CH 28: Protists

Overview of Protistan Diversity and Classification

General Definition of Protists: Protists are members of diverse, mostly unicellular groups of eukaryotes. They belong to domain Eukarya, alongside plants, animals, and fungi.
Taxonomic Status: The former kingdom Protista has been abandoned because some protists are more closely related to plants, fungi, or animals than to other protists. Various protist lineages are now recognized as major groups in their own right. The term "protist" is now used informally to refer to eukaryotes that are not plants, animals, or fungi.
Evolutionary Context: Most eukaryotic lineages are protists, and most protists are unicellular. Multicellular organisms (plants, animals, and fungi) represent only a few branches on the tree of life.
Key Concepts by Section: * 28.1: Most eukaryotes are single-celled organisms. * 28.2: Excavates include protists with modified mitochondria and unique flagella. * 28.3: SAR is a highly diverse group defined by DNA similarities. * 28.4: Red algae and green algae are the closest relatives of plants. * 28.5: Unikonts include protists closely related to fungi and animals. * 28.6: Protists play key roles in ecological communities.

Concept 28.1: Structural and Functional Diversity

Eukaryotic vs. Prokaryotic Structure: * Eukaryotic cells have a nucleus and membrane-enclosed organelles (mitochondria, Golgi apparatus). * A well-developed cytoskeleton enables eukaryotes to have asymmetric (irregular) forms and to change shape during feeding, growth, or movement.
Complexity at the Cellular Level: * Unicellular protists are considered the simplest eukaryotes but are the most elaborate of all cells. * Essential functions performed by organs in multicellular organisms are carried out by subcellular organelles in protists. * Unique Organelles: Some protists use contractile vacuoles to pump excess water. Certain dinoflagellates possess an ocelloid, a complex eye-like organelle with a "lens" and "retina" resembling vertebrate eyes.
Nutritional Diversity: * Photoautotrophs: Contain chloroplasts. * Heterotrophs: Absorb organic molecules or ingest food particles. * Mixotrophs: Combine photosynthesis and heterotrophic nutrition.
Reproduction and Life Cycles: Protists utilize asexual and sexual reproduction (meiosis and fertilization). Life cycles include all three basic sexual types plus unique variations.

The Role of Endosymbiosis in Eukaryotic Evolution

Definition: Endosymbiosis is a relationship where one organism (the endosymbiont) lives inside the cell of another (the host).
Mitochondrial Origin: * All eukaryotes descended from a host cell that engulfed an alpha proteobacterium. * DNA analysis (mtDNA) indicates mitochondria arose only once from a single common ancestor. * The host cell is hypothesized to be an archaean or a close relative, such as the recently discovered lokiarchaeotes.
Plastid Origin: * Plastids descended from a cyanobacterium engulfed by a heterotrophic eukaryotic host. * This primary endosymbiotic event created red algae and green algae.
Secondary Endosymbiosis: * Red and green algae were ingested in food vacuoles of other heterotrophic eukaryotes and became endosymbionts themselves. * Chlorarachniophytes: Likely evolved when a heterotrophic eukaryote engulfed a green alga; they contain a vestigial nucleus called a nucleomorph.

Scientific Skills Exercise: Genetic Sequence Comparison

Research Objective: Identify which bacteria are most closely related to mitochondria using rRNA (ribosomal RNA) encoding genes.
Comparison Matrix Data (Standardized to 617 Nucleotide Positions): * Wheat mitochondrion vs. A. tumefaciens: $48\%$ similarity. * Wheat mitochondrion vs. C. testosteroni: $38\%$ similarity. * Wheat mitochondrion vs. E. coli: $35\%$ similarity. * C. testosteroni vs. E. coli: $55\%$ similarity.
Interpretation: Higher percentage values indicate closer evolutionary relationships. Gaps in tables indicate identical positions across all sequences or comparisons of an organism to itself.

The Four Eukaryotic Supergroups

Excavata: Characterized by an "excavated" feeding groove on one side. Includes diplomonads, parabasalids, and euglenozoans.
SAR: A large, monophyletic group named after its three clades: Stramenopila, Alveolata, and Rhizaria.
Archaeplastida: Includes red algae, green algae, and plants. These are key producers that form the base of aquatic food webs.
Unikonta: Includes amoebozoans (lobe-shaped pseudopodia) and opisthokonts (animals, fungi, and related protists). Also known as Amorphea.

Concept 28.2: Supergroup Excavata

Diplomonads: * Possess reduced mitochondria called mitosomes (lack functional electron transport chains). * Derive energy from anaerobic pathways. * Structure: Two equal-sized nuclei and multiple flagella. * Example: Giardia intestinalis, an intestinal parasite spread via contaminated water.
Parabasalids: * Possess reduced mitochondria called hydrogenosomes, generating energy anaerobically and releasing $H_2$ gas. * Example: Trichomonas vaginalis, a sexually transmitted parasite. It may have acquired genes for feeding on vaginal lining via horizontal gene transfer from bacteria.
Euglenozoans: * Distinguished by a rod with a spiral or crystalline structure inside their flagella. * Kinetoplastids: Feature a single large mitochondrion containing a mass of DNA called a kinetoplast. Includes Trypanosoma, which causes sleeping sickness (vectored by tsetse flies) and Chagas' disease. They use a "bait-and-switch" defense by continually changing surface proteins. * Euglenids: Have a pocket at one end with one or two flagella. Euglena features an eyespot and light detector to move toward light for photosynthesis. They are often mixotrophic and have a pellicle for flexibility.

Concept 28.3: Supergroup SAR

Stramenopiles: Characterized by a "hairy" flagellum paired with a "smooth" flagellum. * Diatoms: Unicellular algae with silicon dioxide walls. They sustain pressures up to $1.4 \times 10^6\,kg/m^2$ . In "blooms," dead diatoms sink, pumping $CO_2$ to the ocean floor. * Brown Algae: Largest/most complex algae; all are multicellular and marine. Structure includes holdfast (rootlike), stipe (stemlike), and blades (leaflike). Some have gas-filled floats. Used for food (Laminaria or kombu) and algin (thickener). * Oomycetes: Water molds and relatives. Have cell walls of cellulose (unlike fungal chitin). Phytophthora infestans caused the Irish potato famine.
Alveolates: Have membrane-enclosed sacs (alveoli) beneath the plasma membrane. * Dinoflagellates: Reinforced by cellulose plates; two flagella in grooves cause spinning. Cause "red tides" due to carotenoids and toxins. * Apicomplexans: Parasites with an apical complex for cell penetration. Possess a modified plastid called an apicoplast. Plasmodium causes malaria and continually changes surface proteins. * Ciliates: Use cilia for movement/feeding. Have two nuclei: macronuclei (daily function) and micronuclei (reproduction). Exchange micronuclei via conjugation.
Rhizaria: Many are amoebas with threadlike pseudopodia. * Radiolarians: Symmetrical silica skeletons. Pseudopodia radiate from the central body. * Forams (Foraminiferans): Have porous shells called tests made of calcium carbonate. $90\%$ of known species are fossils, used to track climate change and age rocks. * Cercozoans: Amoeboid/flagellated. Paulinella chromatophora illustrates a second case of primary endosymbiosis involving a different cyanobacterium.

Concept 28.4: Red Algae and Green Algae

Archaeplastida: The monophyletic group containing red algae, green algae, and land plants.
Red Algae (Rhodophytes): * Red color from phycoerythrin, allowing absorption of blue/green light in deep water (up to $260\,m$ ). * Most are multicellular seaweeds, e.g., Porphyra (nori). * Lack flagellated gametes; depend on water currents.
Green Algae: Grass-green chloroplasts similar to plants. Divided into charophytes (closest to plants) and chlorophytes. * Chlorophytes: Include unicellular Chlamydomonas, colonial Pediastrum, and multicellular Ulva (sea lettuce). * Caulerpa: A "supercell" created by repeated nuclear division without cytokinesis.

Concept 28.5: Supergroup Unikonta

Amoebozoans: Amoebas with lobe- or tube-shaped pseudopodia. * Tubulinids: Ubiquitous in soil and water (e.g., Amoeba proteus). * Slime Molds (Mycetozoans): Resemble fungi due to evolutionary convergence. * Plasmodial Slime Molds: Form a single mass of cytoplasm with many nuclei (the plasmodium). * Cellular Slime Molds: Solitary cells aggregate into a slug-like unit when food is scarce. Dictyostelium discoideum is a model for multicellularity. * Entamoebas: Parasites. Entamoeba histolytica causes amoebic dysentery, killing up to $110,000$ people annually.
Opisthokonts: Include animals, fungi, and protist groups nucleariids (close to fungi) and choanoflagellates (close to animals).

Concept 28.6: Ecological Roles of Protists

Symbiotic Protists: * Mutualisms: Photosynthetic dinoflagellates nourish coral polyps; wood-digesting protists inhabit termite guts. * Parasitism: Plasmodium (malaria), Phytophthora ramorum (sudden oak death), and Pfiesteria shumwayae (fish kills).
Photosynthetic Producers: * Protists perform approximately $30\%$ of global photosynthesis. * Aquatic producers are limited by nitrogen, phosphorus, or iron. * Climate Change Impact: Rising sea surface temperatures create warm layers that prevent the upwelling of cold, nutrient-rich water, causing declines in marine producer biomass.