Bacteria and Archaea: Prokaryote Characteristics

• Bacteria and Archaea are the focus of chapter 27.

Characteristics of Prokaryotes

• Enables them to reach huge population sizes and thrive in diverse environments.
• Single-celled organisms which make up domains Bacteria and Archaea
• They are well-adapted to diverse and extreme environments
• They are the most abundant organisms on Earth

Structural and Functional Adaptations

• Contribute to prokaryotic success
• Prokaryotes were the first organisms to inhabit Earth
• Most are unicellular, however, some species form colonies
• Most prokaryotic cells are 0.5–5 µm, which is much smaller than the 10–100 µm of many eukaryotic cells
• They have a variety of shapes including spheres (cocci), rods (bacilli), and spirals

Cell-Surface Structures

• The cell wall maintains shape, protects the cell, and prevents it from bursting in a hypotonic environment.
• Most prokaryotes lose water and experience plasmolysis in hypertonic environments
• Cells have defense structures that help them to survive
• Cells can also have projections to aid in cell communication, survival, and motility

Cell wall

• Most bacterial cell walls contain peptidoglycan, a network of sugar polymers cross-linked by polypeptides
• Archaeal walls contain a variety of polysaccharides and proteins, but lack peptidoglycan
• Scientists use the Gram stain to classify bacteria by cell wall composition
• Gram-positive bacteria have simpler walls with a large amount of peptidoglycan
• Gram-negative bacteria walls have less peptidoglycan and are more complex with an outer membrane that contains lipopolysaccharides
• Gram-negative bacteria tend to be more resistant to antibiotics than gram-positive bacteria
• Many antibiotics target peptidoglycan and damage gram-positive bacterial cell walls
• Human cells lack peptidoglycan and are unaffected by antibiotics

Capsules

• Many prokaryotes have a sticky layer of polysaccharide or protein surrounding the cell wall
• A capsule is defined as dense and well-defined, or a slime layer if it is not well organized
• Both types enable adherence to a substrate, prevent dehydration, and protect the cell from the host's immune system

Endospores

• Some bacteria form metabolically inactive endospores
• A cell copies its chromosome and surrounds it with a multilayered structure
• The endospores can withstand extreme conditions and remain viable for centuries

Hair

• Some prokaryotes have hairlike appendages called fimbriae that allow them to stick to their substrate or other individuals in a colony
• Pili (or sex pili) are longer than fimbriae and function to pull cells together enabling the exchange of DNA

Motility

• About half of all prokaryotes exhibit taxis, which is the ability to move toward or away from a stimulus
• For example, chemotaxis is the movement toward or away from a chemical stimulus
• Flagella are the most common structures used by prokaryotes for movement
• They are scatted over the entire surface or concentrated at the ends of the cell
• Flagella of prokaryotes and eukaryotes differ in structure, mechanism of propulsion, and molecular composition

Internal organization and DNA

• Prokaryotic cells lack complex compartmentalization
• Some prokaryotes have specialized membranes that perform metabolic functions
• These are usually infoldings of the cell membrane

Comparison

• Prokaryotes vs Eukaryotes
• Prokarytoes*:
• less DNA and produce fewer proteins
• one circular chromosome
• lack a nucleus; the chromosome is in the nucleoid, a region with no membrane
• may also have smaller rings of independently replicating DNA called plasmids
• Transcription and translation can occur at the same time
• Targeted by antibiotics
• Eukaryotes*:
• produce more proteins and have more DNA
• multiple linear chromosomes
• contain a nucleus with a double membrane
• do not have plasmids, but do have mitochondrion
• transcription, translation, and replication occur stepwise because of the compartmentalization
• Not necessarily killed by antibiotics

Reproduction

• Prokaryotes reproduce quickly by binary fission and can divide every 1–3 hours under optimal conditions
• There are three key features of prokaryote biology:
  • They are small
  • They reproduce by binary fission
  • They have short generation times

Genetic Diversity

• Rapid reproduction, mutation, and genetic recombination promote genetic diversity in prokaryotes
• Three factors contribute to the high levels of genetic diversity observed in prokaryote populations:
  • Rapid reproduction
  • Mutation
  • Genetic recombination
• Cells produced by binary fission are generally identical, but differences can arise through mutation
• Mutation rates are typically low, but mutations accumulate rapidly with short generation times and large populations
• Genetic recombination, the combining of DNA from two sources, contributes to prokaryote diversity
  • DNA from different individuals can be combined by transformation, transduction, or conjugation
  • Movement of genes between individual prokaryotes of different species is called horizontal gene transfer

Transformation and Transduction

• In transformation, prokaryotic cells incorporate foreign DNA taken up from their surroundings
• In transduction, phages (bacteriophages) carry prokaryotic genes from one host cell to another

Conjugation and Plasmids

• Conjugation is the process through which DNA is transferred between two prokaryotic cells
• In bacteria, the DNA transfer is always one way and one cell donates the DNA and the other receives it
• In E. coli, conjugation occurs in the following steps:
  • a pilus of the donor cell attaches to the recipient
  • the pilus retracts, pulling the two cells together
  • DNA is transferred through a temporary structure called the "mating bridge"
• a piece of DNA called the F factor (F for fertility) is required for the production of pili
• The F factor can exist either as a plasmid or a segment of DNA within the bacterial chromosome

F Factor as Plasmid

• Cells containing the F plasmid (F+ cells) function as DNA donors
• Cells lacking the F factor (F- cells) are recipients
• An F+ cell can convert an F− cell to an F+ cell if the F+ cell transfers an entire F plasmid to the F- cell.
• If only part of the F plasmid’s DNA is transferred, the recipient cell will be recombinant.

F Factor in the Chromosome

• Cells that have the F factor in their chromosome (Hfr cells, high frequency of recombination), function as donors during conjugation.
• Homologous segments of the chromosomal DNA from the Hfr cell recombine with that of the F cell. The recombinant recipient cell becomes a new genetic variant on which evolution can act.

R Plasmids

• Antibiotic Resistance Antibiotics kill most bacteria, but not those with R plasmids, plasmids that carry resistance genes
• Some R plasmids carry genes for resistance to multiple antibiotics
• R plasmids also have genes that encode the pili used to transfer DNA between cells, enabling the rapid spread of resistance

Nutritional and Metabolic Adaptations

• Prokaryotes can be categorized by how they obtain energy and carbon:
• Phototrophs obtain energy from light
• Chemotrophs obtain energy from chemicals
• Autotrophs require CO2 or related compounds as a carbon source
• Heterotrophs require an organic nutrient to make other organic compounds
• Energy and carbon sources are combined to give four major modes of nutrition:
  • Photoautotroph
  • Chemoautotroph
  • Photoheterotroph
  • Chemoheterotroph

Role of Oxygen

• Prokaryotic metabolism varies with respect to O₂
  • Obligate aerobes require O₂for cellular respiration
  • Obligate anaerobes are poisoned by O₂and live by fermentation or use substances other than O₂for anaerobic respiration
  • Facultative anaerobes can use O₂ if it is present or carry out fermentation or anaerobic respiration if not

Nitrogen Metabolism

• Nitrogen is essential for the production of amino acids and nucleic acids in all organisms
• Prokaryotes metabolize nitrogen in many forms
  • For example, some prokaryotes convert atmospheric nitrogen (N₂) to ammonia (NH₃) in a process called nitrogen fixation

Metabolic Cooperation

• Prokaryote cells may cooperate to use resources unavailable to individual cells
  • Nitrogen-fixation is isolated in cells called heterocysts that prevent oxygen penetration
  • Photosynthetic cells exchange carbohydrates for the fixed nitrogen produced by the heterocysts
• Cells of one or more prokaryote species cooperate to form surface-coating colonies called biofilms
• Cells near the edge release signaling molecules to recruit new cells
• Channels in the biofilm allow nutrients to reach cells in the interior and wastes to be expelled
• Biofilms are common in nature, but can cause many problems for humans including
  • Corrosion of industrial structures and products
  • Contamination of medical devices
  • Tooth decay
  • Chronic, antibiotic-resistant infections

Diverse lineages

• Prokaryotes have radiated into diverse lineages
• Horizontal gene transfer has played a key role in the evolution of prokaryotes
• Significant portions of the genomes of prokaryotes are mosaics of genes imported from other species
• For example, in a study of 329 bacterial genomes, an average of 75% of the genes in each genome had been horizontally transferred at some point

Bacteria

• Bacteria include the vast majority of prokaryotic species familiar to most people
• Every major mode of nutrition and metabolism is represented among bacteria
• Proteobacteria*:
• Gram-negative bacteria including photoautotrophs, chemoautotrophs, and heterotrophs
  • For example, the sulfur bacterium Thiomargarita namibiensis, is an autotroph that obtains energy by oxidizing H₂S and producing sulfur as a waste product
• Heterotrophic proteobacteria include several pathogens
  • Neisseria gonorrhoeae causes gonorrhea
  • Vibrio cholerae causes cholera
  • Helicobacter pylori causes stomach ulcers
• Chlamydias*:
• All species parasitize animal cells and have gram-negative walls lacking peptidoglycan
  • For example, Chlamydia trachomatis causes nongonococcal urethritis, the most common sexually transmitted disease in the United States
• Spirochetes*:
• These bacteria are helical gram-negative heterotrophs that spiral through the environment by rotating internal filaments
• Many are free-living, but others are pathogens
  • For example, Treponema pallidum, causes syphilis, and Borrelia burgdorferi, causes Lyme disease
• Cyanobacteria*:
• These bacteria are gram-negative photoautotrophs
• Plant chloroplasts likely evolved from cyanobacteria by the process of endosymbiosis Solitary and filamentous cyanobacteria are abundant components of freshwater and marine phytoplankton
• Gram-Positive Bacteria*:
• Gram-positive bacteria are a diverse group
  • Actinomycetes are colony forming bacteria including pathogens and soil decomposers
  • Soil-dwelling species of Streptomyces are cultured as a source of antibiotics, including tetracycline
  • Other subgroups include pathogens such as Staphylococcus aureus; Bacillus anthracis, the cause of anthrax; and Clostridium botulinum, the cause of botulism

Archaea

• Archaea share certain traits with bacteria and other traits with eukaryotes
• They also have many unique characteristics
• Extremophiles*:
• Archaea that live in extreme environments, uninhabitable for most organisms
  • Extreme halophiles either tolerate or require highly saline environments
  • Extreme thermophiles have adaptations that make their DNA and proteins stable at high temperatures (even above 100°C)
• Methanogens*:
• Obligate anaerobes that produce methane as a by-product of their metabolism
• They are found in diverse environments
  • Under kilometers of ice in Greenland
  • In swamps and marshes
  • In the guts of cattle, termites, and other herbivores
• Euryarchaeota is the clade that includes many of the extreme halophiles, most methanogens, and some extreme thermophiles
• Most of the extreme thermophiles belong to another clade TACK is a supergroup composed of the remaining, closely-related clades of archaea
• The group is named for its component clades
  • Thaumarchaeota
  • Aigarchaeota
  • Crenarchaeota—includes most extreme thermophiles
  • Korarchaeota

Crucial Roles

• Prokaryotes play crucial roles in the biosphere
• If prokaryotes were to disappear, the prospects for any other life surviving on Earth would be dim
• Prokaryotes play a major role in the recycling of chemical elements between the living and nonliving components of the environment
  • For example, some chemoheterotrophic prokaryotes are decomposers; they break down dead organisms and wastes and release carbon and other elements
• Prokaryotes can also "immobilize" or decrease the availability of nutrients by using them within their own cells

Ecological Interactions

• Symbiosis: an ecological relationship in which two species live in close contact, a larger host with a smaller symbiont

Prokaryotes often form symbiotic relationships with larger organism

• in mutualism both symbiotic organisms benefit
• in commensalism one organism benefits while neither harming nor helping the other
• in parasitism an organism called a parasite harms, but does not usually kill its host
• Parasites that cause disease are called pathogens*

Humans Impacts

• Prokaryotes have both beneficial and harmful impacts on humans
• the best-known prokaryotes are human pathogens but they represent a small fraction of prokaryotes
• Many others have positive interactions with people and some play essential roles in both agriculture and industry
• Mutualistic Bacteria*:
• Human intestines are home to about 500–1,000 species of bacteria
• Intestinal bacteria cells collectively outnumber all human cells in the body by a factor of ten
• Many intestinal bacteria are mutualists
  • For example, Bacteroides thetaiotaomicron, has genes involved in synthesizing carbohydrates, vitamins, and other important nutrients
  • It also produces signals that activate human genes involved in absorption and antimicrobial production
• Pathogenic Bacteria*:
• All known pathogenic prokaryotes are bacteria
• Bacteria cause about half of all human diseases For example, more than 1.5 million people die each year of tuberculosis, a lung disease caused by Mycobacterium tuberculosis Some bacterial disease is transmitted by other spices Lyme disease affects 300,000 causes arthritis, hearth disease nerous disorder and death Caused by bacterium carried by ticks

Pathogenic prokaryotes

• Cause disease by releasing exotoxins and endotoxins
• Exotoxins* are proteins secreted by bacteria that can cause disease even if the bacteria are no longer present
• Cholera
• Endotoxins* are lipopolysaccharide components released only when bacteria die and their cells break down
• Salmonella (Food poisoning)

Horizontal Gene Transfer Can spread genes with virulence to normally harmful bacteria Pathogenic E.coli strains produced by horizontal transfer of genes from other pathogenic species

Antibiotic Resistance

• Since the 1940s, Bacteria has evolved rapidly
• New Antibiotics has not kept pace with the Bacteria that ha evolved in resistance
• Rapid reproduction enables bacterial cells carrying resistance genes to produce lager amounts of resistant offspring
• Resistant genes spread rapidly between bacterial cells via horizontal gene transfer.
• Benefits of bacteria*:
• Production of ethanol from Agricutural and can help reduce dependence on petroleum
• Humans reap many benefits from Bacteria:
  • Cheese and yogurt from milk
  • Production of food from Cheese and yogurt from milk (beer and wine and soy sauce)
  • Product of natural product (Plastic made by PHA Bacteria)
• Prokaryotes can also be used to reduce pollutions
• Bioremediation* the use of organisms to remove pollutants from soil, air, of water Bacteria that metabolize oil can to used to increase the breakdown of oil following a spill

Chapter 27 focuses on Bacteria and Archaea. Prokaryotes, single-celled organisms, are well-adapted to diverse environments and achieve large populations. They are the most abundant organisms on Earth. Most are unicellular, with varied shapes like spheres, rods, and spirals.