Three Domains of Living Organisms

• Domain Bacteria – Most of the Known Prokaryotes
  • Although it is clear that the bacteria need to be separated into kingdoms, they are not well enough studied for this to have been done yet. At present, they are separated into five phyla.
  • Phylum Proteobacteria: Nitrogen-fixing bacteria
  • Phylum Cyanobacteria: Photosynthetic bacteria (formerly blue-green algae)
  • Phylum Eubacteria: True gram-positive bacteria
  • Phylum Spirochetes: Spiral bacteria
  • Phylum Chlamydiae: Intracellular parasites
• Domain Archaea – Prokaryotes of Extreme Environments
  • Kingdom Crenarchaeota: Thermophiles
  • Kingdom Euryarchaeota: Methanogens and halophiles
  • Kingdom Korarchaeota: Some hot-springs microbes
• Domain Eukarya – Eukaryotic Cells
  • Protista (Informal Group): Single-celled organisms that have a nucleus and other internal structure in the cell (e.g., diatoms, dinoflagellates, foraminifera, radiolaria, marine algae, seaweeds)
  • Kingdom Fungi: Multicelled organisms that are not able to photosynthesize (or chemosynthesize)
  • Kingdom Plantae (or Metaphyta): Multicelled photosynthetic autotrophs (e.g., kelp)
  • Kingdom Animalia (or Metazoa): Multicelled heterotrophs (invertebrates and vertebrates)

Viruses have traditionally been considered to be non-living (since they cannot reproduce without a host).However, this view is now changing, and viruses may soon be recognized as life.In addition, there is now evidence that viruses may have preceded all of the other existing kingdoms, that they stand somewhere at the base of the tree of life, and may have evolved into cellular organisms.Some may even have devolved from a member of the 3 domains, losing (as no longer necessary) their prior cellular structure and ability to breed without a host, two of the characteristics recognized as generally defining life. As a result, it is likely that viruses will have to be found a place within the taxonomic hierarchy. Whether this will require reorganization of the 3 Domain structure shown in the table above to include a new Domain, a new Kingdom or lower order, or even a new classification level above Domain is not yet clear.

The taxonomic hierarchy generally has nine levels, although sometimes one or another level is omitted, sometimes intermediate levels are added within the hierarchy, and there is, as yet, no universal agreement on the use of the top level domains. The major levels in the hierarchy are as follows:

Domain

   Kingdom

      Phylum

         Subphylum

            Class

               Order

                  Family

                     Genus

                        Species

The principal phyla and classes to which all common marine species belong, and some examples of each type are listed at the end of this appendix.

Scientific names of organisms are important for many reasons, one of which is that common names are often confusing. For example, the common name “red snapper” is used in the Gulf of Mexico for the species Lutjanus campechanus. In the Pacific Ocean the same common name, “red snapper,” is used for at least three different species (Lutjanus bohar, Lutjanus malabaricus, and Lutjanus gibbus) that are related but very different from one another. This difference does not matter to the local populations who eat these fishes (indeed, when you order red snapper in a restaurant, you may be served any one of many species that may not even be snappers). However, scientists must be able to distinguish them in the literature, and they do so by using scientific names.

The scientific names given to species always consist of two parts: a genus name followed by a species name. For example, mussels are classified as follows:

• Domain: Eukarya
• Kingdom: Animalia (Metazoa)
• Phylum: Mollusca
• Class: Bivalvia
• Order: Mytiloida
• Superfamily: Mytilacea (this is good example of an intermediate level used in the taxonomic hierarchy for only some orders)
• Family: Mytilidae
• Genus: Mytilus

The common blue mussel of the east coast of North America is Mytilus edulis, and a different species, Mytilus californianus, is present only on the west coast.

These and other scientific names may seem complicated, but they are either Latin or Greek words modified to explain something that the taxonomist considers important in identifying the organism. For example, “Mytilus” is derived from the Greek word for sea mussels, “californianus” expresses that this species is present only on the West Coast; and “edulis” means “edible,” a suitable term for this species that is so good to eat. Similarly, the genus name Sargassum is applied to species of algae present in the Sargasso Sea, and Enterococcus is the genus name for species of bacteria (“-coccus”) that are present in vertebrate intestines (“Entero-”).

Scientific names can be complicated and sometimes obscure, but in general, they follow an internationally accepted set of rules. Note that the convention is to use italics for scientific names and to capitalize the genus name only. In addition, shortening the genus name is acceptable when clear. For example, this text refers to mussels as M. edulis and M. californianus after the full names have been used once. There are other conventions as well. For example, “sp.” after the genus name refers to a single species of the genus whose species name is not known, and “spp.” after the genus name indicates that all (or many) of the species of that genus are being referred to (e.g., “Mytilus sp.” refers to an unstated or unknown species of mussel, and “Mytilus spp.” refers to all or any species of mussel). The “sp.” and “spp.” are often omitted, as is done for simplicity in many cases in this text. Sometimes the genus name is followed by abbreviations such as “cf.” and “aff.” The first of these abbreviations (“cf.”) means that the genus listed is thought to be correct and that the species is very similar to the species identified by the name following the genus name and “cf.” but there are enough differences to lead the investigator to believe that this may turn out to be a new, but very closely related, species or a subspecies. The second abbreviation (“aff.”) means that the species is very similar to the species identified by the name following the genus name and “aff.” but it is sufficiently different that it is most likely an undescribed species similar to the one named.

Taxonomic Classification

Phyla that have no members in the marine environment, as well as phyla in which all species are extinct, are omitted from the following list. The list includes general descriptions of members of each classification and, in some cases, examples of common species and a listing of figures in this text that show a photograph of a member of this classification. The classification presented is not accepted by all taxonomists. Classifications, including the distinctions between phyla, continually change as more is learned.

Domain Archaea. Organisms that have no nucleus, predominantly single-celled. Occur primarily in extreme environments.

Kingdom Crenarchaeota. Thermophiles.

Kingdom Euryarchaeota. Methanogens and halophiles.

Kingdom Korarchaeota. Some hot-springs microbes.

Domain Bacteria. Organisms that have no nucleus, predominantly single-celled.

Phylum Proteobacteria. Nitrogen-fixing bacteria.

Phylum Cyanobacteria. Photosynthetic bacteria (formerly blue-green algae).

Phylum Eubacteria. True gram-positive bacteria.

Phylum Spirochetes. Spiral bacteria.

Phylum Chlamydiae. Intracellular parasites.

Domain Eukarya, Protista (Informal). Organisms with a nucleus confined by a membrane, predominantly single-celled. This group may eventually be broken up and reclassified.

Phylum Chrysophyta. Diatoms (Figs. 6-6; 12-16a), coccolithophores (Figs. 6-7; 12-16c), silicoflagellates.

Phylum Pyrrophyta. Autotrophic dinoflagellates (Fig. 12-16b), zooxanthellae.

Phylum Chlorophyta. Green algae (Fig. 13-4a,d; 15-13f).

Phylum Phaeophyta. Brown algae (Fig. 13-4a). Kelps (Figs. 12-4a,b; 15.3a,c; 15-7c), Sargassum (Figs. 15-8; 15-15), and others.

Phylum Rhodophyta. Red algae (Fig. 13-4a,b,e).

Phylum Zoomastigophora. Flagellated protozoa, including heterotrophic dinoflagellates.

Phylum Sarcodina. Amoebas and relatives, including foraminifera (Figs. 6-8a; 12-19d) and radiolaria (Figs. 6-9; 12-19e).

Phylum Ciliophora. Protozoa with cilia.

Domain Eukarya, Kingdom Fungi. Fungi, lichens.

Phylum Mycophyta. Marine fungi are primarily benthic decomposers. Marine lichens are primarily intertidal.

Domain Eukarya, Kingdom Plantae (Metaphyta). Auto­trophic multicelled plants.

Phylum Tracheophyta. Plants with roots, stems, leaves, and special cells that transport nutrients and water.

Class Angiospermae. Flowering plants with seeds contained in a closed seedpod. Turtle grass (Thalassia; Fig. 14-12b), marsh grasses (Spartina; Fig. 14-12c).

Domain Eukarya, Kingdom Animalia (Metazoa). Multicelled heterotrophs (animals).

Phylum Placozoa. Amoeba-like multicelled animals.

Phylum Mesozoa. Wormlike parasites of cephalopods.

Phylum Porifera. Sponges (Fig. 14-28m).

Phylum Cnidaria (Coelenterata). Jellies and related organisms, all of which have stinging cells.

Class Hydrozoa. Polypoid colonial animals, most with a medusa-like stage. Includes Portuguese man-of-war (Fig. 12-20d).

Class Scyphozoa. Jellies with no (or reduced) polyp stage in life cycle. Medusa stage dominates (Fig. 12-20a,b).

Class Anthozoa. Zooanthids (Fig. 14-8h), anemones (Figs. 14-6c; 14-8g,i; 14-20a; 14-35a; 15-9b), sea pens (Fig. 14-6a,b), and corals (Figs. 13-12; 14-8a-f; 14-28a; 15-5e,f; 15-7; 15-9a) that have only a polypoid body form.

Phylum Ctenophora. Comb jellies (Fig. 12-20d), “sea gooseberries.” Predatory, predominantly planktonic.

Phylum Platyhelminthes. Flatworms, flukes, tapeworms. Many are parasitic; many others are free-living predators.

Phylum Nemertea. Ribbon worms. Benthic and pelagic.

Phylum Gnathostomulida. Microscopic, wormlike, meiofaunal (small organisms that live in the spaces between sediment grains).

Phylum Gastrotricha. Microscopic, ciliated, meiofaunal.

Phylum Rotifera. Ciliated, less than about 2 mm long. Most species freshwater. Planktonic or epibenthic.

Phylum Kinorhyncha. Small, spiny, segmented worms; meiofaunal.

Phylum Acanthocephala. Spiny-headed worms. All are intestinal parasites of vertebrates.

Phylum Entoprocta. Small polyplike suspension feeders.

Phylum Nematoda. Roundworms. Most are 1 to 3 mm; marine species are infaunal.

Phylum Bryozoa. Small moss animals that form encrusting or branching colonies on the seafloor.

Phylum Phoronida. Suspension-feeding tube worms. Infaunal; inhabit shallow and temperate sediments.

Phylum Brachiopoda. Lamp shells. Bivalve animals that superficially resemble clams. Mostly deep-water.

Phylum Mollusca. Soft-bodied animals with a mantle and muscular foot. Most species secrete a calcium carbonate shell.

Class Monoplacophora. Limpetlike shells, segmented bodies, abyssal only.

Class Polyplacophora. Chitons (Fig. 15-13d). Oval, flattened body covered by eight overlapping plates.

Class Aplacophora. Worm-shaped mollusks; soft-sediment infauna.

Class Gastropoda. Snails (Figs. 14-3b; 14-19b; 14-28h; 15-13a), limpets (Fig. 15-13b), abalones, pteropods (Figs. 6-8b; 14-3a), nudibranchs (Figs. 3-1c; 14-11c,d; 14-28d–g; 15-9f), and many others (Figs. 14-11b; 14-19c; 14-34s).

Class Bivalvia. Clams (Fig. 14-35d), scallops, oysters (Fig. 14-7b), mussels (Figs. 14-7a; 15-13e; 15-14). Bivalves (shell with two fitted segments). Mostly filter-feeding.

Class Scaphopoda. Tusk shells. Soft-sediment infauna.

Class Cephalopoda. Squid (Figs. 12-24a, 14-28i), octopi (Figs. 12-1, 14-18e; 15-18), cuttlefish (Figs. 12-24b–d, 14-1; 14-28j), Nautilus (Figs. 12-24e,f). No external shell except in Nautilus sp.

Phylum Priapulida. Small, wormlike, subtidal.

Phylum Sipuncula. Peanut worms, benthic, exclusively marine.

Phylum Echiura. Spoon worms. Spoon-shaped proboscis. Infaunal or live under rocks.

Phylum Annelida. Segmented worms. Mostly benthic. Includes feather duster worms (Fig. 14-6d), scale worms (Fig. 14-34r), and Christmas tree worms (Figs. 14-10c,d).

Phylum Tardigrada. Meiofaunal. Eight-legged. Can hibernate for long periods.

Phylum Pentastoma. Tongue worms. Parasites of vertebrates.

Phylum Pogonophora. Tube-dwelling worms with no digestive system. Absorb food through body wall. All species are marine. Mostly deep-water (Fig. 15-20b).

Phylum Echinodermata. Spiny-skinned animals. Most are benthic epifaunal or infaunal.

Class Asteroidea. Sea stars (Figs. 12-21c; 15-5b, 15-9e).

Class Ophiuroidea. Brittle stars, basket stars (Fig. 14-33e).

Class Echinoidea. Sea urchins (Figs. 14-10b; 14-11a; 14-18d; 14-35b; 15-5c; 15-10b), sand dollars (Fig. 15-5d), sea biscuits.

Class Holothuroidea. Sea cucumbers (Figs. 14-10a; 14-28l; 15-5a).

Class Crinoidea. Sea lilies and feather stars (Figs. 14-16a,b; 14-34g).

Phylum Chaetognatha. Arrowworms, stiff-bodied, mostly planktonic.

Phylum Hemichordata. Unsegmented infauna with primitive nerve cord. Acorn worms. All marine.

Phylum Arthropoda. Jointed, legged animals with segmented body covered by an exoskeleton.

Subphylum Crustacea. Copepods (Figs. 12-19a, 14-32a), krill (Fig. 14-2a), barnacles (Figs. 14-7c,d; 15-13c), amphipods, shrimp (Figs. 14-2b,c; 14-16a,b,j-l; 14-18a; 14-34h-q; 14-35c,e; 15-9d), lobster, crabs (Figs. 12-21a; 14-16f,g; 14-18c; 14-34a-e; 14-35a,b; 15-9c; 15-13g), euphausiids (Figs. 12-19b; 14-2a), isopods (Fig. 14-32b,c).

Subphylum Chelicerata. Horseshoe crabs, sea spiders.

Subphylum Uniramia. Insects. Only five species of a single genus are present in the ocean.

Phylum Chordata. Animals with a nerve cord and gills, gill slits, or lungs.

Subphylum Urochordata. Tunicates (Fig. 14-9), sea squirts, salps (Fig. 12-20e; 14-4).

Subphylum Cephalochordata. Lancelets, Amphioxus. Found in coarse temperate and tropical sediments.

Subphylum Vertebrata. Spinal column of vertebrae, internal skeleton, brain.

Class Agnatha. Jawless fishes. Cartilaginous skeletons. Lampreys, hagfishes.

Class Chondrichthyes. Cartilaginous skeletons. Rays (Fig. 12-23f,h,i), sharks (Fig. 12-23a-e,g; 14-25e), skates, sawfishes, chimeras.

Class Ostreichthyes. Bony fishes (Figs. 12-22; 14-13d; 14-14; 14-15; 14-16c-e,h,i; 14-17; 14-18b; 14-19a,d-f; 14-20b-f; 14-21; 14-22; 14-23; 14-24; 14-25a–d; 14-26; 14-27; 14-28b,c,k,n; 14-32; 14-34f,g; 14-35c; 15-7; 15-9g).

Class Amphibia. No marine species, but one species (Asian mud frog) is known to tolerate marine water. Frogs, toads, salamanders.

Class Reptilia. Turtles (Figs. 12-28a,b; 14-12d), sea snakes (Fig. 12-28c,d). One species of iguana (Fig. 12-28e,f) and one species of crocodile are marine.

Class Aves. Birds (Figs. 12-29; 16-9b). Many species live on and feed in the ocean, but all must return to land to breed.

Class Mammalia. Warm-blooded animals that have mammary glands and hair, bear live young.

Order Cetacea. Whales (Fig. 12-25a-d), porpoises, dolphins (Fig. 12-25e).

Order Sirenia. Sea cows. Manatee (Fig. 12-26), dugong.

Order Carnivora. Marine species in two suborders.

Suborder Pinnipedia. Seals (Figs. 12-27a,b; 15-16; 16-9a), sea lions (Fig. 12-27c), walrus (Fig. 12-27d).

Suborder Fissipedia. Sea otters (Figs. 12-27e; 15-10a).

Order Primates. Primates. Apes, human beings. Only one species is known to tolerate marine water—surfers, swimmers, scuba divers.

The phyla Porifera, Cnidaria, Platy­hel­minthes, Nematoda, Mollusca, Arthropoda, Arthropoda, and Chordata each have more than 10,000 known member species. The phyla Cyanobacteria, Chrysophyta, Pyrrophyta, Chlorophyta, Phaeophyta, Rhodophyta, Zoomastigophora. Sarcodina, Ciliophora, Mycophyta, and Echinodermata each have between approximately 1000 and 10,000 known member species. All other phyla listed have fewer than about 1000 known species. However, it is estimated that there may be between 1 and 10 million species in the oceans, of which only a few hundreds of thousands have yet been identified.