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Bacterial and Archaeal Diversity*

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 with neither a membrane-bound nucleus nor other lipid membrane-bound organelles. They are composed of two phylogenetically 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 nevertheless, represent evolutionarily distinct domains of life. The figure below shows a simple phylogenetic tree with the three main domains of life: Bacteria, Archaea, and Eukarya. This means that the use of the term prokaryote should not be used with the intention to group the bacteria and archaea on the basis of shared evolutionary history.  It is, however, convenient to use the term "prokaryote" when describing the groups of organisms that share the common morphological characteristics (i.e. no nucleus) and some of your instructors will likely do so.  When you hear or use the term "prokaryote", therefore, make sure that it is not being used to or implying that the bacteria and archaea are part of the same phylogenetic group. Rather make sure that the use of the term "prokaryote" is limited to describing the common physical characteristics of these two microbial groups.  


Figure 1. 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 exact 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, the chemical composition of the cell wall, and the makeup of the information processing machinery (e.g., replication, DNA repair, and transcription).

Bacterial and archaeal diversity

Bacteria and archaea were on Earth long before multicellular life appeared. They are ubiquitous and have highly diverse metabolic activities. This diversity allows different species within clades to inhabit every imaginable surface where there is sufficient moisture. For example, some estimates suggest that 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. Certain bacterial and archaeal species can thrive in environments that are inhospitable for most other life. 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 (natural or man-made).

The first inhabitants of Earth

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 Earth's surface. 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, therefore, needed to be able to withstand all these harsh conditions.

So, when and where did life begin? What were the conditions on Earth when life began?  What did LUCA (the Last Universal Common Ancestor), the predecessor to bacteria and archaea look like?  While we don't know exactly when and how life arose and what it looked like when it did, we do have a number of hypotheses based on various biological and geological data that we briefly describe below.

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 Earth's formation. Then, cyanobacteria, also known as blue-green algae, evolved from these simple phototrophs one billion years later. Cyanobacteria began oxygenating 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.


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 comparative genetics which, as its name suggests, is a domain of biology that makes quantitative comparisons of the genetic information between two or more species.  A core assumption in the field of comparative genetics is that the more recently two species have diverged, the more similar their genetic information will be. Conversely, species that diverged long ago will have more genes that are dissimilar.  Therefore, by comparing genetic sequences between organisms can shed light on their evolutionary relationships and allow scientists to create models of what the genetic makeup of the ancestors of the organisms being compared might have looked like.  

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. The model they derived from their data indicates that three important groups of bacteria—Actinobacteria, Deinococcus, and Cyanobacteria (which the authors call Terrabacteria)—were likely the first to colonize land. Organisms in the genus Deinococcus are bacteria that tend to be highly resistant to ionizing radiation. Cyanobacteria are photosynthesizers, while Actinobacteria are a group of very common bacteria that include species important in decomposition of organic wastes.

The timelines of species 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 radiation. It has been proposed that the emergence of cyanobacteria with its ability to conduct photosynthesis and produce oxygen was a key event in the evolution of life on Earth.

Microbial mats

Microbial mats (large biofilms) may be representative of the earliest visible structure formed by 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, forming an 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 harvested energy through redox reactions (discussed elsewhere) 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 depended on chemicals from hydrothermal vents for energy and food.

Figure 2. (a) This 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.”  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)


A stromatolite is a sedimentary structure formed when minerals precipitate out of water due to the metabolic activity of 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.

Figure 3. (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).

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 forms 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, such as in the depths of the oceans and the earth; in hot springs, the Artic, and the Antarctic; in very dry places; in harsh chemical environments; and in high-radiation environments, just to mention a few. These organisms help to give us a better understanding of the diversity of life and open up the possibility of finding microbial 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. Other extremophiles, like radioresistant organisms, do not prefer an extreme environment (in this case, one with high levels of radiation) but have adapted to survive in it.

Table 1. This table lists some extremophiles and their preferred conditions.

Extremophile Type Conditions for Optimal Growth
Acidophiles      pH 3 or below
Alkaliphiles      pH 9 or above
Thermophiles      Temperature of 60–80 °C (140–176 °F)
Hyperthermophiles      Temperature of 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


Figure 4. 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.