Some of the Clermont Biology students at the picnic Box Turtle decided to go for a hike and explore the farm. They tried to make a list of all the plants and animals they saw, but soon realized there were so many, they couldn’t possibly list them all. Thus, they decided to include just the most “interesting” or “unusual” plants and animals on their list, and to try to find representatives of as many taxonomic categories as possible. They were able to find members of all the kingdoms except Kingdom Monera (the bacteria), but they knew that was just because bacteria are too small to see without a microscope. In the creek, they found algae in Kingdom Protista, and in the woods, they saw mushrooms in Kingdom Fungi. In Kingdom Plantae, they saw everything from moss and ferns to pine trees, grass, and maple trees. In Kingdom Animalia, they found earthworms, snails, spiders, fish, a toad and a box turtle, many kinds of birds and mammals, and lots and lots of ants.

Taxonomy of Various Groups of Organisms

The Taxonomic Hierarchy

Biologists group/classify all living organisms into five (for our purposes, anyway) big groups called “kingdoms,” and into various levels of sub-categories within those kingdoms. This ranking system is not a totally static thing, for especially at the lower levels, organisms may be re-classified within a different group as new information becomes available. The levels in this hierarchy are:

The taxonomic hierarchy was developed by Carolus Linnaeus, who also came up with the idea of using the genus and species names as an organism’s scientific name. While an organism’s common name might vary from language to language, or even among different regions of a country, the scientific name is one, standard, Latin name used around the world for that organism. For example, Homo sapiens is the scientific name for humans. “Homo” is the genus and “sapiens” is the species. Genus names always begin with a capital letter (like Homo) whereas species names are always lower case (like sapiens). After being stated in full at least once in a publication, it is then acceptable to abbreviate the genus name by using just the first letter. Thus, for example, someone might be writing about the bacterium Escherichia coli and in a subsequent sentence or paragraph, refer to that as E. coli. Since these names are Latin, therefore a foreign language when used in a publication that is otherwise in English, Spanish, German, Chinese, Arabic, or whatever, they properly should be italicized, as they have been here (though that is a bit harder to see with Arial font). Newspaper and magazine journalists are notorious for getting it all wrong! I’ve seen everything from not using italics to putting a hyphen in the middle of E. coli, to not using proper capitalization, etc., etc. If you are hand-writing a scientific name, the proper thing to do is to underline it to show the italics, so for example, Homo sapiens.


Kingdom Monera

Pneumonia
Pneumonia
bacteria
This kingdom includes various kinds organisms which are commonly called bacteria (note: “bacterium” is singular, “bacteria” is plural – make sure to use the proper, matching verbs, etc.). Some kinds have chlorophyll and can do photosynthesis, and those are called blue-green algae. They all are microscopic, one-celled organisms. Their cell structures are fairly simple, without many of the interior membranes that cells in the other kingdoms possess. One of the most significant differences is that members of Kingdom Monera do not possess a true nucleus in their cells. They are called prokaryotic cells or prokaryotes because while they do have DNA, typically grouped into one, circular chromosome, that genetic material is not enclosed within a nuclear envelope liked cells of organisms within the other kingdoms. (Those cells with a true nucleus surrounded by a nuclear envelope are called eukaryotic cells or eukaryotes.) Many biologists now split the Monera into several kingdoms based on slightly different cell structures, but for our purposes, we will simplify things by continuing to regard them as one kingdom.
Some kinds of bacteria are beneficial to humans. For example Lactobacillus acidophilus turns milk into yogurt. Some are harmful, such as Staphylococcus aureus, which causes staph (note the spelling!) infections. (As a reminder, hopefully you remember reading about the problem with overuse of antibiotics “causing” antibiotic-resistant bacteria, as discussed on the immune system Web page.) Overall, there are far more beneficial or neutral bacteria in the world around us than the harmful ones about which we hear so much in the news.


Kingdom Protista

Plasmodium vivax
A photo, taken by Dr. Fankhauser, of a prepared slide
of blood cells infected with Plasmodium vivax
This kingdom includes some one-celled organisms such as Amoeba, Paramecium, and Euglena, which you may have studied in junior- or senior-high school biology. It also includes a number of colonial and multicellular organisms such as various types of algae and seaweed. A number of types of seaweed, such as nori and kelp, are used by humans as food, and because they come from the ocean, they are high in a number of minerals, notably iodine. Perhaps one of the “strangest” uses for a protist is the gynecological use of Laminaria sp. This seaweed is harvested from the ocean, rolled up (like cinnamon sticks?), and dried. When a gynecologist needs to dilate a woman’s cervix to access her uterus, rather than quickly forcing the cervix open with medical instruments, a much gentler, more comfortable method is to place a piece of rolled-up Laminaria into the woman’s cervical opening a day or so before the scheduled procedure. As the Laminaria gradually absorbs some of the woman’s body fluids, it slowly expands, thereby gently enlarging the opening of the cervix.
There are also a few protists that are parasites which invade humans’ bodies and cause disease. One which has been in the news lately is Plasmodium vivax, the parasite which causes malaria. P. vivax has a complex life cycle, spending part of its life in the gut of a mosquito. Then, when the mosquito bites a person to suck his/her blood, some of the P. vivax parasites are transferred into the person’s bloodstream. From there, the parasites invade red blood cells (RBCs) and reproduce, killing those RBCs which they have invaded, thus potentially causing anemia. The newly-produced parasites go find other RBCs to invade, and the cycle continues. Malaria is a major problem in some tropical areas of the world, including large portions of Africa. Many babies and young children, as well as pregnant women, die from malaria, and it is not uncommon for young children to come down with and need to be treated for malaria perhaps even several times within one year — if medical care is available where they live. Recently, in an effort to reduce the incidence of malaria, a number of organizations are working together to provide bed nets to people in areas where malaria is common. Because it is not unusual for several family members to share a mattress/bed at night, by blocking mosquitoes from reaching those people, one bed net can, thus, save several lives.


Kingdom Fungi

Amanita muscari
A photo, taken by Dr. Fankhauser, of Amanita muscari
This kingdom includes things like various kinds of mold, many species of mushrooms, and yeast. Some of these, such as mushrooms, are “good” because they are decomposers and break dead trees, etc. back down into soil so more, new trees can grow. Many mushrooms are edible, and are considered to be a delicacy. Other mushrooms secrete chemicals which make them deadly toxic, while still other mushrooms secrete chemicals which have mind-altering effects. Amanita muscari (Fly Agaric) is a mushroom which is probably familiar-looking to anyone who likes to read fairy tales (or who is familiar with Smurfs) — it has a bright red (or orangish) cap specked with white flecks. Any “official” government-type Web site will state that they are deadly toxic, while counterculture Web sites mention that they are hallucinogenic Some fungi, such as bakers’/brewers’ yeast (Saccharomyces cerevisia), used in making bread, beer, and wine, as well as Penicillium roqueforti, used to make Roquefort and blue cheese, are of significant economic importance to humans. Some, such as Penicillium notatum, are used as a source of life-saving drugs (P. notatum is the source of penicillin.). Other fungi, such as Candida albicans, are considered to be “bad” because they are parasitic, causing things like athelete’s foot, vaginal “yeast” infections, thrush, and other similar skin and mucus membrane problems.
Fungi are referred to as being organisms which absorb their food. They typically secrete digestive enzymes into their environment, then absorb the resulting nutrients.


Kingdom Plantae

Many of the members of this kingdom are of great economic significance to humans and have served as extremely important food sources for just about all of human history. Plants also serve as sources of paper, wood for building, fiber for cloth, and various drugs (both legal and illegal). A major characteristic of plants is that they possess chlorophyll and do photosynthesis, thereby capturing the energy of sunlight and turning it into a form usable as food, directly or indirectly, by humans and most other animals on earth. Some of the major subgroups include:

Division Bryophyta (Mosses)
Moss
Moss
These have no true roots, no true leaves. They must live close to the ground and directly absorb water. Reproduction is via swimming sperm fertilizing an egg, and by spores.
Division Pterophyta (Ferns)
Fern
Fern
These do have true roots and true leaves. Reproduction is via swimming sperm fertilizing an egg, and by spores which typically form on the undersides of specialized leaves. Fern leaves are called “fronds.”
Gymnospermae (such as pine)
Pine
Pine
This is the “lowest” group of plants in which seeds are present. Sperm are transferred within the body of a wind-blown male gametophyte (pollen). Eggs are produced within female gametophytes that stay within a “female” cone (pine cone). A fertilized egg and its surrounding structures turn into a seed, and two seeds are found on the upper surface of each scales in the cone. Pine trees are in Division Coniferophyta, but other gymnosperms include things like cycads and ginkgo trees.
Division Angiospermae
This group is the “flowering plants.“ Pollen is transferred via wind, various insects, or other animals to the “female” structure where it, then, releases sperm cells. The resulting seeds are embedded within an ovary, and the ovary, typically, when fully mature, is modified in some way for dispersal of the seeds. A fruit is a ripened, mature ovary. There are two main subdivisions within the Angiosperms. These are

Kingdom Animalia

Animals are said to be organisms which ingest (eat) their food. Often, when people think of “animals,” they tend to refer only to mammals (milk-producing animals with hair) or to vertebrates (animals with backbones), but there are far, far more invertebrates, especially insects, than there are vertebrates. A few of the major subgroups include:

Cnidaria (or Coelenterata)
Hydra
Hydra
While most of these are marine organisms (jellyfish, sea anemones, and coral), hydra are fresh-water members of this phylum that live in streams here in the Cincinnati area. However, since they are only a few millimeters long, they don’t get noticed very often. Cnidarians have one body opening that serves both to ingest food and expel waste. That is surrounded by a ring of tentacles which, in turn, bear specialized stinging cells to capture and paralyze their prey.
Platyhelminthes (flatworms)
Probably the most “notorious” members of this phylum are the tapeworms, which are parasites. Free-living members of this phylum include planarians. While planarians have many of the “usual” body parts that might be expected, because tapeworms (which live in the intestines of their host) are totally surrounded by pre-digested food, many of their body systems are greatly reduced because they’re not needed. Thus the main organ in each segment is an ovary full of developing eggs. Segments are broken off the posterior end of the tapeworm and shed along with the feces, and if another animal would happen to eat that segment, at least some of those eggs would develop into new tapeworms.
Nematoda (roundworms)
The roundworms are the “lowest” group of animals with a “tube-within-a-tube” body plan. They have both a mouth and an anus, and food goes in one end and out the other. All of their muscles go from front to back (none go around the worm), so they move by thrashing around. Some roundworms are free-living, mostly in soil, and some of those are beneficial or neutral, while others are considered harmful. Other roundworms are parasites, including things like hookworms and pinworms.
Mollusca
Snail
Snail
Mollusks are soft-bodied, and some have shells to protect themselves. Snails and slugs have eyes on long stalks. Snails have one, coiled shell, while slugs have none. Clams and their relatives have two shells that are hinged at the back, and have numerous eyes all along the front edge of their body. Octopus and squid are free-swimming in the ocean.
Snail Eye
Snail Eye
Squid have an internal shell (sold at pet stores as “cuttlebone”) for support. Squid and octopus have tentacles with suckers on them. Octopus are famous for their well-developed brain, excellent vision, and intelligence.
One of the most interesting species of slug I’ve seen is one called a Banana Slug that comes from the redwood forests of California. The name Banana Slug is very appropriate. They are about the size of a small banana (up to around 4 in. or so long and approximately ¾ in. diameter), and are bright yellow, just like a banana.
Snails (escargot) and squid (calamari) are among the mollusks eaten by humans.
Annelida
The earthworms and leeches are included in this phylum. Members of this phylum have bodies that are clearly divided into numerous segments. While earthworms are free-living and help to aerate the soil with their digging, leeches are infamous blood-suckers. As leeches suck blood, they also secrete a powerful anticoagulant to keep the blood flowing, and that is being studied as a potential drug for treating people who need “blood thinners.”
Back in the 1700s, people thought that many diseases were caused by too much blood, and leeches were used to “bleed” people in an effort to cure their diseases. A medicinal leech can easily hold a tablespoon or two of blood, and the tiny hole that it makes will continue to bleed for hours after the leech is full and has dropped off. Interestingly, medicinal leeches are still used, occasionally, in modern medicine. I read an account of a man who had severed his thumb, which had to be surgically re-attached. Because of that, the circulation to/in that thumb wasn’t very good so a) it was swollen, and b) it wasn’t getting as many nutrients, etc., as it needed to heal. His doctors created artificial circulation in the re-attached thumb by letting a leech suck on the tip of it. That both drew out the accumulated lymph and reduced the swelling as well as created space so new blood/lymph could enter, bringing needed nutrients.
Biologists are finding out that earthworms aren’t always as good for the soil in some areas as was thought. In the forests of northern Minnesota, there were, originally, not very many earthworms, and thus the leaf litter made a “blanket” over the soil that helped to retain moisture and warmth in winter, thereby helping new seeds to germinate. However, so many fishermen in the boundary water area have dumped left-over earthworms onto/into the soil, and those earthworms have successfully reproduced, that the net effect has been a significant change in the soil in those forests. Now, the earthworms break down and eat all the leaf litter with the consequence that new seeds are not able to germinate like they used to. Less cover for the soil also means a warmer soil temperature and increased erosion.
Arthropoda
This is the most numerous group of all the plants and animals. There are more species (and more individuals) of arthropods — specifically, of insects — than all the rest of the plants and animals put together. In terms of species, there are more kinds of beetles than anything else, and in terms of numbers of individuals, there are more ants than anything else. The word “arthropod” literally means “jointed foot,” and arthropods have a hard exoskeleton (no bones inside) and jointed appendages and other body parts, which allows for movement. Some of the main classes within this order include: Many arthropods are part of the diets of various cultures and ethnic groups around the world.
Echinodermata
This phylum includes starfish, sand dollars, and their relatives. Their hardened “skeleton” (not bones like ours) is covered with a layer of skin, and so is considered an internal skeleton. They have hundreds of suction-cup-like tube feet which allow them to grab on to things for movement, or in the case of the starfish, to open the clams and oysters upon which they feed. Because these tube feet operate via hydraulic pressure (by moving water around within the body), they don’t get tired like muscles do. That’s why when a starfish is trying to open an oyster to eat it and the oyster is using its muscles to stay shut, the starfish will always “win” when the oyster’s muscles get tired. Starfish are really good at regenerating a whole new body from one chopped-off arm – oyster fishermen used to “destroy” any starfish they found by chopping them up and throwing the remains back into the water, until they realized they now had even more starfish competing with them for the oysters.
Chordata (Subphylum Vertebrata)
This phylum includes all the animals with backbones. All these animals have bones, including a skull and vertebrae. This comparatively-small group of animals is what many people think of as “animals.” Several of the main classes include:

Background Information

Links to Related Information on Our Web Server

The following Web pages contain information related to the taxonomy of various groups of organisms.

Bio Lecture Human Genetics
Pay special attention to the section on sickle cell anemia and malaria
Bio Lecture Natural Selection
Pay special attention to the section on the five kingdoms and the taxonomic hierarchy near the bottom of the page
Bio Lecture Bacteria
General information on Kingdom Monera
Bio Lecture Protista
Information on Kingdom Protista
Bio Lecture Fungi
Information on Kingdom Fungi
Bio lecture Mosses, Ferns, and Other Lower Plants
General Information on Kingdom Plantae and more-detailed information on the “lower” plants
Bio Lecture Gymnosperms
Information on the Gymnosperms, especially pine
Bio Lecture Angiosperms
Information on the Angiosperms
Bio Lecture Coevolution and Pollination
Information on special relationships which have developed between certain pairs of species which are totally dependent on each other
Bio Lecture Invertebrates
Information on the non-vertebrate animals, except the arthropods
Bio Lecture Arthropods
Information on Phylum Arthropoda
Bio Lecture Chordates
Information on Phylum Chordata, especially Subphylum Vertebrata
Checklist of Species Seen on the Clermont Campus
A list of all the organisms we’ve recorded as occuring on the Clermont campus
Practice Wildflower Quiz
A game to practice identification of commonly-seen local wildflowers
Bio Lab Bird-Feeding Activity
An activity to feed and observe local birds
Bio Lab Sprout-Growing Activity
An activity to grow and study one’s own monocot and dicot sprouts
Bio lab Eyelash Mite Activity
An activity to examine eyelash mites from a person’s face
Bio Lab Local Animals Activity
A dichotomous key to major groups of local animals
Bio Lab Worm Bin Activity
Instructions for setting up a worm bin in a 2-liter bottle
Photos
Photos of a variety of organisms
Dr. Fankhauser’s Mushroom Photos
A directory full of mushroom photos
Dr. Fankhauser’s Wildflower Photos
A directory full of wildflower photos
Dr. Fankhauser’s Animal Photos
A directory full of animal photos

Your Assignment
A Scavenger Hunt

There will be one, combined assignment for the topics of Taxonomy, Evolution, Ecology, and Human Intervention. Thus, even though this will appear on each of those pages to remind you, you only need to do it once. You will need to go somewhere where there are lots of living organisms. Assuming you’re here in the Cincinnati area, you might go (with your family?) to the Cincinnati Zoo, Krohn Conservatory, the Newport Aquarium, one of the local parks, or someplace similar to that. If you’re not in the Cincinnati area, there are probably similar places to visit near wherever you are. However, if finances are tight and/or you’re short on time, your back yard would work, too! Then, you need to try to find organisms in as many taxonomic groups/categories as possible. You need to observe and take notes on each organism you find — you do not need to try to catch them or pick them up, but rather, observe their natural behavior — then go look up further information on each of those organisms. The grading criteria for this assignment are given below, and you should also refer to those as you work on the assignment. A total of 26 points is possible.

  1. Kingdoms: Finding organisms in Kingdoms Fungi, Plantae, and Animalia should be fairly easy. If you look in just the right place, you might also be able to see some of the larger organisms from Kingdom Protista. You probably will not be able to see any of the organisms in Kingdom Monera without a microscope.
  2. Phyla (Divisions): Figuring out to what phylum (botanists use the word “division” instead of “phylum”) organisms in Kingdoms Protista and Fungi belong would be difficult, but there are a number of Phyla/Divisions in Kingdoms Plantae and Animalia that are fairly easy to identify. These includethe following.
    Within Kingdom Plantae it should be fairly easy to find representatives of
    plus, if you are fortunate enough to be in just the right place, you may see representatives of Division Lycophyta or Division Sphenopytya.
    Within Kingdom Animalia, you can probably find representatives of
    plus, if you go to the Aquarium or the Zoo, you may also be able to find representatives of Phylums Porifera, Cnidaria/Coelenterata, and/or Echinodermata.
  3. Phylum Arthropoda: Finding members of the following classes is possible, but you probably will not find representatives of all of these groups at once unless you are able to go somewhere like the Insect World at the Zoo. These include
    plus, if you are able to go to the Zoo or the Aquarium, you might also be able to find members of Class Xiphosura.
  4. Phylum Chordata, Subphylum Vertebrata: If you’re using your back yard, several of these might be difficult to find if you live in an urban area, but in general, the possibilities include
    plus if you are able to go to the Zoo or Aquarium, you can probably also see members of Class Chondrichthyes.
  5. Note that because the taxonomic heirarchy is “nested,” a given organism may represent several taxa. For example, a cat would represent Kingdom Animalia, Phylum Chordata–Subphylum Vertebrata, and Class Mammalia. Also, note that you will only get credit for organisms that are correctly placed — for example, credit would not be given for a domestic dog listed as a plant.
  6. For as many as possible of the organisms you find, look up and include their scientific names. The list of species seen on campus may be of help. Do not expect to find scientific names for everything you see. For example, there are so many kinds of flies that look so similar, it takes a PhD to identify them to species, but if you would see something like a Monarch butterfly, that species name is “easy” to find.
  7. For each organism, take notes on their characteristics: what do they look like, do they have any “unusual” body parts, what are they doing, how do they move, etc.
  8. Describe the habitat/environment in which each organism is found. If you’re at the Zoo, Aquarium, etc., these habitats may be very different, but if you’re in your back yard, it may seem, at first glance, like all the same habitat. Look more carefully, then — for example, the habitat in a flower bed would be different than the habitat in the middle of a lawn area. Notice (and take notes on) the amount of light (shady under trees and plant leaves vs bright sun in open lawn area), temperature/heat (cooler under trees, really cold in a penguin exhibit at the Zoo), humidity, soil conditions, etc. in the organism’s environment.
  9. Describe the organisms’ interactions with other organisms that share their habitats: what do they eat or how do they get food, who eats them, how do they defend themselves from predators (chemical defenses, camouflage, teeth and claws, or whatever). Do you see anything that looks like mating behavior? If they eat food, how do they eat their food (chew it up, suck it up, etc.)? How do they communicate with other members of their species and with other organisms? Are they solitary organisms or do they typically live in a social group such as a colony or pack? What is each organism’s “job” within its environment — what does it do there? Do you see any other interesting behavior patterns?
  10. Describe how human intervention, “good” or “bad,” has influenced each organism and its environment. For captive organisms, you may wish to consider both their normal, natural environment as well as the artificial or display environment in which they are currently living. Is there anything that we could/should be doing to improve and/or properly manage those environments?
  11. At this point, if you are a registered student, you should submit your work.

Grading Criteria

1.   Taxonomy:
2 — Representatives of 4(+) kingdoms were included
1 — Representatives of 2-3 kingdoms were included
0 — Representatives of only 1 kingdom were included
2 — Representatives of 4(+) plant divisions were included
1 — Representatives of 2-3 plant divisions were included
0 — Representatives of only 0-1 plant division were included
2 — Representatives of 4(+) animal phyla were included
1 — Representatives of 2-3 animal phyla were included
0 — Representatives of only 0-1 animal phylum were included
2 — Representatives of 4(+) arthropod classes were included
1 — Representatives of 2-3 arthropod classes were included
0 — Representatives of only 0-1 arthropod class were included
2 — Representatives of 4(+) vertebrate classes were included
1 — Representatives of 2-3 vertebrate classes were included
0 — Representatives of only 0-1 vertebrate class were included
2 — 11 or more total organisms were included
1 — 6-10 total organisms were included
0 — 5 or less total organisms were included
2 — 5(+) scientific names were included
1 — 2-4 scientific names were included
0 — 0-1 scientific names were included
2.   Ecology:
2 — Descriptions of the organisms’ traits/characteristics were thorough and showed that the student was extremely observant
1 — Descriptions of the organisms’ traits/characteristics were adequate and showed that the student was fairly observant
0 — Descriptions of the organisms’ traits/characteristics were too sketchy and showed that the student wasn’t very observant
2 — Descriptions of the organisms’ habitat and environmental conditions were thorough and showed that the student was extremely observant
1 — Descriptions of the organisms’ habitat and environmental conditions were adequate and showed that the student was fairly observant
0 — Descriptions of the organisms’ habitat and environmental conditions were too sketchy and showed that the student wasn’t very observant
2 — Descriptions of the organisms’ interactions and behaviors were thorough and showed that the student was extremely observant
1 — Descriptions of the organisms’ interactions and behaviors were adequate and showed that the student was fairly observant
0 — Descriptions of the organisms’ interactions and behaviors were too sketchy and showed that the student wasn’t very observant
2 — Descriptions of the human impact on these organisms’ environments were thorough and showed that the student was extremely observant and thoughtful
1 — Descriptions of the human impact on these organisms’ environments were adequate and showed that the student was fairly observant and thoughtful
0 — Descriptions of the human impact on these organisms’ environments were too sketchy and showed that the student wasn’t very observant and/or gave little evidence of putting much thought into it
3.   Overall:
2 — The student, obviously, went beyond the minimum requirements of the assignment
1 — The student adequately completed the assignment
0 — The student completed considerably less of the assignment than what was required
2 — It is evident that the student used much insight, thoughtfulness, and critical thinking when completing this assignment
1 — The student adequately thought about the assignment – there was, perhaps, a bit of “fuzzy thinking” in a couple places
0 — The assignment gives the appearance of being “slapped together” just to get it done, with little evidence of thoughtfulness
Total Possible:
26 — total points

Copyright © 2006 by J. Stein Carter. All rights reserved.
This page has been accessed Counter times since 18 Nov 2006.