The Microbial World

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Chapter 1 The Relevance and History of Microbiology
1-1 Introduction
1-2 Microbes have a large impact on human health
1-3 Microbes are often helpful, not harmful
1-4 Microbes have profound effects on the environment
1-5 Studying microbes helps us to understand the world around us
1-6 The history of microbiology is a web of discoveries
1-7 Microscopes allowed the discovery of microbes
1-8 Robert Koch developed many microbiological techniques
1-9 Spontaneous generation was an attractive theory to many people, but was ultimately disproven.
1-10 Microbes are discovered to cause disease
1-11 Viruses are shown to parasitize organisms
1-12 The power of vaccination is discovered
1-13 Antimicrobial compounds are developed to kill microorganisms
1-14 Beijerinck and Winogradsky initiate the field of environmental microbiology
1-15 Studying microbes provides insight into life at the molecular level
1-16 Work on microbes paves the way to taking control of the genome
1-17 Summary
Chapter 2 Cell structure and organization
2-1 Introduction
2-2 Sugars are common in the cell
2-3 Nucleic acids store information and process it
2-4 Proteins are made of amino acids
2-5 The primary structure of proteins is the amino acid sequence
2-6 Secondary structure is the local geometry of the protein
2-7 Tertiary structure is the 3D structure of individual polypeptides
2-8 Quaternary structure is the total complex of a functional protein
2-9 Lipids are the building blocks of membranes
2-10 Small molecules are also important in the cell
2-11 The cell is organized into functional units
2-12 Membranes surround the cell and hold it in
2-13 Membranes are a selective barrier
2-14 Membranes can help generate energy
2-15 Membranes are also important in their own synthesis and can fold inward for specialized functions
2-16 The cytoplasm is the area inside the membrane
2-17 Enzymes serve as catalysts in the cytoplasm
2-18 The cell DNA is organized into a nucleoid
2-19 Transcription and translation occur on the surface of the nucleoid
2-20 Translation involves messenger RNA
2-21 Ribosomes are composed of RNA and protein
2-22 Transfer RNA is the ferry for amino acids
2-23 Inclusions and other internal structures are found in many prokaryotic cells
2-24 The periplasm is between the cytoplasmic and outer membranes in gram-negative bacteria
2-25 The cell wall surrounds and holds in the microbe
2-26 Some bacteria lack cell walls
2-27 The cell surface extends into the environment
2-28 Flagella are one type of structure used for motility
2-29 Advantages of motility
2-30 Some bacteria move by gliding motility
2-31 Pili and fimbriae are involved in adhesion, motility and DNA exchange
2-32 Bacterial cells are often covered in glycocalyx
2-33 Bacteria can exist in different cell states
2-34 Endospores are very resistant structures
2-35 Some microbes make other types of spores
2-36 Heterocysts are differentiated cells that specialize in nitrogen fixation
2-37 Archaea, a different type of microbe
2-38 The major differences between Archaea and other domains of life
2-39 Eukaryotic cells have much in common with prokaryotic cells
2-40 Things that are different between eukaryotes and prokaryotes
2-41 Unique structures in eukaryotes
2-42 Eukaryotic cells absorb things by endocytosis
2-43 The nucleus holds the cells genetic material in eukaryotes
2-44 Mitochondria and plastids are organelles of energy generation in eukaryotic cells
2-45 The implications of eukaryotic structures on their growth
2-46 Summary
Chapter 3 Viral Structure and function
3-1 Introduction
3-2 Viruses face several common obstacles that they must overcome to successfully replicate
3-3 Viruses often have common structures
3-4 The genome of viruses can be DNA or RNA
3-5 Viruses are classified by the nature of their viral nucleic acid
3-6 The life cycle of a virus is divided into several phases
3-7 To infect cells, viruses first need to attach to them.
3-8 Bacterial viruses almost always enter cells by injecting their nucleic acid.
3-9 Entry of eukaryotic viruses can involve penetration at the membrane or use of natural uptake pathways.
3-10 Viruses are lytic or lysogenic
3-11 The lytic cycle requires copying of the nucleic acid genome.
3-12 Viruses regulate viral protein production in a manner consistent with their host
3-13 After the parts of the virus are synthesized, they assemble into complete virions.
3-14 The lytic cycle ends with release of the finished virions from the cell.
3-15 Summary
Chapter 4 The Central Dogma
4-1 Introduction
4-2 The DNA sequence directs the synthesis of proteins
4-3 DNA Replication uses a collection of proteins called a replication complex
4-4 After replication, the two copies of the chromosome move to opposite ends of the microbe
4-5 Not all DNA in the prokaryotic cell is chromosomal: the specific case of plasmids
4-6 Plasmids can vary in size and number
4-7 Errors can occur in DNA replication that create potential mutations
4-8 Errors in DNA can also occur outside of replication
4-9 SOS repair can fix serious errors in the DNA, but is error prone
4-10 Recombination repair can accurately fix large errors in the DNA
4-11 There are more complicated mutations: deletions, duplications, and amplifications
4-12 Mobile genetic elements can also cause mutations in the chromosome
4-13 Genetic changes do not become fixed in the DNA until they are copied
4-14 Transcription involves the copying of DNA into RNA
4-15 The level of mRNA is a common regulatory point in prokaryotes
4-16 Prokaryotic mRNAs are typically more than one gene long
4-17 Differential transcription and stability of mRNA can also be used as points of regulation
4-18 Translation is the conversion of mRNA into protein at the ribosome
4-19 Translation is initiated at the Shine-Dalgarno sequence and involves formyl methionine (fMet)
4-20 Some interesting facts about translation
4-21 Chapter summary
Chapter 5 Microbial Nutrition
5-1 Introduction
5-2 The cell is made up of a few common elements
5-3 Microbes can be classified based upon their nutritional requirements
5-4 Examples of Nutritional Classifications
5-5 Culture Media
5-6 Media can come in both liquid and solid form.
5-7 Culture media is as varied as the microorganisms that grow in it.
5-8 Media can be classified into several different categories
5-9 Sterilization of media
5-10 Chapter Summary
Chapter 6 Microbial Growth
6-1 Introduction
6-2 Growth for microorganisms is defined as an increase in numbers
6-3 Unicellular microbes grow by cell division
6-4 Cell division is a complex process
6-5 Measurement of cell growth can be accomplished in a number of ways
6-6 Growth in batch culture has four separate phases
6-7 Lag phase is the time before cell growth begins
6-8 In exponential phase, cells begin to divide
6-9 The growth rate in exponential phase can be modeled mathematically
6-10 Cells stop increasing in number during stationary phase
6-11 Cells at some point can no longer sustain themselves and death phase begins
6-12 Continuous culture is an open system where microbes can be maintained in exponential phase
6-13 The environment greatly affects the growth of microbes
6-14 Temperature affects the rate of growth.
6-15 Microbes respond differently to the presence of oxygen.
6-16 The hydrogen ion concentration (pH) affects growth of microbes
6-17 The availability of water or concentration of solutes influences the ability of microbes to grow
6-18 Summary
Chapter 7 Control of Microbes
7-1 Introduction
7-2 Temperature is a common physical method for controlling microbes
7-3 Empirical data can be used to predict the success of a heat treatment
7-4 Some historical methods of heat treatment are still useful in certain situations
7-5 Autoclaving, dry heat and pasteurization are common methods of heat treatment
7-6 Low temperature slows or stops the growth of microbes
7-7 Irradiation damages critical cellular processes, killing microbes
7-8 Filtration physically removes microbes from a solution
7-9 Reducing the water activity of a sample can prevent the growth of microbes
7-10 Chemical treatments act on microbes to prevent their growth
7-11 Antiseptics and disinfectants control microbes on surfaces
7-12 Preservatives control the growth of microbes in foods
7-13 Antibiotics and chemotherapeutic agents help to control pathogenic microbes in the body
7-14 Antimicrobial activity is measured using standard tests
7-15 Summary
Chapter 8 Metabolism
8-1 Introduction
8-2 As are all things, microbes are subject to the laws of thermodynamics
8-3 Free Energy (&豌G) is what cells are after
8-4 Cells often perform useful work through oxidation-reduction reactions (redox reactions)
8-5 Energy in the cell is carried by special molecules
8-6 Enzymes are biological catalysts
8-7 Enzymes are often organized in the cell into functional units
8-8 Bacterial diversity is mainly manifested as catabolic diversity
8-9 Fermentations in microbes share some common properties
8-10 The Embden-Meyerhof-Parnas pathway (EMP) is a very common glycolytic pathway
8-11 For anaerobes, the EMP pathway results in an excess of NADH, which is dealt with by reducing pyruvate to fermentation end products.
8-12 The Entner-Doudoroff pathway is a third common pathway for the catabolism of glucose
8-13 Respiration involves donation of electrons to an inorganic terminal electron acceptor
8-14 Catabolism of sugar (glucose) through respiration involves the tricarboxylic acid cycle
8-15 Catabolism of fats (lipids) uses &豪-oxidation
8-16 High-energy electrons are converted into ATP using a membrane
8-17 Protons move across the membrane during ETS
8-18 ATP synthesis involves protons moving through ATP synthase
8-19 Many microbes are capable of anaerobic respiration
8-20 Nitrate reduction can generate energy, but not as much as aerobic respiration
8-21 Sulfate reduction is common in anaerobic environments
8-22 Carbonate can also serve as a terminal electron acceptor
8-23 Some microbes can grow completely on inorganic sources of carbon, energy and electrons
8-24 Nitrifying bacteria are chemoautotrophic lithotrophs that use ammonia as a source of energy and electrons.
8-25 Chapter Summary
Chapter 9 Photosynthesis
9-1 Introduction
9-2 Photosynthetic microbes have several common characteristics
9-3 Light is collected by protein complexes containing photopigments
9-4 Chlorophyll is the molecule that collects light and energizes an electron, while carotenoid protects the cell from the damaging effects of light
9-5 The placement of the photopigments is important in the performance of their function
9-6 Light energy is focused at the reaction center
9-7 Photosynthetic microorganisms are classified as oxygenic and anoxygenic
9-8 Purple bacteria are anoxygenic photosynthetics that are metabolically versatile
9-9 Purple bacteria house their photosynthetic apparatus in intracytoplasmic membranes
9-10 The reaction center of purple bacteria is made of three polypeptides and contains many photopigments
9-11 Three systems regulate photosynthesis in the purple bacteria
9-12 The green bacteria are anoxygenic photosynthetics that form a chlorosome
9-13 The reaction center in green bacteria contains an iron-sulfur center
9-14 The cyanobacteria perform oxygenic photosynthesis
9-15 Cyanobacteria contain two reaction centers
9-16 Photosynthesis in cyanobacteria is constitutively expressed
9-17 The energy generated by photosynthesis is used to drive the dark reactions
9-18 Summary
Chapter 10 Anabolism
10-1 Introduction
10-2 Microbes must first find and transport the elements that they need
10-3 Carbon can be assimilated from organic source or synthesized from CO2
10-4 Nitrogen assimilation can involve the uptake of reduced nitrogen compounds or nitrogen fixation
10-5 Sulfur can come from organic or inorganic sources
10-6 Phosphate enters metabolism by ATP synthesis and substrate-level phosphorylation.
10-7 Metal ions, important components of many enzymes, must be taken up from the environment
10-8 The environment influences the ability of a microbe to make monomers
10-9 Amino acids that are simple in structure have simple biosynthetic pathways
10-10 The synthesis of some amino acids share common steps
10-11 Amino acids with more complex structures have longer biosynthesis pathways
10-12 Nucleotide synthesis is complex and expensive
10-13 Lipid synthesis involves a carrier protein
10-14 Monomers are assembled to form polymers
10-15 Peptidoglycan begins in the cytoplasm and ends in the periplasm
10-16 Synthesized polymers combine in orderly fashion to make cellular stuctures.
10-17 Summary
Chapter 11 Regulation of Metabolism
11-1 Introduction
11-2 Regulation is a way to respond to a changing environment
11-3 There are common steps in regulation
11-4 Allosteric proteins sense small molecules and change their activity because of them
11-5 Regulation occurs at many different points during gene expression
11-6 Positive and negative regulation involves proteins that bind to DNA
11-7 Attenuation is regulatory mechanism in which translation affects transcription
11-8 Protein activity in prokaryotes is also regulated at the post-transcriptional and translational level
11-9 Expression of the lac operon requires the presence of lactose and the absence of glucose
11-10 The tryptophan operon is controlled by repression, attenuation and feedback inhibition
11-11 Sporulation in Bacillus subtilis is directed by sigma factors and turned on by a phosphorelay system
11-12 Vibrio fischerii senses cell density using a small diffusible molecule that binds to an activator
11-13 Heat-shock gene expression is controlled by &豻 factors, mRNA secondary structure, and protein stability
11-14 Nitrogen fixation can be controlled by a positive activator, mRNA stability, and enzyme modification
11-15 Summary
Chapter 12 Genomics and genetics
12-1 Introduction
12-2 Sequence information is obtained by performing enzymatic reactions on small amounts of pure DNA
12-3 What does sequence information look like?
12-4 What conclusions can you draw about the function of the protein product of your new ORF?
12-5 What are the applications of the information gained through genomics?
12-6 In addition to insights about gene products, what else can be learned from studying genomes?
12-7 An introduction to genetics and genetic engineering
12-8 How to find a needle in a hay stack
12-9 Generation of random mutations
12-10 Effects of mutations
12-11 Engineering specific mutations in the lab
12-12 Gene Transfer Systems
12-13 Genetic Mapping
12-14 Complementation Analyses
12-15 There can be complications in complementation analysis
12-16 Gene fusions can be used to make large quantities of a protein or to monitor the regulation of a gene
12-17 Suppressors are second-site mutations that change the phenotype of a mutant to be more like that of the wild type
12-18 Summary
Chapter 13 Bacterial Viruses
13-1 We can monitor bacterial viruses with the naked eye by seeing their effects on the bacterial hosts.
13-2 Lambda phage is a lysogenic virus with double-stranded DNA.
13-3 DNA damage causes lambda to enter the lytic cycle.
13-4 T4 is a large, lytic phage with a large double-stranded DNA genome
13-5 Restriction-modification systems limit the host range of T4.
13-6 Viruses need to pack virions with complete genomes and also provide energy for entry into a new host
13-7 P22 is a lysogenic, double-stranded DNA phage that was important in the development of bacterial genetics.
13-8 P1 is a double-stranded DNA phage with an unusual ability to infect different hosts
13-9 P1 replicates its DNA independently of the host chromosome when in a lysogenic state.
13-10 Q&豪 is a small, single-stranded RNA virus.
13-11 As an RNA virus, Q&豪 has special problems to overcome.
13-12 Q&豪 packs a great deal of information into its small RNA genome.
13-13 M13 has a genome composed of a single-stranded, circular DNA molecule.
13-14 M13 expresses all of its genes at the same time and produces progeny without killing the host cell.
13-15 Some phage lysogens cause their hosts to become pathogenic.
13-16 Summary
Chapter 14 Host-Microbe Interactions
14-1 Introduction
14-2 Microbes that interact with eukaryotes face some common challenges and utilize similar strategies
14-3 Types of host-microbe interactions
14-4 Microbes face many challenges when associating with a host
14-5 Once a microbe detects a host, it then attaches to it
14-6 Microbes may invade deeper into host tissues once attached
14-7 Mutualistic outcomes
14-8 Pathogenic outcomes
14-9 Direct damage to host
14-10 The nature and role of Exotoxins
14-11 The nature and action of endotoxins
14-12 Indirect damage to host
14-13 Three examples of host-microbe interactions
14-14 Vibrio fischeri and squid form a mutualistic relationship under the sea
14-15 Quorum sensing and autoinduction
14-16 The process of autoinduction
14-17 Biochemistry of bioluminescence
14-18 Euprymna scolopes selects for V. fischeri
14-19 Microbes that live in close association with plants
14-20 How plants recognize the proper rhizobia
14-21 Not all associations between plants and nitrogen-fixing bacteria is as involved as the rhizobial system
14-22 The normal flora of humans
14-23 The skin and eyes as habitats
14-24 The microbial population in the mouth
14-25 The respiratory tract has mostly harmless bacteria, but can contain pathogens.
14-26 The gastrointestinal tract has the largest number and greatest diversity of microbes in our body.
14-27 The urogenital tract
14-28 Benefits of the normal flora
14-29 Summary
Chapter 15 Animal defenses against microbes
15-1 Introduction
15-2 Important introductory concepts of the immune system
15-3 Susceptibility to a pathogen varies between and even within species
15-4 The immune system is a complex collection of organs and tissues
15-5 The circulatory system transports the components of the immune system
15-6 Bone marrow is the origin of all immune cells
15-7 Lymphoid tissue is a separate vascular system through which lymph and immune cells move
15-8 The MALT and spleen are collections of immune cells that work to fight infection
15-9 Animal defenses can be classified into innate and adaptive immune systems
15-10 Complement is a set of proteins that detect and kill microbes
15-11 Inflammation is a response to tissue damage that can activate the immune system
15-12 Phagocytes engulf and kill foreign cells
15-13 Phagocytes can detect pathogens and move toward them
15-14 After attaching to a microbe, phagocytes ingest them
15-15 Natural killer cells attack pathogens, but are not inducible
15-16 The adaptive immune system increases its response to a pathogen after initial exposure
15-17 Lymphocytes make antibodies and regulate the immune system
15-18 Antibodies come in five different classes
15-19 Important properties of antibodies
15-20 T lymphocytes regulate the immune system and fight intracellular infections, viral infection and cancer
15-21 Major histocompatibility complex (MHC) molecules are the signal beacons of the immune system
15-22 There are several types of T cells, but all mature in the thymus
15-23 T cell activation occurs when an antigen is presented to a T cell and reacts with its T cell receptor
15-24 Natural killer cell activation involves interferon or IL-2, and IgG
15-25 Putting it all together - examples of responses of the immune system to different types of pathogens
15-26 Host response to viral pathogens relies heavily on T cells
15-27 The immune system is not perfect - Allergies
15-28 Autoimmune diseases involve the host immune system attacking host proteins
15-29 Summary
Chapter 16 Treatment and prevention of disease
16-1 Introduction
16-2 As disease became more common, efforts were made to combat them
16-3 Quarantine can be an effective method of limiting the spread of disease
16-4 Good water sanitation can prevent the spread of many gastrointestinal diseases
16-5 Control of insects can prevent the spread of some diseases
16-6 Vaccines train the immune system to fight disease
16-7 Many of the recommended vaccines are live attenuated viruses
16-8 Another common vaccine type are component vaccines
16-9 Some groups are wrongly advocating stopping vaccination
16-10 Antimicrobial compounds directly inhibit or kill pathogens, thus curing infectious diseases
16-11 Bacterial cell wall synthesis enzymes are a common target for antibiotics
16-12 A second class targets the cell membrane, but they are often toxic to humans
16-13 A third class of antibiotics target the 70S ribosome
16-14 A fourth class targets nucleic acid metabolism
16-15 A fifth class of antimicrobials are competitive inhibitors of metabolism
16-16 Resistance to antibiotics has diminished the effectiveness of antibiotics
16-17 The overuse of antibiotics is one reason that drug resistance has developed
16-18 Summary
Chapter 17 Bacterial Pathogens
17-1 Introduction
17-2 A microbe must first find a host
17-3 Once a host is found, a pathogen must colonize (possibly invade) and cause damage
17-4 Pathogens have a collection of properties that are major determinants in pathogenesis
17-5 Bacillus anthracis is an endospore forming microbe that can causes a lethal toxic infection called anthrax
17-6 Anthrax toxin and the polypeptide capsule are key aspects of pathogenesis
17-7 Yersinia pestis is the causative agent of plague
17-8 Y. pestis delivers toxic substances to the host using a type III secretion apparatus and defends itself using LPS
17-9 Bordetella pertussis causes whooping cough and was a major killer of children
17-10 Adhesins and toxins are important in the virulence of Bordetella pertussis
17-11 Streptococcal diseases are major causes of infectious disease
17-12 The pathogenesis of S. pyogenes is understood, while that of S. pnemoniae is less clear.
17-13 Staphylococcus aureus causes a large number of human infections
17-14 S. aureus produces a deadly cocktail of enzymes, polysaccharides, and toxins
17-15 The microbes of the tuberculosis complex are slow-growing pathogens that gradually destroy the host
17-16 Virulence factors of M. tuberculosis allow it to survive the host's defenses
17-17 Tetanus and botulism are intoxications caused by clostridia
17-18 The major virulence factors for botulism and tetanus are the toxins produced
17-19 Helicobacter pylori is the cause of many ulcers
17-20 H. pylori creates a collection of enzymes that allow it to colonize the stomach
17-21 Some Escherichia coli strains cause diarrheal diseases by colonizing the intestine, while others are capable of extraintestinal infections.
17-22 Five different strains of E. coli cause five different gastointestinal infections
17-23 Other E. coli strains are the major cause of urinary tract infections
17-24 Salmonella enterica causes a common form of gastroenteritis
17-25 S. enterica uses a type III secretion system to deliver a toxic mix of proteins into host cells
17-26 Chlamydia are intracellular pathogens that cause the most common forms of venereal disease
17-27 Chlamydial infection causes a strong immune response that results in tissue damage
17-28 Treponema pallidum is the cause of syphilis
17-29 T. pallidum cannot survive outside the host
17-30 T. pallidum spreads rapidly during infection, but can be cured with antibiotics
17-31 Neisseria gonorrhoeae causes the common sexually transmitted disease gonorrhea
17-32 Pili are the major virulence factor for N. gonorrhoeae
17-33 Borrelia burgdorferi causes the tick-borne Lyme disease
17-34 Little is known about the mechanisms of pathogenesis of B. burgdorferi, but the disease can be sucessfully treated with antibiotics
17-35 Vibrio cholerae is the cause of cholera
17-36 Pili and cholera toxin are major determinants in pathogenesis
17-37 Corynebacterium diphtheriae is the cause of diphtheria
17-38 Diphtheria toxin causes most of the symptoms of diphtheria
17-39 Summary
Chapter 18 Eukaryotic Pathogens
18-1 Introduction
18-2 Infection by eukaryotic pathogens is importantly different from infection by bacterial pathogens.
18-3 Plasmodium species cause malaria
18-4 Cryptosporidiosis, a gastrointestinal infection, is caused by Cryptosporidium species
18-5 Infection with Giardia intestinalis causes giardiasis
18-6 Toxoplasmosis is caused by Toxoplasma gondii
18-7 Trypanosomes cause two forms of trypanosomiasis
18-8 Superficial fungal infections are bothersome, but normally not serious
18-9 Sporotrichosis is caused by Sporothrix schenckii
18-10 Candidiasis is infection with Candida species, a yeast
18-11 Histoplasmosis is caused by two closely related species of fungi
18-12 Blastomycosis is caused by Blastomyces dermatitidis
18-13 Chapter Summary
Chapter 19 Viral Pathogens
19-1 Introduction
19-2 Rhinovirus is the most common causes of colds
19-3 Rhinoviruses are single-strand RNA viruses that replicate in the cytoplasm of the host cell.
19-4 Adenoviruses also infect the respiratory tract, but can cause illness elsewhere
19-5 The adenovirus is a double-stranded DNA virus with a complex viral capsid
19-6 Influenza virus causes a lower respiratory viral infection with fever
19-7 The influenza viral genome contains eight single-stranded RNAs, which are replicated in the nucleus.
19-8 Human Immunodeficiency virus z(HIV) causes acute immune deficiency syndrome (AIDS).
19-9 HIV contains two copies of a single-stranded RNA that is copied into DNA as part of its replication
19-10 Hepatitis viruses infect the liver
19-11 HAV and HEV are transmitted by enteric routes
19-12 HBV, HCV and HDV are transmitted by blood and other bodily fluids
19-13 Diagnosis of hepatitis depends on blood tests while treatment varies with the specific virus
19-14 Hepatitus viruses have different replication systems
19-15 Herpes viruses cause cold sores and genital herpes
19-16 HSV is a enveloped virus with a double-stranded DNA genome.
19-17 West Nile Virus causes a viral infection that can result in deadly encephalitis
19-18 West Nile Virus (WNV) has a single-stranded RNA genome that is translated as a large polyprotein.
19-19 Ebola virus causes hemorrhagic disease with a high fatality rate
19-20 Ebola is a filamentous virus with a single-stranded RNA genome.
19-21 Satellite viruses are important in some infections.
19-22 Viroids and prions are infectious agents that are very different from viruses.
19-23 Chapter summary
Chapter 20 Evolution: Implications for microbiology
20-1 What aspects of evolution are we talking about?
20-2 Organisms are similar because of their common ancestry
20-3 A consequence of common ancestry is residual similarity of species
20-4 Macromolecular sequence data shows how microbes evolve
20-5 Ribosomal RNA genes are useful for determining phylogenetic relationships.
20-6 Sequence analysis supports our view of evolution
20-7 A classification scheme that flows from evolution has many advantages over other methods
20-8 The mechanisms of evolution involve genetic change and natural selection
20-9 Limitations and implications of the classifications of organisms
20-10 The difficulty of classifying microorganisms by their obvious properties
20-11 Molecular phylogeny
20-12 The results of molecular phylogenies - the tree of life
20-13 Mitochondria and chloroplasts originated as bacteria
20-14 Eurakyotes are metabolically similar, but morphologically very different.
20-15 Archaea are fundamentally different from bacteria and eukaryotes
20-16 Bacteria
20-17 Properties in bacteria and their importance to phylogeny
20-18 Summary
Chapter 21 Eukaryotic Microbial Diversity
21-1 Introduction
21-2 Dinoflagellates are photosynthetic eukaryotes found in many fresh water and marine habitats
21-3 Ciliates contain hair-like structures on their surface involved in motility.
21-4 Apicomplexa are obligate parasites that infect many animal species
21-5 Stramenopiles are photosynthetic and nonphotosynthetic microbes whose evolutionary relationship has been shown by molecular analysis
21-6 Rhodophyta are a third group of photosynthetic protists that grow in coastal areas
21-7 Some protists are related to green plants
21-8 Fungi are critical heterotrophs in the environment
21-9 Different species of fungi are classified by morphology, nutrition and molecular data
21-10 Chytridiomycota look like protists, but are actually fungi
21-11 Zygomycota can be obligate pathogens or free-living saprophytes that live in moist environments
21-12 Glomeromycota form symbiotic relationships with higher plants.
21-13 Dikaryomycota are species of fungi that can form cells with two separate nuclei.
21-14 Ascomycota create complex networks of fruiting bodies
21-15 Basidiomycota are organized as macrofungi, rusts, and smuts
21-16 Smuts and rusts are important agricultural pathogens
21-17 Yeasts are a morphological stage of some fungi.
21-18 Primitive protists
21-19 Some protozoa are closely related to animals
21-20 Amoeba are unicellular protozoa with a naked outer layer
21-21 Flagellates are motile protozoa with flagella
21-22 Slime molds are unusual organisms that share both protozoan and fungal properties
21-23 Summary
Chapter 22 Archaeal Diversity
22-1 Introduction
22-2 Methanogens produce methane as an end product and form a deep branch of the Archaea.
22-3 The reactions of methanogenesis utilize unique cofactors
22-4 The genomic comparisons of Methanothermobacter thermautotrophicus and Methanococcus jannaschii are informative.
22-5 Extreme halophiles can generate energy using bacteriorhodopsin
22-6 Extreme halophiles survive high-salt conditions by having enzymes that function at high concentrations of potassium.
22-7 Bacteriorhodopsin pumps protons across the membrane using a conformational shift activated by light
22-8 Thermoacidophilic archaea grow in high-temperature acidic environments
22-9 Extreme thermophiles grow at temperatures above 75°C
22-10 Many cultured Crenarchaeota are hyperthermophilic
22-11 Kornarchaeota and Nanoarchaeota have been defined 16S rRNA sequences
22-12 Chapter Summary
Chapter 23 Bacterial Diversity
23-1 Introduction
23-2 Proteobacteria
23-3 &豩 subdivision - rhizobia are plant symbionts
23-4 &豩-subdivision - Caulobacter are dimorphic prosthecate bacteria
23-5 Methanotrophs used methane as their carbon and energy source
23-6 &豩 subdivision - Agrobacterium species often colonize plants, not as symbionts, but as pathogens
23-7 Purple non-sulfur bacteria are facultative phototrophs
23-8 &豩 subdivision - Pelagibacter ubique (SAR11), a previously unculturable microbe is present at high populations in many environments
23-9 Ammonia oxidizers, mostly members of the &豪 subdivision, only grow using inorganic chemicals.
23-10 Thiobacillus are chemoautolithotrophic bacteria that use reduced sulfur compounds as a source of energy
23-11 &豫 subdivision - enteric bacteria contain species that are important pathogens and are ubiquitous in the environment
23-12 Vibrio and Photobacterium
23-13 &豫 subdivision - pseudomonads are a large group of commonly found microbes that grow on organic compounds.
23-14 &豫 subdivision - SAR86 may be a new kind of primary producer
23-15 &豬 subdivision - sulfate-reducing bacteria use sulfur compounds as their terminal electron acceptor
23-16 &豬 subdivision - myxobacteria are social microbes capable of forming fruiting bodies
23-17 &豬 subdivision - bdellovibrio are fast-moving predators of other microbes
23-18 &豭 subdivision - some Campylobacter strains are intestinal pathogens
23-19 High GC - mycobacteria are slow-growing microbes with unusual cell walls.
23-20 High GC - Streptomycetaceae are spore-forming, filamentous microbes that are a major source of antibiotics
23-21 Low GC - Staphylococci are common parasites of animals
23-22 Low GC - lactic acid bacteria are fermentative microbes important in many food processes
23-23 Low GC - Bacillus species are aerobic microbes that form endospores
23-24 Low GC - clostridia are anaerobic, endospore-forming bacteria.
23-25 Low GC - Heliobacteriaceae have the unusual combination of photosynthesis and endospore formation
23-26 Low GC - mycoplasma lack a cell wall and are obligate parasites of eukaryotes.
23-27 Cyanobacteria are microbes that carry out oxygenic photosynthesis
23-28 Spirochetes are one of the few groups whose morphology indicates their phylogeny
23-29 Planctomyces and related species contain cells walls lacking peptidoglycan
23-30 Deinococcaceae are highly resistant to radiation
23-31 Cytophagales are pigmented gliding bacteria
23-32 Chlorobiaceae - green sulfur bacteria
23-33 Chloroflexaceae are gliding photosynthetic microbes
23-34 Thermotogales grow at the highest temperature of any bacteria
23-35 Chapter Summary
Chapter 24 Microbial Ecology
24-1 Introduction
24-2 Determining what microbes are present in an environment is difficult
24-3 With modern molecular techniques, scientists are able to identify organisms in the environment
24-4 Counting all microbes is becoming possible
24-5 Scientists are just beginning to learn the metabolic activities of microbe in the environment
24-6 The surface soil environment is heterogeneous and contains many biological activities
24-7 Microbes cooperate in the soil to degrade biopolymers
24-8 Subsurface environments are hot, high-pressure environments
24-9 Aquatic environments are the largest surface environments on earth
24-10 Environments with running water often contains biofilms
24-11 Microbial communities in lakes and ponds depend upon nutrients and predation
24-12 Oceans contain photosynthetic microbes and chemoheteroorganotrophs
24-13 Microbial life below the surface of the ocean has fewer nutrients, except at deep sea ocean vents.
24-14 Shore habitats contain higher concentrations of microbes due to warmer temperatures, more light and the nutrient run-off from surrounding land.
24-15 Microbes participate in the cycling of elements
24-16 Carbon cycles between organic compounds and carbon dioxide
24-17 Nitrogen gas is converted into biochemically accessible forms by microbes
24-18 H2S and SO4 are important inorganic sources of sulfur
24-19 Chapter summary
Chapter 25 Applied Microbiology
25-1 Introduction
25-2 The difference between primary and secondary metabolites
25-3 Pharmaceutical microbiology uses microbes for the production of medically important compounds
25-4 Finding new antibiotics can involve several different approaches
25-5 Enzyme screens can find inhibitors of important pathogenic proteins
25-6 Once a strain is found that produces something desirable, its growth conditions need to be optimized
25-7 Culture conditions must be optimized for large scale production.
25-8 Methods have been developed to detect pathogens in food and for diagnosis of disease
25-9 Wastewater treatment prevents contamination of our environment
25-10 Water purification ensures safe drinking water
25-11 Food microbiology increases understanding of food fermentations and works to prevent spoilage
25-12 Yogurt is a fermentation of milk by lactic acid bacteria
25-13 Cheese production involves milk fermentation, pressing and ripening
25-14 Beer brewing involves alcoholic fermentation by yeast in the presence of barley and hops.
25-15 Wine is an alcoholic fermentation of grapes by yeast
25-16 Bread making uses yeast to create CO2, which causing the dough to rise
25-17 Vinegar is made by the action of microbes on sugar or starchy material to produce acetic acid
25-18 Sauerkraut involves a fermentation of cabbage by lactic acid bacteria
25-19 Food processes can be spoiled by the action of undesirable microbes
25-20 Enzymes from microorganisms are used in a wide variety of products
25-21 Some vitamins are manufactured using microorganisms
25-22 Some amino acids are manufactured using microorganisms
25-23 Bioconversion involves catalyzing one or several steps of the synthesis of a complex molecule using microorganisms
25-24 Industrial microbiology is also important in agriculture
25-25 Summary
Chapter 26 Microbial Methods

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