Prokaryotic Diversity Quiz

PDF page 899: a nucleus and cytoplasmic organelles. In the late 20 century, scientists compared sequences of small-subunit ribosomal RNA, which resulted in a more fundamental way to group organisms on Earth. Based on the differences in the structure of the cell membranes and in rRNA, Carl Woese and his colleagues proposed the three domain system. The domain Bacteria comprises all organisms in the kingdom Eubacteria (bacteria), the domain Archaea comprises the rest of the prokaryotes, and the domain Eukarya comprises all eukaryotes, including protists, fungi, plants, and animals. Prokaryotes exhibit great diversity in form and function and are abundant and ubiquitous. In addition to inhabiting moderate environments like the human digestive system, prokaryotes are found in extreme conditions (extremophiles), from boiling hot springs to the Great Salt Lake and to frozen environments in Antarctica. Because prokaryotes inhabit many different environments, they have evolved multiple strategies for meeting their energy demands, including chemosynthesis, photosynthesis, anaerobic cellular respiration, and aerobic cellular respiration. Hot springs and hydrothermal vents may have been the environments in which life began, and there is fossil evidence of the presence of microbial mats about 3.5 billion years ago. During the first two billion years of Earth’s history, the atmosphere lacked sufficient quantities of oxygen, 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 allows the evolution of other life forms with other metabolic processes. Most prokaryotes prefer to live in communities, often forming biofilms.

PDF page 899: a nucleus and cytoplasmic organelles. In the late 20 century, scientists compared sequences of small-subunit ribosomal RNA, which resulted in a more fundamental way to group organisms on Earth. Based on the differences in the structure of the cell membranes and in rRNA, Carl Woese and his colleagues proposed the three domain system. The domain Bacteria comprises all organisms in the kingdom Eubacteria (bacteria), the domain Archaea comprises the rest of the prokaryotes, and the domain Eukarya comprises all eukaryotes, including protists, fungi, plants, and animals. Prokaryotes exhibit great diversity in form and function and are abundant and ubiquitous. In addition to inhabiting moderate environments like the human digestive system, prokaryotes are found in extreme conditions (extremophiles), from boiling hot springs to the Great Salt Lake and to frozen environments in Antarctica. Because prokaryotes inhabit many different environments, they have evolved multiple strategies for meeting their energy demands, including chemosynthesis, photosynthesis, anaerobic cellular respiration, and aerobic cellular respiration. Hot springs and hydrothermal vents may have been the environments in which life began, and there is fossil evidence of the presence of microbial mats about 3.5 billion years ago. During the first two billion years of Earth’s history, the atmosphere lacked sufficient quantities of oxygen, 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 allows the evolution of other life forms with other metabolic processes. Most prokaryotes prefer to live in communities, often forming biofilms.

PDF page 899: In the recent past, scientists grouped living organisms into five kingdoms based on several criteria, including the absence or presence of a nucleus and other membrane-bound organelles, the absence or presence of cell walls, multicellularity, and so on. As we learned earlier, prokaryotes were the first cells to evolve on Earth 3.5 to 4.5 millions of years ago and lacked

PDF page 900: Objective scientific questions about the origin of life on Earth. Essential 1.D.2 Life on Earth evolved between 3.5 and 4.5 billion years ago. Knowledge

PDF page 903: 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 (Figure 22.5), 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 (Table 22.1). 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 (Figure 22.5).

PDF page 903: 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 (Figure 22.5), 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 (Table 22.1). 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 (Figure 22.5).

PDF page 905: 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.

PDF page 899: a nucleus and cytoplasmic organelles. In the late 20 century, scientists compared sequences of small-subunit ribosomal RNA, which resulted in a more fundamental way to group organisms on Earth. Based on the differences in the structure of the cell membranes and in rRNA, Carl Woese and his colleagues proposed the three domain system. The domain Bacteria comprises all organisms in the kingdom Eubacteria (bacteria), the domain Archaea comprises the rest of the prokaryotes, and the domain Eukarya comprises all eukaryotes, including protists, fungi, plants, and animals. Prokaryotes exhibit great diversity in form and function and are abundant and ubiquitous. In addition to inhabiting moderate environments like the human digestive system, prokaryotes are found in extreme conditions (extremophiles), from boiling hot springs to the Great Salt Lake and to frozen environments in Antarctica. Because prokaryotes inhabit many different environments, they have evolved multiple strategies for meeting their energy demands, including chemosynthesis, photosynthesis, anaerobic cellular respiration, and aerobic cellular respiration. Hot springs and hydrothermal vents may have been the environments in which life began, and there is fossil evidence of the presence of microbial mats about 3.5 billion years ago. During the first two billion years of Earth’s history, the atmosphere lacked sufficient quantities of oxygen, 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 allows the evolution of other life forms with other metabolic processes. Most prokaryotes prefer to live in communities, often forming biofilms.

PDF page 901: 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 (Figure 22.4) 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.

PDF page 901: 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 (Figure 22.4) 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.

PDF page 900: 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 22.2) 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.

PDF page 901: 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) 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 22.3). 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.

PDF page 903: 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

PDF page 903: 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