BSC 1011C
General Biology II
Dr. Graeme Lindbeck
glindbeck@valenciacollege.edu

Prokaryotes And The Origins of Metabolic Diversity

Outline

A. The World of Prokaryotes

1. They're (almost) everywhere! An overview of prokaryotic life

Prokaryotes were the earliest organisms on Earth and evolved alone for 1.5 billion years.

Today, prokaryotes still dominate the biosphere.

Their collective biomass outweighs all eukaryotes combined by at least tenfold.
More prokaryotes inhabit a handful of fertile soil or the mouth or skin of a human than the total number of people who have ever lived.

Prokarytes are wherever there is life and they thrive in habitats that are too cold, too hot, too salty, too acidic, or too alkaline for any eukaryote.

We hear most about the minority of prokaryote species that cause serious illness.

During the 14th century, a bacterial disease known as bubonic plague, spread across Europe and killed about 25% of the human population.
Other types of diseases caused by bacteria include tuberculosis, cholera, many sexually transmissible diseases, and certain types of food poisoning.

However, more bacteria are benign or beneficial.

Bacteria in our intestines produce important vitamins.
Prokaryotes recycle carbon and other chemical elements between organic matter and the soil and atmosphere.

Prokaryotes often live in close association among themselves and with eukaryotes in symbiotic relationships.

Mitochondria and chloroplasts evolved from prokaryotes that became residents in larger host cells.

Modern prokaryotes are diverse in structure and in metabolism.

About 5,000 species of prokaryotes are known, but estimates of actual prokaryotic diversity range from about 400,000 to 4 million species.

2. Bacteria and archaea are the two main branches of prokaryote evolution

Molecular evidence accumulated over the last two decades has lead to the conclusion that there are two major branches of prokaryote evolution, not a single kingdom as in the five-kingdom system.

These two branches are the bacteria and the archaea.

The archaea inhabit extreme environments and differ from bacteria in many key structural, biochemical, and physiological characteristics.

Current taxonomy recognizes two prokaryotic domains: domain Bacteria and domain Archaea.

A domain is a taxonomic level about kingdom.
The rationale for this decision is that bacteria and archaea diverged so early in life and are so fundamentally different.
At the same time, they both are structurally organized at the prokaryotic level.

B. The Structure, Function, and Reproduction of Prokaryotes

Most prokaryotes are unicellular.

Some species may aggregate transiently or form true colonies, even extending to division of labor between specialized cell types.

The most common shapes among prokaryotes are spheres (cocci), rods (bacilli), and helices.

Most prokaryotes have diameters in the range of 1-5 um, compared to 10-100 m for most eukaryotic cells.

However, the largest prokaryote discovered so far has a diameter of 0.75 mm.
It is a sulfur-metabolizing marine bacterium from coastal sediments off Namibia.

1. Nearly all prokaryotes have a cell wall external to the plasma membrane

In nearly all prokaryotes, a cell wall maintains the shape of the cell, affords physical protection, and prevents the cell from bursting in a hypotonic environment.

Most bacterial cell walls contain peptidoglycan, a polymer of modified sugars cross-linked by short polypeptides.

The walls of archaea lack peptidoglycan.

The Gram stain is a valuable tool for identifying specific bacteria, based on differences in their cell walls.

Gram-positive bacteria have simpler cell walls, with large amounts of peptidoglycans.

Gram-negative bacteria have more complex cell walls and less peptidoglycan.

An outer membrane on the cell wall contains lipopolysaccharides, carbohydrates bonded to lipids.

Among pathogenic bacteria, gram-negative species are generally more threatening than gram-positive species.

The lipopolysaccharides on the walls are often toxic and the outer membrane protects the pathogens from the defenses of their hosts.
Gram-negative bacteria are commonly more resistant than gram-positive species to antibiotics because the outer membrane impedes entry of antibiotics.

Many antibiotics, including penicillins, inhibit the synthesis of cross-links in peptidoglycans, preventing the formation of a functional wall, particularly in gram-positive species.

These drugs are a very selective treatment because they cripple many species of bacteria without affecting humans and other eukaryotes, which do not synthesize peptidoglycans.

Many prokaryotes secrete another sticky protective layer, the capsule, outside the cell wall.

Capsules adhere the cells to their substratum.
They may increase resistance to host defenses.
They glue together the cells of those prokaryotes that live as colonies.

Another way for prokaryotes to adhere to one another or to the substratum is by surface appendages called pili.

Pili can fasten pathogenic bacteria to the mucous membranes of its host.
Some pili are specialized for holding two prokaryote cells together long enough to transfer DNA during conjugation.

2. Many prokaryotes are motile

About half of all prokaryotes are capable of directional movement.

The action of flagella, scattered over the entire surface or concentrated at one or both ends, is the most common method of movement.

The flagella of prokaryotes differ in structure and function from those of eukaryotes.

In a prokaryotic flagellum, chains of a globular protein wound in a tight spiral from a filament which is attached to another protein (the hook), and the basal apparatus.

Rotation of the filament is driven by the diffusion of protons into the cell through the basal apparatus after the protons have been actively transported by proton pumps in the plasma membrane.

A second motility mechanism is found in spirochetes, helical bacteria.

Two or more helical filaments under the cell wall are attached to a basal motor attached to the cell.
When the filaments rotate, the cell moves like a corkscrew.

A third mechanism occurs in cells that secrete a jet of slimy threads that anchors the cells to the substratum.

The cell glides along at the growing end of threads.

In a relatively uniform environment, a flagellated cell may wander randomly.

In a heterogenous environment, many prokaryotes are capable of taxis, movement toward or away from a stimulus.

With chemotaxis, binding between receptor cells on the surface and specific substances results in movement toward the source (positive chemotaxis) or away (negative chemotaxis).
Other prokaryotes can detect the presence of light (phototaxis) or magnetic fields.

3. The cellular and genomic organization of prokaryotes is fundamentally different from that of eukaryotes

Prokaryotic cells lack a nucleus enclosed by membranes.

The cells of prokaryotes also lack the other internal compartments bounded by membranes that are characteristic of eukaryotes.

Instead, prokaryotes used infolded regions of the plasma membrane to perform many metabolic functions, including cellular respiration and photosynthesis.

Prokaryotes have smaller, simpler genomes than eukaryotes.

On average, a prokaryote has only about one-thousandth as much DNA as a eukaryote.

Typically, the DNA is concentrated as a snarl of fibers in the nucleoid region.

The mass of fibers is actually the single prokaryotic chromosome, a double-stranded DNA molecule in the form of a ring.

There is very little protein associated with the DNA.

Prokaryotes may also have smaller rings of DNA, plasmids, that consist of only a few genes.

Prokaryotes can survive in most environments without their plasmids because essential functions are programmed by the chromosomes.
However, plasmids provide the cell genes for resistance to antibiotics, for metabolism of unusual nutrients, and other special contingencies.
Plasmids replicate independently of the chromosome and can be transferred between partners during conjugation.

Although the general processes for DNA replication and translation of mRNA into proteins are alike for eukaryotes and prokaryotes, some of the details differ.

For example, the prokaryotic ribosomes are slightly smaller than the eukaryotic version and differs in its protein and RNA content.
These differences are great enough that selective antibiotics, including tetracycline and chloramphenicol, can block protein synthesis in many prokaryotes but not in eukaryotes.

4. Populations of prokaryotes grow and adapt rapidly

Prokaryotes reproduce only asexually via binary fission, synthesizing DNA almost continuously.

A single cell in favorable conditions will produce a colony of offspring.

While lacking meiosis and sex as seen in eukarotes, prokaryotes have several mechanisms to combine genes between individuals.

In transformation, a cell can absorb and integrate fragments of DNA from their environment.
- This allows considerable genetic transfer between prokaryotes, even across species lines.
In conjugation, one cell directly transfers genes to another cell.
In transduction, viruses transfer genes between prokaryotes.

Lacking meiotic sex, mutation is the major source of genetic variation in prokaryotes.

With generation times in minutes or hours, prokaryotic populations can adapt very rapidly to environmental changes, as natural selection screens new mutations and novel genomes from gene transfer.

The word growth as applied to prokaryotes refers to multiplication of cells and population increases, rather than enlargement of individual cells.

Conditions for optimal growth vary according to species.

Variables include temperature, pH, salt concentrations, nutrient sources, among others.

In the absence of limiting resources, growth of prokaryotes is effectively geometric.

The number of cells doubles each generation.
Typical generation times range from 1-3 hours, but some species can double every 20 minutes in an optimal environment.

Prokaryotic growth in the laboratory and in nature is usually checked at some point.

The cells may exhaust some nutrient.
Alternatively, the colony poisons itself with an accumulation of metabolic waste.

Prokaryotes can also withstand harsh conditions.

Some bacteria form resistant cells, endospores.

In an endospore, a cell replicates its chromosome and surrounds one chromosome with a durable wall.
While the outer cell may disintegrate, an endospore, such as this anthrax endospore, dehydrates, does not metabolize, and stays protected by a thick, protective wall.

An endospore is resistant to all sort of trauma.

Endospores can survive lack of nutrients and water, extreme heat or cold, and most poisons.
Sterilization in an autoclave kills even endospores by heating them to 120^oC.
Endospores may be dormant for centuries or more.
When the environment becomes more hospitable, the endospore absorbs water and resumes growth.

In most environments, prokaryotes compete with other prokaryotes (and other microorganisms) for space and nutrients.

Many microorganisms release antibiotics, chemicals that inhibit the growth of other microorganisms (including certain prokaryotes, protists, and fungi).
Humans have learned to use some of these compounds to combat pathogenic bacteria.

C. Nutrition and Metabolic Diversity

1. Prokaryotes can be grouped into four categories according to how they obtain energy and carbon

Nutrition here refers to how an organism obtains energy and a carbon source from the environment to build the organic molecules of cells.

Species that use light energy are phototrophs.
Species that obtain energy from chemicals in their environment are chemotrophs.
Organisms that need only CO₂ as a carbon source are autotrophs.
Organisms that require at least one organic nutrient as a carbon source are heterotrophs.

These categories of energy source and carbon source can be combined to group prokaryotes according to four major modes of nutrition.

Photoautotrophs are photosynthetic organisms that harness light energy to drive the synthesis of organic compounds from carbon dioxide.

Among the photoautotrophic prokaryotes are the cyanobacteria.
Among the photosynthetic eukaryotes are plants and algae.

Chemoautotrophs need only CO2 as a carbon source, but they obtain energy by oxidizing inorganic substances, rather than light.

These substances include hydrogen sulfide (H₂S), ammonia (NH₃), and ferrous ions (Fe²⁺) among others.
This nutritional mode is unique to prokaryotes.

Photoheterotrophs use light to generate ATP but obtain their carbon in organic form.

This mode is restricted to prokaryotes.

Chemoheterotrophs must consume organic molecules for both energy and carbon.

This nutritional mode is found widely in prokaryotes, protists, fungi, animals, and even some parasitic plants.

The majority of known prokaryotes are chemoheterotrophs.

These include saprobes, decomposers that absorb nutrients from dead organisms, and parasites, which absorb nutrients from the body fluids of living hosts.
Some of these organisms (such as Lactobacillus) have very exacting nutritional requirements, while others (E. coli) are less specific in their requirements.
With such a diversity of chemoheterotrophs, almost any organic molecule, including petroleum, can serve as food for at least some species.
Those few classes or syntheticorganic compounds that cannot be broken down by bacteria are said to be nonbiodegradable.

Accessing nitrogen, an essential component of proteins and nucleic acids, is another facet of nutritional diversity among prokaryotes.

Eukaryotes are limited in the forms of nitrogen that they can use.
In contrast, diverse prokaryotes can metabolize most nitrogenous compounds.

Prokaryotes are responsible for the key steps in the cycling of nitrogen through ecosystems.

Some chemoautotrophic bacteria convert ammonium (NH₄⁺) to nitrite (NO₂^-).
Others "denitrify" nitrite or nitrate (NO₃^-) to N₂, returning N₂ gas to the atmosphere.
A diverse group of prokaryotes, including cyanobacteria, can use atmospheric N₂ directly.
During nitrogen fixation, they convert N₂ to NH₄⁺, making atmospheric nitrogen available to other organisms for incorporation into organic molecules.

Nitrogen fixing cyanobacteria are the most self-sufficient of all organisms.

They require only light energy, CO₂, N₂, water and some minerals to grow.

The presence of oxygen has a positive impact on the growth of some prokaryotes and a negative impact on the growth of others.

Obligate aerobes require O₂ for cellular respiration.
Facultative anerobes will use O₂ if present but can also grow by fermentation in an anaerobic environment.
Obligate anaerobes are poisoned by O₂ and use either fermentation or anaerobic respiration.
- In anaerobic respiration, inorganic molecules other than O₂ accept electrons from electron transport chains.

2. Photosynthesis evolved early in prokaryotic life

Early prokaryotes were faced with constantly changing physical and biological environments.

All of the major metabolic capabilities of prokaryotes, including photosynthesis, probably evolved early in the first billion years of life.
It seems reasonably that the very first prokaryotes were heterotrophs that obtained their energy and carbon molecules from the pool of organic molecules in the "primordial soup" of early Earth.

Glycolysis, which can extract energy from organic fuels to generate ATP in anaerobic environments, was probably one of the first metabolic pathways.

Presumably, heterotrophs depleted the supply of organic molecules in the environment.

Natural selection would have favored any prokaryote that could harness the energy of sunlight to drive the synthesis of ATP and generate reducing power to synthesize organic compounds from CO₂.

Photosynthetic groups are scattered among diverse branches of prokaryote phylogeny.

While it is possible that photosynthesis evolved several times independently, this seems unlikely because of the complex molecular machinery required.

The most reasonable or parsimonious hypothesis, is that photosynthesis evolved just once.
Heterotrophic groups represent a loss of photosynthetic ability during evolution.
Although the very first organisms may have been heterotrophs from which autotrophs evolved, the diversity of heterotrophs we observe today probably descended secondarily from photosynthetic ancestors.

The early evolution of cyanobacteria is also consistent with an early origin of photosynthesis.

Cyanobacteria are the only autotrophic prokaryotes that release O₂ by splitting water during the light reaction.
Geological evidence for the accumulation of atmospheric O₂ at least 2.7 billion years ago suggests that cyanobacteria were already important by this time.
- Fossils from stromatolites that look like modern cyanobacteria are as old as 3.5 billion years.

Oxygenic photosynthesis is especially complex because it requires two cooperative photosystems.

Some modern groups of prokaryotes use a single photosystem to extract electrons from compounds such as H₂S instead of splitting water.
A logical inference is that cyanobacteria which split water and released O₂ evolved from ancestors with simpler, nonoxygenic photosystems.

The evolution of cyanobacteria changed the Earth in a radical way, transforming the atmosphere from a reducing one to an oxidizing one.

Some organisms took advantage of this change through the evolution of cellular respiration which used the oxidizing power of O₂ to increase the efficiency of fuel consumption.
In fact, photosynthesis and cellular respiration are closely related, both using electron transport chains to generate protons gradients that power ATP synthase.
It is likely that cellular respiration evolved by modification of the photosynthetic equipment for a new function.

D. A Survey of Prokaryotic Diversity

1. Molecular systematics is leading to phylogenetic classification of prokaryotes

The limited fossil record and structural simplicity of prokaryotes created great difficulties in developing a classification of prokaryotes.

A breakthrough came when Carl Woese and his colleagues began to cluster prokarotes into taxonomic groups based on comparisons of nucleic acid sequences.

Especially useful was the small-subunit ribosomal RNA (SSU-rRNA) because all organisms have ribosomes.

Woese used signature sequences, regions of SSU-rRNA that are unique, to establish a phylogeny of prokarotes.

Before molecular phylogeny, phenotypic characters, such as nutritional mode and gram staining behavior, were used to establish prokaryotic phylogeny.

While these characters are still useful in the identification of pathogenic bacteria in a clinical laboratory, they are poor guides to phylogeny.
For example, nutritional modes are scattered through the phylogeny, as are gram-negative bacteria.
Some traditional phenotype-based groups do persist in phylogenetic classification, such as the cyanobacteria and spirochetes.

More recently, researchers have sequenced the complete genomes of several prokaryotes.

Phylogenies based on this enormous database have supported most of the taxonomic conclusions based on SSU-rRNA comparisons, but it has also produced some surprises.

Among the surprises is rampant gene-swapping within early communities of prokaryotes, and the first eukaryotes.

2. Researchers are identifying a great diversity of archaea in extreme environments and in the oceans

Early on prokaryotes diverged into two lineages, the domains Archaea and Bacteria.

A comparison of the three domains demonstrates that Archaea have at least as much in common with eukaryotes as with bacteria.

The archaea also have many unique characteristics.

Most species of archaea have been sorted into the kingdom Euryarchaeota or the kingdom Crenarchaeota.

However, much of the research on archaea has focused not on phylogeny, but on their ecology - their ability to live where no other life can.

Archaea are extremophiles, "lovers" of extreme environments.

Based on environmental criteria, archaea can be classified into methanogens, extreme halophiles, and extreme thermophilies.

Methanogens obtain energy by using CO₂ to oxidize H₂ replacing methane as a waste.

Methanogens are among the strictest anaerobes.
They live in swamps and marshes where other microbes have consumed all the oxygen.
Methanogens are important decomposers in sewage treatment.
Other methanogens live in the anaerobic guts of herbivorous animals, playing an important role in their nutrition.
They may contribute to the greenhouse effect, through the production of methane.

Extreme halophiles live in such saline places as the Great Salt Lake and the Dead Sea.

Some species merely tolerate elevated salinity; others require an extremely salty environment to grow.
Colonies of halophiles form a purple-red scum from bacteriorhodopsin, a photosynthetic pigment very similar to the visual pigment in the human retina.

Extreme thermophiles thrive in hot environments.

The optimum temperatures for most thermophiles are 60^oC-80^oC.
Sulfolobus oxidizes sulfur in hot sulfur springs in Yellowstone National Park.
Another sulfur-metabolizing thermophile lives at 105^oC water near deep-sea hydrothermal vents.

If the earliest prokaryotes evolved in extremely hot environments like deep-sea vents, then it would be more accurate to consider most life as "cold-adapted" rather than viewing thermophilic archaea as "extreme".

Recently, scientists have discovered an abundance of marine archaea among other life forms in more moderate habitats.

All the methanogens and halophiles fit into Euryarchaeota.

Most thermophilic species belong to the Crenarchaeota.

Each of these taxa also includes some of the newly discovered marine archaea.

3. Most known prokarotes are bacteria

The name bacteria was once synonymous with "prokaryotes," but it now applies to just one of the two distinct prokaryotic domains.

However, most known prokaryotes are bacteria.

Every nutritional and metabolic mode is represented among the thousands of species of bacteria.

The major bacterial taxa are now accorded kingdom status by most prokaryotic systematists.

E. The Ecological Impact of Prokaryotes

1. Prokaryotes are indispensable links in the recycling of chemical elements in ecosystems

Ongoing life depends on the recycling of chemical elements between the biological and chemical components of ecosystems.

If it were not for decomposers, especially prokaryotes, carbon, nitrogen, and other elements essential for life would become locked in the organic molecules of corpses and waste products.
Prokaryotes also mediate the return of elements from the nonliving components of the environment to the pool of organic compounds.

Prokaryotes have many unique metabolic capabilities.

They are the only organisms able to metabolize inorganic molecules containing elements such as iron, sulfur, nitrogen, and hydrogen.
Cyanobacteria not only synthesize food and restore oxygen to the atmosphere, but they also fix nitrogen.
- This stocks the soil and water with nitrogenous compounds that other organisms can use to make proteins.
When plants and animals die, other prokaryotes return the nitrogen to the atmosphere.

2. Many prokaryotes are symbiotic

Prokaryotes often interact with other species of prokaryotes or eukaryotes with complementary metabolisms.

Organisms involved in an ecological relationship with direct contact (symbiosis) are known as symbionts.

If one symbiont is larger than the other, it is also termed the host.

In commensalism, one symbiont receives benefits while the other is not harmed or helped by the relationship.

In parasitism, one symbiont, the parasite, benefits at the expense of the host.

In mutualism, both symbionts benefit.

Prokaryotes are involved in all three categories of symbiosis with eukaryotes.

Legumes (peas, beans, alfalfa, and others) have lumps in their roots which are the homes of mutualistic prokaryotes (Rhizobium) that fix nitrogen that is used by the host.
- The plant provides sugars and other organic nutrients to the prokaryote.
Fermenting bacteria in the human vagina produce acids that maintain a pH between 4.0 and 4.5, suppressing the growth of yeast and other potentially harmful microorganisms.
- Other bacteria are pathogens.

3. Pathogenic prokaryotes cause many human diseases

Exposure to pathogenic prokaryotes is a certainty.

Most of the time our defenses check the growth of these pathogens.
Occasionally, the parasite invades the host, resists internal defenses long enough to begin growing, and then harms the host.

Pathogenic prokaryotes cause about half of all human disease, including pneumonia caused by Haemophilus influenzae bacteria.

Some pathogens are opportunistic.

These are normal residents of the host, but only cause illness when the host's defenses are weakened.
Louis Pasteur, Joseph Lister, and other scientists began linking disease to pathogenic microbes in the late 1800s.

Robert Koch was the first to connect certain diseases to specific bacteria.

He identified the bacteria responsible for anthrax and the bacteria that cause tuberculosis.

Koch's methods established four criteria, Koch's postulates, that still guide medical microbiology.

The researcher must find the same pathogen in each diseased individual investigated,
Isolate the pathogen form the diseased subject and grow the microbe in pure culture,
Induce the disease in experimental animals by transferring the pathogen from culture, and
Isolate the same pathogen from experimental animals after the disease develops.

These postulates work for most pathogens, but exceptions do occur.

Some pathogens produce symptoms of disease by invading the tissues of the host.

The actinomycete that causes tuberculosis is an example of this source of symptoms.

More commonly, pathogens cause illness by producing poisons, called exotoxins and endotoxins.

Exotoxins are proteins secreted by prokaryotes.

Exotoxins can produce disease symptoms even if the prokaryote is not present.
- Clostridium botulinum, which grows anaerobically in improperly canned foods, produces an exotoxin that causes botulism.
- An exotoxin produced by Vibrio cholerae causes cholera, a serious disease characterized by severe diarrhea.
- Even strains of E. coli can be a source of exotoxins, causing traveler's diarrhea.

Endotoxins are components of the outer membranes of some gram-negative bacteria.

The endotoxin-producing bacteria in the genus Salmonella are not normally present in healthy animals.
- Salmonella typhi causes typhoid fever.
- Other Salmonella species, including some that are common in poultry, cause food poisoning.

Since the discovery that "germs" cause disease, improved sanitation and improved treatments have reduced mortality and extended life expectancy in developed countries.

More than half of our antibiotics (such as streptomycin and tetracycline) come from the soil bacteria Streptomyces.
- This genus uses these antibiotics to prevent encroachment by competing microbes.

The decline (but not removal) of bacteria as threats to health may be due more to public-health policies and education than to "wonder-drugs."

For example, Lyme disease, caused by a spirochete spread by ticks that live on deer, field mice, and occasionally humans, can be cured if antibiotics are administered within a month after exposure.

If untreated, Lyme disease causes arthritis, heart disease, and nervous disorders.
The best defense is avoiding tick bites and seeking treatment if bit and a characteristic rash develops.

Today, the rapid evolution of antibiotic-resistant strains of pathogenic bacteria is a serious health threat aggravated by imprudent and excessive antibiotic use.

Although declared illegal by the United Nations, the selective culturing and stockpiling of deadly bacterial disease agents for use as biological weapons remains a threat to world peace.

3. Humans use prokaryotes in research and technology

Humans have learned to exploit the diverse metabolic capabilities of prokaryotes, for scientific research and for practical purposes.

Much of what we know about metabolism and molecular biology has been learned using prokaryotes, especially E. coli, as simple model systems.
Increasing, prokaryotes are used to solve environmental problems.

The application of organisms to remove pollutants from air, water, and soil is bioremediation.

The most familiar example is the use of prokaryote decomposers to treat human sewage.
Anaerobic bacteria decompose the organic matter into sludge (solid matter in sewage), while aerobic microbes do the same to liquid wastes.
Soil bacteria, called pseudomonads, have been developed to decompose petroleum products at the site of oil spills or to decompose pesticides.

Humans also use bacteria as metabolic "factories" for commercial products.

The chemical industry produces acetone, butanol, and other products from bacteria.
The pharmaceutical industry cultures bacteria to produce vitamins and antibiotics.
The food industry used bacteria to convert milk to yogurt and various kinds of cheese.

The development of DNA technology has allowed genetic engineers to modify prokaryotes to achieve specific research and commercial outcomes.

Course Pages maintained by
Dr. Graeme Lindbeck .