CHAPTER 14

13.10 The Evolution of Microbial Genomes

• Components of Microbial Genomes

  • Core Genome: Contains genes shared by all strains of a species.

  • Pan Genome: Includes core genome plus additional genes not shared by all strains.

• Microbes continuously sample genes from surrounding organisms, leading to variations in genome size, gene content, and functional traits.

Figure 13.23: Chromosomal Islands and Pathogenicity Islands in Escherichia coli

• PAIs: Critical regions in the E. coli genome that encode virulence factors, contributing to pathogenic traits.

  • Multiple pathogenicity islands (PAI I - PAI VII) enrich the E. coli genome.

  • encode functions related to virulence, metabolism, environmental adaptability and antibiotic resistance

• Evidence where genetic regions are acquired through HGT

  • flanked by inverted repeats, suggests transposition

  • base composition and coach bias influence adaptability

  • found in some but not others (pan)

• Outer Ring: facilitate interactions with TFs

• Inner Ring: shows GC frequency

Chromosomal Islands

• Pathogenicity Islands (PAI): Encompass virulence factors aiding in diseases caused by bacteria such as uropathogenic E. coli (UTI) and Staphylococcus aureus (skin infection).

  • need to be able to colonize host and replicate to establish infection.

  • Capsules: help bacteria evade immune system by inhibiting phagocytosis

• Other Chromosomal Islands encode functionalities like pollutant degradation and symbiotic relationships (e.g., Rhizobium).

PCR Amplification of 16S rRNA Gene (Figure 14.5)

• Procedure:

  1. Isolate DNA from microbial culture.

  2. Amplify 16S gene using PCR.

  3. Run PCR products on agarose gel for size verification.

  4. Sequence the gene, align sequences, and construct phylogenetic tree.

Phylogenetic Trees and Their Interpretation (Figure 14.27)

• Structure:

  • Tree topology remains unchanged with rotation of branches around nodes.

  • Nodes: divergence, common ancestor

  • Branch lengths: represent evolutionary time or genetic distance

  • Monophyletic groups: include an ancestor and all its descendants

  • Paraphyletic groups: include an ancestor and some, but not all, of its descendants

  • Polyphyletic groups: do not include the most recent common ancestor of the group.

Horizontal Gene Transfer (Figure 14.30)

• Process:

  • Unrelated species can exchange genes (Gene 2 and Gene 3) leading to incongruence in evolutionary history compared to the core genome.

• Results in diverse genetic repertoires across species.

Introduction to Metabolic Diversity

• Energy Source Classifications:

  • Phototroph: Energy from light.

  • Chemotroph: Energy from chemical compounds.

    Reducing Power Source:

  • Lithotroph: Uses inorganic sources.

  • Organotroph: Requires organic compounds.

  • Autotroph: Uses inorganic carbon.

  • Heterotroph: Uses organic carbon.

• All Eukaryotes:

  • unique trait: chloroplasts

    • photolithoautotrophs, e.g plants and algae

    • Chemoorganoheterotrophs, e.g. animals and fungi.

      • restricted to these 2 because derived from cyanobacteria and chloroplasts, which are believed to have originated from endosymbiotic relationships with these organisms.

• All Prokaryotes:

  • photolitho-hetero/autotroph

  • chemolitho-hetero/autotroph

  • mixotroph (hetero+auto)

  • chemoorganoheterotroph

• Phototrophy and respiration (must involve membrane): involve ETC and PMF, which are essential for ATP synthesis in both phototrophic and heterotrophic organisms. In phototrophs, light energy is captured and converted into chemical energy, while in chemoorganoheterotrophs, organic molecules are oxidized to release energy.

Autotrophic Pathways

can assimilate CO2 into cellular materials e.g. photo/chemolithotrophs

• Calvin Cycle:

  • Primary CO2 fixation method, common in cyanobacteria, algae, and plants (oxygenic phototrophs), purple bacteria, aerobic chemolithotrophic bacteria.

  • Key enzyme: RubisCO (located in carboxysomes).

    • reduces CO2 → G3P

  • Requires 12 NADPH (reducing power) and 18 ATP to create 1 fructose-6-phosphate from CO2.

• Reverse Citric Acid Cycle (rTCA):

  • Used by green sulfur bacteria and anaerobic or mircoaerophilic chemolithotrophic bacteria.

  • Functions in CO2 reduction; efficient with lower energy requirement compared to Calvin Cycle.

  • 24H and 10 ATP to fix 6 CO2 into 1 glucose molecule

  • requires enzymes not found in citric acid cycle

    • alpha-ketoglutarate, pyruvate synthase, etc.

• reverse/opposite from “Can I Keep Selling Sex For Money Officer”

  • citrate → Acetyl-CoA → pyruvate → phosphoenolpyruvate → G3P

• Photosynthesis Patterns: Illustrated different photosynthetic pathways, crucial for energy conversion in various organisms.

Comparison of Electron Flow

Water in cyclic photophosphorylation provides electrons and protons

• Purple Bacteria:

  • cyclic electron flow

  • an-oxygenic photosynthesis, produce energy without O2 as byproduct

  • coverts weak electron donor to strong donor

  • use hydrogen sulfide for reducing power

• Green Sulfur Bacteria

  • not cyclic

  • anoxygenic

  • rely on hydrogen sulfide as electron donor

  • contains chlorosomes, house bacteriochlorophylls.

• Cyanobacteria:

  • water as electron donor

  • oxygenic bc O2 is produced

  • oxygenic photosynthesis

• Oxygenic vs Anoxygenic Phototrophs:

  • Highlight differences in electron transport during photophosphorylation.

  • Oxygenic phototrophs release oxygen, while anoxygenic ones do not.

• Oxygenic: H2O electron donor → split and release O2 during photosynthesis.

• Anoxygenic: H2S electron donor → sulfur as byproduct made.

  • Both produce ATP

  • if the membrane is damaged (thylakoid) → disrupts ETC = ATP production will decrease or stop

• Oxygenic Photosynthesis:

  • Eukaryotes (plants and algae): occur in chloroplast

  • Cyanobacteria: occur in stacked membrane (thylakoids) in cytoplasm

    • stacked thylakoids = increase space/size in membrane

    • inner membrane: for energy

    • thylakoid space = lowest pH

• Electron Transport in Oxygenic Photosynthesis

  • Cyanobacteria acquire PS1 and PSt2 through HGT which allows them to harness energy for photosynthesise

  • PSI and PSII → noncyclic

  • noncyclic electrons: reduce NADP+ → NADPH

  • From PS1, electrons pass through ETC then they return to PS1

  • Photophosphorylation: Sunlight → PMF → ATP production

Photophosphorylation vs. Oxidative Phosphorylation

• Photophosphorylation:

  • occurs in the thylakoid membranes of chloroplasts

  • utilize light energy to generate a proton motive force (PMF),

• oxidative phosphorylation:

  • occurs in the inner mitochondrial membrane

  • use energy released from electron transport to create ATP.

• BOTH:

  • PMF

  • ATP synthase

  • ETC

  • membrane

Sulfur Bacteria

• Sox system used to oxidize sulfur = genes have been transferred multiple times through HGT

• Sox/Dsr system:

  • ATP produced through substrate level oxidative phosphorylation

• Sulfate and Sulfur Reduction:

  • Sulfate reduction:

    • sulfate (SO4²-) is reduced to sulfide (H2S) by sulfate-reducing bacteria

  • Sulfur Reduction;

    • sulfur (S) is reduced to sulfide (H2S) through the metabolic processes of sulfur-reducing bacteria

  • Sulfide → sulfate = decrease pH

Iron Oxidation

• Chemolithotrophic Bacteria:

  • Oxidize ferrous iron (Fe2+) to ferric iron (Fe3+) which is easily oxidized in the presence of air

  • ferric hydroxide plays precipitates water, affecting environmental pH.

  • Many Fe oxidizers strongly acidophilic

Nitrification Process

• Chemolithotrophic Nitrifying Bacteria:

  • Convert ammonia (NH3) → nitrite (NO2−) → nitrate (NO3−) through specific oxidation processes.

  • Important contributors in soil, water, and wastewater systems.

  • Nitrifiers can only catalyze one set of reactions

    • e.g. ammonia → nitrite by nitrosomonas and nitrosopumilus

    • nitrite → nitrate by nitrobacter

• Nitrate Reduction and Denitrification:

  • Nitrate reduction: aerobic

    • nitrate (NO3-) → nitrite (NO2-) or further to nitrogen gas (N2) and other nitrogenous compounds.

  • Denitrification: anaerobic

    • final step in the nitrogen cycle, where denitrifying bacteria convert nitrates back into nitrogen gas, releasing it into the atmosphere and completing the cycle.

Respiratory Processes

• Assimilative:

  • process that consumes energy

  • reduced form of element becomes part of the biomass of the organism

  • autotrophic pathways

  • e.g. bacteria that take in sulfur from the environment to make cysteine is assimilative sulfate reduction

• Dissimilative:

  • energy conserved, sulfate reduction is used to convert sulfate into hydrogen sulfide

  • Steps:

    1. Nitrate → Nitrite → Nitric Oxide → Nitrous Oxide → Dinitrogen

    2. enzymes in order: Nitrate reductase → nitrite reductase → nitric oxide reductase → nitrous oxide reductase

       Gases: nitric oxide, nitrous oxide, and dinitrogen

Key Nitrogen Compounds and Oxidation States

• Oxidation States:

  • Includes ammonia (−3), nitrate (+5), and nitric oxide (+2), indicating the versatility of nitrogen transformations in ecosystems.

Methanogenesis

• Process:

  • Biological methane production catalyzed by methanogens (strictly anaerobic Archaea).

  • Important in ecological settings like wetlands and digestive systems.

  • methanogenesis is also a from of anaerobic respiration (CO2 reduction by H2)

  • uses coenzyme M to transfer electron and reduce carbon

Energetic and Redox Considerations

Fermentation Characteristics

• Energy Conservation:

  • Lacks electron transport chain or PMF; thus, lower energy yield compared to respiration.

  • Achieves balance through substrate-level phosphorylation.

Common Fermentations and Their Organisms

• Detailed reactions and energy yields from various fermentation processes illustrated with representative organisms.

  • Includes alcoholic fermentation, lactic fermentation, and butyric fermentation among others.

CHAPTER 16

Phylogenetic Diversity of bacteria

• distinguished based on 16S ribosomal RNA

• 4 main phyla

  • Proteobacteria

  • Actinobacteria

  • firmicutes

  • bacteroidetes.

Proteobacteria

• largest and most metabolically diverse due to HGT

• ALL gram (-)

• relationships to oxygen:

  • anaerobic, microaerophilic, and facultatively aerobic

• Morphologically divers:

  • rods, cocci, spirilla, filamentous, budding and appendage forms

• 6 classes

  1. Alpha

  2. beta

  3. delta

  4. gamma

  5. epsilon

  6. zeta

Alphaproteobacteria

• second largest class

• obligate intracellular parasites or mutualists of animals

• most are obligate or facultative aerobes

• Diverse:

  • phototrophs, nitrogen-fixing bacteria, pathogens, and oligotrophs.

• Main orders

  • Rhizobiales:

  • Rickettsiales

    • obligate intracellular parasites or mutualists

    • cant be cultivated outside host cell

  • Caulobacterales

Betaproteobacteria

• 3rd largest

• Diversity:

  • chemolithotrophs, nitrogen fixers, pathogens, and waste water treatment bacteria

• Main orders:

  • Burkholderiales

  • Hydrogenophilales

  • Methylophilales

  • Neisseriales

  • Nitrosomonadales

  • Rhodocyclales

Gammaproteobacteria

• Largest and most diverse class

• well-known human pathogens

• Enterobacteriales (Enteric bacteria):

  • Escherichia, Salmonella, Shigella, Klebsiella, Proteus

• Pseudomonadales and Vibrionales:

  • pseusomonas: opportunistic pathogens, biofilm formers

  • Vibrio, Aliivibrio: marine bacteria, includes pathogens (V.cholera)

Deltaproteobacteria and Epsilonproteobacteria

• Deltaproteobacteria: Includes sulfate-reducing bacteria and some predatory species, playing significant roles in biogeochemical cycles.

  • Key Genera:

    • Bdellovibrio, Myxococcus, Desulfovibrio, Geobacter

  • predatory bacteria→ Bdellovibrio

  • sulfate-reducing → Desulfovibrio

  • metal-reducing → Geobacter

• Epsilonproteobacteria: Often found in extreme environments, such as deep-sea vents and gastric systems of animals, with some members being pathogenic.

  • Key Genera:

    • campylobacter: causes gastroenteritis

    • helicobacter: causes gastric ulcers

Gram + bacteria and relatives

• Firmicutes

  • low G+C (Gram +)

  • includes lactic acid bacteria, endospore formers, and pathogenic species

• Lactobacillales

  • Key Genera:

    • lactic acid bacteria

    • lactobacillus: dairy fermentation

    • streptococcus: strep throat and dental caries

    • enterococcus: fecal origin

    • leuconostoc: produces dextran slimes and flavor compounds in dairy

  • Sporulating Bacillales and Clostridiales

    • endospore (survival advantage) formers found in soil, adapted for survival in extreme conditions

    • pathogenic species infect incidentally

      • Key Genera:

        • Bacillus: produce antibitoics

        • Clostridium:

          • obligate anaerobes, ferment sugars or amino acids.

          • generate ATP through Sub-level phosphorylation

        • Sporosarcina: highly alkaline tolerant, coccoid shape = unusual among spore formers

  • Aerobic conditions: Bacillus species grow

  • anaerobic conditions: Clostridium species grow

• Tenericutes

  • Lack cell wall

  • includes Mycoplasma which is phylogenetically related to Firmicutes

• Mycoplasma

  • Key Genera: mycoplasma, spiroplasma

    • resistant to antibiotics targeting peptidoglycan

    • requires sterols for membrane stability

    • fried egg morphology

• Actinobacteria

  • high G+C (Gram +)

  • includes Mycobacterium, Streptomyces, and other filamentous soil bacteria

• Mycobacterium

  • acid-fast staining for identification

  • waxy, lipid rich cell wall

  • mycolic acids

  • cord factor

  • Mycobacterium tuberculosis: Causes tuberculosis, requires long incubation times for visible colony formation.

  • Mycobacterium leprae: Causes leprosy.

Orders of chlamydiae, planctomycetes, and verrucomicrobia

• Planctomyces

  • gram (-) found in orders planctomycetales and brocadiales

  • stalked bacterium composed of protein

  • facultatively aerobic chemoorganotrophs

  • grow by fermentation or respiration of sugar

  • found in freshwater, marine, and soil habitats

• Verrucomicrobia

  • found in freshwater, marine, forest, and agricultural soils

  • aerobic or facultatively aerobic bacteria that ferment sugar

  • some symbiotic relationships with protists

  • membrane bound intracellular structures

  • cytoplasmic appendages

  • present peptidoglycan

  • bacteria divide symmetrically

• Chlamydiae

  • obligate intracellular parasites

  • gram (-) but lack peptidoglycan, cysteine-rich proteins for stability instead

  • respiratory, ocular, and sexually transmitted infections

    Infection Cycle:

    1. Attachment and entry: elementary body attaches to host cell and is internalized through phagocytosis

    2. Conversion to Reticulate Body (RB): within host endosome, EB → RB = active = replication

    3. Reconversion to Elementary Bodies: RBs reorganize into EBs making them infectious again

    4. Cell Lysis: rupture and release of EBs that infect nearby cells

Hyperthermophilib Bacteria

• in geothermal aquatic systems

• Thermotoga

  • ancient lineage, archaeal genes (suggest HGT), toga structure (sheath-like envelope), rod shaped

  • stain gram (-)

  • fermantative anaerobes

• Thermodesulfobacterium

  • sulfate reducer with ether-linked lipids

  • uses pyruvate, lactate, and ethanol as electron donors

Radiation Resistant Deinococcus Radiodurans

• highly efficient in repairing damaged DNA

  • RecA-dependent and independent repair systems

  • single and double stranded DNA breaks

  • reassembles chromosome from fragments

• resistant to radiation and desiccation

• pink and red because of carotenoids

  • Deinococcus radiodurans: Radiation-resistant, superior DNA repair.

  • Thermus aquaticus: Source of Taq polymerase for PCR.