Lecture Notes: Prokaryotes, Phylogeny, Endosymbiosis, and Protists
Prokaryotes: Overview and Timeline
Lecture aims: explore diversity of life by examining major groups; focus on prokaryotes (bacteria and archaea) and later a brief intro to protists (referred to as protease in the transcript).
Prokaryotes have dominated Earth for most of life's history; they were alone for a long span before eukaryotes appeared.
Timeline (Earth’s evolutionary calendar, not to scale):
Origin of life:
Prokaryotes arrive:
Photosynthesis arises:
Eukaryotic cells arise:
Prokaryotes alone on Earth for ~
First major atmospheric change driven by photosynthesis: oxygen as a byproduct leading to two key consequences.
Aerobic metabolism becomes possible (presence of oxygen enables much higher energy yield in cellular respiration).
Accumulation of atmospheric oxygen leads to ozone formation, creating an ozone layer that protects from UV rays and enables life on land.
Visual: a cartoon of aquatic organisms transitioning from water to land (illustrative; not scientifically to scale).
Phylogeny and Classification
Phylogeny: the hierarchical organization of life; the three-domain system recognizes domains: .
Simplified evolutionary timeline on a phylogenetic tree (time shown for context):
Origin of life:
Prokaryotes (common bacterial ancestry) split:
Archaea and Eukarya diverged:
Important relationships:
Although both Archaea and Bacteria are prokaryotes, Archaea are more closely related to Eukarya than to Bacteria (in the three-domain model).
Traditional seven/five-kingdom framework (Plants, Animals, Fungi, Protists, and Monera/Bacteria) is outdated; the three-domain system is more reflective of evolutionary relationships.
The “old” idea (often used in intro courses) is the eight- or so kingdoms within Eukarya; the lecture notes mention a remaining usage of the older plants/fungi/animals/protists framework for familiarity, but newer systems organize by lineage and genetics rather than just kingdoms.
Key terms:
Monophyletic group: a group consisting of an ancestor and all its descendants.
Protists (protists/proteas) are described as not a monophyletic group; rather, they form multiple lineages within Eukarya and are often collectively paraphyletic.
Genomic insight (genome sequencing):`
The first archaeal/bacterial genome sequencing (1996) revealed major differences despite superficial similarities.
Bacteria vs. Archaea differences include cell wall composition (peptidoglycan in many bacteria; archaea have different polysaccharides/glycoproteins) and membrane composition, among others (RNA sequences, membrane structure).
These findings helped substantiate the three-domain model.
Extremophiles: many archaea thrive in extreme environments (e.g., high temperature, acidity); example: Sulfolobus species living in hot, acidic environments.
Prokaryotes: Diversity, Ecology, and the Human Microbiome
Prokaryotes are the most numerous and diverse organisms on Earth; ecological and metabolic diversity exceeds that of many eukaryotes.
Culturing limitations historically: only ~1% of prokaryotes could be cultured in the lab; modern DNA sequencing from environmental samples (soil, sludge, seawater) via metagenomics has unveiled vast, previously unseen diversity.
Human microbiome: vast communities of prokaryotes living inside and on the human body.
Gut: at least ~thousands of species; likely many more; estimated >10× more prokaryotic cells than human cells in the body; roughly a kilogram of body weight is bacteria.
Skin: diverse communities across different skin regions (forearm, underarm, forehead, between fingers, etc.); different habitats harbor distinct microbiota; the interdigital spaces show particularly high diversity.
Functions: gut microbiota aid in gut development and calibrating the immune system; modulate calorie extraction from food; skin microbiota protect against pathogens and stimulate local immunity.
Metagenomics: technique focused on sequencing DNA from entire microbial communities to assess diversity and functional potential.
Notable example of prokaryote influence: endosymbiotic associations can dramatically affect host biology (e.g., bacteria in parasitic wasps can manipulate sex ratios; antibiotics can reverse effects by killing the symbiont).
Prokaryotes can affect their environment and other organisms in impactful ways despite their small size.
Prokaryote Cell Structure, Morphology, and the Endomembrane Concept
Prokaryotes (bacteria and archaea) generally lack a nucleus and have a single, undivided compartment where DNA resides (the nucleoid region).
Cell wall differences:
Bacteria often have peptidoglycan in their cell walls.
Archaea have cell walls made of different substances (polysaccharides or glycoproteins) and lack peptidoglycan.
Size and organization:
Prokaryotic cells are typically much smaller than eukaryotic cells and lack a true nucleus; DNA floats in the cytoplasm.
Eukaryotic cells have a nucleus bounded by a nuclear envelope and contain membrane-bound organelles; this compartmentalization is a major difference from prokaryotes.
Eukaryotic features (contrast to prokaryotes):
Nuclear envelope enclosing DNA in the nucleus.
Cell membrane (plasma membrane) plus a cytoskeleton for structure and transport; eukaryotes generally lack a rigid cell wall (except many plants and some fungi/algae) but have a more flexible plasma membrane.
Organelles (mitochondria, chloroplasts, endoplasmic reticulum, Golgi, lysosomes, peroxisomes, etc.) bounded by membranes, specialized for distinct functions.
Vesicles for intracellular transport and digestion; complex endomembrane system.
A common misconception to note: ribosomes are not membrane-bound in both prokaryotes and eukaryotes (though they are in the cytosol of both), whereas many organelles are membrane-bound in eukaryotes.
Importance of membranes: membranes regulate the selective passage of molecules (solutes, water, ions) and define compartments; they host enzymes and facilitate complex cellular processes; they are dynamic and responsive to environmental cues.
The membrane as a selective gateway:
Permeability is selective; some molecules pass freely, others require transport mechanisms.
Membranes create and maintain distinct internal environments and enable specialized functions in different organelles.
Endosymbiosis and the Origin of Eukaryotic Cells
Endosymbiotic theory (evidence discussed): ancestral free-living prokaryotes were incorporated into a larger host cell and became organelles.
Mitochondria and chloroplasts retain their own DNA and ribosomes, supporting a prokaryotic origin.
Chloroplasts share features with cyanobacteria; mitochondria share features with proteobacteria.
Chloroplasts have chlorophyll and galactolipids in their membranes, consistent with photosynthetic ancestry.
Implications: mitochondria and chloroplasts likely originated from endosymbiotic events where a primitive eukaryotic cell engulfed aerobic bacteria (proto-mitochondrion) and, later, a photosynthetic cyanobacterium (proto-chloroplast).
The endosymbiotic origin of organelles explains why these organelles contain their own circular DNA and ribosomes and why they reproduce by a division process resembling binary fission.
Key takeaways for exam readiness:
Endosymbiosis explains the origin of mitochondria and chloroplasts.
Organelles are membrane-bound, have their own DNA, and bear similarities to ancient prokaryotes.
Prokaryote Physiology and Metabolism
Reproduction: prokaryotes reproduce asexually by fission (binary fission), splitting into two or more parts that form new cells.
Genetic exchange mechanisms between prokaryotes:
Conjugation: DNA transfer via a cytoplasmic bridge between two cells.
Transformation: uptake of extracellular DNA from the environment.
Transduction: DNA transfer mediated by bacteriophages (virus that infects bacteria).
Metabolic diversity and energy sources:
All organisms need energy and a carbon source to survive; most bacteria and archaea are heterotrophic (obtain carbon from organic compounds) though some are autotrophic.
Autotrophs: obtain carbon from CO₂ and use light or inorganic chemical reactions for energy.
Photoautotrophs (e.g., cyanobacteria): use light for energy and CO₂ for carbon; CO₂ is inorganic and lacks C–H bonds.
Chemolithotrophs: obtain energy from inorganic compounds (e.g., hydrogen sulfide) and carbon from CO₂; common among archaea; can inhabit extreme environments (deep-sea hydrothermal vents).
Notable nuance: some prokaryotes use light for energy but rely on organic compounds for carbon (photoheterotrophs).
Cyanobacteria and primary production:
Cyanobacteria are photosynthetic bacteria that contribute to atmospheric O₂ and the global carbon cycle.
Metabolic strategies enabling life in extreme environments:
Chemolithotrophy enables life in places without light (e.g., deep-sea vents) and contributes to primary production via chemosynthesis.
Notable ecological example: hydrothermal vent communities are based on chemosynthesis conducted by archaea and bacteria; life here is independent of sunlight and relies on chemical energy from the Earth’s crust.
Protists (Protista) and Eukaryotic Diversity
Protists are not a monophyletic (single-ancestral) group; they are diverse and arise from multiple eukaryotic lineages.
Eight major eukaryotic lineages are recognized; most lineages include protists. Protists are often unicellular, though some (e.g., kelp) are multicellular.
Mutualisms and symbioses involving protists have been historically important:
Termites host cellulose-digesting protists in their gut, enabling wood digestion.
Coral symbiosis with dinoflagellates (dinoflagellates living inside corals) is essential for coral reef ecosystems.
Protists are associated with various parasites (e.g., Giardia, malaria-causing Plasmodium, trypanosomes causing sleeping sickness).
Examples of protist diversity:
Kelp (brown algae): a multicellular protist; can reach lengths up to about ; forms important coastal ecosystems.
Diatoms: phytoplankton with silica-based cell walls; highly ornate and well-preserved; contribute to ~ of global primary productivity and fix ~ of global carbon; silica cell walls provide useful morphological features for paleoecology and are used in diatomaceous earth filtration and as fertilizer.
Diatoms as a key example of protist productivity and ecological impact:
Silica-based shells give diatoms distinct, highly preserved ornamentation.
The fossil and ecological significance of diatoms extends to their role in paleoecology and commercial filtration technologies; their unique morphology is exploited in various applications.
Nitrogen Cycling and Microbial Ecology
Prokaryotes play central roles in nutrient cycling, including the global nitrogen cycle:
Nitrogen fixation: atmospheric N₂ is converted to ammonia (NH₃) or ammonium (NH₄⁺) by certain bacteria/archaea (e.g., rhizobium associated with legumes).
Nitrification: ammonia (NH₄⁺) is oxidized to nitrite (NO₂⁻) and then to nitrate (NO₃⁻).
Denitrification: nitrate (NO₃⁻) is reduced back to atmospheric N₂.
Rhizobium and nitrogen fixation:
Rhizobium bacteria live in root nodules of legumes, converting atmospheric N₂ into ammonium that plants can assimilate; this enriches soils and supports plant communities in nutrient-poor environments.
Ecological significance of nitrogen-cycling microbes:
These processes are essential for soil fertility, plant growth, and ecosystem productivity.
Prokaryotes link energy capture and carbon cycling to broader nutrient dynamics in soils, oceans, and symbiotic relationships.
Prokaryotes, Antibiotics, and Bioactive Compounds
Prokaryotes produce diverse bioactive compounds, including cellulose-degrading enzymes and toxins with potential pharmaceutical applications (e.g., polyketides like poderine used in defense by symbiotic bacteria in podrid beetles; some polyketides possess anticancer properties).
Rhizobium’s nitrogen fixation and root nodules illustrate the ecological and agricultural relevance of prokaryotes in plant communities.
Methanogens (a subset of archaea) produce methane as a key energy form in anaerobic metabolism; methane is a potent greenhouse gas when released to the atmosphere.
Methane production is substantial in both natural and agricultural systems; up to roughly 80–90% of atmospheric methane is derived from archaea, with a notable share (about 30%) arising from the intestinal tracts of grazing herbivores.
Methane is eventually consumed by other microbes; the global methane cycle involves both production and consumption, influencing climate dynamics.
Protists Revisited: Ecology, Evolution, and Practical Relevance
Protists (protists) include diverse lineages with varied lifestyles, from unicellular to multicellular (e.g., kelp).
Diatoms provide a striking example of protist-driven primary production and biogeochemical cycles, particularly carbon fixation and silica-based morphology.
The study of protists has informed our understanding of endosymbiosis, mutualism, and the evolution of eukaryotic cellular complexity.
Snippets and Real-World Connections
Endosymbiosis evidence is embedded in organelles:
Mitochondria and chloroplasts contain their own DNA and ribosomes and resemble proteobacteria and cyanobacteria, respectively.
They harbor pigments and lipids (chlorophyll, galactolipids) characteristic of ancestral prokaryotes.
The large-scale ecological roles of prokaryotes: nitrogen cycling, methane production/consumption, nutrient recycling, and energy flow in extreme environments (hydrothermal vents) illustrate how microbial life underpins global biogeochemical processes.
Human health context: the microbiome’s influence on development, immune system calibration, metabolism, and disease resistance underscores the functional importance of prokaryotes in human biology.
Quick Recap of Key Terms and Concepts
Domains:
Major differences: cell wall composition (peptidoglycan vs. archaeal polysaccharides/glycoproteins); presence vs. absence of a nuclear envelope; membrane-bound organelles in Eukarya.
Endosymbiosis: mitochondria and chloroplasts originated from free-living bacteria; evidence includes own DNA, ribosomes, and shared features with prokaryotes.
Metabolic diversity in prokaryotes: photoautotrophs, chemolithotrophs, photoheterotrophs, and heterotrophs; energy and carbon source strategies.
Nitrogen cycle steps: fixation (N₂ → NH₄⁺), nitrification (NH₄⁺ → NO₂⁻ → NO₃⁻), denitrification (NO₃⁻ → N₂).
Protists: diverse, often not monophyletic; includes diatoms (silica walls; major carbon fixation; 40% of primary productivity; 20% of global carbon), kelp (multicellular algae up to ~), and mutualistic/parasitic interactions (e.g., termite gut symbionts, coral-dinoflagellate symbioses).
Methanogenesis and methane cycling: archaea produce significant methane; methane dynamics are globally relevant to climate.
Notes and examples discussed in class were used to illustrate core concepts like endosymbiosis, microbial ecology, and the vast diversity of life beyond visible organisms. The lecture emphasizes both historical context (timeline, phylogeny) and contemporary discoveries (metagenomics, human microbiome, extreme environments).
Prokaryotes: Overview and Timeline
Prokaryotes (bacteria and archaea) dominated Earth for ~ before eukaryotes.
Key Timeline:
Origin of life:
Prokaryotes:
Photosynthesis:
Eukaryotes:
Photosynthesis led to:
Oxygen accumulation, enabling aerobic metabolism.
Ozone layer formation, protecting from UV rays, allowing life on land.
Phylogeny and Classification
Three-domain system: . This reflects evolutionary relationships better than older kingdom models.
Key relationship: Archaea are more closely related to Eukarya than to Bacteria.
Monophyletic group: An ancestor and all its descendants. Protists are not monophyletic.
Genomic insight: First genome sequencing (1996) revealed major differences between Bacteria and Archaea (cell wall, membrane composition, RNA).
Bacteria: often peptidoglycan cell walls.
Archaea: different polysaccharides/glycoproteins in cell walls, no peptidoglycan.
Extremophiles: Many archaea thrive in extreme environments.
Prokaryotes: Diversity, Ecology, and the Human Microbiome
Most numerous and diverse organisms on Earth.
Metagenomics: DNA sequencing from environmental samples, revealing vast uncultured diversity (~99% of prokaryotes).
Human microbiome: Thousands of prokaryotic species in/on the body (gut, skin).
Functions: aid gut development, calibrate immune system, modulate calorie extraction, protect against pathogens.
Endosymbiotic associations: Prokaryotes can dramatically affect host biology (e.g., bacteria in parasitic wasps).
Prokaryote Cell Structure, Morphology, and the Endomembrane Concept
Prokaryotes lack: a true nucleus (DNA in nucleoid region) and membrane-bound organelles.
Eukaryotes have: a nuclear envelope, membrane-bound organelles (mitochondria, chloroplasts, ER, Golgi), and a cytoskeleton.
Cell wall differences: Bacteria have peptidoglycan; Archaea do not.
Membranes: Regulate passage of molecules, define compartments, host enzymes, facilitate processes.
Endosymbiosis and the Origin of Eukaryotic Cells
Endosymbiotic theory: Ancestral free-living prokaryotes were incorporated into larger host cells, becoming organelles.
Evidence for endosymbiosis: Mitochondria and chloroplasts:
Retain their own circular DNA and ribosomes.
Reproduce by binary fission.
Similarities: mitochondria to proteobacteria; chloroplasts to cyanobacteria (e.g., chlorophyll, galactolipids).
Prokaryote Physiology and Metabolism
Reproduction: Asexually by binary fission.
Genetic exchange mechanisms:
Conjugation: DNA transfer via a cytoplasmic bridge.
Transformation: Uptake of extracellular DNA from the environment.
Transduction: DNA transfer mediated by bacteriophages (viruses).
Metabolic diversity (all need energy and carbon source):
Autotrophs: Carbon from CO₂.
Photoautotrophs (e.g., cyanobacteria): Energy from light.
Chemolithotrophs: Energy from inorganic compounds (e.g., H₂S); common in archaea, deep-sea vents.
Heterotrophs: Carbon from organic compounds.
Photoheterotrophs: Energy from light, carbon from organic compounds.
Cyanobacteria: Photosynthetic, vital for atmospheric O₂ and global carbon cycle.
Protists (Protista) and Eukaryotic Diversity
Protists are diverse, not a monophyletic group, arising from multiple eukaryotic lineages.
Often unicellular, some multicellular (e.g., kelp, up to ~).
Mutualisms: Termites host cellulose-digesting protists; corals host dinoflagellates.
Parasites: Giardia, Plasmodium (malaria), trypanosomes (sleeping sickness).
Diatoms: Phytoplankton with silica cell walls.
Contribute ~40 \text{%} of global primary productivity and fix ~20 \text{%} of global carbon.
Used in filtration and as fertilizer.
Nitrogen Cycling and Microbial Ecology
Prokaryotes are central to the global nitrogen cycle:
Nitrogen fixation: N₂ (atmospheric) → NH₃/NH₄⁺ (by bacteria/archaea, e.g., Rhizobium in legumes).
Nitrification: NH₄⁺ → NO₂⁻ → NO₃⁻.
Denitrification: NO₃⁻ → N₂.
Rhizobium: Symbiotic bacteria enriching soil, vital for plant growth.
Prokaryotes, Antibiotics, and Bioactive Compounds
Prokaryotes produce bioactive compounds (e.g., antibiotics, anticancer polyketides, cellulose-degrading enzymes).
Methanogens (Archaea): Produce methane (CH₄), a potent greenhouse gas, from anaerobic metabolism.
~80-90% of atmospheric methane from archaea; ~30% from grazing herbivores.
Quick Recap of Key Terms and Concepts
Domains: Bacteria, Archaea, Eukarya.
Major differences: Cell wall (peptidoglycan vs. archaeal polysaccharides); nuclear envelope (absent vs. present); membrane-bound organelles (absent vs. present).
Endosymbiosis: Explains origin of mitochondria and chloroplasts (from proteobacteria and cyanobacteria).
Metabolic diversity: Photoautotrophs, chemolithotrophs, photoheterotrophs, heterotrophs.
Nitrogen cycle: Fixation, nitrification, denitrification.
Protists: Diverse eukaryotic lineages, not monophyletic; diatoms (silica walls, primary productivity, carbon fixation), kelp, mutualists, parasites.
Methanogenesis: Archaea produce methane, a climatically relevant greenhouse gas.