Protists

• Paraphyletic grouping of unicellular and multicellular eukaryotes
• Algae, Protozoa, Slime Molds
• Photosynthetic, Heterotrophic, Mixotrophic
• Various sexual life cycles
• Studied via samples, DNA fragments and overlapping sequence analysis; environmental sequencing/metagenomics
• Studied for…
  • Human Health Concerns (Giardia lamblia, Trypanosome, Malaria)
  • Ecological Issues
    • Primary producers/consumers
    • CO₂ drawdown to benthic reservoirs, outside of atmosphere
    • Algal blooms (red tides, toxins)

Origin of Protists

• Mitochondria: Endosymbiosis Theory
  1. archaeal cell engulfed aerobic bacterium
  2. bacterium survived and formed an endosymbiotic relationship
  3. formation of mitochondria
• Nuclear Envelope: Infolding Hypothesis
  • infolding of plasma membrane surrounded chromosomes
  • created a double membrane with organelles (endoplasmic reticulum)
• Chloroplast: Primary and Secondary Endosymbiosis
  • Primary Endosymbiosis:
    • engulfed cyanobacteria; endosymbiosis theory
    • consider Gram bacteria
      • Gram-positive: thick cell wall of peptidoglycan on the outside
      • Gram-negative: thin cell wall of peptidoglycan with an outer phospholipid bilayer membrane (double membrane wall)
    • food vacuole contained one membrane, then cyanobacterium contained 2 membranes
    • one membrane was lost, resulting in a chloroplast with two bounding membranes
  • Secondary Endosymbiosis:
    • algal cell engulfed by a non-photosynthetic, heterotrophic eukaryote
      • either red or green algae
    • outer membrane of food vacuole, algal cell membrane, and two membranes of cyanobacterium
    • results in up to four membranes around chloroplast
    • also sometimes contains a remnant nucleus from the algal cell: nucleomorph
      • reduced set of genes and often a membrane
    • may have occurred multiple times depending on algaee
  • occurred in Archaeplastida (Plantae)

Eukaryotic supergroups/clade

Excavata

• excavated feeding groove
• Diplomonads, Parabasalids, Eugleenozoans

Archaeplastida

• AKA Plantae supergroup
  • “Ancient plastids” — first evolution of plastids
• Underwent two endosymbiotic events:
  • primary endosymbiosis in all cases
  • secondary endosymbiosis in many cases

Red Algae

• Marine and benthic; tropical and warm waters
• Unicellular, filamentous, pseudoparenchymatous, and parenchymatous forms
• Chlorophyll A only, carotenoids, phycoerythrin
• Can grow to greatest depths of algae; 200m deep
• Cellulose and mucilage
  • Agar and carrageenan
• Porphyra — Nori
• Complex life cycles with a 3rd stage
• Agar and carrageenan emulsifiers/stabilizers; Irish Moss

Coralline Algae

• Cell walls have calcium carbonate deposits (CaCO₃)
• Structures coral reefs
• Aids reef productivity
• Articulate corallline algae and crustose

Green Algae

• Paraphyletic group distinguished as chlorophytes and charophytes
• Mostly freshwater, aquatic algae; grow in damp soil, snow
• ~7,000 sp.
• Haploid lifecycle
• Many similarities to plants
  • Chlorophyll A and B, carotenoids
  • Food is stored in starches in plastids
  • Cell walls
  • Some make phytochrome
• Forms can not be used for clarification; diverse forms
  • Unicellular
  • Filamentous
  • Non-filamentous colonies
  • Multicellular
  • Coenocytic/Siphonous
    • Multinucleated algae in one cytoplasm shared
• Chlamydomonas nivalis
  • more pigments protect chlorophyll
  • snow; “red snow”
• Chlamydomonas
  • green snow
• Algae are divided into clades (classes) based on three synapomorphies:
  1. Cytokinetic mode of division
  2. Characteristics of the flagella: location, symmetry, anchoring
  3. How cellulose is produced

Chlorophytes (Chlorophyceae)

Aphragmoplastic Division

• No phragmoplast, and different orientation of microtubules
• Phycoplast: Horizontal/lateral orientation of phragmoplast that is parallel to the cell plate/line of cell division and parallel to the cytokinins

Apical Flagella

• On symmetric cells
• Apical flagella extending forward
• Anchored by two broad bands of microtubules; cross-like shape

Charophytes (Charophyceae)

• Closer related to plants
  • Rings of cellulose/rosette in the cell membrane synthesize enzymes
  • Phragmoplastic division of cytokinesis
  • Land plants

Phragmoplastic Division

• Shared with all plants; present in most Charophyceae
• Phragmoplast is made of microtubule rings that are parallel to the cytokinins and perpendicular to the cell plate/line of cell division

Anapical Flagella

• Subapical or lateral flagella
• Extends at right angles
• Anchored to membrane via a broad band of microtubules
• On asymmetric cells

Plants

Stramenophiles

• SAR Supergroup
• Synapomorphy: One hairy flagellum at some point in development, one smooth flagellum
• “Heterokonts”

Diatoms

• Mostly unicellular and photosynthetic
• Marine and freshwater
• Chlorophyll A+ C, carotenoids
• Frustules: hard, petri-plate-like structures made of sillicon dioxide; glass-like
  • Encases the cell membrane
  • Girdle plates hold frustules together
• Pores on the valve view
• Pennate and centric symmetry
  • Pennate: cylindrical on valve view; centric: round
  • Pennates are isogamous, centric are oogamous
• No flagella on adults
• Girdle view
• Raphe on modal ones: secretes hydrative crystals that form sticky rod to push along surface
• Centric have surface area and oils to float near surface vs. raphe
• Diatoms leave frustules on death (silica); diatomaceous earth sediment
• Dessicative use
• Blooms; most are not toxic, but some are
  • Pseudo-nitzchsia domoic acid blooms

Water Molds

• Non-photosynthetic
• Pathogenic to plants
  • Downy mildew in grapes (Bordeaux collapse)
  • Late potato blight — Phytophtora infestans (Irish potato famine)
    • Genetically identical potatoes
    • Blighted, inedible
  • Sudden oak death — Phytophtora ramorum
    • Coastal CA, 2000
• Fungal-like; fungal-like terms
• Sporangia
• Spreads are modal; spread in moist conditions

Brown Algae

• Multicellular
• Marine benthic
• Cool/temperate waters
• Chlorophyll A and C, fucoxanthin
• Multiple forms: filamentous, pseudoparenchymatous, parenchymatous
  • Fliamentous: One filament, two-dimensional, not interlocked
  • Pseudoparenchymatous: Filaments divide and lengthen by mitosis individually, creating a three-dimensional structure
  • Parenchymatous: Not interwoven; analogous to 3D apical meristems, large
• Cell walls are not rigid: cellulose and mucilaginous component
  • No lignin
  • Mucilage helps with flexibility, dessication, protection
    • Algin (Alginic acid) — Creamy texturee; stabilizer and emulsifier
    • Fucoidin
• Life cycles include alternation of generation and diploid
• Sea palm, Ectocarpus siliculosis, Kelps (Laminariales), Sargassum

Laminariales

• Largest brown algae
• Up to 30m
• Three parts: Holdfast, stipe, blade
  • Holdfast is only for anchoring
  • Stipe
  • Blade is specialized for photosynthesis
• Some in deeper water have sacs/air bladders used for buoyancy
• Has a transport tissue that reseembles phloem — convergent evolution
• Alternation of generations
  • Multicellular adults; Diploid adult (sporophyte) is the larger recognized kelp
  • Sporangia on the blades: elongate cells that produce spores via meiosis
  • Gametophytes are benthic and filamentous
  • Heteromorphic alternation of generations vs. isomorphic
• Macrocystis
• Nereocystis
• Fucus
• Kelp forests are highly productive habitats and provide shelter

Golden Algae

Alveolates

• SAR Supergroup
• Synapomorphic alveoli: membrane sacs inside the cell membrane

Dinoflagellates

• 3um
• modal unicellular organisms
• mostly marine and planktonic
• feeding…
  • ~50% are photosynthetic
  • ~50% lost chloroplast over time
  • some mixotrophic dinoflagellates
• transport…
  • two flagella:
    • one lines the equatorial groove, ribbon flagellum
    • one lines sulcus
    • 90 degrees/perpendicular to each other in most dinoflagellates
  • twirling in water
• armored dinoflagellates… possess hard parts known as thecae
  • thecae are made of cellulose
  • inside alveoli (inside cell membrane)
• pigments:
  • chlorophyll a and chlorophyll c
  • carotenoid
    • distinct reddish-brown coloring
• complex life cycle…
  • resting cysts: protected
  • multiple lifestages
• ecological importance…
  • primary producers as plankton and endosymbionts
  • zooxanthellae are endosymbiotic to corals, sponges, sea anemones, octopus
    • no armor; exchanges materials
    • 30,000 dinoflagellates per cubic millimeter of a coral polyp
    • produces glycerol instead of starch for use in cell respiration
  • red tides are dinoflagellate blooms
    • population explosion
    • 20% dinoflagellate species have toxins
      • assumed to deter predators (copepod zooplankton)
      • aerosolized can kill fish, make people ill/rashed
      • can accumulate in shellfish; bioaccumulation; neurotoxins
  • bioluminescence
    • glows/emits light when disturbed via wave action
      • assumed to protect against predators (cause to be consumed by another consumer)
• Pfiesteria piscicida
  • fish killer in southeast river deltas
  • peduncle: feeding tube
  • amoeboid stage and amoeboid cysts
  • undetected by fish

Apicomplexans

Ciliates

Rhizarians

• SAR Supergroup

Radiolarians

Foraminifera

Cercozoans

Amoebozoa

• Unikonta Supergroup
• Synapomorphic lobe-shaped, wide pseudopodia
• Non-photosynthetic ingesting/engulfing
• Otherwise fungal-like
• Amoeba, plasmodial slime molds, cellular slime molds

Plasmodial Slime Molds

• multinucleated, unicellular
• plasmodium feeding stage
  • cytoplasm ebbing
• separate to genus Plasmodium
• Physarum polycephalum
• Diploid life cycle
  • Feeds, then matures
  • Fruits/aggregates with an upward structure: sporangium with a stalk at maturity
  • Produces spores from meiosis
  • Releases spores in air and germinates
    • Haploid amoeboid cells → move as individual uninucleate amoeboid cells
    • Haploid flagellated cells → move via flagella
  • Fertilizes → Diploid zygote
  • Mitosis
  • Feeding plasmodium

Tubulinids

Entamoebas

Ophistokonts

• Unikonta Supergroup

Nucleariids

Choanoflagellates

Aquatic Producers/Consumers

• Phytoplankton: photosynthetic, free-floating/swimming surface protists in salt and freshwater; includes some cyanobacteria
• Zooplankton: non-photosynthetic
• Benthic producers are multicellular protists anchored to a substrate in the subtidal or intertidal zones
• Dinoflagellates: endosymbiont protists

Fungi

• One of three eukaryotic kingdoms — Mycota
• Branches from common ancestor with animals around Ophistokont period
  • Fungi and nucleariids
• Fungi thought to be necessary for land plants ~470 MYA
  • Land was covered by algal slime, cyanobacteria, and some heterotrophs such as fungi
  • Evidence: Sym genes that initiate symbiotic reelationships with fungi are present in all
• Diverse radiation:
  • 1969 classification of 4 major phyla:
    • Chytridiomycota
    • Zygomycota
    • Ascomycota
    • Basidiomycota
    • (Deuteromycota)
  • 2005 with molecular data:
    • Chytridiomycota and Zygomycota were paraphyletic
    • Basal fungi: Cryptomycetes and Microsporidians
    • Chytrids
    • Zoopagomycetes
    • Mucoromycetes
    • Ascomycetes
    • Basidiomycetes
• Most of a fungus’s body is underground or in its food
• Heterotrophic absorptive consumers
• Saprobe/saprophytic decomposers
  • Feeds on dead organisms;
  • Nutrients are recycled into the soil
• All fungi can digest cellulose
  • Like bacteria
  • Some can digest lignin (esp. Basidiomycota)
    • White rot — Eudicot/Hardwood, Shiitake, mycoremediation
      • Lignin peroxidase class; free radical → enzymatic combustion, oxidation
    • Brown rot — conifers/softwood, partial lignin degradation
• Parasitism and mutualism
  • Human parasitism, fungal disease
  • Lichens and Mycorrhizae
• Use in medicine; Penicillium, cyclosporins (organ transplants)
• Sheer number of species; largest organism is considered fungus
  • 145,000 known sp. with 1-2000 learned per year

Characteristics

Morphology

• Two growth forms
  • Unicellular growth form → Yeast
  • Most are multicellular and filamentous: filaments are hyphae, and masses of hyphae are mycelium
    • High surface area to volume ratio from thin hyphae
    • Vulnerable to dessication
• Hyphae have different septation
  • Crosswalls between hyphae: Septate
  • No crosswalls: Aseptate/Coenocytic
• Cell walls are made of chitin; no cellulose
  • Chitin polymer; B1, 4 linkages
  • Polysaccharide with highly modified sugars
    • Glucose replaced by a nitrogen containing group
  • Straight, stronger than cellulose, more possibilities for hydrogen bonding between parallel molecules due to nitrogen-containing group
• Hyphae undergo hyphal extension
  • Hypha tip is not hardened, plastic
  • Tip of hypha extends due to increased turgor pressure
  • Growth is performed throughout the hypha, but material is sent through the hypha to the tip
  • Older cell walls are hardened and do not expand
  • Most hyphae grow away from other hyphae
    • If they find food, they branch towards it extensively and may fuse with other hyphae
• Cell wall formation in cytokinesis is different from both plants and animals; no pinching in, no formation of new cell wall

Spores

• Fungi make spores through sexual and asexual lifecycles; generally thrrough both in most fungi
  • Main reproductive cells
• Unicellular, dispersal spores that do not fuse/fertilize; can divide by mitosis to make mycelium without fertilization
  • Thick walls, protective against dessication
  • Some are not thick and softer
  • Carried by wind currents

Life Cycle

• Modified haploid life cycle
• Deuteromycetes: “unable to see” sexual reproduction
  • No longer used

Asexual Reproduction

• Genetically identical haploid spores
• Developed via mitosis

Sexual Reproduction

• Fertilization is separated into two parts/sections: plasmogamy and karyogamy
  • These phases occur in all fertilization, but are so divided in fungi they can be distinguished as two phases
  • Plasmogamy fuses cytoplasm
  • Karyogamy fuses nuclei
  • In between plasmogamy and karyogamy: cell/hypha is heterokaryotic as it has two types of nuclei in the cell
    • Monokaryotic: One nucleus in the cell
    • Heterokaryotic: Two types of many haploid nucleus in the cell
    • Dikaryotic: A specialization of heterokaryotic; two nuclei in each cell, both which are heterokaryotic

Basal Fungi

• Generally parasitic, unicellular
• Some differences between phyla

Cryptomycetes

• Flagellated spores
• Rozella
• attacks fungi and protists

Microsporidia

• Non-flagellate spores
• Reduced genomes and mitochondria; relies on hosts for ATP
• Nosema sp. — (honeybee) colony collapse disorder
  • harms worker bees, so colonies collapse
  • other possible factors: insecticides, mite species
  • affects hormones in worker bees, delaying role reception

Chytridiomycota

• Chytrids
• Common to soil and water
• Decomposers/saprophytic
• More advanced to basal groups: may have hyphae and flagella
• Different functions
  • Digests cellulose in guts of cattle and sheep after consuming grass
  • Causes chytridiomycosis in amphibians (chytrid disease)
    • Disease of the skin
    • Worldwide decline in amphibian populations such as frogs
    • Skin thickens and prevents breathing through skin

Zoopagomycota

• Diverse: parasitic, saprophytic

Mucoromycota

• True mycelia and no flagellated cells
• Mucus
• Only ~750 species; small phylum
  • True molds (small invisible reproductive structures; no mushrooms/large flowering body)
  • Endomycorrhizal species
  • Household and forest floor spores
    • Rhizopus stolonifer (black bread mold)
  • Mutualists, parasites, fast-growing molds
  • Asexual reproduction is more common via sporangia
    • Sexual reproduction is performed through zygosporangium in life cycle
  • Aseptate/coenocytic hyphae
• Pilobolus (hat thrower; dung; bends toward light)

Rhizopus stolonifer

• Black Bread Mold
• Rhizoids underground/in host
• Aerial coenocytic cells
• Sporangium forms around/in a hollow columella
  • Asexual spores made via mitosis
  • Spores spread once sporangium is broken open
• Sexual life cycle is heterothallic; must have different mating genes (+/-)
  • Constantly secreting materials into environment and able to detect mating partners
  • Gametangia from mating strains held together by suspensors
  • Merging of gametangia forms zygosporangium
  • Zygosporangium stores zygospore with two nuclei
  • Zygosporangium produces hypha and spores that are genetically different

Glomeromycotina

• Subphylum
• An endomycorrhizae phylum; arbuscular mycorrhizae
  • Found in 80% of land plants, but only 160 species of fungi important to arbuscular mycorrhizae
  • No 1:1 relationship between fungi and land plants
• Oldest filamentous fungi in record
• Hypha forms highly branched structures inside plant cell: arbuscule
  • Arbuscule transfers material
• Ballooning vesicles formed by fungus for storage of material
• Found in grasslands and tropical forests; absorbs Phosphorus for plants
• Builds soils; breaks down parent rocks and adds organic material from decomposition
• Cell walls have glomalin glycoprotein
• Up to 25% soil organic composed of Glomeromycotina

Dikarya

Ascomycota

• Dikaryotic hyphae
• “Sac fungi” — cell in sexual reproductioon
• 990,000 species
• hyperdiverse; many yeasts, colored molds, lichens, truffles, moreels
• hyphae are septate with porees
• some arre saprophytic, parasitic, mycorrhizae
• Neurospora crassa
  • one gene one enzyme hypothesis
• Penicillium, Aspergillus, Morchella esculenta (morels), Tuber, Claviceps purpurea
• Most reproduction is asexual
  • Conidia spores, produced via budding
  • Conidogenous cells and conidiophores
  • Germination produces more hyphae
• Some sexual reproduction
  • Mycelia fuse, specific cells fuse together
  • Plasmogamy forms a large fruiting body: ascocarp
    • Usually visible to eye
    • Made of many hyphae
    • Cup-shaped with protrusions in the center: hymenium
    • Hymenium: Layer of asci (ascus) sacs and ascospores
      • End cell of dikaryotic hyphae is the ascus
      • Ascus: Karyogamy occurs; diploid cell
      • Meiosis → Haploid state
      • Mitosis → 8 nuclei
      • Spores → 8 spores (ascospores) produced in each ascus
  • Spore germination breaks through ascus
  • Ascus is necessary, but not ascocarp to be part of phylum
• Tubers are ectomycorrhizal
  • Attached to a plant: oak, birch, beech, poplars, pines
  • Difficult to cultivate, expensive
  • Tuber magnatum, melanosporum, aestivum
• Ergotism is caused by ergots in grains
  • Ergotamine, similar to epinephrine, LSD; neurotransmitter, vasoconstrictive
  • Convulsive or gangrenous ergotism
  • Pear-shaped asci

Yeasts

• non-taxonomic grroup
• budding or fission yeasts
• occurs in both dikarya

Lichens

• mycobiont and photobiont mutualism
• over 98% mycobionts are ascomycetes
• green algae or cyanobacterial photobionts
• about 13,250 species of fungi form lichens; 4 genera of photobionts
• prominent in cool and humid areas
• non-stratified and stratified
• stratified has three forms: fruticose, foliose, crustose
  • 3-4 layers of tightly woven hyphae (upper/lower cortex), central loose woven hyphae (medulla) and photosynthetic layer with mycobiont and photobiont
• asexual reproduction
  • fragmentation; broken in half
  • special reproductive structures; powdery, soredia
  • cuplike ascocarp reproduces by self; later meets with another photobiont partner
• yeast partners caused different growths in ascomycete lichens
• nitrogen fixation if mutualistic to cyanobacteria; forms soil and breaks down rocks and organic material
  • lichen acids; ~40% dry weight in a lichen is from acids
  • susceptible to air pollution as they absorb nutrients from moist air and soil

Basidiomycota

• Dikaryotic hyphae