12.1: How do we describe life?

Before we examine the many complex physical, chemical, and biological interactions that are the foundations of life in the oceans, it will help to look briefly at how biologists group and classify living organisms. All living things are arranged into formal groups according to their anatomy, physiology, and, more recently, genetic differences, through a system known as “taxonomy.” Taxonomy is discussed more fully in Appendix 3. For now, we need to know that, at the highest level of organization, called the “tree of life,” all species are classified into one of three domains (Fig. 12-2, Table 12-1): Bacteria, Archaea, and Eukarya.

Figure 12-2. The tree of life. The prokaryotes—Bacteria and Archaea—are single-celled organisms with no membrane-bound (enclosed by a membrane) organelles, including a nucleus. The eukaryotes (Eukarya)—protists, fungi, plants, and animals— are single- or multicellular organisms whose cells contain membrane-bound organelles (e.g., nucleus, mitochondria, endoplasmic reticulum, golgi apparatus). All life is assumed to derive from a common ancestor, a progenote, referred to as LUCA (Last Universal Common Ancestor of all life). Bacteria and Archaea are known to have developed before Eukarya (to which humans belong). DNA indicates that the Eukarya developed from Archaea but Eukarya also inherited one or more genes from Bacteria through endosymbiotic events and horizontal gene transfer (represented conceptually by the dashed lines in the figure). Horizontal gene transfer (transfer of one or more genes between species) is now known to be common so the original Darwinian theory of evolution of one species into another in a linear fashion that was the basis for the tree of life concept must now be revised. Protists include diatoms, dinoflagellates, foraminifera, radiolaria, marine algae and others (see Table 12-1).

As technology continues to advance, our ability to look at organisms on a molecular level continues to shed light on relatedness and unrelatedness of organisms. For example, Archaea were once considered part of the Bacteria domain but are now considered separately. While the three-domain tree is the widely accepted model, there is now some evidence that suggests that the tree of life might only contain two branches with the Eukarya being considered simply a subbranch of Archaea. As advances in genome sequencing progress, there may be a move toward a wider acceptance of the two-domain model.

Together, bacteria and archaea make up a group of species known as prokaryotes. All other living species belong to a group called eukaryotes. Scientists traditionally divided eukaryotes into four groups, three kingdoms Fungi (fungi), Plantae (plants), and Animalia (animals) and a fourth group, the protists. However, the protists, traditionally assigned as kingdom Protista, is not a single, unified group, but rather a designation of diverse organisms, most of which are single-celled, that do not fit into the other eukaryotic kingdoms. Viruses have traditionally been considered to be non-living because they cannot reproduce without a host, are acellular, not made of cells, and cannot generate energy. However, this view has more recently been debated and there is now evidence that viruses may have preceded all of the other kingdoms and that they stand at the base of the tree of life and may have evolved into cellular organisms and LUCA, the last universal common ancestor of all species of cellular life. However, the origin of viruses remains unknown and the issue of whether they are a branch of “life” remains controversial.

As discussed in Appendix 3, species within each kingdom are classified into groups that are arranged in a hierarchy containing a number of levels. All species eventually are given a formal name that consists of genus and species, the two lowest levels in the hierarchy. For example, humans are genus Homo, species sapiens; we are all members of the species Homo sapiens (note the italics always used for genus and species names).

Although the formal taxonomic classification of species addresses the need to classify organisms according to their physiological and genetic differences, it does not always serve well to classify species with regard to their functions in the ecosystem. Therefore, many other functional grouping schemes are used for specific situations. For example, marine biologists may group organisms according to whether they live in the water column or on the seafloor, or whether they are able to swim against currents or primarily drift with the water, or whether they are capable of synthesizing living organic matter from inorganic matter or not.

Table 12-1. The Major Taxonomic Groupings of Living Organisms

Group	Description
Prokaryotes	Generally microscopic, single-celled organisms that have no membrane-bound (enclosed by a membrane) organelles (e.g., nucleus, mitochondria, endoplasmic reticulum, golgi apparatus, etc.). May be photosynthetic, chemosynthetic, or heterotrophic.
Domain Bacteria	Generally, microscopic and relatively simple single-celled organisms. Bacteria have no organelles (membrane-bound nucleus or internal structural features). However, most possess a carbohydrate-based cell wall composed of peptidoglycan.
Domain Archaea	Archaea are similar to bacteria but have different cell wall structures, different constituent organic compounds, and many different genes. Many archaea live in extreme environments, such as those found at hydrothermal vents, those where the temperature exceeds the boiling point of water (e.g., geysers), those where salinities are extremely high (e.g., salt lakes), or those that are strongly acidic or alkaline. Some archaea are single-celled, whereas others form filaments or aggregates.
Eukaryotes: Domain Eukarya	Single-celled or multicellular organisms whose cells have a nucleus and other internal structure. Generally larger than prokaryotes.
Protists Informal Group	A diverse group of species, including all the eukaryotes except for the plants, fungi, and animals. The vast majority of protists are single-celled organisms, typically only 0.01 to 0.5 mm in size, yet generally larger than the prokaryotes. Examples are diatoms and dinoflagellates, foraminifera, radiolaria, marine algae, and seaweeds. Protists commonly can survive dry periods in the form of cysts; some are important parasites; a few forms are multicelled—for example, the brown and red algae.
Kingdom Fungi	Mostly multicellular organisms but single-celled organisms exist (yeast), including many decomposers and parasites that infect animals and plants. Fungi release enzymes that break down organic matter that they absorb for food and energy. Examples are molds and mushrooms.
Kingdom Plantae	Multicellular photosynthetic autotrophs. Flowering plants, including sea grasses, mangroves, ferns, and mosses. Note that marine algae and seaweeds are not generally considered to be plants as they are non-vascular lacking roots, stems, and leaves.
Kingdom Animalia	Multicellular heterotrophs, including all invertebrates and vertebrates.