Prokaryotes I – Background Reading

Prokaryotes are single-celled organisms of Domain Bacteria and Domain Archaea. They are generally small, typically 0.2-5.0mm, although larger prokaryotic cells exist. Their cells have the four components shared by all cells – plasma membrane, cytosol, DNA, and ribosomes. However, they lack nuclei and other membrane-bound organelles. Other cell structures may be present. For example, fimbriae, which allow attachment to other cells or the substrate, are present in many proteobacteria, while some cyanobacteria have gas vacuoles for buoyancy control.

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Comparison of prokaryotic and eukaryotic cells. Not to scale. 
(image credit: NCBI, public domain)
Comparison of eukaryotic and prokaryotic cells.
NCBI, public domain.

Prokaryotes are a critical component of all ecosystems. They are present in soil, in the oceans, and in freshwater environments. Additionally, a significant number of species are symbiotic, meaning they live in close association with other organisms. Humans have trillions of prokaryotic cells living on and in them. Some prokaryotes are mutualists, beneficial to their host, others are commensal, and many are parasitic, living at the expense of their host organism. Some parasitic bacteria are pathogens, or disease-causing agents.

Types of Symbiosis
MutualismBoth partners benefit from the interaction
CommensalismOne partner benefits; the other is unaffected by the interaction
ParasitismOne partner benefits; the other is harmed by the interaction

Prokaryotes play a crucial role in nutrient cycling. The carbon cycle is dependent on fixation of carbon dioxide from the atmosphere, which is mainly accomplished by photosynthetic prokaryotes and eukaryotes. Carbon dioxide is returned to the atmosphere by decomposition of organic matter by decomposers, which are mainly bacteria and fungi. Prokaryotes are also essential to the nitrogen cycle. Nitrogen-fixing bacteria, for example, transform atmospheric nitrogen into ammonia, which can then be used by plants.

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Phylogenetic tree showing relationships of the three Domains
Phylogenetic relationships of the three domains of life.
Melissa Hardy, public domain.

Prokaryote Evolution

Prokaryotes were the first organisms to live on earth. The fossil record indicates that they were present at least 3.5 billion years ago, although geochemical evidence suggests that they may have evolved much earlier.

Biologists classify life according to characteristics thought to be shared due to common ancestry. The largest and most inclusive taxonomic rank is called a Domain. Two of the three domains of life – Bacteria and Archaea – are comprised of prokaryotes. The third, Eukarya, includes organisms with eukaryotic cells, and will be considered in later labs.

Bacteria and Archaea are both considered to be prokaryotes, and share some morphological characteristics. However, they are genetically and biochemically distinct.


Bacteria are extremely diverse. There are many different groups of bacteria, including large clades that are known only from environmental sequencing. We will consider some of the major clades this week and next: proteobacteria, spirochetes, gram-positive bacteria, and cyanobacteria. Bacteria come in many shapes, but the three most common are cocci (spherical), bacilli(rod-shaped), and spirilli (spiral-shaped).

Common prokaryotic shapes. (a) cocci, or spherical (a pair is shown); (b) bacilli, or rod-shaped; and (c) spirilli, or spiral-shaped. (credit a: modification of work by Janice Haney Carr, Dr. Richard Facklam, CDC; credit c: modification of work by Dr. David Cox; scale-bar data from Matt Russell). From OpenStax Biology 2e, CC BY 4.0.


Archaea are considered a unique Domain of life, along with Bacteria and Eukarya. They were originally classified as bacteria, but reclassified as a separated domain based on information obtained from DNA sequencing and careful observation of cellular structure. The classification of Archaea is an ongoing and difficult endeavor. It is complicated by the fact that most Archaea cannot be cultured in a laboratory setting, and are only known from environmental DNA sequencing. However, today we will be working with an archeon that is easy to culture – Halobacterium sp.

Many Archaea are extremophiles, living in environments that are hostile to most organisms. These include thermophiles, which tolerate high temperatures, halophiles, which inhabit environments with high salinity, and acidophiles, which live in highly acidic conditions. Not all Archaea, however, are extremophiles. They are also found in soil, the ocean, and inside other organisms. Like bacteria, some are mutualists or commensals. No known Archaea are parasites, although there may be undiscovered archaeal parasites.


One of the lab exercises you will complete is to test prokaryotes from the environment for antibiotic resistance. Many species of prokaryotes have evolved resistance to antibiotics. To quickly review, recall that evolution is impossible without genetic variation. Genes can exist in multiple versions, or alleles. All variation is ultimately derived from mutation, which is random with respect to fitness. Different alleles can be inherited from a parent or, in the case of prokaryotes, transmitted by horizontal gene transfer.

Selection sorts this genetic variation. Alleles that are favorable – in other words, that confer a benefit in terms of survival or reproduction – persist and are present at higher frequencies in subsequent generations. On the other hand, unfavorable alleles will decrease in frequency over time and perhaps eventually be eliminated from the population.

Penicillin was discovered in 1928 by Alexander Fleming, and has been widely used to fight infection in humans and animals since the 1940s. Alleles that confer antibiotic resistance were present in bacterial populations before the use of penicillin. Widespread antibiotic use selected for bacteria with these alleles, increasing their frequency in the population. Today, antibiotic resistance is a major threat to public health.