A Systematic Approach

Learning Objectives

  • Describe how microorganisms are classified and distinguished as unique species
  • Compare historical and current systems of taxonomy used to classify microorganisms


The Science of Taxonomy

A painting of Carolus Linnaeus holding a flower.

Figure 1. Swedish botanist, zoologist, and physician Carolus Linnaeus developed a new system for categorizing plants and animals. In this 1853 portrait by Hendrik Hollander, Linnaeus is holding a twinflower, named Linnaea borealis in his honor.



Evolving Trees of Life (Phylogenies)


Linnaeus’s tree of life contained just two main branches for all living things: the animal and plant kingdoms. In 1866, Ernst Haeckel, a German biologist, philosopher, and physician, proposed another kingdom, Protista, for unicellular organisms (Figure 2). He later proposed a fourth kingdom, Monera, for unicellular organisms whose cells lack nuclei, like bacteria.

A drawing of a tree. The base of the tree reads: Radix Monera. This branches into three branches labeled Plantae, Protista, and Animalia. Each of these branches branch further; each new branch Is labeled in small text and clusters of branches are identified. For example, clusters of branches in the protista include: Diatomase, flagellate, protoplasta, and spongae.

Figure 2. Ernst Haeckel’s rendering of the tree of life, from his 1866 book General Morphology of Organisms, contained three kingdoms: Plantae, Protista, and Animalia. He later added a fourth kingdom, Monera, for unicellular organisms lacking a nucleus.



This timeline begins with Carolus Linnaeus who developed a new way to categorize plants and animals in 1758. The image above Linnaeus shows a forked line with one branch labeled plants and the other labeled animals. In 1866, Ernst Haeckel wrote General Morphology of Organisms, proposing four kingdoms. The image above Haeckel shows a central line with Monera branching off the bottom, protists branching off next, then plants and finally animals. In 1969 Robert Whittaker proposed adding a fifth kingdom – fungi – to the tree of life. The image above Whittaker is the same as the one above Haeckel but includes an additional branch labeled fungi between plants and animals.

Figure 3. This timeline shows how the shape of the tree of life has changed over the centuries. Even today, the taxonomy of living organisms is continually being reevaluated and refined with advances in technology.

Think about It


Clinical Focus: Cora, Part 2

This example continues Cora’s story that started in What Our Ancestors Knew.



  • What types of microorganisms could be causing Cora’s symptoms?

We’ll return again to Cora’s example in later pages.

The Role of Genetics in Modern Taxonomy



The phylogenetic Tree of Life. A drawing of branching lines. The central line at the bottom branches into two main branches. On the left branch is the bacterial group. The branch to the right subdivides to the Archaea and Eukarya groups. Additional branches on the Eukarya group from bottom to top are: Diplomonads, Microsporidia, Trichomonads, Flagellates, Entamoebae, Smile molds, Ciliates, Plants, Fungi and Animals (which has a star labeled

Figure 4. Woese and Fox’s phylogenetic tree contains three domains: Bacteria, Archaea, and Eukarya. Domains Archaea and Bacteria contain all prokaryotic organisms, and Eukarya contains all eukaryotic organisms. (credit: modification of work by Eric Gaba)

Scientists continue to use analysis of RNA, DNA, and proteins to determine how organisms are related. One interesting, and complicating, discovery is that of horizontal gene transfer—when a gene of one species is absorbed into another organism’s genome. Horizontal gene transfer is especially common in microorganisms and can make it difficult to determine how organisms are evolutionarily related. Consequently, some scientists now think in terms of “webs of life” rather than “trees of life.”

Think about It

  • In modern taxonomy, how do scientists determine how closely two organisms are related?

Naming Microbes




Bergey’s Manuals


Think about It


Same Name, Different Strain

Within one species of microorganism, there can be several subtypes called strains. While different strains may be nearly identical genetically, they can have very different attributes. The bacterium Escherichia coli is infamous for causing food poisoning and traveler’s diarrhea. However, there are actually many different strains of E. coli, and they vary in their ability to cause disease.



Learn more about phylogenetic trees by exploring the Wellcome Trust’s interactive Tree of Life. The website contains information, photos, and animations about many different organisms. Select two organisms to see how they are evolutionarily related.

Key Concepts and Summary


Multiple Choice

Which of the following was NOT a kingdom in Linnaeus’s taxonomy?

  1. animal
  2. mineral
  3. protist
  4. plant

Which of the following is a correct usage of binomial nomenclature?

  1. Homo Sapiens
  2. homo sapiens
  3. Homo sapiens
  4. Homo Sapiens

Which scientist proposed adding a kingdom for protists?

  1. Carolus Linnaeus
  2. Carl Woese
  3. Robert Whittaker
  4. Ernst Haeckel

Which of the following is NOT a domain in Woese and Fox’s phylogenetic tree?

  1. Plantae
  2. Bacteria
  3. Archaea
  4. Eukarya

Which of the following is the standard resource for identifying bacteria?

  1. Systema Naturae
  2. Bergey’s Manual of Determinative Bacteriology
  3. Woese and Fox’s phylogenetic tree
  4. Haeckel’s General Morphology of Organisms

Fill in the Blank

In binomial nomenclature, an organism’s scientific name includes its ________ and __________.

Whittaker proposed adding the kingdoms ________ and ________ to his phylogenetic tree.

__________ are organisms without membrane-bound nuclei.

______ are microorganisms that are not included in phylogenetic trees because they are acellular.

Think about It

  1. What is a phylogenetic tree?
  2. Which of the five kingdoms in Whittaker’s phylogenetic tree are prokaryotic, and which are eukaryotic?
  3. What molecule did Woese and Fox use to construct their phylogenetic tree?
  4. Name some techniques that can be used to identify and differentiate species of bacteria.
  5. Why is using binomial nomenclature more useful than using common names?
  6. Label the three Domains found on modern phylogenetic trees.

The phylogenetic Tree of Life. A drawing of branching lines. The central line at the bottom branches into two main branches. On the left branch is a purple branch that contains the following sub-branches: Green filamentous bacteria, Gram positives, Cyanobacteria, Proteobacteria, and Spirocheres. The branch to the right subdivides into a red and a brown branch. The brown branch contains the following sub-branches: Smile molds, Plants, Fungi and Animals. The red branch contains the following sub-branches: Thermoproteus, Methanococcus, Methanobacterium, and Halophiles.