VALDOSTA STATE UNIVERSITY

LECTURE NOTES FOR PHYCOLOGY

SPRING 2002

UNIT 6. DIVISION CHLOROPHYTA--THE GREEN ALGAE
  1. Basic features
    1. one of the largest groups, with representatives in marine, freshwater, and terrestrial systems
    2. plastid structure
      1. two-membrane envelope without any chloroplast ER
      2. thylakoids in stacks
      3. chlorophyll a and b
      4. stores alpha-1,4 linked glucans (only group with storage product in the plastid)
    3. flagella, if present, in multiples of 2, without tripartite hairs (mastigonemes); structure useful for phylogenetic and taxonomic purposes
      1. start with an axoneme of 9 doublets of microtubules surrounding an inner core of 2 microtubules, which is covered by the cell membrane
      2. as the flagellum enters the body of the cell, the 2 central tubules end in a plate and the 9 doublets are converted to 9 triplets, leading to 2 to 4 basal bodies
      3. in most cases microtubular roots are attached to the basal bodies in a cruciate pattern of 2-tubule roots alternately with 3-to-many microtubular roots and are connected by two patches of connecting fibers; the basal bodies can be clockwise, anticlockwise, or directly opposed
      4. in at least one lineage, the basal bodies meet in an asymmetric pattern and are anchored by single broad band of microtubules associated with a multi-layered structure
    4. eyespots, if present, always in the plastid
      1. the eyespot consists of a number of layers of carotenoid-containing lipid droplets between the chloroplast envelope and the outermost thylakoids
      2. the photoreceptor is in the cell membrane above the eyespot; contains a chromophore containing 11-cis-retinol, a rhodopsin that also functions as a photoreceptor in animals
    5. enzymes for photorespiration can be either a glycolate dehydrogenase or glycolate oxidase
      1. both enzymes catalyze the reaction convert glycolate to glyoxalate with the production of hydrogen peroxide
      2. the peroxide is converted to water and oxygen by catalase, the glyoxalate is converted to glycine by the addition of an amino group
      3. reactions are localized in peroxisomes
    6. patterns of cell division
      1. mitosis can be either closed (with a persistent nuclear membrane) or open (nuclear membrane disappears)
      2. three versions of cytokinesis
        1. mitotic spindle collapses, a set of microtubules (the phycoplast) forms parallel to the division plane, and a cleavage furrow forms
        2. mitotic spindle remains and a cleavage furrow forms (similar to protozoans and animals)
        3. mitotic spindle remains and a new wall forms through a phragmoplast (similar to higher plants)
    7. life histories
      1. basic patterns
        1. habits and morphologies
          1. monadoid - flagellated vegetative cells (Chlamydomonas)
          2. palmelloid - separate vegetative cells in a common mucilage
          3. coccoid - unicellular vegetative cells with a cell wall but without flagella
          4. filamentous - thallus of linked cells
          5. coenobial - thallus with a definite shape and number of cells
          6. coenocytic - large multinucleate cells, often with a macroscopic thallus without cross-walls separating cells
        1. reproduction
          1. asexual division
            1. vegetative reproduction (desmoschisis) - results in the formation of non-reproductive cells that include parts of the cell wall of the mother cell
            2. zoospore production
            3. autospores and aplanospores - non-motile spores produced through subdivision of the protoplast
          2. sexual reproduction
            1. isogamy vs anisogamy vs oogamy
            2. heterothallic vs homothallic
            3. conjugation (scalariform and lateral)
          3. alternation of generations
            1. haploid dominant (haplontic, zygotic meiosis) - most common
            2. more or less equal stages - diplohaplontic; can be isomorphic or heteromorphic
            3. diploid dominant (diplontic, gametic meiosis) - rare among chlorophytes
      2. life history examples
        1. Chlamydomonas
          1. typical cell is a haploid flagellate formed in multiples of 2 within the envelope of the mother cell using phycoplast-style cell division
          2. under certain conditions (limited flowing water) the vegetative cells resorb their flagella and enter the palmelloid stage; these reform flagella when conditions are reversed
          3. under other conditions (limited nitrogen) the cells develop into gametes by forming special structures in the cell membrane at the anterior end and special agglutinins on the surfaces of the flagella; cells then form clumps attached by flagella, these eventually break into pairs; the cells in a pair fuse to form a zygote with 4 flagella; the zygote eventually resorbs its flagella and forms a thick wall - it is now called a hypnozygote; the zygotes germinate by meiosis, producing 4 or 8 haploid vegetative cells
        2. Volvox
          1. large colonies of flagellated Chlamydomonas-like cells
          2. asexual reproduction occurs through the division of special cells (gonidia); these initially form small balls of cells with the flagella pointed inward; when the colony reaches a certain size it inverts; it is released when the mother colony is broken apart
          3. under certain conditions some of the colony will begin to form sperm; the male (sperm-producing colonies) produce a potent pheromone that causes the other colonies to begin egg formation; the sperm are eventually released in packets, digest their way into a female colony and fuse, separately with eggs; zygotes germinate into a single meiotic flagellate cell which then develops into a flagellated colony
        3. Chlorococcum
          1. individual coccoid cells
          2. under certain conditions, asexual reproduction is through aplanospores, under other conditions through biflagellate zoospores; in either case, the cells develop into nonmotile vegetative cells
          3. sexual reproduction is through isogamous flagellated gametes
        4. Pediastrum
          1. coenobia of large cells linked in a star-like pattern
          2. asexual reproduction involves the multiple division of the cytoplasm into as many biflagellate zoospores as the mother colony has cells; the spores are not released, instead they join together into the pattern of the original on a miniature scale; these are released by the rupture of the parent cell wall
          3. occasionally zoospores are released; these form special polyhedral cells called polyeders; these then make internal zoospores that join up to form a small colony
          4. sexual reproduction involves the release of flagellated gametes that fuse to form a zygote; the zygote germinates after meiosis to release four zoospores that then form polyeders
        5. Oedogonium
          1. unbranched filaments formed by vegetative cell division; in this case cell expansion occurs after cytokinesis and the break in the old wall occurs near one end; result is a shingled appearance in some of the older cells
          2. under certain conditions stephanokont zoospores are formed
          3. sexual reproduction is oogamous; the formation of the egg occurs within an oogonium joined to a support cell; sperm production is macrandrous or nannandrous
            1. in macrandous forms, the antheridial mother cell produces a long and a short cell, the long cell produces a number of antheridia, and each antheridium produces two sperm
            2. in nannandrous forms each antheridium forms a single androspore which is attracted to the oogonial mother cell; it attaches and grows into a short (2-celled) filament; the upper cell of the filament produces two sperm which eventually make their way to the oogonium
  2. Classification--Chlorophyta exhibits at least three major lineages; this have been subdivided into up to 10 classes; we will use the five class system found in your text.
    1. Prasinophyceae
      1. small group (16 genera, 180 species) of flagellates with a large number of primitive characters, but no defining set of characters (may be polyphyletic)
      2. basic characters include
        1. most bear 1 to 8 flagella inserted either laterally or apically, usually near the base of a depression
        2. a flagellar root system that is either cruciate or unilateral with a broad band of microtubules and a multilayered structure; most also have a striated rhizoplast; the diversity of flagellar apparatuses is unique
        3. mitosis can be either open or closed
        4. cytokinesis can involve a persistent spindle and a cleavage furrow or follow the phycoplast system
        5. cell body covered with multiple layers of scales of a pectin-like substance formed in the Golgi apparatus; occasionally the scales are fused to form a solid theca
        6. some with extrusosomes
        7. some of the members exhibit mixotrophy
      3. examples
        1. Pyramimonas - widespread flagellate in fresh or salt water
        2. Bathycoccus - a tiny (0.5 to 2.0 micrometers in diameter) flagellate found in the picoplankton of the North Atlantic
        3. Pterosperma - forms an encysted stage (the phycoma) with an especially resistant wall; fossil phycomata have been found in 1,200 mya sediments
    2. Ulvophyceae
      1. diverse group with over 100 genera and 1100 species, including many macrophytes
      2. basic characters
        1. motile cells with apical flagella; a cruciate root system without an MLS, but possibly with a rhizoplast of striated fibers; no wall, but possibly scales
        2. mitosis is closed and cytokinesis involves a persistent spindle and cleavage furrow
        3. each cell with one cup-shaped or parietal plastid, many plastids in siphonous forms
        4. use glycolate dehydrogenase
      3. orders
        1. Ulotrichales
          1. nonflagellate unicells or branched or unbranched filaments
          2. all with an attached (Codiolum) stage formed by the zygote; the zygote undergoes meiosis, producing flagellated zoospores (meiospores)
          3. gametes not formed in special cells
          4. examples
            1. Ulothrix – unbranched filaments with a parietal plate-type plastid and an attachment organ
        2. Trentepohliales
          1. small group of terrestrial algae with branched filaments
          2. cytokinesis involves a phragmoplast-like array of microtubules
          3. gametes and zoospores formed in special cells; the flagellate cells lack eyespots; the flagella have a wing-like structure
          4. examples
            1. Trentepohlia – branched filaments forming fuzzy growths on tree-bark, rocks and buildings
            2. Cephaleuros – circular colonies with reproductive structures similar to those of Trentepohlia, but growing as a parasite within the cuticle of tropical and subtropical trees such as Magnolias
        3. Ulvales
          1. marine macrophytes with a thallus composed of one- or two-layered sheets of cells, each with a large parietal plastid
          2. isomorphic diplohaplontic lifecycle with biflagellate gametes and quadriflagellate zoospores (meiospores) not made in specialized structures
          3. examples
            1. Ulva – large two-layered sheets
            2. Enteromorpha – large tubes, whose walls are one-cell thick
        4. Siphonocladales (Cladophorales)
          1. branched or unbranched filaments of multinucleate cells with periodic cross-walls and occasional segregating cell division where the cytoplasm is suddenly divided by cellwalls
          2. either a highly dissected (reticulate) plastid or a number of discoid plastid in a network framework
          3. examples
            1. Cladophora – branched filaments composed of large multinucleate cells
            2. Rhizoclonium – large, sparsely branched or unbranched filaments
            3. Valonia – appears in the form of huge balloon-like cells
        5. Dasycladales
          1. tropical and subtropical marine macrophytes, usually calcified
          2. siphonous structure with radial symmetry and an erect axis with many branches
          3. uninucleate vegetative thallus; multinucleate condition immediately prior to reproduction
          4. examples
            1. Acetabularia – parasol structure; extensively used to demonstrate the importance of the nucleus in morphology, circadian rhythms, etc.
        6. Caulerpales
          1. marine tropical and subtropical macrophytes
          2. multinucleate siphonous forms, without cross-walls or segregative division, numerous plastids
          3. sometimes with a multiaxial construction, sometimes with calcium carbonate in the walls
          4. examples
            1. Caulerpa – similar in external appearance to fern fronds; with ingrowths of the cell wall called trabeculae; reproduction involving holocarpy, in which the entire protoplasm gives rise to flagellated cells at once
            2. Udotea – forms carbonate-encrusted fans
            3. Halimeda – jointed, carbonate encrusted thallus, fossil record extending back 100’s of millions of years
            4. Penicillus – shaving-brush morphology based on a multiaxial construction
            5. Codium – dead-man’s finger morphology; filaments expanded at the surface to form utricles, inner filaments colorless
    3. Trebouxiophyceae
      1. basic characters
        1. predominantly unicellular aerial forms, similar in appearance to members of the Chlorophyceae (and usually included in the chlorophycean order Chlorococcales), but differing on the basis of ssu sequences and mitochondrial genomes and on feature of cell division
        2. cruciate roots with the basal bodies arranged counter-clockwise
        3. metacentric spindles (an alternative form of mitosis in which the centrioles are at the side of the spindle)
      2. examples
        1. Chlorella – elliptical to spherical cells with a parietal plastid; reproduction by autospores only; often an endosymbiont of protozoans and simple animals used extensively in studies of single-cell-protein and life-support systems
        2. Trebouxia – spherical cells with an axial stellate plastid, usually found as part of a lichen
        3. Stichococcus – small rod-shaped cells with a single parietal plastid common in subaerial environments
        4. Prasiola – sheets of cells, similar to members of the order Ulvales, but with axial, stellate plastids
    4. Chlorophyceae
      1. one of the most diverse groups in the division Chlorophyta, with over 7000 species described, almost all from freshwater; thallus morphology and reproductive types run the gamut of what has previously been discussed for the division
      2. basic characters
        1. almost all lifecycles involve flagellate cells with a theca (wall) at some stage
        2. sexual life-cycles are haplontic
        3. mitosis is closed, the spindle is non-persistent and cytokinesis is by means of a phycoplast
      3. taxonomic considerations
        1. Chlorophyceans appear to fall into two major lineages (clades) in the basis of sequence analysis and flagellar structure; however this work is still being sorted out, and the information is difficult to work with; therefore we will follow a more traditional division of the class into orders
        2. major orders
          1. Volvocales
            1. large order of unicellular and colonial flagellates, some with palmelloid stages
            2. examples
              1. Chlamydomonas – unicellular with two flagella
              2. Gonium – flat plates of flagellated cells
              3. Pandorina – solid globular balls of flagellated cells
              4. Eudorina – small hollow balls of flagellated cells
              5. Volvox – large hollow balls of flagellated cells
          2. Chlorococcales
            1. non-flagellate cells reproducing by means of zoospores and aplanospores, without vegetative cell division
            2. examples
              1. Chlorococcum – similar in appearance to Chlorella
              2. Characium – an epiphytic form with a short stalk
              3. Scenedesmus – a coenobial form with 2, 4, or 8 cells
              4. Hydrodictyon – the water-net
              5. Pediastrum – coenobia in the appearance of flat stars
          3. Tetrasporales
            1. unicellular forms with immobile vegetative cells capable of vegetative cell-division as well as zoospore and aplanospore production
            2. examples
              1. Tetraspora – vegetative cells enclosed in a colonial mucus in groups of two or four, each with two pseudocilia (projections with a 9+0 construction)
              2. Palmella – similar to Tetraspora, but without the pseudocilia
          4. Sphaeropleales
            1. filamentous forms whose walls are composed of articulated H-shaped segments
            2. examples
              1. Sphaeroplea – a siphonous form
              2. Microspora – unbranched filaments with reticulate plastids and H-pieces
          5. Chlorosarcinales
            1. form packets of cells
            2. example
              1. Chlorosarcina – a common soil alga
          6. Chaetophorales
            1. branched and unbranched filaments with plasmodesmata
            2. examples
              1. Chaetophora – branched filaments with a parietal plate-like plastid and tapering into multicellular hairs; thallus usually in a thick mucilage
              2. Stigeoclonium – similar to Chaetophora, but without the thick mucilage
          7. Oedogoniales
            1. branched and unbranched filaments with reticulate plastids, stephanokont motile cells, and cytokinesis involving the formation of caps and shingles
            2. examples
              1. Oedogonium – unbranched filaments
              2. Bulbochaete – branched filaments with unicellular hairs
    5. Charophyceae
      1. lineage of freshwater green algae leading to higher plants; phylogeny based on molecular and morphological evidence
      2. basic characters
        1. flagellate cells, if present, with an asymmetric (lateral) insertion of flagella
        2. flagellar root consisting of a broad band of microtubules with a smaller secondary root; rhizoplast absent; multilayered structure may be present
        3. persistent spindle with phragmoplast cell wall construction; cell walls contain cellulose, which is formed in membrane complexes similar to those of higher plants (other cellulose containing green algae use a different kind of complex and produce a larger cellulose fiber
        4. glycolate oxidase
        5. haplontic life-histories with hypnozygotes
      3. orders
        1. Klebsormidiales
          1. coccoid to filamentous forms, filaments without plasmodesmata
          2. cells uninucleate with a parietal cup-shaped or plate-like plastid
          3. example
            1. Klebsormidium – freshwater and terrestrial unbranched filaments similar in overall appearance to Ulothrix, but the zoospores lack eyespots
        2. Zygnematales
          1. widespread, species rich group of common freshwater filaments and coccoid forms that reproduce sexually through conjugation
          2. examples
            1. Zygnemataceae – filamentous forms composed of cylindrical cells, cell walls without pores
              1. Spirogyra
              2. Mougeotia
            2. Mesotaniaceae (saccoderm desmids) – unicellular forms whose cell wall does not consist of two halves (semicells) held joined by an isthmus or a suture
              1. Spirotaenia – unicellular form with a spiral plastid
              2. Netrium – cylindrical unicellular form with rounded ends
            3. Desmidaceae (placoderm desmids or desmids) – unicellular or filamentous forms with each cell consisting of two semicells; wall contain pores for the secretion of mucus
              1. Closterium – banana-shaped cells with barium sulfate containing vacuoles at the ends
              2. Cosmarium – usually composed of two semicells that are nearly circular in face-view, elliptic in side-view
              3. Staurastrum – semicells are triradiate to hexaradiate
              4. Microasterias – large flat cells with many rays
              5. Desmidium – a filamentous form with bi- tri- or quadri-radiate cells
        3. Coleochaetales
          1. branched filaments whose crosswalls are pierced by plasmodesmata; most cells bear hairs that may be sheathed and contain cytoplasm
          2. example
            1. Coleochaete – flat disc of cells with sheathed hairs; egg cells and zygotes are retained in the thallus; the surrounding thallus cells develop into a nourishment organ similar in some respects to nourishment cells in embryophytes; sperm development is reminiscent of that in bryophytes
        4. Charales
          1. macrophytes with a long fossil record and a complex filamentous structure consisting of a central axis with whorls of branches at defined nodes
          2. growth is by means of apical meristem cells without centrioles; these divide transversely once to create a segmental cell; the segmental cell divides transversely to form two cells, the upper of which continues to divide to form complex nodes, the lower of which expands to form an internode – internode cells can grow to lengths up to 15 centimeters
          3. gametes are produced in specialized structures (gametangia) covered by a layer of non-reproductive cells, highly unusual among the algae
            1. antheridia – bright orange at maturity, because of lipid droplets in the outer layer of shield cells; sperm are produced by the internal cells of the primary capitulum
            2. oogonia – egg cell surrounded by a helical arrangement of five peripheral cells capped by a corona of five or ten crown cells
            3. zygotes germinate by meiosis
          4. examples
            1. Chara – characterized by unicellular stipules just below the branchlets at the node; usually a layer of cortical cells; corona of five cells; often smell of garlic
            2. Nitella – characterized by very regular branching and uncorticated main axes; oogonia with two tiers of coronal cells
UNIT 7. DIVISION OCHROPHYTA--THE CHROMISTAN (GOLDEN-BROWN, STRAMENOPILE) ALGAE
  1. Basic characteristics
    1. an diverse group, ranging from flagellate unicells to giant kelps; related to closely to oomycetes, less so to a number of colorless protozoans, then alveolates and haptophytes
    2. flagellar apparatus – the defining feature of the group
      1. typically two flagella
      2. leading flagellum with two rows of tripartite hairs (mastigonemes); formed in the endoplasmic reticulum either near the plastid or near the nucleus
      3. trailing whiplash flagellum; often with a basal swelling involved in phototropic responses
      4. usually with a helical structure above the basal plate
      5. usually four microtubules, two associated with the anterior flagellum, two with the posterior
      6. one of the anterior roots is associated with the cytoskeleton in general, one of the posterior roots is associated with a feeding apparatus
    3. plastid structure and photosynthetic apparatus
      1. pigments
        1. chlorophyll a in reaction centers and antennae
        2. chlorophyll c acts as a free-floating (lacks the phytol tail of chlorophylls a and b) accessory pigments
        3. other accessory pigments include beta-carotene, fucoxanthin (brown forms), and vaucheriaxanthin (in green forms)
      2. storage products are beta-1, 3 glucans (chrysolaminarin), stored in vacuoles outside of the plastid
      3. plastids structure
        1. within periplastidal endoplasmic reticulum, which usually joins with the nuclear envelope
        2. thylakoids usually in stacks of three, with a girdle lamella running just below the chloroplast envelope
  2. Classification – Ochrophyta exhibits at least five major lineages, traditionally divided into at least nine classes (often 9 divisions); again we will follow the system used by Graham
    1. Bacillariophyceae (the diatoms)
      1. large group of fresh and salt water unicellular forms; extreme estimates suggest that there are over 10,000,000 species
      2. basic characteristics
        1. coccoid habit dominates, the only flagellate cells are the male gametes of centric diatoms
          1. flagellate cells, when present, have a single flagellum with mastigonemes, but without the two central microtubules of the axoneme
        2. plastid morphology
          1. basic features are those of the division (chloroplast ER continuous with the nuclear envelope, presence of a girdle lamella, chlorophyll c, golden brown color, etc.)
          2. some difference in whether the cell has numerous discoid plastids or a few parietal plates that may be lobed or not
        3. each cell is enclosed in a two-part siliceous shell (frustule) whose parts overlap--this is the defining characteristic of the group
          1. frustule features
            1. the upper valve of the frustule is called the epitheca, the lower is the hypotheca
              1. the epitheca consists of an epivalve and epicingulum (girdle), the lower of an hypovalve and hypocingulum
              2. the cingulum consists of a number of separate bands, the valvocopula next to the valve, and additional girdle elements
            2. all parts of the valve can be penetrated by pores called areolae, usually with a complex structure
              1. if the hole goes straight through it is called a poroid areola, if constricted at one side it is called loculate
              2. one side or both may be partially occluded by a velum
                1. cribrum - velum with an organized series of pores
                2. rota - solid plate attached by spokes
                3. vola - flap-like growth from the sides
            3. may also be penetrated by pore-fields of varying structure
            4. some valves with rib-like costae
            5. some valves with processes
              1. rimoportulae (labiate processes) – fairly common, usually associated with mucus secretion
              2. fultoportulae (strutted processes) – restricted to a few centric genera
            6. many pennate forms with a raphe system
              1. longitudinal slit, usually with an s-shaped or zigzag cross-section
                1. in some forms the raphe is on a raised structure (keel); this type is usually called a canal raphe
              2. the raphe is involved in movement of the diatom; the mechanism is not clear, but seems to involve the exocytosis of polysaccharide fibrils that bind to the substrate
          2. frustule formation
            1. wall composed of silicic acid deposited on an organic matrix in a silicon deposition vesicle (SDV)
            2. in some forms silica deposition begins with an annular ring with radiating ribs, in others with a solid central rib (sternum); in raphid forms silicon deposition begins in a long tube to one side of what will become the raphe (this side is called the primary side); the tube gradually curves around to form the slit of the raphe on the secondary side
            3. when the frustule formation is complete, the inner membrane of the deposition vesicle becomes the new cell membrane; the old cell membrane and the outer membrane of the vesicle are lost
            4. because new frustules are always made inside of the old frustule, one of the new cells has a slightly smaller diameter than the original cell leading to a gradual reduction in the diameter of the cells; this can be compensated in part by increasing the number of girdle bands, but ultimately leads to smaller cells
            5. silica deposition is inhibited by the presence of germanium acting as a competitive inhibitor of the enzymes; copper also inhibits diatoms and copper sulphate is widely used as an algicide
        4. sexual life cycles
          1. basic life-cycle is diplontic
          2. sexual reproduction is triggered in part by the reduction in the size of frustules: when the cell reaches certain size and it meets another cell in the same state, the two undergo meiosis; gametes are formed and fuse; the resulting zygote swells to form a large auxospore with a differently-structured wall; the auxospore germinates by first one mitotic division, resulting in the formation of the epitheca, and then a second, resulting in the formation of the hypotheca; one of the nuclei from each of these divisions degenerates
      3. other features of diatoms
        1. mucilage secretion
          1. can be through pore fields, processes, or raphes
          2. used for attachment to the substratum (Gomphonema) or to other diatoms (Biddulphia) or for movement
            1. movement usually associated with secretion through raphe systems
            2. motive force may come from microtubule/kinesin or dynein interactions
        2. toxin production - some diatoms (memebers of Pseudonitzschia) secrete domoic acid, a cause of amnesic shellfish poisoning (symptoms include nausea, vomiting, and diarrhea after 3 hours, dizziness, hallucinations, short-term memory loss, decreased reaction to pain, and seizures in extreme cases) where it acts on glutamate receptors in the brain
        3. nutrition
          1. diatoms require relatively high concentrations of silica; where exists in the ocean, diatoms predominate (20% of the ocean area); these areas are characterized by diatomaceous sediments
          2. diatom growth triggered by iron addition in high nitrate, low chlorophyll regions
          3. some (Rhizosolenia) contain endosymbiotic cyanobacteria
          4. some can function as heterotrophs
      4. classification - traditionally based on valve symmetry, which may not hold up as more molecular data is added; we will follow the basic scheme in Tomas's Identifying Marine Diatoms and Dinoflagellates
        1. Biddulphiales (Centrales) -- radially symmetric valves
          1. Coscinodiscineae -- valves usually with a ring of marginal processes and radial symmetry
            1. Thalassiosira, Cyclotella, Skeletonema -- with strutted processes
            2. Melosira
            3. Coscinodiscus
            4. Actinocyclus
            5. Actinoptychus
            6. Asteromphalus
          2. Rhizosoleniineae -- valves unipolar, without a ring of processes
            1. Rhizosolenia
          3. Biddulphiineae -- valves bipolar, without a ring of processes
            1. Biddulphia, Odontella
            2. Chaetoceros, Bacteriastrum
            3. Cerataulina
        2. Bacillariales (Pennales) -- valves with bilateral symmetry
          1. Fragilariineae -- usually with a sternum, without a raphe
            1. Fragilaria, Synedra, Tabellaria
            2. Rhaphoneis
            3. Thalassionema
          2. Bacillariineae -- valves with a sternum and a raphe
            1. Eunotia -- arced valves with a short raphe
            2. Achnanthes, Cocconeis -- one valve without a raphe
            3. Navicula, Pinnularia, Frustulia, Stauroneis
            4. Nitzschia, Bacillaria
            5. Epithemia, Surirella
    2. Chrysophyceae -- the golden-brown algae
      1. basic characteristics
        1. unicellular or colonial organisms, primarily freshwater
        2. plastids with chlorophylls c1 and c2 and fucoxanthins; plastid morphology follows the basic ochrophyte plan
        3. flagellate stages with typical ochrophyte flagellar apparatus:
          1. two flagella, a long one with mastigonemes and a short, trailing one without
            1. mastigonemes on the leading flagellum - help pull cell through water(?)
            2. short flagellum with a basal swelling thought to have a function in light sensing (fluoresces green when illuminated with blue or near UV light)
          2. flagella terminate in a helical transition structure
          3. each basal body has two set of microtubules
            1. one of the sets on the leading flagellum appears to contain an MTOC
            2. one of the sets on the trailing flagellum loops around to form part of a feeding apparatus in mixotrophic forms
          4. basal bodies are connected by fibrous bands; there is a banded rhizoplast extending to the nuclear envelope
        4. many genera form siliceous scales in special silica deposition vesicles
        5. all form statospores or stomatocysts
          1. special resting stages almost completely covered in silica; there is an organic plug allowing the cell to exit at germination; the wall is formed in a silica deposition vesicle
          2. can be formed in conjunction with either asexual or sexual reproduction
          3. fossil cysts date back 80 million years; can be used to estimate paleoclimates
        6. exhibit a range of nutritional modes, from photoautotrophy to mixotrophy to heterotrophy -- possibly related to high requirements for phosphorus, iron, and vitamins
      2. classification and diversity -- traditionally, the taxonomy of this group has been based on habit; this is a notoriously poor method, so we will just look at a few examples spanning the range of diversity
        1. Chromulina and Ochromonas -- wall-less flagellate forms. both with two golden-brown plastids
        2. Dinobryon -- loricate flagellates forming branched colonies
        3. Uroglena and Uroglenopsis -- wall-less flagellates in a colonial slime; Uroglenopsis colonies resemble Volvox
        4. Chrysamoeba -- an amoeboid form
    3. Synurophyceae -- a second group of golden-brown algae that was included in the Chrysopheae until recently
      1. basic characteristics
        1. plastids similar to those of chrysophyceans, but without chlorophyll c2
        2. flagellar apparatus is similar to that of chrysophyceans, except that the flagella, both extend forward, so there is no trailing flagellum, the flagellar root system includes a banded rhizoplast
          1. at mitosis, two new long flagella are produced; the short flagellum is formed from the old long flagellum later
        3. flagellate cells retain the photoreceptor, but lack an eyespot
        4. no member of the group is phagotropic
        5. surface usually covered in overlapping siliceous scales
      2. classification and diversity -- again,  a small group, but with two important freshwater genera
        1. Synura -- motile colonies
        2. Mallamonas -- scaled, unicellular flagellates
    4. Dictyochophyceae -- silicoflagellates, a very small group of flagellates, fairly common in colder waters
      1. basic characteristics
        1. single flagellum, with mastigonemes
        2. ochrophyte plastid with chlorophylls a and c, and fucoxanthin
        3. siliceous external skeleton in the form of a basket
      2. classification and diversity
        1. only a few living species all in the genus Dictyocha
        2. extensive fossil record dating back to the Cretaceous (100 million years)
    5. Raphidophyceae (chloromonads)
      1. basic characteristics
        1. relatively large flagellates with the typical set of ochrophyte flagella, but without parabasalar swellings or eyespots
        2. naked (without scales, walls, or thecae)
        3. numerous trichocysts and, possibly, mucocysts
        4. usually with numerous green to golden-brown plastids; brown forms contain fucoxanthin, green forms do not
      2. classification and diversity -- because this is a small group, we will only note differences between marine and freshwater forms
        1. marine raphidophyceans -- tend to be golden-brown, with pyrenoids in the plastids
          1. Heterosigma -- bloom-forming species, sometimes toxic
          2. Chattonella -- another bloom-forming species
        2. freshwater raphidophytes -- tend to be green, without pyrenoids
          1. Gonyostomum -- large form common in acidic waters rich in organic matter (Lake Louise); has a large triangular cavity in the front of the cell
          2. Merotrichia, Vacuolaria
    6. Tribophyceae (Xanthophyceae) -- the yellow-green algae
      1. small group of mostly freshwater and terrestial algae, similar in overall appearance to chlorophytes
      2. basic characteristics
        1. numerous discoid plastids, possibly containing pyrenoids, chlorophylls a and c, and xanthophylls, but no fucoxanthin or violaxanthin (see table 15-1)
        2. flagellate stages with the typical ochrophyte flagellar apparatus, but neither flagellum bears mastigonemes
      3. classification and diversity -- a small group, with the traditional classification based on habit; we follow Graham's lead and just point out a few important genera
        1. Chloridella -- similar in form to Chlorella
        2. Characiopsis -- similar in form to Characium and Pseudocharaciopsis
        3. Ophiocytium -- fairly common curved cylinders
        4. Stipitococcus -- small loricate forms found as epiophytes on filamentous algae
        5. Tribonema -- robust filamentous form with walls composes of two pieces,similar in appearance to those of Microspora
        6. Vaucheria -- large coenocytic filaments forming coarse mats; zoospores are large and multinucleate; sexual reproduction is oogamous
    7. Eustigmatophyceae -- recently identified group of  yellow-green algae
      1. basic characteristics
        1. small unicellular coccoid algae
        2. flagellate cells have a very short trailing flagellum and a large orange-red eyespot outside of the plastid
        3. plastids more or less normal for the ochrophytes: girdle lamella usually missing, chloroplast ER does not connect with the nuclear envelope, usually pyrenoid on a stalk, violaxanthin usually present as accessory pigment
      2. classification -- a small group (but possibly many more, hard to tell from green and yellow-green algae) with a single order (Eustigmatales)
        1. Eustigmatos
        2. Pseudocharaciopsis
        3. Nannochloropsis
    8. Phaeophyceae -- the brown algae
      1. large group of marine macrophytes with over 250 genera and 1500 species
      2. basic characteristics
        1. plastids and photosynthetic apparatus
          1. one to many plastids per cell
          2. plastid construction and pigment composition follow the typical ochrophyte plan with large amounts of fucoxanthin
          3. reserve products include laminarin, mannitol, sucrose, and glycerol
        2. flagellate stages (only zoospores and gametes) with typical ochrophyte flagella
        3. cell walls
          1. cellulose (1-10% of dry weight)
          2. alginates  -- polymer of mannuronic and guluronic acids
          3. fucoidin and other sulfated sugars
        4. physodes
          1. vesicles filled with fucosan (phaeophycean tannin) a colorless liquid that turns black on exposure to air
          2. fucosans apparently inhibit the growth of unicellular algae keeping the thallus relatively free of epiphytes
        5. life histories -- basically haplodiplontic with heteromorphic generations; diploid dominates
          1. gametophyte reproduction
            1. sexual reproduction can be isogamous or oogamous
            2. gametes are produced by mitosis in special gametangia (plurilocular gametangia or sporangia)
              1. products of gametophyte plurilocs sometimes develop into multicellular gametophytes without benefit of fertilization (parthenogenetically); if this is the common mode of reproduction the algae, the alga is called monophasic
            3. most groups studied has some sort of pheromone produced by the female that influences sperm develop and attracts the sperm to the egg
          2. sporophyte reproduction
            1. also produce plurilocular sporangia; the products in this case are zoospores that develop into another sporophyte generation
            2. other structures (unilocular sporangia) are used to produce haploid spores by meiosis; in this case, walls are not formed between the cells, giving the appearance of a single (unilocular) chamber
        6. modes of growth
          1. primitive version is apparently a diffuse growth occuring throughout the thallus
          2. advanced versions involve the formation of definite meristems; the occurrence and position of these has been used to define the orders
            1. apical meristems with division in one plane resulting in filamentous growth
            2. rows of marginal meristem cells giving rise to a broad blade
            3. trichothallic growth - division of  a cell at the base of a long uniseriate filament (hair); below the meristematic cell, division can be in multiple planes
            4. intercalary meristems, between stipes and blades, adding new tissue to both
            5. mersitoderms that increase the girth
        1. habit
          1. brown algae can be filamentous as individual filaments or packed together into pseudoparenchymatous thalli or composed of true parenchymatous thalli arising through the division of cells in multiple planes of division
          2. evolutionarily advanced forms may display a marked amount of differentiation of tissues and structures
            1. thallus can be divided into holdfast, stipe, and blade, with the stipe and/or the blade capable of forming air bladders (gas vesicles or pneumocysts) filled with atmospheric gases, sometimes enriched with CO
            2. within the stipe and blade can be three well-defined tissues
              1. meristoderm -- photosynthetic, meristematic tissue, usually covered by a layer of mucilage
              2. cortex -- mass of larger cells
              3. medulla -- composed of several different cell types
                1. cells that extend from one side of the thallus to the other; develop from outgrowths of inner cortex cells
                2. hypae -- longitudinally arranged cells with sieve plates at the junctions; transport soluble storage products via active transport(?) from sources to sinks; appear trumpet-shaped as they are stretched by the growth of the thallus
      3. classification and diversity
        1. Phaephyceae is normally divided into 14 orders; however, because these are primarily marine macrophytes, we will only treat a few of the major orders displaying the range of form
        2. Ectocarpales -- forms with a thallus consisting of individual (branched) filaments or filaments bunched together to give a compact thallus; reproduction isogamous (this version of the order lumps together a number of the more primitive orders)
          1. Ectocarpus -- both generations composed of uniseriate branched filaments, with plurilocs on the gametophyte, and plurilocs and unilocs on the sporophyte
          2. Scytosiphon -- gametophyte is a large tube-shaped organism, with true parenchymatous growth, attached to the substrate by a basal disc; sporophytes are inconspicuous crusts
        3. Sphacelariales -- branched multiseriate thalli with true tissues growing from a definite and conspicuous apical cell; isomophic alternation of generations
          1. Sphacelaria
        4. Dictyotales -- complex thalli with true tissues developing from apical cells; isomophic alternation of generations; non-motile meiospores
          1. Dictyota -- dichotomously branched thalli
          2. Padina -- flattened, fan-like thalli
        5. Desmarestiales -- pseudoparenchymatous habit derived from a trichothallic growth pattern; oogamous sexual reproduction
          1. Desmarestia -- well-known from polar regions; apparently one form stores sulfuric acid at pH 1 in vacuoles
        6. Laminariales -- also known as the kelps; large sporophytes differentiated into holdfast, stipe, and blades, with intercalary meristems; thallus morphology is that describe previously as an example of the evolutionary extreme; sporophytes produce only unilocs, sometimes in localized patches (sori), sometimes on specializes blades (sporophylls); gametophytes are microscopic
          1. Laminaria -- common in polar and temperate waters; cultivated for food in Asia (undari)
          2. Postelsia -- intertidal form with the appearance of small flattened palm-trees
          3. Nereocystis -- annual reaching up to 30 m in length
          4. Macrocystis -- responsible for large forests off the coast of California, harvested for chemicals since World War II; female gametophytes are unicellular
          5. Ecklonia -- forms underwater forests in warm temperate waters
          6. Egregia
        7. Fucales -- complex thallus arising from apical growth; diplontic life-cycle with gametes formed in conceptacles (chambers) located in receptacles (branch tips)
          1. Fucus -- common intertidal form with flattened thallus with dichotomous or pinnate fronds; medullary region full of water-holding polysaccharides; photosynthesis continues when exposed
          2. Ascophyllum -- similar to Fucus, but without a midrib; sometimes used as animal feed or as a source of thickeners in cooking
          3. Sargassum -- highly differentiated thallus with air bladders in the axils of the fronds; usually attached, but some forms can continue growth while free-floating, forming large rafts with a distinctive animal fauna
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