Bacteria, Archaea, and Eukarya

• Prokaryotes are a non-monophyletic group biologically.
• "Prokaryote" is not a biologically sensible term.
• Bacteria and Archaea are prokaryotes.

Adaptability and Diversity

• Life is mostly single-celled.
• Bacteria and Archaea are highly adaptable.
• They live nearly everywhere, including hot, cold, acidic, sulfurous, and salty conditions.
• The number of bacteria is vast.
• A cup of soil has more bacteria than the number of humans that have ever existed.
• Bacteria and Archaea have high genetic diversity.

Microbiome Influence

• There are more cells in humans that are not human than are human cells.
• Humans are much bigger by volume than their microbiome.
• Gut bacteria influences obesity (in mice), sexual behavior (in flies), stress and depression (in mice), and may affect OCD (in humans).

Mutualisms with Humans

• Bacteria provides mutualistic benefits to humans.
• Bacteria directly inhibit pathogens.
• They aid in digestive processes.
• Short Chain Fatty Acids come from bacterial fermentation.
• Bacteria metabolize drugs.
• They aid the development of the immune system and the fine control of cytokines, which manage the inflammatory response.
• Antibiotics can harm beneficial bacteria.
• Bacteria facilitate the absorption of minerals and synthesize certain vitamins.

Beware of News

• Articles connecting the microbiome to inflammatory bowel disease, diabetes, and cancer may present correlations without causation.

Bacterial Cell Characteristics

• Bacteria are unicellular, but some species can form colonies.
• Bacterial cells range from 0.5–5 μm making them much smaller than eukaryotic cells which range between 10–100 μm.
• Bacterial cells vary in shape.
• The most common shapes are spheres (cocci), rods (bacilli), and spirals.

Bacteria Cell Walls

• Gram-positive bacteria have thick, complex peptidoglycan networks and contain lipoteichoic and teichoic acid.
• Gram-negative bacteria have thin peptidoglycan layers and a second outer membrane with lipopolysaccharide.
• Gram-negative bacteria are often resistant to antibiotics.

Gram Stain Process

• Eukaryotes and Archaea possess polysaccharides and proteins while lacking peptidoglycan.
• Gram stains make bacteria visible and classify many bacterial species.
• Gram-positive bacteria are one classification.
• Gram-negative bacteria are another classification.
• Gram-negative bacteria have less peptidoglycan.
• These have an outer membrane, which can be toxic, and are likely to be antibiotic resistant.

Fimbriae

• Some bacteria have fimbriae, also called attachment pili that allow them to stick to substrates or to other individuals in a colony, also referred to as biofilms.

Flagella and Taxis

• Flagella are slender, rigid, and helical structures composed of the protein flagellin.
• Flagella allow cells to move in response to stimuli, called taxis.
• These are involved in locomotion, and spin like a propeller.
• Flagella are structurally and functionally different from eukaryotic flagella.

Bacteria and Archaea Cell Structure

• Bacteria and archaea cells usually lack complex compartmentalization.
• They generally don't have membrane-bound organelles.
• Some bacteria and archaea have specialized membranes that perform metabolic functions.
• Respiratory membranes are in aerobic bacteria.
• Thylakoid membranes are in photosynthetic bacteria.

Bacteria DNA

• The genome of bacteria is smaller than eukaryotic genomes.
• Most of the bacterial genome consists of a circular chromosome.
• Some bacterial species also have smaller rings of DNA called plasmids.
• The bacterial genome is a ring of DNA not surrounded by a membrane and located in a nucleoid region.

Bacterial Spores

• Bacteria can form either exospores or endospores.
• Endospores are internal to the bacterium.
• These are resistant to heat, UV radiation, desiccation, alcohol, and chemicals.
• Endospores can survive for extended periods.
• Bacteria causing tetanus, botulism, and anthrax produce endospores.
• Exospores are formed differently, and are less robust.

Reproduction and Mutation

• Bacteria reproduce through binary fission quickly, dividing every 1–3 hours.
• Offspring are generally genetically identical.
• Mutations cause variation in offspring, but are rare.
• Reproduction occurs very fast.

Genetic Diversity

• Bacteria and archaea have considerable genetic variation.
• Rapid reproduction, mutation, and genetic recombination contribute to genetic diversity.

Genetic Recombination

• Bacterial DNA from different individuals is brought together by transformation, transduction, and conjugation.
• A bacterial cell can take up foreign DNA from the surrounding environment in a process called transformation.
• Transduction is the movement of genes between bacteria via bacteriophages (viruses that infect bacteria).

Transformation

• Transformation was first shown in 1928.
• Bacteria that can transform are competent, about 1% of bacteria species are naturally competent under laboratory conditions.
• Techniques can make bacteria artificially competent.

Transduction, Generalized and Specialized

• Generalized transduction is the process where virtually any gene is transferred.
• This process occurs via accidents in the lytic cycle.
• Viruses package bacterial DNA, and transfer it in a subsequent infection.
• Specialized transduction occurs via accidents in the lysogenic cycle.
• In specialized transduction, prophage DNA is excised imprecisely.
• The phages involved carry both phage genes and chromosomal genes.

Conjugation

• Conjugation is the process where genetic material is transferred between bacterial cells.
• Sex pili allow cells to connect and pull together for DNA transfer.
• The F factor is required for the production of sex pili.
• The F factor can exist as a separate plasmid or as DNA within the bacterial chromosome.

F Plasmid Transfer

• F+ cells produce F pilus that connects to F- cells.
• Transfer of F plasmid occurs through conjugation bridges.
• F plasmids are copied through rolling circle replication, which results in two F+ cells.
• The F plasmid can integrate into the bacterial chromosome, events which are similar to crossing over in eukaryotes.
• Hfr cells have a high frequency of recombination.
• The F plasmid can also excise itself by reversing the integration process.

R Plasmids

• R plasmids carry genes for antibiotic resistance
• Antibiotics select for bacteria with genes resistant to them.
• Antibiotic-resistant strains of bacteria are becoming more common.
• Misuse and overuse of antibiotics contributes to antibiotic resistance.
• Agricultural uses and patients demanding antibiotics for nonbacterial infections contributes to this problem.
• Soaps and toys that are treated with antibiotics exacerbate the problem, as does lateral gene transfer allows multiple resistance.

Antibiotic Resistance - MRSA

• MRSA, or Methicillin Resistant Staphylococcus aureus, first appeared in 1961, two years after Methicillin was first used.
• MRSA is resistant to penicillin, oxacillin, amoxicillin, tetracycline, erythromycin, and clindamycin.
• 85% of MRSA infections happen in hospitals.
• As of 2011, MRSA caused over 11,000 deaths.
• Infections are mostly skin infections, although the infections can spread to other organs.

Bacterial Nutritional Adaptations

• Phototrophs obtain energy from light.
• Chemotrophs obtain energy from chemicals.
• Autotrophs require CO₂ as a carbon source.
• Heterotrophs require an organic nutrient to make organic compounds.
• Chemoautotrophs are found in black smoker deep sea vents and are major primary producers.

Oxygen Metabolism

• Bacteria metabolism varies based on oxygen requirements.
• Obligate aerobes require O₂ for cellular respiration.
• Obligate anaerobes are poisoned by O₂ and must use fermentation or anaerobic respiration.
• Facultative anaerobes can survive with or without O₂.

Nitrogen Metabolism

• Bacteria can metabolize nitrogen in a variety of ways.
• In nitrogen fixation, some bacteria convert atmospheric nitrogen, N₂, to ammonia, NH₃.

Metabolic Cooperation

• Cooperation between bacteria means they can use resources they couldn't use on their own.
• In the cyanobacterium Anabaena, photosynthetic cells and nitrogen-fixing cells called heterocytes exchange metabolic products.

Proteobacteria

• These gram-negative bacteria include photoautotrophs, chemoautotrophs, and heterotrophs.
• Some are anaerobic while others are aerobic.

Subgroup: Alpha Proteobacteria

• Many species have close relationships with eukaryotic hosts.
• Mitochondria evolved from aerobic alpha proteobacteria through endosymbiosis.
• Rhizobium, which forms root nodules in legumes fixes atmospheric N₂.

Subgroup: Gamma Proteobacteria

• Examples are sulfur bacteria such as Chromatium, and pathogens such as Legionella, Salmonella, and Vibrio cholerae.
• Escherichia coli resides in the intestines of many mammals and is not normally pathogenic.

Subgroup: Epsilon Proteobacteria

• This group contains pathogens including Campylobacter which causes blood poisoning, and Helicobacter pylori which causes stomach ulcers.
• Drs. Marshall and Warren won a Nobel Prize in 2005 for their work helping define the concept by researching ulcers.

Gram-Positive Bacteria

• Gram-positive bacteria include Actinobacteria, which decompose soil.
• Bacillus anthracis causes anthrax.
• Clostridium botulinum causes botulism.
• Staphylococcus and Streptococcus can be pathogenic.
• Mycoplasms are the smallest known cells.
• Streptomyces are the source of many antibiotics, anticancer, and antiviral drugs.

Ecological Relationships

• Symbiosis relates to ecological relationships in which 2 species live in close contact: larger host and smaller symbiont.
• Bacteria often form symbiotic relationships with larger organisms.
• Parasites that cause disease are called pathogens.

Bacteria Benefitting People

• Bacteria are used for fermentation.
• Used for waste management.
• Used for toxic spill cleanup.
• Used for genetic engineering.
• Antibiotics derive from bacteria.

Traits shared or unqiue to Bacteria, Archaea, and Eukarya

• Nuclear Envelope
  • Present = Eukarya, Absent = Bacteria and Archaea
• Peptidoglycan
  • Present = Bacteria, Absent = Archaea and Eukarya
• Introns
  • Very Rare = Bacteria, Present/Some Genes = Archaea, Present/Many Genes = Eukarya
• Histones
  • Absent = Bacteria, Present/Some Species = Archaea, Present = Eukarya
• Circular Chromosome
  • Present = Bacteria and Archaea, Absent = Eukarya
• Growth at Temps > 100° C
  • No = Bacteria and Eukarya, Some Species = Archaea

Archaea and Environment

• Some archaea live in extreme environments and are called extremophiles.
• Extreme halophiles live in highly saline environments.
• Extreme thermophiles thrive in very hot environments.
• Methanogens live in swamps and marshes and produce methane as a waste product.
• Methanogens are strict anaerobes and are poisoned by O₂.

Archaea and Humans

• Archaea produce methane in the human digestive tract.
• These are found in the mouth and can influence tooth heath.
• Many species are found in the intestine.

Explore the unique characteristics, extremophiles, and metabolic processes of Bacteria, Archaea, and Eukarya. Understand the roles of bacteria in different environments. Learn about lateral gene transfer, antibiotic resistance, and bacterial nutrition.