Chapters 34-35-disease transmission

Transmission of Diseases
Chapter 34
Organisms Disease(s)
Strep Strep throat, Rheumatic Fever, Toxic Shock, Scarlet Fever
Corynebacterium Diphtheria
Bordetella Whooping Cough
Mycobacterium TB and Leprosy
Neisseria Gonorrhea and Meningitis
Virus Measles
Virus Mumps
Rubella German Measles
Varicella Chickenpox/Shingles
Rhinovirus, Coronovirus Colds
Influenza Flu
Staphylococcus Skin Infections, Toxic Shock, Food-borne illness,
Helicobacter Ulcers
Hepatitis A-E
Gonorrhea STI
Treponema pallidum Syphilis
Chlamydia STI and Blindness
Herpes STI and Cold Sores
Trichomonas STI
HIV STI
Chapter 35
Rabies Zoonosis
Hantavirus Pulmonary Syndrome
Rickettsia Rocky Mountain Spotted Fever, Typhus
Ehrlichia Ehrlichiosis
Borrelia Lyme Disease
West Nile Meningitis, systemic infection
Yersinia pestis Plague
Fungi Table in book
Clostridium tetanus Tetanus

Group A Streptococcal Diseases
Pharyngitis (“strep throat”)-inflammation of the pharynx
Scarlet fever-rash that begins on the chest and spreads across the body
Pyoderma-confined, pus-producing lesion that usually occurs on the face, arms, or legs
Streptococcal toxic shock syndrome-bacteremia and severe multisystem infections

Streptococcus pneumoniae
Gram-positive cocci in pairs
Alpha-hemolytic colonies when grown on blood agar (anaerobic incubation produces beta-hemolytic colonies)
Can be carried in nasopharynx but can cause disease if travels to the lungs, blood or CNS
Disease is highest in children and the elderly
Corynebacterium and Diphtheria
Corynebacterium diphtheriae, the cause of diphtheria, is the most widely known
Transmitted from person to person via respiratory droplets or skin contact
Diphtheria toxin is responsible for the signs and symptoms of diphtheria

Bordetella and Whooping Cough
Inadequately immunized children are at high risk for acquiring pertussis.
Adult Carriers

Mycobacterium
Cell wall contains waxy lipid -mycolic acid
This cell wall results in unique characteristics
Slow growth
Protection from lysis once the bacteria are phagocytized
Capacity for intracellular growth
Resistance to Gram-staining, detergents, many antimicrobial drugs, and dessication
Cellular immune response
3 main mycobacterial diseases
Tuberculosis
Leprosy
Opportunistic infections in AIDS patients


Tuberculosis (TB)
Respiratory disease cause by M. tuberculosis
Virulent strains of M.tuberculosis contain the cell wall component, cord factor, necessary for disease
3 types of tuberculosis
Primary TB
Results from the initial infection with M.tuberculosis
Secondary TB
Reestablishment of an active infection after a period of dormancy
Disseminated TB
Results when the infection spreads throughout the body



Diagnosis, Treatment, and Prevention
Diagnosis
Tuberculin skin test identifies individuals with previous exposure to M. tuberculosis by the presence of a hard, red swelling at the test site
Chest x-rays are used to identify individuals with active disease
Isolation of organism from specimen and ID.
Treatment
Treatment: special anti-mycobacterial drugs.
Combination therapy must be used for a number of months to treat the disease

Neisseria gonorrhoeae
Cause of Gonorrhea
Can adhere to mucous membrane epithelial cells lining genital, urinary, and digestive tracts. Area of infection: age dependent
Gonorrhea in men
Usually symptomatic producing inflammation that causes painful urination and pus-filled discharge
Gonorrhea in women
Often asymptomatic
Can infect the cervix, parts of the uterus, and fallopian tubes
Can result in pelvic inflammatory disease (PID)
Can result in ectopic pregnancy or sterility

Viruses and Respiratory Infections
The common childhood viral diseases:
measles
mumps
rubella
chickenpox
controllable with appropriate immunization.

Antigenic Shift
Occurs when major changes in antigens occur due to gene reassortment in influenza virus.

Antigenic drift

Occurs when minor changes in antigens occur due to gene mutation in influenza virus.

Staphylococcal Diseases
Noninvasive Disease
Food poisoning from the ingestion of enterotoxin-contaminated food

Cutaneous Disease
Various skin conditions including scalded skin syndrome, impetigo, folliculitis, and furuncles

Systemic Disease
Toxic shock syndrome-TSS toxin is absorbed into the blood and causes shock
Bacteremia-presence of bacteria in the blood
Endocarditis- bacteria attack the lining of the heart
Pneumonia-inflammation of the lungs-alveoli and bronchioles become filled with fluid
Osteomyelitis-inflammation of the bone marrow and the surrounding bone

Helicobacter pylori
Slightly helical, highly motile bacterium that colonizes the stomach of its hosts
Causes most (if not all) peptic ulcers
H.pylori produces numerous virulence factors that enable it to colonize the stomach
Hepatitis Viruses
Hepatitis caused by viruses can cause cirrhosis, an acute liver disease.

Symptoms include fever and jaundice (production and release of excess bilirubin by the liver due to destruction of liver cells, resulting in yellowing of the skin),


STIs
Gonorrhea: Neisseria gonorrhoeae
Syphilis: Treponema pallidum
During pregnancy, syphilis can be transmitted from an infected woman to the fetus; the disease acquired by the infant is called congenital syphilis
Chlamydia
Chlamydia, the most prevalent STI, is caused by infection with the bacterium Chlamydia trachomatis.
Untreated chlamydial urethritis causes serious complications in males and females.
Blindness due to Chlamydia trachomatis
Herpes
Herpes lesions can also be transmitted sexually and are caused by herpes simplex virus type 1 and herpes simplex virus type 2.
HSV-2 is generally associated with sexual transmission and infection of the anogenital regions.
Genital herpes infections are presently incurable
Trichomonas vaginalis
Trichomonas vaginalis is a protozoan responsible for trichomoniasis, another STI.



Zoonosis
Zoonosis: an animal disease transmissible to humans, generally by direct contact, aerosols, or bites.
Rabies occurs primarily in the U.S.
Rabies can be transmitted from the wild animal reservoir to domestic animals or, very rarely, to humans
Bats are the source of most cases of rabies Transmission: Break in the skin or inhalation


Hantavirus Pulmonary Syndrome
Hantaviruses occur worldwide in rodent populations and
Cause serious diseases such as hantavirus pulmonary syndrome (HPS) when accidentally spread to humans.
In the U S, not recognized until 1993.
Rickettsias
Rickettsias are obligate intracellular parasitic Bacteria that are transmitted by arthropods.

Rickettsias cause a variety of diseases in humans and animals, of which the most important are typhus fever, Rocky Mountain spotted fever, and ehrlichiosis.

Controlled by antibiotic therapy

Borrelia
Gram-negative spirochetes
Cause two diseases in humans
Lyme disease
Relapsing fever

Borrelia burgdorferi is the causative agent

Bacteria are transmitted to humans via a tick bite
Hard ticks of the genus Ixodes are the vectors of Lyme disease

The tick life cycle is important in understanding the spread of Lyme disease

Malaria
Malaria is a widespread, mosquito-borne disease occurring in tropical and subtropical regions.
Sickle cell anemia is a genetic trait that confers resistance to malaria but reduces the oxygen-binding affinity of hemoglobin.
Thalasemia is a genetic trait that confers resistance to malaria but alters a red blood cell enzyme


West Nile fever
The disease involves infections of birds by the bite of an infected mosquito.
Humans and other vertebrates are occasional terminal hosts.
Most human infections are asymptomatic, but diagnosed infections can cause up to 3% mortality due to encephalitis and meningitis.


Plague
Plague is confined to individuals who come into contact with rodent populations that are endemic reservoirs for Yersinia pestis.
A systemic infection or a pneumonic infection leads to rapid death, but the bubonic form is treatable with antibiotics if rapidly diagnosed.

Mycoses
A variety of soilborne fungi produce disease in humans. Categories:
Superficial
Subcutaneous
Systemic
Fungal infections cause serious systemic disease in immunocompromised patients.


Tetanus
Clostridium tetani is a ubiquitous soilborne microorganism that can cause tetanus, a disease characterized by toxin production and rigid paralysis.
Tetanus is preventable with appropriate immunization

lab exam 3 review-lecture and lab exam May 12

Read the explanatory sections of your lab manual for each experiment performed since lab exam 2.

1. Know what TSI agar is and the reactions
2. Know what PEA and EMB agars are and do.
3. Know what happens during a carbohydrate fermentation reaction.
4. Know what Mannitol Salt agar and Enterococcosel agar are and do.
5. Know what a differential and/or selective medium is. Be able to categorize the agar you used in lab as differential or selective or both.
6. Know what a durham tube is and does.
7. Know the three types of hemolytic reactions on Blood agar.
8. Know the parts of a mould as listed in your lab manual. What is the agar used for mould growth? How does it work.
9. Know the reactions of the tubes/agars plates you set up for your unknowns-citrate, urea, TSI etc.
10. Know the purpose of food and water testing in microbiology. What are you looking for? What is important?
11. How do you work up an unknown organism?

Exam Review 4

Exam Review 4

Chapters 28
• Know the difference between resident, transient, and opportunistic members, and all other definitions in presentation
• Identify the portals through which pathogens invade the body.
• Know how extracellular enzymes, toxins, and antiphagocytic factors affect virulence. Know 3 types of toxins. Know list of steps of how organism infects cell
• Know non-specific lines of defense in the human body. (
• Explain non-specific lines of defense. Identify physical and chemical factors that inhibit pathogens.

Chapter 29-31
•Know the components of blood and their functions. Be able to ID the different types of white blood cells.
• Know the 2 types of macrophages
• Know the process of phagocytosis.
• Describe the role of eosinophils and NK cells in extracellular killing.
• Describe the complement system, including its classical and alternate pathways. How are they different? How are they the same?
• Know the process of inflammation.
• Define antigen
• What is the lymphatic system. .
• What are B lymphocytes.
• Describe the basic structure of an antibody (immunoglobulin) molecule.
• Contrast the structure and function of the five classes of immunoglobulins.
• Describe five functions of antibodies.
• Know the three types of T lymphocytes covered in lecture/text.
• What are cytokines.
• Describe the two classes of major histocompatibility complex (MHC) proteins.
• Describe antigen processing.
• Describe the functions of plasma cells and memory B cells.
• Describe cytotoxic T-cell action.
• Describe the establishment of B and T-cell memory.
• Describe the three types of vaccines.
• Compare active immunization versus passive immunization.
• Describe the four types of hypersensitivity.
• What cells and antibody are involved in allergic response.
• Describe immune complex disease.
• What is type IV hypersensitivity.
• Define autoimmunity.

Chapter 33
• Know the Keywords for Chapter 33
• Differentiate between the terms endemic, sporadic, epidemic, and pandemic.
• List and describe the five stages of the disease process.
• Define nosocomial infection.

Chapter 34
• Organisms Disease(s)
• Strep Strep throat, Rheumatic Fever, Toxic Shock, • Corynebacterium Diphtheria
• Bordetella Whooping Cough
• Mycobacterium TB and Leprosy
• Neisseria Gonorrhea and Meningitis
• Virus Measles
• Virus Mumps
• Rubella German Measles
• Varicella Chickenpox/Shingles
• Rhinovirus, Coronovirus Colds
• Influenza Flu
• Staphylococcus Skin Infections, Toxic Shock, Food-borne illness,
• Helicobacter Ulcers
• Hepatitis A-E
• Gonorrhea STI
• Treponema pallidum Syphilis
• Chlamydia STI and Blindness
• Herpes STI and Cold Sores
• Trichomonas STI
• HIV STI

Chapter 35
• Rabies Zoonosis
• Hantavirus Pulmonary Syndrome
• Rickettsia Rocky Mountain Spotted Fever, Typhus
• Ehrlichia Ehrlichiosis
• Borrelia Lyme Disease
• West Nile Meningitis, systemic infection
• Yersinia pestis Plague
• Fungi
• Clostridium tetanus Tetanus

Chapter 33-Epidemiology

Principles of Epidemiology  
Epidemiology
Epidemiology is the study of disease in populations.
Includes the study of the interactions of the pathogen with the host population.
Pathogens can be selective forces in the evolution of the host and visa versa.

Etiology
Study of the cause of disease

Germ theory of disease- disease caused by infections of pathogenic microorganisms

Robert Koch developed a set of postulates one must satisfy to prove a particular pathogen causes a particular disease

Infection
Chronic (long-term) infection
Lives in balance with the host
Minimum harm
Acute infections
Characterized by rapid onset and, often, rapid recovery.
Mortality: death
Morbidity: Infection/Disease

Symptoms
Symptoms: subjective characteristic of a disease. A symptom perceived by the patient but not by the examiner
Signs: objective characteristics of disease (verifiable).
Syndrome: group of symptoms and signs that collectively characterizes a particular disease
Asymtomatic or subclinal: No observable symptoms.
Pathogenicity
Pathogenicity: the ability of a microorganism to cause disease

Virulence: the degree of pathogenicity

Virulence Factors: traits that enable pathogens to cause infections.
The Vocabulary of Epidemiology
Prevalence: the proportion of diseased individuals in a population in a given time period.
Incidence: the number of cases of an individual disease in a population in a given time period.

Definitions
Endemic disease: constantly present at low incidence in a specific population.
Epidemic: an unusually high incidence of disease which occurs in a specific population.
Pandemic: A worldwide epidemic.

Reservoirs of Infection
Most pathogens cannot survive long outside of their host
Reservoirs of infection
pathogens that are maintained as a source of infection are termed reservoirs. 3 types of reservoirs:
Animal reservoir
Human carriers
Nonliving reservoir

Opportunistic Pathogens
Normal microbiota that cause disease
Conditions that provide opportunities for pathogens
Immune suppression
Changes in the normal microbiota- changes in relative abundance of normal microbiota may allow opportunity for a member to thrive and cause disease
Introduction of normal microbiota into unusual site in the body

Animal Reservoirs
Zoonoses- diseases that are naturally spread from their usual animal host to humans
Acquire zoonoses through various routes
Direct contact with animal or its waste
Eating animals
Bloodsucking arthropods
Humans are usually dead end host to zoonotic pathogens

Vectors
Biological vectors: hosts for the multiplication of the pathogen during some stage of the pathogen’s life. Plague: Rodents: Fleas
Mechanical: passively carry pathogens to new hosts (fomites)
Some pathogens exist in soil, water, or animals.
Others exist only in humans and are maintained solely by person-to-person contact.

Severe Acute Respiratory Syndrome
Zoonosis: an infection that occurs primarily in animals and is transferred to humans.
SARS-CoV: zoonotic virus that causes severe acute respiratory syndrome (SARS).
Person-to-person spread is by respiratory means.

Infectious Disease Transmission
Transmission: A pathogen spread directly from one host to another, or indirectly by living vectors or
Fomites: inanimate objects.
Vehicles: food and water.

AIDS
AIDS is one of the most studied disease pandemics.
AIDS will continue to be a major public health problem, especially in developing countries.
There is no effective cure or immunization to prevent AIDS

Nosocomial Infections
Infections acquired while in a health care facility
Types of nosocomial infections
Exogenous- pathogen acquired from the health care environment
Endogenous- pathogen arise from normal microbiota due to factors within the health care setting
Iatrogenic- results from modern medical procedures

Control of Nosocomial Infections
Involves precautions designed to reduce the factors that result in disease

Universal (Standard) Precautions instituted by the CDC to limit exposure to pathogens

Hand washing is the most effective way to reduce nosocomial infections

Control of Disease
Public health measures that play a major role in reduction of disease incidence:

Food and water purity regulations, vector control
immunization
quarantine
disease surveillance
pathogen eradication

Virulence-enhancing Mechanisms
Virulence-enhancing mechanisms:
include the mobile genetic elements-

bacteriophages
plasmids
transposons.

Biological Warfare and Biological Weapons
Biological warfare: the use of biological agents to incapacitate or kill a military or civilian population in an act of war or terrorism.
Mode of inoculation:common sources such as food and water are the most likely
Anthrax as a Biological Weapon
Bacillus anthracis has emerged as an important pathogen because of its use as a bioweapon.
Endospores are form of transmission
> 90% mortality rate in untreated individuals
Effective treatment relies on timely observation and diagnosis of symptoms

Chapter 29,30,31-Immunology

Whole blood is composed of plasma, a liquid containing proteins ,other solutes and suspended cells.

Outside the body, plasma forms an insoluble clot. Plasma remains liquid only when an anticoagulant (anticlotting agent) is added.

After clotting, the remaining fluid, called serum, contains no cells or clotting proteins. Serum does, however, contain a high concentration of other proteins, including soluble antibody proteins, and is widely used in immunological investigations.

The Innate Immune Response
Not antibody mediated

Innate immunity is mediated by phagocytes.

Phagocytes recognize pathogen-associated molecular patterns (PAMPs) via a family of membrane-bound pattern-recognition molecules (PRMs)

Cytokines participate in cellular signals

Leukocytes
A variety of leukocytes participate in immune responses. Be able to name and recognize. Neutrophils, Eosinophils, Basophils, Monocytes/Macrophages, Lymphocytes

Phagocytosis-Ingestion and killing of invader by phagocytic cells (neutrophil)

Inflammation, Fever, and Septic Shock
Inflammation is characterized by pain, swelling (edema), redness (erythema), and heat. The inflammatory response is a normal and generally desirable outcome of an immune response.
Uncontrolled systemic inflammation, called septic shock, can lead to serious illness and death.

Adaptive Immune Response
In adaptive immunity, nonspecific phagocytes present antigen to specific T cells, triggering the production of effector T cells and antibodies. Immune T cells and antibodies react directly or indirectly to neutralize or destroy the antigen.
The adaptive immune response is characterized by

Specificity for the antigen
Memory-the ability to respond more vigorously when reexposed to the same antigen
Tolerance- the ability to discriminate self antigens from nonself antigens

B Cell Receptor (BCR)
B lymphocytes have multiple copies of a BCR type
BCR is identical to that of the secreted antibody for that particular cell
The randomly generated antibody variable region determines the BCR (not in response to antigens)
Each BCR is complementary to one antigen

Specific-Adaptive Immunity
Cell-mediated immunity leads to killing of pathogen-infected cells through recognition of pathogen antigens found on infected host cells.
Humoral immunity –killing of cells by antibodies and complement

Immunogens
Immunogens are foreign molecules that induce an immune response. Molecular size, complexity, and physical form are intrinsic properties of immunogens.
Antigens are molecules recognized by antibodies or by T-cell receptors (TCRs).

Presentation of Antigen to T Lymphocytes
T cells recognize antigens presented by antigen-presenting cells (APCs) or by pathogen-infected cells.
At the molecular level, TCRs bind peptide antigens presented by major histocompatibility complex (MHC) proteins. Class I MHC proteins are found on the surfaces of all nucleated cells.
Class II MHC proteins are found only on the surface of B lymphocytes, macrophages, and dendritic cells, all of which are APCs

Cytokines
These molecular interactions stimulate T cells to kill antigen-bearing cells or to produce cell-stimulating proteins known as cytokines.


Natural Killer Cells
Natural killer (NK) cells use the same effectors to kill virus-infected cells and tumors. However, NK cells do not require stimulation, nor do they exhibit memory. NK cells respond in the absence of MHC proteins.

T-Helper Cells: Activating the Immune Response
TH1 and TH2 cells play pivotal roles in cell-mediated and antibody-mediated immune responses.
Following the initial antigen exposure, each antigen-stimulated B cell multiplies and differentiates to form both antibody-secreting plasma cells and memory cells . TH1 inflammatory and TH2 helper cells each stimulate effector cells through the action of cytokines.

Antibody
The amino-terminal region is a variable domain, meaning that the amino acid sequence in this structural region differs in each different antibody.

The antigen-binding site is formed by the interaction of variable regions of heavy and light chains

Antibody Production
Antibody production is initiated by antigen contact with an antigen-specific B cell that processes the antigen and presents it to an antigen-specific TH2 cell.

The activated TH2 cell then signals the antigen-specific B cell to produce antibody.


Plasma Cells
Plasma cells are relatively short-lived (less than 1 week), but produce and secrete large amounts of IgM antibody in this primary antibody response.

Memory B Cells
The memory B cells generated by the initial exposure to antigen may live for years. If reexposure to the immunizing antigen occurs at a later time, memory cells need no T-cell activation; they quickly transform to plasma cells and begin producing IgG.

Secondary Antibody Response
Upon reexposure, the antibody titer rises rapidly to a level 10–100 times greater than the titer achieved following the first exposure. This rise in antibody titer is referred to as the secondary antibody response.

Complement, Antibodies, and Pathogen Destruction-Know complement and alternate pathways

Passive Immunity
Occurs naturally during pregnancy
IgG from mother crosses placenta
Infers protection to the baby
Occurs naturally as result of breast feeding
IgA antibodies in breast milk given to child
Artificial passive immunity involves transfer of antibodies produced by another person or animal
Can be used to prevent disease before or after likely exposure

Vaccines and Immunization
Attenuated vaccines
Weakened form of pathogen
Generally unable to cause disease
Strain replicates in vaccine recipient
Causes infection with undetectable or mild symptoms
Results in long lasting immunity

Vaccines and Immunization
Inactivated vaccines
Unable to replicate in vaccinated individual
Retains immunogenicity of infectious agent
Immunogenic not pathogenic
Inactivated vaccines fall into two categories
Whole agents
Contain killed organisms of inactivated virus
Fragments
Portions of organisms or agents including toxins proteins and cell wall components

Hypersensitivity Reactions
Hypersensitivity results when foreign antigens induce cellular or antibody immune responses, leading to host tissue damage.

Type I-IgE allergic response
Type II-Cytotoxic-complement and antibodies
Type III-Immune Complexes
Type IV-Cell-mediated-Delayed response

Type II (Cytotoxic) Hypersensitivity
Results when cells are destroyed by an immune response, often due to the combined activities of complement and antibodies
Component of many autoimmune diseases
2 examples
Destruction of blood cells following an incompatible blood transfusion
Destruction of fetal red blood cells in hemolytic disease of the newborn


Type III (Immune-Complex Mediated) Hypersensitivity
Due to the formation of antigen-antibody complexes, also called immune-complexes
Can cause systemic or localized reactions
Systemic
Systemic lupus erythematosus
Rhematoid arthritis
Localized
Hypersensitivity pneumonitis
Glomerulonephritis

Type IV Hypersensitivity

Type IV hypersensitivity, or delayed-type hypersensitivity (DTH), is cell-mediated hypersensitivity characterized by tissue damage due to inflammatory responses produced by TH1 inflammatory cells.

Autoimmune Diseases
Body usually recognizes self antigens
Destroys cells that would destroy self
Malfunction in immune recognition basis for autoimmunity
Autoimmune diseases may result from reactions to antigens that are similar to MHC self antigens
Autoimmunity may occur after tissue injury
Self antigens released from injured organ
Autoantibodies form and interact with injured tissues

Chapter 28 Host Microbe Interactions

Microbial Interactions with Humans 

Pathogenicity
Pathogens: Microorganisms that cause harm.
Pathogenicity: the ability of a pathogen to cause disease.
Opportunistic : causes disease only in the absence of normal host resistance.
Host-parasite interactions: The ability of a microorganism to cause or prevent disease is influenced by complex

Wound
Normal Flora
Moist areas, especially around sweat glands, are colonized by gram-positive Bacteria and other members of the skin normal flora.
Environmental and host factors influence the quantity and quality of the normal skin microflora.
Normal Flora
Influences on composition:
Weather
Age
Personal Hygiene
Antibiotic Therapy
Transient
Colonizers/Residents
Bacteremia
Normal Flora
Chemoorganotrophs
Fermenters/Non-fermenters
Methanogenic
Pathogenesis
Exposure
Adherence
Invasion
Colonization/growth
Toxicity or Invasion
Damage and Disease

Dental Caries
Plaque microorganisms produce adherent substances.
Acid produced by microorganisms in plaque damages tooth surfaces, and dental caries result.
A variety of microorganisms contribute to caries and periodontal disease.
Intestinal Tract
The stomach is very acidic and is a barrier to most microbial growth.
The intestinal tract is slightly acidic to neutral and supports a diverse population of microorganisms in a variety of nutritional and environmental conditions.

Upper Respiratory Tract
In the upper respiratory tract (nasopharynx, oral cavity, and throat), microorganisms live in areas bathed with the secretions of the mucous membranes.
The normal lower respiratory tract (trachea, bronchi, and lungs) has no resident microflora, despite the large numbers of organisms potentially able to reach this region during breathing.

Adherence
Pathogen invasion starts at the site of adherence and may spread throughout the host via the circulatory systems.
Capsule: A polymer coat consisting of a dense, well-defined layer surrounding the cell.
Slime Layer: A loose network of polymer fibers extending outward from a cell
Fimbriae and pili
Colonization factors
Colonization and Growth
A pathogen must gain access to nutrients and appropriate growth conditions before colonization in host tissue can occur.
Organisms may grow locally at the site of invasion or may spread through the body.
If extensive bacterial growth in tissues occurs, some of the organisms are usually shed into the bloodstream in large numbers, a condition called bacteremia
Virulence
Virulence is determined by invasiveness, toxicity, and other factors produced by a pathogen.

Various pathogens produce proteins that damage the host cytoplasmic membrane, causing cell lysis and death.

Because the activity of these toxins is most easily detected with red blood cells (erythrocytes), they are called hemolysins.

In most pathogens, a number of factors contribute to virulence.
Attenuation is loss of virulence

Virulence
Pathogens produce a variety of enzymes that enhance virulence by breaking down or altering host tissue to provide access and nutrients.

Still other pathogen-produced virulence factors provide protection to the pathogen by interfering with normal host defense mechanisms. These factors enhance colonization and growth of the pathogen

Clots, enzymes, Toxins
Exotoxins
Toxicity: ability to casue disease by preformed toxin that inhibits or kills cells.
Invasiveness: ability of an organism to grow in host tissue
The most potent biological toxins are the exotoxins produced by microorganisms.
Each exotoxin affects specific host cells, causing specific impairment of a major host cell function.

Enterotoxins
Enterotoxins: toxins that specifically affect the small intestine, causing changes in intestinal permeability that lead to diarrhea.

Many enteric pathogens colonize the small intestine and produce A-B enterotoxins.

Food-poisoning bacteria often produce cytotoxins or superantigens.

Endotoxins
Endotoxins are lipopolysaccharides derived from the outer membrane of gram-negative Bacteria.

Released upon lysis of the Bacteria, endotoxins cause fever and other systemic toxic effects in the host.

Endotoxins are generally less toxic than exotoxins

Limulus amebocyte lysate assay
The presence of endotoxin detected by the Limulus amebocyte lysate assay indicates contamination of a substance by gram-negative Bacteria.
White blood cells of Horseshoe Crab
Debilitation
Conditions of age, stress, diet, general health, lifestyle, prior or concurrent disease, and genetic makeup may compromise the host's ability to resist infection.

Many hospital patients with noninfectious diseases (for example, cancer and heart disease) acquire microbial infections because they are compromised hosts.

Nosocomial Infections: hospital-acquired infections are called
Innate Resistance to Infection
Nonspecific physical, anatomical, and chemical barriers prevent colonization of the host by most pathogens.

Lack of these defenses results in susceptibility to infection and colonization by a pathogen.


Definitions
Parasites: organisms on or in a host that cause damage
Opportunistic pathogen: causes disease only in absence of normal resistance
Infection: when a microbe lives and grows in a host.
Disease: damage to the host that impairs body function.

Definitions
Mucous membranes: epithelial cells that line the lumen(opening) of various tissues
Mucus: glycoproteins
Digestive tract: stomach, small intestine (duodenum, ileum and jejunum)
Methane producers: H2 + CO2=CH4
Upper Respiratory tract: nasopharynx, oral cavity and throat
Lower Respiratory tract: trachea, bonchi and lungs
Ciliated epithelial cells: have cilia on surface/line upper respiratory tract

Homework assignments until end of term

Assignments are due as you finish them or by last lab or the term.

Unknown Table Results

Unknown Info and Example

Unknown Paper: At least (minimum) one page on why you came to the conclusion that your organism was of a particular identification based on the reactions you did and did not get. Give the reactions that supported what it was and the reactions that told you what it was not. Also give brief description of the organism and the potential diseases it causes. The more complete the paper, the better the grade. DUE on last day of LAB CLASS.

Example

Proteus vulgaris is a rod-shaped, Gram negative bacterium that inhabits the intestinal tracts of humans and animals. It can be found in soil, water and faecal matter. It is grouped with the enterobacteriaceae and is an opportunistic pathogen of humans. It is known to cause urinary tract infections and wound infections.
When P. vulgaris is tested using standard biochemical assays, it is discovered that it provides a positive result for: sulfur reduction, urease production, tryptophan deaminase production, and indole production. I identified my unknown as P. vulgaris because it presented with a ……..and negative reactions for.
The optimal growing conditions of this organism is in a facultative anaerobic environment with an average temperature of about 23-37 degrees Celsius .

Exam Review 3: Exam April 21/ Review April 16

Exam 3 Review
Know the Following:

Prokaryotes/Archaea/Eukaryotes
Anoxic- anaerobic and much hotter than the present Earth

Abiotic non-living syntheses that set the stage for the origin of life.

The first life forms may have been self-replicating RNAs (RNA life).

Autotrophy-Use of CO2 for metabolite

Chemolithotrophic-use of inorganic compounds for metabolites

The phylogeny of microorganisms is their evolutionary relationships

SSU (small subunit) RNA sequencing is synonymous with 16S or 18S sequencing.

Phylogenetic trees based on ribosomal RNA have now been prepared for all the major prokaryotic and eukaryotic groups. The amplification of the gene encoding 16S ribosomal RNA, sequencing it, and analyzing the sequence in reference to other sequences.

Bacterial taxonomy places emphasis on analyses of phenotypic properties of the organism.

Taxonomy: The science of classification.. Consists of two major subdisciplines, identification and nomenclature

Horizontal/Lateral Gene flow: Transduction, Conjugation, Transformation

Largest group: The Proteobacteria

Phenotypic
Gram stain
Morphology
Metabolism
Biochemical reactions

Genotypic
16rRNA:genes for 16S rRNA and related molecules are amplified, treated with one or more restriction enzymes, separated by electrophoresis and then probed with complementary rRNA.

The Archaea can be divided into four groups: the methanogens, the halophiles, the hyperthermophiles and the genus Thermoplasma

Found in: Soil, Mineral deposits, Aquatic areas, Volcanic areas, Animals

Archaeal cell walls do not contain muramic acid and D-amino acids, the building blocks of peptidoglycan.

The Archaeal membranes differ from Bacterial membranes in that they contain ether-linked lipids bonded to glycerol

The eukaryotic microbes: algae, fungi, slime moulds and protozoa.

Eukaryotic microorganisms differ from Bacteria and Archaea.
These differences include:
cell size
internal structure
genetic arrangement
evolutionary history.

Know Eukaryotic organelles
The endoplasmic reticulum
The golgi apparatus
Lysosomes
The peroxisome
3 energy organelles: mitochondria, hydrogenosome, chloroplast

The chloroplast is the site of photosynthetic energy production and CO2 fixation in eukaryotic phototrophs (algae).

Instead, chlorophyll and all other components needed for photosynthesis are located in a series of flattened membrane discs called thylakoids

Endosymbiosis

Microbiological Eukaryotes: Protozoa, flagellates, ciliates, sporozoa, fungi, slime moulds, algae

Genomics
Genes: A hereditary unit consisting of a sequence of DNA that occupies a specific location on a chromosome and determines a particular characteristic in an organism.

Genome: entire complement of genes

Sequencing: determining the total bases - that make up the DNA

Cloning vectors: A carrier, such as a bacterial plasmid or bacteriophage.

Genomic sequencing:
Reveals genes
Reveals functions of organism
Evolutionary history
Transcription and translation of genetic
information in the genome

An open reading frame or ORF is a portion of a prokaryotic organism's genome which contains a sequence of bases that could potentially encode a protein.

Bacterial Artificial Chromosomes
The use of the F plasmid to carry large amounts of chromosomal DNA

Yeast Artificial Chromosomes
Vectors which replicate in yeast like normal chromosomes but can carry large fragments of DNA

Shotgun techniques use random cloning and sequencing of relatively small genome fragments

Annotation: conversion of raw sequence data into a list of the genes present in the genome.

Bioinformatics: the use of computer tools to acquire, analyze, store, and access DNA and protein sequences

The purpose of genomics is to determine the number, sequence and function of genes in an organism

Gene families: genes that are related to other genes within the organism

Microarrays are genes or gene fragments attached to a solid support in a known pattern


Diversity
Photoautotrophs
Carbon source is carbon dioxide
Energy source is sunlight
Reduction of CO2 to organic compounds

Photoheterotrophs: Use organic carbon as their carbon source


Light-Dependent Reactions-Purpose: to produce ATP from light energy

Pigments:

Chlorophylls a and b
Bacteriochlorophyll
Carotenoids

Chlorophyll Pigment of oxygenic phototrophs.

Bacteriochlorophyll: the chlorophyll pigment of anoxygenic phototrophs.

Prokaryotes-No chloroplasts

Pigments are integrated into the internal membrane system

Carotenoids:
Most widespread accessory pigments
Hydrophobic pigments embedded in membrane
Photoprotective role: Quench toxic oxygen
Transfers energy to the reaction center which is used to make ATP

Antenna: chlorophyll molecules harvest light energy and transfer it on to reaction center of the pigments.

Exciton: mobile forms of energy (photons)
Pigments absorb light energy, give up electron, which enter electron transfer chains.
Water molecules split, ATP and NADH form, and oxygen is released

Anoxygenic Photosynthesis: Photosynthesis in which O2 is not produced

In oxygenic photosynthesis, water donates electrons to drive CO2 production, and oxygen is produced as a by-product.

Two separate light reaction center are involved, photosystems I and II.

Photosystem I resembles the system in anoxygenic photosynthesis. Photosystem II splits H2O to yield O2


Light Independent reactions:

Synthesis part of photosynthesis
Can proceed in the dark
Calvin-Benson cycle

Most phototrophic and other autotrophic organisms accomplish fixation of CO2 via the Calvin cycle, in which the enzyme ribulose bisphosphate carboxylase (RubisCO) plays a key role

Assimilative Metabolism: When an inorganic compound such as NO3, SO4 or CO2 is reduced for biosynthesis

Dissimilative metabolism : The reduced product is excreted into the environment

Phototrophic: obtains energy from light

Chemolithotrophic: oxidize inorganic compounds for energy(some facultative)

Chemoorganotrophic: obtains energy from the oxidation of organic compounds.

Autotrophic: use CO2 as nutrient source

Methanotrophs: use methane for energy

Decomposition: the breakdown of organisms, and the release of nutrients back into the environment.

Nitrogen Cycling: Plants rely on nitrogen from the soil and cannot acquire it from the gaseous nitrogen in the atmosphere.

Under anoxic conditions, organic matter is degraded principally to methane and carbon dioxide by syntrophic bacteria

The principal form of nitrogen on Earth is nitrogen gas (N2), which can be used as a nitrogen source only by the nitrogen-fixing bacteria.

Nitrogen fixation: the microbiological reduction of nitrogen to ammonia

Ammonia produced by nitrogen fixation or by ammonification from organic nitrogen compounds can be assimilated into organic matter.

Nitrification: The process by which ammonia is oxidized to nitrate

Denitrification: the microbial process by which nitrate is reduced to gaseous nitrogenous compounds (N2)

Methane is decomposed to ammonia

Utilization of sulfur and Iron as electron donors. Changes in soil or water content.

Microbial decomposition is the single largest source of CO2 released to the atmosphere.

Syntrophy: a metabolic process in which two or more organisms cooperate in the degradation of some compound.

The principal form of nitrogen on Earth is nitrogen gas (N2), which can be used as a nitrogen source only by the nitrogen-fixing bacteria.

Sulfate reduction is an important biogeochemical process

Bacterial reduction of ferric iron occurs in anoxic environments causes acid mine drainage.

Methods:
Enrichment culture: technique is a means of obtaining microorganisms from natural samples.

The Winogradsky column is a miniature anoxic ecosystem that can be used as a long-term source of bacteria for enrichment culture purposes

A pure culture can be obtained by conventional microbiological procedures, including streak plates, agar shakes, and dilution methods.

MPN: Most probable number: method of measuring the numbers of microbes in different media and conditions

DAPI is a general stain for identifying microorganisms in natural samples

The green fluorescent protein makes cells autofluorescent and is a means for tracking cells introduced into the environment.

Some stains can differentiate live versus dead cells-Viability stains.

Fluorescent antibodies that are specific for one or a small group of related cells can be prepared

Nucleic acid probes and PCR=highly specific


Microbial Ecology
Microbial ecology: how microorganisms interact with one another and their environment.


Guild: A microbial community which consist of metabolically related organisms.

Ecosystem: a community of organisms and their natural environment.

Biogeochemistry: the study of microbial energy transformations and biogeochemical processes that result in the recycling of elements.

Microenvironment: the place where the microorganism actually lives.

Oxic: the outer zones of a small soil particle containing O2

Anoxic: the center of a soil particle only a very short distance away which is completely anoxic (O2-free)

Biofilms are bacterial colonies, encased in slime, that form on surfaces. Biofilms can lead to damage as a result of the products excreted by the cells. Biofilm involves cell-to-cell communication (quorum sensing) COOPERATION

“A” horizon of soil : where most microbes exist.

The most important factor influencing microbial activity in surface soil is the availability of water
In deep soil (the subsurface environment), nutrient availability plays a major role.

Primary producers: Phototrophs in aquatic ecosystems

Marine waters have less nutrients for bacteria. Many use light to drive ATP synthesis.
Proteorhodopsin

Bacteria -oceanic surface waters
Archaea - deeper waters

Barophiles grow best under pressure.

Barotolerants can grow under elevated pressures but grow best at atmospheric pressures

Extreme barophiles: obtained from the greatest depths, require high pressure for growth.


Bioremediation: the cleanup of oil, toxic chemicals and pollutants by microbes.

Key microbial habitats on plants include the rhizoplane/rhizosphere(root) and the phyllosphere.

The plant provides the energy source needed by the root nodule bacteria, and the bacteria provide fixed nitrogen for the growth of the plant. The bacteria induce the formation of root nodules within which the nitrogen-fixing process occurs.

Chapter 22-Methods in Microbial Ecology

Microbial ecology
Microbial ecology: how microorganisms interact with one another and their environment.
Enrichment culture: technique is a means of obtaining microorganisms from natural samples.
Enrichment Culture Technique
Enrichment Culture Technique:
A medium and set of incubation conditions are established (highly selective)
Conditions are selective for desired organism and counter selective for undesired organisms
Inoculum: Sample
Resources and Conditions


The Winogradsky column is a miniature anoxic ecosystem that can be used as a long-term source of bacteria for enrichment culture purposes
Enrichment Culture
Enrichment bias is demonstrated by comparing the results obtained in dilution cultures with classical liquid enrichment.
Some organisms will grow more rapidly and “take over” culture
Isolation in Pure Culture
Once an enrichment culture is established, a pure culture can be obtained using streak plates, agar shakes, or dilution methods.
MPN: Most probable number: method of measuring the numbers of microbes in different media and conditions.



Fluorescent stains
DAPI (4’, 6-diamido2-phenylindole) is a general stain for identifying microorganisms in natural samples.
Some stains can differentiate live versus dead cells- Viability stains.
Fluorescent antibodies that are specific for one or a small group of related cells can be prepared


Fluorescent stains
The green fluorescent protein makes cells autofluorescent and is a means for tracking cells introduced into the environment.
Unlike in pure cultures, morphologically similar cells may actually be quite different genetically in natural samples.

Genetic Stains
A variety of fluorescent-staining methods employ the power of nucleic acid probes and thus are highly specific in their staining properties.

These include phylogenetic staining, chromosome painting, and reverse transcription fluorescent in situ hybridization (FISH).
FISH
The sample DNA is separated into complimentary strands within the DNA double helix structure.

The fluorescently labeled probe of interest is then added to one sample mixture and binds with the sample DNA at the target site.

The probe signal can then be seen through a fluorescent microscope as a colored spot located in the target area/cell/chromosome. 
The assay uses fluorescence-labeled peptide nucleic acid (PNA) probes that target the species-specific ribosomal RNA (rRNA) in an organism. 

Results are visualized using fluorescence microscopy to see green fluorescing cells. 
Other Methods
FISH
Chromosome painting: DNA probe used to ID cells with specific highly conserved genes within groups of bacteria.
ISRT (in situ reverse transcription):
Used to measure gene expression.
Use of a probe that hybridizes with a specific mRNA.
Electrophoresis
PCR
Environmental Genomics


Electrophoresis
Denaturing gradient gel electrophoresis (DGGE) can be used to resolve difference in genes present in the various species inhabiting a natural sample.


Radioisotopes
Isotopes: Different forms of the same element containing the same number of protons and electrons but different numbers of neutrons

Microautoradiography (MAR): Radioisotopes used as measures of microbial activity in a microscopic technique

Isotope fractionation: can reveal the biological origin of various substances

FISH MAR: Technique that allows the metabolic activity to be measured and the organism to be identified

Chapter 23-Microbial Ecology

Microbial Ecosystems
Chapter 23

Ecological Concepts
Many microbes establish relationships with other organisms (symbioses)
Parasitism
One member is harmed and the other benefits
Mutualism
Both species benefit
Commensalism
One species benefits and the other is neither harmed nor helped

Ecological Concepts
The diversity of microbial species in an ecosystem can be expressed in two ways
Species richness: the total number of different species present
Species abundance: the proportion of each species in an ecosystem
Microbial species richness and abundance is a function of the kinds and amounts of nutrients available in a given habitat

Microbial Ecosystems and Biogeochemical Cycling
Guilds
Metabolically related microbial populations
Sets of guilds form microbial communities that interact with macroorganisms and abiotic factors in the ecosystem

Microbial Ecosystems and Biogeochemical Cycling
Biogeochemistry: the study of biologically mediated chemical transformations
A biogeochemical cycle defines the transformations of a key element that is catalyzed by biological or chemical agents
Typically proceed by oxidation-reduction reactions
Microbes play critical roles in energy transformations and biogeochemical processes that result in the recycling of elements to living systems

Environments and Microenvironments
Difference in the type and quantity of resources and the physiochemical conditions of a habitat define the niche for each microbe
For each organism there exists at least one niche in which that organism is most successful (prime niche)
Microenvironment
The immediate environmental surroundings of a microbial cell or group of cells

Environments and Microenvironments
Physiochemical conditions in a microenvironment are subject to rapid change, both spatially and temporally
Resources in natural environments are highly variable and many microbes in nature face a feast-or-famine existence
Growth rates of microbes in nature are usually well below maximum growth rates defined in the laboratory
Competition and cooperation occur between microbes in natural systems
Biofilms: Microbial Growth on Surfaces

Surfaces are important microbial habitats because
Nutrients adsorb to surfaces
Microbial cells can attach to surfaces

Biofilms: Microbial Growth on Surfaces
Biofilms
Assemblages of bacterial cells adhered to a surface and enclosed in an adhesive matrix excreted by the cells
The matrix is typically a mixture of polysaccharides
Biofilms trap nutrients for microbial growth and help prevent detachment of cells in flowing systems

Biofilms: Microbial Growth on Surfaces

Biofilm formation is initiated by attachment of a cell to a surface followed by expression of biofilm-specific genes

Genes encode proteins that synthesize intercellular signaling molecules and initiate matrix formation

Biofilms: Microbial Growth on Surfaces
Intracellular communication (quorum sensing) is critical in the development and maintenance of a biofilm
The major intracellular signaling molecules are acylated homoserine lactones
Both intra- and interspecies signaling likely occurs in biofilms

Biofilms: Advantages and Control
Bacteria form biofilms for several reasons
Self-defense
Biofilms resist physical forces that sweep away unattached cells, phagocytosis by immune system cells, and penetration of toxins (e.g., antibiotics)
Allows cells to remain in a favorable niche
Allows bacterial cells to live in close association with one another

Biofilms: Advantages and Control
Biofilms are important in human health and commerce
Biofilms have been implicated in several medical and dental conditions
Including periodontal disease, kidney stones, tuberculosis, Legionnaire’s disease, and Staphylococcus infections
In industrial settings, biofilms can slow the flow of liquids through pipelines and can accelerate corrosion of inert surfaces
Few highly effective antibiofilm agents are available
Freshwater Environments
Freshwater environments are highly variable in the resources and conditions available for microbial growth

The balance between photosynthesis and respiration controls the oxygen and carbon cycles

Phytoplankton: oxygenic phototrophs suspended freely in water; include algae and cyanobacteria

Benthic species are attached to the bottom or sides of a lake or stream
Freshwater Environments
The activity of heterotrophic microbes in aquatic systems is highly dependent upon activity of primary producers; oxygenic phototrophs produce organic material and oxygen

Oxygen has limited solubility in water; once consumed in freshwater lakes the deep layers can become anoxic

Oxygen concentrations in aquatic systems is dependent on the amount of organic matter present and the physical mixing of the system
Freshwater Environments

In many temperate lakes the water column becomes stratified during the summer

Freshwater Environments
Rivers
May be well mixed because of rapid water flow
Can still suffer from oxygen deficiencies due to high inputs of
Organic matter from sewage
Agricultural and industrial pollution

Freshwater Environments

Biochemical Oxygen Demand (BOD)
The microbial oxygen-consuming capacity of a body of water

Terrestrial Environments
Soil
The loose outer material of Earth’s surface
Distinct from bedrock
Soil can be divided into two broad groups
Mineral soils
Derived from rock weathering and other inorganic materials
Organic soils
Derived from sedimentation in bogs and marshes

Terrestrial Environments
Soils are composed of
Inorganic mineral matter (~40% of soil volume)
Organic matter (~5%)
Air and water (~50%)
Living organisms

Terrestrial Environments
Most microbial growth takes place on the surfaces of soil particles

Soil aggregates can contain many different microenvironments supporting the growth of several types of microbes





Terrestrial Environments

The availability of water is the most important factor in influencing microbial activity in surface soils
Nutrient availability is the most important factor in subsurface environments

Plants as Microbial Habitats
Rhizosphere
The region immediately outside the root
Zone where microbial activity is usually high
Phyllosphere
The surface of plant leaf
Microbial communities form in both the rhizosphere and phyllosphere of plants

Open Oceans
Compared with most freshwater environ-ments, the open ocean environment is
Saline
Low nutrient; especially with respect to nitrogen, phosphorus, and iron
Cooler
Due to the size of the oceans, the microbial activities taking place in them are major factors in the Earth’s carbon balance
Open Oceans

Nearshore marine waters typically contain higher microbial numbers than the open ocean because of higher nutrient levels

Open Oceans
Most of the primary productivity in the open oceans is due to photosynthesis by prochlorophyte
Prochlorococcus accounts for
> 40% of the biomass of marine phototrophs
~50% of the net primary production

Open Oceans

The planktonic filamentous cyanobacterium Trichodesmium is an abundant phototroph in tropical and subtropical oceans
Small phototrophic eukaryotes, such as Ostreococcus, inhabit coastal and marine waters and are likely important primary producers

Open Oceans
Small planktonic heterotrophic prokaryotes are abundant (105–106 cells/ml) in pelagic marine waters

The most abundant marine heterotroph is Pelagibacter, an oligotroph

Oligotroph: an organism that grows best at very low nutrient concentrations

Open Oceans
Pelagibacter and other marine heterotrophs contain proteorhodopsin, a form of rhodopsin that allows cells to use light energy to drive ATP synthesis
Aerobic anoxygenic phototrophs
Another class of marine microbes that use light energy but do not fix carbon dioxide
Light is used for ATP synthesis via photophosphorylation

Open Oceans
Prokaryote densities in the open ocean decrease with depth
Surface waters contain ~106 cells/ml; below 1,000 m cell numbers drop to 103–105/ml
Bacterial species tend to dominate in surface waters and Archaeal species dominate in deeper waters

Open Oceans
Viruses are the most abundant microorganisms in the oceans (107 virion particles/ml)

Viruses affect prokaryotic populations and are highly diverse

The Deep Sea and Barophilism
> 75% of all ocean water is deep sea, lying primarily between 1000 and 6000 m
Organisms that inhabit the deep sea must deal with
Low temperature
High pressure
Low nutrient levels
Absence of light energy

The Deep Sea and Barophilism

Deep sea microbes are
Psychrophilic (cold-loving) or psychrotolerant
Barophilic (pressure-loving) or barotolerant

Chapter 20-Microbial Metabolic Diversity

Microbial Diversity 

REDOX
Oxidative/reduction reaction

One molecule gives another molecule an e-
Carbon and Energy Sources
Photoautotrophs
Carbon source is carbon dioxide
Energy source is sunlight
Reduction of CO2 to organic compounds
Photoheterotrophs: Use organic carbon as their carbon source
Energy is through a series of oxidation/reductions
Photosynthesis
Photosynthesis: The conversion of light energy to chemical energy.
Photosynthesis involves reactions in which ATP is generated and reactions in which ATP is consumed in the reduction of NADH.


Photoautotroph
Two distinct set of reactions
ATP production and
CO2 reduction to organic compounds
Energy is supplied from ATP
Electrons for the reduction of CO2 come from NADH or NADPH
Produced by electrons originating from various electron donors
Variety of Pigments
Chlorophylls a and b
Bacteriochlorophyll
Carotenoids
Anthocyanins
Phycobilins
Light reaches phototrophic organisms in units of energy called quanta.

Photosynthetic Pigments
In the photosynthetic membrane, chlorophyll or bacteriochlorophyll are associated with proteins to form complexes consisting of 50 to 300 molecules.

Chlorophyll: light sensitive, Mg++ containing porphyrin of photosynthetic organisms that initiates the process of photophosphorylation. Pigment of oxygenic phototrophs.

Bacteriochlorophyll: the chlorophyll pigment of anoxygenic phototrophs.

Photophosphorylation: the production of ATP in photosynthesis


Prokaryotes
No chloroplasts
Pigments are integrated into the internal membrane system
Within invaginations of the cytoplasmic membrane
Or within cytoplasmic membrane itself
Chlorosomes: specialized non-unit membrane enclosed structures.
Chlorophylls
Main pigments in most photoautotrophs
Carotenoids and Phycobilins
Carotenoids:
Most widespread accessory pigments
Hydrophobic pigments embedded in membrane
Photoprotective role: Quench toxic oxygen
Transfers energy to the reaction center which is used to make ATP
Phycobilins
Cyanobacteria and red algae
Accessory Pigments

Light-Dependent Reactions
Pigments absorb light energy, give up electron, which enter electron transfer chains.
Water molecules split, ATP and NADH form, and oxygen is released.
Pigments that give up electrons get replacement electrons.
Photosystem Function: Harvester Pigments
Most pigments in photosystem are harvester pigments

When excited by light energy, these pigments transfer energy to adjacent pigment molecules. Each transfer involves energy loss.

Antenna: chlorophyll molecules harvest light energy and transfer it on to the reaction center of the pigments.

Exciton: mobile forms of energy (photons) that migrate through the antenna pigments to the reaction center

Oxygenic Photosynthesis
In oxygenic photosynthesis, water donates electrons to drive autotrophy (CO2), and oxygen is produced as a by-product.

Two separate light reaction center are involved, photosystems I and II.

Anoxygenic Photosynthesis
Anoxygenic Photosynthesis: Photosynthesis in which O2 is not produced
Photosynthesis begins when exciton energy strikes the bacteriochlorophyll a molecules.
The absorption of energy excites the pigments, converting them to strong electron donors with a low reduction potential.
The energy is then released when electrons are transported through the membrane.

Reverse Electron Flow
Electrons from the quinone pool must be forced backward to reduce NAD to NADH
Light-Independent Reactions
Synthesis part of photosynthesis
Can proceed in the dark
Takes place in the stroma
Calvin-Benson cycle
Autotrophic Fixation: The Calvin Cycle
Most phototrophic and other autotrophic organisms accomplish fixation of CO2 by the Calvin cycle, in which the enzyme ribulose bisphosphate carboxylase (RubisCO) plays a key role.

Calvin-Benson Cycle
Overall reactants
Carbon dioxide
ATP
NADPH oxidized to
Overall products
Glucose
ADP
NADP+

Other Types of Energy Production
Chemolithotrophs oxidize inorganic chemicals as their sole sources of energy and reducing power.

Most chemolithotrophs are also able to grow autotrophically.

Mixotrophic: able to obtain energy from the oxidation of an inorganic compound. They require an organic compound as a carbon source.

Chemolithotrophs: ATP generation is similar to that in chemo-organotrophs, except that the electron donor is inorganic.

Chemolithotrophy-Misc.
Sources of inorganic electron donors: geological, biological or anthropogenic in nature.
The hydrogen bacteria can oxidize H2 compounds
The sulfur bacteria can oxidize reduced sulfur compounds such as H2S and S0
The iron bacteria are chemolithotrophs that use ferrous iron (Fe2+)
Anaerobes reduce CO2 to acetate, usually with H2 as the electron donor

Energy Yields from Oxidation of Inorganic Electron Donors
Sulfur Bacteria
Iron-Oxidizing Bacteria
Electron Flow During Fe2+ Oxidation
Nitrification
NH3 and NO2- are oxidized by nitrifying bacteria during the process of nitrification
Two groups of bacteria work in concert to fully oxidize ammonia to nitrate
Key enzymes are ammonia monooxygenase, hydroxylamine oxidoreductase, and nitrite oxidoreductase
Only small energy yields from this reaction
Growth of nitrifying bacteria is very slow

Oxidation of Ammonia by Ammonia-Oxidizing Bacteria
Oxidation of Nitrite to Nitrate by Nitrifying Bacteria
Anammox
Anammox: anoxic ammonia oxidation
Performed by unusual group of obligate aerobes
Anammoxosome is compartment where anammox reactions occur
Protects cell from reactions occuring during anammox
Hydrazine is an intermediate of anammox
Anammox is very beneficial in the treatment of sewage and wastewater
Anammox

Anaerobic Respiration
The use of an alternate electron acceptor other than O2 for reduction.
Assimilative Metabolism: When an inorganic compound such as NO3, SO4 or CO2 is reduced for biosynthesis
Dissimilative metabolism : The reduced product is excreted into the environment

Fermentation
When inorganic electron acceptors are not present in anoxic environments, carbon is catabolized( broken down) by fermentation.
Fermentations are classified in terms of either the substrate fermented or the fermentation products formed.
Products: Amino acids, organic acids, purines and pyrimidines, alcohols, sugars

Lactic and Mixed-Acid Fermentations

Lactic acid fermentation can occur by homofermentative and heterofermentative pathways

Mixed-Acid Fermentations
Generate acids
Acetic, lactic, and succinic
Sometimes also generate neutral products
E.g., butanediol
Characteristic of enteric bacteria
The Butyric Acid and Butanol/Acetone Fermentation-Clostridia
Entner-Doudoroff Pathway-pathway of sugar carabolism for pseudomonas.
Some Clostridium species ferment amino acids using a complex biochemical pathway known as the Strickland reaction
Propionic Acid fermentation-P. acnes

Non-Substrate-Level Phosphorylation Fermentations
Fermentations of certain compounds do not yield sufficient energy to synthesize ATP
Catabolism of the compound can then be linked to ion pumps that establish a proton or sodium motive force

Nitrification
Nitrate is commonly used as an electron acceptor in anaerobic respiration. Its use requires the enzyme nitrate reductase, which reduces nitrate to nitrite.
Nitrification: the use of ammonia and nitrite as electron donors.
NH4 + NO2 N2 + 2 H20
Ammonia + nitrite Nitrous gas
Denitrification: use of nitrate (NO4) in anaerobic respiration to produce N2
Nitrogen fixation —the reduction of N2 to NH3 (ammonia)
The most widespread inorganic nitrogen compounds in nature are ammonia and nitrate, both formed in the atmosphere.

Methanotrophy, Methylotrophyand Methanogenisis
Methanogenesis is the biological production of CH4 (methane) either from CO2 plus H2 or from methylated compounds

Methanotrophy is the use of CH4 as a carbon and energy source.

Methylotrophs use C1 compounds (or other organic compounds lacking C–C bonds) for energy metabolism and biosynthesis.
Polysaccharides, Organic Acids, Fats
Polysaccharides are abundant in nature and can be broken down, usually by phosphorolysis, into hexose (6) or pentose (5) monomers and used as energy sources
Starch and cellulose are common polysaccharides.
Organic acids are frequently metabolized through the citric acid cycle.
Fats are metabolized via hydrolysis by lipases or phospholipases to free fatty acids.
The fatty acids are oxidized by beta oxidation to acetyl-CoA units, which are subsequently oxidized to CO2 by the citric acid cycle

Chapter 13 Microbial Genomics

Microbial Genomics
Chapter 13
A Short History of Genomics
Genome
Entire complement of genetic information
Includes genes, regulatory sequences, and noncoding DNA
Genomics
Discipline of mapping, sequencing, analyzing, and comparing genomes

Prokaryotic Genomes: Sizes and ORF Contents

On average a prokaryotic gene is 1,000 bp long
1,000 genes per megabase (Mbp; 1,000,000 bp)
As genome size increases gene content proportionally increases

Prokaryotic Genomes: Sizes and ORF Contents

Prokaryotic genomes range in size from those of large viruses to those of eukaryotic microbes
Unlike prokaryotes, eukaryotic genomes contain a large fraction of non-coding DNA
Prokaryotic Genomes: Sizes and ORF Contents
Smallest cellular genomes to date belong to parasitic or endosymbiotic prokaryotes
Obligate parasites range from 490 kbp (Nanoarchaeum equitans) to 4,400 kbp (Mycobacterium tuberculosis)
Endosymbionts can be even smaller (e.g., 160 bp genome of Carsonella ruddii)
Estimates suggest minimum number of genes for a viable cell is 250–300 genes

Prokaryotic Genomes: Sizes and ORF Contents

Largest prokaryotic genomes comparable to those of some eukaryotes
Sorangium cellulosum (Bacteria)
Largest prokaryotic genome to date at 12.3 Mbp
Largest Archaeal genomes tend to be smaller (~ 5 Mp)
Prokaryotic Genomes: Bioinformatic Analyses
Bioinformatics
Science that applies powerful computational tools to DNA and protein sequences
For the purpose of analyzing, storing, and accessing the sequences for comparative purposes

Prokaryotic Genomes: Bioinformatic Analyses

Complement of genes in a particular organism defines its biology but genomes are also molded by an organism’s lifestyle

Prokaryotic Genomes: Bioinformatic Analyses

Many genes can be identified by sequence similarity to genes found in other organisms (comparative analysis)
Comparative analyses allow for predictions of metabolic pathways and transport systems

Prokaryotic Genomes: Bioinformatic Analyses
Gene Distribution in Prokaryotes
Metabolic genes typically most abundant class
DNA replication and transcription genes make up minor fraction of genome
Nontranslated RNA genes are typically prevalent
I.e., rRNA, tRNA, small regulatory RNAs

Prokaryotic Genomes: Bioinformatic Analyses
Number of genes with role that can be clearly identified in a given genome is 70% or less of total ORFs detected
Hypothetical proteins: uncharacterized ORFs; proteins that likely exist but whose function is presently unknown
Likely encode nonessential genes
In E. coli, many predicted to encode regulatory or redundant proteins
Prokaryotic Genomes: Bioinformatic Analyses

Inaccuracies in some annotations are problematic
As many as 10% of annotated genes are incorrectly annotated
Percentage of an organism’s genes devoted to a specific cell function is to some degree a function of genome size

Prokaryotic Genomes: Bioinformatic Analyses
Gene Distribution in Bacteria and Archaea
Archaea typically devote a higher percentage of their genomes to energy and coenzyme production than do Bacteria
Archaea contain fewer genes for carbohydrate metabolism or cytoplasmic membrane functions than do Bacteria

The Genomes of Eukaryotic Organelles
Mitochondria and chloroplasts contain a small genome
Also contain the necessary machinery for protein synthesis
Including ribosomes, tRNAs, and all other components necessary for translation formation of functional proteins

The Genomes of Eukaryotic Organelles
Known Chloroplast Genomes
Circular DNA molecules
Typically 120–160 kbp
Contain two inverted repeats of 6–76 kbp
Many genes encode proteins for photosynthesis and autotrophy
Introns common; primarily of self-splicing type

The Genomes of Eukaryotic Organelles
Known Mitochondrial Genomes
Diverse structures; some linear
Typically smaller than chloroplast genomes
Primarily encode proteins for oxidative phosphorylation
Use simplified genetic codes rather than “universal” code
Some contain small plasmids

The Genomes of Eukaryotic Organelles

Many genes in the nucleus encode proteins required for organelle function
E.g., translational machinery, energy generation

Eukaryotic Microbial Genomes
The Haploid Yeast Genome
Contains 16 chromosomes, ranging in size from 220 kbp to 2,352 kbp
Entire genome is ~ 13,392 kbp; encodes ~ 6600 ORFs; ~3,500 encode proteins with known function
At least 877 ORFs are essential at least 3,121 are not
Contains a large amount of repetitive DNA

Eukaryotic Microbial Genomes
Smallest eukaryotic cellular genome belongs to Encephalitozoon cuniculi
Intracellular pathogen
Haploid genome contains 11 chromosomes
Genome size 2.9 Mbp; ~ 2,000 genes
Smallest eukaryotic genome belongs to a nucleomorph
Degenerate remains of a eukaryotic endosymbiont
Ranges in size from 0.45 to 0.85 Mbp
Eukaryotic Microbial Genomes

Largest eukaryotic genome belongs to Trichomonas
Parasite
~ 60,000 genes (nearly twice as many as humans)
Microarrays and the Transcriptome
Transcriptome
The entire complement of RNA produced under a given set of conditions
Hybridization techniques can be used in conjunction with genomic sequence data to measure gene expression
Microarrays
Small solid-state supports to which genes or portions of genes are fixed and arrayed spatially in a known pattern

Microarrays and the Transcriptome
DNA segments on arrays are hybridized with mRNA from cells grown under specific conditions and analyzed to determine patterns of gene expression
Arrays are large and dense enough that the transcription pattern of an entire genome can be analyzed

Microarrays and the Transcriptome
What can be learned from microarray experiments?
Global gene expression
Expression of specific groups of genes under different conditions
Expression of genes with unknown function; can yield clues to possible roles
Comparison of gene content in closely related organisms
Identification of specific organisms
Proteomics
Proteomics
Genome-wide study of the structure, function, and regulation of an organism’s proteins
Two-dimensional (2-D) polyacrylamide gel electrophoresis
Technique for the separation, identification, and measurement of all proteins present in a sample
In first (horizontal) dimension, proteins separated by differences in isoelectric points
In second (vertical) dimension, proteins separated by size

Proteomics
Proteins with > 50% sequence identity typically have similar functions
Proteins with > 70% sequence identity almost certainly have similar functions
Protein domains
Distinct structural modules within proteins
Have characteristic functions that can reveal much about a protein’s role, even in the absence of complete sequence homology

Nucleic Acid and Amino Acid Sequence Similarities

Metabolomics
Metabolome
The complete set of metabolic intermediates and other small molecules produced in an organism
Mass spectrometry is one of the primary techniques for monitoring metabolites
 Gene Families, Duplications, and Deletions
Homologous: related in sequence to an extent that implies common genetic ancestry
Gene families: groups of gene homologs
Paralogs: genes within an organism whose similarity to one or more genes in the same organism is the result of gene duplication
Orthologs: genes found in one organism that are similar to those in another organism but differ because of speciation
 Gene Families, Duplications, and Deletions
Gene duplications thought to be mechanism for evolution of most new genes

Deletions can eliminate gene no longer needed

Gene analysis in the three domains of life suggests that many genes present in all organisms have common evolutionary roots
 Mobile DNA: Transposons and Insertion Sequences
Horizontal Gene Transfer
The transfer of genetic information between organisms, as opposed to vertical inheritance from parental organism(s)
May be extensive in nature
May cross phylogenetic domain boundaries
Mobile DNA: Transposons and Insertion Sequences
Detecting Horizontal Gene Flow
Presence of genes typically found only in distantly related species
Presence of a DNA with GC content or codon bias that differs significantly from remainder of genome
 Mobile DNA: Transposons and Insertion Sequences

Horizontally transferred genes typically encode non-core metabolic functions

Horizontal Gene Transfer and Genome Stability
Transposons may transfer DNA between different organisms
Transposons may also mediate large-scale chromosomal changes within a single organism
Presence of multiple insertion sequences (IS)
Recombination among identical IS can result in chromosomal rearrangements
E.g., deletions, inversions, or translocations

Horizontal Gene Transfer and Genome Stability
Integrons
Genetic elements that collect and express genes carried on mobile segments of DNA (cassettes)
Of those known, most carry genes for antibiotic resistance

Evolution of Virulence: Pathogenicity Islands
Chromosomal Islands
Region of bacterial chromosome of foreign origin that contains clustered genes for some extra property such as virulence or symbiosis
Pathogenicity islands: chromosomal islands containing genes for virulence

Evolution of Virulence: Pathogenicity Islands
Chromosomal islands believed to have a “foreign” origin based on several observations
Extra regions often flanked by inverted repeats
Base composition and codon usage in chromosomal islands often differ from rest of genome
Often found in some strains of a species but not others
Evolution of Virulence: Pathogenicity Islands
Chromosomal islands contribute specialized functions not essential to growth
Virulence
Biodegradation of recalcitrant compounds
E.g., hydrocarbons and herbicides
Symbiosis

Evolution of Virulence: Pathogenicity Islands
The “pan”/ “core” concept: bacterial species consist of two components
Core genome: shared by all strains of the species
Pan genome: includes all the optional extras present in some but not all strains of the species

Detecting Uncultured Microorganisms
Metagenome
The total gene content of the organisms present in an environment
Several environments have been surveyed by large-scale metagenome projects
E.g., acid mine run-off waters,deep sea sediments, fertile soils

Viral Genomes in Nature
Viruses are more prevalent than bacteria in the environment
Most are bacteriophages and have populations that turn over rapidly
Most of the genetic diversity on Earth thought to reside in viruses
Most virus genes are uncharacterized and show little or no sequence similarity to known genes

Lab exam 2 review with answers for Tues. 3/31

What are organisms grown on? agar
What is nutrient agar? Beef extract and peptone
What are the purposes of growth on agar? Colony morphology, amount, isolation in mixed culture
What is agar? Sea weed-kelp derivative
What is the best temperature for culture growth of most microbes? 37oC
What is sterilization of prepared agar? 121oC for 15 min
What are the two methods of agar inoculation? Loop dilution and streak method
Describe the two methods. Pour plate vs. streak plate
The streak method depends on inoculation into how many areas of the agar? 4 What is accomplished by using the streak method? To gradually dilute colonies What should be the outcome? Pure culture

What two methods of determination of bacterial populations were performed in class? Standard Plate Count/Serial dilutions and Turbidity
What are major differences between the two methods? Use of agar; use of spectrophotometer
How is the outcome of the standard count different from the turbidity method? Colony number versus turbidity reading
How does the spectrophotometer work? Light shown through specimen recorded by photodetector
What is the difference between turbidity ( absorbance) and percent transmission? Turbidity: light absorbed %P: light transmitted
As the percent transmission increases, what is observed about the organisms in the broth? Fewer numbers
Answer the same question for absorbance. More organisms
What is the optimum growth temperature for most bacteria? 37oC
What is room temperature? 25oC
At what temperatures, would you expect to have growth and in what amount? 5C: +-; 23C: +; 37C: ++; 42C: +\-
What happens when the concentration of solutes in the growth media exceeds that in the organism? Plasmolysis (hypertonic)
What if the solute is lower? hypotonic
What special medium was used for oxygen testing? Thioglycollate. What unique substance did it contain? Oxidation-reduction agent.
What is the thermal death point? Temp that kills in 10 min. What is thermal death time? Time to kill at particular temp.



What is the purpose of U.V light? sterilization How is the damage produced? Thymine dimers Can the damage be repaired? Yes What is the procedure for using U.V. light? In the petri dish, the U.V. light affects what? Colonies on plate

What is the difference between disinfectant and antiseptic? Inanimate Objects vs. skin Antiseptics lower concentration of bugs
Be able to recognize aerobic, anaerobic, facultative anaerobic and microaerophilic.
The pour-plate disk method produces results called the colony forming units/ml? How is the result determined? Colony count-number of colonies on plate times dilution factor.
What is the susceptibility testing method used in lab called? Disk diffusion-Kirby Bauer.
What is the medium used to perform antimicrobial susceptibility? Mueller Hinton
What values are used to determine the susceptibility result? Mm size of zone of inhibition How is it obtained? Measure zone of inhibition

Know how to perform a serial dilution. Know Absorbance and Percent Transmission. Know Thermal Death Point and Death Time. Know Growth in types of Oxygen environments and termperatures.
Know Osmolality Experiment: Hypertonic, hypotonic and plasmolysis
Know pour plate, streak plate and broth loop dilution tube plate
Know how to make a dilution

Chapter 18-Eukaryotes

Eukaryotic Microbes
The eukaryotic microbes: algae, fungi, slime moulds and protozoa.
Eukaryotic microorganisms differ from Bacteria and Archaea.
These differences include:
cell size
internal structure
genetic arrangement
evolutionary history.


Eukaryotic Organelles
The endoplasmic reticulum

The golgi apparatus

Lysosomes

The peroxisome

3 energy organelles
Mitochondria
Respiration and oxidative phosphorylation are localized in mitochondria.
Organelle is surrounded by two membranes, inner and outer.
Outer membrane important in permeability
Cristae form from the invagination of inner membrane.
ATP synthesis occurs in the cristae

Hydrogenosome
Present in some anaerobic eukaryotic organisms that lack mitochondria
The organelle lack cristae and citric acid cycle enzymes
Metabolism of organisms is fermentative
Acetate excreted from organelle into cytoplasm.


Chloroplast
The chloroplast is the site of photosynthetic energy production and CO2 fixation in eukaryotic phototrophs (algae).

Like mitochondria, chloroplasts have a permeable outermost membrane, a much less permeable inner membrane, and an intermembrane space.

Chloroplast
The inner membrane surrounds the lumen of the chloroplast, but it is not folded into cristae like the inner membrane of the mitochondrion.

Instead, chlorophyll and all other components needed for photosynthesis are located in a series of flattened membrane discs called thylakoids.

Endosymbiotic Theory
Mitochondria, chloroplasts and hydrogenosomes originated from the stable incorporation of chemoorganotrophic and phototrophic symbionts from bacteria.
Aerobic bacterium established residency within the cytoplasm of a primitive eukaryote
Mitochondria vs. Chloroplast
Both contain DNA
Eukaryotic nucleus contains bacterially derived genes
Both contain their own ribosomes
Some antibiotics inhibit mitochondria and chloroplast activity
rRNA sequencing has shown that both originated from bacteria
Eukaryotic Organelles
Golgi Apparatus
involved in protein modification and secretion
Endoplasmic Reticulum
Smooth; synthesis of lipids and some carbohydrate metabolism
Rough: producer of glycoproteins and produces new membrane material. Some protein production and post-translations modification.

Lysosome
Peroxisomes
Small vesicles – similar to lysosomes
Arise by dividing of preexisting peroxisomes
Produce hydrogen peroxide (H2O2) as a byproduct
Oxidize a wide variety of chemicals
Detoxify harmful chemicals such as alcohol
Motility Organelles
In addition, proteinaceous tubes called microfilaments and microtubules are present, forming the cell's cytoskeleton.

Flagella and cilia are organelles of motility that have extensive microtubular structure.
Microfilaments
Thinnest elements
Composed of actin
Take part in movement, formation, and maintenance of cell shape
Microtubules
Largest elements
Composed of tubulin
Arise from microtubule organizing centers (MTOCs)
Involved in shape, motility,
cell division


Eukaryotic ReplicationDNA Protein Primer
The ends of linear genetic elements present a problem to the replication machinery that circular genetic elements do not.

Some prokaryotic plasmids and viral linear elements solve this problem by using a protein primer .

DNA replicates 5’-3’ (where OH resides)
Protein primer attaches to 5’ end
Replication occurs
Eukaryotic Chromosome
The DNA molecule of a typical chromosome contains:
a linear array of genes (encoding proteins and RNAs)
much noncoding DNA.
Included in the noncoding DNA are long stretches that make up the centromere and long stretches at the ends of the chromosome, the telomeres

Telomeres are crucial to the life of the cell. They keep the ends of the various chromosomes in the cell from accidentally becoming attached to each other.
Telomerases
Telomerase recognizes the tips of chromosomes also know as telomeres. The DNA sequences of telomeres consist of numerous repeats of a 6 to 8 base long sequence, [TTGGGG].

Telomerase consists of a protein and short RNA molecule that is complementary to the TTGGGG repeat in the telomere. This complementary RNA sequence base pairs with the telomere allowing Telomerase to add additional complementary bases to the 3' terminus of the telomere.

When telomeric length shortens to a critical point the cell dies.

Mitosis vs. Meiosis
Eukaryotic microorganisms can mate and exchange DNA during sexual reproduction.
Mitosis ensures appropriate segregation of the chromosomes during asexual cell division.
Haploid cells formed by meiosis can fuse to form a diploid zygote.(sexual reproduction)

RNA Processing
RNA processing: the processing of eukaryotic pre-mRNAs, is unique and involves three distinct steps:
Capping: addition of methylated guanine nucleotide. Facilitates translation
Splicing: removal of introns by spliceosome
Tailing: adding of poly A tail. Role unclear

Ribozyme
Self-splicing introns: work like enzymes
Excise themselves from RNA while joining exons together.
Catalyze reaction only once unlike protein enzymes

Protozoa
Protozoa are unicellular organisms that lack cell walls and obtain nutrients by ingesting other microbes (phagocytosis), or macromolecules in solution (pinocytosis)
They lack pigments and may be motile.
There are four groups, distinguished by their type of motility and their life cycles.
Mastigophora (flagellates) are motile through the use of flagella,
Sarcodina (amoebas) are motile with amoeboid movement,
Ciliophora use cilia for movement
Sporozoa are non-motile. Each group contains representatives that cause important human diseases. hapter

Sarcodines
The sarcodines include Amoeba—which are naked in the vegetative phase—and foraminifera—amoebae that secrete a shell during vegetative growth.

Flagellates
Flagellates are all motile by the activity of flagella.
Ciliates
Ciliates are protozoa that, in some stage of their life cycle, possess cilia, structures that function in motility.

Sporozoa
Sporozoa are a large group of obligately parasitic protozoa. These parasites can cause severe diseases, such as malaria
Slime moulds
Slime molds are non phototrophic eukaryotic microorganisms that live on decaying plant matter by phagocytizing microorganisms present on the surfaces.
There are two groups of slime molds:
cellular slime molds such as Dictyostelium that undergo a life cycle in which the cells exist independently as single amoebalike cells
acellular slime molds where the vegetative forms are naked masses of protoplasm called plasmodia

Slime Molds
Acellular slime molds are masses of motile protoplasm.
Cellular Slime Moulds
Cellular slime molds are masses of individual cells that aggregate to form fruiting bodies that release spores

Fungi
Fungi are chemoorganotrophs, lack chlorophyll, and have simple nutritional requirements as compared to bacteria.

Fungi can be differentiated from prokaryotes because they are much larger, contain a nucleus, vacuoles, and mitochondria. Fungi have a cell wall and are non-motile. Fungi produce spores.

The three important groups of fungi are:
Yeast
moulds
mushrooms
Yeasts
Yeasts are unicellular fungi usually occurring as spheres, ovals or cylinders. They favor environments rich in sugars, such as plant surfaces. They are the causative agents of a number of important diseases. Asexual division in yeasts involves budding.

Algae
Algae are phototrophic Eukarya that contain chlorophyll and carotenoid pigments within a chloroplast. The chloroplast itself has its roots in the Bacteria.

Chapters 15 and 17

Proteobacteria
Largest group: The Proteobacteria

The Proteobacteria consist of five clusters (a,b,c,d,e) containing several genera. Greek letters: alpha, beta, gamma, delta, or epsilon

You do not have to know individual species
Proteobacter
Purple phototrophic bacteria
Nitrifying Bacteria
Sulfur and Iron-oxidizing
Hydrogen-Oxidizing
Methanotrophs and methylotrophs
Pseudomonas
Nitrogen-fixing

Phylum 1
Purple bacteria
Nitrifying (soil and water)
Sulfur and Iron-oxidizing
Hydrogen-Oxidizing Bacteria
Methanotrophs and methylotrophs
Pseudomonads
Nitrogen-fixing
Neisseria et al
Enterics
Vibrios and photobacterium
Rickettsias
Spirilla
Sheathed Proteobacteria
Budding and Prosthecate/Stalked Bacteria
Gliding Myxobacteria
Sulfate and sulfur- reducing Proteobacteria

Phyla 2 and 3
Non-sporulating, Gram-positive bacteria;Lactic Acid Bacteria and relatives
Staphylococcus;Micrococcus
Lactic Acid Bacteria; Lactobacillus
Streptococcus and other coccus
Listeria

Endospore-Forming, Gram-Positive Bacteria: Bacillus, Clostridium and relatives

Cell-Wall Less, Gram-Positive Bacteria: the Mycoplasma

Gram-Positive Bacteria: Corynebacteriua and Proprionic Acid Bacteria (Propionibacterium)

Mycobacterium

Streptomyces and other Actinomycetes

Human Inhabitants
Enteric rods: E. coli, Salmonella and Shigella, Proteus, Enterobacter, Klebsiella and Serratia
Vibrios
Rickettsias
Campylobacter and Helicobacter
Staphylococcus and Micrococcus
Lactobacillus
Streptococcus
Listeria
Bacillus
Clostridium
Mycoplasma
Corynebacteria
Mycobacteria
Actinomycetes
Chlamydia
Bacteriodes
Non-fermentative gram-negative rods

Taxonomy
Phenotypic
Gram stain
Morphology
Metabolism
Biochemical reactions

Genotypic
16rRNA:genes for 16S rRNA and related molecules are amplified, treated with one or more restriction enzymes, separated by electrophoresis and then probed with complementary rRNA.
G:C Ratios
Multilocus Sequence Typing
DNA:DNA Hybridization

Types of Metabolism
Phototrophic: obtains energy from light

Chemolithotrophic: oxidize inorganic compounds for energy

Chemoorganotrophic: obtains energy from the oxidation of organic compounds.

Autotrophic: use CO2 as nutrient source

Methanotrophs: use methane for energy

Nitrogen-fixing: reduction of nitrogen gas to ammonia

Homofermentative: fermentation of glucose or other sugar to lactic acid

Heterofermentative: fermentation of glucose or another sugar to a mix of reduced products.

Facultative: grows in either the presence or absence of an environmental factor

Oxygen and Temperature Response
Oxygen Response
Aerobic
Anaerobic
Facultative Anaerobic

Temperature Response
Mesophile
Thermophile

Role in Ecosystem
Decomposition: the breakdown of organisms, and the release of nutrients back into the environment.

Nitrogen Cycling: Plants rely on nitrogen from the soil and cannot acquire it from the gaseous nitrogen in the atmosphere.

Nitrogen Fixation: These bacteria convert gaseous nitrogen into nitrates or nitrites as part of their metabolism. The resulting products are released into the environment and used by plants. Some plants, house the bacteria in their own tissues.

Denitrifying bacteria turn nitrates into nitrogen gas or nitrous oxide.

Methane decomposed to ammonia

Utilization of sulfur and Iron as electron donors. Changes in soil or water content.

Cell Division in Bacteria
Binary Fission: The cell grows to twice its size, Duplicates its DNA and other cellular constituents, and lays down a cross-wall called a septum that separates the cells.

Polar Growth: the cell grows from one end and the two cells that result from cell division are similar in size.

Simple Budding:,the cell wall grows from one end of the bacterium, producing a smaller cell that separates off and. grows.

Buds-Hyphae-swarmer: The cell buds at the end of extensions called hyphae. As the bud increases in size, it forms a flagellum. A septum forms between the bud and the hypha,and the cells separate.

The daughter cell, called a swarmer, matures, lengthens, and eventually loses its flagellum,forms a hypha, and begins the cell division process again.

Stalk: The cell creates two distinct cells during division. One has a Stalk from which the cell grows. The cell divides by unequal binary fission,producing a second, slightly smaller swarmer cell with a flagellum. The swarmer cell swims off, and when it comes to rest, it lose its flagellum and forms a stalk,again.

Phyla of Bacteria

Purple Phototrophic Bacteria
Purple Phototrophic Bacteria
Anoxygenic photosynthesis. They contain pigments - purple, red and brown.

They are divided into two groups: use of hydrogen sulfide, H2S, as an electron donor for carbon dioxide reduction. (Redox Reactions)

Purple sulfur bacteria: normally respire anaerobically in aquatic environments.

Purple Non-sulfur bacteria: Most species are aerobic and utilize a variety of carbon sources.

Sulfate and Sulfur Reducing Proteobacteria
About 90 species of bacteria from over 20 genera are known which are anaerobic obligate sulphur or sulphate reducers .
Most species live in aquatic environments.
Nitrifying Bacteria
Most species are obligatory chemolithotrophs.

These bacteria can be divided into two groups, those that:

oxidize ammonia to nitrite
oxidize the nitrite to nitrate.

Nitrifying bacteria are widespread in soil and aquatic environments where they are an important part of the nitrogen cycle.
Sulfur and Iron Oxidizing Bacteria
Beggiatoa is a filamentous gliding bacterium which oxidizes sulfur commonly found in sulfur springs, sewage works and hydrothermal vents, and other environmental areas.

Thioploca, Thiotrix and Leucathrix are also filamentous sulphur-oxidizing bacteria that aggregate within a star or rosette with their filaments in a central core. Primarily found in marine habitats where they can form thick mats.

Hydrogen-Oxidizing Bacteria-A wide variety of bacteria can grow with:
H2 as the sole electron donor and O2 as the electron acceptor

Methanotrophs
These are aerobic methane oxidizing bacteria (methane to methanol). An important aspect of the carbon cycle. CH4-CH3OH

Some Methanotrophs are also Methylotrophs meaning that they are limited to using single carbon sources, thus they cannot utilize even simple sugars to grow.

Pseudomonas and the Pseudomonads
Chemoorganotrophic
Aerobic rods
Nitrogen-fixing
Phylogenetically closely related.
Metabolize glucose via the Entner- doudoroff pathway
Opportunists

Acetic Acid Bacteria
they partially oxidize various organic compounds, particularly ethanol, into acetic acid. Used commercially to make vinegar.

Free-living Aerobic Nitrogen Fixers
These are an ecologically important group of bacteria that live in the soil or in water.
Use gaseous nitrogen (N2) from the atmosphere and combine it with carbon and hydrogen, to make organic molecules.
Nearly all the organic molecules in the world are derived from bacterially fixed nitrogen.

Other Gram Negative Bacteria
This is a group of related bacteria that don't fit into any other group.
They contain both free-living species and species found living inside animals.
Among this latter division is the genus Neisseria including the species Neisseria gonorrhoeae which is responsible for the human sexually transmitted disease gonorrhoea.
Other species of Neisseria plus species of Kingella, Moraxella and Acinetobacter may be pathogenic (disease-causing) at times.

Enteric Bacteria
A large group of facultative aerobic rods. Human faeces generally comprise 30% (dry weight) of dead bacteria
Enteric bacteria are separated by the type of fermentation products produced by anaerobic fermentation of glucose.
Some cause gastroenteritis; others are opportunists

Bioluminescent and Related Bacteria
Gram-negative, facultatively aerobic curved rods with a fermentative metabolism. Both aquatic.
Two species of Vibrio cause disease in humans. V. cholorae causes cholera. V. parahemolyticus, causes gastroenteritis due to ingestion of contaminated seafood.
Photobacterium emit light mediated by the enzyme luciferase, an oxidation reaction. Bioluminescent bacteria are mostly associated with fish.

Rickettsia
Rickettsias are obligate intracellular parasites of eucaryotic cells. They have leaky membranes and are unable to obtain nutrients in an extracellular habitat.
Rickettsias occur in nature in the gut of arthropods (ticks, fleas, lice, etc.). They are transmitted to vertebrates by an arthropod bite and produce typhus fever, Rocky Mountain Spotted Fever, Q fever and canine ehrlichiosis.

Spirilla
Spirilla are chemoorganotrophic prokaryotes widespread in the environment.
Campylobacter and Helicobacter which are pathogenic to humans cause acute enteritis, chronic gastritis and peptic ulcers.

Spirilla
Bdellovibrio are predators on other bacteria. They attack by dissolving a hole in their prey's cell wall feeding on the cytoplasm.

Ancylobacter, a ring-shaped bacterium and Magnetospirillum magnetobacterium, a curved rod shaped bacterium, contain 5 to 40 magnetic particles magnetosomes and they allow the organism to align itself in relationship to magnetic fields.

Sheathed Bacteria
Sheathed filamentous bacteria in which individual cells form chains within an outer layer called the sheath. When nutrients are low, the individual cells develop a flagella tuft and are called swarmers

Gliding Myxobacteria
The fruiting myxobacteria are gliding bacteria that aggregate to form complex masses of cells called fruiting bodies.

Myxobacteria are chemoorganotrophic soil bacteria that live by consuming dead organic matter or other bacterial cells.
Gram-positive Bacteria
Gram-positive Bacteria are a large phylogenetic group that contains rods and cocci, sporulating and nonsporulating species.
The lactic acid bacteria are used in dairy production and are human commensals

Endospore Producers
Production of endospores is a hallmark of the key genera Bacillus and Clostridium.
These bacteria are major agents for the degradation of organic matter in soil, and a few species are pathogenic.(C. tetani and botulinum)

Mycoplasma
Lack cell walls and contain a very small genome.
Several are pathogenic for humans, other animals, and plants.
Walking pneumonia and neonatal infections

Small Gram-Positive Rods
Nonsporulating gram positive bacteria; lactic acid bacterial et al, coryneform and propionic Acid Bacteria
Swiss Cheese
The propionic acid bacteria were first discovered in Swiss cheese, where their fermentative production of CO2 results in the characteristic holes. shows the enzymatic reactions leading from glucose to propionic acid.

Actinobacteria: Mycobacterium
The genus Mycobacterium consists of rod-shaped organisms that are acid-fast.
The surface of the cell has unique lipids called mycolic acids, found only in the genus Mycobacterium
Main Pathogen: M. tuberculosis
Actinomycetes: Streptomyces
The streptomycetes are a large group of filamentous, gram-positive bacteria that form spores at the end of aerial filaments.
Other species: Nocardia causes brain infections and pneumoniae.

Cyanobacteria
Cyanobacteria comprise a large and mixed group of phototrophic Bacteria.
Cyanobacteria are oxygenic phototrophs.
Oxygen in Earth's atmosphere is thought to have originated from cyanobacterial photosynthesis

Chlamydia
Obligate intracellular parasites
The life cycle contains two cell types:
The elementary body: non-multiplying,transmit infection
The reticulate body: noninfectious replication form
Sexually-Transmitted Disease
Trachoma

Planctomyces
The Planctomyces group contains stalked, budding bacteria.
The Verrucomicrobia are distinguished by their multiple prosthecate cells

VerrocomicrobiaPhylum 7
Verrocomicrobia

Bacteroides: Phylum 8
The genus Bacteroides contains obligate anaerobic species.
Bacteroides are normally found in the intestinal tract of humans and animals, and can cause infection.
They are the largest group of bacterial in the human colon.

Phylum 9 and 10
Cytophaga
Green Sulfur Bacteria

Spirochete-Phylum 11
Tightly coiled, motile, helical prokaryotes that contain both free-living and pathogenic species.
Treponema pallidum: syphillis
Borrelia: Lyme Disease

Stalked Bacteria
The new cell wall that separates the cytoplasm into two sections starts from a single point. This is called 'Polar Growth'.
A simple hyphae forms a bud at the distant end of the cell. This bud grows to be a new daughter cell. The daughter cell may develop a flagellum and swims away.

Deinococcus: Phylum 12
Deinococcus radiodurans is the most radiation resistant of all known organisms.

Green non-sulfur bacteria: Phylum 13
Chloroflexus

Branching Hyperthermophilic Bacteria: Phylum 14-16

Grow at temperatures > 80C
Netrospira: Phylum 17

Chemolithotrophs to Chemoorganotrophs
Mesophiles to Thermophiles

Characteristics of Different Organisms
Nitrogen oxidizing
Iron oxidizing
Use of metals for electron acceptors
Budding Bacteria
Budding and prosthecate bacteria are appendaged cells that form stalks or prosthecae used for attachment or nutrient absorption and are primarily aquatic.


Archaea
Archaea were once known as archaebacteria and live in extreme environments.
The Archaea can be divided into four groups: the methanogens, the halophiles, the hyperthermophiles and the genus Thermoplasma
Types of Archaea
Extremely Halophilic
Methane-Producing
Thermophilic/Acidophilic
Hyperthermophilic
Cold Dwelling
Hyperthermophiles from volcanic habitats
Hyperthermophiles for submarine volcanic habitats
Environments
Soil
Mineral deposits
Aquatic areas
Volcanic areas
Animals

Archaeal Cell Walls
Archaeal cell walls do not contain muramic acid and D-amino acids, the building blocks of peptidoglycan.
Particular species may contain pseudopeptidoglycan, polysaccharide, glycoprotein, or protein in their cell walls.
Archaeal Membranes
The Archaeal membranes differ from Bacterial membranes in that they contain ether-linked lipids bonded to glycerol.
Glycerol diethers and diglycerol tetraethers are the major types of lipids present in the cell membrane.
The Archaea also contain large amounts of non-polar lipids.

Metabolism in Archae
Chemoorganotrophic: use organic compounds as energy sources for growth.

Chemolithotrophy: anaerobic growth with H2 being a common electron donor and Sulfur, Nitrite, Iron or Oxygen as electron acceptor.

Autotrophy: Use of CO2 for energy source;widespread in the Archaea

Methanogens
Methanogens are obligate anaerobes

Anaerobic environments include marine and fresh-water sediments, bogs and deep soils, intestinal tracts of animals and humans, and sewage treatment facilities
Methanogens
Methanogens have a type of metabolism that can use H2 as an energy source and CO2 as a carbon source for growth.
In the process of making cell material from H2 and CO2, the methanogens produce methane (CH4) in a unique energy-generating process.
The end product (methane gas) accumulates in their environment.
Halophilic Archaea
Extremely halophilic Archaea require large amounts of NaCl for growth.

These organisms accumulate high levels of KCl in their cytoplasm as a compatible solute.

These salts affect cell wall stability and enzyme activity. The light-mediated proton pump bacteriorhodopsin helps extreme halophiles make ATP
Use of Bacteriorhodopsin
Certain species of Halobacterium can synthesize ATP using light energy.
The process uses a membrane protein called bacteriorhodopsin.
The absorption of light by retinal associated with this protein is used to pump protons across the cell membrane.
The resulting proton motive force can drive ATP synthesis via a membrane-bound ATPase.

Hyperthermophiles
“Hyperthermophiles" require temperatures of 80 degrees to 150 degrees for growth.
Most of these Archaea require elemental sulfur for growth. Some are anaerobes that use sulfur as an electron acceptor for respiration in place of oxygen.
Sulfur-oxidizers grow at low pH (less than pH 2), partly because they acidify their own environment by oxidizing SO (sulfur) to SO4 (sulfuric acid). 
Temperature Limits

Although hyperthermophiles live at very high temperatures, in some cases above the boiling point of water, there are temperature limits beyond which no living organism can survive. This limit is likely 140ºC to 150°C
Molecular chaperones
Assist in the folding process.
Fold newly synthesized proteins
Refolding of partially denatured proteins.
Chaperones =heat shock proteins
Refold before proteases destroy them

Reverse DNA Gyrase. 
All hyperthermophiles produce a DNA topoisomerase called reverse DNA gyrase.

Reverse gyrase introduces positive supercoils into DNA (in contrast to the negative supercoils introduced by DNA gyrase, found in all nonhyperthermophilic prokaryotes).
Supercoils
The structure of supercoils.  (a) Positive supercoils - the front segment of a DNA molecule cross over the back segment from left to right.  (b) Negative supercoils.  (c) The positive supercoil in bacteria during DNA replication.

DNA-Binding Proteins
Proteins may also function to maintain double stranded DNA.
Histones: wind and compact DNA into nucleosome-like structure.

Early Life Forms
Hyperthermophilic Archaea and Bacteria are likely the closest living relatives to early life forms that remain today.

Hydrogen catabolism may have been the first energy-yielding metabolism of cells.

Pyrodictium and Pyrolobus
Pyrodictium and Pyrolobus are examples of prokaryotes whose growth temperature optimum lies above 100ºC. The optimum for Pyrodictium is 105ºC and for Pyrolobus is 106ºC.

Cells of Pyrodictium are irregularly disc-shaped and grow in culture in a mycelium-like layer attached to crystals of elemental sulfur.

Nanoarchaeum
Nanoarchaeum is a small, parasitic, early-branching member of the Archaea. Its genome is the smallest of all known organisms.
Nanoarchaeum lacks genes for all but core molecular processes and thus depends on its host, Ignicoccus, for most of its cellular needs.