In our previous presentation about phylogenetic classification, we introduced classifying organisms under a broad three-domain system versus classifying organisms using a five, six, or more kingdom approach. For the purpose of this discussion, we will refer to the traditional five-kingdom system.  Organisms are divided into each of five kingdoms based on defining characteristics, such as: cell type; cell structures; whether the organism is unicellular, multicellular, or has both forms; and nutrition.  As new information is gathered, classifying approaches are constantly being refined.

By themselves, viruses do not have all the characteristics of living organisms and are not considered "alive" by most definitions. Viruses are not cells, but consist of single or double stranded RNA or DNA surrounded by a protein shell called a capsid. The two major shapes of viruses are helical and polyhedral.  Some viruses also have a protein/lipid outer membrane or envelope surrounding the capsid.  Viruses do not grow, maintain homeostasis or metabolize on their own.   

The structure and replication mode of viruses varies widely; however, all viruses can multiply only within a host cell (including bacteria). Phages (viruses that infect bacteria) are the best understood of all viruses and research has led to the discovery that some double stranded DNA viruses are able to reproduce using two alternative processes, the lytic and the lysogenic cycles.  In the lytic cycle, the virus attaches to the host cell, injecting its DNA.  The viral nucleic acid directs the host to produce new viral DNA and phage proteins.  After assembly, new viral offspring particles are released when the host cell disintegrates, or "lyses."  In the lysogenic cycle, viral genomes remain dormant for long periods of time inside the host cell.

Bacteria are the most numerous and ancient life forms found on Earth.  They can live in places normally found inhospitable to other organisms (too cold, too dark, too hot, etc.).  Bacteria are unicellular organisms that do not contain a nucleus or internal compartments, and their genome does not contain introns.  Most species of bacteria can be assigned to two groups, based on the amount of peptidoglycan found in their cell walls.  Bacteria with a thick layer of peptidoglycan in their cell walls are called "gram-positive" because they retain a blue color after staining (following a technique developed by Christian Gram.)  Bacteria with a thin layer of peptidoglycan sandwiched between other layers stain orange-red following the same procedure and are called "gram-negative."  The three most common shapes of bacteria are spherical (cocci), rod (bacilli), and helices (spirilla).

The number of ways that bacteria can obtain nutrition and respire contributes to their ability to inhabit so many diverse places on Earth.  To obtain energy and carbon, bacteria can be photoautotrophic- harness light energy to drive metabolic processes and use CO2 as a carbon source, while others are chemoautotrophic- oxidize inorganic substances for energy and use CO2 as a carbon source, photoheterotrophic- use light to generate energy but obtain carbon from other organic molecules, or chemoheterotrophic- consume organic molecules for both energy and carbon.   The chemoheterotrophs include saprobes, decomposers that absorb their nutrients from the body fluids of living hosts.  Bacteria also form many diverse symbiotic relationships with other organisms.

Bacteria exhibit wide variation in their use of oxygen and can be classified based on their dependence upon it.  Obligate aerobes must have oxygen for cellular respiration; facultative anaerobes use oxygen if it is present, but also can grow by fermentation in an anaerobic environment.  Obligate anaerobes can not tolerate oxygen at any level. 

Bacterial reproduction normally occurs asexually by binary fission.  Bacteria do have the ability to transfer genes or segments of genes, and they do so using three mechanisms: conjugation, transformation and transduction.  Conjugation involves the direct transfer of genetic material between prokaryotes.  In transformation, the cells absorb fragments of DNA from the surrounding environment (even from other species).  Transduction occurs when bacterial viruses play a role in transferring genetic material between prokaryotes. 

These abilities, along with a rapid reproductive rate, leaves little surprise as to why bacteria are "masters" of change and adaptation.

A research team led by Carl Woese at the University of Illinois, first recognized the distinction between bacteria and archaea, also known as archaebacteria.  By analyzing RNA in subunits of ribosomes, they defined the early branching of the prokaryotes into Archaea and Eubacteria.  In addition to their unique composition of ribosomal RNA, archaea also are distinguished by the lack of peptidoglycan in their cell walls and their unusual membrane lipids not found in other organisms.  Unlike traditional bacteria, archaebacterial genes contain introns similar to those found in eukaryotes.

Archaea live in the most extreme or harsh environments on Earth and are classified based on the environment in which they can be found.  Methanogens produce energy from organic compounds in the presence of carbon dioxide, nitrogen and water.  They produce methane and can not live in an oxygen-containing environment.  Thermophiles live in very hot water found in areas around hot springs and ocean hydrothermal vents, and Halophiles are found in water with a high saline content, like the Great Salt Lake in Utah.

The majority of bacteria are not harmful and, in many cases, are beneficial to survival.  Prokaryotes are the decomposers of the Earth.  Many prokaryotes obtain energy by breaking down organic molecules and, in the process, make nutrients available for use by other organisms. Prokaryotes are the only organisms to metabolize inorganic nutrients such as sulfur, iron and nitrogen.  Nitrogen recycling, or nitrogen fixation, is unique to Prokaryotes and is the only biological mechanism that makes atmospheric nitrogen available for the production of organic compounds.  Mutualistic bacteria live inside our intestines aiding in digestion while other bacteria suppress the growth of yeasts and other microbes by altering pH levels in our body.
  
In the late 1800s, Louis Pasteur and other scientists linked bacteria to disease.  Robert Koch was the first to identify the organisms that cause tuberculosis and anthrax.  Since then, other pathogenic prokaryotes have been identified and linked to diseases, such Lyme's disease, tetanus, cholera, diarrhea, botulism and syphilis. In industry, bacteria have been used in bioremediation and as metabolic "factories" that produce acetone as well as pharmaceuticals like insulin and antibiotics.  Bacterial metabolic abilities are useful in separating sulfur compounds from copper and uranium in mining low grade ores.

Members of the microbial kingdom Protista originally were defined by structure (mainly unicellular eukaryotes) and by the difficulty to classify them as either plant, fungi or animal.  More recently, the concept of protists was expanded to include certain multicellular organisms such as kelp (Copeland, 1956). Thus defined, members of Protoctista range from microscopic one-celled organisms like dinoflagellates, to multicellular organisms, like seaweed. To untangle this confusing kingdom, biologists now are turning to molecular analysis. 

When following the traditional five- or six-kingdom classification, the Protist group contains all eukaryotes that are not fungi, plants or animals. There are unicellular, colonial, and multicellular forms, some of which show cell specialization.  Protists groups include both autotrophs and heterotrophs, some of which function as detrivores.

Animal-like groups are often referred to as Protozoans.  The term Protozoa dates back to when members of this group were considered "first animals."  Plant-like forms are generally called algae.

Traits such as method of motility, presence or absence of a shell, manner of obtaining nutrition, and reproducing, are used to categorize and discuss this diverse group, but it is important to remember that these traits do not necessarily reflect evolutionary history.  Recent work suggests that green and red algae are more closely allied with land plants, and that slime molds are more closely allied to animals (Baldauf, et al. 2000).

Protists form a broad base across the bottom of the food chain, and they supply approximately one-half of the world's oxygen (unicellular algae compose a large portion of the world's phytoplankton).  Protists, along with bacteria and fungi, are responsible for decomposing and recycling nutrients.

Many protist are helpful.  Euglena are used to help treat sewage because of their unique ability to switch from an autotrophic to a heterotrophic nutritional mode, helping to maintain oxygen levels in the balance.  Another helpful protist is Trichonympha which lives in the digestive system of termites and produces cellulase, an enzyme that enables termites to digest wood.

Animal-like protists are responsible for diseases such as malaria, amoebic dysentery, toxoplasmosis, African Sleeping Sickness and Giardiasis in humans.  Some protists dramatically have affected human history.  Phytopthana infestans, a water mold, destroyed potato crops throughout Ireland in the 1840s, leading to the Great Potato Famine and the eventual migration of large numbers of people into the United States. 

Some protists have medicinal and industrial uses.  Carrageenan, from algae, is used to produce a thickening agent in ice cream, pudding, and candy.  Chemicals from algae are used to manufacture waxes, plastics, paints and lubricants.  Other chemicals made from Protists are used in treatment of ulcers, high blood pressure, and arthritis.

Members of the kingdom Fungi are eukaryotic, heterotrophic, multicelled organisms (except for yeasts).  Examples of fungi are "mushrooms," puffballs, bracket fungi, molds, and mildews.  Fungi cell walls contain chitin, which is the same material found in the exoskeletons of arthropods.  Fungi are important decomposers in ecosystems as they break down organic materials such as dead organisms, leaves, old wood, and feces.

The body of the multicellular fungi consists of long, slender hyphae, some of which can specialize to hold spores, to anchor its body, to secrete enzymes, and to absorb decomposing material.  Fungi break down potential food sources by excreting strong hydrolytic enzymes (exoenzymes).  Once the food is broken down into smaller molecules, the fungi then absorb them into their bodies. 
 
Fungi are generally described and grouped according to the way they reproduce.  Reproduction can be both sexual and asexual, producing spores that disperse by wind or water.

As major decomposers, fungi serve an important role in ecosystems.  Without decomposition, there would not be enough available nutrients to sustain or create new life. 

Many fungi are parasites and thrive on living things, which is an association harmful to the host.  Fungi cause plant diseases such as black spot, corn smut, wheat rust, and mildews that affect a variety of fruits.  Most of us are familiar with fungi that cause human discomforts like athlete's foot, ringworm, and thrush.

Other kinds of fungi live together in a mutually beneficial relationship with other organisms.  Lichens are symbionts of a fungus and a green algae, or a cyanobacterium.  Mycorrhizae are mutualistic relationships between fungi and the roots of vascular plants.  Fungi cells supply the plant with more nutrients and water than normally would be absorbed by the roots alone, and the plant provides the fungus with products of photosynthesis.