22: Prokaryotes - Bacteria and Archaea Flashcards
Prokaryotic Diversity, Structure of Prokaryotes, Prokaryotic Metabolism, Bacterial Diseases in Humans, Beneficial Prokaryotes (188 cards)
1
Q
Who pioneered the discovery of the three domains of life?
A
In the late 20th century, the pioneering work of Carl Woese and others compared sequences of small-subunit ribosomal RNA (SSU rRNA), which resulted in a more fundamental way to group organisms on Earth than before. Based on the differences in the structure of cell membranes and in rRNA, Woese and his colleagues proposed that all life on Earth evolved along three lineages, called domains, Bacteria, Archaea, and Eukarya.
2
Q
When did prokaryotes first appear on Earth?
A
About 3.5 to 3.8 billion years ago, indicated by the presence of fossilized microbial mats. The first microbial mats likely obtained their energy from chemicals found near hydrothermal vents. Fossilized microbial mats represent the earliest record of life on Earth.
3
Q
What are some examples of environments that are inhabited by prokaryotes?
A
Prokaryotes are abundant and ubiquitous. They are found in both moderate and extreme environments, such as boiling springs to permanently frozen environments in Antarctica; from salty environments like the Dead Sea to environments under tremendous pressure, such as the depths of the ocean; and from areas without oxygen, such as a waste management plant, to radioactively contaminated regions, such as Chernobyl. Prokaryotes reside in the human digestive system and on the skin, are responsible for certain illnesses, and serve an important role in the preparation of many foods.
4
Q
What is an acidophile?
A
Organism with optimal growth in pH of three or below.
5
Q
What is an alkaliphile?
A
Organism with optimal growth pH of nine or above.
6
Q
What are anaerobic organisms?
A
Refers to the organisms that grow without oxygen.
7
Q
What does it mean to be anoxic?
A
Without oxygen.
8
Q
What is a biofilm?
A
Microbial community that is held together by 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.
9
Q
What is an extremophile?
A
Organism that grows under extreme or harsh conditions.
10
Q
What is a halophile?
A
Organism that requires a salt concentration of at least 0.2 M.
11
Q
What is a hydrothermal vent?
A
Fissure in Earth’s surface that releases geothermally heated water.
12
Q
What is a hyperthermophile?
A
Organism that grows at temperatures between 80-122 C.
13
Q
What is a microbial mat?
A
Multi-layered sheet of prokaryotes that may include bacteria and archaea. They are a few centimeters thick, and 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.
14
Q
What is a nutrient?
A
Essential substances for growth, such as carbon and nitrogen.
15
Q
What is an osmophile?
A
Organism that grows in a high sugar concentration.
16
Q
What is a phototroph?
A
Organism that is able to make its own food by converting solar energy to chemical energy.
17
Q
What is a psychrophile?
A
Organism that grows at temperatures of -15 C or lower.
18
Q
What is a radioresistant organism?
A
Organism that grows in high levels of radiation.
19
Q
What is resuscitation?
A
Process by which prokaryotes that are in the VBNC state return to viability.
20
Q
What is a stromatolite?
A
Layered sedimentary structure formed by precipitation of minerals by prokaryotes in microbial mats. Stromatolites form layered rocks made of carbonate or silicate.
21
Q
What is a thermophile?
A
Organism that lives at temperatures between 60-80 C.
22
Q
What is a viable-but-non-culturable (VBNC) state?
A
Survival mechanism of bacteria facing environmental stress conditions.
23
Q
What were the conditions on earth likely like when the first organisms arose?
A
Earth had a very different atmosphere (containing less molecular oxygen) and was subjected to strong radiation, so the first organisms would have flourished where they were more protected, such as in ocean depths or beneath the surface of the Earth. Strong volcanic activity was also common, so life was likely adapted to very high temperatures and other harsh conditions.
24
Q
Are stromatolites formed present day?
A
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, and in Shark Bay, Australia. Fossilized stromatolites found in Glacier National Park, Montana, are nearly 1.5 billion years old.
25
What was the constitution of the atmosphere of early Earth and how did aerobic organisms evolve?
Evidence indicates that during the first two billion years of Earth's existence, the atmosphere was anoxic (lacking molecular oxygen). Phototrophs appeared within one billion years of the formation of Earth. Cyanobacteria evolved from these simple phototrophs one billion years later, which 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 ozone, and ozone effectively absorbs the ultraviolet light that would otherwise cause lethal mutations in DNA. Ultimately, the increased in O2 concentrations allowed the evolution of other life forms.
26
How do cell walls help prokaryotes survive?
Almost all prokaryotes have a cell wall, which allows them to survive in both hyper- and hypo-osmotic conditions.
27
What is an endospore?
A dormant, tough, and non-reproductive structure produced by some soil bacteria. Endospores resist heat and drought, which allows the organism to survive until favorable conditions recur.
28
What are some environments that extremophiles have been found in?
The depth of the oceans, hot springs, the Artic and Antarctic, in very dry places, deep inside the Earth, in harsh chemical environments, and in high radiation environments.
29
What is *Deinococcus radiodurans*?
A prokaryote 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.
30
What is the Dead Sea?
A hypersaline basin that is located between Jordan and Israel. 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. 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.
31
What is a divalent ion?
Doubly-charged monatomic ions, such as Fe2+, Ca2+, and Mg2+.
32
What is hard water?
Water that has high mineral content, such as iron, calcium, and magnesium divalent cations.
33
What sort of prokaryotes live in the Dead Sea?
Extremely salt-tolerant microbial mats, including *Halobacterium*, *Haloferax volcanii*, *Halorubrum sodomense*, *Halobaculum gomorrense*, and *Haloarcula marismortui*.
34
How are prokaryotes grown in culture?
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. The process of culturing bacteria is complex and is one of the greatest discoveries of modern science.
35
How was the process of culturing bacteria discovered?
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.
36
What were Robert Koch's postulates?
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.
37
Why are some prokaryotes 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.
38
Where can biofilms be found?
Biofilms are present almost everywhere: they can cause the clogging of pipes and readily colonize surfaces in industrial settings. In 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.
39
Why are biofilms more robust than free-living prokaryotes?
Interactions among the organisms that populate a biofilm, together with their protective exopolysaccharide (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.
40
What are the five stages of biofilm development?
During stage 1, initial attachment, bacteria adhere to a solid surface via weak van der Waals interactions. During stage 2, irreversible attachment, hairlike appendages called pili permanently anchor the bacteria to the surface. During stage 3, maturation I, the biofilm grows through cell division and recruitment of other bacteria. An extracellular matrix composed primarily of polysaccharides holds the biofilm together. During stage 4, maturation II, the biofilm continues to grow and takes on a more complex shape. During stage 5, dispersal, the biofilm matrix is partly broken down, allowing some bacteria to escape and colonize another surface.
41
Why do bacteria in biofilms often show increased resistance to antibiotics and detergents?
The extracellular matrix and outer layer of cells protects the inner bacteria. The close proximity of cells also facilitates later gene transfer (of genes with antibiotic resistance, for example). Exo-enzymes that destroy antibiotics may save neighboring bacteria as well.
42
What is a capsule?
External structure that enables a prokaryote to attach to surfaces and protects it from dehydration. It can also protect the organism from attack by phagocytic cells, and makes pathogens more resistant to host organism immune responses.
43
What is conjugation?
Process by which prokaryotes move DNA from one individual to another using a pilus. The DNA transferred can be in the form of a plasmid or as a hybrid, containing both plasmid and chromosomal DNA.
44
What are some characteristics of the cell wall and envelope of Gram-negative bacteria?
Bacterium whose cell wall contains little peptidoglycan but has an outer membrane. They have a relatively thin cell wall composed of a few layers of peptidoglycan (only 10% of the total cell wall), surrounded by an outer envelope containing lipopolysaccharides (LPS) and lipoproteins. Porins are proteins in this cell membrane that allow substances to pass through the outer membrane. This outer envelope is sometimes referred to as a second lipid bilayer. The chemistry of this outer envelope is very different, however, from that of the typical lipid bilayer that forms plasma membranes.
45
What is a Gram-positive bacterium?
Bacterium that contains mainly peptidoglycan in its cell walls. They typically lack the outer membrane found in Gram-negative organisms. Up to 90% of the cell wall is composed of peptidoglycan, and most of the rest is composed of acidic substances called teichoic acids. Teichoic acids may be covalently linked to lipids in the plasma membrane to form lipoteichoic acids. Lipoteichoic acids anchor the cell wall to the cell membrane.
46
What is peptidoglycan?
Material composed of polysaccharide chains cross-linked to unusual peptides.
47
What is a pilus?
Surface appendage of some prokaryotes used for attachment to surfaces including other prokaryotes.
48
What is pseudopeptidoglycan?
Component of archaeal cell walls that is similar to peptidoglycan in morphology but contains different sugars.
49
What is an S-layer protein?
Surface-layer protein present on the outside of cell walls of archaea and bacteria.
50
What is teichoic acid?
Polymer associated with the cell wall of Gram-positive bacteria.
51
What is transduction?
Process by which a bacteriophage moves DNA from one prokaryote to another.
52
What is transformation?
Process by which a prokaryote takes in DNA found in its environment that is shed by other prokaryotes.
53
What are the three basic categories of prokaryotes, according to their shape?
Cocci (spherical), bacilli (rod-shaped), and spirilli (spiral-shaped).
54
What are proteobacteria?
A major phylum of Gram-negative bacteria. There are five primary classes of proteobacteria: alpha, beta, gamma, delta, and epsilon.
55
What are alpha proteobacteria?
Some species are photoautotrophic but some are symbionts of plants and animals and others are pathogens. Eukaryotic mitochondria are thought to be derived from bacteria in this group.
56
What are beta proteobacteria?
This group of bacteria is diverse. Some species play an important role in the nitrogen cycle.
57
What are gamma proteobacteria?
Many are beneficial symbionts that populate the human gut, but others are familiar human pathogens. Some species from this subgroup oxidize sulfur compounds.
58
What are delta proteobacteria?
Some species generate a spore-forming fruiting body in adverse conditions. Others reduce sulfate and sulfur.
59
What are epsilon proteobacteria?
Many species inhabit the digestive tract of animals as symbionts or pathogens. Bacteria from this group have been found in deep-sea hydrothermal vents and cold seep habitats.
60
What are some representative organisms of alpha proteobacteria?
* *Rhizobium*: nitrogen-fixing endosymbiont associated with the roots of legumes
* *Rickettsia*: obligate intracellular parasite that causes typhus and Rocky Mountain Spotted Fever (but not rickets, which is caused by vitamin D deficiency)
61
What are some representative organisms of beta proteobacteria?
* *Nitrosomonas*: species from this group oxidize ammonia into nitrite
* *Spirillum minus*: causes rat-bite fever
62
What are some representative organisms of gamma proteobacteria?
* *Escherichia coli*: normally beneficial microbe of the human gut, but some strains cause disease
* *Salmonella*: certain strains cause food poisoning or typhoid fever
* *Yersinia pestis*: causative agent of Bubonic plague
* *Pseudomonas aeruginosa*: causes lung infections
* *Vibrio cholera*: causative agent of cholera
* *Chromatium*: sulfur-producing bacteria that oxidize sulfur, producing H2S
63
What are some representative organisms of delta proteobacteria?
* *Myxobacteria*: generate spore-forming fruiting bodies in adverse conditions
* *Desulfovibrio vulgaris*: anaerobic, sulfate-reducing bacterium
64
What are some representative organisms of epsilon proteobacteria?
* *Campylobacter*: causes blood poisoning and intestinal inflammation
* *Helicobacter pylori*: causes stomach ulcers
65
What is a cold seep?
An area of the ocean floor where hydrogen sulfide, methane, and other hydrocarbon-rich fluid seepage occurs, often in the form of a brine pool.
66
What is *Chlamydias*?
Gram-negative bacterial phylum where all members are obligate intracellular parasites of animal cells. Cell walls lack peptidoglycan.
67
What is Spirochetes?
Gram-negative bacterial phylum where most members, which have spiral-shaped cells, are free-living anaerobes, but some are pathogenic. Flagella run lengthwise in the periplasmic space between the inner and outer membrane.
68
What are Cyanobacteria?
Also known as blue-green algae, these Gram-negative bacteria obtain their energy through photosynthesis. They are ubiquitous, found in terrestrial, marine, and freshwater environments. Eukaryotic chloroplasts are thought to be derived from bacteria in this group.
69
What are Gram-positive bacteria?
Soil-dwelling members of this subgroup decompose organic matter. Some species cause disease. They have a thick cell wall and lack an outer membrane.
70
What are some representative organisms of *Chlamydias*?
* *Chlamydia trachomatis*: common sexually transmitted disease that can lead to blindness
71
What are some representative organisms of Spirochetes?
* *Treponema pallidum*: causative agent of syphilis
* *Borrelia burgdorferi*: causative agent of Lyme disease
72
What are some representative organisms of Cyanobacteria?
* *Prochlorococcus*: believed to be the most abundant photosynthetic organism on earth; responsible for generating half the world's oxygen
73
What are some representative organisms of Gram-positive Bacteria?
* *Bacillus anthracis*: causes anthrax
* *Clostridium botulinum*: causes botulism
* *Clostridium difficile*: causes diarrhea during antibiotic therapy
* *Streptomyces*: many antibiotics, including streptomyocin, are derived from these bacteria
* *Mycoplasmas*: these tiny bacteria, the smallest known, lack a cell wall. Some are free-living, and some are pathogenic.
74
What is Euryarchaeota?
Archaeal phylum which includes methanogens, which produce methane as a metabolic waste product, and halobacteria, which live in an extreme saline environment.
75
What is Crenarchaeota?
Archaeal phylum whose members are ubiquitous and play an important role in the fixation of carbon. Many members of this group are sulfur-dependent extremophiles. Some are thermophilic or hyperthermophilic.
76
What is Nanoarchaeota?
Archaeal phylum which contains only one species, *Nanoarchaeum equitans*.
77
What is Korarchaeota?
Archaeal phylum whose members, considered to be one of the most primitive forms of life, have only been found in the Obsidian Pool, a hot spring at Yellowstone National Park.
78
What are some representative organisms of Euryarchaeota?
* Methanogens: methane production causes flatulence in humans and other animals
* Halobacteria: large blooms of this salt-loving archaea appear reddish due to the presence of bacteriorhodopsin in the membrane. Bacteriorhodopsin is related to the retinal pigment rhodopsin
79
What are some representative organisms of Crenarchaeota?
* *Sulfolobus*: members of this genus grow in volcanic springs at temperatures between 75 C and 80 C and at a pH between 2 and 3.
80
What are some representative organisms of Nanoarchaeota?
* *Nanoarchaeum equitans*: this species was isolated from the bottom of the Atlantic Ocean and from a hydrothermal vent at Yellowstone National Park. It is an obligate symbiont with *Ignicoccus*, another species of archaea.
81
What are some representative organisms of Korarchaeota?
No members of this species have been cultivated.
82
How do archaeal plasma membranes differ from those of bacteria and eukaryotes?
Archaeal phospholipids differ from those found in Bacteria and Eukarya in two ways. First, they have branched phytanyl (isoprene) sidechains instead of linear fatty acids. Second, an ether bond instead of an ester bond connects the lipid to the glycerol. Additionally, some archaeal membranes are lipid monolayers instead of bilayers.
83
What are some features of prokaryotic cell walls?
The cytoplasm of prokaryotic cells has a high concentration of dissolved solutes. Therefore, the osmotic pressure within the cell is relatively high. The cell wall is a protective layer that surrounds some cells and gives them shape and rigidity. It is located outside the cell membrane and prevents osmotic lysis. The chemical composition of the cell walls varies between archaea and bacteria, and also varies between bacterial species.
84
What is peptidoglycan?
Polysaccharide chain that is cross-linked by unusual peptides containing both L- and D-amino acids including D-glutamic acid and D-alanine. There are more than 100 different forms of peptidoglycan.
85
How do many antibiotics work?
Because proteins normally have only L-amino acids, many antibiotics work by mimicking D-amino acids and therefore have specific effects on bacterial cell wall development.
86
Who is the Gram staining method named after?
Its inventor, Danish scientist Hans Christian Gram (1853-1938).
87
What are the four different types of Archaean cell walls composed of?
Pseudopeptidoglycan, polysaccharide, glycoprotein, pure protein.
88
What do fossils of ancient prokaryotes look like?
Tiny bubbles in rock.
89
What were the first groups of bacteria thought to colonize land, and who derived these results?
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 prokaryotes. The model they derived from their data indicates that three important groups of bacteria - Actinobacteria, Deinococcus, and Cyanobacteria - were the first to colonize land.
90
What are actinobacteria?
A group of very common bacteria that include species important in decomposition of organic wastes.
91
What is the timeline of divergence of the three domains of life?
The timelines of divergence suggest that Bacteria diverged from the common ancestral species between 2.5 and 3.2 billion years ago, where archaea diverged earlier, between 3.1 and 4.1 billion years ago. Eukarya later diverged off the Archaean line.
92
What is ammonification?
Process by which ammonia is released during the decomposition of nitrogen-containing organic compounds.
93
What is a chemotroph?
Organism that obtains energy from chemical compounds.
94
What is a decomposer?
Organism that carries out the decomposition of dead organisms.
95
What is denitrification?
Transformation of nitrate from soil to gaseous nitrogen compounds such as N2O, NO, and N2.
96
What is nitrification?
Conversion of ammonium into nitrite and nitrate in soils.
97
What is nitrogen fixation?
Process by which gaseous nitrogen is transformed, or "fixed" into more readily available forms such as ammonia.
98
What are some prokaryotic macronutrients?
Carbon, Hydrogen, Oxygen, Nitrogen, Phosphorus, Sulfur. Carbon accounts for about 50% of the composition of the cell. Nitrogen represents 12% of the total dry weight of a typical cell and is a component of proteins, nucleic acids, and other cell constituents. Most of the nitrogen available in nature is either atmospheric nitrogen (N2) or another inorganic form. Diatomic nitrogen can be converted into an organic form only by nitrogen-fixing organisms. Both hydrogen and oxygen are part of many organic compounds and of water. Phosphorus is required by all organisms for the synthesis of nucleotides and phospholipids. Sulfur is part of the structure of some amino acids such as cysteine and methionine, and is also present in several vitamins and coenzymes. Other important macronutrients are potassium (K), magnesium (Mg), calcium (Ca), and sodium (Na).
99
What is one example of how iron is used in prokaryotic cells?
Iron is necessary for the function of the cytochromes involved in electron-transport reactions.
100
What are some micronutrients required by some prokaryotes, primarily as cofactors?
Boron (B), chromium (Cr), and manganese (Mn).
101
What is a chemoorganotroph?
Chemotroph that can use organic compounds as energy sources.
102
What are chemolitotrophs?
Chemotrophs that can use inorganic compounds as energy sources.
103
What is an autotroph?
Organism that is capable of fixing inorganic carbon.
104
What are autotrophic prokaryotes?
Prokaryote that synthesizes organic molecules from carbon dioxide.
105
What are heterotrophic prokaryotes?
Prokaryote that obtains carbon from organic compounds.
106
What is a photoautotroph?
Organism that uses energy from sunlight, and carbon from carbon dioxide and water.
107
What is a chemoheterotroph?
Organism that obtains energy and carbon from an organic chemical source.
108
What is a chemolitoautotroph?
Organism that obtains its energy from inorganic compounds, and that builds its complex molecules from carbon dioxide.
109
What is the carbon cycle?
Carbon is cycled through Earth's major reservoirs: land, the atmosphere, aquatic environments, sediments and rocks, and biomass. The movement of carbon is via carbon dioxide, which is removed from the atmosphere by land plants and marine prokaryotes, and is returned to the atmosphere via the respiration of chemoorganotrophic organisms, including prokaryotes, fungi, and animals. The most important contributor of carbon dioxide to the atmosphere is microbial decomposition of dead material that undergo respiration. Although the largest carbon reservoir in terrestrial ecosystems is in rocks and sediments, that carbon is not readily available.
110
What is humus?
Mixture of organic materials from dead plants and prokaryotes that have resisted decomposition.
111
What carbon cycle takes place in anoxic sediments?
In aqueous environments and their anoxic sediments, there is another carbon cycle taking place. In this case, the cycle is based on one-carbon compounds. In anoxic sediments, prokaryotes, mostly archaea, produce methane. The methane moves into the zone above the sediment, which is richer in oxygen and supports bacteria called methane oxidizers that oxidize CH4 to CO2, which then returns to the atmosphere.
112
What is the nitrogen cycle?
Nitrogen is recycled from organic compounds to ammonia, ammonium, nitrate, nitrite, and nitrogen gas by myriad processes, many of which are carried out only by prokaryotes. Prokaryotes are key to the nitrogen cycle. The largest pool of nitrogen available in the terrestrial ecosystem is gaseous nitrogen from the air, but this nitrogen is not usable by plants, which are primary producers. Gaseous nitrogen is fixed into more readily available forms such as ammonia through the process of nitrogen fixation. Ammonia can be used by plants or converted to other forms, such as through anaerobic catabolism by some prokaryotes, releasing N2.
113
Ammonia constitutes what percent of the total nitrogen released to the atmosphere?
15% - the rest is N2 and N2O.
114
What bacterial species perform nitrification?
It is carried out by bacteria belonging to the genera *Nitrosomonas*, *Nitrobacter*, and *Nitrospira*.
115
What is an antibiotic?
Biological substance that, in low concentration, is antagonistic to the growth of prokaryotes.
116
What was the Black Death?
One of the most devastating pandemics, 1346 to 1361, that is believed to have been an outbreak of bubonic plague caused by the bacterium *Yersinia pestis*. It is thought to have originated initially in China and spread along the Silk Road to the Mediterranean region and Europe, carried by rat fleas living on black rats that were always present on ships. The Black Death reduced the world's population from an estimated 450 million to about 350-375 million.
117
What is botulism?
A potentially fatal disease produced by a toxin from the anaerobic bacterium *Clostridium botulinum*. Some of the most common sources for this bacterium were non-acidic canned foods, homemade pickles, and processed meat and sausages. The can, jar, or package created a suitable anaerobic environment where *Clostridium* could grow. Proper sterilization and canning procedures have reduced the incidence of this disease.
118
What is CA-MRSA?
MRSA acquired in the community rather than in a hospital setting. It can appear in healthy people who haven't been hospitalized but who live or work in tight populations (like military personnel and prisoners).
119
What is an emerging disease?
Disease making an initial appearance in a population or that is increasing in incidence or geographic range.
120
What is an endemic disease?
Disease that is constantly present, usually at low incidence, in a population.
121
What is an epidemic?
Disease that occurs in an unusually high number of individuals in a population at the same time.
122
What is a foodborne disease?
Any illness resulting from the consumption of contaminated food, or of the pathogenic bacteria, viruses, or other parasites that contaminate food.
123
What is MRSA (methicillin-resistant *Staphylococcus aureus*)?
Very dangerous *Staphylococcus aureus* strain resistant to multiple antibiotics, such as methicillin, amoxicillin, penicillin, and oxacillin. MRSA can cause infections of the skin, but it can also infect the bloodstream, lungs, urinary tract, or sites of injury.
124
What is a pandemic?
Widespread, usually worldwide, epidemic disease.
125
What is a serotype?
Strain of bacteria that carries a set of similar antigens on its cell surface, often many in a bacterial species.
126
What is zoonosis?
Disease that primarily infects animals that is transmitted to humans.
127
What was the scope and impact of the Plague of Athens?
The Plague of Athens in 430 BC killed ¼ of the Athenian troops that were fighting in the great Peloponnesian War and weakened Athens' dominance and power. The plague impacted people living in overcrowded Athens as well as troops aboard ships that had to return to Athens.
128
What is *Salmonella enterica* serovar Typhi?
A gram-negative, rod-shaped gamma proteobacterium, and the causative agent of Typhoid fever.
129
What is Typhoid fever?
A disease spread through feces that causes intestinal hemorrhage, high fever, delirium, and dehydration. Carriers of the disease can be asymptomatic.
130
How prevalent is Typhoid fever?
Today, between 16 and 33 million cases of this re-emerging disease occur annually, resulting in over 200,000 deaths.
131
What is an example of an asymptomatic carrier of Typhoid fever?
In the early 1900s, a cook named Mary Mallon unknowingly spread the disease to over 50 people, three of whom died.
132
What was the likely source of the Plague of Athens?
The source of the plague may have been identified recently when researchers from the University of Athens were able to use DNA from teeth recovered from a mass grave. The scientists identified nucleotide sequences from *Salmonella enterica* serovar Typhi, which causes typhoid fever and is commonly seen in overcrowded areas and has caused epidemics throughout recorded history.
133
What was the scope and impact of the Plague of Justinian?
From 541 to 750, an outbreak of what was likely bubonic plague, which eliminated ¼ to ½ of the human population in the eastern Mediterranean region. The population in Europe dropped by 50% during this outbreak.
134
What is the Bubonic plague?
A disease caused by the bacterium *Yersinia pestis*. The disease is transmitted through the bite of an infected flea, which is infected by a rodent. Symptoms include swollen lymph nodes, fever, seizure, vomiting of blood, and gangrene.
135
When was the Great Plague of London?
An outbreak of bubonic plague that occurred in the mid-1600s which killed an estimated 200,000 people (about 20% of the city's population).
136
What is *Yersinia pestis*?
A gram-negative, rod-shaped bacterium from the class Gamma Proteobacteria. It is the causative agent of bubonic plague.
137
What was the impact of European diseases on Native Americans?
It has been estimated that up to 90% of Native Americans died from infectious diseases after the arrival of Europeans, who had no natural resistance to them.
138
What is brucellosis?
An example of a prokaryotic zoonosis that is re-emerging in some regions.
139
What is necrotizing fasciitis?
Flesh-eating bacteria, has been increasing in virulence for the last 80 years for unknown reasons.
140
What are some examples of diseases that the WHO has identified whose worldwide re-emergence should be monitored?
Two viral diseases - dengue fever and yellow fever - and three bacterial diseases - diphtheria, cholera, and bubonic plague.
141
What is Lyme disease?
A disease which often, but not always, results in a characteristic bullseye rash. It is caused by a Gram-negative spirochete bacterium of the genus *Borrelia*. The bacteria infect ticks, which in turn infect mice. Deer are the preferred secondary host, but the ticks may also feed on humans. Untreated, the disease causes chronic disorders in the nervous system, eyes, joints, and heart. The disease is named after Lyme, Connecticut, where an outbreak occurred in 1995 and has subsequently spread. The disease is not new, as genetic evidence suggests that Otzi the Iceman, a 5300-year-old mummy found in the Alps, was infected with *Borrelia*.
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How do biofilms cause disease?
Biofilms are responsible for diseases such as infections in patients with cystic fibrosis, Legionnaires' disease, and otitis media. They produce dental plaque and colonize catheters, prostheses, transcutaneous and orthopedic devices, contact lenses, and internal devices such as pacemakers. They also form in open wounds and burned tissue. In healthcare environments, biofilms grow on hemodialysis machines, mechanical ventilators, shunts, and other medical equipment. 65% of all infections acquired in the hospital (nosocomial infections) are attributed to biofilms. Biofilms are also related to diseases contracted from food because they colonize the surfaces of vegetables, leaves and meat, as well as food-processing equipment that isn't adequately cleaned.
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Why are biofilm infections difficult to eradicate?
Biofilm infections develop gradually; sometimes they do not cause symptoms immediately. They are rarely resolved by host defense mechanisms. They tend to be resistant to most of the methods used to control microbial growth, including antibiotics. They respond poorly or only temporarily to antibiotics, and it has been said that they can resist up to 1000x the antibiotic concentrations used to kill the same bacteria when they are free-living or planktonic. An antibiotic dose that large would harm the patient; therefore, scientists are working on new ways to get rid of biofilms.
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What is the main cause of antibiotic resistance in bacteria?
The abuse (imprudent and excessive use) of antibiotics. One major misuse of antibiotics is in patients with colds or the flu, for which antibiotics are useless. Another problem is the excessive use of antibiotics in livestock. The routine use of antibiotics in animal feed promotes bacterial resistance. In the United States, 70% of the antibiotics produced are fed to animals. They are given to livestock in low doses, which maximize the probability of resistance developing, and these resistant bacteria are readily transferred to humans.
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What is *Staphylococcus aureus*?
"Staph", a common bacterium that can live in the human body and is usually treated with antibiotics.
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How do foodborne diseases affect Americans?
Although the United States has one of the safest food supplies in the world, the CDC has reported that "76 million people get sick, more than 300,000 are hospitalized, and 5,000 Americans die each year from foodborne illness."
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What is *E. coli* serotype O157:H7?
Bacteria which caused an outbreak in 2006 in raw spinach. Though most *E. coli* are not particularly dangerous to humans, O157:H7 can cause bloody diarrhea and is potentially fatal.
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What is *E. coli* serotype O104:H4?
Bacteria which caused an outbreak in Germany in 2011 that killed 32 people and sickened 3800. It grew on vegetable sprouts grown at an organic farm. It produced Shiga toxin, a substance that inhibits protein synthesis in the host cell. The toxin destroys red blood cells resulting in bloody diarrhea. Deformed red blood cells clog the capillaries of the kidney, which can lead to kidney failure, which happened to 845 patients in the 2011 outbreak. Kidney failure is usually reversible, but some patients experience kidney problems years later.
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What is epidemiology?
The study of the occurrence, distribution, and determinants of health and disease in a population, and is a part of public health. An epidemiologist studies the frequency and distribution of diseases within human populations and environments.
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What do epidemiologists do?
Epidemiologists collect data about a particular disease and track its spread to identify the original mode of transmission. They sometimes work in close collaboration with historians to try to understand the way a disease evolved geographically and over time, tracking the natural history of pathogens. They gather information from clinical records, patient interviews, surveillance, and any other available means. That information is used to develop strategies, such as vaccinations, and design public health policies to reduce the incidence of a disease or to prevent its spread. Epidemiologists also conduct rapid investigations in case of an outbreak to recommend immediate measures to control it.
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What degrees do epidemiologists typically have?
Epidemiologists have bachelor's degrees, plus a master's degree in public health (MPH). Many epidemiologists are also physicians (and have an MD), or they have a Ph.D. in an associated field, such as biology or microbiology.
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What is biological nitrogen fixation (BNF)?
Conversion of atmospheric nitrogen into ammonia (NH3) exclusively carried out by prokaryotes. After photosynthesis, BNF is the second most important biological process on Earth.
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What is bioremediation?
Use of microbial metabolism to remove pollutants.
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What is biotechnology?
Any technological application that uses living organisms, biological systems, or their derivatives to produce or modify other products.
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What is a nodule?
Novel structure on the roots of certain plants (legumes) that results from the symbiotic interaction between the plant and soil bacteria (rhizobia), is the site of nitrogen fixation. Nitrogenase, the enzyme that fixes nitrogen, is inactivated by oxygen, so the nodule provides an oxygen-free area for nitrogen fixation to take place.
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Why is nitrogen important to living things?
Because it is part of nucleotides and amino acids that are the building blocks of nucleic acids and proteins, respectively.
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Where can nitrogen be found?
Nitrogen is usually the most limiting element in terrestrial ecosystems, with atmospheric nitrogen, N2, providing the largest pool of available nitrogen. However, eukaryotes cannot use atmospheric, gaseous nitrogen to synthesize macromolecules. Nitrogen can be fixed biologically or abiotically.
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How can abiotic nitrogen fixation occur?
As a result of lightning or by industrial processes.
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Which prokaryotes carry out biological nitrogen fixation?
Soil bacteria, cyanobacteria, *Frankia* spp.
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What is *Frankia* spp?
Filamentous bacteria interacting with actinorhizal plants such as alder, bayberry, and sweet fern.
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What is the equation representing BNF?
N2 + 16ATP + 8e– ⇒ 2NH3 + 16ADP + 16Pi + H2, where Pi = inorganic phosphate
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What is the total fixed nitrogen through BNF per year?
About 100 to 180 million metric tons per year. Biological processes contribute 65% of the nitrogen used in agriculture.
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What are the most important nitrogen fixers in aquatic environments?
Cyanobacteria.
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What is an example of a nitrogen fixer in soil environments?
Members of the genus *Clostridium* are examples of free-living, nitrogen-fixing bacteria in soil.
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What is the most important source of BNF?
Bacteria that live symbiotically with legume plants. Symbionts may fix more nitrogen in soils than free-living organisms by a factor of 10.
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What are some of the benefits of using rhizobia as a biofertilizer?
Nitrogen fixation by rhizobia provides a natural and inexpensive plant fertilizer, as it reduces atmospheric nitrogen to ammonia, which is easily usable by plants. Through symbiotic nitrogen fixation, the plant benefits from using an endless source of nitrogen: the atmosphere. Bacteria benefit from using photosynthates (carbohydrates produced during photosynthesis) from the plant and having a protected niche. Additionally, the soil benefits from being naturally fertilized.
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What are the most important legumes?
Some legumes, such as soybeans, are key sources of agricultural protein. Some of the most important grain legumes are soybeans, peanuts, peas, chickpeas, and beans. Other legumes, such as alfalfa, are used to feed cattle.
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What is a soybean?
A legume (*Glycine max*) that interacts symbiotically with *Bradyrhizobium japonicum* to form nodules where nitrogen fixation occurs.
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What are some current topics of study in biotechnology?
Genetic engineering, artificial selection, antibiotic production, and cell culture.
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What are some examples of food products derived from the use of prokaryotes?
Cheese, bread, wine, beer, yogurt. They employ both bacteria and other microbes, such as yeast, a fungus.
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How long have prokaryotes been used in early biotechnology?
Cheese production began around 4000-7000 years ago when humans began to breed animals and process their milk. Fermentation in this case preserves nutrients: Milk will spoil relatively quickly, but when processed as cheese, it is more stable. As for beer, the oldest records of brewing are about 6000 years old and refer to the Sumerians. Evidence indicates that the Sumerians discovered fermentation by chance. Wine has been produced for about 4500 years, and evidence suggests that cultured milk products, like yogurt, have existed for at least 4000 years.
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How has bioremediation been used to remove pollutants from an environment?
Bioremediation has been used to remove agricultural chemicals (pesticides, fertilizers) that leach from soil into groundwater and the subsurface. Certain toxic metals and oxides, such as selenium and arsenic compounds, can be removed from water by bioremediation. The reduction of SeO4-2 to SeO3-2 and to Se0 (metallic selenium) is a method used to remove selenium ions from water. Mercury is an example of a toxic metal that can be removed from an environment by bioremediation. As an active ingredient of some pesticides, mercury is used in industry and is also a by-product of certain processes, such as battery production. Methyl mercury is usually present in very low concentrations in natural environments, but it is highly toxic because it accumulates in living tissues.
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What is an example of bacteria that can carry out the biotransformation of toxic mercury into nontoxic forms?
*Pseudomonas aeruginosa*, which can convert Hg+2 into Hg0, which is nontoxic to humans.
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How is bioremediation used to help cleanup oil spills?
To clean up oil spills, bioremediation is promoted by the addition of inorganic nutrients that help bacteria to grow. Hydrocarbon-degrading bacteria feed on hydrocarbons in the oil droplets, breaking down the hydrocarbons. In the case of oil spills in the ocean, ongoing, natural bioremediation tends to occur, inasmuch as there are oil-consuming bacteria in the ocean prior to the spill. In addition to naturally occurring oil-degrading bacteria, humans select and engineer bacteria that possess the same capability with increased efficiency and spectrum of hydrocarbon compounds that can be processed. Under ideal conditions, it has been reported that up to 80% of the nonvolatile compounds in oil can be degraded within one year of the spill. Other oil fractions containing aromatic and highly branched hydrocarbon chains are more difficult to remove and remain in the environment for longer periods of time.
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What are some examples of oil spills that have been bioremediated?
The Exxon Valdez spill in Alaska (1989), the Prestige oil spill in Spain (2002), the spill into the Mediterranean from a Lebanon power plant (2006), and the BP oil spill in the Gulf of Mexico (2010).
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What is an example of bacteria used for bioremediation of oil spills?
*Alcanivorax borkumensis*, which produce surfactants that solubilize the oil, whereas other bacteria degrade the oil into carbon dioxide.
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How was the Exxon Valdez spill in Alaska cleaned up?
Workers hosed oil from the beaches and then used a floating boom to corral the oil, which was finally skimmed from the surface.
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What are some activities of commensal bacteria?
The commensal bacteria that inhabit our skin and gastrointestinal tract do a host of good things for us. They protect us from pathogens, help us digest our food, and produce some of our vitamins and other nutrients. Scientists have gathered evidence that these bacteria may also help regulate our moods, influence our activity levels, and help control weight by affecting food choices and absorption patterns. The Human Microbiome Project has begun the process of cataloging our normal bacteria and archaea so we can better understand these functions.
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How does *Clostridium difficile* grow in human digestive systems?
People who take high doses of antibiotics tend to lose many of their normal gut bacteria, allowing a naturally antibiotic-resistant *Clostridium difficile* to overgrow and cause severe gastric problems, especially chronic diarrhea. Treating this problem with antibiotics only makes it worse. However, it has been successfully treated by giving the patients fecal transplants from healthy donors to reestablish the normal intestinal microbial community. Clinical trials are underway to ensure the safety and effectiveness of this technique.
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What is *Clostridium difficile*?
A Gram-positive, rod-shaped bacterium that causes severe diarrhea. Infection commonly occurs after the normal gut fauna is eradicated by antibiotics.
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What do studies suggest may be caused by the absence of certain microbes from the human intestinal tract?
They may contribute to the development of allergies and some autoimmune disorders. Research is underway to determine whether adding certain microbes may help in the treatment of these problems as well as in treating some forms of autism.
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Why is foodborne disease caused by E. coli not prevented by washing spinach with water several times?
E. coli colonizes the surface of the leaf, forming a biofilm that is more difficult to remove than free (planktonic) cells. Additionally, bacteria can be taken up in the water that plants are grown in, thereby entering the plant tissues rather than simply residing on the leaf surface.
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What are xenobiotics?
Synthetic compounds found in an organism but not normally produced or expected to be present in that organism.
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What bacterium was used when Robert Koch developed Koch's postulates?
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.
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What is the average age of people afflicted by MRSA?
The Journal of the American Medical Association has reported that, among MRSA-afflicted persons in healthcare facilities, the average age is 68, whereas people with CA-MRSA have an average age of 23.
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What percentage of prokaryotes are unculturable?
Over 99% of bacteria and archaea are unculturable.
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How can non-culturable prokaryotes be detected?
The presence of non-culturable prokaryotes can be detected through molecular techniques, such as PCR.
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What is the impact of bubonic plague?
In modern times, approximately 1000 to 3000 cases of plague arise globally each year. Although contracting bubonic plague before antibiotics meant almost certain death, the bacterium responds to several types of modern antibiotics, and mortality rates from plague are now very low.
