Chapter 4- Prokaryotic diversity Flashcards
3 domains are all living organisms are classified into
Archaea, Bacteria, and Eukarya. Archaea and bacteria are unicellular prokaryotes
How abundant are prokaryotes on and within the human body?
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
How are bacteria essential to ecosystems?
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
Why are bacteria able to exist in so many different environments on earth?
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.
Carbon fixation
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
Nitrogen fixation
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
How are prokaryotes responsible for cleaning up the environment?
Some bacteria play a role in degrading toxic chemicals that pollute water and soil.
Negative impacts of prokaryotes (2)
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.
Community
A group of interacting populations of organisms. Prokaryotes live in a community
Population
A group of individual organisms belonging to the same biological species and limited to a certain geographic area
Cooperative interactions
Interactions that benefit the populations in a community
Competitive interactions
Interactions in which one population competes with another for resources
Microbial ecology
The study of the cooperative and competitive interactions between microbial populations and their environment
Symbiosis
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
Mutualism
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
Amensalism
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
Commensalism
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
Neutralism
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)
Parasitism
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
Microbiome
Refers to all prokaryotic and eukaryotic microorganisms, and their genetic material, that are associated with a certain organism or environment.
Subtypes of microbiota in the human microbiota
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
How does the resident microbiota differ between each area of the body?
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
How does an individual’s microbiome change over time?
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.
Why is an individual’s microbiota important for their health?
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.
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
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
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
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
Classes of Proteobacteria (5)
Alpha, beta, gamma, delta, and epsilon proteobacteria
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.
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
Oligotrophs
Organisms capable of living in low nutrient environments such as deep oceanic sediments, glacial ice, or deep undersurface soil
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
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
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
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.
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.
Microaerophilic
Organisms that require low levels of oxygen
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
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
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.
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
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
Enteric
Refers to the intestine
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