Prokaryotes: Bacteria & Archaea

Learning Objectives

  1. Differentiate between Bacteria, Archaea, and Eukarya
  2. Draw and recognize the phylogenetic relationships between Bacteria, Archaea, and Eukarya
  3. Define horizontal gene transfer and explain the challenges presented by horizontal gene transfer for phylogenetic classification of prokaryotes
  4. Identify ways that Archaea and Bacteria get energy and carbon, and use this information to classify example organisms as photo-, chemo-, auto-, and/or hetero-trophs
  5. Identify the fossil, chemical, and genetic evidence for key events for evolution of the three domains of life (Bacteria, Archaea, and Eukarya)
  6. Explain why the flourishing of cyanobacteria led to the oxygenation of the atmosphere.
  7. Place the evolution of the three domains of life on the geologic time scale
  8. Describe the importance of prokaryotes (Bacteria and Archaea) with respect to human health and environmental processes

Three Domains of Life on Earth

DNA sequence comparisons and structural and biochemical comparisons consistently categorize all living organisms into 3 primary domains: Bacteria, Archaea, and Eukarya (also called Eukaryotes; these terms can be used interchangeably). Both Bacteria and Archaea are prokaryotes, single-celled microorganisms with no nuclei, and Eukarya includes us and all other animals, plants, fungi, and single-celled protists; all Eukarya are organisms whose cells have nuclei to enclose their DNA apart from the rest of the cell. The fossil record indicates that the first living organisms were prokaryotes (Bacteria and Archaea), and eukaryotes arose a billion years later.

Study Tip: It is suggested that you create a chart to compare and contrast the three domains of life as you read.

The information below was adapted from OpenStax Biology 22.2

Archaea and Bacteria share a number of features with each other, but they are also distinct domains of life:

  • Both Archaea and Bacteria are unicellular organisms. In contrast, eukaryotes include both unicellular and multicellular organisms.
  • Archaea and bacterial cells lack organelles or other internal membrane-bound structures; unlike eukaryotes, archaea and bacteria do not have a nucleus separating their genetic material from the rest of the cell.
  • Archaea and Bacteria generally have a single circular chromosome: a piece of circular, double-stranded DNA located in an area of the cell called the nucleoid. In contrast, many eukaryotes have multiple, linear chromosomes. (Note that DNA genomes are always composed of double-stranded DNA molecules, whether they are circular or linear chromosomes.)
  • Archaea and Bacteria reproduce asexually through binary fission, a process where an individual cell reproduces its single chromosome and splits in two. In contrast, eukaryotes reproduce asexually through mitosis, which includes additional steps for replicating and correctly dividing multiple chromosomes between two daughter cells. Many eukaryotes also reproduce sexually, where a process called meiosis reduces the number of chromosome by half to produce haploid cells (typically called sperm or eggs), and then two haploid cells fuse to create a new organism. Archaea and bacteria cannot reproduce sexually.
  • Archaea and Bacteria can share genomic information between individual cells which result in a phenomenon called horizontal gene transfer, also called lateral gene transfer. (Horizontal gene transfer is in contrast to vertical gene transfer, which is where offspring inherit genetic information from a parent as a result of reproduction). Horizontal gene transfer occurs when an cell acquires DNA from an external source, and it results in shared DNA between individuals that may not be genetically related. Horizontal gene transfer is the primary way that antibiotic resistance spreads through microbial populations.
  • Almost all prokaryotes have a cell wall, a protective structure that allows them to survive in extreme conditions, which is located outside of their plasma membrane. In contrast, some eukaryotes do have cell walls, while others do not. The composition of the cell wall differs significantly between the domains Bacteria and Archaea:
    • Bacterial cell walls are composed of peptidoglycan, a complex of protein and sugars. Some bacteria have an outer capsule outside the cell wall.
    • Archaeal cell walls are composed of polysaccharides (sugars).
    • The composition of their cell walls also differs from the eukaryotic cell walls found in plants (cellulose) or fungi and insects (chitin).
  • Other structures are present in some prokaryotic species, but not in others. For example:
    • The capsule found in some species enables the organism to attach to surfaces, protects it from dehydration and attack by phagocytic cells, and makes pathogens more resistant to our immune responses.
    • Some species also have flagella (singular, flagellum) used for locomotion, and pili (singular, pilus) used for attachment to surfaces.
    • Plasmids, which consist of extra-chromosomal DNA, are also present in many species of bacteria and archaea.
  • Prokaryotes, especially Archaea, can survive in extreme environments that are inhospitable for most living things.

The features of a typical prokaryotic cell are shown. Image credit: OpenStax Biology 22.2

Phylogenetic Relationships Between Archaea, Bacteria, and Eukarya

While the term prokaryote (“before-nucleus”) is widely used to describe both Archaea and Bacteria, you can see from the phylogenetic Tree of Life below that the term “prokaryote” does not describe a monophyletic group (i.e., it is impossible to draw a circle around bacteria, archaea, and their common ancestor without leaving out one of the decedents of the common ancestor):

A phylogenetic tree of living things, based on RNA data and proposed by Carl Woese, showing the separation of bacteria, archaea, and eukaryotes. By This vector version: Eric Gaba (Sting – fr:Sting) – NASA Astrobiology Institute, found in an article, Public Domain,

In fact, Archaea and Eukarya form a monophyletic group, not Archaea and Bacteria. These relationships indicate that archaea are more closely related to eukaryotes than to bacteria, even though superficially archaea appear to be much more similar to bacteria than eukaryotes.

Horizontal Gene Transfer and Prokaryotic Phylogenies

As previously discussed, genetic information is a commonly used data source to identify evolutionary relationships in phylogenetic trees. However, the prevalence of horizontal gene transfer among prokaryotes presents a challenge to using exclusively genetic approaches to resolving phylogenetic relationships among Bacteria and Archaea, because the presence of a particular gene in two different microbial species may not indicate homology but instead an instance of horizontal gene transfer. This is not to say that phylogenetic classification of prokaryotes is impossible (for example, phylogenetic analyses take advantage of genes that are less likely to be exchanged via HGT such as ribosomal gene sequences), just that some of the tools that work readily for most groups of eukaryotes do not work as well for most groups of prokaryotes.

Metabolic Diversity of Prokaryotes 

The information below was adapted from OpenStax Biology 22.3 

Because phylogenetic relationships among prokaryotes can be challenging to resolve to great details, prokaryotes are often instead classified based on metabolic and other traits. Prokaryotes have been and are able to live in every environment by using whatever energy and carbon sources are available. Prokaryotes fill many niches on Earth, including being involved in nutrient cycles such as nitrogen and carbon cycles, decomposing dead organisms, and thriving inside living organisms, including humans. This incredibly broad range of environments that prokaryotes occupy is possible because there is incredible metabolic diversity represented among different prokaryotic species. We can classify organisms by how they obtain their energy, and how they obtain their carbon:

  • Classification by source of energy:
    • Phototrophs (phototrophic organisms) obtain their energy from sunlight.
    • Chemotrophs (chemosynthetic organisms) obtain their energy from chemical compounds.
  • Classification by source of carbon:
    • Autotrophs (autotrophic organisms) are able to fix (reduce) inorganic carbon such as carbon dioxide
    • Heterotrophs (heterotrophic organisms) must obtain carbon from an organic compound

These terms can be combined to classify organisms by both energy and carbon source:

  • Photoautotrophs obtain energy from sunlight and carbon from carbon dioxide
  • Chemoheterotrophs obtain energy and carbon from an organic chemical source
  • Chemoautotrophs obtain energy from inorganic compounds, and they build their complex molecules from carbon dioxide.
  • Photoheterotrophs use light as an energy source, but require an organic carbon source; they cannot reduce (fix) carbon dioxide into organic carbon.

In contrast to the great metabolic diversity of prokaryotes, eukaryotes are only photoautotrophs (plants and some protists) or chemoheterotrophs (animals, fungi, and some protists). The table below summarizes carbon and energy sources in prokaryotes.

The videos below provide more detailed overviews of Bacteria and Archaea, including general features and metabolic diversity (please note, you can disregard the discussion on lithotrophs and organotrophs for the purposes of this course; in this course, we are using the term chemotroph to refer to all organisms that obtain energy from chemical oxidation, irrespective of whether they use organic or inorganic compounds):

Key events and Evidence in the Evolution of the Three Domains of Life on Earth

Early life on Earth: The Earth is approximately 4.6 billion years old based on radiometric dating. While it is formally possible that life arose during the Hadean eon, conditions may not have been stable enough on the planet to sustain life because large numbers of asteroids were thought to have collided with the planet during the end of the Hadean and beginning of the Archean eons.

Physical and chemical evidence suggest life arose on earth during the Archean eon: Evidence from microfossils (literally “microscopic fossils”) suggests that life was present on Earth at least 3.8 billion years ago, during the Archean. The earliest chemical evidence of life, in the form of chemical signatures produced only by living organisms, dates to approximately 3.6 billion years ago. What were these early life forms like? For the first billion years of Earth’s existence, the atmosphere was anoxic, meaning that there was no molecular oxygen (O2). Thus the first living things were single-celled, prokaryotic anaerobes (living without oxygen) and likely chemotrophic. 

The Oxygen Revolution: The evolution of water-splitting and oxygen-generating photosynthesis by cyanobacteria led to the first free molecular oxygen about 2.6 billion years ago, near the end of the Archean eon. The free oxygen produced by cyanobacteria immediately reacted with soluble iron in the oceans, causing iron oxide (rust) to precipitate out of the oceans. Oxygen didn’t accumulate all at once, and evidence indicates that the oceans weren’t fully oxygenated until 850 million years ago (Mya) near the end of the Proterozoic eon. Today we see evidence of the slow accumulation of oxygen in the atmosphere through banded iron formations present in sedimentary rocks from that period.

Banded iron formation, Karijini National Park, Western Australia. By Graeme Churchard from Bristol, UK – Dales GorgeUploaded by PDTillman, CC BY 2.0,

The increase in oxygen, called “The Oxygen Revolution,” “the Great Oxidation Event,” or the “Oxygen Catastrophe,” enabled the evolution of larger bodies and organs and tissues, such as brains, with high metabolic rates; it also resulted in mass extinction of many obligate anaerobic organisms (organisms that cannot survive in the presence of oxygen). The increase in oxygen is a dramatic example of how life can alter the planet. Evolution of oxygenic photosynthesis changed the planet’s atmosphere over billions of years, and in turn caused radical shifts in the biosphere: from an anoxic environment populated by anaerobic, single-celled prokaryotes, to eukaryotes living in a micro-aerophilic (low-oxygen) environment, to multicellular-organisms in an oxygen-rich environment. The video below provides an overview of the Oxygen Revolution (aka, the Oxygen Catastrophe), including its detrimental effects on the organisms that lived at the time:

Origins of eukaryotes: How did eukaryotes arise? The leading hypothesis, called the endosymbiotic theory, is that eukaryotes arose during the Proterozoic eon as a result of a fusion of Archaean cells with bacteria, where an ancient Archaean engulfed (but did not eat) an ancient, aerobic bacterial cell. The engulfed (endosymbiosed) bacterial cell remained within the archaean cell in what may have been a mutualistic relationship: the engulfed bacterium allowed the host archean cell to use oxygen to release energy stored in nutrients, and the host cell protected the bacterial cell from predators. Microfossil evidence suggests that eukaryotes arose sometime between 1.6 and 2.2 billion years ago during the Proterozoic. The descendants of this ancient engulfed cell are present in all eukaryotic cells today as mitochondria. We’ll discuss the endosymbiotic theory for the origin of eukaryotes more in the next reading. 

Complex multicellular life forms: Much of the life on Earth was singled celled until near the end of the Proterozoic eon, and shortly before the Cambrian “explosion,” when we see emergence of all modern animal phyla at the start of the Phanerozoic eon. The Cambrian radiation (“radiation” in this case meaning rapid evolutionary diversification) occurred approximately 542 Mya. The “explosion” term refers to an increase in biodiversity of multicellular organisms at the start of the Cambrian, 540 million years ago. Multicellular life appeared only several tens of millions of years before the start of the Cambrian, as bizarre-looking fossils (Ediacaran biota/Doushantuo fossils) and exhibiting body plans unlike anything seen present-day animals. These species largely disappeared and were replaced by Cambrian fauna, whose variety includes all of the body plans found in present-day animal phyla. The appearance of Cambrian fauna span millions of years; they did not all appear simultaneously as the term “explosion” inaccurately implies.

Placing Key Events on the Geologic Time Scale

How do each of these events map onto geologic time? Most of them are not “instantaneous” events, and they often span multiple time periods. Please note that the approximate dates below may change as research continues and new evidence is discovered surrounding these events in the origin and evolution of life on Earth:

  • Hadean eon (4.6-4 BYA): No life present on Earth
  • Archean eon (4 to 2.5 BYA)
    • Origin of life (prokaryotic, anaerobic), 3.8-2.6 BYA
    • First cyanobacteria, capable of producing oxygen through photosynthesis, ~2.5 BYA
  • Proterozoic eon (2.5 BYA to 542 MYA)
    • Oxygen revolution (or catastrophe, depending on your point of view) and formation of Banded Iron Formations, occurs over a period from 2.5 to 1.9 BYA
    • First single-celled eukaryotes, ~1.6 BYA
    • First multicellular algaes, ~1.4 BYA
    • First multicellular animals, ~635 MYA
  • Phanerozoic eon (542 MYA to present day)
    • Cambrian explosion (most major animal phyla appeared in the fossil record), 542 MYA
    • Obviously many other events occur in the Phanerozoic, and we’ll spend most of the rest of this module discussing them

Links to Human Health and Environmental Processes

The information below was adapted from OpenStax Biology 22.4 and OpenStax Biology 22.5

Some prokaryotic species can harm human health as pathogens: Devastating pathogen-borne diseases and plagues, both viral and bacterial in nature, have affected humans since the beginning of human history. In the 21st century, infectious diseases remain among the leading causes of death worldwide, despite advances made in medical research and treatments in recent decades. Of particular concern today is the increasing prevalence of antimicrobial resistance, facilitated by misuse of antibiotics and the capacity of many prokaryotes to readily share genetic information resulting in horizontal gene transfer.

But pathogenic prokaryotes represent only a very small percentage of the diversity of the microbial world. In fact, our life would not be possible without prokaryotes, and some prokaryotic species are directly beneficial to human health:

  • The bacteria that inhabit our skin and gastrointestinal tract do a host of good things for us: They protect us from pathogens, help us digest our food, and produce some of our vitamins and other nutrients. They may even help regulate our moods, influence our activity levels, and even help control weight by affecting our food choices and absorption patterns. The Human Microbiome Project has begun the process of cataloging our normal bacteria (and archaea) so we can better understand these functions. In addition, the absence of certain key microbes from our intestinal tract may set us up for a variety of problems, particularly regarding the appropriate functioning of the immune system. There are intriguing findings that suggest that the absence of these microbes is an important contributor to the development of allergies and some autoimmune disorders. Research is currently underway to test whether adding certain microbes to our internal ecosystem may help in the treatment of these problems as well as in treating some forms of autism.
  • A particularly fascinating example of our normal flora relates to our digestive systems. People who take high doses of antibiotics tend to lose many of their normal gut bacteria, allowing a naturally antibiotic-resistant species called Clostridium difficile to overgrow and cause severe gastric problems, especially chronic diarrhea. Obviously, trying to treat this problem with antibiotics only makes it worse. However, it has been successfully treated by giving the patients fecal transplants (so-called “poop pills”) from healthy donors to reestablish the normal intestinal microbial community. Clinical trials are underway to ensure the safety and effectiveness of this technique.

Carbon cycle; Image modified from “Nitrogen cycle” by Johann Dréo (CC BY-SA 3.0). The modified image is licensed under a CC BY-SA 3.0 license._

Other prokaryotes indirectly, but dramatically, impact human health through their roles in environmental processes:

  • Prokaryotes play a critical role in biogeochemical cycling of nitrogen, carbon, phosphorus, and other nutrients. The role of prokaryotes in the nitrogen cycle is especially critical to other living things. Nitrogen is part of nucleotides and amino acids that are the building blocks of nucleic acids and proteins, respectively. Nitrogen is usually the most limiting element in terrestrial ecosystems, with atmospheric nitrogen, N2, providing the largest pool of available nitrogen. However, eukaryotes cannot use atmospheric, gaseous nitrogen to synthesize macromolecules. Fortunately, nitrogen can be “fixed,” (reduced) meaning it is converted into ammonia (NH3) either biologically or abiotically. Abiotic nitrogen fixation occurs as a result of lightning or by industrial processes. Biological nitrogen fixation (BNF) is exclusively carried out by prokaryotes: soil bacteria, cyanobacteria, and Frankia spp. (filamentous bacteria interacting with actinorhizal plants such as alder, bayberry, and sweet fern). After photosynthesis, BNF is the second most important biological process on Earth.
  • Prokaryotes are also essential in microbial bioremediation, the use of prokaryotes (or microbial metabolism) to remove pollutants, such as agricultural chemicals (pesticides, fertilizers) that leach from soil into groundwater and the subsurface, and certain toxic metals and oxides, such as selenium and arsenic compounds. One of the most useful and interesting examples of the use of prokaryotes for bioremediation purposes is the cleanup of oil spills, including the Exxon Valdez spill in Alaska (1989), and more recently, the BP oil spill in the Gulf of Mexico (2010). To clean up these spills, additional inorganic nutrients that help bacteria to grow are added to the area, and the growth of bacteria breaks down the excess hydrocarbons.

a) Cleaning up oil after the Valdez spill in Alaska, workers hosed oil from beaches and then used a floating boom to corral the oil, which was finally skimmed from the water surface. Some species of bacteria are able to solubilize and degrade the oil. (b) One of the most catastrophic consequences of oil spills is the damage to fauna. (credit a: modification of work by NOAA; credit b: modification of work by GOLUBENKOV, NGO: Saving Taman; from