Chapter 6 - Bacteria, Protists, Plants, and Fungi

Notes for Chapter 6:
Bacteria, Protists, Plants, and Fungi

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Case History: Emperor of Japan His Majesty, Hirohito
- Marine Biologist

Featured Organisms and Locality (p. 127):
Spider crabs and sea slugs of Sagami Bay, Japan

I. Classification
   a) The Five Kingdoms System of Whittaker
        (Note: While still wildly popular with textbook
        authors, and advocated by some biologists such
        as Lynn Margulis, this is really a breakdown of
        life by functional and nutritional categories.
        An alternative view, proposed by Carl Woese,
        is gaining in popularity because it more accurately
        reflects the actual historical relationships of life forms:
        This view is called the Three Domains of Life System -
        Bacteria, Archaea, Eukarya)
        terms: kingdoms, Plantae = vascular plants, Fungi,
            Animalia = Metazoa or multicellular animals,
     Protista = arbitrary grouping of organisms whose
            cells have a nucleus (i.e., eukaryotes) but excluding
            multicellular plants, fungi, and animals,
            not to be confused with prokaryotes (or Monera)
            = arbitrary grouping of all organisms except those
            whose cells have a nucleus (eukaryotes)
            Note: Most current taxonomists try to only formally name
            groupings that are clearly monophyletic. In contrast, many
            traditional names, including "prokaryotes," "protists,"
            "invertebrates," and "agnathans" are paraphyletic groupings
            defined by features they lack, such as a cell nucleus, multicellularity,
            a backbone, or a jaw, respectively. Another way to try to carve
            up biotic diversity into monophyletic groups is to increase the
            number of kingdoms, for example with the 10 Kingdom approach.

RQ 6.1: Contrast how life is classified in the Five Kingdoms System
        vs. the Three Domains System. Which kingdom is broken up
        into separate domains and which kingdoms are combined into
        a single domain?

    b) The Names of Organisms
        terms: phylum, class, order, family, genus, species
            (these are "ranks" used in a "ranked" hierarchical
           taxonomy - it is also possible to classify all of life
            without them in an "unranked" hierarchical taxonomy)
            taxon (plural is taxa), taxonomist, systematist,
            taxonomy (= classifying life), systematics (taxonomy
            + evolutionary history of life, includes taxonomy),
            scientific binomial name, e.g., Glyptocephalus zachirus
            abbreviated G. zachirus. Note genus is capitalized,
            species is not, scientific name is always in italics or
            underlined, common name is not: West Coast flatfish;
            but note this common name refers to multiple species
            of other "flatfish" species, and even if one refers to
            a more specific common name, such as "Rex sole,"
            this has problems because it is known by different
            common names elsewhere. See Fig. 6.4 for more
            examples of a common name varing with location.
            The definition of a species is also problematic. The
            most popular (but not necessarily the best) is the
      biological species concept, proposed by Ernst Mayr.
            This species concept generally works best for
            living populations whose members engage in sexual
            interbreeding, and less well for fossils or "species"
            that reproduce without sexual cross-fertilization.

Featured Organism (p. 131):
Rex sole (Glyptocephalus zachirus)

RQ 6.2: Why is a scientific binomial name sometimes more
precise than a common name?

II. Bacteria (includes Cyanobacteria)
        terms (Box 6.1, p. 134): meter (m), millimeter (mm),
            micrometer (µm), nanometer (nm) (1 m = 1000 mm,
            1 mm = 1000 µm, 1 µm = 1000 nm)
        terms (p. 135): anaerobic or aerobic photosynthesis

RQ 6.3: How big are typical "microbial" organisms?

    a) Cyanobacteria - Ancient Transformers of the Earth
        terms: formerly known as "blue-green algae" but
        cyanobacteria are bacteria that engage in aerobic
        photosynthesis, stromatolites are the fossilized
        slime secreted by ancient cyanobacteria, as still
        being produced in some salty bays such as
     Sharks Bay, Australia

RQ 6.4: Based on abundant ancient stromatolite fossils, it
        is apparent that cyanobacteria had an extremely important
        role in transforming the Earth as a habitat for life billions
        of years ago. What did they do that was so important?

    b) (Other) Bacteria - Essential to Closure of Ecological Cycles
        Note: Bacteria reproduce very rapidly so can quickly exhaust
        available O₂ dissolved in seawater (see Chapter 3 notes).
        terms: refractory materials (are indigestable to all but
        bacteria, who make them available to other organisms)

    c) Archaea (no section in the book but there should be; we
        are just beginning to characterize the diverse organisms
        included in this domain of life - including some that live
        at near boiling temperatures in deep-sea-hot vents)

RQ 6.5: Give three examples of where one could find a
member of the most recently recognized domain of life,
Archaea?

III. Protists (i.e., members of Eukarya that are not plants,
fungi, or animals)

    a) Photosynthetic Protists
        terms: plankton, phytoplankton (especially - diatoms and
     dinoflagellates)

        1) Diatoms are single cells enclosed in silica (glass) shells
        terms: tests, epitheca (top) and hypotheca (bottom),
        cytoplasm (cellular fluid), parent and daughter cells,
     auxospore

RQ 6.6: What problem do auxospores help solve for diatoms?

        2) Dinoflagellates are distinguished by cellulose, flagella,
        and diversity
        terms: armored (with cellulose plates) vs. unarmored, flagella,
     bioluminescence, red tides, toxic red tides, paralytic shellfish poisoning,
     ciguatera (important concern in Caribbean and elsewhere in tropics),
     zooxanthellae (symbiotic cells in corals and anemones), coral reef
     bleaching

RQ 6.7: How do zooxanthellae and their anemone, coral (or other animal)
hosts mutually benefit from their association?

        3) Microflagellates are tiny, diverse, abundant, and dominant?
        terms: microflagellates (includes coccolithophores with coccolith
        plates, also green flagellates such as Chlamydomonas)

    RQ 6.8: If microflagellates are sometimes even more abundant than
        diatoms and dinoflagellates, why was this not generally appreciated
        until recently?

b) Nonphotosynthetic Protists
terms: forams, ciliates, cilia, radiolarians

IV. Plants in the Sea

a) Seaweeds, Kelp, and Other Algae
terms: gametophyte, sporophyte, gametes, meiosis, spores, zygote

        1) Brown algae are the largest and most structurally complex seaweeds
        terms: kelp, giant kelps, Macrocystis, kelp forest, rockweeds, Sargassum,
     fucoxanthin pigment, alginate/agar (used in ice cream, etc.)

RQ 6.9: Why are brown algae brown? What are some ways they are
important?

2) Green algae resemble land plants in several ways
terms: chlorophyll a, starch, chlorophytes (green algae + land plants)

RQ 6.10: What main evidence suggests land (vascular) plants share a
common ancestor with green algae, relative to other algae?

        3) Red algae are strangely dissimilar to other photosynthesizers
        terms: rhodophytes, phycobilin pigments, leafy or filamentous red
        algae or coralline algae: coralline - tufts or crusts

b) Land Plants in the Sea
terms: vascular tissue, roots

    RQ 6.11: What is at least one advantage that land plants have, relative
        to algae, for life in the sea? Why, then, are land plants not more
        common in the sea?

        1) Grasses and grasslike plants are prominent in salt marshes
            and submerged meadows
        terms: salt marsh plants (Spartina), eelgrass, rhizomes, sea grasses

2) Mangroves form low forests around quiet, warm shores

V. Marine Fungi
terms: lichens (symbiosis between fungus and alga and
common in intertidal splash zones on rocks)

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