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Introduction to Prokaryotes

Introduction to Bacterial and Archaeal Diversity

Perhaps bacteria may tentatively be regarded as biochemical experiments; owing to their relatively small size and rapid growth, variations must arise much more frequently than in more differentiated forms of life, and they can in addition afford to occupy more precarious positions in natural economy than larger organisms with more exacting requirements.

-Marjory Stephenson, in Bacterial Metabolism, (1930)

Prokaryotes are single celled organisms that have neither a distinct nucleus with a membrane nor other organelles. They are composed of two distinct groups of organisms: bacteria and archaea. In recent years, the term prokaryote has fallen out of favor for many microbiologists. The reason is that while bacteria and archaea share many morphological characteristics, they represent evolutionary distinct domains of life. The figure below shows a simple evolutionary tree with the three main domains of life: bacteria, archaea, and eukaryota. Some instructors in BIS2A will continue to use the term "prokaryote" when describing the morphological characteristics of the organism, but use the terms "bacteria" and "archaea" when discussing the unique characteristics of these two domains of life.

Although Bacteria and Archaea are both described as prokaryotes, they have been placed in separate domains of life. An ancestor of modern Archaea is believed to have given rise to Eukarya, the third domain of life. Archaeal and bacterial phyla are shown; the evolutionary relationship between these phyla is still open to debate.

Although bacteria and archaea share many morphological, structural and metabolic attributes, there are numerous differences between the organisms in these two clades. The most notable differences are in the chemical structure and compositions of membrane lipids (see Module 10.1), the chemical composition of the cell wall, and the make-up of the information processing machinery (e.g. replication, DNA repair, transcription).

Bacterial and Archaeal Diversity

Bacteria and Archaea were on Earth long before multicellular life appeared. They are ubiquitous and are highly diverse in their metabolic activities. This diversity allows different species within these clades to inhabit every imaginable surface where there is sufficient moisture. For example, in the typical human body, bacterial cells outnumber human body cells by about ten to one. Indeed, bacteria and archaea comprise the majority of living things in all ecosystems. Bacterial and archaeal species have been identified that thrive in environments that are inhospitable for most other living things. Bacteria and archaea, along with microbial eukaryotes, are also critical for recycling the nutrients essential for creating new biomolecules. They also drive the evolution of new ecosystems, some of which are natural and others man-made.

The First Inhabitants of Earth

When and where did life begin? What were the conditions on Earth when life began? Based on the fossil record, LUCA, Last Universal Common Ancestor, was the predecessor to bacteria and archaea. While we don't know what these organsims were like genetically, we do know that they had no true nucleus and were morphologically similar to bacteria and archaea. They were the first forms of life on Earth and they existed for billions of years before plants and animals appeared. The Earth and its moon are thought to be about 4.54 billion years old. This estimate is based on evidence from radiometric dating of meteorite material, together with other substrate material from Earth and the moon. Early Earth had a very different atmosphere (contained less molecular oxygen) than it does today and was subjected to strong radiation; thus, the first organisms would have flourished in areas where they were more protected, such as in ocean depths or beneath the surface of the Earth. During this time period, strong volcanic activity was common on Earth, so it is likely that these first organisms were adapted to very high temperatures. Early Earth was also bombarded with mutagenic radiation from the sun. The first organisms needed to be able to withstand all these harsh conditions.

Note: The Evolution of Bacteria and Archaea

How do scientists answer questions about the evolution of bacteria and archaea? Unlike with animals, artifacts in the fossil record of bacteria and archaea offer very little information. Fossils of ancient bacteria and archaea look like tiny bubbles in rock. Some scientists turn to genetics and to the principle of the molecular clock, which holds that the more recently two species have diverged, the more similar their genes (and thus proteins) will be. Conversely, species that diverged long ago will have more genes that are dissimilar.

Scientists at the NASA Astrobiology Institute and at the European Molecular Biology Laboratory collaborated to analyze the molecular evolution of 32 specific proteins common to 72 species of bacteria.1 The model they derived from their data indicates that three important groups of bacteria—Actinobacteria, Deinococcus, and Cyanobacteria (which the authors call Terrabacteria)—were the first to colonize land. Deinococcus is a bacterium that is highly resistant to dessication. Cyanobacteria are photosynthesizers, while Actinobacteria are a group of very common bacteria that include species important in decomposition of organic wastes.

The timelines of divergence suggest that bacteria (members of the domain Bacteria) diverged from common ancestral species between 2.5 and 3.2 billion years ago, whereas archaea diverged earlier: between 3.1 and 4.1 billion years ago. Eukarya diverged off the Archaean line later. Furthermore, there were bacteria able to grow in the anoxic environment that existed prior to the advent of cyanobacteria (about 2.6 billion years ago). These bacteria needed to be resistance to drying and to possess compounds that protect the organism from UV light. It has been proposed that the emergence of cyanobacteria with its ability to conduct photosynthesis and produce oxygen, as well as the ozone (O3) that is derived from O2, and protects us from most of the sun's UV rays) was a key event in the evolution of life on earth.

Microbial Mats

Microbial mats or large biofilms may represent the earliest forms of life on Earth; there is fossil evidence of their presence starting about 3.5 billion years ago. A microbial mat is a multi-layered sheet of microbes composed mostly of bacteria, but that may also include archaea. Microbial mats are a few centimeters thick and they typically grow at the interface between two materials, mostly on moist surfaces. Organisms in a microbial mat are held together by a glue-like sticky substance that they secrete, called extracellular matrix. The species within the mat carry out different metabolic activities depending on their environment. As a result, microbial mats have been identified that have different textures and colors reflecting the mat composition and the metabolic activities conducted by the microorganisms that make up the mat.

The first microbial mats likely obtained their energy from chemicals found near hydrothermal vents. A hydrothermal vent is a breakage or fissure in the Earth’s surface that releases geothermally heated water. With the evolution of photosynthesis about 3 billion years ago, some organisms in microbial mats came to use a more widely available energy source — sunlight — whereas others were still dependent on chemicals from hydrothermal vents for energy and food.

This (a) microbial mat, about one meter in diameter, grows over a hydrothermal vent in the Pacific Ocean in a region known as the “Pacific Ring of Fire.” The mat helps retain microbial nutrients. Chimneys such as the one indicated by the arrow allow gases to escape. (b) In this micrograph, bacteria within a mat are visualized using fluorescence microscopy. (credit a: modification of work by Dr. Bob Embley, NOAA PMEL, Chief Scientist; credit b: modification of work by Ricardo Murga, Rodney Donlan, CDC; scale-bar data from Matt Russell)


Fossilized microbial mats represent the earliest record of life on Earth. A stromatolite is a sedimentary structure formed when minerals precipitate out of water by organisms in a microbial mat. Stromatolites form layered rocks made of carbonate or silicate. Although most stromatolites are artifacts from the past, there are places on Earth where stromatolites are still forming. For example, growing stromatolites have been found in the Anza-Borrego Desert State Park in San Diego County, California.

(a) These living stromatolites are located in Shark Bay, Australia. (b) These fossilized stromatolites, found in Glacier National Park, Montana, are nearly 1.5 billion years old. (credit a: Robert Young; credit b: P. Carrara, NPS)

The Ancient Atmosphere

Evidence indicates that during the first two billion years of Earth’s existence, the atmosphere was anoxic, meaning that there was no molecular oxygen. Therefore, only those organisms that can grow without oxygen — anaerobic organisms — were able to live. Autotrophic organisms that convert solar energy into chemical energy are called phototrophs, and they appeared within one billion years of the formation of Earth. Then, cyanobacteria, also known as blue-green algae, evolved from these simple phototrophs one billion years later. Cyanobacteria began the oxygenation of the atmosphere. Increased atmospheric oxygen allowed the development of more efficient O2-utilizing catabolic pathways. It also opened up the land to increased colonization, because some O2 is converted into O3 (ozone) and ozone effectively absorbs the ultraviolet light that would otherwise cause lethal mutations in DNA. Ultimately, the increase in O2 concentrations allowed the evolution of other life forms.

Bacteria and Archaea Are Adaptable: Life in Moderate and Extreme Environments

Some organisms have developed strategies that allow them to survive harsh conditions. Bacteria and archaea thrive in a vast array of environments: some grow in conditions that would seem very normal to us, whereas others are able to thrive and grow under conditions that would kill a plant or an animal. Almost all bacteria and archaea have some form of a cell wall, a protective structure that allows them to survive in both hyper- and hypo-osmotic conditions. Some soil bacteria are able to form endospores that resist heat and drought, thereby allowing the organism to survive until more favorable conditions recur. These adaptations, along with others, allow bacteria to be the most abundant life form in all terrestrial and aquatic ecosystems.

Some bacteria and archaea are adapted to grow under extreme conditions and are called extremophiles, meaning “lovers of extremes.” Extremophiles have been found in all kinds of environments: the depth of the oceans, hot springs, the Arctic and the Antarctic, in very dry places, deep inside Earth, in harsh chemical environments, and in high radiation environments, just to mention a few. These organisms give us a better understanding of prokaryotic diversity and open up the possibility of finding new prokaryotic species that may lead to the discovery of new therapeutic drugs or have industrial applications. Because they have specialized adaptations that allow them to live in extreme conditions, many extremophiles cannot survive in moderate environments. There are many different groups of extremophiles. They are categorized based on the conditions in which they grow best, and several habitats are extreme in multiple ways. For example, a soda lake is both salty and alkaline, so organisms that live in a soda lake must be both alkaliphiles and halophiles Table 1.  

Table 1: Extremophiles and Their Preferred Conditions
Extremophile Type Conditions for Optimal Growth
Acidophiles   pH 3 or below
Alkaliphiles   pH 9 or above
Thermophiles   Temperature 60–80 °C (140–176 °F)
Hyperthermophiles   Temperature 80–122 °C (176–250 °F)
Psychrophiles   Temperature of -15 °C (5 °F) or lower
Halophiles   Salt concentration of at least 0.2 M
Osmophiles   High sugar concentration

Deinococcus radiodurans, visualized in this false color transmission electron micrograph, is a bacterium that can tolerate very high doses of ionizing radiation. It has developed DNA repair mechanisms that allow it to reconstruct its chromosome even if it has been broken into hundreds of pieces by radiation or heat. (credit: modification of work by Michael Daly; scale-bar data from Matt Russell)


1. Battistuzzi, FU, Feijao, A, and Hedges, SB. A genomic timescale of prokaryote evolution: Insights into the origin of methanogenesis, phototrophy, and the colonization of land. BioMed Central: Evolutionary Biology 4 (2004): 44, doi:10.1186/1471-2148-4-44.

Cellular Structure of Bacteria and Archaea

In this section we will discuss the basic structural features of both bacteria and archaea. There are many structural, morphological and physiological similarities between bacteria and archaea. As discussed in the previous section, these microbes inhabit many ecological niches and carry out a great diversity of biochemical and metabolic processes. Both bacteria and archaea lack a membrane-bound nucleus and membrane-bound organelles which are hallmarks of eukaryotes. 

While bacteria and archaea are separate domains, morphologically they share a number of structural features. As a result, they face similar problems, such as the transport of nutrients into the cell, the removal of waste material from the cell, and the need to respond to rapid local environmental changes. In this section, we will focus on how their common cell structure allows them to thrive in various environments and simultaneously puts constraints on them. One of the biggest constraints is related to cell size. 

Although bacteria and archaea come in a variety of shapes, the most common three shapes are as follows: cocci (spherical), bacilli (rod-shaped), and spirilli (spiral-shaped) (figure below). Both bacteria and archaea are generally small compared to typical eukaryotes. For example, most bacteria tend to be on the order of 0.2 to 1.0 micrometers (µm) in diameter and 1-10 µm in length. However, there are exceptions. Epulopiscium fishelsoni is a bacillus-shaped bacterium that is typically 80 µm in diameter and 200-600 µm long. Thiomargarita namibiensis is a spherical bacterium between 100 and 750 µm in diameter, which is visible to the naked eye. For comparison, a typical human neutrophil is approximately 50 µm in diameter.

A thought question:

One question that comes to mind is: why are bacteria and archaea typically so small? What are the constraints that keep them microscopic? How could bacteria such as Epulopiscium fishelsoni and Thiomargarita namibiensis overcome these constraints? Think of possible explanations or hypotheses that might explain this phenomena. We'll explore and develop an understanding of this question in more detail below and in class.

The Bacterial and Archaeal Cell: common structures

Introduction the basic cell structure

Bacteria and archaea are unicellular organisms, which lack internal membrane-bound structures that are disconnected from the plasma membrane, a phospholipid membrane that defines the boundary between the inside and outside of the cell. In bacteria and archaea, the cytoplasmic membrane also contains all membrane-bound reactions, including the electron transport chain, ATP synthase, and photosynthesis. By definition, these cells lack a nucleus. Instead, their genetic material is located in a defined area of the cell called the nucleoid. The bacterial and archaeal chromosome is often a single covalently closed circular double stranded DNA molecule. However, some bacteria have linear chromosomes and some bacteria and archaea have more than one chromosome or small non-essential circular replicating elements of DNA called plasmids. Besides the nucleoid, the next common feature is the cytoplasm (or cytosol), the "aqueous" jelly-like region encompassing the internal portion of the cell. The cytoplasm is where the soluble (non-membrane associated reactions) occur and contains the ribosomes, the protein-RNA complex where proteins are synthesized. Many prokaryotes have more than one cell membrane- and outer an inner membrane. The outer membrane often includes large pores that are large enough allow "goodies" such as sugars and amino acids drift into the intermembrane space. The inner membrane does not include these pores, and we'll discuss transport across these membranes in a later section. Finally, many bacteria and archaea also have cell walls, the rigid structural feature surrounding the plasma membrane that helps provide protection and constrain the cell shape. You should learn to create a simple sketch of a general bacterial or archaeal cell from memory.

 The features of a typical prokaryotic cell are shown.

Constraints on the bacterial and archaeal cell

One common, almost universal feature of bacteria and archaea is that they are small, microscopic to be be exact. Even the two examples given as exceptions, Epulopiscium fishelsoni and Thiomargarita namibiensis still face the basic constraints all bacteria and archaea face; they simply found unique strategies around the problem. So what is the largest constraint when it comes to dealing with the size of bacteria and archaea? Think about what the cell must do to survive.

Some basic requirements

So what do cells have to do to survive? They need to transform energy into a usable form. This involves making ATP, maintaining an energized membrane, and maintaining productive NAD+/NADH2 ratios. Cells also need to be able to synthesize the appropriate macromolecules (proteins, lipids, polysaccharides etc) and other cellular structural components. To do this, they need to be able to either make the core key precursors for more complex molecules or get them from the environment. Even if they are autotrophs, they still need to obtain their basic building materials from their environment.

Diffusion and its importance to bacteria and archaea

Movement by diffusion is passive and proceeds down the concentration gradient. For compounds to move from the outside to the inside of the cell, the compound must be able to cross the phospholipid bilayer. If the concentration of a substance is lower inside the cell than outside and it has chemical properties that allow it to move across the cell membrane, that compound will energetically tend to move into the cell. Nonpolar substances like CO2 can easily diffuse across a cell's membrane- we'll deal with more difficult substances in the next reading.

Diffusion can also used to get rid of some waste materials. As waste products accumulate inside the cell, their concentration rises compared to the outside environment and the waste product can leave the cell. Movement within the cell works the same way, compounds will move down their concentration gradient, away from where they are synthesized to places where their concentration is low and therefore may be needed. Since diffusion is a random process - the ability of two different compounds or reactants for chemical reactions to interact becomes a meeting of chance. In small confined spaces, random interactions or collisions occur more frequently than in large spaces. Keep in mind that prokaryotes are extremely small!

The ability of a compound to diffuse is dependent upon the viscosity of the solvent. For example, it is a lot easier for you to move around in air than in water (think about moving around underwater in a pool). Likewise, it is easier for you to swim in a pool of water than in a pool filled with peanut butter. If you put a drop of food coloring into a glass of water, it quickly diffuses until the entire glass has changed color. Now what do you think would happen if you put that same drop of food coloring into a glass of corn syrup (very viscus and sticky)? It will take a lot longer for the glass of corn syrup to change color.

The relevance of these examples is to note that the cytoplasm tends to be very viscous. It contains many proteins, metabolites, small molecules, etc. and has a viscosity more like corn syrup than water. So, diffusion in cells is slower and more limited than you might have originally expected. Therefore, if cells rely on solely on diffusion to move compounds around what do you think happens to the efficiency of these processes as cells increase in size and their internal volumes get bigger? Is there a potential problem to getting big that is related to the process of diffusion? 

So how do cells get bigger?

As you've likely concluded from the discussion above, cells that rely on diffusion to move things around the cell - like bacteria and archaea - size does matter. So how do you suppose Epulopiscium fishelsoni and Thiomargarita namibiensis got so big? Take a look at these links and see what these bacteria look like morphologically and structurally. Epulopiscium fishelsoni and Epulopiscium fishelsoni and Thiomargarita namibiensis

Based on what we have just discussed, in order for cells to get bigger, that is, for their volume to increase, intracellular transport must somehow become less dependent on diffusion. One of the great evolutionary leaps was the ability of cells (eukaryotic cells) to transport materials- particularly very large materials that essentially do not diffuse- around the cell. Compartmentalization also provided a way to localize processes to smaller organelles, which overcame another problem caused by the large size. Compartmentalization and the complex intracellular transport systems have allowed eukaryotic cells to become very large in comparison to the diffusion-limited bacterial and archaeal cells. We'll discuss specific solutions to these challenges in later sections.