34 Bacteria and Archaea: The Prokaryotic Domains

Introduction

· · Some bacteria are quite large, 0.75 mm in diameter. (A typical human somatic cell is only about 10 mm.)

· · The smallest organisms on Earth are also species of prokaryotes (0.2 mm).

· · There are two kinds of prokaryotes: bacteria(eubacteria) and archaea.

· · The DNA sequencing of a species of archaea in 1996 provided evidence of substantial differences between archaea and both eukaryotes and bacteria.

· · Biologists now generally categorize all life first into three domains: Bacteria, Archaea, and Eukarya.

Why Three Domains?

· · Members of all three domains metabolize glucose, have double-stranded DNA information molecules, and share a common genetic code.

· · Archaea share a more recent common ancestor with eukaryotes than with bacteria.

· · The three domain names are a higher taxonomic category than kingdoms.

· · The common ancestor of all three domains was prokaryotic.

· · It likely had a circular chromosome and structural genes organized into operons.

· · All three domains are over a billion years old.

· · None are "primitive" today because all cellular life has come from previously existing life. All species are in essence the same age.

· · The earliest prokaryotic fossils date back to 3.5 billion years.

· · Prokaryotes were the only life forms for billions of years.

General Biology of the Prokaryotes

· · Prokaryotes live all around and even within us.

· · The bacteria in one person's intestinal tract outnumber all the people who have ever lived.

· · They even outnumber the total number of human cells in that person’s body.

· · Prokaryotes are important to the biosphere.

· · Some perform key steps in the cycling of nitrogen, sulfur, and carbon.

· · Some trap energy from the sun and from inorganic chemical sources.

· · Some help animals digest their food.

· · Prokaryotes are found in every conceivable habitat on the planet.

· · They live at extremely hot temperatures.

· · They can survive extreme alkalinity and saltiness.

· · Some survive in the presence of oxygen, while others survive without it.

· · Some live at the bottom of the sea.

· · Some live in rocks more than 2 km into Earth's solid crust.

Prokaryotes and their associations take a few characteristic forms

· · Three shapes are common to prokaryotes: spheres, rods, and curved or spiral forms

· · Spherical prokaryotes are called cocci (singular coccus). Cocci might live singly or in two- or three-dimensional arrays of chains, plates, or blocks, depending on the species.

· · Rod-shaped prokaryotes are called bacilli. These live in chains or singularly.

· · Prokaryotes, with just a few exceptions, are unicellular.

· · Chains and other associations do not signify multicellularity because each cell is viable independently.

· · Some bacteria that associate in chains become enclosed within delicate tubular sheaths.

· · These associations are called filaments. All the cells of the filament divide simultaneously.

Prokaryotes lack nuclei, organelles, and a cytoskeleton

· · Most of what is currently known about prokaryotic cellular structure has been learned from bacteria.

· · The DNA of the prokaryotic cell is not organized within a membrane-enclosed nucleus.

· · Prokaryotes have no membrane-bound cytoplasmic organelles—mitochondria, Golgi apparatus, etc. Some do have plasma membrane infoldings.

· · Prokaryotes lack a cytoskeleton and thus do not divide by mitosis. Instead, they divide by fission after replicating their DNA.

Prokaryotes have distinctive modes of locomotion

· · Some prokaryotes are motile.

· · Some spiral bacteria called spirochetes use a rolling motion.

· · Many cyanobacteria and some other bacteria use a gliding mechanism.

· · Some aquatic prokaryotes move slowly up and down in the water by adjusting the amount of gas in gas vesicles.

· · Bacterial flagella, which are entirely different from those of eukaryotes, consist of a single fibril, made of the protein flagellin, projecting from the surface.

· · The prokaryotic flagellum rotates about its base, rather than beating, as a eukaryotic flagellum does.

Prokaryotes have distinctive cell walls

· · Most prokaryotes have a thick and stiff cell wall of peptidoglycan (a polymer of amino sugars).

· · Archaean cell walls are of different types, but most contain significant amounts of protein.

· · The Gram stain, developed by Hans Christian Gram in 1884, separates bacteria into two distinct groups, Gram-positive and Gram-negative, based on the nature of their cell walls.

· · To obtain a Gram stain, cells on a microscope slide are soaked in violet dye and treated with iodine.

· · The slide is then washed with alcohol and counterstained with safranine.

· · Gram-positive bacteria stain violet.

· · Gram-negative bacteria stain pink to red.

· · Gram staining correlates with the structure of the cell wall.

· · Gram-positive cell walls have a thicker layer of peptidoglycan than Gram-negative cell walls.

· · Gram-negative cell walls have a second outer membrane outside the cell wall, and the cell wall has only a fifth as much peptidoglycan.

· · The space between the outer membrane and the cell wall is called the periplasmic space.

· · The periplasmic space contains enzymes important to the digestion and transport of some materials.

· · Many antibiotics act by disrupting cell wall synthesis. Antibiotics that interfere with the synthesis of bacterial cell walls tend to have little or no effect on eukaryotic cells.

Prokaryotes reproduce asexually, but genetic recombination does occur

· · Prokaryotes reproduce asexually by fission.

· · Prokaryotes can exchange genetic material through transformation, conjugation, and transduction.

· · Rates of division vary with species. E. coli divides about once every 20 minutes. The shortest known generation time for prokaryotes is about 10 minutes. Bacteria living in rock deep in Earth's crust might not divide for as long as 100 years.

Prokaryotes have exploited many metabolic possibilities

· · Anaerobic versus aerobic metabolism:

· · Obligate anaerobes live only in the absence of oxygen. Oxygen is toxic to them.

· · Facultative anaerobes can shift between anaerobic and aerobic modes.

· · Some cannot use oxygen but are not damaged by it.

· · Others can shift from aerobic and anaerobic metabolisms.

· · Obligate aerobes are unable to survive for extended periods in the absence of oxygen.

· · Nutritional categories:

· · The four nutritional categories of organisms include photoautotrophs, photoheterotrophs, chemoautotrophs, and chemoheterotrophs.

· · Photoautotrophs are photosynthesizers.

· · Photoautotrophs use light for energy and carbon dioxide as a carbon source.

· · Cyanobacteria use chlorophyll a and produce oxygen as a by-product.

· · Other photosynthetic bacteria use bacteriochlorophyll.

· · These bacteria do not produce oxygen.

· · Some produce particles of pure sulfur, because H₂S is used instead of H₂O as an electron donor.

· · Bacteriochlorophyll uses longer wavelengths than chlorophylls. This longer wavelength of light penetrates farther into water and is not absorbed by plants.

· · Photoheterotrophs use light as a source of energy but must get carbon from other organisms.

· · They use carbohydrates, fatty acids, and alcohols for carbon.

· · Purple nonsulfur bacteria are photoheterotrophs.

· · Chemoautotrophs obtain energy from oxidizing inorganic substances.

· · Chemoautotrophs use some of the energy to fix carbon dioxide.

· · Some use pathways to fix CO₂ identical to those of the Calvin cycle.

· · Others use alternative pathways to fix CO₂.

· · Some use ammonia as the chemical source of energy; others use hydrogen gas, hydrogen sulfide, sulfur, or methane.

· · Some deep-sea ecosystems are based on chemoautotrophic prokaryotes.

· · They form the basis for a food chain that includes giant worms, crabs, and mollusks.

· · These bacteria live around the thermal vents of underwater volcanoes.

· · Chemoheterotrophs typically obtain energy and carbon atoms from one or more organic compounds.

· · Most known bacteria and archaea are chemoheterotrophs, as are all animals, fungi, and many protists.

· · Nitrogen and sulfur metabolism:

· · Some bacteria use electron acceptors other than oxygen.

· · Some use oxidized nitrogen, such as ammonia or nitrite, or sulfur, such as sulfur or sulfite, as electron acceptors.

· · Denitrifiers return nitrogen to the atmosphere.

· · All nitrogen fixers are bacteria.

· · They provide the enzymes and environment to conduct the following reaction: N₂ + 6 H ® 2 NH₃.

· · All organisms require fixed nitrogen for their proteins, nucleic acids, and other nitrogen-containing compounds.

· · Nitrifiers oxidize ammonia to nitrate.

· · Bacteria of two genera, Nitrosomonas and Nitrosococcus, convert ammonia to nitrite.

· · Nitrobacter oxidizes nitrite to nitrate.

· · The bacteria harvest energy from the conversion of ammonia to nitrite and nitrite to nitrate.

Prokaryotes in Their Environments

Prokaryotes are important players in element cycling

· · Plants depend on prokaryotes for sources of nitrogen.

· · Prokaryotes that are denitrifiers prevent accumulation of toxic levels of nitrogen in lakes and oceans.

· · Cyanobacteria have had a powerful effect on changing Earth by generating atmospheric O₂.

· · The accumulation of O₂ in the atmosphere made the evolution of more efficient glucose metabolism possible and caused the extinction of many species that couldn't tolerate oxygen.

Prokaryotes live on and in other organisms

· · Mitochondria and chloroplasts are assumed to be descendants of free-living bacteria.

· · Cows depend on prokaryotes in their digestive tract to digest cellulose, which makes up the bulk of their food.

· · Humans use vitamins B₁₂ and K produced by our intestinal bacteria.

A small minority of bacteria are pathogens

· · In the late nineteenth century, Robert Koch formulated rules for determining that a particular microorganism causes a particular disease. These are called Koch's postulates:

· · The microorganism must always be found in individuals with disease.

· · The microorganism can be taken from the host and grown in pure culture.

· · A sample of the culture produces the disease when injected into a new, healthy host.

· · The newly infected host yields a new, pure culture of microorganisms identical to those obtained in the second step.

· · Only a tiny proportion of prokaryotic species are pathogens. All known prokaryotic pathogens are bacteria (not archaea).

· · For an organism to be a pathogen, it must:

· · Arrive at the body surface

· · Enter the body

· · Evade detection and defenses

· · Multiply inside the host

· · Infect new hosts

· · For the host, the seriousness of the infection depends on:

· · The invasiveness of the pathogen

· · The toxigenicity of the pathogen

· · Corynebacterium diphtheriae, the agent that causes diphtheria, has low invasiveness but produces powerful toxins.

· · Bacillus anthracis, which causes anthrax, has low toxigenicity, but is so invasive that the bloodstream of infected animals teems with organisms.

· · There are two major types of toxins:

· · Endotoxins are lipopolysaccharides from the outer membrane of Gram-negative bacteria, which cause vomiting, fever, and diarrhea.

· · Salmonella and Escherichia produce endotoxins.

· · Exotoxins are produced and released by living, multiplying bacteria.

· · These can be highly toxic, even fatal.

· · They don't cause fever.

· · Tetanus (from Clostridium tetani), botulism (from Clostridium botulinum), cholera (from Vibrio cholerae), and plague (from Yersinia pestis) are all examples of exotoxins.

Prokaryote Phylogeny and Diversity

Nucleotide sequences of prokaryotes reveal their evolutionary relationships

· · The three primary motivations for classification schemes are:

· · To help identify unknown organisms

· · To reveal evolutionary relationships

· · To provide universally recognized names for organisms

· · In the past, phenotypic characters such as color, shape, antibiotic resistance, and staining were used to classify organisms.

· · These were the best clues available until recently.

· · Now, nucleic acid sequencing is providing clues to evolutionary relationships.

· · Ribosomal RNA's (rRNA's) have been studied.

· · rRNA is evolutionarily ancient.

· · All organisms have rRNA.

· · rRNA functions the same way in all organisms.

· · rRNA changes slowly enough that sequence similarities between groups of organisms are easily found.

· · Signature sequences of rRNA are compared.

· · The sequence AAACUUAAAG occurs about 910 bases from one end of the RNA of the light subunit of ribosomes in all Archaea and Eukarya, but it fails to exist as such in any bacteria.

· · Results so far have provided some contradictory phylogenetic patterns.

Mutations are the most important source of prokaryotic variation

· · The rapid multiplication of many prokaryotes—coupled with mutation, selection, and genetic drift—causes rapid changes.

· · An example is the acquiring of resistance to antibiotics.

The Proteobacteria are a large and diverse group

· · The Proteobacteria is the largest group in terms of the number of species.

· · Proteobacteria are sometimes referred to as the purple bacteria.

· · Some are Gram-negative, bacteriochlorophyll-containing, and sulfur-using photoautotrophs.

· · Mitochondria were derived from proteobacteria by endosymbiosis.

· · Figure 26.12 shows the evolution of proteobacterial metabolisms.

· · The common ancestor to all proteobacteria was probably a photoautotroph.

· · Early in evolutionary history, two groups lost the ability to photosynthesize and became chemoheterotrophs.

· · There are also chemoautotrophs and chemoheterotrophs in all three of the other groups.

· · Some fix nitrogen (Rhizobium), and some help cycle nitrogen and sulfur.

· · E. coli, Yersinia pestis, Vibrio cholerae, and Salmonella typhimurium are all proteobacteria.

· · Agrobacterium tumefaciens is also a proteobacterium.

· · This bacterium causes crown gall and is currently being used by plant molecular biologists as a vector for gene transfer in plants due to its Ti plasmid. (See Figure 26.13. The Instructor’s Resource CD-ROM includes images of A. tumefaciens and the gall it causes.)

The Cyanobacteria are important photoautotrophs

· · Cyanobacteria (blue-green bacteria) require only water, N₂, CO₂, a few mineral elements, light, and O₂ (this they actually produce from water).

· · Cyanobacteria have highly organized internal membranes called photosynthetic lamellae. (See Figure 26.14. The Instructor’s Resource CD-ROM includes images of cyanobacteria; Chapters 4 and 5 have micrographs showing photosynthetic membranes in cyanobacteria.)

· · Chloroplasts are derived from an endosymbiotic cyanobacterium.

· · Cyanobacteria grow free or in colonies. (See Figure 26.15.)

· · Filamentous colonies differentiate into three cell types: vegetative cells, spores, and heterocysts.

· · Heterocysts are specialized for nitrogen fixation.

Spirochetes look like corkscrews

· · Spirochetes are Gram-negative bacteria with axial filaments, which are fibrils running through the periplasmic space. (See Figure 26.5a.)

· · The cell body is a long cylinder coiled into a spiral.

· · Many spirochetes live in humans as parasites. Others live free in mud or water. (See Figure 26.16.)

Chlamydias are extremely small

· · Chlamydias are among the smallest bacteria (0.2 to 1.5 mm in diameter).

· · They are intracellular parasites.

· · They change form during their life cycle. (See Figure 26.17. The Instructor’s Resource CD-ROM includes the micrograph from this figure.)

· · In humans, they cause eye infections, sexually transmitted disease, and some forms of pneumonia.

Most Firmicutes are Gram-positive

· · Most firmicutes are Gram-positive but some are Gram-negative. (See Figure 26.19.)

· · Some produce endospores, which are heat-resistant resting structures.

· · The bacterium replicates its DNA.

· · It encapsulates one copy in a tough cell wall, thickened with peptidoglycan and covered with a spore coat. (See Figure 26.18. The Instructor’s Resource CD-ROM includes a freeze-etch TEM of a Clostridium bacterium with an endospore.)

· · The parent cell then breaks down, releasing the endospore.

· · Some endospores can be reactivated after more than a thousand years of dormancy.

· · Members of this endospore-forming group include Bacillus and Clostridium.

· · Just 1 mg of toxin from Clostridium botulinum is lethal to a human.

· · Staphylococcus includes pathogens that cause boils on skin, as well as respiratory, intestinal, and wound infections.

· · Actinomycetes are firmicutes that develop an elaborately branched system of filaments. (See Figure 26.20. The Instructor’s Resource CD-ROM includes a TEM of part of an actinomycete filament.)

· · Some form chains of spores at the tips of filaments.

· · Mycobacterium tuberculosis causes tuberculosis.

· · Streptomyces produces the antibiotic streptomycin, as well as hundreds of other antibiotics.

· · Most of our antibiotics are from actinomycetes.

· · Mycoplasmas have the least amount of DNA and are the smallest bacteria. (See Figure 26.21.)

· · Mycoplasmas lack cell walls.

· · Some are 0.2 mm in size.

· · They may have the minimum amount of DNA necessary to code for the essential properties of a living cell.

The Archaea

· · The study of archaea is still in its very early stages.

· · It is possible that the domain Archaea is paraphyletic.

· · Most archaea live in environments that are extreme in one way or another: temperature, salinity, oxygen concentration, or pH. (The Instructor’s Resource CD-ROM includes images of thermoacidophiles, halophiles [salt lovers], and methanogens.)

The Archaea share some unique characteristics

· · The Archaea lack peptidoglycan in their cell walls.

· · They have distinctive lipids. (See Figure 26.22.)

· · When biologists sequenced the first archaean genome, of its 1,738 genes, more than half were unlike any found in the other two domains.

· · Long fatty acids are bonded to glycerol via an ether linkage instead of the ester linkage found in other organisms.

Most Crenarchaeota live in hot, acidic places

· · Most Crenarchaeota are both thermophilic and acidophilic.

· · The genus Sulfolobus live in hot sulfur springs at temperatures of 70 to 75^oC.

· · They die of "cold" at 55^oC (131^oF).

· · They grow best at pH 2 to 3 but can survive pH 0.9.

The Euryarchaeota live in many amazing places

· · Some species of Euryarchaeota produce methane from CO₂.

· · All methanogens are obligate anaerobes.

· · Methanogens release approximately 2 billion tons of methane gas into Earth's atmosphere.

· · Approximately a third of this methane comes from methanogens in the guts of grazing herbivores.

· · Methanopyrus lives on the ocean bottom near volcanic vents. These can live at 110^oC.

· · Some Euryarchaeota, called extreme halophiles, live exclusively in very salty environments. (See Figure 26.24.)

· · These grow in the Dead Sea.

· · Some of these organisms survive a pH of 11.5.

· · Some of the extreme halophiles use bacteriorhodopsin to make ATP using a chemiosmotic mechanism.

· · Thermoplasma is thermophilic and acidophilic.

· · It is aerobic and lives in coal deposits.

· · It has no cell wall.

· · It has the smallest genome of any archaea: 1,100,000 base pairs.