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 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.

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 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.

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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 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 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 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.

Figure 2. 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)

Stromatolites

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.

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)

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 Artic 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. 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 .

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)

Footnotes

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.