VALDOSTA STATE UNIVERSITY
LECTURE NOTES FOR PHYCOLOGY

SPRING 2004

UNIT I. INTRODUCTORY MATERIAL

  1. Introduction to phycology
    1. phycology (Greek) vs algology (Latin)--both mean study of algae
    2. What are the algae? (some images)
      1. pond scum, frog spawn or frog spittle, insect excreta, substances bred of putrefaction
      2. thallophytes (not embryophytes)
        1. lacking roots, stems, and leaves
        2. no protective layer around reproductive cells
        3. photosynthetic
          1. usual definition includes chlorophyll a, but we will also consider photosynthetic bacteria using bacteriochlorophyll
  2. Historical background
    1. The First Age of Phycology
      1. reported from an archeological site in Chile dated at 12,500 bp
      2. possible reference in the Epic of Gilgamesh as plant giving everlasting life (problem is that its spike pricks like a bramble)
      3. algae definitely referred to in ancient Chinese classics as food and medicine
      4. Greeks (Theophrastus and Dioscorides) refer to phykos (seaweed) -- later becomes fucus in Latin
      5. seaweed gradually grouped into: Fucus, Corallina, Ulva, Conferva
        1. names lasted from 1620 to well into the 1700's
        2. Linnaeus recognized five genera: Tremella, Fucus, Ulva, Conferva, Corallina, plus Chara and Volvox ( zoophyte)
    2. The Golden Age of Plant Taxonomy and the Second Age of Phycology
      1. huge interest in naming plants of all sorts from a scientific viewpoint
      2. J. Stackhouse given credit for beginning the transformation of phycology into a science with his description zygote germination in Fucus around 1800 and his initial attempts at breaking Fucus into multiple genera; part of the dawning realization of the importance of life-histories and, especially, of flagellate stages (but some thought indicated metamorphosis into animals) in the classification of lower plants
      3. this was also a period of improved microscopy
      4. a few names still recognized today: Vaucher, Hedwig, Roth, Trentepohl, C. A. Agardh J. G. Agardh, Kützing, Rabenhorst, Pringsheim, Bornet and Flahault, Gomont, Borzi, and de Toni
    3. Modern phycology
      1. systematics
        1. based primarily on cell structure: plastid structure, flagellar apparatus, cell wall structure, other cytoplasmic structures with more and more detail added as more tools become available--value of structure varies from group to group (diatoms and cell wall, green algae and flagellar apparatus)
          1. new phylogenies being developed based on small subunit ribosomal RNA sequences
        2. a few important early figures: Pascher, Prescott, Geitler, Iyengar, Fritsch, West and West; helped define the divisions (phyla) still commonly used today without access to either electron microscopes or DNA-based techniques
      2. ecology and economics
        1. important components of aquatic systems as phytoplankton and benthic growths
          1. kelp forests
          2. corals and coral reefs
        2. phytoplankon and periphyton in rivers, streams, ponds, and lakes
        3. terrestrial algae
        4. biological indicators and occurrences of harmful algal blooms
        5. diatomaceous earth and other industrial products
          1. salt production
          2. polysaccharide gums
          3. multitude of uses for diatoms
        6. food and drugs for man and animal
        7. waste water recovery and life-support systems
          1. sewage treatment
          2. paper mills


UNIT 2. MAJOR GROUPS OF ALGAE

  1. An introduction to nomenclature
    1. species concepts in phycology
      1. biological species--interbreed with viable offspring
      2. morphological species--distinguished by unique repeatable morphological features
      3. phylogenetic species--smallest related group; exhibit some morphological, biochemical similarity; all descended from a common ancestor
    2. Latin binomial plus authority
    3. description (Latin)
    4. diagnosis (Latin)
    5. phylogenetic groupings
      1. -phyta designates a division (phylum)
      2. -phyceae designates a class within a division
      3. -ales designates an order within a class
      4. -aceae desgnates a family within an order
  2. Classification of the algae
    1. distinguishing features
      1. cell structure
        1. in the prokaryotes look at photosynthetic apparatus then shape and arrangement of cells
        2. in the eukaryotes look at
          1. chloroplast structure
            1. nature of the photosynthetic apparatus
            2. types of chlorophyll
              1. nature of accessory pigments
              2. pyrenoids and storage products
            3. arrangement of thylakoids
            4. chloroplast endoplasmic reticulum
          2. type of storage products
            1. alpha 1,4-linked glucans (starches) vs beta 1,3-linked glucans (laminarins and paramylon)
            2. low-moleculular weight products: sugars, polyols, glycosides
          3. flagellar structure
            1. number and arrangement
            2. presence of mastigonemes and other appendages (tinsel flagella)
            3. eyespots
          4. wall structure
            1. chemical make up: polysaccharide, proteinaceous, siliceous
            2. structure: scales, frustules, plates, etc.
          5. nuclear structure
            1. ploidy level and number
            2. mesokaryon vs eukaryon
              1. mesokaryon
                1. chromosomes always somewhat condensed
                2. nucleolus persistent
                3. chromosomes attached to nuclear membrane
                4. nuclear membrane remains intact
              2. eukaryon
                1. chromosomes condense at prophase, disperse at telophase
                2. nucleolus disperses during prophase
                3. chromosomes attach to mitotic spindle
                4. nuclear membrane may disperse during mitosis (or it may not)
            3. cell division
          6. habit
            1. motile flagellate forms
              1. found in all groups except red algae
              2. probably the primitive condition
              3. may be naked (without the rigid cell wall usually thought of with plants)
            2. motile amoeboid forms
            3. motile colonies
            4. palmelloid habit - algal cell type, but no flagella; lots of mucilage
              1. may be a stage in a flagellate life-cycle
            5. coccoid habit - without flagella for most of the life of the cell
              1. may have contractile vacuoles and eyespots usually associated with flagellate forms
            6. filamentous habit - based on vegetative reproduction--mother cell wall retained as part of the wall of the new cell
              1. unbranched vs branched vs heterotrichous
            7. siphonous growth
            8. parenchymatous growth
      2. nucleotide sequences
        1. thought to give direct evidence of phylogeny and phylogenetic relationships
        2. methods
          1. RFLP--restriction-fragment length polymorphism
          2. RAPD--randomly amplified polymorphic DNA
          3. microsatellites
          4. ribosomal RNA genes
            1. SSU and LSU--used for large-scale phylogeny
            2. ITS--used for fine-scale phylogeny
    2. major groups of photosynthetic or plastid-containing organisms  (grouped on structure of the host cell, if exist)
      1. Domain Archaea
        1. Phylum Euryarchaeota, Class Halobacteria
      2. Kingdom Bacteria (prokaryotic)
        1. Phylum Chloroflexi--anaerobic, with bacteriochlorophyll; filamentous anoxygenic phototrophic bacteria
        2. Phylum Chlorobi--anaerobic, with bacteriochlorophyll; the green sulfur bacteria
        3. FamilyHeliobacteriaceae--anaerobic, with bacteriochlophyll g
        4. Purple sulfur and non-sulfur bacteria--anerobic, with bacteriochlorophyll
        5. Phylum Cyanobacteria/Cyanophyta--oxygenic, with chlorophyll a and phycobilisomes
      3. Kingdom Protozoa
        1. Sarcomastigota--flagellate or amoeboid with tubular cristae
          1. Chlorachniophyta--with grass-green plastids, 4 chloroplast membranes, and nucleomorph
        2. Discicristata--flagellate or amoeboid with discoid cristae
          1. Euglenophyta--also grass-green, but always with flagellum, eyespot; mostly freshwater
        3. Alveolata--with cortical alveolae
          1. Dinophyta--brown to reddish because of xanthophylls but plastids highly variable in structure; unique flagellar apparatus; mostly marine
          2. Sporozoa (Apicomplexans)?
      4. Kingdom Plantae
        1. Glaucophyta--with unusual plastids (cyanelles) that retain a bit of peptidoglycan; with phycobilisomes
        2. Rhodophyta--usually multicellular forms with phycobilisomes
        3. Chlorophyta--green because of chl a and b with limited carotenoids; mostly freshwater, about half of the terrestrial forms; microscopic or macroscopic
      5. Kingdom Chromista
        1. Cryptophyta--use some of the phycobilins as accessories, but without phycobilisomes; secondary/tertiary endosymbiosis
        2. Chromophyta (Ochrophyta)--Stramenopiles, major classes Chrysophyceae, Synurophyceae, Bacillariophyceae, Phaeophyceae, Xanthophyceae, Raphidiophyceae, Eustigmatophyceae--usually golden because of the presence of lots a xanthophylls as accessories to chlorophylls a and c, but may appear greenish with a slight yellowish tinge; with unique system of two unequal flagella
        3. Prymnesiophyta (Haptophyta)--unique accessory organ, the haptonema


UNIT 3. A QUICK REVIEW OF OXYGENIC PHOTOSYNTHESIS

  1. Light and photosynthesis
    1. spectrum/photon types
      1. action spectrum vs absorption spectrum
      2. photosynthetically active region of the spectrum
      3. units of measurement
    2. photosynthetic structures
      1. thylakoids and other photosynthetic membranes
        1. contain the photosynthetic pigments and electron transport chains
        2. usually not arranged in the grana of higher plants; instead there are bands of thylakoids, usually containing three to five thylakoids per band; sometimes an additional thylakoid (the girdle lamella) is found under the chloroplast envelope
      2. pyrenoids
        1. in stroma
        2. RuBP carboxylase in some sort of package, may be with carbonic anhydrase
        3. sometimes penetrated by thylakoids
    3. light reactions of photosynthesis
      1. review of cyclic and non-cyclic photophosphorylation
      2. pigments
        1. chlorophyll a most common--in all cells using noncyclic photophosphorylation
          1. 0.3 to 3.0% of dry weight
          2. porphyrin ring with a magnesium atom in the center and lipid chain to anchor into thylakoids
        2. accessory pigments
          1. chlorophylls b (prochlorophytes, chlorophytes, euglenoids), c1 and c2 (chromophytes, dinoflagellates), or d (rhodophytes)
          2. carotenoids and/or biliproteins
            1. carotenoids are lipids, soluble in nonpolar solvents
              1. carotenes (without oxygen) vs xanthophylls (with oxygen)
              2. over 60 known, most important: beta-carotene, fucoxanthin, peridinin
                1. beta-carotene widespread
                2. fucoxanthin in brown chromophytes
                3. peridinin in dinoflagellates
              3. biliproteins are hydrophilic proteins with an attached chromophore
                1. found in cyanobacteria, glaucophytes, rhodophytes, cryptophytes
                2. form phycobilisomes which are visible with EM
                3. allophycocyanin core -- transfers energy to reaction center
                4. stack of phycocyanin antenna molecules - blue, absorb 620-640
                5. stacks of phycoerythrin antenna molecules - red, absorb 565
                6. serve as light gathering pigments, can be cannibalized if amino acids needed
                7. chromatic adaptation
    4. dark reactions (almost universal)
      1. carbon fixation using RuBP carboxylase (pyrenoid)
      2. Calvin-Benson cycle leading to the production of phosphoglyceraldehyde
        1. three CO2 used to form 6 PGA
        2. PGA's reduced and energized to form 6 PGAL
        3. one PGAL saved, five used to make 3 RuBP
          1. two join to make fructose
          2. third joins fructose to make a 5-carbon sugar and a 4-carbon sugar (erythrose)
          3. fourth joins with erythrose to make sedheptulose
          4. fifth joins with sedheptulose to form two 5-carbon sugars
          5. the three 5-carbon sugars are energized to form three RuBP
    5. storage products
      1. high molecular weight compounds
        1. starch, either in cytoplasm or in chloroplast (alpha-1,4 linked glucose)
          1. cyanobacterial starch in cyanobacteria
          2. floridean starch in cytoplasm of red algae
          3. starch in chloroplast envelope in cryptophytes
          4. dinophycean starch in cytoplasm of dinoflagellates
          5. starch in chloroplast in chlorophytes
        2. laminarin or chrysolaminarin (beta-1,3 linked glucose)
          1. laminarin in oil-like droplets in the cytoplasm near pyrenoid in phaeophytes
          2. chrysolaminarin similar, in cytoplasm of chrysophytes, bacillariophytes, prymnesiophytes
        3. paramylon (beta-1,3 linked glucose), bounded by a membrane, in cytoplasm of euglenoids, xanthophytes, and some prymnesiophytes
        4. fructosans (1,2 linked fructose) in some chlorophytes
      2. low molecular weight
        1. sucrose (chlorophytes and euglenoids) or trehalose (rhodophytes)
        2. glycosides (glucose attached to glycerol) in rhodophytes
        3. polyols like mannitol, glycerol, etc. in phaeophytes and numerous other groups
    6. RuBP carboxylase problems
      1. carbon-isotope discrimination
        1. RuBP carboxylase slightly favors carbon-12 carbon dioxide over carbon dioxide using other isotopes; as a result, the products of the Calvin-Benson cycle are enriched in carbon-12 relative to the air
        2. the degree of enrichment is standardly given as the delta-13 value, which compares the carbon-13/carbon-12 ratio of the plant with the carbon-13/carbon-12 ratio in a standard rock formation (a particular Cretaceous limestone)
          1. delta-13 is calculated as  [(Rsample - Rstandard)/Rstandard] x 1000, where R refers to the ratio of carbon-13 to carbon-12
          2. if an organism preferentially uses carbon-12, Rsample will be smaller than Rstandard and the value of delta-13 will be more negative; this is generally true of C3 plants
      2. oxygen-discrimination
        1. molecular oxygen acts as a competitive inhibitor of RuBP carboxylase; the competing reaction produces phosphoglycolate which can result in a net loss of carbon from the cell (photorespiration)
        2. solutions
          1. evolutionary trend toward smaller half-saturation constants for RubisCO binding CO2
            1. Km often found from   P = Pmax* [S/(Km + S)], where S is the substrate concentration
            2. Km for cyanobacteria typically in the range 80 to 330 micromoles, Km for eukaryotic algae are in the range 45-70 micromoles, while those for higher plants are in the range 10 to 25 micromoles
          2. evolutionary trend toward more discrimination against oxygen (measured as tau--organisms with high tau are less susceptible to oxygenase activity
          3. recovery of energy stored in phosphoglycolate through conversion to glyoxylate
            1. glycolate oxidase in peroxisomes
            2. glycolate dehydrogenase in cyanobacteria and in mitochondria
          4. development of carbon concentrating mechanisms
            1. similar in function to C4 metabolism in higher plants
            2. in algae, most seem to revolve around the concentration bicarbonate ions and the conversion of bicarbonate to carbon dioxide via carbonic anhydrase
              1. bicarbonate ions are more common in slightly basic waters
              2. bicarbonate does not cross membranes as easily as carbon dioxide
              3. concentrating mechanism can be intracellular or extracellular
              4. in some instances the mechanism is tied to external carbonate formations
                1. basic reaction:  HCO3- + H+ == CO2 + H20
                2. need source of H+:  CO2 +Ca2+ + H2O == CaCO3 + 2H+
            3. in cyanobacteria, both carbonic anhydrase and RubisCO are located in carboxysomes
            4. in algae, mechanisms are diverse, sometimes associated with pyrenoids, sometimes carbonic anhydrase associated with membrane
    7. measurement of photosynthesis
      1. increase in dry weight
      2. 14CO2 uptake
        1. dark reactions
        2. measures gross primary production if time is short
      3. net CO2 uptake using infrared gas analyzers
        1. dark reactions
        2. measures net primary production (gross uptake is partially obscured by CO2 release through respiration)
      4. net O2 production using oxygen electrodes
        1. light reactions
        2. partially obscured by oxygen uptake for respiration
      5. chlorophyll fluorescence
        1. light reactions
        2. monitors transfer of electrons between reaction centers
    8. photosynthetic response to light
    9. photosynthetic response to carbon dioxide
    10. other interactions with light
      1. phototaxis
        1. involves eyespot but eyespot is not the photoreceptor (photoblocker)
        2. receptor often in swelling in base of flagellum
      2. diurnal rhythms
      3. sporogenesis

UNIT 4. PHOTOSYNTHETIC PROKARYOTES

  1. Review evolution and phylogeny of non-oxygenic photosynthetic prokaryotes
    1. origins of cells
    2. origins of photosynthesis
    3. diversity of organisms
      1. Halobacteriaceae (Halobacterium, etc.)
        1. halophilic archaebacteria
          1. significantly different ribosomal RNA
          2. cell walls without peptidoglycan
          3. frequently with branched hydrocarbons and etherr-linked phosphoglycerides in the cell membrane
          4. most require at least 1.5 molar salt in their surroundings
          5. most are pink or reddish in color because of high concentrations of C50 carotenoids
        2. most store light energy using bacteriorhodopsin in special purple membranes to transfer hydrogen ions outward
          1. absorption peak at 568
          2. similar molecules used to pump chloride ions inward
        3. possibly fixes carbon dioxide via the reductive acetyl-CoA pathway; some reports suggest RuBP carboxylase is present; whether or not true phototrophs is a matter of debate
          1. one molecule of CO2 is reduced to form an enzyme-bound carbonyl
          2. a second CO2 is reduced to form a tetrahydropterin-bound methyl group
          3. the carbonyl and the methyl are then condensed to form acetyl-CoA by the enzyme carbon monoxide dehydrogenase/acetyl-CoA synthetase
          4. the acetyl is carboxylated to form pyruvate
      2. bacteriochlorophyll-using bacteria (all are eubacteria)
        1. use photosystem I to produce ATP; variety of bacteriochlorophylls (at least 6)
          1. bacteriochlorophylls very similar in structure to chlorophyll a
          2. absorption peaks at 800 and 870 nm, instead of 680 nm
          3. pigments in patches of cell membrane, in cytoplasmic tubes, vesicles, etc., derived from cell membrane or in chlorosomes (phospholipid monolayers associated with cell membrane)
          4. electron transport chain uses cytochrome bc1, c also found in respiratory chains
        2. NADPH produced through either the oxidation of hydrogen or through reversed electron transport
          1. hydrogen oxidation requires the enzyme hyrogenase
          2. reverse electron transport requires an electron donor (hydrogen sulfide, hydrogen thiosulfate, some organics, Fe+2 ions) and energy in the form of a charged membrane; sulfide and thiosulfate enter the electron transport chain at cytochrome c
        3. most can fix nitrogen
        4. can be divided into 7 subgroups
          1. Rhodospirillaceae (purple non-sulfur bacteria; alphaproteobacteria and betaproteobacteria)
            1. photoheterotrophs
            2. hydrogen sulfide is toxic, but can tolerate oxygen
          2. Heliobacteriaceae (Heliobacillus and Heliobacterium)
            1. similar to purple non-sulfur but strictly photoheterotrophs; different chlorophyll; no internal membranes
          3. Chromatiaceae (purple sulfur bacteria, gammaproteobacteria)
            1. true photoautotrophs
            2. produce sulfur droplets internal during NADPH formation
            3. a subgroup produces external droplets
          4. Chlorobiaceae (green sulfur bacteria)
            1. true photoautotrophs
              1. bacteriochlorophyll in chlorosomes
              2. fix carbon via the reductive (reverse) TCA cycle
            2. deposit sulfur externally under some conditions
            3. acidophilic and anaerobic
          5. Chloroflexaceae - filamentous green bacteria
            1. flexible walls and gliding motility
            2. Chloroflexus fixes CO2 by unique pathway
              1. acetyl-CoA is carboxylated, then reduced to form proprionyl-CoA
              2. proprionyl-CoA is carboxylated to form methyl-malonyl CoA from which malate or oxaloacetate can be formed
          6. Erythrobacter (alphaproteobacteria)
            1. aerobic, chemotrophic, mostly respiratory
            2. does contain bacteriochlorophyll , etc.; production stimulated by oxygen
  2. Oxygen producing prokaryotes – cyanobacteria
    1. most important group of photosynthetic bacteria; one of the most important groups of algae
      1. possibly 150 genera, 2000 species, possibly many more, possibly many less
      2. possibly responsible for changing the atmosphere to an oxygen containing atmosphere
      3. as picoplankton, may be the largest group of photosynthetic organisms in the ocean
      4. an important component of the nitrogen cycle, especially in the tropics
      5. produce toxic blooms
      6. sold in health-food stores
    2. important features
      1. normal eubacterial, Gram-negative cell
        1. wall contains peptidoglycan layer covered by a membrane of lipopolysaccharides
        2. may be covered by a sheath or capsule of sugars, proteins, etc.
        3. genetic material consists of nucleoid; translation using 70S ribosomes
        4. generally large for prokaryote cells (internal compartments formed by thylakoids)
      2. basic morphologies
        1. coccoid, bacilloid, spiral forms with and without sheaths
        2. how many planes of division?
        3. production of small cells (baeocytes) by repeated or simultaneous cell division
        4. polarity of the cell
        5. filamentous forms with and without sheath
          1. the filament of cells, excluding any sheath is called a trichome
          2. most important features are the degree of branching and the presence of special cells (heterocysts and akinetes)
      3. photosynthetic apparatus
        1. thylakoids in various arrangements - continuous with cell membrane?
        2. embedded in the thylakoids are the reaction centers and the electron transport chains
        3. attached to the reaction center are the water-soluble phycobilisomes
        4. normally produce oxygen during photosynthesis, but many capable of switching to system similar to that of the sulfur-bacteria, especially in sulfide-rich environments with lots of light (stratified shallow lakes and lagoons)
      4. inclusion bodies in the cytoplasm
        1. cyanophycean starch granules (alpha-1,4-linked glucose)
        2. cyanophycin granules - large granules, often found near the cross-walls of filamentous forms, composed of a polymer of arginine and asparagine (one of very few proteins known not to be made on a ribosome) - functions as a nitrogen reserve
        3. polyphosphate granules (volutin) - phosphate "rocks" which act a reserve for phosphate; stain with toluidine blue
        4. carboxysomes - polyhedral accumulations of RuBP carboxylase (similar to pyrenoids?)
        5. poly-beta-hydroxybutyric acid - storage product in a few cyanobacteria
        6. gas vacuoles in cyanobacteria
          1. composed of bundles of hollow protein cylinders filled with gas
          2. serve a buoyancy tanks to regulate the position of the alga in the water column
            1. if light is low, more vesicles are formed and the alga floats to more brightly lit layers
            2. in brightly lit layers more photosynthesis; more photosynthesis increases the number of small sugars, etc., in the cell, decreasing the osmotic pressure (makes more negative)
            3. as osmotic pressure becomes more negative, water enters the cell; this increases the hydrostatic pressure; as the hydrostatic pressure increases, the gas vesicles collapse and the alga sinks
      5. special cells
        1. akinetes - large resting stages
          1. relatively thick wall
          2. full of cyanophycin granules and cyanophycean starch, but no volutin
          3. formation may be triggered by phosphate deficiency
          4. resistant to environment, surviving years in lake sediments
            1. this may be important since some of the toxic forms are also akinete formers; stirring up the bottom by dredging may trigger a bloom
        2. heterocysts - special cells designed for nitrogen fixation
          1. nitrogen fixation is a high energy process
            1. need to reduce nitrogen to ammonium
              1. requires 16 ATP and 8 electrons for each molecule of N2 reduced
                1. ATP from photosynthesis
                2. electrons supplied by organic molecules via NADPH and reduced ferrodoxin
                3. ferrodoxin is a water soluble, iron and sulfur containing molecule
            2. ammonium is immediately attached to glutamate to make glutamine
          2. enzyme for the reduction step is nitrogenase
            1. enzyme is reasonably well-conserved over a variety of bacteria
              1. two components, both necessary, both oxygen sensitive
                1. Fe component that binds MgATP and transfers electrons to second
                2. MoFe component that reduces dinitrogen
          3. special structures of heterocysts help protect nitrogenase
            1. visually, heterocysts appear as thick-walled structures with a pale color, no inclusions
              1. closer examination reveals reduced thylakoids, no photosystem II, only photosystem (cyclic photophosphorylation), numerous plasmodesmata
                  1. free from oxygen, source of energy, means to pass material to rest of cells
            2. should be noted that non-heterocystous forms may also fix nitrogen
              1. at night, so that oxygen production limited (quickly make nitrogenase at sunset
              2. in anoxic regions of the environment
          4. should also be noted that enzyme not very specific
            1. standard test for nitrogen fixation monitors the reduction of acetylene to ethylene
          5. under some conditions, nitrogenase shunts electrons off to H+, producing hydrogen gas; during the Carter years there was a federal program to see if this could be made into a reliable source of H2
      6. toxins
        1. over 30 species implicated in toxic water blooms
        2. three major categories of toxins
          1. hepatatoxins (microcystin, nodularin, cylindrospermopsin, etc.) can lead to intrahepatic hemorrhage and hypovolemic shock,  death within days; upto 90% of lethal dose can be injested safely; present in strains of Anabaena, Microcystis, Nodularia, Nostoc, Oscillatoria
          2. anatoxins increase the effects acetylcholine (block cholinesterase), causing paralysis, death in minutes to hours because breathing paralyzed; present in strains of Anabaena, Aphanizomenon, Lyngbya
          3. saxitoxins block sodium channels, preventing transmission of impulses and paralysis--a form of paralytic shellfish poisoning; present in strains of Anabaena circinalis and Aphanizomenon flos-aquae
      7. habitats
        1. important constituent of marine picoplankton
        2. common in freshwater and terrestrial environments
        3. found in some of the most extreme environments
          1. thermal springs
          2. hot deserts
          3. Antarctica
      8. taxonomic concepts
        1. species concept - what constitutes a species in asexual organisms
          1. broad species with ecological variants
          2. narrow species with similar morphology
          3. are strains the only real category
        2. higher level taxonomic relations
          1. Geitlerian vs Drouetian vs Stanierian vs Anagnostidis and Komarek vs ???
          2. many arguments based on disagreement concerning the way the group should be treated
            1. blue-green algae (cyanophytes) vs blue-green bacteria (cyanobacteria)
            2. botanical vs bacteriological codes of nomenclature
          3. currently, molecular phylogenies based on small-subunit ribosomal RNA sequences are redefining (yet again) the major grouping; until sorted out we will stick with a somewhat classical-botanical approach
        3. major taxonomic groups
          1. Chroococcales (Anagnostidis and Komarek)
            1. all of the unicellular cyanobacteria (and old orders Chamaesiphonales, Pleurocapsales)
            2. families distinguished by: shape of cell, planes of division, formation of baeocytes and nanocytes, presence and type of sheath
            3. important genera: Microcystis, Gloeocapsa, Chroococcus, Synechococcus, Synechocystis, Anacystis
          2. Oscillatoriales (Anagnostidis and Komarek)
            1. characterized by uniseriate trichomes with or without sheaths (trichomes and filaments may be bundled), without special cells or true branching (false branching rare)
            2. families and genera are based on the type and color of the sheath, the shape and color of the cells, motility of filaments and hormogonia, false branching
            3. some important genera: Oscillatoria, Phormidium, Lyngbya, Plectonema, Spirulina
          3. Nostocales (Anagnostidis and Komarek)
            1. characterized by uniseriate trichomes with or without sheaths, with heterocysts and/or akinetes, without true branching
            2. families and genera based on: the type and color of sheath, the shape and color of cells, the shape and relative position of heterocysts and akinetes, the type of false branching, tapering of the trichomes and filaments
            3. some important genera: Nostoc, Anabaena, Aphanizomenon, Scytonema/Tolypothrix,Rivularia
          4. Stigonematales (Anagnostidis and Komarek)
            1. characterized by uniseriate or multiseriate trichomes with true banching and heterocysts and possibly akinetes
            2. families and genera distinguished by shape of cells, the nature of the trichome, the type of branching, the shape and relative positions of heterocysts and akinetes
            3. some important genera: Stigonema, Fischerella, Hapalosiphon
        4. Prochlorophytes—not a taxonomic group
          1. first discovered living as symbionts of sea squirts, now known from the picoplankton of some lakes and from blooms of filamentous forms
          2. photosynthetic apparatus
            1. chlorophyll a and b with carotene and other carotenoids as accessory pigments in stacked thylakoids, and using non-cyclic photophosphorylation
          3. cyanobacteria-like carboxysomes and starch
          4. peptidoglycan wall
          5. once thought to be implicated in the origin of mitochondria and chloroplasts, but now considered to be an interesting group of unrelated cyanobacteria
UNIT 5.  THE ORIGINS OF EUKARYOTE ALGAE
  1. Review of major events leading to eukaryotic forms
    1. origin of life in an anoxic world
      1. first cells simple getting energy by anaerobic fermentation
      2. origins of electron transport systems and carbon and nitrogen fixation
      3. origins of anoxygenic photosynthesis
      4. origins of oxygenic photosynthesis (cyanobacteria)
      5. increasing oxygen in the environment lead to selection for
        1. oxygen tolerance
        2. advanced oxygen tolerance (catalase, etc.)
        3. aerobic respiration
    2. in the meantime, early cells quickly split into two major lineages, the eubacteria and the archaebacteria and from the archeabacterial lineage (?) arose proto-eukaryotes
      1. major features of the proto-eukaryotes probably include:
        1. anaerobic fermentation; eventually oxygen tolerance (catalase)
        2. complex internal membrane system
          1. nucleus
        3. complex cytoskeleton including microtubules
        4. phagocytic life-style in at least many of them
    3. rise of oxygen lead to selection among eukaryotes for those forms capable of maintaining some organisms as endosymbionts
      1. anoxygenic photosynthetic bacteria, which eventually evolved into mitochondria and hydrogenosomes, possibly during the anoxic stages of Earth's history
        1. process must have begun very early, because mitochondria now highly modified
          1. ribosomes don't match the bacterial type any more
          2. most of the genes have been transferred into the nucleus
        2. three types - flattened, disk-like, and tubular - repesenting three events or three lineages (?)
        3. hydrogenosomes in Giardia appear to represent an extreme case, in which all DNA has been transferred
      2. cyanobacteria as plastids, other plastid containing eukaryotes as plastids
  2. Examples of modern equivalents of some of the stages in the process of plastid incorporation
    1. endosymbiosis with living cells
      1. Aphanocapsa - common cyanobacterial endosymbiont of warm-water sponges
      2. inclusions in some open ocean diatoms - under EM can be seen to contain thylakoids with phycobilisomes and to undergo cell division - probably cyanobacteria
      3. Chlorella in Hydra and in numerous ciliates
        1. live in special vacuoles that block normal digestion and cause production of maltose
        2. only a few species in the genus can cause the formation of special vacuoles
      4. most large foraminifera contain some sort of algal symbiont
      5. corals contain up to 2 million zooxanthellae per square millimeter
    2. cyanelles
      1. photosynthetic structures in the glaucophytes
      2. clearly modified cyanobacteria
        1. contain peptidogycan and lipopolysaccharide layers
        2. thylakoids with phycobilisomes, but lack phycoerythrin
        3. can make glucose but not starch
        4. more DNA than normal plastids, but 90% of proteins made by nuclear genes
      3. some well-known forms include Cyanophora and Glaucocystis
    3. primary endosymbiosis in the green and the red algae
      1. plastids with two membranes in the envelope
      2. most of the photosynthesis genes now in the nucleus
      3. some no longer photosynthetic at all but still with sizable genome
    4. secondary endosymbiosis
      1. in chlorarchiophytes
        1. in this case a green alga has been incorporated as a plastid into a eukaryotic amoeba
        2. the plastid retains several features hinting at its origins
          1. surrounded by four membranes
          2. between the inner two and the outer two is a nucleomorph containing tiny chromosomes and just ennough genes to keep it alive and capable of division - clearly the remains of a nucleus from an endosymbiont
        3. best-known genus is Chlorarachnion
      2. the situation is similar in cryptophytes
      3. secondary endosymbiosis in ochrophytes, euglenoids, etc., has progressed to the stage where the nucleomorph has been lost
    5. tertiary endosymbiosis
      1. in this case an organism with secondary plastids is eaten by a third organism
      2. most common examles are the dinoflagellates (always a good group to look for interesting plastids)
        1. Peridinium balticum contains two nuclei and a plastid without peridinin that probably derieves from a diatom ancestor
    6. kleptoplastidy
      1. some organisms harvest just the plastids and keep them alive for months in special pouches
        1. oligotrich ciliates (Strombidium) - from lots of unicellular algae
        2. the sea slug Elysia - Cladophora
        3. Gymnodinium acidotum - cryptomonad plastids
    7. cryptic endosymbiosis and gene transfer