Bacterial Diversity
Prokaryotes represent a broad group of organisms that for
many years were classified by R.H. Whittaker in a five
kingdoms system as Monerans. The five-kingdom system,
proposed in 1968, has become a popular standard and with
some refinement is still used in many works, or forms the
basis for newer multi-kingdom systems.
The Monerans include all of the prokaryotic cells and
reflects collectively close to 4 billion years of
evolution. Until recently (the last 10 – 20 years)
scientist (biologists) were restricted in the means by
which they could organize or relate these organisms in a
meaningful context. And yet it is fair to say that they
have been for practical purposes fairly successful.
The classical approach to prokaryote identification relied
on three criteria.
1 – shape of cell, and colony morphology
2 – nutritional capabilities
3 – staining properties
Without much more to go on these properties were used with
a fair amount of sophistication in order to identify an
organism. More recently, Carl Woese, at the University of
Illinois, embraced a comprehensive molecular study that has
shed a tremendous amount of light upon our understanding of
bacterial diversity and evolutionary relatedness. The term
molecular systematics uses molecular analysis in order to
organize and arrange different organisms in an evolutionary
context.
Molecular systematic approaches have resulted in a new
paradigm that employs a new and more inclusive level in the
hierarchical scheme used by biologist for purposes of
classification. This higher order level is the domain.
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Interestingly, all of the eukaryotic organisms that were
once organized within the four kingdoms (protists, plants,
animals and fungi) are now represented by a single domain,
the Eukarya. The prokaryotes, which originally were
organized into a single kingdom, monara, have now been
expanded to include two separate domains. These two domains
are identified the Eubacteria and the Archaea.
Part Ahttp://www.uphs.upenn.edu/bugdrug/antibiotic_manual/Gram1.h
tm
The web page cited discusses the culture and identification
of infectious agents.
Read through these pages and try to answer some of these
basic questions.
Who first developed the Gram stain?
What are the two major groups identified by this method of
staining?
What does Gram staining rely on?
What are some organisms that do not readily stain with the
gram stain?
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http://www.uphs.upenn.edu/bugdrug/antibiotic_manual/Gram3.h
tm
Identify some of major gram-positive organisms.
Identify some of the major gram-negative organisms.
Now go to http://pathmicro.med.sc.edu/fox/culture.htm and
consider the molecular analysis described?
Part B.
Each group of organisms has signature sequences, regions of
its SSU-rRNA (this is RNA associated with the small subunit
of the ribosome) that have unique nucleotide sequences
acquired by an accumulation of mutations in the ancestor of
that taxonomic group. These can be domain-specific
sequences at comparable locations in ribosomal RNA or other
nucleic acids. They can even be species specific.
Analysis of what important molecule is used for as the
“gold standard” for species classification.
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How is one able to get this information from organisms that
are not easily cultured in the laboratory?
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http://euarch.blogspot.com/2007/11/archaea.html
In this unit you will explore the some of the major clades
of each of these groups.
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The two major prokaryotic domains resulting from the work
of Carl Woese are the Eubacteria and the Archeabacteria.
Although both are prokaryotes they show some major
distinctions. Try to answer the following questions using
the following link. Click here for an excellent overview of
the Archaea and the Bacteria.
Sometimes the Archaea are referred to as the
“extremophiles” or lover of the extremes.
These are further divided into major phyla. What are some
of the major groupings or phyla represented in the Archea?
How is the cell wall of the Archaea different from the true
bacteria? For example, what does it lack? What contributes
to its capacity to withstand extreme conditions?
The Eubacteria or true bacteria are divided into a number
of major clades:
Proteobacteria
This large and diverse clade of gram-negative bacteria
includes photoautotrophs, chemoautotrophs, and
heterotrophs. Proteobacteria include both anaerobic and
aerobic species. Molecular systematists recognize three to
five major subgroups of proteobacterial species depending
on whose system you are reading.
I. The purple bacteria include photo-autotrophic and photoheterotrophic bacteria. Many of which contain
bacteriochlorophylls located in membrane invaginations.
Many species are obligate anaerobes and are found in mud,
ponds, lakes and sediment.
The ancestral bacterium that evolved into mitochondria
through endosymbiosis is thought to be a relative of the
purple non sulfur bacteria. This conclusion is based on
similar metabolic features of mitochondria and purple non
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sulfur bacteria and on comparisons of the base sequences in
their 16S rRNAs.
II. Next, there are the chemoautotrophic proteobacteria.
Many of these organisms play key ecological roles in
nitrogen metabolism . They can be free living or symbionts.
Rhizobium which is found in the root nodules of leguminous
plants such as alfalfa, pea and clover and Agrobacterium
tumerfacians, which is an important organism adapted by
researchers as a tool for gene transfer in dicots.
III. The chemoheterotrophic bacteria include the enterics,
which are important residents of the intestinal flora of
animals. They include E. coli, Shigella dysenteriae and
Salmonella.
Other organisms included in the proteobactera include the
myxobacxteria and bdellovibrios
The Myxobacteria form the most elaborate colonies of all
prokaryotes. The cells secrete a slimy ooze which permits
them to glide through soil. Under certain conditions of
stress they can form a "fruiting" body, which may be
brightly colored and as large as a millimeter in diameter.
The fruiting body releases spores that will become active
in favorable environments.
Another proteobacterim includes bdellovibrios. These are
predators that attack other bacteria. A bdellovibrio canl
drill boring into its prey by spinning at relatively very
high speeds.
Major clades of Eubacteria other than the proteobacteria
include:
Clamidyas - These parasites can survive only within the
cells of animals, depending on their hosts for resources as
basic as ATP. The gram-negative walls of chlamydias are
unusual among bacteria in that they lack peptidoglycan. One
species, Chlamydia trachomatis , is the most common cause
of blindness in the world and also causes nongonococcal
urethritis, the most common sexually transmitted disease
(STD) in the United States.
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Spirochetes - Rotation of internal flagellum-like filaments
produces a corkscrewlike movement. Many spirochetes are
free- living, but the group also includes some notorious
pathogens: Treponema pallidum causes the STD syphilis, and
Borrelia burgdorferi is the pathogen of Lyme disease.
Gram positive bacteria
Many mycoplasmas are soil bacteria, one species of
mycoplasma causes "walking pneumonia" in humans.
Which species is responsible for "walking pneumonia" in
humans?
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How many genes are found in the mycoplasma?
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How dos this compare with the genome of Escherchia coli?
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Actinomycetes – These are a large group of gram positive
bacteria that take on a filimentous phenotype. Some are
branched forms and superficially resemble molds.
The resemblance of fungi and the filamentous forms of
actinomycetes is an example of
__________________ evolution between the prokaryotes and
the eukaryotes in the soil environment.
Actinomycetes and streptomycetes are associated with
insects and provide a rich source of antibiotics. This fact
has not escaped the attention of the pharmaceutical
companies. Actinomycetes are the primary source of which
antibiotic?
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Actinomycetes such as Streptomyces have a world-wide
distribution in soils. They are important in aerobic
decomposition of organic compounds and have an important
role in biodegradation and the carbon cycle. Also included
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with the gram positive bacteria are Bacillus and
Clostridium; anthrax is caused by Bacillus anthracis,;
Clostridium botulinum produces the toxin that causes the
potentially fatal disease botulism. Staphylococcus
associated with skin infections, Streptococcus, is the
agent of strep throat, and the mycoplamas which are the
smallest of all known cells.
The pyogenic cocci (pyogenic refers to bacterial infections
that make pus or form abscesses.)
Which organisms are responsible for producing 1/3 of all
human infections?
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Cyanobacteria - These photoautotrophs are the only
prokaryotes with plantlike, oxygenic photosynthesis.
Chloroplasts evolved from a cyanobacterium. They provide
enormous amounts of food for freshwater and marine
ecosystems and play important ecological roles in global
nitrogen, carbon and oxygen cycles. Some filamentous
colonies like Anabanea have cells specialized for nitrogen
fixation.
What is the name of the specialized cells that are able to
fix nitrogen?
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What is the name of the cyanobacterium that is the leading
candidate for the type of bacterium that might have
undergone endosymbiotic events that led to the development
of the plant chloroplast.
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These structures are layered chalk deposits, which exhibit
a continuous geologic record covering 2.7 billion years.
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How do cyanobacteria maintain buoyancy in the aquatic
environments?
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Summer 2008 Workshop in Biology and Multimedia for High School
Teachers
Harvard University Life Sciences – HHMI Outreach Program