Classifying the Microbial World

     The science of classification is called taxonomy .  Classification systems are based upon distinguishing between characteristics different populations of organisms have.

    Carolus Linnaeus (1707-1778), a Swiss botanist, was the first researcher to formalize the science of taxonomy.  Linnaeus realized that the names given to organisms varied from language to language, and proposed that all living things be given formal, two-part names, via a process he called binomial nomenclature.  The binomial would consist of a generic name (the genus) and a specific epithet (specific name) called the species.  He also proposed that all naming be done in Latin, since this language was no longer used in any country, thus preventing the confusion associated with differences in the names of living things based upon the native language of the researcher.

     With a working system for naming organisms, it would now be possible to construct larger taxons to further group organisms.  These groups are placed into heirarchical order from the largest and most general, to the smallest and most specific, such that at the most specific level only those organisms which share many characteristics are included.  While all of these groupings, called taxons, are essentially artificial constructs, they serve to allow investigators to differentiate between populations in an efficient and logical manner, and gain some understanding about how each population is related to all of the others.

A Brief History of Taxonomic Systems

    The placement of organisms into various kingdoms and other taxons has changed many times throughout history.  Aristotle (4 B.C.) classified all living things as either animals or plants.  Linnaeus classified organisms this way as well, but also included a kingdom he called Chaos, in which he placed all microorganisms.  In 1866, Ernst Haeckel, who was heavily influenced by the recent works of Charles Darwin, proposed that the classification of living things be based upon evolutionary considerations.  His system included Kingdoms Plantae, Animalia, and Protista, which included the bacteria, fungi, and protists.  In 1969, the American ecologist Robert Whittaker proposed a five-kingdom system based both upon evolution and ecology which included Kingdoms Plantae, Animalia, Protista, Fungi, and Monera (in which he placed the bacteria).  Whittaker's system is the most widely accepted today.  With the development of molecular techniques for the study of living organisms beginning in the 1970s, however, other scientists such as Carl Woese have developed new classification schemes.  Woese's system is based upon molecular evidence gathered through a comparison of ribosomal RNA (rRNA) taken from eukaryotes and prokaryotes.  While studying prokaryotes, Woese found that the Archaebacteria, a group of organisms which vary in some characteristics from the Eubacteria and Cyanobacteria had significant differences in their rRNA from all other groups.  He proposed that since there were differences in the rRNA between Archaebacteria, Eubacteria, and Eukaryotes, but no significant differences among the members of the Eukaryotes themselves, only three Domains (superkingdoms), Archaebacteria, Eubacteria, and Eukaryotae were necessary.

Classifying Microorganisms

     Biological entities such as viruses, viroids and prions, obligate intracellular parasites which do not share many of the characteristics of living things, are not included in the classification scheme proposed by Whittaker, but have been classified based upon their own characteristics. True microbes can be found in three of Whittaker's Kingdoms- Monera, which includes all of the bacteria, Fungi, and Protista.  Some organisms which are often studied in microbiology are also found in Kingdom Animalia, including the parasitic flat and round worms .

     Prions are bits of infective protein which can replicate in animal host cells and have been implicated in such diseases as kuru, a disease of the brain which is found only among certain tribes of New Guinea who at one time practiced cannibalism, scrapie, a disease found in sheep, bovine spongiform encephalopathy (mad-cow disease), Creutzfeldt-Jacob disease, and possibly Alzheimer's disease in humans.

    Viroids are infectious RNA particles which cause plant disorders such as potato spindle-tuber disease, Chrysanthemum stunt, and tomato atypical stunt diseases.

     Viruses are obligate intracellular parasites composed of a protein coat called a capsid surrounding nucleic acids (either DNA or RNA) which can infect bacteria (the bacteriophages), and have been implicated in many diseases of plants and animals.  Viruses use the host cell's own biosynthetic activities to replicate themselves, which eventually leads to cell death.  This occurs either through loss of cellular energy, or the destruction of the host cell by lysis (bursting), which releases all of the newly replicated viral particles, freeing them to infect new host cells.  Some viruses wrap themselves in bits of the host cell plasma membrane which becomes a viral envelope that can help to prevent the virus from being recognized by the body of the host as a foreign invader and attacked by the body's defense mechanisms.  Classification of the viruses is based upon their structure, including the presence or absence of an envelope, the symmetry (shape) of the capsid and the type and nature of the nucleic acid the virus contains (DNA or RNA, single-stranded, double-stranded, linear or circular).

     Prokaryotes include the Archaebacteria, the Eubacteria, and the Cyanobacteria.  Classification of these organisms is based upon cell morphology (shape), cell arrangement (single cells, chains, or clusters), staining reactions (Gram and acid-fast stains), cultural characteristics (appearance in broth and on media, such as colony shape, size, and pigmentation), nutrition (oxygen requirements, energy sources, carbon and nitrogen sources, modes of metabolism), biochemical characteristics (cell wall components, type of pigment chemicals, inclusion bodies, RNA type, cell antigen types), and genetic characteristics (guanine + cytosine content, percent DNA, DNA hybridization with other species).  Unlike most organisms, the genetic component of prokaryote classification is highly variable, such that organisms having as much as 30% variation in their genetic code are still considered as belonging the same species.  The difference in genetic makeup can be used to place these organisms into various types or strains.

     Protists include unicellular and multicellular organisms which have characteristics which are similar to those found in plants, animals, and fungi.  The major groups of protists are:

 1. The protozoa, which are eukaryotic, unicellular organisms including the following phyla:

  a. Euglenophyta- organisms such as Euglena, which which has the ability to ingest particles of food
      through a gullet, but can also undergo photosynthesis, using a chloroplast.

  b. Ciliophora- organisms such as Paramecium, which are covered with short, hairlike structures
      called cilia that are used for motility.

  c. Mastogophora- organisms such as Trypanosoma, which have a long  flagellum (similar to
      a cilium) for motility.

  d. Sarcodina- organisms such as Amoeba, which lack cilia and flagella, and move via the
      formation of pseudopodia ("false-feet"; extensions of the plasma membrane).

  e. Foraminifera- organisms similar to the sarcodinids which have a hard outer shell composed
      of silica.

  f. Sporozoa- organisms such as Plasmodium, which are non-motile.

 2. Plant-like protists, including the algaes, which are found in both unicellular and multicellular
     forms.  Major phyla include:

  a. Chlorophyta- green algaes such as Chlorella (unicellular), Spyrogyra (muticellular filaments),
      and Ulva (multicellular flat body called a thallus).

  b. Rhodophyta- red algae such as Hypnea, Porphyra (called Nori; used as food), Gracilaria
      (used to produce agar), and Chondrus (Irish moss; used to produce carrageenans used in
      dairy products).

  c. Phaeophyta- brown algaes such as Laminaria (Kelp; used for food) and Sargassum.

  d. Chrysophyta- golden brown algaes commonly called diatoms.

  e. Pyrrophyta- flagellate fire algae, including Gonylaux, which causes red tide.

 3. Fungus-like protists which reproduce primarily by spores including the following phyla:

  a. Oomycota- these are the "water molds" including Saprolegnia and Phytopthera (the agent of
      late-blight of potato; responsible for the Irish potato famine of the Nineteenth Century).

  b. Myxomycota- the acellular slime molds, including Physarum.

  c. Acrasiomycota- the cellular slime molds, including Dictyostelium.

 Fungi are organisms which are heterotrophic and occur in both unicellular (yeast) and multicellular (mold) forms.  All fungi are dispersed in the form of spores.  Fungi are classified based on the type of spores they produce and whether or not they have a sexual stage.  Major fungal classes include:

 1. Zygomycetes- these fungi produce zygospores and have both sexual and asexual forms of
     reproduction.  Examples include Rhizopus (bread mold) and Mucor.

 2. Ascomycetes- these fungi produce ascospores, have both sexual and asexual means of
     reproduction, and include yeast and mold forms. Examples include Saccharomyces (brewer's
     yeast), Candida (agent of yeast infections), and Morchella (edible morel).

 3. Basidiomycetes- these fungi produce basidiospores and have both sexual and asexual means
     of reproduction.  Examples include mushrooms such as Amanita (the poisonous fungi called
     "angel of death") and Coprinus (the common inky cap mushroom), bracket fungi which grow
     on trees, rusts and smuts, which are pathogens of ornamental and crop plants.

 4. Deuteromycetes- these fungi have no known means of sexual reproduction, including
     genera such as Penicillium (P. notatum produces the antibiotic penicillin) and Aspergillus.

     Animals which are often studied in microbiology include the helminth worms which act as parasites, including Clonorchis (a flatworm; sheep-liver fluke), Taenia (tapeworm), Enterobius (pinworm), Ascharis and Trichina (roundworms).

Concepts of Phylogenetics

     The study of phylogenetics is concerned with the evolutionary relationships between organisms.  This study has its roots in the taxonomic systems of Haeckel and Whittaker, as well as the study of numerical taxonomy, which places organisms into groupings based upon clusters of numbered characteristics which they share.  Like taxonomy, the basis of phylogenetic studies is the species.  What makes a population of organisms a species has been and is still a topic of great and heated debate, but the most commonly held view was proposed by the evolutionary biologist Ernst Mayer and is called the Biological Species Concept (BSC).  The BSC is based on the concept of reproductive isolation, which means that an organism can be included in a species if it is a part of a population of organisms which can interbreed with themselves, but cannot do so with other populations of other organisms and produce reproductively viable offspring. This system works reasonably well for organisms which reproduce sexually, but is violated by those organisms which reproduce by asexual means, such as binary fission in bacteria, fragmentation in algaes and cyanobacteria, budding, and parthenogenic (without sex) reproduction in organisms such as rotifers and aphids, as well as some fish and reptiles.  These violations have lead to the proposal of other species concepts on which taxonomies can be based.  One of the most interesting of these is called the Phylogenetic Species Concept (PSC), which groups organisms into species and other taxa according to diagnosable clusters of characteristics.

    Ultimately, the goal of phylogenetics is to produce phylogenetic trees, which can be used as hypotheses to test theories concerning the evolution of groups of organisms from a common ancestor, and can also serve as a means of producing more meaningful systems of classification.  Phylogenetic trees  separate organisms from one another based on ancestral characteristics found in all of themembers of the taxon, and derived characteristics which have arisen through evolution, shared by only a few organisms, or in only one species.

  Test Yourself Take this quiz on microbial taxonomy.

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