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Taxonomy

Taxonomy

Classification

In this last section, we're going to take a whirlwind tour through all of the biggest taxa on Earth. We hope you get a sense of just how diverse life on our planet is. Before we get into the details, we'll study a few more terms that will help us describe the various organisms.

Prokaryotes v. Eukaryotes

We've tossed these words around already, but now we'll really unpack them. The root "karyon" comes from the Greek word for nucleus. "Pro" means "before" and "eu" means "true." Therefore, the major distinction between prokaryotes and eukaryotes is that the former organisms do not have a nucleus and the latter ones do. But the differences don't stop there.

The nucleus is one type of membrane-bound organelle. Prokaryotes aren't just lacking nuclei; they don't have any organelles. Both prokaryotes and eukaryotes have plasma membranes and most prokaryotes have cell walls, which they share with some eukaryotic cells, like plants.

Prokaryotes are haploid, meaning they only have a single copy of their genes, which is contained within a circular molecule of DNA. Prokaryotes reproduce asexually, whereas eukaryotes usually reproduce sexually and are always diploid, meaning they have two different copies (alleles) of each gene. That said, prokaryotes could share some of their genes with non-offspring in what is called horizontal gene transfer. This is a more primitive, less complete way of increasing the genetic diversity within a population.

The final difference we'll consider is size. Prokaryotes are almost always unicellular. Only a few species can create colonies containing cells with different tasks. The simplest eukaryotes are also unicellular, but most eukaryotes are multicellular once they get past the awkward fertilization stage.

Human egg cells are among the largest cells on Earth. They tend to be somewhere over 100 μm in diameter, which is about the size of the period at the end of this sentence. Adults are made of 60-90,000,000,000,000 (trillion) cells—if you could only get a penny for every cell in your body.
  
Prokaryotes Eukaryotes
Nucleus? No Yes
Other organelles? No Yes
Plasma membrane? Yes Yes
Cell wall? Usually Sometimes
Gene copies 1 (haploid) 2 (diploid)
DNA form Circular Chromosomes
Organization Unicellular Uni- to multicellular
Reproduction Asexual Usually sexual
Average diameter 0.5 – 1.0 μm 5 – 50 μm

Metabolic Options

All living things need energy to survive. This energy fuels the reactions that build the molecules that they need and recycle the ones that they don't need.

Organisms can either get their energy from chemical compounds, in which case they're called chemotrophs, or they can capture it from sunlight, giving them the name phototrophs. All organisms also need a source of carbon atoms to make most of the molecules in their bodies. When an organism's carbon source is the organic molecules of other organisms, it is called a heterotroph. Heterotrophs must consume other organisms, which is why they are often called consumers. When an organism is able to use (inorganic) carbon dioxide to create its own organic molecules, it is called an autotroph. Autotrophs are also called producers because they can produce their own carbon compounds.Based on their needs for both energy and carbon, we can combine these terms and classify organisms into four categories.

1) Chemoheterotrophs need organic molecules as a carbon and an energy source. We, for example, eat plants and animals, which are made up of organic molecules. We then digest those molecules by breaking their bonds, which releases energy that can be harnessed and used to do work. Breaking down large molecules has the added benefit of creating many smaller molecules that can then by reworked and made into the proteins and other molecules that we need. All animals are chemoheterotrophs.

2) Photoheterotrophs get their carbon from other organisms but also get their energy from the sun. This means that they must somehow digest or decompose matter from other organisms but they have chlorophyll or other pigments that can capture energy from the sun. Purple non-sulfur bacteria are fun examples that use a purple pigment to absorb sunlight instead of chlorophyll, which is green.

3) Photoautotrophs capture energy from the sun to make their own organic molecules out of inorganic molecules, like carbon dioxide. In this way, photoautotrophs are the least dependent on other organisms. Unicellular photoautotrophs were probably the first form of life on Earth. Almost all plants are photoautotrophs.

4) Chemoautotrophs are quite special because they can use inorganic molecules both to make organic molecules and as an energy source. Therefore they can survive in weird, extreme environments, like deep in the ocean where the sun doesn't shine. They use carbon dioxide as a carbon source and they oxidize molecules like ammonia (NH3) and hydrogen sulfide (H2S) for energy. Most archaea are chemoautotrophs.
  
Kingdom Bacteria Archaea Protista Fungi Plantae Animalia
Cell Type Prokaryotic Prokaryotic Eukaryotic Eukaryotic Eukaryotic Eukaryotic
Cell Wall present (usually containing peptidoglycan) present (no peptidoglycan) present in some present (no cellulose) present (cellulose) absent
Body Organization cellular cellular cellular multicellular, loose tissues tissues, organs tissues, organs, organ systems
Metabolic Mode autotrophs & heterotrophs autotrophs photo-autotrophs & heterotrophs chemo-heterotrophs photo-autotrophs chemo-heterotrophs
Reproductive Mode asexual, some produce spores asexual, no spores asexual, sexual, or both most sexual and asexual, spores sexual, spores, often seeds sexual
A summary of the major characteristics of each of the six kingdoms.

These are the characteristics that most of the members of these kingdoms share in common. Just remember that there's an exception to practically every rule. Look for the evolutionary trends moving from left to right across the table. Remember that evolutionary advances are usually reflected in taxonomic categories.

Here are the types of Autotrophs.
Here are the types of Heterotrophs.

Domain Bacteria

All members of the Domain Bacteria are prokaryotic. Under the Domain Bacteria, there is a single Kingdom, also called Bacteria. Within that kingdom, there are more than 20 recognized phyla. They are generally classified based on their shape, the characteristics of their cell walls, and their type of metabolism.

Pathogenic bacteria are the ones everyone thinks of when they hear the word "bacteria." They're the ones that can get us sick. They cause everything from mild stomach upset and severe food poisoning to deadly spinal meningitis. They can also cause epidemics, especially chlamydia, tuberculosis, and cholera. The bacterium Yersinia pestis was the cause of the Black Death plague that decimated Europe's population in the mid-14th century (and wiped out large portions of the Middle East and Asia, too). Luckily, antibiotics and good hygiene are generally effective against bacteria. Don't forget to wash your hands.

For an organism that can kill us, bacteria are small. They're definitely microscopic, but just because we can't see something doesn't mean that it isn't there. In fact, there are more than 10 times as many bacterial cells in your body than human cells. Because they are so small, though, they only take up a half-gallon of space. (To keep learning more, go here.) Don't be grossed out. Bacteria have gotten a bad rap. Most of them are actually quite helpful. The ones in our bodies are generally helping us to digest our food, develop our immune systems, and keep "bad bacteria" and other microscopic organisms in check.

Bacteria are a very diverse group of organisms. Most of them are chemoheterotrophs. If they decompose dead matter, they are called saprotrophs. The ones that feed off of living matter (like the ones inside of us) are not necessarily pathogenic, but some are. Other bacteria are photoautotrophs, like cyanobacteria, or photoheterotrophs, like purple nonsulfur bacteria. They contain chlorophyll or other pigments that can trap the energy contained in sunlight. Iron bacteria are one type of chemoautotrophic bacteria. They form that brownish residue around the insides of toilet tanks. They're harmless but they sure don't look nice.

Domain Archaea

All archaea are also prokaryotic. They were originally thought to be the most ancient, living life form, which is where they get their name (think "archaic").

For a long time, they were also thought to be a type of bacteria, which is understandable because they are often rod- or sphere-shaped, just like bacteria. They are also prokaryotic, like bacteria. But molecular systematics has recently shown us that they are more similar to eukaryotes than bacteria are, suggesting that bacteria are actually the more ancient organisms.

We also now know about some of their genetic and biochemical differences with bacteria, which we have summarized for you below

Archaea
  • No peptidoglycan* in cell walls
  • Different phospholipids in cell membranes
  • 3 RNA polymerases, like eukaryotes
  • Ribosomes similar to eukaryotic ribosomes
Bacteria
  • Peptidoglycan* in cell walls
  • Different phospholipids in cell membranes
  • One RNA polymerase
  • Ribosomes not so similar to eukaryotic ribosomes
* Peptidoglycan is a repeating macromolecule (polymer) made of amino acids and sugars that form an interconnecting web that gives bacterial cell walls structure and strength.

Archaea are generally classified into five phyla (Crenarchaeota, Euryarchaeota, Korarchaeota, Nanoarchaeota, and Thaumarchaeota). Since these tiny cells are often hard to find and study, there isn't always agreement on which organism belongs where. Instead of getting "political," we'll just discuss them in three broad, sometimes overlapping, groups.

Methanogens like to live in places that are void of oxygen because their cellular respiration is anaerobic. They can be found in swamps and in the guts of many animals, including us. As their name suggests, they produce methane gas as a byproduct of their respiration. (Pop Quiz! Which gas do we produce as a byproduct of cellular respiration?)

Extreme halophiles love to live in environments that are very salty, like the Dead Sea in Israel/Jordan or the Great Salt Lake, UT. The water in these places can be ten times as salty as regular ocean water. Due to osmosis, if these little cells didn't have some intense protections, their insides would be sucked right out of them.

Extreme thermophiles like it hot (> 113 ºF/45 ºC). They are usually found in hydrothermal vents in the ocean or in hot springs like those in Yellowstone National Park. The record for bearing the heat stands at 248 ºF/121 ºC. (That's way above the boiling point for water.) Most proteins denature (or unfold) at high temperatures. Since most of the structure and function of a cell comes from proteins, these tiny creatures have to have super special proteins that can withstand that kind of heat without losing their function.

(For more on Archaea, go to here.)


Rings of golden color formed by mats of bacteria and archaea that love the heat of Great Prismatic Spring, Yellowstone National Park. The center of the spring is so blue because it is pure, sterile water. It is so hot in the center that no living things are found there.

Brain Snack

No pathogenic Archaea are known.

We owe much of what we know about molecular biology to a bacterium. Polymerase chain reaction (PCR) is a technique used in every molecular biology lab in the world. It allows a small section of DNA to be copied over and over again to create enough of it to study. The reaction requires a DNA polymerase that can withstand temperatures high enough to separate the double strands of the DNA template (~205 ºF/96 ºC). Such a polymerase was found and isolated from a bacterial thermophile called Thermus aquaticus. If you ever hear of "Taq polymerase," you now know where it came from and why it is so special.

Domain Eukarya

Ah, eukaryotes. We just took a major step up the evolutionary ladder. Now cells themselves are getting organized and using organelles to help them divide their work and conquer. (For a review of eukaryotic cells, check here.) As we move through the kingdoms within the eukaryotic domain, cells begin to work together in tissues to perform specialized tasks. Then the tissues begin to work together as organs and the organs and tissues work together in organ systems. Social animals specialize and work together in communities, adding the final level of collaboration to the hierarchical nature of life. Remember that each of these advances is an evolutionary adaptation, which also means that they represent new categories being formed within our taxonomic hierarchy.

Kingdom Protista

Protists are an odd bunch of characters. They are usually microscopic and unicellular but that's where their similarities end. They are, of course, eukaryotic, too, since they belong to the Domain Eukarya. They are actually thought to be direct descendants of the earliest eukaryotes and fungi, plants, and animals probably evolved from different branches of the protist family tree.

Though they are usually unicellular, some live together in colonies of loosely connected cells and others are made up of many cells. Some are even made of a single cell with multiple nuclei. Weird.

To move, some push their cell mass around and extend it to create "fake feet" (pseudopods) for pulling themselves forward; others use long, rope-like structures (flagella) that whip around to propel them through their environments; and others have hair-like cilia covering their little bodies to push them through liquids.

Eating—or obtaining nutrients—is also accomplished in many different ways. Some protists are photoautotrophs, like plants and algae, because they contain chloroplasts and undergo photosynthesis. Some are more like heterotrophic fungi because they digest food outside of themselves and then absorb the nutrients. Others remind us of animals because they actually take food particles into their bodies and digest them there.

Some of Kingdom Protista's Usual Suspects:


Paramecium aurelia.


Assorted Diatoms


Kelp looks like a plant but is a kind of brown algae and is one of the largest organisms in Kingdom Protista.

Kingdom Fungi

These fun guys (it never gets old) don't have the best of reputations. Even if some people enjoy mushrooms pizza, they are rarely found growing in gardens—at least not on purpose. Not only are they rarely considered beautiful, they are usually decomposers (chemoheterotrophs) that break down dead things. Fungi are an important worker, together with bacteria, in any compost pile. Without these decomposers, your beloved pile of grass and leaves in the back yard would just sit there and never become the rich fertilizer you wants for the garden.

All fungi are made of eukaryotic cells whose cell walls contain complex carbohydrates, usually chitin. Fungi are generally considered to be yeast or molds, depending on whether they are unicellular or multicellular.

Yeasts are found all over the place: in dirt, on plants, on our skin, and in our bodies. They are also responsible for making bread and alcoholic beverages, and even some medicines.


A moldy pear. Image from here.

Molds begin as unicellular spores that begin to replicate, creating long, branching filaments (hyphae) that allow them to penetrate food sources. These filaments then mature into tangled webs (mycelia).

Reproduction in fungi is varied. It usually happens through the creation of spores, but this can happen both sexually (through meiosis) and asexually (through mitosis) in the same organism, though not at the same time. Creating the spores sexually has the advantage of producing genetic variety, and is therefore better for evolution in the long run, but it isn't as fast as asexual spore formation. Spores are hard to kill. If a fungus feels threatened, it's going to quickly make asexual spores and hope that its descendants will live to see a better day. Oh, the humanity.

There are five distinct phyla in this kingdom: Chytridiomycota, Zygomycota, Glomeromycota, Ascomycota, and Basidiomycota. Guess what scientists who study fungi are called. Mycologists.

Kingdom Plantae

All plants are eukaryotes and most plants are photoautotrophs, but there are exceptions to most biological rules. We'd hate to play Monopoly with these guys. A few plants are actually carnivorous, and thus photoheterotrophs, like the Venus fly trap. They are still capable of obtaining nutrients from the air and soil, but they tend to live in places with nutrient-poor soil. They decided it was best to start catching and digesting bugs to supplement their diets.

All plant cells are surrounded by a plasma membrane, which is then surrounded by a stiff cell wall. The cell wall gives structure and support to the plant, helping it to stand upright. It's an advantage for a plant to stand tall. There is less competition for space in the ground. By going all Michael Jordon, they might be able to catch more rays of sun, which is necessary for photosynthesis.

Most plants get tall enough that they need a way to transport water and nutrients from their roots in the soil up to their top parts. They have vascular tissues that are analogous to our blood vessels, except they are tougher and there is no heart to pump liquids through. They actually have two different sets of vessels: xylem that carry water and dissolved inorganic minerals and phloem that carry dissolved organic molecules like sugar. Both of these tissues contain the polymer lignin to strengthen and support them.

All plants have the same life cycle, called alteration of generations. It is covered more thoroughly here in Shmoop's chapter on plants. Alternation of generations basically involves a diploid phase and a haploid phase. Different plants spend different portions of their lives in each phase and the structures and mechanisms used in each phase vary with phyla.


Plant life cycle: alternation of generations

Plants can be classified into five broad categories, each containing a few phyla. Nonvascular bryophytes (Phyla Bryophyta, Hepatophyta, Anthocerophyta) include mosses, liverworts, and hornworts. (No, we're not referencing Harry Potter. Though they might be part of a potion or two.) These short plants are so short that they don't need the vascular network that other plants need. They also don't have real roots, leaves, or stems. All together, that means they need to live in moist environments. You may have heard that moss only grows on the north side of trees and that's true-ish. In lands north of the equator, the sun will never directly shine on the north side of a tree so it will tend to be cooler and more moist on that side so there will tend to be more moss there. However, if you're in a cool, moist climate like Washington State, it probably doesn't matter which side of the tree you're on. The moss will be happy anywhere.

Once vascular tissues evolved, the Plant Kingdom really took off. There are two big groups of vascular plants: those with seeds and those without. The vascular seedless plants (Phyla Lycopodiophyta, Pteridophyta) may not have had seeds but they have all of the other "normal" trappings of a plant, like roots, leaves, and stems.

Vascular seeded plants are then divided into two more groups: those with "naked" seeds (the gymnosperms) and those with fruit surrounding their seeds (the angiosperms). Fruit is actually the wall of a plant's ovary nourishing and protecting its developing seed(s).


The pericarp of this peach formed from the wall of an ovary surrounding an egg at the base of a peach flower.

Gymnosperms include the Phyla Coniferophyta, Cycadophyta, Ginkgophyta, Gnetophyta. The first phylum is the conifers: evergreens with their seeds in cones. The cycads and some of the Gnetophyta also bear their seeds in cones. Ginkgo biloba trees (the only living species in the Ginkgophyta phylum) and some of the plants in Gnetophyta have seeds that look something like berries but they aren't made from the ovary wall or they would be classified as angiosperms.


The unique leaves of a Gingko biloba tree.

Angiosperms are just one big phylum, Anthophyta. The ovaries of angiosperms mature into a thick coating around the seeds, which we technically call fruit. This is not your typical "fruits and vegetables" fruit, though. Angiosperms include wheat, corn, and cacti, to name just a few "non-fruits." The fruits of angiosperms help to protect and disperse the seeds. How do they help disperse them? When eating fruit, most animals besides humans don't bother to spit out the seeds. So, the seeds travel through the gut of the animal for a while as it wanders in search of more food. Eventually, the seeds are deposited on the ground again, leaving the animal from the end opposite that through which they came in, if you catch our drift.

Kingdom Animalia

At long last, we reach the animals. We're glad you've stuck with us this far. Now we're in even more familiar territory, but we'll still keep you on your toes.

These guys are all eukaryotes. They are all multicellular in their adult forms and have the most complex body plans of all organisms on Earth. Some are more complex than others, but they all have their cells arranged and working together in tissues, which work together to create organs, which work with other organs and tissues to create organ systems.


This sponge is nicknamed a Venus Flower Basket but its scientific name is Euplectella aspergillum.

All animals can reproduce sexually, but a few have some creative alternatives. Some simple animals, like sponges, can reproduce asexually by creating a new adult from a fragment that breaks off from a parent organism. It would be cool, but way too creepy if humans could break off body parts and grow them into new humans. Some animals, including sponges, are hermaphrodites, meaning that a single organism can produce both eggs and sperm. In sponges, a given organism will only produce one type of gamete at a time. Fertilization happens when its gametes are released and fuse with those of a sponge producing the opposite kind of gamete. Other hermaphrodites, like Ctenophores (comb jellies), are capable of fertilizing their own gametes because they produce both eggs and sperm simultaneously.

Among some of the most important evolutionary developments of animals are those that protect their young as they mature. The location of both fertilization and embryonic development have much to do with the survival of young animals and is a useful characteristic to look for when classifying animals.

Most amphibians reproduce in the water. Females lay many jelly-like eggs in a mass. Males then release their sperm in the water nearby. Because fertilization is external to the animals, many of the eggs will go unfertilized and the ones that do get fertilized are left to develop on their own in the water where they are very vulnerable to hungry prey. That is why so many eggs are laid in the first place: very few will become adults.


Two egg masses in a stream. Top: Rana aurora, Northern red-legged frog, Bottom: Amybstoma gracile, Northwestern salamander. 

In birds, fertilization is internal and therefore more successful. Eggs, either fertilized or unfertilized are laid with a hard, protective shell; the mother watches over and warms the eggs until they hatch. In placental mammals, fertilization and embryonic development occur within the protective environment of the mother's uterus. This gives the young their best chance for survival. Because it takes so much energy from the mom, usually only a few offspring are born at a time.

All animals are chemoheterotrophs. They usually take food into their bodies and digest it there. Sugars and starches are broken down and combined with oxygen to generate ATP, or energy. (That's the "chemo" part.) Proteins are broken down into amino acids and recycled to create the proteins needed by each particular cell at any given moment. (That's the heterotroph part.)

Most animals move around to find their food – mobility is an important evolutionary adaptation—but a few, like sponges and coral, are sedentary. They have to sit and wait for their food to come to them. They have filters that let water through but capture the tiny food particles floating in the water. Most animals also have a highly developed nervous system and muscle system, which they use not only to get from point A to B but also to find and ingest food and water, react to predators or falling trees, or pull a bow across a few taut strings to make hauntingly beautiful music.

We've already gone through many of the animal phyla in the EvoDevo section. The main thing to remember is that animals share similar patterns of development because we share similar genes because we share (way back when) a common ancestor. Scientists think that the first animal was probably derived from a protist called a choanoflagellate. As their name implies, the cells of these colonial organisms are flagellated. The theory is that some of these colonies began to evolve so that some cells worked together to perform particular tasks in a way that was coordinated with other cells working on other tasks. That was the big step needed to begin building the complex organ systems that exist today.

As we saw earlier, taxonomists classify animals into five major clades based on their macro similarities and differences, confirmed at a molecular level. Below are the five clades and some of the phyla included within them. The hierarchy takes you to the "Class" level for the animals that are most familiar to us.

1. Parazoa (Phylum Porifera)
2. Radiata
a. Phylum Cnidaria
b. Phylum Ctenophora
3. Lophotrochozoan Protostomes
a. Phylum Platyhelminthes
b. Phylum Nemertea
c. Phylum Mollusca
d. Phylum Annelida
e. Lophophorates (Phyla Brachiopoda, Bryozoa, Entoprocta, and Phoronida)
f. Phylum Rotifera
4. Ecdysozoan Protostomes
a. Phylum Nematoda
b. Phylum Arthropoda
5. Deuterostomes
a. Phylum Echinodermata
b. Phylum Hemichordata
c. Phylum Chordata
i. Subphylum Urochordata
ii. Subphylum Cephalochordata
iii. Subphylum Vertebrata
-jawless fish (Classes Myxini, Cephalaspidomorphi)
-sharks (Class Chondrichthyes)
-bony fish (Classes Actinopterygii, Actinistia, Dipnoi)
-Class Amphibia (amphibians)
-Class Reptilia (reptiles)
-Class Aves (birds)
-Class Mammalia

We are members of the Domain Eukarya, Kingdom Animalia, Phylum Chordata, Subphylum Vertebrata, Class Mammalia, Order Primates, Family Hominidae, Genus Homo, Species Homo sapiens.

Brain Snack

Watch a Venus fly trap eat a spider.

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