Biological Concepts — Lab 9 online
BIOLOGICAL DIVERSITY:
Microbial life; fungi; symbiotic relationships

Instructions:
Study all the visual information in this online lab, plus the accompanying explanations.
Be prepared to answer a few "check-in" questions to show that you were paying attention.


PREFACE:
This lab and the next three together illustrate the vast biological diversity, or BIODIVERSITY, of planet Earth.
This biodiversity, emphasized in Chapter 18, also includes the many types of plants described in Chapter 11
    and the microbial life forms emphasized in today's lab.
PLEASE REVIEW the second half of Chapter 6 for a discussion of the classification by which our knowledge of this biodiversity is organized.




MICROBIAL DIVERSITY
PROCARYOTES
Procaryotes are one-celled organisms whose cells lack a true (membrane-bounded) nucleus and other eucaryotic organelles. Procaryotes include the Archaebacteria, true bacteria, and Cyanobacteria.

Procaryotic cells: Cells without true nuclei, lacking many other structures found in eucaryotic cells.

Procaryotic cell walls: Contain substances like muramic acid, absent in eucaryotes.
  • Gram-negative cell walls: two membranes, separated by a thin layer of peptidoglycan.
  • Gram-positive cell walls: one membrane, surrounded by a very thick peptidoglycan layer.

    Chemical diversity: Procaryotes have greater chemical diversity than eucaryotes. They can subsist on a greater variety of foodstuffs, have a greater range of chemical substances that can be tolerated, and can subsist in a variety of atmospheres, both with and without oxygen.
  • Energy sources:   Phototrophic (sunlight) vs. Chemotrophic (chemical energy)
  • Carbon sources:   Autotrophic (inorganic carbon incl. CO2) vs.
          Heterotrophic (organic molecules, mostly from other organisms)
  • Anaerobic (oxygen-intolerant) vs. Aerobic (oxygen-dependent) vs. Facultative (OK either way)


  • Cell shapes: Commonly "rod"-shaped, but many are spherical ("cocci").
          Less common shapes: bent rods, pear-like, gentle spirals, corkscrews ("spirochete")

    Procarytoic chromosomes: Generally arranged in a single circular loop containing DNA but no histone proteins. Partial recombination may occur during conjugation. Most procaryotes also have small chromosome fragments that can detach from the main chromosome and exist separately for long periods as plasmids, small, circular samples of DNA similar to certain viruses.

    Archaea (Archaebacteria): A group of strict anaerobes (killed by oxygen) that include the methane-producers (methanogens), the extreme halophiles, and the extreme thermophiles. Their RNA sequences have only minimal homology to the RNA of other procaryotic or eucaryotic organisms, and the cell walls are also unique.

    True bacteria: The majority of procaryotes, with RNA sequences homologous to those of Cyanobacteria and eucaryotes (but not Archaebacteria). Most are heterotrophs. A few autotrophs use a variety of energy sources, but none contains chlorophyll a and none can split water in the Hill reaction.

    Cyanobacteria (= Cyanophyta, blue-green bacteria, or blue-green algae): All are similar to bacteria in structure and their RNA sequences are homologous. All are oxygen-tolerant autotrophs that can use sunlight for energy and CO2 as a carbon source. They contain chlorophyll a and can split water in the Hill reaction.


    A possible classification of Bacteria:
    • Proteobacteria (includes the majority of bacteria):
      • "Alpha proteobacteria":   includes Rhizobium and other symbiotic bacteria
      • "Beta proteobacteria":   includes Nitrosomonas and other soil bacteria
      • "Gamma proteobacteria":   a great variety, incl. sulfur bacteria, Escherichia coli,
            and many pathogenic species (e.g., Salmonella, Legionella, Vibrio)
      • "Delta proteobacteria":   slime-secreting bacteria (myxobacteria) and bacteria
            that attack other bacteria (Bdellovibrio, etc.)
      • "Epsilon proteobacteria":   includes mostly pathogens (Campylobacter, Helicobacter, etc.)
    • Chlamidias: obligate energy parasites that can only survive inside animal cells
    • Spirochetes: motile, corkscrew-shaped bacteria
    • Gram-positive bacteria: a great variety of mostly pathogenic species (Bacillus, Clostridium, Streptococcus, Staphylococcus, Streptomyces, Mycoplasma)
    • Cyanobacteria: photoautotrophs possessing chlorophyll a



    Viruses are fragments of nucleic acid (DNA or RNA, never both), often surrounded by protein, that can replicate only with the help of intact cells. (A few viruses also have capsules derived from host cell membranes.)
    • All viruses have a lytic cycle, in which they invade a cell, replicate inside, then rupture the cell and release their progeny.   Some viruses also have a lysogenic cycle, in which they lie dormant and replicate as part of the host DNA.
      • Lytic cycle (in all viruses):
        1. Virus first attaches to host cells and injects nucleic acid only.
        2. Viral DNA or RNA is replicated using the host cell's enzymes.
        3. Host cell ruptures, releasing thousands of new virus particles.
      • Lysogenic cycle (in some viruses only):
        1. Viral DNA inserts into the host cell chromosome.
        2. Virus then hides (lysogenic stage), replicating as part of host DNA.
        3. Upon "activation," the virus takes over the cell's reproductive machinery and resumes the lytic cycle.
    • Viral shapes can be helical, icosahedral (20-sided), or complex (with head and tail).
    • Viruses have very few of the characteristics of life; they cannot reproduce without the gene-replicating machinery of the host cell.
    • Viruses are classified by the the type of nucleic acid (either DNA or RNA).



    • EUCARYOTE DIVERSITY

    The study of RNA sequences offers new insights into the evolution of diversity among the Eucarya. One-celled eucaryotes (formerly called Protista) possess a diversity of locomotor adaptations: pseudopods for amoeboid locomotion, flagella, and cilia. Some are non-motile.
    Photosynthesizing eucaryotes that do not develop from multicellular embryos are called Algae; a diversity of photosynthetic pigments exists among brown algae (Phaeophyta), green algae (Chlorophyta), red algae (Rhodophyta), and several groups of microscopic algae.
    The Eucarya are now classified into about five major groups: Unikonta (including amoebozoans, animals, and fungi), Excavata (Diplomonads, etc.), Rhizaria, Chromalveolata (a large and possibly heterogeneous group including ciliates, brown algae, and many others), and Archaeplastida (a group of photosynthetic organisms including red algae, green algae, and plants).

    Different locomotor adaptations have arisen among the Eucarya:
    • Amoeboid locomotion using protoplasmic extensions called pseudopods. Amoebozoans, one of the largest and most diverse group of one-celled eycaryotes, use broad, lobe-like pseudopods; their body changes shape continually as it moves. Another group, the Rhizaria, use thin, needle-like pseudopods. Most of these organisms are predators, engulfing their prey by phagocytosis.
    • Flagella: Flagellated cells move by beating a long, whip-like flagellum with a "9 + 2" grouping of microtubules, or sometimes more than one flagellum. A few species show both flagellar and amoeboid locomotion.
    • Cilia: Some cells are covered with thousands of hairlike cilia whose rhythmic beating controls both locomotion and feeding. Cilia have the same "9 + 2" internal structure as flagella.
    Chloroplasts and other plastids are thought to have originated by endosymbiotic capture of photosynthetic Cyanobacteria containing chlorophyll a.
    • Brown algae have chloroplasts that also contain chlorophyll c and certain yellowish pigments (carotenes and xanthophylls) not found in any Archaeplastida, leading to the hypothesis that these chloroplasts were captured independently. Dinoflagellates and a few other unicellular algae have similar pigments (and similar flagella) and are thought to be related to brown algae for this reason.
    • Red algae have chloroplasts that also contain chlorophyll d; they also have certain phycobilin and phycoerythrin pigments not found in any other eucaryotes (but found in Cyanobacteria).
    • Green algae and plants have chloroplasts that also contain chlorophyll b, xanthophylls, and α- and β-carotenes. Cell walls contain cellulose and pectin. Starch is the main storage product.
    • A few eucaryotes have plastids that no longer contain chlorophyll. Some "chromoplasts" contain other pigments; some "leucoplasts" contain stored food (starch).

    CLASSIFICATION OF THE EUCARYA
    Starting in 2004, whole genome sequences became available for many eucaryotes. As a result, the classification of Eucarya changed dramatically, and is now based on similarities in RNA sequences. The following major groups (subdomains) of Eucarya are now recognized:
    • UNIKONTA:
      Most organisms in this group are motile, either by amoeboid locomotion or by a single posterior (rear-facing) flagellum (or both). This large group includes the Amoebozoa, the slime molds, the Fungi (Mycota), the choanoflagellates, and the Animal Kingdom.
    • EXCAVATA:
      This small group includes the Diplomonads such as the parasite Giardia. Two smaller groups, the Parabasalids, and the photosynthetic Euglenoids, may also belong here. Many experts consider this group close to the ancestry of all Eucarya (possibly excluding Unikonta).
    • RHIZARIA:
      These one-celled predators all secrete a hard shell enclosing a cell body from which radiate numerous thin, needle-like pseudopods that are used to trap and engulf their prey.
      • Radiolaria:  shell is usually a beautiful sphere made of silica (SiO2).
      • Foraminifera:  shell is coiled, perforated with many tiny holes, and usually made of calcium carbonate (CaCO3).
    • CHROMALVEOLATA:
      This large group is often subdivided into two subgroups:
      • ALVEOLATA,   with bubble-like spaces (alveoli) just beneath the plasma membrane.
        Included here are:
        • Ciliata, whose entire cell surface is clothed in cilia. Paramecium is a familiar example. All ciliates have two nuclei (macronucleus, micronucleus) and a unique type of sexual conjugation in which two cells exchange micronuclei.
        • Apicomplexa, a group of parasites that use a sharp apical complex to penetrate host cells. Reproduction by spores. The malaria parasite Plasmodium belongs to this group.
      • STRAMENOPILES,  characterized by two unequal flagella (one simple, one with feathery branches) and by chloroplasts containing chlorophylls a and c and several unique xanthins and other pigments not found in the Archaeplastida. This group is hypothesized to have originated by a symbiotic capture of plastids, independently of the Archaeplastida.
        Included are:
        • Brown algae (Phaeophyta), often large, structurally complex; ecologically dominant in temperate and colder marine waters.
        • Dinoflagellates, unicellular, marine and planktonic, with two flagella at right angles to one another.   Mitosis unusual: no histones, no centrioles, no spindle fibers; nucleolus and nuclear envelope remain visible throughout mitosis.
        • Diatoms, especially abundant in plankton; the major primary producers in most marine (and several freshwater) ecosystems.
    • ARCHAEPLASTIDA:
      These organisms are all photosynthetic and all have plastids containing chlorophyll a and either chlorophyll b or chlorophyll d, but never chlorophyll c. Included here are the following:
      • Red algae (Rhodophyta), containing chlorophylls a and d, plus other pigments resembling those of Cyanobacteria. No "9 + 2" organelles (centrioles or flagella); no motile cells, not even gametes. Unique storage products include "floridean starch" in cell walls. Ecologically dominant in tropical marine waters.
      • Green algae (Chlorophyta), containing chlorophylls a and b, xanthophylls, and α- and β-carotenes. Cellulose, pectins, and starch are also present. Ecologically dominant in freshwater ecosystems, but many are also marine.
      • Plants (Kingdom Plantae), sharing cellulose, starch, and all the pigments found in green algae, but differing from algae in developing from multicellular embryos.



    ONE-CELLED PROTISTS

    Animal-like (non-photosynthetic)




    Trypanosoma life cycle


    Amoeboid locomotion (movie clip)

    Slime mold (J.T. Bonner film)




    Plant-like (photosynthetic)


    Possible family trees of Eucarya




      CHARACTERISTICS OF GROUPS in the preceding family trees:
    • Excavata: Energy-dependent parasites with degenerate or vestigial mitochondria; feeding groove "excavated" from one side.
    • Chromalveolata: A possibly heterogeneous group, possessing cellulose cell walls, and thought by some experts to have originated by a "secondary endosymbiosis" in which a red algal cell became a secondary chloroplast. (Many experts have questioned the validity of this group.)
    • Rhizaria: Mostly planktonic predators using needle-like pseudopods to capture prey; usually with hardened shells.
    • Archaeplastida: Photosynthetic organisms with plastids (but excluding those with chlorophyll c).
    • Unikonta: Organisms with a single flagellum (or none) and/or lobe-like pseudopods.
      • Amoebozoans: move principally by lobe-like pseudopods.
      • Opisthokonts: move principally by a posterior flagellum (lost in many advanced species)







    PHOTOSYNTHETIC PROTISTS ("ALGAE")

























    FUNGI (Kingdom MYCOTA)
    FUNGI (MYCOTA)

    The Mycota or Fungi are non-photosynthetic eucaryotes adapted to absorptive nutrition. Slime molds have motile, unicellular, vegetative stages, while true fungi form branched filaments (hyphae) that invade dead or decaying material. All fungi form spores; the various groups of fungi are distinguished by their means of spore formation.

     General characteristics of fungi: Plastids and chlorophyll are absent. Cell walls are made of chitin, not cellulose. Cell membranes sometimes break down to form binucleated cells or multinucleated aggregates. Reproductive structures vary, but spores are always produced. Nutrition is usually absorptive; many fungi live on dead or decaying matter (saprophytic), but some are parasitic instead. Fungi are important as decay organisms in freshwater and terrestrial ecosystems. Most prefer moist conditions for optimal growth.

    Slime molds: Organisms whose unicellular vegetative stages are either amoeboid or flagellated and resemble Amoebozoans. All types have a multinucleated or multicellular creeping stage that forms spore-producing bodies. Each spore develops into a new vegetative cell.
    Formerly considered to be fungi, but now usually put in their own group.

    True fungi (Eumycota): Fungi whose vegetative structure typically consists of a series of branching filaments (hyphae) forming a tuft (mycelium).
    • Chytrids: Primitive, aquatic fungi that reproduce by flagellated cells (zoospores).
      Includes Phytophthora, responsible for the 1841 devastation of the Irish potato crop.

    • Glomerulomycota: Fungi that are often attracted to plant roots, where they form symbiotic associations (mycorrhizae) that benefit both species.

    • Zygomycota (black bread molds, etc.): Reproduce by conjugation of hyphae that come together and form nonmotile spores.

    • Ascomycetes (Ascomycota) (yeasts, cup fungi, truffles, etc.): spores are produced, 4 or 8 at a time, in sacs (asci).
      Included genera of commercial or medical importance:
      • Saccharomyces, a yeast used commercially in the production of both bread and beer.
      • Penicillium, responsible for penicillin, also for roquefort and camembert cheeses.
      • Candida, responsible for vaginal yeast infections, also for mouth infections ("thrush").
      • Several genera of "dermatophyte" fungi, responsible for ringworm and athlete's foot.

    • Basidiomycetes (Basidiomycota) (mushrooms, puffballs, rusts, smuts, etc.): spores are produced, usually 4 at a time, at the tips of club-like organs (basidia).
    Lichens: Very intimate symbiotic associations of fungi with either algae or cyanobacteria. The fungus absorbs and retains sufficient moisture for both partners; the green partner photosynthesizes and provides food. Lichens are often the first colonizers of bare rock surfaces.

    FUNGUS (etc.) VIDEOS:
  • Slime mold (J.T. Bonner film) (no longer considered fungi)
  • Mycelium trapping nematode
  • Pilobolus spore discharge
  • Pilobolus spores (time lapse)


    • FUNGI (MYCOTA)







    ZYGOMYCETES


    ASCOMYCETES




    BASIDIOMYCETES






    SYMBIOTIC RELATIONSHIPS
    Symbiosis consists of two (or more) species living together. Symbiosis greatly increases biodiversity because, as ecologists often say, every new species creates many new niches and many new habitats for other species to live either inside it or upon it:
    "The big bug has a little bug,  upon his back to bite him;
    The little bug has a little'er bug, and so on, ad infinitum!"

    Most cases of symbiosis begin as parasitism, a symbiosis where the parasitic species does harm to the host species, usually by feeding off its tissues. In such situations, natural selection among hosts favors those that can detect and defend against parasites, while natural selection among parasites favors those that can evade host defenses by causing as little pain and harm as possible. One big problem for parasites is that their habitat is the mortal body of their host; if they cause too much harm, they kill their host, and lose their habitat. Parasites therefore evolve smaller sizes and other adaptations that minimize the harm they do to the health and well-being of their hosts.

    Over the course of evolution, some parasites evolve to return some benefit to their hosts and keep the host alive and well. When the benefit and harm are balanced and equal, the relationship is called commensalism. Some parasitic or commensal species go even further and return more benefit to their hosts than the harm that they do, a situation called mutualism. (This is measured by determining that an increase in the formerly parasitic species results in an increase, not a decrease, in the host species population.) Mutualism benefits both species, so that natural selection favors adaptations in each that benefit the other species and make the relationship stronger.

    Among fungi (above), the Glomerulomycota exist almost exclusively as symbiotic colonies called mycorrhizae, living in associations with plant roots. The fungi benefit the plants by retaining moisture during dry periods, and the plant provides habitat for the fungus, including small compartments that maintain the conditions needed for fungal growth.

    Other fungi grow in symbiotic associations with algae (or sometimes Cyanobacteria) known as lichens. In a lichen, the photosynthetic partner uses sunlight to make sufficient food for both itself and the fungus. The fungus, in turn, retains moisture during dry periods and allows the moisture-dependent photosynthetic partner to grow on tree trunks or bare rock surfaces.


    Ants of the genus Pseudomyrmyx live inside the hollow "swollen thorns" of the
    bull-horn acacia tree (Vachellia cornigera). They actively defend the tree against
    herbivores such as goats.   In return, the tree houses them inside the hollow
    thorns and feeds them with sugary nectar from nectaries and protein-rich
    secretions on the ends of leaflets.


       
    These plants of the genus Yucca are pollinated by certain moths of the genus Megathymus.
    Both species are dependent on this mutualism: the moth can only complete its life cycle
    by laying its eggs inside the yucca that its caterpillars feed upon, and the yucca plants
    cannot reproduce without the pollinating activity of the adult moths.



    Several species get their teeth cleaned by smaller symbiotic species. The smaller "cleaning" species gets a free meal.



    On occasion, an aggressive species take advantage of symbiosis by mimicking a "cleaning" species.
    In this example, the saber-tooth blenny is able to get close enough to attack its prey
    because it mimics a cleaning species, the cleaning wrasse.








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    ——     Rev. Oct. 2020     ——