Chapter 4- Prokaryotic diversity Flashcards
1
Q
3 domains are all living organisms are classified into
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Archaea, Bacteria, and Eukarya. Archaea and bacteria are unicellular prokaryotes
2
Q
How abundant are prokaryotes on and within the human body?
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Prokaryotes outnumber human cells 10:1 in some estimates, but the ratio is 1:1 in others. They are found in the mouth, nasal cavity, throat, ears, gastrointestinal tract, and vagina. There are also large colonies of bacteria on the skin
3
Q
How are bacteria essential to ecosystems?
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Bacteria are part of soil formation and stabilization processes through the break down of organic matter and the development of biofilms. Some species of bacteria use acids and carbohydrates released from plant roots as nutrients. They metabolize these substances and release the products of metabolism into the soil to enhance the soil’s fertility. In salty lakes like the Dead Sea, bacteria decompose dead shrimp to nourish young shrimp and flies with the products of bacterial metabolism
4
Q
Why are bacteria able to exist in so many different environments on earth?
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Because they are extremely resilient and adaptable. They are metabolically flexible, so they can switch from one energy source or metabolic pathway to another, based on the availability of resources.
5
Q
Carbon fixation
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Animals require organic carbon to grow, but they can’t use inorganic carbon sources like carbon dioxide. Therefore, animals rely on prokaryotes to convert carbon dioxide into organic carbon products. This process is called carbon fixation
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Q
Nitrogen fixation
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The conversion of atmospheric nitrogen into ammonia, which plants use to form many biomolecules they need to survive. Legume plants rely on specific nitrogen fixing bacteria to help them make the building blocks of nucleic acids. These plants can also be eaten by animals, which will sustain their growth and survival. If the plants aren’t eaten and die, the products of nitrogen fixation will then enrich the soil and be used by other plants
7
Q
How are prokaryotes responsible for cleaning up the environment?
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Some bacteria play a role in degrading toxic chemicals that pollute water and soil.
8
Q
Negative impacts of prokaryotes (2)
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Around 1% of prokaryotes are human pathogens, but collectively, these species are responsible for a large number of diseases that affect humans. In addition, prokaryotes may play a role in climate change. As earth’s temperature rises, soil that used to be frozen year round (permafrost) has been to thaw. Carbon trapped in the permafrost is released and metabolized by prokaryotes, which releases large amount of greenhouse gases such as carbon dioxide and methane.
9
Q
Community
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A group of interacting populations of organisms. Prokaryotes live in a community
10
Q
Population
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A group of individual organisms belonging to the same biological species and limited to a certain geographic area
11
Q
Cooperative interactions
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Interactions that benefit the populations in a community
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Q
Competitive interactions
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Interactions in which one population competes with another for resources
13
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Microbial ecology
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The study of the cooperative and competitive interactions between microbial populations and their environment
14
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Symbiosis
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Any interaction between between species that are associated with each other within a community. These interactions fall in a spectrum between opposition and cooperation, and these interactions can be beneficial or harmful
15
Q
Mutualism
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Symbiosis where two species benefit from each other. Humans have a mutualistic relationship with some strains of E. coli, which obtain nutrients living in the intestines and produces vitamin K (which is required to make blood clotting factors) in return
16
Q
Amensalism
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A type of symbiosis where one population is harmed and the other is unaffected. Some bacteria on the skin produce bacteriocins that kill pathogenic bacteria
17
Q
Commensalism
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A type of symbiosis where one population receives a benefit and the other population is unaffected. Some species of bacteria on the skin uses dead human skin cells as a source of nutrients, but we don’t react to this bacteria in any way
18
Q
Neutralism
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A type of symbiosis where neither of the populations are affected. An example is the coexistence of metabolically active bacteria and endospores (dormant, metabolically passive bacteria)
19
Q
Parasitism
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A type of symbiosis where one population benefits and the other population is harmed. This occurs when humans are infected with pathogenic bacteria that invade the body and produce toxic substances or cause disease. This includes the bacteria that causes tetanus and diphtheria
20
Q
Microbiome
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Refers to all prokaryotic and eukaryotic microorganisms, and their genetic material, that are associated with a certain organism or environment.
21
Q
Subtypes of microbiota in the human microbiota
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Resident microbiota and transient microbiota. Resident microbiota consists of microorganisms that constantly live in or on our bodies. Transient microbiota is microorganisms that are only temporarily found in the human body, including pathogenic microbes
22
Q
How does the resident microbiota differ between each area of the body?
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The resident microbiota is diverse in terms of the preference of different microorganisms in different areas of the human body. In the mouth alone, some bacteria prefer the front or back teeth, while others prefer the gums. The inner surface of the cheek has the least diverse microbiota because of its exposure to oxygen, while the spaces between teeth have the most diverse microbiota since they have limited oxygen exposure. Different species of bacteria are most prevalent in different areas of the body
23
Q
How does an individual’s microbiome change over time?
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Before birth, there is a rapid increase in the population of Lactobacillus in the vagina. This provides the first colonization of microbiota during birth. After birth, additional microbes are acquired when the baby comes into contact with other individuals. The microbiome continues to evolve over the course of an individual’s life as new microbes colonize and are eliminated from the body. Babies born vaginally have different microbiota and are less prone to disease than babies born by C-section.
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Q
Why is an individual’s microbiota important for their health?
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Resident microbiotas occupy niches that might otherwise be taken by pathogenic microbes. The Lactobacillus population in the vagina produces lactic acid, which contributes to the acidity of the vagina and inhibits the growth of pathogenic yeasts. If the population of resident microbiota is decreases, like by antibiotics, the vagina becomes a more favorable environment for the growth of yeasts.
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Which characteristics of prokaryotes are used to classify them?
Prokaryotes are challenging to classify because they don't reproduce sexually and don't have many morphological features. They are classified based on shape, staining patterns, biochemical or physiological differences, and nucleotide sequences in genes. The manual in determinative bacteriology and the newer Bergey's manual of systematic bacteriology list the biological properties of bacterial species and their taxonomy
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How are bacteria classified based on staining patterns?
Bacteria can be classified as gram positive, gram negative, or atypical. Gram positive bacteria have a thick peptidoglycan cell wall that retains the primary crystal violet stain and stain purple. Gram negative bacteria have a thin cell wall, so the crystal violet stain is not retained. They are stained by safranin and appear pink or red. There are certain species that are considered atypical because they can't be evaluated by gram staining
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How are gram negative bacteria further classified?
They are classified into proteobacteria, cytophaga-flavobacterium-bacteroides (CFB), and spirochetes. This is based on physiological, biochemical, and genetic features. Proteobacteria is a diverse group that includes some human pathogens like E. coli. The CFB group contains components of normal human gut microbiota. The spirochetes are spiral shaped bacteria that include the pathogen that causes syphilis
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How are gram positive bacteria further classified?
They are classified into low G+C and high G+C bacteria, based on their prevalence of guanine and cytosine nucleotides. Low G+C bacteria have less than 50% of guanine and cytosine nucleotides in their DNA. This includes human pathogens like those that cause anthrax and tetanus. High G+C bacteria have more than 50% guanine and cytosine nucleotides in their DNA. This includes the bacteria that causes diphtheria and tuberculosis
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Classes of Proteobacteria (5)
Alpha, beta, gamma, delta, and epsilon proteobacteria
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Proteobacteria
A phylum of gram negative bacteria within the domain bacteria. Proteobacteria is a diverse group that is defined based on the similarity of nucleotide sequences in their genome.
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Alphaproteobacteria
Many of these bacteria are obligate or facultative intracellular bacteria. Some species are characterized as oligotrophs. Ricksettsias are considered alphaproteobacteria, which are obligate intracellular pathogens and include a number of human pathogens. C. trachomatis is another example, which causes trachoma, a disease of the eyes that can cause blindness
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Oligotrophs
Organisms capable of living in low nutrient environments such as deep oceanic sediments, glacial ice, or deep undersurface soil
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Obligate intracellular pathogens
Pathogens that require part of their life cycle to occur inside other celled called host cells. This includes Rickettsia, which is metabolically inactive outside of their host cell. They can't synthesize their own ATP, so they rely on cells for their energy needs
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Rickettsia
Alphaproteobacteria that are obligate intracellular pathogens. R. rickettsii causes rocky mountain spotted fever, which is a life threatening form of meningoencephalitis. This bacteria infects ticks and can be transmitted to humans by a bite from an infected tick. Another species of rickettsia is spread by lice and causes epidemic typhus, a severe disease causing high fever, abdominal pain, and delirium. A relative called R. typhi causes less sever endemic typhus
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Betaproteobacteria
A diverse group of bacteria. The different species in this group utilize a wide range of metabolic strategies and can survive in a range of environments. Includes the genus Neisseria and the bacterium Bordetella pertussis that is responsible for pertussis
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Neisseria
Betaproteobacteria. They are cocci that live on mucosal surfaces of the human body. They require high levels of moisture, nutrients, and carbon dioxide. They are also microaerophilic and have diplococcal growth in culture. They include the bacteria N. gonorrhoeae, which is the causative agent of gonorrhea.
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Bordetella pertussis
A member of betaproteobacteria. It produces several toxins that paralyze the movement of cilia in the human respiratory tract and directly damage the cells of the respiratory tract, causing a severe cough.
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Microaerophilic
Organisms that require low levels of oxygen
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Gammaproteobacteria
The most diverse class of gram negative bacteria. Includes many human pathogens, such as P. aeruginosa, which is responsible for diverse infections in many areas of the body. Also includes the family Pasteurellaceae, which contains human and animal pathogens
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P. aeruginosa
A gammaproteobacterium that is responsible for a wide range of human infections. It is an aerobic, nonfermenting, high motile bacterium. It infects wounds and burns, can be the cause of chronic UTIs, and can be the cause of respiratory infections in ventilated patients and patients with cystic fibrosis. Infections by this bacteria are difficult to treat because the bacterium is resistant to many antibiotics and forms biofilms
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Pasteurellaceae
A family of gammaproteobacteria. Pasteurella hemolytica causes severe pneumonia in sheep and goats. The genus haemophilus contains two human pathogens, H. influenzae and H. ducreyi. H. influenzae does not cause influenza (which is a viral infection). It can cause respiratory tract infections, like pneumonia, ear infections, and bronchitis.
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Vibrionales
An order that belongs to gammaproteobacteria. It is an aquatic bacterium that lives in highly alkaline environments like sea ports. A toxin produced by V. cholerae causes hypersecretion of electrolytes and water in the large intestine, leading to profuse watery diarrhea and dehydration. V. parahaemolyticus is a cause of gastrointestinal disease in humans, while V. vulnificus causes serious cellulitis (infection of the skin and deeper tissues) and blood borne infections
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Legionella
A genus that belongs to gammaproteobacteria. L. pneumophila is the pathogen that is responsible for Legionnaires disease. It is an aquatic bacterium that inhabits pools of warm water, like those found in air conditioning units in large buildings, and can spread via aerosols, infecting the residents of large buildings
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Enteric
Refers to the intestine
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Enterobacteria
A large family of enteric bacteria that belongs to gammaproteobacteria. They are facultative anaerobes and are able to ferment carbohydrates. They have two categories: coliforms (E. coli) and noncoliforms
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E. coli
A category of enterobacteria, which belongs to gammproteobacteria. Coliforms are able to ferment lactose completely (with the production of acid and gas). Many strains of E. coli are in mutualistic relationships with humans. However, some strains produce potentially deadly Shiga toxins. When they enter target cells, Shiga toxins interact with ribosomes and stop protein synthesis. This leads to cellular death and hemorrhagic colitis, characterized by inflammation of the intestinal tract and bloody diarrhea
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Noncoliforms
A category of enteric bacteria that is considered part of gammaproteobacteria. They either can't ferment lactose or can only ferment it incompletely (producing either acid or gas, but not both). Includes human pathogens like Salmonella, shigella, and Y. pestis
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Salmonella
A genus that belongs to the noncoliform group of Enterobacteriaceae. There is no consensus about how many species it includes. Their classification is based on patterns of reactivity by animal antisera against molecules on the surface of the bacterial cells. Some serotypes of Salmonella can cause salmonellosis, characterized by inflammation of the small and the large intestine, accompanied by fever, vomiting, and diarrhea. The species S. enterobacterica causes typhoid fever, with symptoms including fever, abdominal pain, and skin rashes
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Serotypes
Strains or variations of the same species of bacteria
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Deltaproteobacteria
A small class of gram negative proteobacteria that includes sulfate reducing bacteria (SRBs). SRBs use sulfate as the final electron acceptor in the electron transport
chain. Few SRBs are pathogenic. However, the SRB Desulfovibrio orale is associated with periodontal disease (disease of the gums)
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Bdellovibrio
A genus of deltaproteobacteria. Species of this genus are parasites of other gram-negative bacteria. This genus invades the cells of the host bacterium and positions itself in the periplasm, feeding on the host's proteins and polysaccharides. This infection is lethal for host cells
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Periplasm
The space between the plasma membrane and the cell wall
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Myxobacteria
A type of deltaproteobacteria that lives in the soil and scavenges inorganic compounds. They are motile and interact with other bacteria within and outside their own group. They can form multicellular, macroscopic "fruiting bodies", structures that are being studied by biologists. These bacteria can also form metabolically inactive myxospores
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Epsilonproteobacteria
The smallest class of proteobacteria. They are gram negative and microaerophilic. It contains two clinically relevant genera called campylobacter and helicobacter, which are both spiral shaped rods
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Campylobacter
A genus of epsilonproteobacteria. It can cause food poisoning that manifests as severe enteritis (inflammation in the small intestine). It is usually caused by consuming contaminated poultry products
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Helicobacter
A genus of epsilonproteobacteria. Includes the bacterium H. pylori, which is a member of typical stomach microbiota. It is also the most common cause of chronic gastritis and ulcers of the stomach and duodenum. It is also linked to stomach cancer. H. pylori can survive in the highly acidic environment of the stomach, which is unusual. It produces urease and other enzymes that modify its environment and make it less acidic.
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4 classes of gram-negative nonproteobacteria
1. Chlamydia
2. Spirochetes
3. CFB
4. Planctomycetes
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Chlamydia
A class of nonproteobacteria. They are gram negative, obligate intracellular pathogens that are extremely resistant to cellular defenses. This gives them the ability to spread from host to host rapidly via elementary bodies
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Elementary bodies
Endospore-like forms of intracellular bacteria that enter an epithelial cell, where they become active. They are metabolically and reproductively inactive before they enter the cell. This is characteristic of the class chlamydia
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Spirochetes
A class of nonproteobacteria that is spiral shaped. Most of them are very thin and are therefore usually examined under darkfield fluorescent microscopy. They are highly motile and use an axial filament to propel themselves. The subspecies T. pallidum pallidum causes the STD syphilis, other subspecies of T. pallidum cause tropical infectious diseases of the skin, bones, and joints
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Axial filament
Found in spirochetes. They are similar to a flagellum, but wrap around the cell and run inside the cell body of a spirochete in the periplasmic space
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CFB group
The gram-negative nonproteobacteria of the genera Cytophaga, Fusobacterium, and Bacteroides, which are classified together as a phylum. They share some similarities in the sequence of nucleotides in their DNA. They are rod shaped bacteria adapted to anaerobic environments, like the tissue of the gums and the gut. CFB bacteria are fermenters and are able to process cellulose in rumen, therefore enabling ruminant animals to obtain carbon and energy from grazing.
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Cytophaga
Part of the CFB group. They are motile aquatic bacteria that glide
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Fusobacteria
Part of the CFB group. They inhabit the human mouth and can cause severe infectious diseases
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Bacteroides
The largest genus of the CFB group. They are prevalent in the human large intestine and make up about 30% of the entire gut microbiome. Most Bacteroides are mutualistic, the bacteria benefit from nutrients in the gut and humans benefit from their ability to prevent pathogens from colonizing the large intestine. When populations of Bacteroides are reduced in the gut, like when a patient takes antibiotics, the gut becomes a more favorable environment for pathogenic bacteria and fungi. Only a few species are pathogenic- some can cause wound infections
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Planctomycetes
A class of nonproteobacteria. They are found in aquatic environments, including saltwater and freshwater. They are unusual in that they produce by budding. Their cells are motile and not attached to a surface, but they will differentiate into immobile cells with an appendage that allows them to attach to surfaces in the water. Only sessile cells can reproduce.
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Budding
A reproductive process of bacteria where instead of one maternal cell splitting into two equal daughter cells in the process of binary fission, the mother cell forms a bud that
detaches from the mother cell and lives as an independent cell.
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Phototrophic bacteria
A group of bacteria that use sunlight as their main source of energy. They use sunlight to synthesize ATP through photosynthesis. This group contains both proteobacteria and nonproteobacteria. The majority of phototrophic bacteria form anoxygenic photosynthesis, where they do not produce oxygen. Cyanobacteria is one species that performs oxygenic photosynthesis (they produce oxygen).
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Bacteriochlorophylls
Green, purple, or blue pigments that are similar to the chlorophyll found in plants. They are used by a large group of phototrophic bacteria that includes green and purple bacteria. Some of these bacteria have a varying amount of red or orange pigments called carotenoids, so their color varies. They are able to absorb light of various wavelengths. These bacteria are classified into sulfur and nonsulfur bacteria and are further classified by color
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Classes of bacteriochlorophyll bacteria (4)
1. Purple sulfur bacteria
2. Green sulfur bacteria
3. Purple nonsulfur bacteria
4. Green nonsulfur bacteria
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How do sulfur bacteria differ physiologically from nonsulfur bacteria?
The sulfur bacteria perform anoxygenic photosynthesis, using sulfites as electron donors and releasing free elemental sulfur. Nonsulfur bacteria use organic substrates, such as succinate and malate, as donors of
electrons.
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Purple sulfur bacteria
Oxidize hydrogen sulfide into elemental sulfur and sulfuric acid. They get their purple color from the pigments bacteriochlorophylls and carotenoids. The genus chromatium is an example of purple sulfur gammaproteobacteria. These bacteria are anaerobic and live in water. They use carbon dioxide as their only source of carbon, but require sulfites for their survival and growth- they use sulfites as electron donors. Chromatium has been used as a model for studies of bacterial photosynthesis since the 1950s
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Green sulfur bacteria
Use sulfide for oxidation and produce large amounts of green bacteriochlorophyll. The genus Chlorobium is a green sulfur bacterium that is implicated in climate change because it produces methane. These bacteria use at least four types of chlorophyll for photosynthesis. The most prevalent of these, bacteriochlorophyll, is stored in special vesicle-like organelles called chlorosomes.
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Purple nonsulfur bacteria
Similar to purple sulfur bacteria, except they use hydrogen rather than hydrogen sulfide for oxidation. Includes the genus Rhodospirillum. These microorganisms are facultative anaerobes, which are actually pink rather than purple, and can metabolize
(fix) nitrogen. They may be valuable in the field of biotechnology because of their potential ability to produce biological plastic and hydrogen fuel
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Green nonsulfur bacteria
Similar to green sulfur bacteria, but they use substrates other than sulfides for oxidation. Chloroflexus is an example of a green nonsulfur bacterium, which is orange when growing in the dark but green when growing in sunlight. It stores bacteriochlorophyll in
chlorosomes, similar to Chlorobium, and performs anoxygenic photosynthesis, using organic sulfites (low concentrations) or molecular hydrogen as electron donors, so it can survive in the dark if oxygen is available.
Chloroflexus does not have flagella but can glide, like Cytophaga. It grows at a wide range of temperatures and can therefore be thermophilic.
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Cyanobacteria
A group of phototrophic bacteria. They get their blue-green color from the chlorophyll contained in their cells. They perform oxygenic photosynthesis and therefore produce gaseous oxygen- they may have played a role in converting our atmosphere to oxygenated. Cyanobacteria are very adaptable and live in many different habitats, like marine and freshwater environments, soil, and rocks. They live at a wide range of temperatures. They can live as unicellular organisms or in colonies, and they can be filamentous, forming sheaths or biofilms. Many of them fix nitrogen, converting molecular nitrogen into nitrites and nitrates that other bacteria, plants, and animals can use. Some genera of cyanobacteria produce harmful toxins that cause diseases of the nervous system and liver tumors
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How does photosynthesis occur in cyanobacteria?
It is oxygenic and uses the same type of chlorophyll A found in plants and algae as its photosynthetic pigment. They use phycocyanin and cyanophycin as their secondary photosynthetic pigments, which give them their blue color. They are located in special organelles called phycobilisomes and in folds of the cellular membrane called thylakoids, similar to plants. Plants may have originated from endosymbiosis of ancestral eukaryotic cells and ancestral photosynthetic bacteria
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What makes a bacterium gram positive?
A bacterium is gram positive if they have multiple layers of peptidoglycan forming the cell wall. The cell wall retains the crystal violet stain and the cell appears purple under the microscope
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Actinobacteria
A class of gram positive bacteria that can be classified as high G+C gram positive bacteria or low G+C gram positive bacteria. High G+C bacteria have more than 50% guanine and cytosine nucleotides in their DNA. Actinobacteria are very diverse in terms of appearance and size. Most live in soil, but some are aquatic. The majority are aerobic. They have several different peptidoglycans in their cell wall
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Actinomyces
A genus of actinobacteria that plays an important role in soil ecology. Some inhabit the human mouth and are opportunistic pathogens- they can cause infectious diseases like periodontitis and oral abscesses. The species A. israelii is an anaerobe notorious for causing endocarditis (inflammation of the inner lining of the heart)
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Mycobacterium
A genus of actinobacteria- contains bacilli covered with a mycolic acid coat. The mycolic acid is waxy and protects the bacteria from some antibiotics, dehydration, and blocks penetration by Gram stain reagents. This requires an acid-fast staining procedure to visualize the bacteria. It contains multiple human pathogens, including the bacterium that causes tuberculosis (many strains are drug resistant). M. leprae causes leprosy (a disease of the peripheral nerves, skin, and mucosal surface of the respiratory tract).
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Corynebacterium
A genus of mycobacterium. These bacteria contain diaminopimelic acid in their cell walls and form pairs of rod shaped cells that resemble the letter V (palisades). Cells store inorganic phosphates in metachromatic granules. Most of these bacteria are nonpathogenic, but the genus includes the causative agent of diphtheria- it produces a toxin that forms a pseudomembrane in the patient’s throat, causing swelling, difficulty breathing, and other symptoms that can become serious if untreated
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Bifidobacterium
A genus of mycobacterium. It consists of filamentous anaerobes. They are commonly found in the GI tract, vagina, and mouth. They are part of the gut microbiota and are used in probiotics and in yogurt production
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Gardnerella
A genus of mycobacterium that contains one species- G. vaginalis. This species is gram variable because it's too small for gram staining. It is placed in the high G+C gram positive group based on its genome. G. vaginalis can cause bacterial vaginosis in
women; symptoms are typically mild or even undetectable, but can lead to complications during pregnancy.
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Clostridia
A diverse class of low G+C gram positive bacteria. Clostridium is one genus
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Clostridium
A genus of clostridia (low G+C gram positive). They are rod shaped obligate anaerobes that produce endospores and can be found in anaerobic habitats like soil and aquatic sediments that have nutrients. Their endospores can survive for many years. Many pathogens are included in that genus
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Which pathogens are included in the clostridium genus?
C. perfringens causes food poisoning and a disease called gas gangrene. Gas gangrene occurs when the bacteria's endospores enter a wound and germinate, producing a toxin that causes necrosis. C. tetani causes tetanus and produces a neurotoxin that enters neurons and blocks the inhibition of nerve impulses involved in muscle contractions- this causes deadly spastic paralysis. C. botulinum produces botulinum neurotoxin- it blocks the release of acetylcholine in neuromuscular junctions, causing flaccid paralysis. C. difficile is a common source of hospital acquired infections and can result in serious cases of colitis.
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Lactobacillales
An order of low G+C gram positive bacteria. It includes both bacilli and cocci in 4 genera
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4 genera of Lactobacillales
1. Lactobacillus
2. Leuconostoc
3. Enterococcus
4. Streptococcus
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Streptococcus
A genus of Lactobacillales. Species in this genus are classified by serotypes called Lancefield groups and by their ability to lyse red blood cells when grown on blood agar. It contains multiple human pathogens
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S. pyogenes
Belongs to the Lancefield group A, β-hemolytic Streptococcus. This species is considered a pyogenic pathogen because of the associated pus production observed with infections it causes. It is the most common cause of bacterial pharyngitis (strep throat), skin infections like impetigo, and necrotizing fasciitis
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Nonpyrogenic streptococci
These bacteria are not associated with pus production. They are a group of streptococcal species that are grouped together because they inhabit the human mouth. They don't belong to any of the Lancefield groups. Most are commensals, but some cause dental caries
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S. pneumoniae (pneumococcus)
A Streptococcus species that also does not belong to any Lancefield group. S. pneumoniae cells appear microscopically as diplococci rather than the chains typical of streptococci. They cause a wide range of infections, like pneumonia and other respiratory infections, meningitis, septicemia, osteomyelitis, and endocarditis, especially in newborns, the elderly, and patients with immunodeficiency
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Bacilli
A morphologically diverse class of bacillus and coccus shaped genera- Bacillus and Staphylococcus are clinically important. Part of low G+C gram positive bacteria.
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Bacillus
A genus that is part of the class bacilli of low G+C gram positive bacteria. They are bacillus in shape, produce endospores, and can include aerobes or facultative anaerobes. They are used in the production of antibiotics, enzymes, and detergents. Includes the pathogen that causes anthrax- manifests in humans as charcoal-black ulcers on the skin, severe enterocolitis, pneumonia, and brain damage due to swelling. B. cereus causes food poisoning
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Staphylococcus
A genus that belongs to the class Bacilli. Its shape is a coccus. They are facultative anaerobic, halophilic, and nonmotile. The two best-studied species of this genus are S. epidermidis and S. aureus.
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S. epidermidis
A species of the genus staphylococcus. Its main habitat is the human skin. It is nonpathogenic for healthy people, but in patients with immunodeficiency, it can cause infections in skin wounds and prostheses (artificial joints, heart valves). It is also a cause of infections associated with IV catheters
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S. aureus
A species of the genus staphylococcus. It causes skin infections that produce boils, cellulitis, and impetigo. Certain strains produce enterotoxin, which can cause severe enteritis (staph food poisoning). It some strains produce the toxin responsible for toxic shock syndrome, which can result in cardiovascular collapse and death. Many strains have developed resistance to antibiotics. Some strains are considered methicillin resistant (MRSA) or vancomycin resistant (VRSA)- these strains exhibit resistance to nearly all available antibiotics
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Mycoplasmas
A genus of low G+C gram positive bacteria, however, they don't have a cell wall and can't be stained by gram staining. The genus contains very small cells that are smaller than some viruses. Because they have no cell walls, they are considered pleomorphic and can be difficult to identify. One species called M. pneumoniae causes a mild form of pneumonia called walking pneumonia
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Pleomorphic
Cells with no cell wall that can take on a variety of shapes and can even resemble very small animal cells. Because they lack a characteristic shape, they can be difficult to identify
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Deeply branching bacteria
The first non last universal common ancestor forms of life produced by evolution billion of years ago. When placed on the phylogenetic tree, they stem from the common root of life, closest to the LUCA root. This is where the deeply branching name comes from
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What is the evolutionary significance of deeply branching bacteria?
They can provide clues regarding the structure and function of ancient and now extinct organisms. We can hypothesize that ancient bacteria, similar to currently existing deeply branching bacteria, were thermophiles (thrived at high temperatures). The class Aquificae includes deeply branching bacteria that are adapted to the harshest conditions on our planet, resembling the conditions thought to dominate the earth when life first appeared. Some species in this class use inorganic substances as nutrients. They also have resistance to UV light and ionizing radiation. This evidence supports the hypothesis that deeply branching bacteria began evolving more than 3 billion years ago when the earth was hot and lacked an atmosphere, exposing the bacteria to radiation
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Thermotogae
A class of deeply branching bacteria that is mostly hyperthermophilic. Some are mesophilic (prefer moderate temperatures). They are anaerobic gram negative bacteria whose cells are wrapped in a sheath-like membrane called a toga. Their cell wall contains a thin layer of peptidoglycan with an unusual structure- it contains diaminopimelic acid and D-lysine. These bacteria use a variety of organic substrates and produce molecular hydrogen. One species, T. maritima, lives near the thermal ocean
vents and thrives in temperatures of 90 °C; another species, T. subterranea, lives in underground oil reservoirs
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Deinococcus radiodurans
A deeply branching bacterium that is considered a polyextremophile because of its ability to survive in many different extreme conditions- heat, drought, acidity, radiation. It can withstand high doses of ionizing radiation in contrast to other bacteria species, likely due to unique mechanisms of DNA repair
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How do archaea different from bacteria? (3)
1. The archaeal cell membrane is composed of ether linkages with branched isoprene chains (as opposed to the bacterial cell membrane, which has ester linkages with unbranched fatty acids).
2. Archaeal cell walls lack peptidoglycan, but some contain a structurally similar substance called pseudopeptidoglycan or pseudomurein.
3. The genomes of Archaea are larger and more complex than those of bacteria.
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Domain archaea
All organisms in this domain are unicellular. The domain is diverse and its representatives can be found in any habitat. Organisms can exist in extreme temperatures, extreme salinity, and other hostile conditions. Their metabolism is adapted to the harsh environments. They can perform methanogenesis in contrast in bacteria. Archaea are not typically present in the human microbiota, and none are currently known to be associated with infectious diseases in humans, animals, plants, or microorganisms.
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5 major phyla of archaea
Crenarchaeota, Euryarchaeota, Korarchaeota,
Nanoarchaeota, and Thaumarchaeota
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Crenarchaeota
A diverse class of archaea. All Crenarchaeota are aquatic organisms, and they are thought to be the most abundant microorganisms in the oceans. Most, but not all are hyperthermophiles
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Sulfolobus
A genus of archaea in the class Crenarchaeota. They are thermophiles and acidophiles that prefer a pH of 2-3. They can live in aerobic or anaerobic environments. In the presence of oxygen, they use metabolic processes similar to those of heterotrophs. In anaerobic environments, they oxidize sulfur to produce sulfuric acid, which is stored in granules. They are used in biotech to produce proteins called affitins
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Affitins
Acid-resistant proteins that can bind and neutralize various antigens (molecules found in toxins or infectious agents that provoke an
immune response from the body).
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Thermoproteus
A genus of the class Crenarchaeota. It contains only anaerobic organisms with an optimal growth temperature of 85 degrees Celsius. They are motile and use a flagella to move. This genus has a cellular membrane with a lipid monolayer, which is typical of archaea. Its metabolism is autotrophic.
To synthesize ATP, they reduce sulfur or molecular hydrogen and use carbon dioxide or carbon monoxide as a source of carbon. Thermoproteus is thought to be the deepest-branching genus of Archaea and is therefore a currently living example of some our planet's earliest forms of life
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Euryarchaeota
A phylum of archaea with 3 methanogen classes: Methanobacteria,
Methanococci, and Methanomicrobia
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Methanogens
They can reduce carbon dioxide in the presence of hydrogen, producing methane. They can live in the most extreme environments and can reproduce at temperatures varying from below freezing to boiling. Methanogens have been found in hot springs as well as deep under ice in Greenland. They also produce gas in humans, and the mixture of gases produced by methanogens resembles the makeup of the atmosphere on Mars
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Halobacteria
A class of archaea in the phylum Euryarcheota. Includes halophilic (salt loving) archaea. Halobacteria require a very high concentrations of sodium chloride in their aquatic environment. The required concentration is found in environments like the Dead Sea as well as some salty lakes in Antarctica and south-central Asia. One
distinctive feature of these organisms is that they perform photosynthesis using the protein bacteriorhodopsin, which gives them, and the bodies of water they inhabit, a purple color. One species in this class, Halobacterium salinarum, may be the oldest living organism on earth.
