Week Six: Classification of Marine Organisms

"What's in a name?" asked Shakespeare, but what he didn't appreciate was the fact that names not only help us identify an organism and its relatives, but it gives us clues about the organism's ancestry and the role it has played in the physical, chemical, biological and geological evolution of our planet. All that from a name? You betcha!

In this section, we explore why classification of organisms is such a hot topic, how we distinguish the three major types of cells on our planet, what are the major divisions of life and who are some of the major marine representatives of these divisions. It may seem like stamp collecting, but if you keep an open mind, you will begin to see things in the natural world of your daily life that you never even knew existed!

6.1 Why Classify?

Before we look at why classification of organisms is important, let's define what we mean by classification and how it impacts our daily lives.

The word "classify" means quite simply "to arrange in classes or categories." It is synonymous with sort, group, catalog, grade, pigeonhole and type (as in stereotype). This verb permeates our daily lives, as we separate persons, places and things into tidy little categories.

Think about it: classification starts from the time you are a baby, when your parents give you those "round peg-square peg" games. It stays with us in school--"oh, she's an A-student" or "he's failing." It carries into our adult life: "how ghetto" or "they're so upper class now." And it follows us beyond the grave: "tombstone, monument or cremation?"

Here's a few more examples:

When you sort pens and pencils from paperclips and tacks on your desktop, you are classifying. When you arrange food in the refrigerator, frozen foods in the freezer, dairy in the dairy case, eggs in the egg holes, meats in the meat bin and everything else in the main compartment, you are classifying. When you sort your clothes and put the socks in one drawer, the undies in another drawer, your shirts and pants in another, you are classifying. Look around you. What are some other examples of activities in your home and daily life in which you actively classify (and probably weren't aware of it)?

Humans are basically sorters. We like to divide material things into nice discrete groups. It makes it easier for us to comprehend the complexity of the world that way. Sometimes, it's not always just or desired to classify; sometimes we put our friends or people we meet into categories that are unfair or unwarranted. No one said classification was perfect. But if we observe more carefully and look at the details, we may find re-arrange our classifications and a group of people who you may once have feared may now be classified among your friends.

But the kind of classification we are talking about goes beyond the practical and sociological dimensions of the human species. Classification of organisms involves creating categories for every living organism on our planet so that we may better understand the natural order of life on our planet. When we group plants and animals and fungi and bacteria into groups, we find an amazing network of relationships, an ancestry with tremendous implications for our own species and a beauty to life that can only be appreciated by understanding these relationships.

Here's my list of ten reasons for classifying organisms on Planet Earth. Perhaps you can think of some others.

  1. provide an unambiguous name and grouping for all organisms
  2. avoid the pitfall of common names where dolphin can be a fish or a marine mammal
  3. find commonalities among organisms on molecular, biochemical, physiological, developmental, organismal, behavioral and ecological levels
  4. understand the origin of species
  5. define the evolutionary links between species and groups of species
  6. decipher the fate of organisms who have gone extinct
  7. learn about past climates on Earth
  8. elucidate evolutionary pressures on species
  9. marvel at the incredible variety of adaptations to diverse habitats
  10. appreciate the intricacy and detail of living organisms on molecular, biochemical, physiological, developmental, organismal, behavioral and ecological levels

Oh, and while we're on this subject of classification, let me just say one thing. Life defies classification. Every time we come up with a rule for classifying an organism a certain way, another organism bends the rules. Just like we can't put people into nice tidy categories, you can't pin down life that way either.

However, classification does help us bring order to the world. It helps us make sense of our surroundings. And even though classification is an ongoing process, subject to continuous revision and restructuring (as it has since Linnaeus invented it), it's still darn useful, as we shall see.

6.2 Archaebacteria versus Prokaryotes versus Eukaryotes

Whoa! We're kickin' down some big words here. Take a moment to learn how to pronounce these words—say them out loud—and it will be much easier for you to remember what they mean. Learning how to pronounce a word is the key to understanding its meaning!

Now, what the heck ARE these words? Most simply, they are the three major types of life that occur on our planet. ALL living organisms can be placed into one of these categories. To put it another way, we can classify all living organisms into one of these groups.

In particular, these terms refer to cell types. Cells, as you may have once learned, are the basic unit of life. And every cell of every being, even single-celled beings, belongs to one of these categories.

What makes these categories even more important is that they represent the major branches of the evolutionary tree of life. The story here is a fascinating one and if you open your mind to it, you will be simply amazed. It's kind of like learning that your distant ancestors were aliens.

Let's get familiar with each group separately before we compare them.

Archaebacteria, pronounced ahr-kee-back-teer-eee-uh, refers to a distinct kingdom of primitive bacteria found in extreme environments, such as the hot, acidic thermal pools at Yellowstone National Park, the salt flats near San Francisco Bay or hydrothermal vents at the bottom of the ocean. Besides where they live, they are distinct in their cellular structure and genetic makeup, which is why they have their own kingdom (although there is widespread disagreement about this, which I'll explain later).

Archaebacteria, all of whom are unicellular (i.e. they exist as single cells), live in some pretty weird places and under some pretty weird conditions. The three major types of Archaebacteria include:

halophiles - live in salty or alkaline extreme environments, like the salt evaporation ponds surrounding Owens Lake, San Francisco Bay or the Dead Sea; derive energy from photosynthesis using a special type of bacterial chlorophyll; most prefer aerobic environments

methanogens - live in anaerobic environments in aquatic and marine sediments, swamps, sewage sludge, the rumens of animals and insects (where they aid in the digestion of cellulose); use carbon dioxide as sole carbon source (unlike us who get carbon from a lot of difference sources) and produce swamp gas (methane, hence their name) and if they didn't do this, the carbon cycle (and most likely us) would not exist, i.e. all photosynthetically-derived carbon would be buried and not recycled

thermoacidophiles - prefer hot, acidic pools, at pH values from 0.9 to 5.8 (which basically covers the range from battery acid to coffee) and at temperatures between 130 and 230 degrees Fahrenheit, like the thermal springs at Yellowstone and the hydrothermal vents off the coast of Washington State; live off sulfur and most are obligate aerobes (meaning that can't survive without oxygen, like us)

The coolest thing about Archaebacteria is that they were among the very first life forms to appear on our planet. That's why they are called Archae- (Greek: old or ancient) bacteria (Greek: little stick). It makes sense if you think about it. Conditions on Earth soon after it formed (and before life appeared) were pretty hot and miserable (which is why we call it the Hadean period, i.e. the time of Hades or Hell). It took a pretty hardy organism to get going under those conditions.

Another reason scientists like me are excited about Archaebacteria is the possibility they present for life on other planets. The independent discoveries of Archaebacteria and hydrothermal vents in the 1970s and the subsequent discovery of Archaebacteria on hydrothermal vents soon thereafter got people to thinking that maybe these guys could survive conditions on other planets and planetary bodies. The high likelihood of an ocean on Jupiter's ice-covered moon Europa and the volcanic activity there make people wonder whether Archaebacteria might live there. To put it in Spock's words, the possibilities are "fascinating".

Prokaryotes, pronounced pro-care-eee-ahts, are cellular organisms without distinct internal organelles, including the common bacteria (also known as eubacteria) and blue-green algae. Prokaryotes are also unicellular but unlike Archaebacteria, they live just about everywhere (including inside your mouth where their numbers exceed the total number of people who have ever lived on Earth, according to Margulis!). Prokaryotes and Archaebacteria ruled our planet for the first two billion years of it's existence, from 3.8 to 1.5 billion years ago.

Prokaryotes, like Archaebacteria, are among the oldest living organisms on our planet. In fact, fossil remains of Prokaryotes can be found as far back as 3.8 billion years ago. Some of these Prokaryotes, like the blue-green algae that build stromatolites in Shark's Bay, Australia, are still living. Fossils of stromatolites span the entire history of life on Earth.

At least 10,000 species of Prokaryotes are known and perhaps many more are not known, especially in the marine environment. Prokaryotes are notoriously hard to grow and they are remarkably hardy. Some are able to survive millions of years before being revived again. On October 18, 2000, CBS News reported the following:

(CBS) Scientists have revived a 250 million-year-old unit of bacteria found buried beneath the earth—the oldest living thing ever brought back to life.

The organism was found in a tiny, fluid-filled bubble inside a salt crystal 1,850 feet underground, about 30 miles east of Carlsbad, N.M., when scientists pulled about 220 pounds of rock salt from the Waste Isolation Pilot Plant, an underground nuclear waste dump.

That an organism can survive in a state of suspended animation for that long is truly mind-boggling. But that's the story of these hardy, diverse and all-so-important organisms.

Prokaryotes are nature's little recyclers and without them, we wouldn't be here. Prokaryotic bacteria break down organic matter and remineralize it into basic compounds that can be used once again by plants and other autotrophs (organisms that make their own food). If they didn't, there would be no carbon dioxide left on our planet: all of it would be buried in the form of organic matter. In short, prokaryotic bacteria are the foundation of life; they mediate all the biogeochemical cycles on our planet and for that, we should be very thankful.

We don't have room here to expound on all the wild and wonderful ways that prokaryotes affect our planet and our lives, but hopefully, this brief introduction has given you a better appreciation for their importance.

Eukaryotes, pronounced you-care-eee-ahts, are the most advanced form of cell line on our planet. They are defined as an organism composed of one or more cells with a distinct nucleus and organelles, but that doesn't begin to tell their story. Eukaryotes represent the penultimate in cellular cooperation and diversity. We are eukaryotes, so that should tell you something about their importance (!)

Eukaryotes include both unicellular organisms, like protozoans andn dinoflagellates, and multicellular organisms, from sponges and clams to lizards and mammals. Clearly, this is one large and highly successful cell type!

Numerically, eukaryotes include more species than either of the other two cell lines, with at least 1.3 million species and possibly up to 30 million! Scientists simply do now know how many different species of organisms exist on our planet. Each year, thousands more are described and so, the numbers grow.

Perhaps the most fascinating aspect of eukaryotes is how they originated. There is growing evidence that eukaryotes represent a "joining together" of two or more prokaryotes or, perhaps, a prokaryote and a eukaryote. It is believed that the various organelles within a eukaryotic cell, like the nucleus, mitochondria, chloroplast and possibly other parts, came from prokaryotic bacteria. This process, known as endosymbiosis, occurs when one bacterial cell engulfs (i.e. eats whole) another cell but instead of dissolving, this newly invaginated cell remains intact and begins living within the host cell. Endosymbiosis, then, is the process where one organism enters into another organism and remains in a mutually beneficial and obligate relationship (i.e. endo = within and symbiosis = living together).

Endosymbiosis is a radical concept but one that has gained considerable acceptance in recent years. What it means is that every cell in your body contains an ancient bacterium in the form of a mitochondria, the organelle that supplies energy for every cell in your body. Humans (and every other eukaryotic organism) are, essentially, communities of organisms, as each of our cells contain organelles possibly derived from different primitive bacteria some 1.5 billion years ago.

Two scientists and authors, Lynn Margulis and Dorion Sagan, have written about this process in a wonderfully readable book published in 1986 called Microcosmos: Four Billion Years of Microbial Evolution.

I want to leave you in this section with a few of their words:

The new cells seem to have been bacterial confederacies. They cooperated and centralized and, in doing so formed a new kind of cellular government. The upstarts were increasingly centrally organized. and their various cell organelles became integrated into a new biological unit...Cohabiting symbiotically, the archaebacteria and their eubacterial invaders did what neither could do alone. Their descendants became the foundation of the macrocosm. All the familiar creatures of the Earth today, from seaweed to sea urchin to sea lion to sailor, are composites of nucleated cells. The nucleated cells themselves are the result of prokaryotic mergers. And each cell with a nucleus is packed with the deep-breathing mitochondria that once upon a time were bacteria.

Simply amazing, isn't it?

Now that we have some idea of what these three cell types are, let's take a closer look at the differences between them. Having a sense of why these cell types differ will help us better understand the classification of life into various divisions.

Take a moment to study the internal structure of these cells below. Note that the archaebacteria and prokaryotic cells are very similar morphologically (and shown as one figure on the right). The primary difference between eukaryotes and these other two cell types is the presence of distinct organelles.

from American Scientist,  http://www.sigmaxi.org/amsci/articles/99articles/hoppertcap2.html

Note that even though Prokaryotes don't have organelles, they are not just bags of chemicals. In fact, the internal structure of Prokaryotes is quite well organized. The main difference between Prokaryotes and Eukaryotes is the lack of distinct bodies, such as the mitochondrion (energy supplying organelles), the nucleus (the "brain" of the cell where DNA is housed), the endoplasmic reticulum (aka ER, where DNA is transcribed and proteins and lipids are assembled), and the Golgi apparatus (the shipping department of the cell, packaging cellular products from the ER, modifying some of them, and separating them to be delivered to other parts of the cell), to name a few.

Some scientists, like Margulis, prefer to put Archaebacteria and Prokaryotes in the same grouping. However, I tend to go along with the scientists that split them off from the Prokaryotes because I think it's more instructive to emphasize their differences, not only cellularly but ecologically. Even Margulis notes that Archaebacteria are as different from Prokaryotes as they are from Eukaryotes.

The principal differences among the Archaebacteria, Prokaryotes and Eukaryotes are summarized in the table below.






3.6-3.8 BYA

3.6 BYA

1.5 BYA


0.3 to 1 micron

0.3 to 1 micron

10 - 1000 microns


Typically extreme, but not always



Cell Wall

No peptidoglycan



Cell membrane

Single-layer lipids, ether-linked

Lipid+protein bilayer, ester-linked

Lipid+protein bilayer, ester-linked

Respiratory chains



Mitochondria, bacterial in origin




Chloroplasts, bacterial in origin

30S subunit of RNA




Cellular division



Mitosis, Meiosis,

Those are just a few of the distinctions between these groups and this table and the figure above are meant primarily to give you a flavor for the general differences between these three cell lines. However, with most things in science, the details are far more complex than this simple characterization. Check out your favorite web search engine to learn more about the molecular, biochemical, morphological, physiological and ecological differences between these groups.

6.3 The Kingdoms of Life

Okay, it might seem like we've gone pretty far afield from classification but trust me, that stuff we just went through was important and pretty cool, too. If you never learn anything else about classifying organisms, at least you now know you can divide life into three major groups (even if you don't remember their names ten years from now).

The general field of study of classifying organisms is known as systematics and the people who do the classifying are called systematists. A person who classifies sponges is known as a sponge systematist while a person who classifies birds might be known as a bird systematist.

It's time to get down to the nitty-gritty of classification, a scheme started by Aristotle and refined by a Swedish guy named Linnaeus and several others since then. But before we do, you should know that classification of organisms is never finished. New species evolve and new species are found, changing the relationships among a group of organisms.

It's an ever-changing, ever-evolving, ever-improving system based on our best knowledge at the time. The development of molecular biology has radically transformed how we group organisms and when it comes down to it, Nature defies classification. So just be aware that these are general principles of classification. When applied to specific organisms, certain new schemes may be present.

The system introduced by Linnaeus characterizes all organisms on the basis of a double-name, known as the binomial method of classification. In this scheme, every species of organism is given two names, a genus name and a species name, like Homo sapiens. Note that the genus is always capitalized and the species name is always lower case. In addition, the genus and species names of organisms should be italicized.

The species name of an organism is unique; no other organism within a genus can have it. In fact, the definition of a species is a group of organisms within a genus who are potentially capable of exchanging genes or interbreeding or, if asexual, who are most similar in characteristics.

From the species level, organisms are grouped according to similar characteristics throughout an organism's life, be they molecular, biochemical, morphological or physiological. Part of the reason so many characteristics are necessary is because many organisms are difficult to fully characterize throughout their lives. Many forms of bacteria have not been grown in culture, thus molecular similarities and differences must be used. Many organisms change their morphology (the shape and form of an organism) at different stages in their life (especially seaweeds) so that reliance on just the shape of an organism can be very misleading.

Fortunately, we are not delving so deep into classification that we will be faced with such difficulties. It's just important that you appreciate the great pains that scientists go to to define a particular species.

The major groupings of all organisms follows the general scheme proposed by Linnaeus with a few modifications:


Note that this system is hierarchical, that is, it starts at the most general level and divides into more specific levels. Also, within any of these groupings you may find sub- and super- prefixes added. And instead of Phyla (the plural of phylum), plant systematists use Division.

Recently, some systematists have suggested the use of an additional super-grouping called Domain, to refer to the three major cell lines and we will adopt that here. So the major Domains of life are the Prokaryotes, the Eukaryotes and the Archaebacteria.

The next level is that of the Kingdom. Here’s where there’s quite a bit of disagreement among scientists. Some scientists prefer to lump organisms together and some prefer to split organisms into different groups. It’s analogous to putting all your clothes in a bag dividing them into separate drawers, i.e. your sock drawer, underwear drawer, shirt drawer, etc. For our purposes, which are focused on understanding the importance of classification and its general application in our lives, we recognize six kingdoms of life, creating a separate kingdom for the archaebacteria (which in other schemes is a subkingdom).

Using our scheme, the six kingdoms of life include:

  1. Kingdom Plantae, which includes all the multicellular plants (seaweeds, sea grasses and land plants)
  2. Kingdom Animalia, which includes all the multicellular animals
  3. Kingdom Fungi, which includes the mushrooms
  4. Kingdom Protoctista, which includes all the unicellular eukaryotes (diatoms, dinoflagellates, foraminiferans, radioloarians, etc)
  5. Kingdom Bacteria, which includes all the single-celled prokaryotic bacteria
  6. Kingdom Archaebacteria, which includes the Archaebacteria, as described above.

At the Phylum level, we find tens of different Phyla in each Kingdom but it is not our intention to review them all here. Rather, let’s look at a few examples from the marine environment.

Examples of Classification of Marine Organisms

Common Name

California Kelp

American Lobster

White Shark












Phylum or Division