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22.1: Prokaryotic Diversity - Biology

22.1: Prokaryotic Diversity - Biology


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Skills to Develop

  • Describe the evolutionary history of prokaryotes
  • Discuss the distinguishing features of extremophiles
  • Explain why it is difficult to culture prokaryotes

Prokaryotes are ubiquitous. In the typical human body, prokaryotic cells outnumber human body cells by about ten to one. They comprise the majority of living things in all ecosystems. Some prokaryotes thrive in environments that are inhospitable for most living things. Prokaryotes recycle nutrients—essential substances (such as carbon and nitrogen)—and they drive the evolution of new ecosystems, some of which are natural and others man-made. Prokaryotes have been on Earth since long before multicellular life appeared.

Prokaryotes, the First Inhabitants of Earth

When and where did life begin? What were the conditions on Earth when life began? Prokaryotes 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 where they were more protected, such as in ocean depths or beneath the surface of the Earth. At this time too, strong volcanic activity was common on Earth, so it is likely that these first organisms—the first prokaryotes—were adapted to very high temperatures. Early Earth was prone to geological upheaval and volcanic eruption, and was subject to bombardment by mutagenic radiation from the sun. The first organisms were prokaryotes that could withstand these harsh conditions.

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 prokaryotes (Figure (PageIndex{1})) that includes mostly bacteria, but also archaea. Microbial mats are a few centimeters thick, and they typically grow where different types of materials interface, mostly on moist surfaces. The various types of prokaryotes that comprise them carry out different metabolic pathways, and that is the reason for their various colors. Prokaryotes in a microbial mat are held together by a glue-like sticky substance that they secrete called extracellular matrix.

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 prokaryotes 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.

Stromatolites

Fossilized microbial mats represent the earliest record of life on Earth. A stromatolite is a sedimentary structure formed when minerals are precipitated out of water by prokaryotes in a microbial mat (Figure (PageIndex{2})). 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.

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 (Figure (PageIndex{3})) 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.

Microbes Are Adaptable: Life in Moderate and Extreme Environments

Some organisms have developed strategies that allow them to survive harsh conditions. Prokaryotes 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 animal. Almost all prokaryotes have 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 favorable conditions recur. These adaptations, along with others, allow bacteria to be the most abundant life form in all terrestrial and aquatic ecosystems.

Other 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 ([link]), 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 identified 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 (Figure (PageIndex{4})). 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 (PageIndex{1})).

Table (PageIndex{1}): Extremophiles and Their Preferred Conditions
Extremophile TypeConditions for Optimal Growth
AcidophilespH 3 or below
AlkaliphilespH 9 or above
ThermophilesTemperature 60–80 °C (140–176 °F)
HyperthermophilesTemperature 80–122 °C (176–250 °F)
PsychrophilesTemperature of -15-10 °C (5-50 °F) or lower
HalophilesSalt concentration of at least 0.2 M
OsmophilesHigh sugar concentration

Prokaryotes in the Dead Sea

One example of a very harsh environment is the Dead Sea, a hypersaline basin that is located between Jordan and Israel. Hypersaline environments are essentially concentrated seawater. In the Dead Sea, the sodium concentration is 10 times higher than that of seawater, and the water contains high levels of magnesium (about 40 times higher than in seawater) that would be toxic to most living things. Iron, calcium, and magnesium, elements that form divalent ions (Fe2+, Ca2+, and Mg2+), produce what is commonly referred to as “hard” water. Taken together, the high concentration of divalent cations, the acidic pH (6.0), and the intense solar radiation flux make the Dead Sea a unique, and uniquely hostile, ecosystem1 (Figure (PageIndex{5})).

What sort of prokaryotes do we find in the Dead Sea? The extremely salt-tolerant bacterial mats include Halobacterium, Haloferax volcanii (which is found in other locations, not only the Dead Sea), Halorubrum sodomense, and Halobaculum gomorrense, and the archaea Haloarcula marismortui, among others.

Unculturable Prokaryotes and the Viable-but-Non-Culturable State

Microbiologists typically grow prokaryotes in the laboratory using an appropriate culture medium containing all the nutrients needed by the target organism. The medium can be liquid, broth, or solid. After an incubation time at the right temperature, there should be evidence of microbial growth (Figure (PageIndex{6})). The process of culturing bacteria is complex and is one of the greatest discoveries of modern science. German physician Robert Koch is credited with discovering the techniques for pure culture, including staining and using growth media. His assistant Julius Petri invented the Petri dish whose use persists in today’s laboratories. Koch worked primarily with the Mycobacterium tuberculosis bacterium that causes tuberculosis and developed postulates to identify disease-causing organisms that continue to be widely used in the medical community. Koch’s postulates include that an organism can be identified as the cause of disease when it is present in all infected samples and absent in all healthy samples, and it is able to reproduce the infection after being cultured multiple times. Today, cultures remain a primary diagnostic tool in medicine and other areas of molecular biology.

Some prokaryotes, however, cannot grow in a laboratory setting. In fact, over 99 percent of bacteria and archaea are unculturable. For the most part, this is due to a lack of knowledge as to what to feed these organisms and how to grow them; they have special requirements for growth that remain unknown to scientists, such as needing specific micronutrients, pH, temperature, pressure, co-factors, or co-metabolites. Some bacteria cannot be cultured because they are obligate intracellular parasites and cannot be grown outside a host cell.

In other cases, culturable organisms become unculturable under stressful conditions, even though the same organism could be cultured previously. Those organisms that cannot be cultured but are not dead are in a viable-but-non-culturable (VBNC) state. The VBNC state occurs when prokaryotes respond to environmental stressors by entering a dormant state that allows their survival. The criteria for entering into the VBNC state are not completely understood. In a process called resuscitation, the prokaryote can go back to “normal” life when environmental conditions improve.

Is the VBNC state an unusual way of living for prokaryotes? In fact, most of the prokaryotes living in the soil or in oceanic waters are non-culturable. It has been said that only a small fraction, perhaps one percent, of prokaryotes can be cultured under laboratory conditions. If these organisms are non-culturable, then how is it known whether they are present and alive? Microbiologists use molecular techniques, such as the polymerase chain reaction (PCR), to amplify selected portions of DNA of prokaryotes, demonstrating their existence. Recall that PCR can make billions of copies of a DNA segment in a process called amplification.

The Ecology of Biofilms

Until a couple of decades ago, microbiologists used to think of prokaryotes as isolated entities living apart. This model, however, does not reflect the true ecology of prokaryotes, most of which prefer to live in communities where they can interact. A biofilm is a microbial community (Figure (PageIndex{7})) held together in a gummy-textured matrix that consists primarily of polysaccharides secreted by the organisms, together with some proteins and nucleic acids. Biofilms grow attached to surfaces. Some of the best-studied biofilms are composed of prokaryotes, although fungal biofilms have also been described as well as some composed of a mixture of fungi and bacteria.

Biofilms are present almost everywhere: they can cause the clogging of pipes and readily colonize surfaces in industrial settings. In recent, large-scale outbreaks of bacterial contamination of food, biofilms have played a major role. They also colonize household surfaces, such as kitchen counters, cutting boards, sinks, and toilets, as well as places on the human body, such as the surfaces of our teeth.

Interactions among the organisms that populate a biofilm, together with their protective exopolysaccharidic (EPS) environment, make these communities more robust than free-living, or planktonic, prokaryotes. The sticky substance that holds bacteria together also excludes most antibiotics and disinfectants, making biofilm bacteria hardier than their planktonic counterparts. Overall, biofilms are very difficult to destroy because they are resistant to many common forms of sterilization.

Art Connection

Compared to free-floating bacteria, bacteria in biofilms often show increased resistance to antibiotics and detergents. Why do you think this might be the case?

Summary

Prokaryotes existed for billions of years before plants and animals appeared. Hot springs and hydrothermal vents may have been the environments in which life began. Microbial mats are thought to represent the earliest forms of life on Earth, and there is fossil evidence of their presence about 3.5 billion years ago. A microbial mat is a multi-layered sheet of prokaryotes that grows at interfaces between different types of material, mostly on moist surfaces. During the first 2 billion years, the atmosphere was anoxic and only anaerobic organisms were able to live. Cyanobacteria evolved from early phototrophs and began the oxygenation of the atmosphere. The increase in oxygen concentration allowed the evolution of other life forms. Fossilized microbial mats are called stromatolites and consist of laminated organo-sedimentary structures formed by precipitation of minerals by prokaryotes. They represent the earliest fossil record of life on Earth.

Bacteria and archaea grow in virtually every environment. Those that survive under extreme conditions are called extremophiles (extreme lovers). Some prokaryotes cannot grow in a laboratory setting, but they are not dead. They are in the viable-but-non-culturable (VBNC) state. The VBNC state occurs when prokaryotes enter a dormant state in response to environmental stressors. Most prokaryotes are social and prefer to live in communities where interactions take place. A biofilm is a microbial community held together in a gummy-textured matrix.

Art Connections

[link] Compared to free-floating bacteria, bacteria in biofilms often show increased resistance to antibiotics and detergents. Why do you think this might be the case?

[link] The extracellular matrix and outer layer of cells protects the inner bacteria. The close proximity of cells also facilitates lateral gene transfer, a process by which genes such as antibiotic resistance genes are transferred from one bacterium to another. And even if lateral gene transfer does not occur, one bacterium that produces an exo-enzyme that destroys antibiotic may save neighboring bacteria.

Footnotes

  1. 1 Bodaker, I, Itai, S, Suzuki, MT, Feingersch, R, Rosenberg, M, Maguire, ME, Shimshon, B, and others. Comparative community genomics in the Dead Sea: An increasingly extreme environment. The ISME Journal 4 (2010): 399–407, doi:10.1038/ismej.2009.141. published online 24 December 2009.

Glossary

acidophile
organism with optimal growth pH of three or below
alkaliphile
organism with optimal growth pH of nine or above
anaerobic
refers to organisms that grow without oxygen
anoxic
without oxygen
biofilm
microbial community that is held together by a gummy-textured matrix
cyanobacteria
bacteria that evolved from early phototrophs and oxygenated the atmosphere; also known as blue-green algae
extremophile
organism that grows under extreme or harsh conditions
halophile
organism that require a salt concentration of at least 0.2 M
hydrothermal vent
fissure in Earth’s surface that releases geothermally heated water
hyperthermophile
organism that grows at temperatures between 80–122 °C
microbial mat
multi-layered sheet of prokaryotes that may include bacteria and archaea
nutrient
essential substances for growth, such as carbon and nitrogen
osmophile
organism that grows in a high sugar concentration
phototroph
organism that is able to make its own food by converting solar energy to chemical energy
psychrophile
organism that grows at temperatures of -15 °C or lower
radioresistant
organism that grows in high levels of radiation
resuscitation
process by which prokaryotes that are in the VBNC state return to viability
stromatolite
layered sedimentary structure formed by precipitation of minerals by prokaryotes in microbial mats
thermophile
organism that lives at temperatures between 60–80 °C
viable-but-non-culturable (VBNC) state
survival mechanism of bacteria facing environmental stress conditions

Review Questions

The first forms of life on Earth were thought to be_________.

  1. single-celled plants
  2. prokaryotes
  3. insects
  4. large animals such as dinosaurs

Microbial mats __________.

  1. are the earliest forms of life on Earth
  2. obtained their energy and food from hydrothermal vents
  3. are multi-layered sheets of prokaryotes including mostly bacteria but also archaea
  4. all of the above

The first organisms that oxygenated the atmosphere were

  1. cyanobacteria
  2. phototrophic organisms
  3. anaerobic organisms
  4. all of the above

Halophiles are organisms that require________.

  1. a salt concentration of at least 0.2 M
  2. high sugar concentration
  3. the addition of halogens
  4. all of the above

Many of the first prokaryotes to be cultured in a scientific lab were human or animal pathogens. Why would these species be more readily cultured than non-pathogenic prokaryotes?


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 prokaryotes (Figure) that includes mostly bacteria, but also archaea. Microbial mats are a few centimeters thick, and they typically grow where different types of materials interface, mostly on moist surfaces. The various types of prokaryotes that comprise them carry out different metabolic pathways, and that is the reason for their various colors. Prokaryotes in a microbial mat are held together by a glue-like sticky substance that they secrete called extracellular matrix.

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 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)


22.1: Prokaryotic Diversity - Biology

FB Biologie/Chemie, Universität Osnabrück, Postfach 4469, 49076 Osnabrück, Germany

Albert-Ludwigs Universität, Institut für Biologie II, Mikrobiologie, Schänzlestraße 1, 79104 Freiburg/Br, Germany

Institut für Mikrobiologie, Universität Göttingen, Grisebachstraße 8, 37077 Göttingen, Germany

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Summary

Bacterial Systematics Is the Cradle of Comparative Biology

Numerical Taxonomy Is an Approach to Cluster Strains on the Basis of Large Sets of Unweighted Phenetic Data


Prokaryotic Diversity

Prokaryotes are ubiquitous. They cover every imaginable surface where there is sufficient moisture, and they live on and inside of other living things. In the typical human body, prokaryotic cells outnumber human body cells by about ten to one. They comprise the majority of living things in all ecosystems. Some prokaryotes thrive in environments that are inhospitable for most living things. Prokaryotes recycle nutrients—essential substances (such as carbon and nitrogen)—and they drive the evolution of new ecosystems, some of which are natural and others man-made. Prokaryotes have been on Earth since long before multicellular life appeared.

Prokaryotes, the First Inhabitants of Earth

When and where did life begin? What were the conditions on Earth when life began? Prokaryotes 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 where they were more protected, such as in ocean depths or beneath the surface of the Earth. At this time too, strong volcanic activity was common on Earth, so it is likely that these first organisms—the first prokaryotes—were adapted to very high temperatures. Early Earth was prone to geological upheaval and volcanic eruption, and was subject to bombardment by mutagenic radiation from the sun. The first organisms were prokaryotes that could withstand these harsh conditions.

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 prokaryotes ([link]) that includes mostly bacteria, but also archaea. Microbial mats are a few centimeters thick, and they typically grow where different types of materials interface, mostly on moist surfaces. The various types of prokaryotes that comprise them carry out different metabolic pathways, and that is the reason for their various colors. Prokaryotes in a microbial mat are held together by a glue-like sticky substance that they secrete called extracellular matrix.

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 prokaryotes 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.

Stromatolites

Fossilized microbial mats represent the earliest record of life on Earth. A stromatolite is a sedimentary structure formed when minerals are precipitated out of water by prokaryotes in a microbial mat ([link]). 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.

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 ([link]) 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.

Microbes Are Adaptable: Life in Moderate and Extreme Environments

Some organisms have developed strategies that allow them to survive harsh conditions. Prokaryotes 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 animal. Almost all prokaryotes have 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 favorable conditions recur. These adaptations, along with others, allow bacteria to be the most abundant life form in all terrestrial and aquatic ecosystems.

Other 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 ([link]), 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 identified 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 ([link]). 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 ([link]).

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 -15-10 °C (5-50 °F) or lower
Halophiles Salt concentration of at least 0.2 M
Osmophiles High sugar concentration

Prokaryotes in the Dead Sea

One example of a very harsh environment is the Dead Sea, a hypersaline basin that is located between Jordan and Israel. Hypersaline environments are essentially concentrated seawater. In the Dead Sea, the sodium concentration is 10 times higher than that of seawater, and the water contains high levels of magnesium (about 40 times higher than in seawater) that would be toxic to most living things. Iron, calcium, and magnesium, elements that form divalent ions (Fe 2+ , Ca 2+ , and Mg 2+ ), produce what is commonly referred to as “hard” water. Taken together, the high concentration of divalent cations, the acidic pH (6.0), and the intense solar radiation flux make the Dead Sea a unique, and uniquely hostile, ecosystem 1 ([link]).

What sort of prokaryotes do we find in the Dead Sea? The extremely salt-tolerant bacterial mats include Halobacterium, Haloferax volcanii (which is found in other locations, not only the Dead Sea), Halorubrum sodomense, and Halobaculum gomorrense, and the archaea Haloarcula marismortui, among others.

Unculturable Prokaryotes and the Viable-but-Non-Culturable State

Microbiologists typically grow prokaryotes in the laboratory using an appropriate culture medium containing all the nutrients needed by the target organism. The medium can be liquid, broth, or solid. After an incubation time at the right temperature, there should be evidence of microbial growth ([link]). The process of culturing bacteria is complex and is one of the greatest discoveries of modern science. German physician Robert Koch is credited with discovering the techniques for pure culture, including staining and using growth media. His assistant Julius Petri invented the Petri dish whose use persists in today’s laboratories. Koch worked primarily with the Mycobacterium tuberculosis bacterium that causes tuberculosis and developed postulates to identify disease-causing organisms that continue to be widely used in the medical community. Koch’s postulates include that an organism can be identified as the cause of disease when it is present in all infected samples and absent in all healthy samples, and it is able to reproduce the infection after being cultured multiple times. Today, cultures remain a primary diagnostic tool in medicine and other areas of molecular biology.

Some prokaryotes, however, cannot grow in a laboratory setting. In fact, over 99 percent of bacteria and archaea are unculturable. For the most part, this is due to a lack of knowledge as to what to feed these organisms and how to grow them they have special requirements for growth that remain unknown to scientists, such as needing specific micronutrients, pH, temperature, pressure, co-factors, or co-metabolites. Some bacteria cannot be cultured because they are obligate intracellular parasites and cannot be grown outside a host cell.

In other cases, culturable organisms become unculturable under stressful conditions, even though the same organism could be cultured previously. Those organisms that cannot be cultured but are not dead are in a viable-but-non-culturable (VBNC) state. The VBNC state occurs when prokaryotes respond to environmental stressors by entering a dormant state that allows their survival. The criteria for entering into the VBNC state are not completely understood. In a process called resuscitation, the prokaryote can go back to “normal” life when environmental conditions improve.

Is the VBNC state an unusual way of living for prokaryotes? In fact, most of the prokaryotes living in the soil or in oceanic waters are non-culturable. It has been said that only a small fraction, perhaps one percent, of prokaryotes can be cultured under laboratory conditions. If these organisms are non-culturable, then how is it known whether they are present and alive? Microbiologists use molecular techniques, such as the polymerase chain reaction (PCR), to amplify selected portions of DNA of prokaryotes, demonstrating their existence. Recall that PCR can make billions of copies of a DNA segment in a process called amplification.

The Ecology of Biofilms

Until a couple of decades ago, microbiologists used to think of prokaryotes as isolated entities living apart. This model, however, does not reflect the true ecology of prokaryotes, most of which prefer to live in communities where they can interact. A biofilm is a microbial community ([link]) held together in a gummy-textured matrix that consists primarily of polysaccharides secreted by the organisms, together with some proteins and nucleic acids. Biofilms grow attached to surfaces. Some of the best-studied biofilms are composed of prokaryotes, although fungal biofilms have also been described as well as some composed of a mixture of fungi and bacteria.

Biofilms are present almost everywhere: they can cause the clogging of pipes and readily colonize surfaces in industrial settings. In recent, large-scale outbreaks of bacterial contamination of food, biofilms have played a major role. They also colonize household surfaces, such as kitchen counters, cutting boards, sinks, and toilets, as well as places on the human body, such as the surfaces of our teeth.

Interactions among the organisms that populate a biofilm, together with their protective exopolysaccharidic (EPS) environment, make these communities more robust than free-living, or planktonic, prokaryotes. The sticky substance that holds bacteria together also excludes most antibiotics and disinfectants, making biofilm bacteria hardier than their planktonic counterparts. Overall, biofilms are very difficult to destroy because they are resistant to many common forms of sterilization.

Compared to free-floating bacteria, bacteria in biofilms often show increased resistance to antibiotics and detergents. Why do you think this might be the case?

Section Summary

Prokaryotes existed for billions of years before plants and animals appeared. Hot springs and hydrothermal vents may have been the environments in which life began. Microbial mats are thought to represent the earliest forms of life on Earth, and there is fossil evidence of their presence about 3.5 billion years ago. A microbial mat is a multi-layered sheet of prokaryotes that grows at interfaces between different types of material, mostly on moist surfaces. During the first 2 billion years, the atmosphere was anoxic and only anaerobic organisms were able to live. Cyanobacteria evolved from early phototrophs and began the oxygenation of the atmosphere. The increase in oxygen concentration allowed the evolution of other life forms. Fossilized microbial mats are called stromatolites and consist of laminated organo-sedimentary structures formed by precipitation of minerals by prokaryotes. They represent the earliest fossil record of life on Earth.

Bacteria and archaea grow in virtually every environment. Those that survive under extreme conditions are called extremophiles (extreme lovers). Some prokaryotes cannot grow in a laboratory setting, but they are not dead. They are in the viable-but-non-culturable (VBNC) state. The VBNC state occurs when prokaryotes enter a dormant state in response to environmental stressors. Most prokaryotes are social and prefer to live in communities where interactions take place. A biofilm is a microbial community held together in a gummy-textured matrix.

Art Connections

[link] Compared to free-floating bacteria, bacteria in biofilms often show increased resistance to antibiotics and detergents. Why do you think this might be the case?

[link] The extracellular matrix and outer layer of cells protects the inner bacteria. The close proximity of cells also facilitates lateral gene transfer, a process by which genes such as antibiotic resistance genes are transferred from one bacterium to another. And even if lateral gene transfer does not occur, one bacterium that produces an exo-enzyme that destroys antibiotic may save neighboring bacteria.

Review Questions

The first forms of life on Earth were thought to be_________.

  1. single-celled plants
  2. prokaryotes
  3. insects
  4. large animals such as dinosaurs

Microbial mats __________.

  1. are the earliest forms of life on Earth
  2. obtained their energy and food from hydrothermal vents
  3. are multi-layered sheet of prokaryotes including mostly bacteria but also archaea
  4. all of the above

The first organisms that oxygenated the atmosphere were

  1. cyanobacteria
  2. phototrophic organisms
  3. anaerobic organisms
  4. all of the above

Halophiles are organisms that require________.

  1. a salt concentration of at least 0.2 M
  2. high sugar concentration
  3. the addition of halogens
  4. all of the above

Free Response

Describe briefly how you would detect the presence of a non-culturable prokaryote in an environmental sample.

As the organisms are non-culturable, the presence could be detected through molecular techniques, such as PCR.

Why do scientists believe that the first organisms on Earth were extremophiles?

Because the environmental conditions on Earth were extreme: high temperatures, lack of oxygen, high radiation, and the like.

Footnotes

    Bodaker, I, Itai, S, Suzuki, MT, Feingersch, R, Rosenberg, M, Maguire, ME, Shimshon, B, and others. Comparative community genomics in the Dead Sea: An increasingly extreme environment. The ISME Journal 4 (2010): 399–407, doi:10.1038/ismej.2009.141. published online 24 December 2009.

Glossary


Results

Environmental chemistry

Physicochemical conditions, summarized in Table 1 and S2 Table, were measured on both the shelf and pool at each site and were internally consistent between locations on the day of sampling. Water temperatures were higher in Devils Hole (33.55 and 33.50°C, pool vs. shelf) than in AMFCF (30.35 and 30.78°C, pool vs. shelf) (Table 1 and S1 Table), and higher still in Well P-9 (38.4°C). pH measurements averaged 7.28 in Devils Hole, 7.74 in AMFCF, and 7.58 in Well P-9. Conductivity was relatively low and consistent across all five sampling sites (640–868 μS cm -1 ). Average dissolved oxygen concentrations were 2.6 mg L -1 in Devils Hole (36.5% saturation), 5.3 mg L -1 in AMFCF (78.1% saturation), and 3.9 mg L -1 (59.5% saturation) in Well P-9 at the time of sampling. Consistent with a shared carbonate-buffered aquifer source for Devils Hole and AMFCF, major ions and alkalinity values were equivalent to within a few percent across the dataset. Alkalinity values ranged from 229 mg L -1 in AMFCF to 265 mg L -1 in Devils Hole, and all water samples where characterized by sulfate > sodium > calcium > magnesium/chloride. Dissolved organic carbon concentrations were low (0.127, 0.128, and 0.231 mg L -1 in Devils Hole, Well P-9, and AMFCF, respectively). Bioavailable nitrogen concentrations (primarily dissolved nitrate) were very low in AMFCF and Well P-9 (0.022 and 0.041 mg L -1 ) compared to Devils Hole which, while also low, were greater by nearly an order of magnitude (0.143 and 0.138 mg L -1 , pool and shelf). Nitrite (<0.002 mg L -1 ), ammonia (0.003–0.004 mg L -1 ), and phosphorus (0.003–0.004 mg L -1 ) concentrations were very low, approaching detection limits, in all samples. Correspondingly, N:P molar ratios for the Devils Hole shelf, Devils Hole pool, AMFCF shelf, AMFCF pool, and Well P-9 were 105:1, 108:1, 19:1, 19:1, and 24:1, respectively. Devils Hole, AMFCF, and Well P-9 had remarkably similar dissolved metal concentrations overall (Table 1 and S1 Table). However, dissolved arsenic in Devils Hole (0.125 mg L -1 ) was nearly an order of magnitude higher than all AMFCF-associated sites. Conversely, the concentration of silica in Devils Hole (23.7 mg L -1 ) was lower than in AMFCF and Well P-9 (33.9 and 34.1 mg L -1 ).

Prokaryotic diversity and community structure

Planktonic microbial density was low in all samples from Devils Hole and AMFCF, averaging 7.9E+4 to 9.2E+4 cells mL -1 , with no pattern between sites, and was significantly higher (1.79E+5 cells mL -1 , p≤0.0012, Student’s t-test) in Well P-9 (S3 Table). In total, 2,039 operational taxonomic units (OTUs) were identified at 97% sequence similarity from the 862,307 quality-filtered sequences generated from the twenty-one samples that comprised this study (S1 Appendix). The two most abundant OTUs, an unclassified cyanobacterium (OTU_500, affiliated with the genus Oscillatoria) and an unclassified bacterium in the Verrucomicrobiaceae family of Verrucomicrobia (OTU_1850), accounted for 4.8% and 4.7% of all sequences. The Cyanobacteria OTU was most abundant in Devils Hole water and sediment samples (13.2% mean relative abundance), and nearly completely absent (<0.01%) from AMFCF and Well P-9 samples. Conversely, the Verrucomicrobiaceae OTU was found in high abundances in AMFCF water samples (31.7% mean relative abundance), but was present only at low abundances (≤2.4%) in all Devils Hole samples and AMFCF sediments, and was completely absent from Well P-9.

Devils Hole and AMFCF host diverse prokaryotic communities (Fig 2), with 44 bacterial and archaeal phyla detected, including 23 candidate divisions. Devils Hole planktonic samples were dominated by Cyanobacteria (37.7% mean relative abundance), with Plantomycetes (14.5%), Gammaproteobacteria (9.3%), unassigned taxa (8.7%), Verrucomicrobia (5.5%), and Alphaproteobacteria (5.0%) accounting for large proportions of community structure. Devils Hole sediment communities were dominated by Cyanobacteria (23.6%), unassigned taxa (11.9%), Bacteroidetes (10.2%), Chloroflexi (9.9%), Deltaproteobacteria (6.8%), Alphaproteobacteria (6.3%), Gammaproteobacteria (5.5%), Verrucomicrobia (5.3%), and Chlorobi (5.1%). AMFCF planktonic communities were dominated by Verrucomicrobia (38.7%), Alphaproteobacteria (25.5%), Planctomycetes (11.8%), and Bacteroidetes (8.9%). In contrast, AMFCF sediments were dominated by Deltaproteobacteria (11.3%), unassigned taxa (10.1%), Planctomycetes (9.9%), Cyanobacteria (9.8%), Chloroflexi (8.0%), Betaproteobacteria (7.7%), Alphaproteobacteria (7.6%), Bacteroidetes (7.2%), and Gammaproteobacteria (6.7%). Well P-9 was dominated by Betaproteobacteria (19.5%), Nitrospirae (15.7%), unassigned taxa (13.9%), Deltaproteobacteria (13.3%), and Alphaproteobacteria (9.0%). Across the entire dataset, Bacteria far outnumbered Archaea, but this domain was present and accounted for <0.01–3.16% relative abundance in Devils Hole and AMFCF prokaryotic communities. Twenty-one phyla were present at <1% relative abundance across all sites.

Phylum-level taxonomic bar chart for prokaryotic communities from Devils Hole (DH), Ash Meadows Fish Conservation Facility (AMFCF), and Well P-9 constructed from the final unrarefied OTU table (S1 Appendix). Planktonic samples (“pool”, “shelf”, and “Well P-9”) and sediment samples (“Sed1-Sed16”), each representing a discrete sample, are noted. The Proteobacteria were subdivided into classes. Only microbial groups with abundances ≥ 1% are displayed. Groups with < 1% abundances are included in aggregate as “Phyla < 1%”.

Alpha diversity metrics (observed OTU richness, Chao1 estimated richness, Faith’s Phylogenetic Diversity [Faith’s PD], and Shannon’s index) were calculated from 100 rarefactions of 10,000 sequences per sample (S4 Table). The Devils Hole pool sample had significantly higher alpha diversity values than all other planktonic samples (Devils Hole shelf, AMFCF pool and shelf, and Well P-9) (p<0.0001 for all comparisons, Student’s t-test). The AMFCF shelf sample was significantly more diverse than the AMFCF pool sample and the Well P-9 sample (p<0.0001). Sediment samples, as site-specific groups, were more diverse than their planktonic counterparts (p<0.0001). AMFCF sediments collectively were more diverse than DH sediments (p<0.0001). The least diverse sample in the dataset was the Devils Hole shelf sample, with an observed OTU richness of 101.5 ± 0.59 OTUs.

To evaluate the similarity between prokaryotic communities, particularly between Devils Hole and AMFCF, pairwise unweighted UniFrac, weighted UniFrac, and Bray-Curtis distances were calculated, UPGMA clustering was performed, and ordination diagrams were generated. Principal component analysis of abundance-unweighted (Fig 3a) and abundance-weighted (Fig 3b) UniFrac distances show the distribution of prokaryotic communities in the statistical space formed by the first two components. Unweighted and weighted analyses showed separation of communities based upon both sample location and substrate type (planktonic vs. sediment). Abundance-unweighted and –weighted UPGMA clustering dendrograms (S1 and S2 Figs) validated these observations, with each cluster of samples supported by 100% jackknife support, although the DH Shelf and DH Pool samples clustered independently in the abundance-unweighted dendrogram. The Well P-9 sample clustered independently of all other samples in both of the ordinations (Fig 3a and 3b) and dendrograms. In the abundance-weighted ordination and dendrogram (Fig 3b and S2 Fig), Devils Hole planktonic samples formed their own distinct cluster and were more similar to all sediment samples than to AMFCF planktonic samples. Sediment samples clustered in a site-specific manner.

Principal component analysis ordinations of a) pairwise abundance-unweighted UniFrac distances and b) pairwise abundance-weighted UniFrac distances for all samples show separation of samples by sample location and sample type (planktonic vs. sediment). Individual samples are colored according to sample type (planktonic vs. sediment: Devils Hole (DH) planktonic and sediment samples are shown as light blue and dark blue squares, respectively Ash Meadows Fish Conservation Facility (AMFCF) planktonic and sediment samples are shown as yellow and red triangles, respectively and the Well P-9 sample is shown as an asterisk.

Analysis of similarity (ANOSIM) tests were conducted to identify significant differences in taxonomic similarity (Bray-Curtis distances), qualitative phylogenetic similarity (abundance-unweighted UniFrac distances), and quantitative phylogenetic similarity (abundance-weighted UniFrac distances) between planktonic and sediment samples from Devils Hole and AMFCF (S5 Table). Taxonomic and phylogenetic similarity differed significantly between sample sites (p<0.01). Sediment samples were taxonomically and phylogenetically significantly different between Devils Hole and AMFCF (p<0.05), whereas the planktonic samples between the two sites were not significantly different.

SIMPER analysis was performed to identify the top five OTUs that contributed to the dissimilarity between Devils Hole and AMFCF sediment and planktonic samples (Fig 4, S6 Table). Prokaryotic community dissimilarities (42.82% cumulative contribution) between Devils Hole and AMFCF planktonic samples were driven by two unclassified Cyanobacteria OTUs (OTU_502 and OTU_500), which were abundant in Devils Hole planktonic samples (16.64% and 11.03% mean relative abundance) and undetected in AMFCF planktonic samples, and an OTU in the Verrucomicrobiaceae family (OTU_1850), an OTU in the Hyphomonadaceae family (OTU_1062), and an OTU in the Planctomyces genus (OTU_941), which were more abundant in AMFCF planktonic samples (31.97%, 13.15%, and 9.99%, respectively) compared to Devils Hole planktonic samples (1.21%, 0.01%, and undetected, respectively). Two phyla were detected in Devils Hole planktonic samples but absent from AMFCF planktonic samples (Fusobacteria and Gemmatimonadetes, both <1%). Conversely, six phyla were detected in low abundances in AMFCF planktonic samples (Elusimicrobia, GOUTA4, OC31, OP11, OP3, and SBR1093, all <1%) but were absent in Devils Hole planktonic samples.

Differentially abundant OTUs between a) planktonic samples and b) sediment samples between Devils Hole and Ash Meadows Fish Conservation Facility (AMFCF), along with OTU ID and taxonomy, are shown. Prefixes (p_, o_, f_ and g_) denote phylum, order, family, and genus level OTU identities. See S6 Table for the percent contribution of each OTU to the dissimilarity between each group of samples.

Dissimilarities between Devils Hole and AMFCF sediment samples (15.16% cumulative contribution) were attributed to an unclassified Cyanobacteria OTU (OTU_500), two unassigned OTUs (OTU_2006 and OTU_2023), an OTU in the Chitinophagaceae family (OTU_162), and an OTU in the PK329 order of Chlorobi (OTU_291), which were found in higher abundance in Devils Hole sediments (13.81%, 4.21%, 3.11%, 2.29%, and 1.95%, respectively) compared to AMFCF sediments (0.0038%, 2.54%, 0.36%, 0.033%, and 0.12%, respectively). Three phyla were detected in Devils Hole sediments at low abundances (Euryarchaeota, Caldithrix, and FCPU426, all <0.5%) but were absent from AMFCF sediments. Conversely, the phylum OP11 was detected in a single AMFCF sediment sample but no other sediment samples from either AMFCF or Devils Hole (<0.01%).


Prokaryotes and Eukaryotes

Both prokaryotes and eukaryotes contain DNA however the former have no nuclei while the latter does. The purpose of the nucleus is to enclose the DNA production within one section of the cell thereby increasing efficiency. This is not necessary in prokaryote cells due to the fact that they’re so much smaller in size which means all the cell’s materials are in close proximity to each other.

Another difference between their DNA is that eukaryotic DNA is linear whereas DNA in prokaryotes is circular. While the former contains chromosomes the latter contains only one circular DNA molecule and a number of smaller DNA circlets called plasmids. Basically, the prokaryotic cell doesn’t need as many genes.


22.1: Prokaryotic Diversity - Biology

Biology 213. Diversity and Ecology

Introduction to the evolution of life, the diversity of prokaryotic and eukaryotic organisms, population biology, species interactions, the organization of biological communities and ecosystems. Two lecture hours and one discussion hour a week for one semester. Only one of the following may be counted: Biology 301M, 304, 311D, 213. Prerequisite: Biology 211 and 212 with a grade of at least C in each, or Biology 311C with a grade of at least C.

Each of us quite naturally perceives ourself to be at the center of things, but no one would deny that other events ultimately have their influence, too. Likewise, many people unconsciously place humanity at the exact center of the universe. In this view, the utility of anything is measured by how it can be used by humans. For many, everything has its dollar value. Such anthropocentrism is understandable, but narrow and misguided.


It is a worthwhile exercise to imagine that something else, such as an ant, a lizard, an oak tree, or an HIV virus, is really the focus of the cosmos. From such a perspective, the almighty dollar quickly loses its primacy. Survival (Survival Kit) and reproduction assume a lot more significance. What good are lizards?

Prerequisites:
Bio 211 and 212 with grades of C or higher are required. Students who enroll in 213 who have not met these prerequisites will be dropped after the fourth class day.

This course assumes knowledge of High School algebra and geometry. You will be expected to be able to understand 3-dimensional graphs and be able to manipulate simple equations.

We will attempt to teach you the basic ecology and evolution that everyone should know -- we will also do our utmost to encourage you to think .

[Optional, but recommended] Pianka, E. R. 2000. Evolutionary Ecology,
6th ed. Addison-Wesley Longman.

1: Background
2: History and Biogeography
3: Meteorology
4: Climate and Vegetation
5: Resource Acquisition and Allocation
7: Evolution and Natural Selection
8: Vital Statistics of Populations
9: Population Growth and Regulation
10: Sociality
11: Interactions between Populations
12: Competition
13: The Ecological Niche
14: Experimental Ecology
15: Predation and Parasitism
16: Phylogenetics in Ecology
17: Community and Ecosystem Ecology
18: Biodiversity and Community Stability
19: Island Biogeography and Conservation Biology

Final Exam: Wed. 11 May, 9-12 AM

Best 2 of the above 3 hour exams will count 20% each (40% total)
The comprehensive final exam will count for the other 40% of your course grade

Your performance in discussion sections counts for 20% of your course grade.
There will be NO "make up" exams!

You will be expected to "know" everything the instructors say in lecture and discussion sections, including pauses and nuances, as well as everything assigned in reading assignments. Exams will be in multiple choice format. Each 60 minute exam will cover about one-third of the class. Everyone must take at least two of the three hour exams plus the comprehensive 3 hour final exam. No "Make Up" exams will be given (if you press us on this, you will get grilled by both of us in a 2 hour private oral examination!). No "extra points" are available.

Outline of Subjects to be covered in the Course

Biology 213 - Diversity and Ecology

Definitions and Groundwork the scientific method domain of ecology, environment limiting factors, tolerance limits, the principle of allocation
natural selection, self-replicating molecular assemblages levels of selection,
levels of approach to science, speciation, phylogeny, classification and systematics.

Macroevolution, natural selection and adaptation, the species concept.
Origin of life, prokaryotes and eukaryotes, introduction to the diversity
of organisms. Domains, traits (and example organisms) of kingdoms
[archaebacteria, eubacteria, protists, fungi, plants, animals]
Adaptations, structures, symbiotic relationships, including variations in life cycles

How organisms are classified and why phylogenetic systematics
One major taxon will be examined in depth ( Lizards ) we will investigate
classification, phylogeny, and biogeography
Evolution will be related to the history of earth (plate tectonics)

Physiological Ecology
Physiological optima and tolerance curves, energetics of metabolism and movement energy budgets and the principle of allocation adaptation and deterioration of environment heat budgets and thermal ecology water economy in desert organisms other limiting materials sensory capacties and environmental cues adaptive suites and design constraints.


Principles of Population Ecology
Life tables and schedules of reproduction net reproductive rate and reproductive value stable age distribution intrinsic rate of increase population growth and regulation Pearl-Verhulst logistic equation density dependence and independence r and K selection population "cycles," cause and effect metapopulations evolution of reproductive tactics evolution of old age and death rates use of space evolution of sex sex ratio mating systems sexual selection fitness and the individual's status in the population kin selection, reciprocal altruism, parent-offspring conflict and group selection.

Interactions Between Populations
Complex examples of population interactions indirect interactions competition theory competitive exclusion balance between intraspecific and interspecific competition evolutionary consequences of competition laboratory experiments and evidence from nature character displacement and limiting similarity future prospects Predation predator-prey oscillations "prudent" predation and optimal yield theory of predation functional and numerical responses selected experiments and observations evolutionary consequences of predation: predator escape tactics aspect diversity and escape tactic diversity coevolution plant apparency theory evolution of pollination mechanisms symbiotic relationships.

Community Ecology
Classification of communities interface between climate and vegetation plant life forms and biomes leaf tactics succession transition matrices aquatic systems community organization trophic levels and food webs the community matrix guild structure primary productivity and evapotranspiration pyramids of numbers, biomass, and energy energy flow and ecological energetics saturation with individuals and with species species diversity diversity of lowland rainforest trees community stability evolutionary convergence and ecological equivalents ecotones, vegetational continuua, soil formation and primary succession evolution of communities.

Island Biogeography and Conservation Biology
Classical biogeography biogeographic "rules" continental drift island biogeography species-area relationships equilibrium theory compression hypothesis islands as ecological experiments: Krakatau, Darwin's finches, and other examples metapopulations, conservation biology, human impacts on natural ecosystems, hot spots of biodiversity, applied biogeography and the design of nature preserves.


Prokaryotes - Diversity & Classification

We want you to know that prokaryotes are diverse and we've got the data to back it up. A great way to demonstrate diversity is by graphing a phylogenetic tree. A phylogenetic tree is kind of like a family tree, but for different species of living things. At the root of the tree is a shared ancestor, and at the other end are all the relatives, both close and distant, of the current generation.

If you want to see a good example of a family tree, we recommend checking out the British royal family tree. This family tree traces the links from a common ancestor (in this case, Queen Elizabeth II, who was born in 1926) through to her great grandchildren, including Prince George and Princess Charlotte.

The phylogenetic tree of life is similar to a family tree, except instead of going back to a single person, like Queen Elizabeth II, it's rooted in a shared ancestor for all of the species included. You may not look a lot like a bacterium, but you're very distantly related to it. Of course, any ancestor we shared with bacteria lived very, very, very long ago.

This is a diagram of the phylogenetic tree of life. It separates organisms based on their genomic sequences.


Phylogenetic Tree of Life. Image from here.

The root of the tree lies at the center bottom. This point represents the common ancestor of all living things. Modern organisms span the outer reaches of the tree, from Firmicutes (a type of bacteria) on the left to animals (like us!) on the right. This tree shows two important things:

  • Prokaryotes are really diverse
  • Archaea really are separate from bacteria and eukaryotes.

The diversity of organisms is represented by how much space they take up on the tree. Since prokaryotes take up more space than eukaryotes, they're more diverse.

Looking at the tree, we see that archaea exist in a completely separate branch from bacteria. In fact, they're even grouped a little more closely with the eukaryotes than with the bacteria. This is because when it comes to the enzymes used for several of their most basic processes, notably the enzymes used for transcription and translation, archaea are more like eukaryotes than bacteria. Archaea and bacteria might look similar under a microscope (as you can see in some of the images below), but, genetically, they're made of different stuff.

In the first image below, bacterial cells appear next to a large plant cell. The archaea in the second image (which isn't at the same scale!) looks a lot like bacteria, but are a genetically distinct branch of life.


Image from here.


Image from here.

Prokaryotic Cells

So let's get into the differences between prokaryotic cells. Here's a simple schematic. These prokaryotes have two membranes, a cell wall between them, and, finally some DNA. It doesn't get much simpler than that. Actually, it does get a little simpler. Some prokaryotes don't even have the outer membrane (gasp!). We'll get into that in a bit.


Simple, right?

Differences in the cell wall affect how prokaryotes grow and how we classify them. In archaea, the cell wall, called the S-layer (for surface layer), is made of proteins. In bacteria the cell wall is made up of a material called peptidoglycan. Peptidoglycan molecules consist of a peptide (peptides are like really small proteins) linked with a glycan (aka sugar).

Differences in prokaryotic cell walls also affect how other organisms respond to them. For example, the human immune system has specific receptors that recognize peptidoglycan, enabling it to detect bacteria (though sometimes not soon enough to keep us from feeling their effects). These receptors monitor the presence of bacteria in places where they should and shouldn't be. Think of them like tiny tracking devices that are keeping tabs on their comings and goings.

Gram Staining

Bacteria are divided into two major classes. This process is based on cell walls (are you sensing that these are important yet?). Hans Christian Gram, a Dane (who might have been great) worked in a German morgue and invented the staining process we use to detect which class a particular bacterium has. No relation to the sometimes-morbid Hans Christian Andersen, who wrote The Little Mermaid. Because the stain is named for a person, the first letter of Gram is always capitalized.

The Gram stain is still used as the first step in identifying bacteria. The way it works is that a population of bacteria is exposed to a dye called crystal violet. Initially, this dye colors all the bacteria. When the dye is washed away, the Gram-positive bacteria, which have thick cell walls, hold all the dye in. Bacteria without those thick candy shells lose the dye and are classified as Gram negative. A weaker stain, called a counter stain, is then added so we can see the Gram negative bacteria in a pretty pink hue.


Gram-negative bacteria (rosy pink). Image from here.


Gram-positive bacteria (royal purple). Image is ID# 3079 from the CDC Public Health Image Library.

Both Gram-negative and Gram-positive bacteria have similar cytoplasms and cytoplasmic membranes (also known as plasma membranes) made of phospholipid bilayers. Just like the ones eukaryotic and archaeal cells run around in. If you just can't get enough of plasma membranes, read up on 'em here.

Bottom line, the cell wall is where Gram negatives and Gram positives really show off their differences. Their different outsides strongly affect how they interact with the world. Even at the microbial level, appearances matter.

Gram-positive bacteria have a thick cell wall that surrounds their cytoplasmic membrane. In some species the wall is coated with polysaccharides in a final layer called the capsule. The capsule is slippery, helping bacteria slip and slide away from predators. It also blocks some viruses and detergents from harming the bacteria.

Gram-negative bacteria have an extra membrane, called the outer membrane, that surrounds their cell wall. The inner face of the outer membrane is composed of phospholipids, just like the inner membrane. The outer face is composed of a special material called lipopolysaccharide (LPS). Bet you can guess what LPS is made of too: it's part lipid and part polysaccharide (sugar). The polysaccharide part protrudes outside the cell. And just because they want to play slip and slide too, some Gram-negative bacteria have capsules.

The existence of an outer membrane means that Gram-negative bacteria have an extra cellular compartment between the two membranes. This region is called the periplasm, and it's where the bacterium hides the candy it doesn't want to share with its friends…wait…no. The periplasm is kind of like a giant cellular foyer or "airlock" that surrounds the cytoplasm, giving the cell an extra measure of control to what chemicals and nutrients are allowed to cross each of their membranes.

The Gram-negative bacterial cell wall is located in the periplasm. It is thinner than the Gram-positive cell wall. Gram-negative bacteria are okay with this because they get extra stability from the LPS in their outer membrane.


Gram-positive versus Gram-negative. Who will win?

Shapes

Prokaryotes, both bacteria and archaea, take on some inventive shapes, or morphologies. The shapes depend on the way their cell walls are constructed. The most common shapes are:

  • Rod-shaped (Bacillus)
  • Spherical (Coccus)
  • Spiral-shaped (Spirilla are rigid spirals Spirochetes are flexible)

Warning! Bacillus is both a bacterial shape AND a bacterial genus. Lots of bacteria outside of the genus Bacillus are bacillus-shaped. For example, E. coli, which is in the genus Escherichia, is bacillus-shaped. We're happy to report that species in the genus Bacillus are also bacillus shaped. Otherwise that could have been very confusing…

The images below are presented in false color in order to help distinguish the bacteria from the background (too bad these colors don't actually happen in nature). From top to bottom, they are Spheres, Rods, Spirals, and finally Curved Rods. We threw the curved rods (also called comma-shaped) in there just to point out that variations on the three major shapes are common.


Cocci. Image from here.


Bacillus. Image from here.


Curved rod. Image from here.


Spirochete. Image is ID# 13169 from the CDC Public Health Image Library.

DNA-based Prokaryotic Classification

A lot can be gained from understanding a bacterium's morphology. For example, if you think someone might have the disease cholera, but they don't have cells that look like the bacteria that causes cholera, you might want to try a different treatment. Or get a better doctor.

Prokaryotes are a bit trickier to identify than multicellular eukaryotes. If you're trying to tell if a horse and a zebra are different organisms, all you need to do is open your eyes. We haven't seen too many stripy horses. Prokaryotes don't have stripes or as many obvious features to distinguish one from another, so scientists have figured out other ways of classifying them.

Serotyping

One way that prokaryotes are classified is by determining their serotypes. Serotype is determined by testing which antibodies (generally from an animal, like antibodies from a rabbit immune system) interact with a given sample. American microbiologist Rebecca Lancefield developed the serotype classification system in 1933.

Different antibodies recognize different parts of molecules on the outsides of the prokaryotic cells. A major antigen responsible for serotyping in Gram-negative bacteria is the O-antigen, the polysaccharide component of LPS. While serotyping antibodies often recognize the outer regions of cells, they also respond to virulence factors (called exotoxins) that are released by pathogenic bacteria. Pathogenic bacteria are bacteria that can cause disease. We'll talk more about pathogens and exotoxins later.

Serotyping can be very sensitive and even identify different classes of bacteria of the same species, called strains. For example, the species Vibrio cholerae, which causes the disease cholera, has more than 200 serotypes. We pity the poor little bunny that figured that one out.

DNA Barcodes

Another method that is increasingly used is DNA sequencing. DNA sequencing can be used in one of two ways. In the first option, an entire bacterial genome sequence can be found and compared with known existing sequences. This is expensive, time consuming, and a bit boring if you're not into thousands of pages of As, Ts, Gs, and Cs. A quick and dirty approach involves only sequencing a specific region of the genome known to be variable across species. Such regions are sometimes called DNA barcodes, since they're unique to a given species. The DNA barcode sequence can be used like real-life barcodes to look up the organism attached to it.

Brain Snack

DNA barcoding was used by high school students in New York to investigate if fish used for sushi were the actual fish advertised on the menu. In a big news story dubbed "Sushigate", the students, with the help of university researchers, found that 25% of fish were mislabeled. Check it out here.

The work pioneered by these high school students continues. A more recent investigation in Los Angeles showed that over half of seafood there was labeled as some other fish.


Summary

This tutorial introduced you to the prokaryotes. They are a very diverse group of organisms that are commonly referred to as bacteria however, they are really comprised of two different domains. One domain, the Archaea, usually grow in the most extreme environments. Their ability to occupy extreme habitats is mirrored by their flexibility in utilizing resources some species are photosynthetic, whereas others can live on oil or hydrogen sulfide. The other domain, the Bacteria, is much more abundant. Although diverse, members of both domains share some common features. Prokaryotes lack membrane-bound nuclei, they are generally single-celled or colonial, and they are very small. The genetic organization of prokaryotes and binary fission as a means for replication aids in their fast generation times, which contributes to relatively quick evolutionary changes. We will continue our discussion of prokaryotes in the next tutorial by exploring their morphologies and by describing some of their interactions with other life forms.



Comments:

  1. Skippere

    Thanks for the interesting material!

  2. Vudorisar

    Very excellent idea

  3. Jalil

    You are absolutely right.

  4. Goltitaxe

    Bravo, what words..., a magnificent idea

  5. Geraghty

    The message is removed

  6. Tygok

    OGO, well, finally



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