22: Prokaryotes - Bacteria and Archaea Flashcards
Prokaryotic Diversity, Structure of Prokaryotes, Prokaryotic Metabolism, Bacterial Diseases in Humans, Beneficial Prokaryotes
Who pioneered the discovery of the three domains of life?
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.
When did prokaryotes first appear on Earth?
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.
What are some examples of environments that are inhabited by prokaryotes?
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.
What is an acidophile?
Organism with optimal growth in pH of three or below.
What is an alkaliphile?
Organism with optimal growth pH of nine or above.
What are anaerobic organisms?
Refers to the organisms that grow without oxygen.
What does it mean to be anoxic?
Without oxygen.
What is a biofilm?
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.
What is an extremophile?
Organism that grows under extreme or harsh conditions.
What is a halophile?
Organism that requires a salt concentration of at least 0.2 M.
What is a hydrothermal vent?
Fissure in Earth’s surface that releases geothermally heated water.
What is a hyperthermophile?
Organism that grows at temperatures between 80-122 C.
What is a microbial mat?
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.
What is a nutrient?
Essential substances for growth, such as carbon and nitrogen.
What is an osmophile?
Organism that grows in a high sugar concentration.
What is a phototroph?
Organism that is able to make its own food by converting solar energy to chemical energy.
What is a psychrophile?
Organism that grows at temperatures of -15 C or lower.
What is a radioresistant organism?
Organism that grows in high levels of radiation.
What is resuscitation?
Process by which prokaryotes that are in the VBNC state return to viability.
What is a stromatolite?
Layered sedimentary structure formed by precipitation of minerals by prokaryotes in microbial mats. Stromatolites form layered rocks made of carbonate or silicate.
What is a thermophile?
Organism that lives at temperatures between 60-80 C.
What is a viable-but-non-culturable (VBNC) state?
Survival mechanism of bacteria facing environmental stress conditions.
What were the conditions on earth likely like when the first organisms arose?
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.
Are stromatolites formed present day?
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.
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.
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.
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.
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.
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.
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.
What is a divalent ion?
Doubly-charged monatomic ions, such as Fe2+, Ca2+, and Mg2+.
What is hard water?
Water that has high mineral content, such as iron, calcium, and magnesium divalent cations.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
What is peptidoglycan?
Material composed of polysaccharide chains cross-linked to unusual peptides.
What is a pilus?
Surface appendage of some prokaryotes used for attachment to surfaces including other prokaryotes.
What is pseudopeptidoglycan?
Component of archaeal cell walls that is similar to peptidoglycan in morphology but contains different sugars.
What is an S-layer protein?
Surface-layer protein present on the outside of cell walls of archaea and bacteria.
What is teichoic acid?
Polymer associated with the cell wall of Gram-positive bacteria.
What is transduction?
Process by which a bacteriophage moves DNA from one prokaryote to another.
What is transformation?
Process by which a prokaryote takes in DNA found in its environment that is shed by other prokaryotes.
What are the three basic categories of prokaryotes, according to their shape?
Cocci (spherical), bacilli (rod-shaped), and spirilli (spiral-shaped).
What are proteobacteria?
A major phylum of Gram-negative bacteria. There are five primary classes of proteobacteria: alpha, beta, gamma, delta, and epsilon.
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.
What are beta proteobacteria?
This group of bacteria is diverse. Some species play an important role in the nitrogen cycle.
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.
What are delta proteobacteria?
Some species generate a spore-forming fruiting body in adverse conditions. Others reduce sulfate and sulfur.
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.
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)
What are some representative organisms of beta proteobacteria?
- Nitrosomonas: species from this group oxidize ammonia into nitrite
- Spirillum minus: causes rat-bite fever
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
What are some representative organisms of delta proteobacteria?
- Myxobacteria: generate spore-forming fruiting bodies in adverse conditions
- Desulfovibrio vulgaris: anaerobic, sulfate-reducing bacterium
What are some representative organisms of epsilon proteobacteria?
- Campylobacter: causes blood poisoning and intestinal inflammation
- Helicobacter pylori: causes stomach ulcers
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.
What is Chlamydias?
Gram-negative bacterial phylum where all members are obligate intracellular parasites of animal cells. Cell walls lack peptidoglycan.
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.
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.
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.
What are some representative organisms of Chlamydias?
- Chlamydia trachomatis: common sexually transmitted disease that can lead to blindness
What are some representative organisms of Spirochetes?
- Treponema pallidum: causative agent of syphilis
- Borrelia burgdorferi: causative agent of Lyme disease
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
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.
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.
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.
