Chapter 25

pathogenesis

-In some wasp species, Wolbachia induces parthenogenesis, the development of unfertilized eggs into adult organisms. they affect reproduction and may influence evolutionary divergence and even extinction. They also affect HGT -Some types of bacteria may influence evolution of other species -example: The proteobacteria Wolbachia infect many inver- tebrates, including insects, spiders, crustaceans, and nematodes (roundworms). They limit or eradicate males from the population.

prokaryotes

-assigned to domain Archaea or Bacteria, are cellular organisms. -they are very small measured in micrometers. -most are unicellular but some form colonies or filaments containing specialized cells -have inhabited our planet for more than 3.5 billion years, much longer than eukaryotes, -account for more than half of Earth's bio- mass, the mass of living material. Greater mass than all the eukaryotes, fungi, plants, and animals. -One group of prokaryotes, the cyanobacteria, are producers that carry on photosynthesis, which generates oxygen. 70% to 80% of the oxygen on planet Earth is generated by cyanobacteria and algae. -They DO NOT have membrane-enclosed organelles or nucleus

chemoautotrophs

-autotroph The majority of archaea and some bacteria are chemoautotrophs -which use carbon dioxide as a carbon source, but do not use sunlight as their energy source. -Instead, they obtain energy by oxidizing inorganic chemical sub- stances such as ammonia (NH3) or hydrogen sulfide (H2S). -Energy source: inorganic chemicals (NH3, H2S, Fe2+ ) -Carbon Source: Carbon Dioxide CO2 -Examples of organisms: Certain proteobacteria; most archaea (e.g., methanogens, extreme halophiles)

photoautotrophs

-autotroph such as cyanobacteria, -use the energy from sunlight to synthesize organic compounds from car- bon dioxide and other inorganic compounds. -Energy source: Sunlight -Carbon Source: Carbon Dioxide CO2 -Examples of organisms: Cyanobacteria; purple sulfur bacteria

things that bacteria and eukaryotes share

-bacteria and eukaryotes both have ester linked membrane lipids -some believe that eukaryote are a product of fusion between an archaeon, which contributed components for trancription and translation and a bacterial symbiont, which contributed enzymes necessary for energy metabolism -further molecular analysis hypothesize that eukaryotes arose from an archaea ancestor -then and chest may have been LOKIARCHAEOTA because they have several eukaryotic characteristics many believed that eukaryotes branched from this guy. if the is correct or accurate then eukaroyotes would be a part of the domain archaea eliminating eukarya.

taxonomy of archaea and bacteria

-continously changes -Groups that branched off earlier had more time to accumulate mutations in their SSU rRNA. Their nucleotide sequences are less similar than those of groups that diverged more recently. -The editors of Bergey's Manual of Systematic Bacteriology, considered the definitive reference text by microbiologists, have divided archaea into 4 groups (phyla) and bacteria into more than 30 groups (phyla) based on 16S rRNA analyses. Systematists, however, have proposed addi- tional groups (phyla) of archaea based on the numerous and continuing discoveries of previously unidentified organisms.

Photoheterotrophs

-heterotroph -such as the purple nonsulfur bac- teria -obtain their carbon from other organisms but use chlorophyll and other photosynthetic pigments to trap energy from sunlight. -Energy source: Sunlight -Carbon Source: Organic compounds -Examples of organisms: Purple and green nonsulfur bacteria

similarities between archaea and eukaryotes

-in some ways archaea are more like eukaryotes than bacteria -archaea do not have simple RNA polymerase found in bacteria -like eukaryotes their translation process begins with Methinoine, whereas in bacteria translation begins with formylmethionine -several antibiotics that affect bacteria do not affect archaea or eukaryotes.

evolution of prokaryotes

-it proceeds rapidly in prokaryote populations -mutations are quickly passed on to new generations. Muta- tions that confer some advantage spread through the popula- tion, and the effects of natural selection are quickly evident. -Horizontal gene transfer greatly contributes to the rapid evolution that takes place in prokaryotes. -New DNA introduced into a prokaryote's genome represents raw material for evolution. -New genes are subject to mutation and are acted on by the forces of natural selection. The changes in the genetic material are passed to succeeding generations by binary fission. Changes that result in adaptation can quickly spread through future bacterial and archaeal populations.

domain bacteria

-no nuclear envelope -no membrane- enclosed organelles -circular chromosome present (linear in some species) -number of chromosomes typically are one (may also have plasmids) -no histones associated with DNA -peptidoglycan in cell wall is present -structure of lipids in plasma membrane is straight- chain fatty acids bonded to glycerol by ester linkages -size of ribosomes if 70S1 -One relatively simple RNA polymerase -Translation begins with Formylmethionine -there is growth about 70 degrees Celsius

domain archaea

-no nuclear envelope -no membrane-enclosed organelles -circular chromes is present -Typically one chromosome (may also have plasmids) -there are histones associated with DNA -no peptidoglycan in cell wall -structure of lipids in plasma membrane is branched-chain hydrocarbons linked to glycerol by ether linkages -size of ribosomes is 70S -one relatively complex RNA polymerase -translation begins with Methionine -there is growth above 70 degrees celsius

domain eukarya

-nuclear envelope is present -membrane-enclosed organelle are present -no circular chromosome -typically many for number of chromosomes -histones associated with DNA are present -no peptidoglycan in cell wall -structure of lipids in plasma membrane is straight-chain fatty acids bonded to glycerol by ester linkages -size of ribosomes is 80S except in mitochondria and chloroplasts -Several relatively complex RNA polymerases -translation begins with Methionine -no growth above 70 degrees celsius

use of flagella or archaellum

-other than to win they use it to swarm, adhere to surfaces, and to participate in BIOFILM formation (which is the community of microorganisms attached to a surface) -bacteria use flagella to sense wetness -some archaea can interact with one another by their archaella resulting in biofilm composed of more than one species

conjugation

-two cells of different mating types come together, and genetic material is transferred from one to the other -conjugation involves contact between two cells. STEPS: 1. F+ (donor) cell produces sex pilus. 2. Sex pilus develops into conjugation bridge. 3. Single strand of F plasmid DNA is transferred from F+ cell to F- cell. 4. DNA replicates. Both bacterial cells now contain double- stranded F plasmid. The F- cell has been converted to an F+ cell. -The bacteria are connected by a sex pilus. When stimulated by the contact, the cells pull close together and form a conjugation bridge between donor and recipient cells

nitrogen fixation

All organisms require nitrogen to manufacture amino acids and nucleic acids. Some bacteria (certain cyanobacteria) and archaea (methanogens) can reduce nitrogen in the atmosphere to ammonia. -Ammonia produced by nitrogen fixation is converted to ammonium ions (NH4+) -Nitrogen-fixingprokaryotescanuse these simple forms of nitrogen to produce organic compounds

anthrax

Bacillus anthracis Most commonly occurs in domestic animals such as cattle. Can be transmitted to humans from infected animals or animal products. Endospores can live in soil for many years. Anthrax is not spread from person to person. Infection can occur in three ways: cutaneous, by inhalation, and gastrointestinal.

Bioremediation

Bacteria are used in bioremediation, the process of using microorganisms (and sometimes other organisms) to detoxify or remove oil, gasoline, and other pollutants or toxic chemicals from the environment. Microorganisms break down certain toxins, leav- ing behind harmless metabolic byproducts such as carbon dioxide and chlorides For example, bacteria and other microorganisms are used in oil spills to break down oil, oxidizing it to CO2. Microorganisms are also used in sewage treatment and to break down solid wastes in landfills. -Archaea are also economically important. Archaea that are adapted to high temperatures or extremely acidic conditions, for example, are a source of enzymes that can be used under these extreme conditions. Archaeal enzymes have been added to laun- dry and industrial detergents and to organic solvents to increase performance at higher temperatures and pH levels. Methanogens are important in the biogas production industry and in sewage treatment. Another archaeal enzyme has been useful in the food industry to convert cornstarch to dextrins (low molecular weight carbohydrates produced by hydrolysis of starch or glycogen).

antibiotic resistance

Bacteria mutate frequently and reproduce rapidly, often devel- oping resistance to antibiotics. Many antibiotics target protein synthesis in bacteria. For example, streptomycin and related anti- biotics block the initiation of protein synthesis. The tetracyclines block aminoacyl tRNA from binding to the A site on the ribosome. -Drug resistance may result from an accumulation of muta- tions in plasmid or chromosomal DNA. Plasmids that have genes for antibiotic resistance are called R factors. -Methicillin-resistant Staphylococcus aureus (SA), referred to as MRSA, and vancomycin-resistant Staphylococcus aureus, or VRSA, have been directly linked to the horizontal transfer of antibiotic- resistance genes by plasmids during conjugation. this is a SUPERBUG that can cause infection in individuals with compromised immune systems. -The practice of feeding low-dose antibiotics to farm animals to promote growth has also resulted in many types of antibiotic- resistant bacteria that survive and multiply after susceptible bac- teria are killed. -bioflim strategy- The bacteria subvert the attack by forming biofilms. Each biofilm is sur- rounded by a matrix rich in polysaccharides and by a protective shell. The bacteria in the biofilm are resistant to antibiotics as well as to host defenses.

gram-positive

Bacteria that absorb and retain crystal violet stain in the laboratory are referred to as gram-positive bacteria. -The cell walls of gram-positive bacteria are very thick and consist pri- marily of peptidoglycan. -A thick layer of peptidoglycan molecules is held together by amino acids. -penicillin works most effec- tively against gram-positive bacteria because it interferes with peptidoglycan synthesis.

gram-negative

Bacteria that do not retain the stain when rinsed with alcohol are gram-negative bacteria. -The cell walls of gram-negative bacteria have two layers: a thin peptidoglycan layer and a thick outer membrane. (outer membrane resembles the plasma membrane but contains polysaccharides bonded to lipids)

the two new domains after carl woes's work

Based on Woese's work and on other recent data, systematists now classify the modern descendants of these two ancient lines in two domains: Archaea and Bacteria -using sequence analysis of small sub- unit 16S ribosomal RNA (SSU rRNA), Carl Woese and his co- workers demonstrated that there are two fundamentally different groups of prokaryotes -these groups diverged from a common ancestor about 4 billion years ago. -Archaea and bacteria were the only living organisms on our planet for about 2 billion years. -Horizontal gene transfer has contributed to the diver- sity of these organisms. As a result of gene transfer, sometimes from dis- tantly related species, the genomes of archaea and bacteria are actually a mix of genes from many prokaryotes.

2 types of autotroph

Based on two principal ways of capturing energy, -CHEMOTROPHS obtain their energy FROM CHEMICAL COMPOUNDS -PHOTOTROPHS CAPTURE energy FROM LIGHT. As early as 3.5 billion years ago, the ability to use the sun as an energy source evolved in early prokaryotes. early phototrophs used hydrogen sulfide to reduce carbon dioxide (releasing sulfur as a waste product) -About 2.7 billion years ago, the ability to use water rather than hydrogen sulfide to reduce carbon dioxide evolved in early cyanobacteria, and oxygen was released as a waste product.

Lyme disease

Borrelia burgdorferi Transmitted to humans by bite of infected blacklegged ticks. Symptoms include skin rash, headache, fever, and fatigue. If untreated, infection can spread to joints, heart, and nervous system.

common shapes of prokaryotes

COCCI- spherical prokaryotes, groups in twos (Diplococci), in long chains (Streptococci), irregular clumps that look like bunches of grapes (staphylococci) example: Staphylococcus aureus. These cocci cause skin and wound infections, food poisoning, and toxic shock syndrome. BACILLI- rod shaped prokaryotes example: Salmonella. These bacilli cause food poisoning. SPIROCHETE- prokaryotes that are spiral AND flexible example: Borrelia burgdorferi. These spirochetes cause Lyme disease, transmitted by infected deer ticks. SPIRILLIUM- prokaryotes that are spiral AND rigid, when shaped like a comma it is called a (vibrio)

nitrification

Certain prokaryotes convert ammonia or ammonium ions to nitrite (NO2− ), and others convert nitrite to nitrate (NO3− ). This process, called nitrification, -converts nitrogen to a form that can be used by plants and fungi. -Animals obtain nitrogen from organic compounds when they eat other organisms. They depend on nitrogen fixation and nitrification by prokaryotes for their survival.

Chlamydia

Chlamydia trachomatis One of the most frequently reported sexually transmitted infections in the U.S. About 75% of infected women and 50% of infected men have no symptoms. If untreated, infection spreads and can lead to infertility. Chlamydia can also infect eyes; causes millions of cases of blindness worldwide each year.

other gram negative bacteria

Chlamydias lack peptidoglycan in their cell walls. They are energy parasites, completely dependent on their hosts for ATP. Infect almost every species of bird and mammal.A strain of Chlamydia causes trachoma, the leading cause of blindness in the world. Sexually transmitted chlamydias are the major cause of pelvic inflammatory disease in women. -Spirochetes are spiral-shaped bacteria with flexible cell walls; move by means of unique internal flagella called axial filaments. Some species are free-living, whereas others form symbiotic associations; a few are parasitic. Treponema pallidum causes syphilis.

botulism

Clostridium botulinum Contracted by eating foods that contain the exotoxin or from infected wound. Infant botulism is caused by ingesting endospores. Causes muscle paralysis and can cause death from respiratory failure.

Antibiotic-associated diarrhea; and inflam- mation of colon

Clostridium difficile (common name: C. dif) Risk greatest for older people taking antibiotics, people with compromised immune systems, and patients in hospitals and health care facilities for extended periods

Diphtheria

Corynebacterium diphtheriae Transmitted from person to person by intimate respiratory and physical contact. Endemic in developing countries. Not common in U.S. since vaccine became available in 1920s. Infects the heart muscle and respiratory passageways.

groups, phyla or clades of the domain archaea

Domain Archaea consists of several widely recognized groups (phyla, clades), including Crenarchaeota, Euryarchaeota, Nanoarchaeota, and Korarchaeota. -This phylogeny is based on 16S rRNA and on sequencing of entire genomes. Based on continued detection of previously unidentified archaea and sequencing of archaeal genomes, systematists estimate that more than a dozen additional groups may be added.

endotoxins

Endotoxins are not secreted by pathogens but instead are components of the cell walls of most gram-negative bac- teria. These compounds affect the host only when they are released from dead bacteria. Endotoxins bind to the host's macrophages (large phagocytic cells of the immune system) and stimulate them to release substances that cause fever and other symptoms of infection. -Unlike exotoxins, which cause specific symptoms, endotoxins appear to affect the entire body. Endotoxins are not destroyed by heating.

Peptic ulcer disease

Helicobacter pylori Causes peptic ulcer, a lesion in the lining of the stomach or duodenum (upper part of small intestine).

commensalism

In commensalism, one partner benefits, and the other is neither harmed nor helped. Many prokaryotes that inhabit the human intestine are commensals that live on unused food.

plasma membrane in archaea

In contrast, fatty acid components are not found in archaea. -Instead, branched-chain hydrocarbons (synthesized from isoprene units) are bonded to glycerol by ETHER linkages (C has a bond with O and two H on each side) -The absence of a second electronegative oxygen atom makes ether linkages stronger than ester linkages. -this contributes o the ability of archaea to survive and thrive in harsh environments.

parasitism

In parasitism, one partner lives on or in the other. The parasite benefits, and the host is harmed. Disease-causing bacteria are usually not considered obligate parasites because these pathogens typically can survive in other ways.

plasma membranes of bacteria and eukaryotes

In the plasma membranes of bacteria and eukaryotes, straight-chain fatty acids are linked to glycerol molecules by ESTER linkages (C has a double bond with O and a single bond with another O)

Koch's Postulates

Koch proposed a set of guidelines, now known as Koch's postulates, that are still used to demonstrate that a specific pathogen causes specific disease symp- toms: 1. the pathogen must be pres- ent in every individual with the disease, 2. a sample of the microorganism taken from the diseased host can be grown in pure culture, 3. a sample of the pure culture causes the same disease when injected into a healthy host, and 4. the host can be recovered from the experimentally infected host. Sometimes these guidelines cannot be met, as, for example, when certain microorganisms cannot be grown in pure culture.

microbial fermentation

Microbial fermentation helps produce many foods and beverages. Lactic acid bacteria are used in producing aci- dophilus milk, yogurt, pickles, olives, and sauerkraut. Several types of bacteria are used in the production of cheese. Bac- teria are involved in making fermented meats such as salami and in producing vinegar, soy sauce, chocolate, and certain Bvitamins(B12 andriboflavin).

Pyrococcus furiosus

Molecular biology and forensic biology have greatly ben- efited from heat-resistant DNA polymerase, derived from the archaeon Pyrococcus furiosus -Like heat-resistant Taq polymerase, derived from a bacterium, it is used in the polymerase chain reaction (PCR) -Acidophilic archaea are promising as resources for extracting metal from ores and remediating toxic mining sites.

heterotrophs

Most prokaryotes are heterotrophs that obtain car- bon atoms FROM THE ORGANIC COMPOUNDS of other organisms. -Other heterotrophic bacteria benefit their hosts. For example, some of the bacteria that inhabit the human large intestine produce vitamin K and certain B vitamins that benefit their hosts.

Hansen disease (leprosy)

Mycobacterium leprae Thought to be spread from person to person in nasal secretions. Worldwide, this disease has disabled up to 2 million people.

Gonorrhea

Neisseria gonorrhoeae Common sexually transmitted disease.

Nitrogen

Nitrogen is constantly removed from the soil by plants and other natural processes as well as by human activities such as agriculture. Plant growth depends on the availability of usable nitrogen, so it must be continually added to the soil. Several types of bacteria, including cyanobacteria, and some archaea transform atmospheric nitrogen to forms that can be used by plants. Marine archaea that carry out nitrification are important in the ocean nitrogen cycle.

microbiome

Normal microbial populations have been shown to have multiple effects, including preventing harmful microorgan- isms from flourishing. The term microbiome refers to the community of these microorganisms, including their genomes and all of their interactions. -Rapid DNA sequencing has greatly facilitated microbiome research because there are thousands of species of these organisms and many are difficult to grow in culture. -Through the Human Microbiome Project supported by the National Institutes of Health, investigators have mapped the human microbiome, creating a database of more than 10,000 microorganisms. understanding of the critical control and effects these symbionts have on human health and disease.

obligate anaerobes

Other prokary- otes are obligate anaerobes -carry on anaerobic respiration; they respire with terminal electron acceptors other than oxygen, such as sulfate(SO42−), nitrate(NO3−), or iron(Fe2+). -Some obligate anaerobes, including certain archaea, are actu- ally killed by even low concentrations of oxygen.

pathogenic microorganisms

Pathogenic microorganisms can enter the body in food, dust, or droplets, or through wounds. Many diseases are transmit- ted by insect or animal bites. To cause disease, a pathogen must adhere to a specific cell type, multiply, and produce toxic substances. Adherence and multiplication occur only when the pathogen competes successfully with the normal micro- biota and counteracts the host's defenses against invasion. -Helicobacter pylori, the most common cause of peptic ulcers (ulcers of the stomach and duodenum), is an extremely successful pathogen can become stomach cancer -Helicobacter pylori Among its many adaptations is its ability to produce an alkaline shield around itself that protects it from stomach acid. Also contributing to its suc- cess are several powerful flagella used to propel the pathogen through the thick mucus lining the stomach.

exotoxins

Pathogens produce a variety of substances that increase their success. Some bacteria produce exotoxins, strong poi- sons that are either secreted from the cell or leak out when the bacterial cell is destroyed. -The toxin, not the presence of the bacteria themselves, is responsible for the disease. -Diphtheria is caused by a gram-positive bacillus (Corynebacterium diphtheriae) that produces a toxin only when lysogenized by a phage. The diphtheria toxin kills cells and causes inflammation. -Botulism is caused by an exotoxin released by the gram- positive, endospore-forming Clostridium botulinum. During the canning process, food must be heated sufficiently to kill any highly heat-resistant endospores that may be present. If not, the endospores can germinate. -The botulism exotoxin, marketed under the trade name Botox, is used in extremely tiny amounts to treat several medical conditions involving spasms (involuntary muscle contractions). Botox injections are used to treat migraines, excessive sweat- ing, overactive bladder/incontinence, and crossed eyes. Because Botox is a neurotoxin that works by paralyzing muscles, it can also relax facial wrinkles caused by contraction of the underlying muscles. However, its effects last for only about three months. -Another gram-positive, endospore-forming bacterium, Clostridium difficile, is an anaerobe that produces two exotoxins. It is a common cause of antibiotic-associated diarrhea (AAD)

symbiosis

Prokaryotes interact with other organisms in both bene- ficial and harmful ways. An intimate relationship between members of two or more species is called symbiosis.

archaeocins

Researchers have discovered that some archaea also produce antimicrobial substances, called archaeocins, which may someday be used in the production of new antibiotics. -bacteria are ideal "factories" for the production of biomolecules. -bacteria have been genetically engineered bacteria to produce certain vaccines, human growth hormone, insulin, and many other clinically important compounds

Epidemic typhus

Rickettsia prowazekii Transmitted by infected body lice. After an 8- to 12-day incubation period, symptoms include fever, severe headache, muscle aches, and chills. Several days later, a rash appears. About 40% of untreated patients die.

endospores

Some bacteria survive unfavorable conditions by forming endospores -When the environment becomes unfavorable: when nutrients are limited or the environment becomes very dry or hot—some types of bacteria produce extremely durable, dor- mant cells called endospores. -To form an endospore, the bacterial cell divides by binary fission, forming a large cell that surrounds a smaller cell containing the genome. After an endospore forms, the cell wall of the original cell disintegrates, releasing the endospore. - endospores survive in very dry hot or frozen environments or at times when food is scarce, some can even survive an hour or more of boiling or centuries of freezing. -When environmental conditions are again suitable for growth, the endospore germinates, forming an active, growing bacterial cell. -NOT a type of reproduction in bacteria -One endospore in created per original cell -archaea do not form endospores they instead produce unique enzymes on the cell surface that protect them from cold, heat and desiccation

antibiotics

Some microorganisms produce antibiotics. -These compounds limit competition for nutrients by inhibiting or destroying other microorganisms. By the 1950s, antibiotics had become impor- tant clinical tools that transformed the treatment of infectious disease. -Pharmaceutical companies obtain most antibiotics from three groups of microorganisms: a large group of gram-positive soil bacteria, the actinomycetes; gram-positive bacteria of the genus Bacillus; and molds (eukaryotes belonging to kingdom Fungi).

microbiota

Some prokaryote species have coevolved with eukaryotes and are interdependent with them. All plants and animals harbor a community of microorganisms referred to as microbiota. (This term has replaced microflora, which is a misnomer because "flora" refers to plants.) An estimated 37 to more than 100 trillion sym- biotic bacteria, archaea, and (a few) eukaryotic microorganisms normally inhabit the human body! This number is equal to or up to triple the number of the body's own cells (more than 37 trillion).

autotrophs

Some prokaryotes are autotrophs (-troph comes from a Greek word that means "nutrition") -are able to USE INORGANIC COMPOUNDS, such as carbon dioxide, as a source of carbon for manufacturing their organic molecules.

fragmentation

Some prokaryotes divide by fragmentation. In this process, walls develop within the cell, which then separates into several new cells.

the two supergroups

Supergroup "TACK" includes four groups (Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota). The "Asgard" clade includes the Lokiarchaeota, discussed previously, along with three other newly discovered archaea groups (Thorar- chaeota, Odinarchaeota, and Heimdallarchaeota). Asgard archaea appear to be closely related to TACK archaea. there is more archaea in marine and soil environments that in extreme habitats. archaea are important in biogeochemical cycles and in marine food chains. no pathogenic area have been identified.

Crenarchaeota

The Crenarchaeota include EXTREME THERMOPHILES, archaea that require a very high temperature or very low tem- perature for growth. -The optimum temperature for many is greater than 80°C (176°F) and some thrive at temperatures greater than 100°C. -Some species inhabit acidic environments. One species is found in the hot sulfur springs of Yellowstone National Park at temperatures near 80°C and pH values of 1 to 2, the pH of concentrated sulfuric acid. -Other crenarchaeotes inhabit volcanic areas under the sea./ near deep-sea hydrothermal vents on the seafloor of the Pacific Ocean/ lives at temperatures ranging from 80 degrees celsius to 120 degrees celsius. -in contrast some Crenarchaeota species live in very cold environments (1.8°C) -members of this clade are common to most environments. Crenarchaeotes are a main con- tributor to carbon fixation. They are also an important part of the plankton in cold, oxygen-rich seas. A few are photoheterotrophs.

Euryarchaeota

The Euryarchaeota also include many archaea that inhabit extreme environments. -This group includes methano- gens, extreme aerobic and anaerobic thermophiles, acidophiles, and halophiles (some extreme)

bacteria that can for endospores and cause diseases

The endospore of Bacillus anthracis, the bacterium that causes anthrax, is so hardy that this pathogen has become a con- cern as an agent of biological warfare. -The bacteria (Clostridium tetani) that cause tetanus and the bacteria (C. perfringens) that cause gas gangrene typically enter the body with soil when a per- son suffers a deep cut or puncture wound. Patients may also be exposed to these serious diseases when surgical instruments are not effectively sterilized, allowing endospores to survive.

Nanoarchaeota

The first member of the Nanoarchaeota, Nanoarchaeum equitans, was discovered in a hydrothermal vent in 2002. -it Is a marine microbe very small (400 nm) anaerobic, extreme thermophile with a very small genome (less than 500,000 nucle- otides) -It lives attached to another archaeon, an autotroph, and depends on its host for many of its metabolic needs.

genetic material in prokaryotes

The genetic material of a prokaryote is located in the nuclear area but is not surrounded by a nuclear envelope. - a single, circular DNA molecule. -prokaryote DNA has little protein associated with it -In addition to their genomic DNA, most bacteria and archaea have one or more PLASMIDS, smaller circular fragments of DNA. -plasmids have genes that code for catabolic enzymes for genetic exchange or for resistance to antibiotics - bacterial plasmids replicate independently of the genomic DNA or become integrated into it. We do not know how plasmids replicate yet

methanogens

The methanogens (methane producers) are a large, diverse group that inhabit oxygen-free environments in sewage, swamps, and the digestive tracts of humans and other animals. -They are obligate anaerobes that produce methane gas from simple carbon compounds. -The methanogens are important in recycling components of organic products of organisms that inhabit swamps. Methanogens that inhabit the digestive tracts of cows and other grazing animals produce methane, which is belched out by the animals. Meth- anogens produce more than 80% of the methane (more than 2 billion tons each year) in Earth's atmosphere. -these are also found in marine sediments -it is an important greenhouse gas

symbionts

The partners in a symbiotic relationship are called symbionts. Symbiotic relationships arise by coevolution. Three forms of symbiosis are mutualism, commensalism, and parasitism.

Cholera

Vibrio cholerae Contracted by eating food or drinking water contaminated with the bacteria. Common in areas with inadequate sewage treatment and impure water. Infects intestine and can cause severe diarrhea. Rapid fluid loss can lead to dehydration and death.

peptidoglycan

a complex polymer that consist of two unusual types of sugars (amino sugars) linked with short polypeptides. The sugars and poly- peptides are cross-linked to form a crystalline lattice that sur- rounds the entire plasma membrane. Peptidoglycan is absent in the archaeon cell wall. -Bacterial cell wall includes this

alpha proteobacteria

alpha proteobacteria in the SAR11 clade are among the most successful organisms on Earth. Although they are one of the most abundant organ- isms in the Atlantic Ocean, they were not successfully cultured until 2002, and very little is known about their ecological role. There is evidence that they are important in cycling carbon, nitrogen, and sulfur in the ocean.

nucleioid

also referred to as nuclear area -Although prokaryotes don't have a nucleus they do have a nuclear area also referred to as the nucleoid which contain DNA

archaellum

archaea have a rotating appendage for motility called an archaellum. -It is thinner that a bacterial flagellum. -it is more similar to a bacterial pili -the structure of the motor and the assembly of the flagellum in archaea evolved differently from those of bacteria. Cannulae and hami are extracellular structures that are unique to archaea. -Cannulae are hollow glycoprotein tubes that extend from cells, they are extremely resistant to heat and are produced by pyrodictium (genus of archaea that live in marine hydrothermal habitats) -Hami are complex archaeal cell appendages, entwined with bacterial filaments in sulfurous springs. are helical, have barbs along the length of the filament, and have a three-part hook at the distal end, which facilitates attachment to surfaces. These two things are adaptations to extreme environments that many archaea inhabit

Extreme halophiles

are heterotrophs that require large amounts of Na+ for their growth. -they live in saturates brine solutions like: salt ponds, the Dead Sea, and great salt lake. -use aerobic respiration to make ATP. -However, they also carry out a form of the Calvin cycle (a part of photosynthesis) in which they capture the energy of sun- light using a purple pigment (bacteriorhodopsin). This pigment is very similar to the pigment rhodopsin involved in animal vision.

Cyanobacteria

are the only prokaryotes that carry on pho- tosynthesis using water as the electron source and generating oxygen. During this process they fix huge amounts of carbon dioxide into organic molecules.

budding

bacteria and archaea commonly reproduce by budding - In budding a cell develops a bulge, or bud, that enlarges, matures, and eventually separates from the mother cell.

bacteria

cause many diseases, such as tuberculosis, tetanus, respiratory infections, and food poisoning in humans. However, only a small minority of bacterial species are pathogens. (Although some archaea have been associated with disease, no pathogenic archaea have been identified.)

christian gram

developed the gram staining procedure

Anton van leeuwenhoek

discovered bacteria and other microorganisms in 1674 when he lookedat a drop of lake water through a glass lens.

Louis pasteur

disproved the prevailing views of spontaneous generation by demonstrating that sterilization of a sugar and protein culture prevented bacterial growth. also developed a rabies vaccine, showing that people can be stimulated to develop immunity to disease.

eukaryotes

evolved about 2.2 billion years ago.

cytoplasm

in prokaryotes... The dense cytoplasm of the prokaryotic cell contains ribosomes (smaller than those found in eukaryotic cells) and storage granules that hold glycogen, lipid, and phosphate compounds. -Enzymes needed for metabolic activities may be located in the cytoplasm -in some prokaryotic cells the plasma membrane is extensively folded inward. Enzymes needed for cellular respiration and photosynthesis may be associated with plasma membrane or its folds

capsule/ slime layer

in prokaryotes... -Many prokaryote species produce a capsule or slime layer that surrounds the cell wall. -A slime layer is more loosely attached to the cell wall than a capsule -These outer layers are made of polysaccharide or protein. -may provide the cell with added protection against phagocytosis (engulfment) -In disease-causing bacteria, a capsule or slime layer may protect against phagocytosis by the host's white blood cells. -A strain of S. pneumoniae that lacks a capsule does not cause the disease. -Bacteria also use their capsules to attach to surfaces such as rocks, plant roots, and human teeth (where they cause dental plaque).

flagella

in prokaryotes... -Many types of prokaryotes are motile -for them water is like molasses -Most motile prokaryotes manage to move by means of rotating flagella. -The number and location of flagella are important in classifying some bacterial species. -prokaryotic flagella do not consist of microtubules -a bacteria flagellum is long, thin, consisting of 3 parts: a basal body, a hook, and a single filament. -the basal body anchors the flagellum into the cell wall by disc shaped plates it is also like a motor -the curved hook connects the basal body to the long hollow filament that extends outside the environment -bacterium uses energy from ATPA to pump protons OUT of the cell. DIFFUSION of these protons back into the cell powers the moron that spins the flagellum -flagellum rotates counterclock- wise -Prokaryotes that propel themselves do not move aim- lessly. Many prokaryotes exhibit CHEMOTAXIS, movement in response to chemicals in the environment. -many prokaryotes exhibit PHOTOTAXIS, movement in response to light in the environment.

fimbriae or pili

in prokaryotes... -Some prokaryotes have hundreds of hair-like appendages called fimbriae. Fimbriae, which are made of protein, are shorter than flagella. -Pili are usually longer than fimbriae. -There are typically fewer pili on the cell surface than fimbriae. -Prokaryotes use these to attached to surfaces and in pathogenic bacteria to surfaces they infect - some elongated pili called sex pili are important in transmitting DNA b/n bacteria

binary fission

in prokaryotes... -ability to reproduce rapidly. -reproduce asexually, generally by binary fission -a process in which one cell divides into two similar cells -First the circular DNA replicates, and then an ingrowth of both the plasma membrane and the cell wall forms a transverse wall. -some bacterial species can replicate in under 20 min if under ideal conditions

Korarchaeota

is a clade of Archaea that appears to have branched before the Crenarchaeota and Euryarchaeota branches separated. -Korarchaeota have some characteristics of Crenarchaeota and some features of Euryarchaeota. Korar- chaeotes have been found in terrestrial hot springs.

Mutualism

is a symbiotic relationship in which both part- ners benefit. -Cows and other ruminants (cud-chewing animals) have mutualistic relationships with bacteria and archaea that inhabit their digestive tracts.Ruminants lack enzymes for digest- ing cellulose. They provide the prokaryotes with a nutrient-rich home, and the prokaryotes digest the cellulose for them. -Bacteroides break down indigestible complex carbohydrates into sugars that their human host can absorb. These bacteria also produce certain vitamins that their host absorbs and uses. In addition, Bacteroides promote proliferation of blood vessels that improve intestinal function. these bacteria can Make compound that kills competing bacteria

biofilms

many prokaryotes form biofilms -Many types of bacteria and archaea that inhabit watery environments form biofilms, dense communities of microorganisms that attach to solid surfaces. -The prokaryotes secrete a slimy, gluelike substance rich in polysaccharides and become embedded in this matrix. A biofilm may consist of layers up to 200 μm thick. Biofilms are communities of many microorganisms and may con- sist of many species of bacteria, archaea, fungi, and protists. -The dental plaque that forms on teeth is a familiar example of a biofilm. Dental plaque consists of several hundred different types of bacteria and archaea. Biofilms also commonly form on the surfaces of contact lenses and catheters. They sometimes develop on surgical implants such as pacemakers and joint replace- ments. Biofilms, which form on and inside plants, cause considerable crop loss.

Rhizobial prokaryotes

motile inhabitants of the soil, form mutualistic relationships with the roots of legumes, a large fam- ily of plants that includes important crops such as beans, peas, and peanuts. The infected plant cells form tumorlike nodules in which the microbes reside and fix nitrogen. The prokaryotes supply the plant with the nitrogen it requires, and the plant provides the prokaryotes with organic compounds, including sugar needed for cellular respiration. -When the legumes die and are decomposed, the fixed nitrogen is released and enriches the soil.

horizontal gene transfer

occurs when an organism (or virus) transfers genetic material to another organism that is not its offspring.

cell wall

of prokaryotes.. surrounds tha plasma membrane The cell wall provides a rigid framework that supports the cell and maintains its shape. Bacterial cells have a high concentration of dissolved solutes. The cell wall keeps the cell from bursting under hypotonic conditions -HOWEVER cell walls are of little help when a bac- terium is in a hypertonic environment, as in food preserved by a high sugar or salt content. For this reason, most bacteria grow poorly in jellies, jams, salted fish, and other foods preserved in these ways.

aerobic

require oxygen for cellular respiration -Whether they are heterotrophs or autotrophs, most bacterial cells and many archaeal cells are aerobic

gene transfer

results in genetic recombination

bacteria and archaea

these are two domains and are two of the three main branches of the tree of life. -Both bacteria and archaea play essential roles in the biosphere. As decomposers they break down organic molecules into their components.

vertical gene transfer

transfer of genetic material from parent to offspring

facultative anaerobes

use oxygen for cellular respiration if it is available but can carry on metabolism anaerobically when necessary. -Many are facultative anaerobes

Robert koch

was the first to clearly demonstrate that bac- teria cause infectious disease. he showed that Bacillus anthracis caused anthrax. Using a microscope, Koch observed the bacteria in the blood and spleens of dead sheep.

gram postive bacteria

-Actinomycetes superficially resemble fungi. However, they have peptidoglycan in their cell walls, lack nuclear envelopes. Most are saprotrophs that decompose organic materials in soil. Some are anaerobic. Some cause serious lung disease and other infections in humans and other animals. -Streptomyces produce antibiotics such as streptomycin, erythromycin, chloramphenicol, and the tetracyclines. A. mashuensis produces streptomycin, as well as an antifungal antibiotic. -Lactic acid bacteria ferment sugar, producing lactic acid as the main end product. Among the normal inhabitant of the human mouth and vagina. -Mycobacteria are slender, irregular rods; contain a waxy substance in their cell walls. One species causes tuberculosis; another causes leprosy. -Streptococci inhabit the mouth and digestive tract of humans and some other animals. Among the harmful species are those that cause "strep throat," dental caries, a form of pneumonia, scarlet fever, and rheumatic fever. -Staphylococci normally live in the nose and on skin. Opportunistic pathogens that cause disease when the immunity of the host is lowered. food poisoning, other strains cause toxic shock syndrome. -Clostridia are anaerobic. One species causes tetanus; another causes gas gangrene. Clostridium botulinum can cause botulism, an often fatal type of food poisoning. -The mycoplasmas are a group of very small bacteria that lack cell walls. They may have evolved from bacteria with gram-positive cell walls. They inhabit soil and sewage; some are parasitic on plants or animals. Some inhabit human mucous membranes but do not generally cause disease; one species causes a mild type of bacterial pneumonia in humans.

gram negative bacteria (proteobacteria)

-BETA PROTEOBACTERIA- A large, very diverse clade of GRAM-NEGATIVE BACTERIA. Based on rRNA sequences, the group is divided into five subgroups designated as alpha, beta, gamma, delta, and epsilon. -ALPHA PROTEOBACTERIA- Rhizobia are nitrogen-fixing bacteria., Rickettsias are very small, rod- shaped bacteria. A few species are pathogenic to humans and other animals; transmitted by arthropods through bites or through contact with their excretions. Rickettsias cause typhus (transmitted by fleas and lice) and Rocky Mountain spotted fever (transmitted by ticks). Members of the SAR11 clade are extremely abundant in the ocean. -BETA PROTEOBACTERIA- Several diverse groups, including Nitrosomonas, which oxidizes ammonia. Pathogenic bacteria in this group include Neisseria gonorrhoeae, which causes gonorrhea. -GAMMA PROTEOBACTERIA- Includes the enterobacteria, decomposers that live on decaying plant matter,Escherichia coli, Vibrios are mainly marine; some are bioluminescent. Vibrio cholerae causes cholera. Pseudomonads are heterotrophs that produce nonphotosynthetic pigments; cause disease in plants and animals, including humans. Purple sulfur bacteria are photoautotrophs that do not produce oxygen. -DELTA PROTEOBACTERIA-Includes the myxobacteria (slime bacteria), which secrete slime and glide or creep along. very resistant to heat and drying. -EPSILON PROTEOBACTERIA-A small group of bacteria that inhabit the animal digestive tract. Helicobacter can cause peptic ulcers.

structure of prokaryotic cell

-Fimbriae (Structures used for attachment) -Storage granule -Flagellum -Ribosomes -Bacterial chromosome (DNA) -Plasmid (DNA) -Nuclear area (nucleoid) -Plasma membrane -cell wall: outer membrane and peptidoglycan layer -capsule -Prokaryotic cells typically have a nuclear area with a single, circular DNA molecule. -They may also have one or more plasmids, small rings of DNA that replicate independently.

transduction

-HGT -a phage carries bacterial or archaeal genes from one bacterial or archaeal cell into another -Normally, a phage contains only its own DNA. However, sometimes a phage incorporates some of the DNA of its host. Then, when the phage infects another bacterium or archaeon, it transfers that DNA to its new host. -The chro- mosome of this new host then becomes a recombination of its own original DNA and DNA from another bacterium or archaeon. STEPS: 1. DNA of a phage penetrates bacterial cell. 2. Phage DNA may become integrated with host-cell DNA as a prophage. 3. When the prophage becomes lytic, bacterial DNA is degraded and new phages are produced. New phages may contain some bacterial DNA. 4. Bacterial cell lyses and releases many phages, which can then infect other cells. 5. Phage infects new host cell. 6. Bacterial genes introduced into new host cell are integrated into host's DNA. They become a part of bacterial DNA and are replicated along with it.

transformation

-HGT -when prokaryote dies they release DNA that ban be taken up by other prokaryotes. -in transformation a prokaryotic cell takes up the fragments of foreign DNA or RNA released by another prokaryotic cell. -The foreign DNA must bind to DNA-binding proteins on the surface of the host cell. Once it enters the host cell, segments of the foreign DNA may be exchanged with homologous segments of the host DNA (reciprocal recombination) -Oswald T. Avery and his colleagues identified DNA as the agent that transformed bacterial cells and showed that DNA is the chemical basis of heredity. -Foreign DNA can also be taken up as plasmids. When that occurs, DNA does not undergo recombination; instead, it remains as a plasmid separate from the pro- karyotic chromosome. STEPS 1. Bacterium dies and releases DNA. 2. Fragments of foreign DNA bind to proteins on surface of living bacterium. 3. DNA enters cell, and some DNA is incorporated into host cell by reciprocal recombination.

Chemoheterotrophs

-Heterotroph -The majority of bacteria are chemoheterotrophs. -They depend on organic molecules for both their carbon and energy. -Many prokaryote chemoheterotrophs are free-living DECOMPOSERS that obtain their carbon and energy from dead organic matter.(sometimes called saprotrophs) -some chemoheterotrophs are pathogens and get their nourishment from organisms they infect. harm host by causing diseases. -Energy source: Organic compounds -Carbon Source: Organic compounds -Examples of organisms: Free-living decomposers; most bacterial pathogens