Chapter 27 - Bacteria & Archaea Bacteria and Archaea Lecture Presentation by Nicole Tunbridge and Kathleen Fitzpatrick Unit7: Biological Diversity & Microbiology

Why is Utah’s Great Salt Lake water pink? Chapter 27 - Bacteria & Archaea Why is Utah’s Great Salt Lake water pink? Figure 27.1 Why is this lake’s water pink? Can reach a salt concentration of 32% Pink color comes from living prokaryotes Unit7: Biological Diversity & Microbiology

Chapter 27 - Bacteria & Archaea Concept 27.1: Structural and functional adaptations contribute to prokaryotic success Most likely Earth’s first organisms Divided into 2 Domains: Bacteria and Archaea Most are unicellular: 0.5–5 µm in size Some species form colonies Variety of Shapes: Spherical (cocci) Rods (bacilli) Spirals Unit7: Biological Diversity & Microbiology

Chapter 27 - Bacteria & Archaea Figure 27.2 Chapter 27 - Bacteria & Archaea Figure 27.2 The most common shapes of prokaryotes 1 µm 1 µm 3 µm (a) Spherical (b) Rod-shaped (c) Spiral Unit7: Biological Diversity & Microbiology

Chapter 27 - Bacteria & Archaea Figure 27.UN04 Fimbriae Cell wall Circular chromosome Capsule Sex pilus Internal organization Figure 27.UN04 Summary of key concepts: prokaryote adaptations Flagella Unit7: Biological Diversity & Microbiology

Bacterial Cell Wall & Surface Structures Chapter 27 - Bacteria & Archaea Bacterial Cell Wall & Surface Structures Maintains cell shape, protects cell, and prevents bursting in a hypotonic environment Contains Peptidoglycan: Network of sugar polymers cross-linked by polypeptides Eukaryote Cell Walls: Made of cellulose or chitin Archaea: Contain polysaccharides and proteins Gram Stain: Classify bacteria by cell wall composition Gram-positive: Simpler walls, large amount of peptidoglycan Gram-negative: Less peptidoglycan and toxic outer membrane Unit7: Biological Diversity & Microbiology

Chapter 27 - Bacteria & Archaea Figure 27.3 (a) Gram-positive bacteria (b) Gram-negative bacteria Carbohydrate portion of lipopolysaccharide Peptido- glycan layer Outer membrane Cell wall Cell wall Peptido- glycan layer Plasma membrane Plasma membrane Peptidoglycan traps crystal violet, which masks the safranin dye. Crystal violet is easily rinsed away, revealing the red safranin dye. Gram-positive bacteria Gram-negative bacteria Figure 27.3 Gram staining 10 µm Unit7: Biological Diversity & Microbiology

Chapter 27 - Bacteria & Archaea Antibiotics Target peptidoglycan  Damage bacterial cell walls Gram-negative Bacteria: More likely to be antibiotic resistant Capsule: Polysaccharide or protein layer covers many prokaryotes 200 nm Bacterial cell wall capsule Tonsil cell Unit7: Biological Diversity & Microbiology

Chapter 27 - Bacteria & Archaea Endospores: Many prokaryotes form these Remain viable in harsh conditions for centuries Metabolically inactive Fimbriae: Allow prokaryotes to stick to substrate or individuals in a colony Pili (sex pili): Allow prokaryotes to exchange DNA Longer than fimbriae 0.3 µm Coat Endospore 1 µm Fimbriae Unit7: Biological Diversity & Microbiology

Chapter 27 - Bacteria & Archaea Motility Taxis: Ability to move toward or away from stimuli Heterogeneous environment: Exhibited by many bacteria Chemotaxis: Movement toward or away from a chemical stimulus Flagella: Propel bacteria Scattered across surface Concentrated at one or both ends Flagella of bacteria, archaea, and eukaryotes composed of different proteins Likely evolved independently Unit7: Biological Diversity & Microbiology

Video: Prokaryotic Flagella

Chapter 27 - Bacteria & Archaea Figure 27.7 Flagellum 20 nm Filament Hook Cell wall Motor Figure 27.7 A prokaryotic flagellum Plasma membrane Peptidoglycan layer Rod Unit7: Biological Diversity & Microbiology

Evolutionary Origins of Bacterial Flagella Chapter 27 - Bacteria & Archaea Evolutionary Origins of Bacterial Flagella Bacterial flagella: Composed of a motor, hook, and filament Many proteins are modified versions of proteins that perform other tasks in bacteria Flagella likely evolved as existing proteins were added to an ancestral secretory system Example of Exaptation Existing structures take on new functions via descent with modification Unit7: Biological Diversity & Microbiology

Prokaryotic Cells Internal Organization and DNA Chapter 27 - Bacteria & Archaea Prokaryotic Cells Internal Organization and DNA Lack complex compartmentalization Specialized membranes perform metabolic functions Infoldings of the plasma membrane 0.2 µm 1 µm Respiratory membrane Thylakoid membranes (a) Aerobic prokaryote (b) Photosynthetic prokaryote Unit7: Biological Diversity & Microbiology

Chapter 27 - Bacteria & Archaea Prokaryotic Genome Less DNA than eukaryotic genome Most of genome is circular chromosome Located in nucleoid region No membrane Some species have plasmids, or smaller rings of DNA 1 µm Plasmids Chromosome Unit7: Biological Diversity & Microbiology

Prokaryotes Reproduction Chapter 27 - Bacteria & Archaea Prokaryotes Reproduction Reproduce quickly via binary fission Divide every 1–3 hours Short generation times Differences in prokaryotic/eukaryotic DNA replication, transcription, & translation  Allow antibiotics to inhibit bacterial growth without harming host organism. Unit7: Biological Diversity & Microbiology

Chapter 27 - Bacteria & Archaea Concept 27.2: Rapid reproduction, mutation, and genetic recombination promote genetic diversity in prokaryotes Prokaryotes have considerable genetic diversity: Rapid reproduction Mutation Genetic recombination Unit7: Biological Diversity & Microbiology

Rapid Reproduction and Mutation Chapter 27 - Bacteria & Archaea Rapid Reproduction and Mutation Binary fission  Offspring are generally identical Mutation rates during binary fission are low Rapid reproduction  Mutations accumulate rapidly within population Short generation time  Evolve quickly Prokaryotes not “primitive”  Highly evolved Unit7: Biological Diversity & Microbiology

Genetic Recombination Chapter 27 - Bacteria & Archaea Genetic Recombination Combining DNA from 2 sources  Horizontal gene transfer  Diversity Transformation: Prokaryotic cell incorporates foreign DNA from surrounding environment Transduction: Movement of genes between bacteria by bacteriophages Conjugation: Genetic material transferred between prokaryotic cells DNA transfer is one way: Donor cell attaches to a recipient by a pilus  Pulls it closer  Transfers DNA Unit7: Biological Diversity & Microbiology

Chapter 27 - Bacteria & Archaea Figure 27.11-5 Chapter 27 - Bacteria & Archaea Phage DNA 1 Phage infects bacterial donor cell with A+ and B+ alleles. A+ B+ Donor cell 2 Phage DNA is replicated and proteins synthesized. A+ B+ 3 Fragment of DNA with A+ allele is packaged within a phage capsid. A+ Crossing over Figure 27.11-5 Transduction (step 5) 4 Phage with A+ allele infects bacterial recipient cell. A+ A− B− Recipient cell Recombinant cell 5 Incorporation of phage DNA creates recombinant cell with genotype A+ B−. A+ B− Unit7: Biological Diversity & Microbiology

Chapter 27 - Bacteria & Archaea Figure 27.12 Sex pilus 1 µm Figure 27.12 Bacterial conjugation Unit7: Biological Diversity & Microbiology

The F Factor as a Plasmid Chapter 27 - Bacteria & Archaea The F Factor as a Plasmid F factor: DNA required for production of pili F factor is transferable during conjugation Cells with F plasmid: Function as DNA donors Cells without F factor: Function as DNA recipients Recipient becomes recombinant bacterium with DNA from 2 different cells R plasmids: Carry genes for antibiotic resistance Antibiotics cannot kill bacteria w/specific R plasmids Natural selection: % bacteria with genes for resistance increases in a population exposed to antibiotics Unit7: Biological Diversity & Microbiology

Chapter 27 - Bacteria & Archaea Figure 27.13a-4 Chapter 27 - Bacteria & Archaea Bacterial chromosome F plasmid F+ cell F+ cell (donor) Mating bridge F− cell (recipient) Bacterial chromosome F+ cell 1 One strand of F+ cell plasmid DNA breaks at arrowhead. 2 Broken strand peels off and enters F− cell. 3 Donor and recipient cells synthesize complementary DNA strands. 4 Recipient cell is now a recombinant F+ cell. Figure 27.13a-4 Conjugation and recombination in E. coli (part 1, step 4) (a) Conjugation and transfer of an F plasmid Unit7: Biological Diversity & Microbiology

Chapter 27 - Bacteria & Archaea Figure 27.13b-4 Chapter 27 - Bacteria & Archaea Hfr cell (donor) A+ A+ A+ F factor A+ A− A+ A− A− A+ A− Recombinand F− bacterium F− cell (recipient) 1 An Hfr cell forms a mating bridge with an F− cell. 2 A single strand of the F factor breaks and begins to move through the bridge. 3 Crossing over can result in exchange of homologous genes. 4 Enzymes degrade and DNA not incorporated. Recipient cell is now a recombinant F− cell. Figure 27.13b-4 Conjugation and recombination in E. coli (part 2, step 4) (b) Conjugation and transfer of part of an Hfr bacterial chromosome, resulting in recombination Unit7: Biological Diversity & Microbiology

Chapter 27 - Bacteria & Archaea Concept 27.3: Diverse nutritional and metabolic adaptations have evolved in prokaryotes Prokaryotes can be categorized by how they obtain energy and carbon: 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 Unit7: Biological Diversity & Microbiology

Energy and Carbon Sources are Combined to Give 4 Modes of Nutrition: Chapter 27 - Bacteria & Archaea Energy and Carbon Sources are Combined to Give 4 Modes of Nutrition: Table 27.1 Major nutritional modes Unit7: Biological Diversity & Microbiology

Roles of Oxygen & Nitrogen in Metabolism Chapter 27 - Bacteria & Archaea Roles of Oxygen & Nitrogen in Metabolism Oxygen Metabolism Obligate Aerobes require O2 for cellular respiration Obligate Anaerobes are poisoned by O2 Facultative anaerobes can survive with or without O2 Nitrogen: Essential for production of amino acids and nucleic acids Prokaryotes metabolize nitrogen in a variety of ways Nitrogen Fixation Convert atmospheric nitrogen (N2) to ammonia (NH3) Unit7: Biological Diversity & Microbiology

Metabolic Cooperation Chapter 27 - Bacteria & Archaea Metabolic Cooperation Prokaryotic cells cooperate  Allows use of resources not usable as individual cells Cyanobacterium Anabaena, (photosynthetic cells) and heterocysts (nitrogen-fixing cells) exchange metabolic products Biofilms: Surface-coating prokaryotic colonies Metabolic cooperation occurs between different species Ocean floor: Sulfate-consuming bacteria and methane-consuming bacteria use each other’s waste products Unit7: Biological Diversity & Microbiology

Metabolic cooperation in a prokaryote Chapter 27 - Bacteria & Archaea Metabolic cooperation in a prokaryote Photosynthetic cells Heterocyst Figure 27.14 Metabolic cooperation in a prokaryote 20 µm Unit7: Biological Diversity & Microbiology

Concept 27.4: Prokaryotes have radiated into a diverse set of lineages Chapter 27 - Bacteria & Archaea Concept 27.4: Prokaryotes have radiated into a diverse set of lineages Domains Bacteria and Archaea Genetic analysis  Division of prokaryotes Horizontal gene transfer between prokaryotes obscures the root of phylogeny Bacteria include the vast majority of prokaryotic species familiar to most people Proteobacteria: Gram-negative bacteria Photoautotrophs, chemoautotrophs, and heterotrophs Can be anaerobic or aerobic Unit7: Biological Diversity & Microbiology

Chapter 27 - Bacteria & Archaea Figure 27.15 Chapter 27 - Bacteria & Archaea Domain Eukarya Eukaryotes Korarchaeotes Euryarchaeotes Domain Archaea Crenarchaeotes UNIVERSAL ANCESTOR Nanoarchaeotes Proteobacteria Chlamydias Figure 27.15 A simplified phylogeny of prokaryotes Spirochetes Domain Bacteria Cyanobacteria Gram-positive bacteria Unit7: Biological Diversity & Microbiology

Chapter 27 - Bacteria & Archaea Figure 27.16aa Chapter 27 - Bacteria & Archaea Alpha Beta Gamma Proteobacteria Delta Epsilon Figure 27.16aa Exploring selected major groups of bacteria (part 1a: proteobacteria tree) Unit7: Biological Diversity & Microbiology

Chapter 27 - Bacteria & Archaea Subgroup: Alpha Proteobacteria Species closely associated with eukaryotic hosts May be ancestor of mitochondria Examples: Rhizobium, which forms root nodules in legumes and fixes atmospheric N2 Agrobacterium, which produces tumors in plants and is used in genetic engineering Rhizobium (arrows) inside a root cell of a legume (TEM) 2.5 µm Unit7: Biological Diversity & Microbiology

Chapter 27 - Bacteria & Archaea Subgroup: Beta Proteobacteria Example: the soil bacterium Nitrosomonas, which converts NH4+ to NO2– Nitrosomonas (colorized TEM) 1 µm Unit7: Biological Diversity & Microbiology

Chapter 27 - Bacteria & Archaea Subgroup: Gamma Proteobacteria Examples: Sulfur bacteria (Thiomargarita namibiensis) and pathogens (Legionella, Salmonella, Vibrio cholerae) Escherichia coli resides in the intestines of many mammals and is not normally pathogenic 200 µm Thiomargarita namibiensis containing sulfur wastes (LM) Unit7: Biological Diversity & Microbiology

Chapter 27 - Bacteria & Archaea Subgroup: Delta Proteobacteria Example: Slime-secreting myxobacteria Produces drought resistant “myxospores” Bdellovibrios: Mount high-speed attacks on other bacteria Fruiting bodies of Chondromyces crocatus, a myxobacterium (SEM) 300 µm Unit7: Biological Diversity & Microbiology

Chapter 27 - Bacteria & Archaea Subgroup: Epsilon Proteobacteria Contains many pathogens Campylobacter: Causes blood poisoning Helicobacter pylori: Causes stomach ulcers 2 µm Helicobacter pylori (colorized TEM) Unit7: Biological Diversity & Microbiology

Chapter 27 - Bacteria & Archaea Chlamydias Parasites that live within animal cells Example: Chlamydia trachomatis Causes blindness and nongonococcal urethritis by sexual transmission Chlamydia (arrows) inside an animal cell (colorized TEM) 2.5 µm Unit7: Biological Diversity & Microbiology

Chapter 27 - Bacteria & Archaea Spirochetes Helical heterotrophs Some are parasites: Treponema pallidum: Causes syphilis, and Borrelia burgdorferi: Causes Lyme disease Leptospira, a spirochete (colorized TEM) 5 µm Unit7: Biological Diversity & Microbiology

Chapter 27 - Bacteria & Archaea Cyanobacteria Photoautotrophs that generate O2 Plant chloroplasts likely evolved from cyanobacteria by the process of endosymbiosis Oscillatoria, a filamentous cyanobacterium 40 µm Unit7: Biological Diversity & Microbiology

Video: Cyanobacteria (Oscillatoria)

Chapter 27 - Bacteria & Archaea Gram-Positive Bacteria Actinomycetes: Decompose soil Bacillus anthracis: Cause of anthrax Clostridium botulinum: Cause of botulism Some Staphylococcus and Streptococcus: Can be pathogenic Mycoplasms: Smallest known cells Hundreds of mycoplasmas covering a human fibroblast cell (colorized SEM) 2 µm Streptomyces, the source of many antibiotics (SEM) 5 µm Unit7: Biological Diversity & Microbiology

Chapter 27 - Bacteria & Archaea Table 27.2 Chapter 27 - Bacteria & Archaea Table 27.2 A comparison of the three domains of life Unit7: Biological Diversity & Microbiology

Chapter 27 - Bacteria & Archaea Common traits with bacteria or with eukaryotes Extremophiles: Live in extreme environments Extreme halophiles: Highly saline environments Extreme thermophiles: Thrive in very hot environments Methanogens: Live in swamps and marshes and produce methane as a waste product Strict anaerobes  Poisoned by O2 Unit7: Biological Diversity & Microbiology

Chapter 27 - Bacteria & Archaea Figure 27.17 Chapter 27 - Bacteria & Archaea Figure 27.17 Extreme thermophiles Unit7: Biological Diversity & Microbiology

Video: Tube Worms

Concept 27.5: Prokaryotes play crucial roles in the biosphere Chapter 27 - Bacteria & Archaea Concept 27.5: Prokaryotes play crucial roles in the biosphere Prokaryotes are important to the survival of the entire biosphere. Chemical Recycling Prokaryotes recycle chemical elements between the living and nonliving components of ecosystems Decomposers: Chemoheterotrophic Prokaryotes Break down dead organisms and waste products Increase availability of nitrogen, phosphorus, and potassium for plant growth “Immobilize” or decrease the availability of nutrients Unit7: Biological Diversity & Microbiology

Chapter 27 - Bacteria & Archaea Figure 27.18 Chapter 27 - Bacteria & Archaea 1.0 0.8 0.6 Uptake of K+ by plants (mg) 0.4 0.2 Seedlings grow- ing in the lab Figure 27.18 Impact of bacteria on soil nutrient availability No bacteria Strain 1 Strain 2 Strain 3 Soil treatment Unit7: Biological Diversity & Microbiology

Ecological Interactions Chapter 27 - Bacteria & Archaea Ecological Interactions Symbiosis: Ecological relationship with 2 species living in close contact Larger host and smaller symbiont Prokaryotes often form symbiotic relationships with larger organisms Mutualism: Both organisms benefit Commensalism: Only 1 organism benefits Neither is harmed Parasitism: 1 organism = Parasite Harms but does not kill host Pathogens: Parasites that cause disease Unit7: Biological Diversity & Microbiology

Chapter 27 - Bacteria & Archaea Figure 27.19 Chapter 27 - Bacteria & Archaea Figure 27.19 Mutualism: bacterial “headlights” Unit7: Biological Diversity & Microbiology

Chapter 27 - Bacteria & Archaea Concept 27.6: Prokaryotes have both beneficial and harmful impacts on humans Mutualistic Bacteria Human Intestines: ~500–1,000 species of bacteria Break down food that is undigested by our intestines Pathogenic Prokaryotes Secrete exotoxins or endotoxins  Cause Disease Exotoxins: Cause disease even if prokaryote producing them are not present Endotoxins: Released only when bacteria lyses Horizontal gene transfer: Share virulent genes Example: Pathogenic strains of E. coli Contain genes that were acquired through transduction Unit7: Biological Diversity & Microbiology

Chapter 27 - Bacteria & Archaea Pathogenic Bacteria Bacteria cause ~1/2 of all human diseases Can be transmitted by other species Example: Lyme disease Bacterium carried by ticks 5 µm Unit7: Biological Diversity & Microbiology

Prokaryotes in Research and Technology Chapter 27 - Bacteria & Archaea Prokaryotes in Research and Technology Bacteria can be used to make natural plastics Bioremediation: Use of prokaryotic organisms to remove pollutants from the environment Bacteria can be engineered to produce vitamins, antibiotics, and hormones Bacteria are also being engineered to produce ethanol from agricultural and municipal waste biomass, switchgrass, and corn Advances in DNA Technology E. coli: Used in gene cloning Agrobacterium tumefaciens: Used to produce transgenic plants Unit7: Biological Diversity & Microbiology

Chapter 27 - Bacteria & Archaea Bacteria synthesizing and storing PHA, a component of biodegradeable plastics Figure 27.21 Bacteria synthesizing and storing PHA, a component of biodegradeable plastics Unit7: Biological Diversity & Microbiology