Microbiology, Lec. 5

Our next goal is to gain a broad understanding of the diversity and classification of microorganisms. We will learn the major groups of Bacteria, Archaea and Eukaryotic microbes so that as the course goes on we can place all of the microbes that we talk about into these groups.

Let's start by thinking about the relationship between evolution and classification. It is the goal of systematic biologists to develop classification schemes that reflect true (evolutionary) relatedness among organisms. Such phylogenetic systems not only make organizing all of life a lot easier but they also can have profound practical implications. For example, if you discovered a new bacterium, wouldn't you want to know if it were closely related to a deadly pathogen?

One big problem with microbial systematics is that many microbes (especially bacteria) look alike. We discussed some of the biophysical reasons for this last week but for now just believe me that one rod-shaped bacterium looks pretty much like another under the microscope! With this in mind, let's take a brief journey through the history of microbial systematics. A little after the time of Leeuwenhoek (see lec. 2), a botanist named Linnaeus was attempting to classify all living things. In his 1759 treatise he divided the world into Animal, Vegetable and Mineral and named all organisms that he knew of using the binomial (Genus species) system that we still use today. Obviously not much was known about microbes at that time so Linnaeus gave up in frustration and put all microscopic life into one genus, Chaos!

In the next 100 years enough progress had been made in microbiology so that E. Haeckel at least gave microbes some credit....show 1866 tree (Plants, Animals and Protists=bacteria, fungi, protozoa).

Let's jump another 100 years to 1969 when Whittaker and others introduced the 5 kingdom system for classifying all life (Plants, Animals, Fungi, Protists and Bacteria). This system was based mostly on the 3 main modes of nutrition: photosynthesis, absorption, and ingestion...... draw foot tree. This "tree" of life has been widely accepted but it is no longer believed to be phylogenetically correct and it it implies that all prokaryotes are all closely related to one another (simply because they are small and have simple morphologies) and it also implies that microbes are primitive and haven't been evolving along with everybody else......

Fortunately, there has been a great deal of progress in the last 20 years in classifying microorganisms. Microbiologists have long known that the morphology of a bacterium is not a good character to use in classifying them. The most progress has been made using methods that compare the sequences of bases in DNA or the sequence of monomers in macromolecules coded for by DNA. Many such molecules have been sequenced and a few are now used to classify microbes. Perhaps the most useful sequences have been those of rRNA. This molecule occurs in all forms of life and different parts of it's sequence are thought to have changed at different rates over evolutionary time.

For classifying bacteria we usually compare the sequence of the 16S region of the ribosome of an unknown critter with a data base of sequences from known organisms. Most of the classification scheme given in your book is based on 16S sequences (or 18S in Eukaryotes). There are also a number of other approaches to microbial classification that support the phylogenetic scheme we will discuss in this class. You will also get to use some of these commonly used diagnostic tests in the laboratory part of this course.

Before we get down to specific groups of microbes let's see what sort of tree that sequencing gives for all of life on earth....

Show tree

3 domains of life:



Eucarya = Eukaryotes (including the fungi, protozoa etc.)

Closer look at the differences among the 3 Domains...

Table 19.8 in your book show some of the main differential characteristics of the 3 Domains. Note that the Bacteria and Archaea share certain characteristics - mainly because they both lack certain features of eukaryotic cells (e.g. nucleus, mitochondrion). But also note that Eucarya and Archaea share certain characteristics including:

1) similar RNA polymerases

2) immunity to many well known antibiotics that affect most Bacteria (including rifamycin, which binds to bacterial RNA polymerases, but not to those of Archaea and Eucarya),

3) similar methods of transcribing proteins (e.g. diphtheria exotoxin inhibits protein synthesis in Archaea and Eucarya but not in Bacteria),

4) similar ATPases

The 16S/18S phylogenetic tree (Fig. 19.3) also supports the idea that the Eucarya and Archaea are more closely related than the Eucarya and Bacteria. Note that the initial (deepest) branch of the tree leads to the Bacteria on one side and the Archaea and Eucarya on the other. As long as we have the tree up let's examine a few other ideas. First is the idea that the earth was hot when life evolved. This theory is supported by the fact that some of the deepest divergences in the Bacteria and Archaea are thermophilic organisms (therm = Gr. for heat; philo = Gr. for love) and that thermophiles exist in all of the major lineages of life (e.g., there are many thermophilic fungi).

Another idea that has been supported by 16S rRNA phylogenies is the endosymbiotic theory (put forth mostly by Lynn Margulis). This theory states that mitochondria and chloroplasts are the descendants of ancient bacteria that were incorporated into the cytoplasm of an ancestor of modern eukaryotic organisms (perhaps a relative of the modern Archaea). As it turns out these organelles have their own ribosomes and simple chromosomes. When the 16S rRNA of these organelles is sequenced and compared to all known sequences - the mitochondria end up being classified in the Proteobacteria (a big group within the Bacteria) and the chloroplasts end up in the Cyanobacteria. In other words, these organelles are actually bacteria that have been living quite happily as endosymbionts in eukaryotic organism for millions of years!

Before we get too deeply into the groups of microbes let's review some physiological groupings that we will use in addition to our 16S phylogenies.

Heterotrophs - use organic carbon compounds as their carbon and energy sources (we are heterotrophs as are the fungi and many bacteria).

Autotrophs can fix carbon dioxide (CO2) from the air and turn it into organic molecules.

Photoautotrophs use light energy to do this (plants, cyanobacteria and many other bacteria are photoautotrophs).

Chemoautotrophs use chemical energy to fix CO2 (e.g. sulfur oxidizing bacteria and nitrifiers are chemoautotrophs).

I will also be discussing anaerobes and aerobes (see lec. 2) - facultative anaerobes are organisms that can grow anaerobically or aerobically. Anaerobic organisms use several different physiological ways of making a living, including fermentation reactions and anaerobic respiration, the details of which we will explore in a few weeks.



Proteobacteria (ch. 22) (= Purple Bacteria)

The Proteobacteria are a huge group of organisms with as much metabolic diversity as the Plants and Animals combined. Taxonomy of this huge group is still in a state of flux so we will present them as functional groups with reference to where each genus fits into the Alpha, Beta, Gamma, or Delta Proteobacteria.

Gamma Proteobacteria:

Bacteria in this group include some of the most common human pathogens and bacteria of economic importance.

Let's start with the Gamma Proteobacteria that are fermentative (facultative anaerobes)

Enteric Bacteria (enter = Gr. for gut), Table 19.2 shows some common genera of Enteric Bacteria (Enterobacteriaceae). Note that the habitat for most of them is indeed in the intestines of some sort of animal.

Some Famous genera:

Salmonella (S. typhi causes typhoid fever)

Escherichia (E. coli)

Shigella (S. dysenteriae is closely related to E. coli)

Yersinia (Y. pestis causes plague)

Klebsiella (fixes N2 and can cause pneumonia)


Erwinia (live on plants - some plant pathogens)

Table 22.7 and Fig. 22.27 show some of the common tests for distinguishing between these and other enteric genera (you will do some of these tests in lab).

Other fermentative Gammas include the genera Vibrio (vib = L. for whip mark), Photobacterium (bioluminescent) and Aeromonas (includes fish pathogens).

One common attribute of most of the facultative anaerobes is that they are capable of living dual lives. For example, many bioluminescent bacteria can use their anaerobic capabilities to live in the guts of fish and their aerobic abilities to live in the light organs of fish or to survive in the aerobic waters of the open oceans.

show pictures of bioluminescent Bacteria and Fungi....

Gamma Proteobacteria (cont.)

Strict Aerobes or oxidative Gamma Proteobacteria (can't ferment organic compounds)

Sulfur Oxidizers

Beggiatoa (gliding motility)

Thioploca large (15 - 40 Ám wide) relative of Beggiatoa that form huge mats off the coast of Chile (see Fossing et al. 1995. Nature vol. 374: 713 - 715)

Thiothrix (sheathed sulfur oxidizer)

discuss gradient cultures for Beggiatoa (see Hagen, K.D. and D.C. Nelson. 1996. Appl. Environ. Microbiol. 62: 947-953.)


Pseudomonas - polar flagella and oxidase positive.
A very large genus that is now being broken up into many different genera.

Fluorescent Pseudomonads

P. putida
P. aeruginosa (flowers and burn patients)

fluorescent pigments are iron chelating compounds (siderophores)
discuss difference between fluorescence and bioluminescence