. However, there isn't a lot of
evidence from current cells that shows this type of transition is
possible. Another theory is that they evolved along with living
cells, from genes or proteins that happened to be self-replicating.
It would seem that since the spectrum of viruses around today is so
wide, they likely evolved through many different pathways.
Answer 4:Yes, viruses are interesting. Viruses don't fit the
definition of life, but they're certainly not dead either! They're
an interesting example of how we can't really separate stuff into 2
simple categories - Living and Non-living. Viruses seem to be in
between those 2 categories.
And the question gets even more interesting when scientists talk
about life on other planets, because this might be very different
from life on earth. They call it "Life as we Don't know it."
Some scientists are still debating about What is Life? In fact,
I wrote a little article about it last fall, for a collection of
journal articles all about that subject.
I think viruses probably evolved from simple cells such as
bacteria and archaea that don't have a nucleus. Keep asking
questions!
Best wishes,
Answer 5:Excellent, viruses ARE fascinating! A virus particle is
made up of 2 main parts: genetic material (either RNA or DNA) and a
coat that is made up of protein and sometimes lipids (fats) that
protect the genetic material. A virus can live outside of a host
cell but it can not reproduce without a host!
Scientists argue a lot about whether viruses are in fact living
organisms or just organic structures interacting with living
organisms. Some properties of viruses make them seem alive like the
fact that they have genetic material and that they make copies of
themselves to reproduce. On the other hand, people will argue that
viruses do not have any structure to their cells (which even simple
living organisms have), they do not have the ability to make their
own chemical products and need a host cell to do that for them and
that is why they can not reproduce without a host cell. This debate
is not going to be settled anytime soon, but you can decide for
yourself whether you think viruses are living or not!
Where viruses originated is also something that scientists
disagree about. There are 3 main ideas for how viruses evolved in
the first place. 1) Viruses could have started out as bacteria and
just lost all the genes they needed to survive on their own. 2)
Viruses could have begun as small pieces of genetic material that
escaped from a larger organism and infected another. 3) Viruses
simply started out as viruses when proteins and genetic material
mixed and that these particles have been living this way (infecting
living cells to replicate) for billions of years, ever since life
itself began. Viruses do not form fossils, which makes it really
hard for scientists to determine where exactly they came from.
For some more information on viruses, check out these two
links:
virus1virus2
Answer 6:Viruses are very strange organisms. They are not really
considered to be living creatures. This is because they are not
capable of replicating themselves on their own. Viruses need to
infect another cell in order to replicate. This is because they do
not have all the genes necessary for replication. Viruses are made
up of their genetic material and a few proteins, which is
encapsulated in a protein coat. They attach to a living cell and
inject their nucleic acids (and sometimes release their proteins as
well) into a cell. The viral nucleic acids then takes over the
cell's own proteins and makes the cell replicate the viral genetic
material. Once the virus has replicated its genome and made the
proteins for its coat, it will assemble and then cause its host
cell to burst open. This releases a new set of viruses to infect
other cells. Thus, without another living cell, viruses cannot
replicate and spread.
The evolutionary origin of viruses is something that is unknown.
It is possible that viruses were actually cellular organisms once,
which became adapted to an intracellular life style. This is
similar to how mitochondria are believed to have evolved. However,
it is unlikely that viruses evolved directly from mitochondria.
Viruses were likely around long before mitochondria existed.
Another theory is that viruses originated from genetic material
that co-evolved with cellular organisms to become separate from the
cellular genome and eventually became more complex, resulting in
the virus particles we know today.
Answer 7:Viruses lack the cellular machinery to be able to
reproduce themselves; without using the genetic code of a cell as
their host, the genetic information contained within a virus is
meaningless. An analogy I could make is that viruses are basically
software, and software requires hardware (in this case, a cell) to
run on. For this reason, most definitions of life do not identify
viruses as living organisms, because they aren't actually
*organisms*.
This said, viruses do possess a lot of life- like qualities,
including the ability to carry information, reproduce (with help),
and evolve under natural selection. Saying that viruses aren't
living in some sense is also missing the point.
Viruses are strands of DNA or RNA contained within protein
sheathes and seem to be genetically related to the organisms that
they infect, as if they evolved from their hosts' genomes. This
means that viruses probably evolved multiple times from different
ancestors. I don't know of any viruses thought to have evolved from
mitochondria, or that can even infect mitochondria, but I see no
reason why it isn't possible that some could have.
ClickHereto return to the search form.
http://scienceline.ucsb.edu/getkey.php?key=3316Viruses are in
the news. You've probably heard about Avian Flu, West Nile Virus,
HIV, and SARS. You probably know about chicken pox, measles,
rabies, or polio. I'm sure you've had a "cold." Your nose is runny,
you sneeze a lot and have a sore throat. Your eyes might be red,
and you might feel sore all over and have a fever. A "cold" and
many other diseases are caused by a tiny,microscopicliving thing
called a virus.Photo. Courtesyof the MicrobeLibrary.org; Jean-Yves
Sgro, University of Wisconsin.What is a virus?A virus is amicrobe.
A microbe is a tiny one-celledliving organism, too small to be seen
with just your eyes. Othertypesof microbes are: bacteria, protozoa,
and fungi. Some people call microbes "germs".
Not all microbes are bad... Many bacteria live with us all the
time, and help us do amazing things like make yogurt, pickles,
cheese, and even break down some garbage. Microbes are all around
us. They exist on our skin, and on the skin of
fruit.http://www.microbeworld.org/htm/aboutmicro/microbes/types/bacteria.htm
What is agerm?
Here is aphotoof one type of virus.This photogalleryhas even
more images.
Discoveryof the VirusHow bigis a virus?
How does a virus infect you?Viruses are everywhere but they need
to get inside a human, an animal or a plant to make them sick. In
fact, they must invade a cell, called ahostcell, in order to grow
and reproduce. Most can't survive long unless they're in a living
host. Once inside, though, they can spread and make other people
sick. Some can live awhile on something like a desk, or doorknob so
it's important for you to wash your handsregularly so you don't
becomeinfected!Viruses can enter us through the nose, mouth or
breaks in the skin.
Viruses are made of a small collection ofgenetic material(DNA or
RNA) encased in a protective protein coat called a capsid. Take a
peek at what'sinside a virus...
Is a virus ALIVE? There is some debate about this. However, most
scientists say they are not alive because they cannot grow or
reproduce on their own.They need a host cell to multiply.
Then what happens?Once inside a host cell they follow these
basic steps in order to fool the host cell into making make copies
of the virus that might then infect living organisms. This is
called the lytic cycle.The Lytic Cycle- or how a virus fools a host
cell into making more virusesA virus attaches to a host cell. (All
viruses have some type of protein on the outside coat that
"recognizes" the proper host cell.)
The enzymes make parts for more new virus particles
The virus, or a virus particle, enters or releases itsgenetic
instructionsinto the host cell
The new particles assemble the parts into new viruses.
The injected genetic material gives instructions to the host
cell's enzymes
The new virus particles leave the host cell, ready to infect
other cells
Discover more aboutviruses,bacteria,protozoa,fungi.
Your body's Immune System to the rescue!!!Your body has a
defense against viruses. It is called theImmune System.If a virus
makes it past your tough skin, or the sticky mucus and little hairs
called cilia lining your breathing tube then this system takes
over.Here's how it works...The immune system is an organization of
different types of cells, tissues and enzymes work together to
identify and eliminate all invading substances in your body. Each
part of the immune system has it's own specialized job.White blood
cellsare your main defense. They patrol your body. When they come
across anantigen, they produce anantibodythat only works to fight
against that particular antigen. Some antibodies destroy antigens
while others make it easier for white blood cells to destroy the
antigen.Trillions and trillions of white blood cells gobble the
enemy. Sometimes, though, your body needs help from the medicines
doctors give you.One of these medicines is called avaccine. Learn
about vaccineshere.
There are hundreds of different kinds of viruses, and theyre
constantly changing. You can't catch the same virus teice.
Theimmune system can remember the response later if the foreign
substance invades the body again, and it gets right to work
http://idahoptv.org/dialogue4kids/season8/viruses/facts.cfmVirus
A virus is a microscopic particle that can infect the cells of a
biological organism.
Viruses can only replicate themselves by infecting a host cell
and therefore cannot reproduce on their own.
At the most basic level, viruses consist of genetic material
contained within a protective protein coat called a capsid; the
existence of both genetic material and protein distinguishes them
from other virus-like particles such as prions and viroids.
They infect a wide variety of organisms: both eukaryotes
(animals, fungi and plants) and prokaryotes (bacteria).
A virus that infects bacteria is known as a bacteriophage, often
shortened to phage.
The study of viruses is known as virology, and those who study
viruses are known as virologists.
It has been argued extensively whether viruses are living
organisms.
Most virologists consider them non-living, as they do not meet
all the criteria of the generally accepted definition of life.
They are similar to obligate intracellular parasites as they
lack the means for self-reproduction outside a host cell, but
unlike parasites, viruses are generally not considered to be true
living organisms.
A primary reason is that viruses do not possess a cell membrane
or metabolise on their own - characteristics of all living
organisms.
Examples of common human diseases caused by viruses include the
common cold, the flu, chickenpox and cold sores.
Serious diseases such as Ebola, AIDS, bird flu and SARS are all
also caused by viruses.
http://www.sciencedaily.com/articles/v/virus.htm
