Prokaryotes, Protists, and Endosymbiosis

Pathogenic Bacteria

• Symbiotic relationships exist between bacteria and larger organisms.

• Some bacteria are pathogenic, causing human disease.

• Tuberculosis is an example of a bacterial disease transmitted through a vector.

• Human infection is often part of the disease's life cycle.

Mechanisms of Pathogenic Bacteria

There are three main mechanisms by which bacteria cause illness:

Direct Tissue Invasion

• Bacteria invade tissue and cause problems within the cells.

• Example: Mycobacterium tuberculosis invades lung tissue.

• Helicobacter pylori causes stomach ulcers (researchers drank cultures to prove it).

• Staphylococcus: Many strains exist, some commensal, some opportunistic pathogens.

• MRSA (Methicillin-Resistant Staphylococcus aureus) is an antibiotic-resistant bacterium.

• Anthrax: Inhaled and invades lung tissue.

• Botulism: Clostridium botulinum causes botulism, an anaerobic fermenter. Eating improperly canned or dented food can pose a risk because of this.

Toxins (Exotoxins)

• Bacteria produce toxins in various situations.

• Exotoxins: Proteins secreted by the bacterium that are toxic to the host organism.

• Clostridium botulinum: An anaerobic bacterium that produces a potent toxin.

• One gram of botulism toxin can kill up to a million people if evenly distributed.

• Cholera-is a vibrio, works similarly, produces exotoxins.

• Some Strep and E. coli strains produce exotoxins.

Toxins (Endotoxins)

• Toxic components are part of the outer membrane or cell wall of the bacterium.

• When the cell dies and breaks down, the toxic component is released.

• The toxin is not secreted actively; it's released upon cell breakdown.

• Examples: Salmonella (food poisoning), Lyme disease.

Archaea

• Archaea split off from bacteria early in evolutionary history.

• They are often difficult to study due to their adaptation to extreme environments.

• Many do not grow well in standard laboratory settings.

• Some are ubiquitous and some are endosymbiotes within other organisms.

• Archaea makes up a significant portion of microbial biomass in the oceans (up to 40%).

• Not currently implicated in human diseases.

• The archaea branch of prokaryotes is hypothesized to be where eukaryotic cells came about.

• Many archaea are extremophiles.

Types of Archaea

Methanogens

• Found in swamps, rice paddies, intestines, and wastewater treatment plants.

• Produce methane (CH_4).

• Methanobrevibacter smithii makes up a significant portion of prokaryotic biomass in human guts.

• Used in wastewater treatment plants.

• Cows have methanogens in their gut to break down cellulose, producing methane as a byproduct.

Halophiles

• Tolerate extremely salty environments.

• Found in areas with high evaporation, such as salt flats (e.g., Death Valley).

Thermophiles

• Tolerate extremely high temperatures.

• Found in hot springs and geothermal vent systems.

Protists

• The Kingdom Protista is problematic and may not be a valid kingdom.

• It was a "dumping ground" for organisms that didn't fit into other kingdoms.

• Data suggests it may not represent a monophyletic group.

• Monophyletic Group: A group originating from a single lineage.

• The term "protist" may become an informal name for a group of organisms rather than an official taxonomic grouping.

• Protists are eukaryotic, meaning they have internal organelles.

• They have greater internal complexity than prokaryotic cells.

• Extremely diverse: Metabolic mechanisms, life cycles, unicellular/multicellular/colonial.

• Most are unicellular, but some algae, kelps, etc., are colonial or multicellular.

• Endosymbiosis is the hypothesized mechanism for the origin of algae and heterotrophic protists.

• Algae (photosynthetic) led to plants; heterotrophic protists led to animals and fungi.

• Single-celled eukaryotic cells have internal organelles (nuclear membrane, endoplasmic reticulum, Golgi apparatus, chloroplasts, mitochondria).

• Some reproduce asexually, some sexually.

Nutritional Diversity

Photoautotrophs

• Photosynthesizers with chloroplasts.

• Algae and other single-celled organisms.

Heterotrophs

• Absorb organic molecules or ingest organic particles.

• Amoebas and other protists that engulf cells.

Myxotrophs

• Combine photosynthesis and heterotrophic nutrition.

• Photosynthesize when sunlight is available, but can also metabolize heterotrophically.

Evolutionary Perspective: Endosymbiotic Hypothesis

• Endosymbiotic theory explains the diversity of protists, plants, animals, and fungi.

• Membrane infolding also played a role in eukaryotic evolution.

• Mitochondria and plastids derived from engulfed prokaryotic cells.

• Plastids: Pigment-containing organelles (e.g., chloroplasts).

Primary Endosymbiosis

• Ancestral heterotrophic cell engulfed a photosynthetic cell (likely a cyanobacterium).

• The cyanobacterium took up residence, creating a stable environment for photosynthesis to occur and produce organic molecules.

• Evidence: Chloroplasts have multiple membranes.

• This primary endosymbiosis produced red and green algae lineages.

Secondary Endosymbiosis

• Red and green algae cells were engulfed by other cells.

• Red algae were engulfed to produce dinoflagellates, apicomplexans, and straminophiles (SAR).

• Green algae were engulfed to form euglenids and chlorarachniophytes.

• Occurred millions of years over time.

Supergroups

• Attempts to organize protists phylogenetically.

• Supergroups within the domain Eukarya: Excavata, Sarclade, Archaeplastida, and Uniconta.

• Supergroups include other kingdoms (e.g., Archaeplastida includes land plants; Uniconta includes fungi and animals).

• This organization aims for monophyletic groups.

• Molecular data and structural similarities are used.

Excavata

• Named for a groove or invagination in their cell membrane.

• Flagella or cilia often extend from the excavated area.

• Includes diplomonads(Giardia), parabasalids, and euglenozoans.

• All members have an inpouching within their external cell.

• Examples of Diplomonids: Giardia intestinalis

  • Parasitic organism that causes giardiasis (diarrheal condition).

  • Mitochondria lack electron transport chains (anaerobic).

  • Two nuclei and multiple flagella.

  • Spread via the fecal-oral route (contaminated water).

• Examples of Euglenids

  • Single-celled organisms that are myxotrophic

  • Can either engulf other organisms or photosynthesize.

  • Have chloroplasts inside them for photosynthesis

  • Photosynthesis organelle that tells it where and when there's sunlight (eye spot).

  • Has two long flagella

Sarclade

• Includes the straminophiles, the alveolates, and the riserians.

• Straminophiles: diatoms, golden algae, brown algae.

• Alveolates: dinoflagellates, apicomplexans, ciliates.

• Riserians: forams, cercosoans, radiolarians.

• Diatoms: unicellular algae with cell walls made of hydrated silica (gives them a glassy appearance).

• Their cell walls are three-dimensional structures and often fit together like a shoe box (box and lid).

• Diatoms are a major component of phytoplankton in both marine and freshwater ecosystems.

• Diatoms blooming in excessive amounts can have a carbon sequestration effect.

• Carbon dioxide that it took to make the silica in their cell walls gets embedded in the ocean floor and removes that from the atmosphere.

• Diatoms incorporating carbon dioxide into their bodies helps to remove it from the atmosphere as part of one of the earth's natural pumps to remove carbon dioxide.

  Prokaryotes Overview

  • Prokaryotes include bacteria and archaea, and they are the earliest and simplest forms of life.

  • This study will focus on their evolution, adaptability, diversity, and the hypothesized origins of these traits.

  Evolution of Prokaryotes

  • The first living organisms were likely prokaryotic cells.

  • Archaea branched off from the early lineage of keratotic cells, leading to two main domains: Archaea and Bacteria.

  • Understanding of prokaryotic genetic and species diversity is rapidly evolving.

  • Currently, over 10,000 species of bacteria are known, but the actual number is likely much higher due to unexplored species, especially in human microbiomes.

  Prokaryotic Adaptability

  • Prokaryotes exhibit great adaptability due to various factors:

    • Metabolic Diversity: They can metabolize in extreme environments (extremophiles), thriving in acidic, hot, or saline environments.

    • Rapid Reproduction: They reproduce asexually via binary fission, allowing for exponential growth under favorable conditions.

    • Haploid Nature: Having only one copy of their genome means mutations are immediately expressed in the phenotype.

  • Mutation rates are low (about one in ten million per cell division), but with billions of cells produced, a significant number of mutations can occur daily.

  • Adaptations can be advantageous, leading to the survival and proliferation of specific traits.

  Prokaryotic Cell Structure

  • Basic Shapes: Prokaryotes can be classified into three general shapes:

    • Bacilli: Rod-shaped.

    • Cocci: Spherical.

    • Spirilla: Spiral.

  • Prokaryotes lack a nuclear envelope and membrane-bound organelles. Instead, they possess:

    • A circular chromosome and sometimes additional small circular DNA called plasmids.

    • Cell walls with varying compositions; bacteria contain peptidoglycan, archaea do not.

  • External Structures: Some prokaryotes may have capsules, flagella, or pili for adherence, mobility, and genetic exchange (horizontal gene transfer).

  Phylogenetic Relationships

  • The classification of prokaryotes is complex due to massive genetic diversity and frequent horizontal gene transfer.

  • Early classifications grouped bacteria and archaea, showing substantial differences in genetic and biochemical characteristics.

  • Eukaryotes are hypothesized to have branched off from the archaeal lineage.

  Metabolic Processes

  • Prokaryotes are essential in various ecological processes:

    • Autotrophs: Use inorganic CO₂ to synthesize organic molecules (photoautotrophs/capture sunlight; chemoautotrophs/break down inorganic chemicals).

    • Heterotrophs: Cannot synthesize their own organic molecules, rely on consuming organic compounds.

  • Major roles include:

    • Chemical recycling: Decomposing organic materials and returning nutrients to the soil.

    • Nitrogen fixation: Converting atmospheric nitrogen into forms usable for plants.

    • Photosynthesis: Contributing to the atmosphere's oxygen through photosynthesis.

  Symbiotic Relationships

  • Prokaryotes often exist in symbiosis with other organisms:

    • Mutualism: Both parties benefit (e.g., gut microbiome).

    • Commensalism: One benefits, the other is unaffected (e.g., birds feeding on insects stirred up by large animals).

    • Parasitism: One organism benefits while harming the other.

  • Example: Legumes host nitrogen-fixing bacteria in root nodules, enriching soil nitrogen and supporting agriculture practices.

  Applications of Prokaryotes

  • Bioremediation: Using prokaryotes to clean up environmental pollutants (e.g., sewage treatment, oil spills).

  • Genetic Engineering: Utilizing plasmids to produce medicines (e.g., insulin, vaccines) or genetically modifying crops (e.g., golden rice).

  • Prokaryotes play a crucial role in biotechnology and agricultural enhancements.

  Pathogenic Bacteria

  • Many diseases are caused by pathogenic bacteria, which can lead to serious health issues:

    • Example pathogens include Mycobacterium tuberculosis (tuberculosis) and bacteria causing diarrheal diseases.

Dinoflagellates

• Another group of alveolates.

• Abundant components of phytoplankton; they are producers.

• Have an outer reinforced cell wall made of cellulose.

• Two cellulose plates with a groove where they come together.

• Flagella within the groove beat, causing them to spin in the water.

• Abundant in marine and freshwater systems.

• Form the basis of aquatic food chains.

Red Tides

• Caused by blooms of dinoflagellates (excessive reproduction).

• Often due to excess nitrogenous nutrients.

• Some dinoflagellates secrete neurotoxins.

• Red tides have a red appearance.

Bioaccumulation

• Dinoflagellate neurotoxins can bioaccumulate.

• Moratoria on clam harvesting due to toxin buildup in low-level consumers.

• Similar to mercury accumulation in high-level aquatic predators.

• Toxins concentrate at higher levels in the ecosystem.

• Example: Red tide produced by Gambardiscus toxicus.

Bioluminescence and Symbiotic Relationships

• Some dinoflagellates bioluminesce (glowing waves).

• Zooxanthellae have photosynthetic relationships with corals (mutualism).

• Zooxanthellae photosynthesize within corals, giving them bright colors.

Coral Bleaching

• Rising ocean temperatures cause corals to expel zooxanthellae.

• Collapse of the coral reef ecosystem as the coral organisms become white.

• Caused by climate change.

Diatomaceous Earth

• Diatom composition allows for a porous soil that allows for water drainage.

Diatom Blooms (Green Tide)

• Diatom blooom in the Bering Sea

Radiolarians

• Shells made of silica (glass-like coverings) with holes.

• Extend cytoplasmic extensions via pseudopodia to engulf smaller cells (phagocytosis).

• Pseudopodia extrude from holes to feed and engulf prey.

• Shells are braced internally by microtubules.

• Heterotrophic zooplankton engulfing bacteria and algal cells.

Multicellular Algae

Brown Algae

• Largest and most complex algae (kelps and seaweeds).

• Most brown algae have a brown appearance.

• Kelp forests in shallow waters support diverse organisms (underwater rainforests).

• Bull kelp has a floaty bulb to keep photosynthetic cells exposed to sunlight.

Structures

• Holdfast: Part of the kelp attached to the substrate.

• Thallus: The body of the algae; a long, slender tube.

• Sea palms: Look like tiny palm trees.

• Fucus (Pacific rock weed): Adapted to live in shallow intertidal zones and can photosynthesize when not submerged.

Archaeplastida Supergroup

• Includes heterotrophic protists that acquired cyanobacterial endosymbionts.

• Contains algae close to the development of land plants.

• Includes red algae, green algae, and land plants.

• Hypothesis: Monophyletic group descended from protists with secondary endosymbiosis.

• The closest algal relatives to land plants are red algae, and even closer are green algae such as the chlorophytes and the carophaceans.

Red Algae (Rhodophytes)

• About 6,000 species.

• Most are multicellular.

• Use phycoerythrin (accessory pigment) to mask chlorophyll's green color.

• Absorb blue and green light, adapted to living in shallows.

• Some have alternation of generations (haploid and diploid stages).

• Example: Turkish towel algae in intertidal zones.

Green Algae

• Have chloroplasts and chlorophyll as primary pigments (appear green).

• Freshwater and marine species.

• Example: Sea lettuce.

• Single-celled and multicellular forms.

• Two groups: Chlorophytes and Carofaceans.

Chlorophytes

• Around 7,000 species.

• Freshwater, marine, and quasi-terrestrial (moist environments).

• Unicellular (e.g., Chlamydomonids with biflagellated structure).

• Can live symbiotically with fungi in lichens.

• Colonial (e.g., Volvox) and multicellular forms.

Carofaceans

• All freshwater species.

• Considered closest relatives of true plants based on genetic analysis and cellular morphology.

• Transitioned to land by withstanding desiccation.

Unikonts Supergroup

• Heterotrophic organisms related to animals, fungi, and some protists.

• Amoebas move via pseudopodia (cytoplasm extensions).

• Two major groups: Amoebozoans (amoebas and related organisms) and Apistoconts (lineage leading to animals, fungi, and other related protists).

• Choinoflagellates: Cells similar to choanocytes in sponges; help sponges filter feed.

Ecological Roles of Protists

• Producers or symbionts.

• Dinoflagellates nourish coral polyps (zooxanthellae).

• Wood-digesting protists in termite guts.

• Photosynthetic protists (phytoplankton) are producers in aquatic environments.

• Nutrients come from upwelling currents and terrestrial runoff.

• Warm surface water acts as a barrier to upwelling, affecting marine ecosystems.