Figure 21.12 (a) This colorized electron micrograph shows Zika virus particles (red). (b) Women infected by the Zika virus during pregnancy may give birth to children with microcephaly, a deformity characterized by an abnormally small head and brain. (credit a, b: modifications of work by the Centers for Disease Control and Prevention)


Figure 21.13 Virions of the rabies virus have a characteristic bullet-like shape. (credit: modification of work by the Centers for Disease Control and Prevention)


Figure 21.14 (a) An Emerson respiratory (or iron lung) that was used to help some polio victims to breathe. (b) Polio can also result in impaired motor function. (credit b: modification of work by the Centers for Disease Control and Prevention)


Figure 21.15 (a) Polio is caused by the poliovirus. (b) Two American virologists developed the first polio vaccines: Albert Sabin (left) and Jonas Salk (right). (credit a: modification of work by the Centers for Disease Control and Prevention)


Figure 21.16 The replicative cycle of misfolded prion proteins.


Figure 20.19 A blood smear (human blood stage) shows an early trophozoite in a delicate ring form (upper left) and an early stage schizont form (center) of Plasmodium falciparum from a patient with malaria. (credit: modification of work by Centers for Disease Control and Prevention)


Figure 21.5 (a) A normal human brain removed during an autopsy. (b) The brain of a patient who died from bacterial meningitis. Note the pus under the dura mater (being retracted by the forceps) and the red hemorrhagic foci on the meninges. (credit b: modification of work by the Centers for Disease Control and Prevention)


Figure 21.6 N. meningitidis (arrows) associated with neutrophils (the larger stained cells) in a gram-stained CSF sample. (credit: modification of work by the Centers for Disease Control and Prevention)


Figure 21.7 To prevent campus outbreaks, some colleges now require students to be vaccinated against meningogoccal meningitis. (credit: modification of work by James Gathany, Centers for Disease Control and Prevention)


Figure 21.9 A tetanus patient exhibiting the rigid body posture known as opisthotonos. (credit: Centers for Disease Control and Prevention)


Figure 21.10 (a) An electron micrograph of Listeria monocytogenes infecting a host cell. (b) Listeria is able to use host cell components to cause infection. For example, phagocytosis allows it to enter host cells, and the host’s cytoskeleton provides the materials to help the pathogen move to other cells. (credit a: modification of work by the Centers for Disease Control and Prevention; credit b: modification of work by Keith Ireton)


Figure 21.3 The layers of tissue surrounding the human brain include three meningeal membranes: the dura mater, arachnoid mater, and pia mater. (credit: modification of work by National Institutes of Health)


Figure 21.4 (a) A myelinated neuron is associated with oligodendrocytes. Oligodendrocytes are a type of glial cell that forms the myelin sheath in the CNS that insulates the axon so that electrochemical nerve impulses are transferred more efficiently. (b) A synapse consists of the axonal end of the presynaptic neuron (top) that releases neurotransmitters that cross the synaptic space (or cleft) and bind to receptors on dendrites of the postsynaptic neuron (bottom).


Figure 20.18 The life cycle of Plasmodium. (credit: modification of work by Centers for Disease Control and Prevention)


Figure 20.20 The infectious cycle of Toxoplasma gondii. (credit: “diagram”: modification of work by Centers for Disease Control and Prevention; credit “cat”: modification of work by “KaCey97078”/Flickr)


Figure 20.21 (a) Giemsa-stained Toxoplasma gondii tachyzoites from a smear of peritoneal fluid obtained from a mouse inoculated with T. gondii. Tachyzoites are typically crescent shaped with a prominent, centrally placed nucleus. Microscopic cyst containing T. gondii from mouse brain tissue. Thousands of resting parasites (stained red) are contained in a thin parasite cyst wall. (credit a: modification of work by Centers for Disease Control and Prevention; credit b: modification of work by USDA)


Figure 20.14 An Ebola virus particle viewed with electron microscopy. These filamentous viruses often exhibit looped or hooked ends. (credit: modification of work by Centers for Disease Control and Prevention)


Figure 20.15 This micrograph shows HIV particles (green) budding from a lymphocyte (top right). (credit: modification of work by Centers for Disease Control and Prevention)


Figure 20.17 This graph shows the clinical progression of CD4 T cells (blue line), clinical symptoms, and viral RNA (red line) during an HIV infection. (credit: modification of work by Kogan M, and Rappaport J)


Figure 20.6 Yersinia pestis, the causative agent of plague, has numerous modes of transmission. The modes are divided into two ecological classes: urban and sylvatic (i.e., forest or rural). The urban cycle primarily involves transmission from infected urban mammals (rats) to humans by flea vectors (brown arrows). The disease may travel between urban centers (purple arrow) if infected rats find their way onto ships or trains. The sylvatic cycle involves mammals more common in nonurban environments. Sylvatic birds and mammals (including humans) may become infected after eating infected mammals (pink arrows) or by flea vectors. Pneumonic transmission occurs between humans or between humans and infected animals through the inhalation of Y. pestis in aerosols. (credit “diagram”: modification of work by Stenseth NC, Atshabar BB, Begon M, Belmain SR, Bertherat E, Carniel E, Gage KL, Leirs H, and Rahalison L; credit “cat”: modification of work by “KaCey97078”/Flickr)


Figure 20.7 (a) Yersinia pestis infection can cause inflamed and swollen lymph nodes (buboes), like these in the groin of an infected patient. (b) Septicemic plague caused necrotic toes in this patient. Vascular damage at the extremities causes ischemia and tissue death. (credit a: modification of work by American Society for Microbiology; credit b: modification of work by Centers for Disease Control and Prevention)


Figure 20.8 This Wright’s stain of a blood sample from a patient with plague shows the characteristic “safety pin” appearance of Yersinia pestis. (credit: modification of work by Centers for Disease Control and Prevention)


Figure 20.9 This image shows the 2-year life cycle of the black-legged tick, the biological vector of Lyme disease. (credit “mouse”: modification of work by George Shuklin)


Figure 20.10 (a) A characteristic bull’s eye rash of Lyme disease forms at the site of a tick bite. (b) A darkfield micrograph shows Borrelia burgdorferi, the causative agent of Lyme disease. (credit a: modification of work by Centers for Disease Control and Prevention; credit b: modification of work by American Society for Microbiology)


Figure 20.2 The major components of the human circulatory system include the heart, arteries, veins, and capillaries. This network delivers blood to the body’s organs and tissues. (credit top left: modification of work by Mariana Ruiz Villareal; credit bottom right: modification of work by Bruce Blaus)


Figure 20.3 The essential components of the human lymphatic system drain fluid away from tissues.


Figure 20.5 (a) The spleen is a lymphatic organ located in the upper left quadrant of the abdomen near the stomach and left kidney. It contains numerous phagocytes and lymphocytes that combat and prevent circulatory infections by killing and removing pathogens from the blood. (b) Lymph nodes are masses of lymphatic tissue located along the larger lymph vessels. They contain numerous lymphocytes that kill and remove pathogens from lymphatic fluid that drains from surrounding tissues.


Figure 19.17 (a) Adult Ascaris lumbricoides roundworms can cause intestinal blockage. (b) This mass of A. lumbricoides worms was excreted by a child. (c) A micrograph of a fertilized egg of A. lumbricoides. Fertilized eggs can be distinguished from unfertilized eggs because they are round rather than elongated and have a thicker cell wall. (credit a: modification of work by South African Medical Research Council; credit b: modification of work by James Gathany, Centers for Disease Control and Prevention; credit c: modification of work by Centers for Disease Control and Prevention)


Figure 19.18 (a) E. vermicularis are tiny nematodes commonly called pinworms. (b) This micrograph shows pinworm eggs.


Figure 19.14 Rotaviruses in a fecal sample are visualized using electron microscopy. (credit: Dr. Graham Beards)


Figure 19.12 Clostridium difficile is able to colonize the mucous membrane of the colon when the normal microbiota is disrupted. The toxins TcdA and TcdB trigger an immune response, with neutrophils and monocytes migrating from the bloodstream to the site of infection. Over time, inflammation and dead cells contribute to the development of a pseudomembrane. (credit micrograph: modification of work by Janice Carr, Centers for Disease Control and Prevention)


Figure 19.7 Tooth decay occurs in stages. When bacterial biofilms (plaque) develop on teeth, the acids produced gradually dissolve the enamel, followed by the dentin. Eventually, if left untreated, the lesion may reach the pulp and cause an abscess. (credit: modification of work by “BruceBlaus”/Wikimedia Commons)


Figure 19.8 (a) Tartar (dental calculus) is visible at the bases of these teeth. The darker deposits higher on the crowns are staining. (b) This tooth shows only a small amount of visible decay. (c) An X-ray of the same tooth shows that there is a dark area representing more decay inside the tooth. (d) Removal of a portion of the crown reveals the area of damage. (e) All of the cavity must be removed before filling. (credit: modification of work by “DRosenbach”/Wikimedia Commons)


Figure 19.5 (a) The structure of the wall of the small intestine allows for the majority of nutrient absorption in the body. (b) Villi are folds in the surface of the small intestine. Microvilli are cytoplasmic extensions on individual cells that increase the surface area for absorption. (c) A light micrograph shows the shape of the villi. (d) An electron micrograph shows the shape of the microvilli. (credit b, c, d: Modification of micrographs provided by the Regents of University of Michigan Medical School © 2012)


Figure 18.16 Trichomonas vaginalis is visible in this Gram stained specimen. (credit: modification of work by American Society for Microbiology)


Figure 18.15 Candida can produce germ tubes, like the one in this micrograph, that develop into hyphae. (credit: modification of work by American Society for Microbiology)


Figure 18.9 Virions of the herpes simplex virus are shown here in this transmission electron micrograph. (credit: modification of work by Centers for Disease Control and Prevention)


Figure 18.10 Genital herpes is typically characterized by lesions on the genitals (left), but lesions can also appear elsewhere on the skin or mucous membranes (right). The lesions can be large and painful or small and easily overlooked. (credit b: modification of work by Schiffer JT, Swan D, Al Sallaq R, Magaret A, Johnston C, Mark KE, Selke S, Ocbamichael N, Kuntz S, Zhu J, Robinson B, Huang ML, Jerome KR, Wald A, and Corey)


Figure 18.11 Genital warts may occur around the anus (left) or genitalia (right). (credit left, right: modification of work by Centers for Disease Control and Prevention)


Figure 18.12 In this image, the cervical cells on the left are normal and those on the right show enlarged nuclei and hyperchromasia (darkly stained nuclei) typical of HPV-infected koilocytes. (credit: modification of work by Ed Uthman)


Figure 18.13 Details associated with two different viral infections of the reproductive tract.


Figure 18.5 In this vaginal smear, the cell at the lower left is a clue cell with a unique appearance caused by the presence of bacteria on the cell. The cell on the right is a normal cell.


Figure 18.6 (a) Clinical photograph of gonococcal discharge from penis. The lesions on the skin could indicate co- infection with another STI. (b) Purulent discharge originating from the cervix and accumulating in the vagina of a patient with gonorrhea. (c) A micrograph of urethral discharge shows gram-negative diplococci (paired cells) both inside and outside the leukocytes (large cells with lobed nuclei). These results could be used to diagnose gonorrhea in a male patient, but female vaginal samples may contain other Neisseria spp. even if the patient is not infected with gonorrhoeae. (credit a, b: modification of work by Centers for Disease Control and Prevention; credit c: modification of work by American Society for Microbiology)


Figure 18.4 A urine dipstick is compared against a color key to determine levels of various chemicals, proteins, or cells in the urine. Abnormal levels may indicate an infection. (credit: modification of work by Suzanne Wakim)


Figure 18.2 These structures of the human urinary system are present in both males and females.


Figure 18.3 The female reproductive system is located in close proximity to the urinary system. In males, the urethra is shared by the reproductive and urinary systems.


Figure 17.15 The illustration shows the structure of an influenza virus. The viral envelope is studded with copies of the proteins neuraminidase and hemagglutinin, and surrounds the individual seven or eight RNA genome segments. (credit: modification of work by Dan Higgins, Centers for Disease Control and Prevention)


Figure 17.15


Figure 17.16 (a) Measles typically presents as a raised macular rash that begins on the face and spreads to the extremities. (b) Koplik’s spots on the oral mucosa are also characteristic of measles. (c) A thin-section transmission electron micrograph of a measles virion. (credit a, b, c: modification of work by Centers for Disease Control and Prevention)


Figure 17.17 (a) The characteristic appearance of the pustular chickenpox rash is concentrated on the trunk region. (b) This transmission electron micrograph shows a viroid of human herpesvirus 3, the virus that causes chickenpox in children and shingles when it is reactivated in adults. (credit b: modification of work by Centers for Disease Control and Prevention)


Figure 17.18 (a) An individual suffering from shingles. (b) The rash is formed because of the reactivation of a varicella-zoster infection that was initially contracted in childhood. (credit a: modification of work by National Institute of Allergy and Infectious Diseases (NIAID); credit b: modification of work by Centers for Disease Control and Prevention)


Figure 17.5 This scanning electron micrograph of Streptococcus pyogenes shows the characteristic cellular phenotype resembling chains of cocci. (credit: modification of work by U.S. Centers for Disease Control and Prevention – Medical Illustrator)


Figure 17.6 Streptococcal infections of the respiratory tract may cause localized pharyngitis or systemic signs and symptoms. (a) The characteristic appearance of strep throat: bright red arches of inflammation with the presence of dark-red spots (petechiae). (b) Scarlet fever presents as a rash on the skin. (credit a: modification of work by Centers for Disease Control and Prevention; credit b: modification of work by Alicia Williams)


Figure 17.7 (a) A healthy tympanic membrane; the middle ear bones can be seen behind the membrane. (b) An ear with chronic inflammation that has resulted in a torn membrane, erosion of the inner ear bones, and mucus buildup. (credit a: modification of work by “DrER.tv”/YouTube; credit b: modification of work by Li Mg, Hotez PJ, Vrabec JT, Donovan DT)


Figure 17.8 A chest radiograph of a patient with pneumonia shows the consolidations (lesions) present as opaque patches. (credit: modification of work by Centers for Disease Control and Prevention)


Figure 17.9 (a) This micrograph of Streptococcus pneumoniae grown from a blood culture shows the characteristic lancet-shaped diplococcal morphology. (b) A colorized scanning electron micrograph of S. pneumoniae. (credit a: modification of work by Centers for Disease Control and Prevention; credit b: modification of work by Janice Carr, Centers for Disease Control and Prevention)


Figure 17.10 Culture of Haemophilus influenzae on a chocolate agar plate. (credit: modification of work by Centers for Disease Control and Prevention)


Figure 17.11 The micrograph shows Mycoplasma pneumoniae using their specialized receptors to attach to epithelial cells in the trachea of an infected hamster. (credit: modification of work by American Society for Microbiology)


Figure 17.12 In the infectious cycle of tuberculosis, the immune response of most infected individuals (approximately 90%) results in the formation of tubercles in which the infection is walled off.[footnote]G. Kaplan et al. “Mycobacterium tuberculosis Growth at the Cavity Surface: A Microenvironment with Failed Immunity.” Infection and Immunity 71 no.12 (2003):7099–7108.[/footnote] The remainder will suffer progressive primary tuberculosis. The sequestered bacteria may be reactivated to form secondary tuberculosis in immunocompromised patients at a later time. (credit: modification of work by Centers for Disease Control and Prevention)


Figure 17.13 (a) The Mantoux skin test for tuberculosis involves injecting the subject with tuberculin protein derivative. The injection should initially produce a raised wheal. (b) The test should be read in 48–72 hours. A positive result is indicated by redness, swelling, or hardness; the size of the responding region is measured to determine the final result. (credit a, b: modification of work by Centers for Disease Control and Prevention)


Figure 17.2 (a) The ear is connected to the upper respiratory tract by the eustachian tube, which opens to the nasopharynx. (b) The structures of the upper respiratory tract.


Figure 17.3 The structures of the lower respiratory tract are identified in this illustration. (credit: modification of work by National Cancer Institute)


Figure 16.24 This Loa loa worm, measuring about 55 mm long, was extracted from the conjunctiva of a patient with loiasis. The Loa loa has a complex life cycle. Biting deerflies native to the rain forests of Central and West Africa transmit the larvae between humans. (credit a: modification of work by Eballe AO, Epée E, Koki G, Owono D, Mvogo CE, Bella AL; credit b: modification of work by NIAID; credit c: modification of work by Centers for Disease Controland Prevention)


Figure 16.25 Details associated with loiasis, a parasitic skin and eye infection.


Figure 16.22 Tineas are superficial cutaneous mycoses and are common. (a) Tinea barbae (barber’s itch) occurs on the lower face. (b) Tinea pedis (athlete’s foot) occurs on the feet, causing itching, burning, and dry, cracked skin between the toes. (c) A close-up view of tinea corporis (ringworm) caused by Trichophyton mentagrophytes. (credit a, c: modification of work by Centers for Disease Control and Prevention; credit b: modification of work by Al Hasan M, Fitzgerald SM, Saoudian M, Krishnaswamy G)


Figure 16.19 Warts can vary in shape and in location. (a) Multiple plantar warts have grown on this toe. (b) A filiform wart has grown on this eyelid.


Figure 16.20 This cold sore was caused by HSV-1. (credit: Centers for Disease Control and Prevention)


Figure 16.7 (a) A mannitol salt agar plate is used to distinguish different species of staphylococci. In this plate, S. aureus is on the left and S. epidermidis is in the right. Because S. aureus is capable of fermenting mannitol, it produces acids that cause the color to change to yellow. (b) This scanning electron micrograph shows the characteristic grapelike clusters of S. aureus. (credit a: modification of work by “ScienceProfOnline”/YouTube; credit b: modification of work by Centers for Disease Control and Prevention)


Figure 16.8 Furuncles (boils) and carbuncles are infections of the skin often caused by Staphylococcus bacteria. (a) A furuncle contains pus and exhibits swelling. (b) A carbuncle is a pus-filled lesion that is typically deeper than the furuncle. It often forms from multiple furuncles. (credit a: modification of work by “Mahdouch”/Wikimedia Commons; credit b: modification of work by “Drvgaikwad”/Wikimedia Commons)


Figure 16.9 A newborn with staphylococcal scalded skin syndrome (SSSS), which results in large regions of peeling, dead skin. (credit: modification of work by D Jeyakumari, R Gopal, M Eswaran, and C MaheshKumar)


Figure 16.10 Impetigo is characterized by vesicles, pustules, or bullae that rupture, producing encrusted sores. (credit: modification of work by FDA)


Figure 16.11 Streptococcus pyogenes forms chains of cocci. (credit: modification of work by Centers for Disease Control and Prevention)


Figure 16.12 S. pyogenes can cause a variety of skin conditions once it breaches the skin barrier through a cut or wound. (a) Cellulitis presents as a painful, red rash. (b) Erysipelas presents as a raised rash, usually with clear borders. (c) Erythema nodosum is characterized by red lumps or nodules, typically on the lower legs. (credit a: modification of work by “Bassukas ID, Gaitanis G, Zioga A, Boboyianni C, Stergiopoulou C; credit b: modification of work by Centers for Disease Control and Prevention; credit c: modification of work by Dean C, Crow WT)


Figure 16.13 (a) The left leg of this patient shows the clinical features of necrotizing fasciitis. (b) The same patient’s leg is surgically debrided to remove the infection. (credit a, b: modification of work by Piotr Smuszkiewicz, Iwona Trojanowska, and Hanna Tomczak)


Figure 16.14 (a) Acne is characterized by whitehead and blackhead comedones that result from clogged hair follicles. (b) Blackheads, visible as black spots on the skin, have a dark appearance due to the oxidation of lipids in sebum via exposure to the air. (credit a: modification of work by Bruce Blaus)


Figure 16.15 (a) Cutaneous anthrax is an infection of the skin by B. anthracis, which produces tissue-damaging exotoxins. Dead tissues accumulating in this nodule have produced a small black eschar. (b) Colonies of B. anthracis grown on sheep’s blood agar. (credit a, b: modification of work by Centers for Disease Control and Prevention)


Figure 16.16. Details associated with various bacterial infections of the skin.


Figure 16.17 Acute, purulent, bacterial conjunctivitis causes swelling and redness in the conjunctiva, the membrane lining the whites of the eyes and the inner eyelids. It is often accompanied by a yellow, green, or white discharge, which can dry and become encrusted on the eyelashes. (credit: “Tanalai”/Wikimedia Commons)


Figure 16.18 Details associated with acute bacterial conjunctivitis, a bacterial infection of the eyes.


Figure 16.2 (a) A micrograph of a section through human skin shows the epidermis and dermis. (b) The major layers of human skin are the epidermis, dermis, and hypodermis. (credit b: modification of work by National Cancer Institute)


Figure 16.3 The normal microbiota varies on different regions of the skin, especially in dry versus moist areas. The figure shows the major organisms commonly found in different locations of a healthy individual’s skin and external mucosa. Note that there is significant variation among individuals. (credit: modification of work by National Human Genome Research Institute)


Figure 16.4 The lacrimal apparatus includes the structures of the eye associated with tear production and drainage. (credit: modification of work by “Evidence Based Medical Educator Inc.”/YouTube)


Figure 16.5 Some microbes live on the conjunctiva of the human eye, but the vitreous humor is sterile.


Figure 16.6 (a) Conjunctivitis is inflammation of the conjunctiva. (b) Blepharitis is inflammation of the eyelids. (c) Keratitis is inflammation of the cornea. (credit a: modification of work by Lopez-Prats MJ, Sanz Marco E, Hidalgo- Mora JJ, Garcia-Delpech S, Diaz-Llopis M; credit b, c: modification of work by Centers for Disease Control and Prevention)


Figure 15.11 Hyperpigmentation is a sign of Addison disease. (credit: modification of work by Petros Perros)


Figure 15.12 The radiograph (left) and photograph (right) show damage to the hands typical of rheumatoid arthritis. (credit right: modification of work by “handarmdoc”/Flickr)


Figure 15.13 (a) Systemic lupus erythematosus is characterized by autoimmunity to the individual’s own DNA and/ or proteins. (b) This patient is presenting with a butterfly rash, one of the characteristic signs of lupus. (credit a: modification of work by Mikael Häggström; credit b: modification of work by Shrestha D, Dhakal AK, Shiva RK, Shakya A, Shah SC, Shakya H)


Figure 15.2 (a) Allergens in plant pollen, shown here in a colorized electron micrograph, may trigger allergic rhinitis or hay fever in sensitive individuals. (b) Skin rashes are often associated with allergic reactions. (c) Peanuts can be eaten safely by most people but can provoke severe allergic reactions in sensitive individuals.


Figure 15.3 On first exposure to an allergen in a susceptible individual, antigen-presenting cells process and present allergen epitopes with major histocompatibility complex (MHC) II to T helper cells. B cells also process and present the same allergen epitope to TH2 cells, which release cytokines IL-4 and IL-13 to stimulate proliferation and differentiation into IgE-secreting plasma cells. The IgE molecules bind to mast cells with their Fc region, sensitizing the mast cells for activation with subsequent exposure to the allergen. With each subsequent exposure, the allergen cross-links IgE molecules on the mast cells, activating the mast cells and causing the release of preformed chemical mediators from granules (degranulation), as well as newly formed chemical mediators that collectively cause the signs and symptoms of type I hypersensitivity reactions.


Figure 15.4. This figure shows the isohemagglutinins and antigens associated with the different human blood types.


Figure 15.5 A type II hypersensitivity hemolytic transfusion reaction (HTR) leading to hemolytic anemia. Blood from a type A donor is administered to a patient with type B blood. The anti-A isohemagglutinin IgM antibodies in the recipient bind to and agglutinate the incoming donor type A red blood cells. The bound anti-A antibodies activate the classical complement cascade, resulting in destruction of the donor red blood cells.


Figure 15.6 (a) When an Rh− mother has an Rh+ fetus, fetal erythrocytes are introduced into the mother ’s circulatory system before or during birth, leading to production of anti-Rh IgG antibodies. These antibodies remain in the mother and, if she becomes pregnant with a second Rh+ baby, they can cross the placenta and attach to fetal Rh+ erythrocytes. Complement-mediated hemolysis of fetal erythrocytes results in a lack of sufficient cells for proper oxygenation of the fetus. (b) HDN can be prevented by administering Rho(D) immune globulin during and after each pregnancy with an Rh+ fetus. The immune globulin binds fetal Rh+ RBCs that gain access to the mother ’s bloodstream, preventing activation of her primary immune response.


Figure 15.7 Type III hypersensitivities and the systems they affect. (a) Immune complexes form and deposit in tissue. Complement activation, stimulation of an inflammatory response, and recruitment and activation of neutrophils result in damage to blood vessels, heart tissue, joints, skin, and/or kidneys. (b) If the kidneys are damaged by a type III hypersensitivity reaction, dialysis may be required.


Figure 15.8 Exposure to hapten antigens in poison ivy can cause contact dermatitis, a type IV hypersensitivity. (a) The first exposure to poison ivy does not result in a reaction. However, sensitization stimulates helper T cells, leading to production of memory helper T cells that can become reactivated on future exposures. (b) Upon secondary exposure, the memory helper T cells become reactivated, producing inflammatory cytokines that stimulate macrophages and cytotoxic T cells to induce an inflammatory lesion at the exposed site. This lesion, which will persist until the allergen is removed, can inflict significant tissue damage if it continues long enough.


Figure 14.24 The four classifications of immunity. (credit top left photo: modification of work by USDA; credit top right photo: modification of work by “Michaelberry”/Wikimedia; credit bottom left photo: modification of work by Centers for Disease Control and Prevention; credit bottom right photo: modification of work by Friskila Silitonga, Indonesia, Centers for Disease Control and Prevention)


Figure 14.25 (a) A painting of Edward Jenner depicts a cow and a milkmaid in the background. (b) Lesions on a patient infected with cowpox, a zoonotic disease caused by a virus closely related to the one that causes smallpox. (credit b: modification of work by the Centers for Disease Control and Prevention)


Figure 14.20 B-cell receptors are embedded in the membranes of B cells. The variable regions of all of the receptors on a single cell bind the same specific antigen.


Figure 14.21 T-independent antigens have repeating epitopes that can induce B cell recognition and activation without involvement from T cells. A second signal, such as interaction of TLRs with PAMPs (not shown), is also required for activation of the B cell. Once activated, the B cell proliferates and differentiates into antibody-secreting plasma cells.


Figure 14.22 In T cell-dependent activation of B cells, the B cell recognizes and internalizes an antigen and presents it to a helper T cell that is specific to the same antigen. The helper T cell interacts with the antigen presented by the B cell, which activates the T cell and stimulates the release of cytokines that then activate the B cell. Activation of the B cell triggers proliferation and differentiation into B cells and plasma cells.


Figure 14.23 Compared to the primary response, the secondary antibody response occurs more quickly and produces antibody levels that are higher and more sustained. The secondary response mostly involves IgG.


Figure 14.14 (a) Red bone marrow can be found in the head of the femur (thighbone) and is also present in the flat bones of the body, such as the ilium and the scapula. (b) Red bone marrow is the site of production and differentiation of many formed elements of blood, including erythrocytes, leukocytes, and platelets. The yellow bone marrow is populated primarily with adipose cells.


Figure 14.15 The thymus is a bi-lobed, H-shaped glandular organ that is located just above the heart. It is surrounded by a fibrous capsule of connective tissue. The darkly staining cortex and the lighter staining medulla of individual lobules are clearly visible in the light micrograph of the thymus of a newborn (top right, LM × 100). (credit micrograph: modification of micrograph provided by the Regents of University of Michigan Medical School © 2012)


Figure 14.16 A T-cell receptor spans the cytoplasmic membrane and projects variable binding regions into the extracellular space to bind processed antigens associated with MHC I or MHC II molecules.


Figure 14.17 This illustration depicts the activation of a naïve (unactivated) helper T cell by an antigen-presenting cell and the subsequent proliferation and differentiation of the activated T cell into different subtypes.


Figure 14.18 This figure illustrates the activation of a naïve (unactivated) cytotoxic T cell (CTL) by an antigen- presenting MHC I molecule on an infected body cell. Once activated, the CTL releases perforin and granzymes that invade the infected cell and induce controlled cell death, or apoptosis.


Figure 14.19 (a) The macrophage in this figure is presenting a foreign epitope that does not match the TCR of the T cell. Because the T cell does not recognize the epitope, it is not activated. (b) The macrophage in this figure is presenting a superantigen that is not recognized by the TCR of the T cell, yet the superantigen still is able to bridge and bind the MHC II and TCR molecules. This nonspecific, uncontrolled activation of the T cell results in an excessive release of cytokines that activate other T cells and cause excessive inflammation. (credit: modification of work by “Microbiotic”/YouTube)


Figure 14.11 MHC I are found on all nucleated body cells, and MHC II are found on macrophages, dendritic cells, and B cells (along with MHC I). The antigen-binding cleft of MHC I is formed by domains α1 and α2. The antigen- binding cleft of MHC II is formed by domains α1 and β1.


Figure 14.12 A dendritic cell phagocytoses a bacterial cell and brings it into a phagosome. Lysosomes fuse with the phagosome to create a phagolysosome, where antimicrobial chemicals and enzymes degrade the bacterial cell. Proteases process bacterial antigens, and the most antigenic epitopes are selected and presented on the cell’s surface in conjunction with MHC II molecules. T cells recognize the presented antigens and are thus activated.


Figure 14.2 This graph illustrates the primary and secondary immune responses related to antibody production after an initial and secondary exposure to an antigen. Notice that the secondary response is faster and provides a much higher concentration of antibody.


Figure 14.3 An antigen is a macromolecule that reacts with components of the immune system. A given antigen may contain several motifs that are recognized by immune cells.


Figure 14.5 (a) The typical four-chain structure of a generic antibody monomer. (b) The corresponding three- dimensional structure of the antibody IgG. (credit b: modification of work by Tim Vickers)


Figure 14.6 Details associated with the different human antibodies or immunoglobulin (Ig) classes.


Figure 14.7 Neutralization involves the binding of specific antibodies to antigens found on bacteria, viruses, and toxins, preventing them from attaching to target cells.


Figure 14.8 Antibodies serve as opsonins and inhibit infection by tagging pathogens for destruction by macrophages, dendritic cells, and neutrophils. These phagocytic cells use Fc receptors to bind to IgG-opsonized pathogens and initiate the first step of attachment before phagocytosis.


Figure 14.9 Antibodies, especially IgM antibodies, agglutinate bacteria by binding to epitopes on two or more bacteria simultaneously. When multiple pathogens and antibodies are present, aggregates form when the binding sites of antibodies bind with separate pathogens.


Figure 14.10 In this example of ADCC, antibodies bind to a large pathogenic cell that is too big for phagocytosis and then bind to Fc receptors on the membrane of a natural killer cell. This interaction brings the NK cell into close proximity, where it can kill the pathogen through release of lethal extracellular cytotoxins.


Figure 13.15 (a) Mast cells detect injury to nearby cells and release histamine, initiating an inflammatory response. Histamine increases blood flow to the wound site, and increased vascular permeability allows fluid, proteins, phagocytes, and other immune cells to enter infected tissue. These events result in the swelling and reddening of the injured site, and the increased blood flow to the injured site causes it to feel warm. Inflammation is also associated with pain due to these events stimulating nerve pain receptors in the tissue. The interaction of phagocyte PRRs with cellular distress signals and PAMPs and opsonins on the surface of pathogens leads to the release of more proinflammatory chemicals, enhancing the inflammatory response.


Figure 13.16 A tubercle is a granuloma in the lung tissue of a patient with tuberculosis. In this micrograph, white blood cells (stained purple) have walled off a pocket of tissue infected with Mycobacterium tuberculosis. Granulomas also occur in many other forms of disease. (credit: modification of work by Piotrowski WJ, Górski P, Duda-Szymańska J, Kwiatkowska S)


Figure 13.13 Phagocytic cells contain pattern recognition receptors (PRRs) capable of recognizing various pathogen-associated molecular patterns (PAMPs). These PRRs can be found on the plasma membrane or in internal phagosomes. When a PRR recognizes a PAMP, it sends a signal to the nucleus that activates genes involved in phagocytosis, cellular proliferation, production and secretion of antiviral interferons and proinflammatory cytokines, and enhanced intracellular killing.


Figure 13.14 The stages of phagocytosis include the engulfment of a pathogen, the formation of a phagosome, the digestion of the pathogenic particle in the phagolysosome, and the expulsion of undigested materials from the cell.


Figure 13.9 All the formed elements of the blood arise by differentiation of hematopoietic stem cells in the bone marrow.


Figure 13.10 Granulocytes can be distinguished by the number of lobes in their nuclei and the staining properties of their granules. (credit “neutrophil” micrograph: modification of work by Ed Uthman)


Figure 13.11 Mast cells function similarly to basophils by inducing and promoting inflammatory responses. (a) This figure shows mast cells in blood. In a blood smear, they are difficult to differentiate from basophils (b). Unlike basophils, mast cells migrate from the blood into various tissues. (credit right: modification of work by Greenland JR, Xu X, Sayah DM, Liu FC, Jones KD, Looney MR, Caughey GH)


Figure 13.12 Monocytes are large, agranular white blood cells with a nucleus that lacks lobes. When monocytes leave the bloodstream, they differentiate and become macrophages with tissue-specific properties. (credit left: modification of work by Armed Forces Institute of Pathology; credit right: modification of work by Centers for Disease Control and Prevention)


Figure 13.7 Sebaceous glands secrete sebum, a chemical mediator that lubricates and protect the skin from invading microbes. Sebum is also a food source for resident microbes that produce oleic acid, an exogenously produced mediator. (credit micrograph: Micrograph provided by the Regents of University of Michigan Medical School © 2012)


Figure 13.8 Interferons are cytokines released by a cell infected with a virus. Interferon-α and interferon-β signal uninfected neighboring cells to inhibit mRNA synthesis, destroy RNA, and reduce protein synthesis (top arrow).Interferon-α and interferon-β also promote apoptosis in cells infected with the virus (middle arrow). Interferon-γ alerts neighboring immune cells to an attack (bottom arrow). Although interferons do not cure the cell releasing them or other infected cells, which will soon die, their release may prevent additional cells from becoming infected, thus stemming the infection.


Figure 13.2 Human skin has three layers, the epidermis, the dermis, and the hypodermis, which provide a thick barrier between microbes outside the body and deeper tissues. Dead skin cells on the surface of the epidermis are continually shed, taking with them microbes on the skin’s surface. (credit: modification of work by National Institutes of Health)


Figure 13.3 Rose gardener’s disease can occur when the fungus Sporothrix schenkii breaches the skin through small cuts, such as might be inflicted by thorns. (credit left: modification of work by Elisa Self; credit right: modification of work by Centers for Disease Control and Prevention)


Figure 13.4 This scanning electron micrograph shows ciliated and nonciliated epithelial cells from the human trachea. The mucociliary escalator pushes mucus away from the lungs, along with any debris or microorganisms that may be trapped in the sticky mucus, and the mucus moves up to the esophagus where it can be removed by swallowing.


Figure 13.5 Goblet cells produce and secrete mucus. The arrows in this micrograph point to the mucus-secreting goblet cells (magnification 1600⨯) in the intestinal epithelium. (credit micrograph: Micrograph provided by the Regents of University of Michigan Medical School © 2012)


Figure 13.6 Tears flush microbes away from the surface of the eye. Urine washes microbes out of the urinary tract as it passes through; as a result, the urinary system is normally sterile.


Figure 12.14 Even before the Ebola epidemic of 2014–15, Ebola was considered an emerging disease because of several smaller outbreaks between the mid-1990s and 2000s.


Figure 12.9 Direct contact transmission of pathogens can occur through physical contact. Many pathogens require contact with a mucous membrane to enter the body, but the host may transfer the pathogen from another point of contact (e.g., hand) to a mucous membrane (e.g., mouth or eye). (credit left: modification of work by Lisa Doehnert)


Figure 12.10 Fomites are nonliving objects that facilitate the indirect transmission of pathogens. Contaminated doorknobs, towels, and syringes are all common examples of fomites. (credit left: modification of work by Kate Ter Haar; credit middle: modification of work by Vernon Swanepoel; credit right: modification of work by “Zaldylmg”/Flickr)


Figure 12.11 Food is an important vehicle of transmission for pathogens, especially of the gastrointestinal and upper respiratory systems. Notice the glass shield above the food trays, designed to prevent pathogens ejected in coughs and sneezes from entering the food. (credit: Fort George G. Meade Public Affairs Office)


Figure 12.12 (a) A mechanical vector carries a pathogen on its body from one host to another, not as an infection. (b) A biological vector carries a pathogen from one host to another after becoming infected itself.


Figure 12.13 (a) The Aeromedical Biological Containment System (ABCS) is a module designed by the CDC and Department of Defense specifically for transporting highly contagious patients by air. (b) An isolation ward for Ebola patients in Lagos, Nigeria. (credit a: modification of work by Centers for Disease Control and Prevention; credit b: modification of work by CDC Global)


Figure 12.5 (a) John Snow (1813–1858), British physician and father of epidemiology. (b) Snow’s detailed mapping of cholera incidence led to the discovery of the contaminated water pump on Broad street (red square) responsible for the 1854 cholera epidemic. (credit a: modification of work by “Rsabbatini”/Wikimedia Commons)


Figure 12.6 (a) Outbreaks that can be attributed to point source spread often have a short duration. (b) Outbreaks attributed to propagated spread can have a more extended duration. (credit a, b: modification of work by Centers for Disease Control and Prevention)


Figure 12.7 (a) Florence Nightingale reported on the data she collected as a nurse in the Crimean War. (b) Nightingale’s diagram shows the number of fatalities in soldiers by month of the conflict from various causes. The total number dead in a particular month is equal to the area of the wedge for that month. The colored sections of the wedge represent different causes of death: wounds (pink), preventable infectious diseases (gray), and all other causes (brown).


Figure 12.8 Joseph Lister initiated the use of a carbolic acid (phenol) during surgeries. This illustration of a surgery shows a pressurized canister of carbolic acid being sprayed over the surgical site.


Figure 12.2 This graph compares the incidence of HIV (the number of new cases reported each year) with the prevalence (the total number of cases each year). Prevalence and incidence can also be expressed as a rate or proportion for a given population.


Figure 12.3 The 2007–2008 influenza season in the United States saw much higher than normal numbers of visits to emergency departments for influenza-like symptoms as compared to the previous and the following years. (credit: modification of work by Centers for Disease Control and Prevention)


Figure 11.8 (a) Hyaluronan is a polymer found in the layers of epidermis that connect adjacent cells. (b) Hyaluronidase produced by bacteria degrades this adhesive polymer in the extracellular matrix, allowing passage between cells that would otherwise be blocked.


Figure 11.9. Lipopolysaccharide is composed of lipid A, a core glycolipid, and an O-specific polysaccharide side chain. Lipid A is the toxic component that promotes inflammation and fever.


Figure 11.10 (a) In A-B toxins, the B component binds to the host cell through its interaction with specific cell surface receptors. (b) The toxin is brought in through endocytosis. (c) Once inside the vacuole, the A component (active component) separates from the B component and the A component gains access to the cytoplasm. (credit: modification of work by “Biology Discussion Forum”/YouTube)


Figure 11.11 (a) A micrograph of capsules around bacterial cells. (b) Antibodies normally function by binding to antigens, molecules on the surface of pathogenic bacteria. Phagocytes then bind to the antibody, initiating phagocytosis. (c) Some bacteria also produce proteases, virulence factors that break down host antibodies to evade phagocytosis. (credit a: modification of work by Centers for Disease Control and Prevention)


Figure 11.12 Antigenic drift and antigenic shift in influenza viruses. (a) In antigenic drift, mutations in the genes for the surface proteins neuraminidase and/or hemagglutinin result in small antigenic changes over time. (b) In antigenic shift, simultaneous infection of a cell with two different influenza viruses results in mixing of the genes. The resultant virus possesses a mixture of the proteins of the original viruses. Influenza pandemics can often be traced to antigenic shifts.


Figure 11.3 A graph like this is used to determine LD50 by plotting pathogen concentration against the percent of infected test animals that have died. In this example, the LD50 = 104 pathogenic particles.


Figure 11.3 The progression of an infectious disease can be divided into five periods, which are related to the number of pathogen particles (red) and the severity of signs and symptoms (blue).


Figure 11.4 Shown are different portals of entry where pathogens can gain access into the body. With the exception of the placenta, many of these locations are directly exposed to the external environment.


Figure 11.5 Glycocalyx produced by bacteria in a biofilm allows the cells to adhere to host tissues and to medical devices such as the catheter surface shown here. (credit: modification of work by Centers for Disease Control and Prevention)


Figure 11.2 Blood smears showing two diseases of the blood. (a) Malaria is an infectious, zoonotic disease caused by the protozoan pathogen Plasmodium falciparum (shown here) and several other species of the genus Plasmodium. It is transmitted by mosquitoes to humans. (b) Sickle cell disease is a noninfectious genetic disorder that results in abnormally shaped red blood cells, which can stick together and obstruct the flow of blood through the circulatory system. It is not caused by a pathogen, but rather a genetic mutation. (credit a: modification of work by Centers for Disease Control and Prevention; credit b: modification of work by Ed Uthman)


Figure 10.10 In a dilution test, the lowest dilution that inhibits turbidity (cloudiness) is the MIC. In this example, the MIC is 8 μg/mL. Broth from samples without turbidity can be inoculated onto plates lacking the antimicrobial drug. The lowest dilution that kills ≥99.9% of the starting inoculum is observed on the plates is the MBC. (credit: modification of work by Suzanne Wakim)


Figure 10.11 A microdilution tray can also be used to determine MICs of multiple antimicrobial drugs in a single assay. In this example, the drug concentrations increase from left to right and the rows with clindamycin, penicillin, and erythromycin have been indicated to the left of the plate. For penicillin and erythromycin, the lowest concentrations that inhibited visible growth are indicated by red circles and were 0.06 μg/mL for penicillin and 8 μg/ mL for erythromycin. For clindamycin, visible bacterial growth was observed at every concentration up to 32 μg/mL and the MIC is interpreted as >32 μg/mL. (credit: modification of work by Centers for Disease Control and Prevention)


Figure 10.9 In recent decades, approvals of new antimicrobials by the FDA have steadily fallen. In the five- year period from 1983–1987, 16 new antimicrobial drugs were approved, compared to just two from 2008–2012.


Figure 10.9 There are multiple strategies that microbes use to develop resistance to antimicrobial drugs. (Not shown: target overproduction, target mimicry, and enzymatic bypass). (credit: modification of work by Gerard D Wright)


Figure 10.7 The predominant sterol found in human cells is cholesterol, whereas the predominant sterol found in fungi is ergosterol, making ergosterol a good target for antifungal drug development.


Figure 10.8 Antiretroviral therapy (ART) is typically used for the treatment of HIV. The targets of drug classes currently in use are shown here. (credit: modification of work by Thomas Splettstoesser)


Figure 10.5 The major classes of protein synthesis inhibitors target the 30S or 50S subunits of cytoplasmic ribosomes.


Figure 10.6 Sulfonamides and trimethoprim are examples of antimetabolites that interfere in the bacterial synthesis of folic acid by blocking purine and pyrimidine biosynthesis, thus inhibiting bacterial growth.


Figure 10.2 Broad-spectrum antimicrobial use may lead to the development of a superinfection. (credit: modification of work by Centers for Disease Control and Prevention)


Figure 9.6 A disk-diffusion assay is used to determine the effectiveness of chemical agents against a particular microbe. (a) A plate is inoculated with various antimicrobial discs. The zone of inhibition around each disc indicates how effective that antimicrobial is against the particular species being tested. (b) On these plates, four antimicrobial agents are tested for efficacy in killing Pseudomonas aeruginosa (left) and Staphylococcus aureus (right). These antimicrobials are much more effective at killing S. aureus, as indicated by the size of the zones of inhibition. (credit b: modification of work by American Society for Microbiology)


Figure 9.7 Used disinfectant solutions in a clinical setting can be checked with the in-use test for contamination with microbes.


Figure 9.2 A protective suit like this one is an additional precaution for those who work in BSL-4 laboratories. This suit has its own air supply and maintains a positive pressure relative to the outside, so that if a leak occurs, air will flow out of the suit, not into it from the laboratory. (credit: modification of work by Centers for Disease Control and Prevention)


Figure 9.4 Details associated with the different protocols used for control of microbial growth.


Figure 9.5 Microbial death is logarithmic and easily observed using a semilog plot instead of an arithmetic one. The decimal reduction time (D-value) is the time it takes to kill 90% of the population (a 1-log decrease in the total population) when exposed to a specific microbial control protocol, as indicated by the purple bracket.


Figure 8.5 Gene therapy using an adenovirus vector can be used to treat or cure certain genetic diseases in which a patient has a defective gene. (credit: modification of work by National Institutes of Health)


Figure 8.2 (a) The gene encoding green fluorescence protein is a commonly used reporter gene for monitoring gene expression patterns in organisms. Under ultraviolet light, GFP fluoresces. Here, two mice are expressing GFP, while the middle mouse is not. (b) GFP can be used as a reporter gene in bacteria as well. Here, a plate containing bacterial colonies expressing GFP is shown. (c) Blue-white screening in bacteria is accomplished through the use of the lacZ reporter gene, followed by plating of bacteria onto medium containing X-gal. Cleavage of X-gal by the LacZ enzyme results in the formation of blue colonies. (credit a: modification of work by Ingrid Moen, Charlotte Jevne, Jian Wang, Karl-Henning Kalland, Martha Chekenya, Lars A Akslen, Linda Sleire, Per Ø Enger, Rolf K Reed, Anne M Øyan, Linda EB Stuhr; credit b: modification of work by “2.5JIGEN.com”/Flickr; credit c: modification of work by American Society for Microbiology)


Figure 8.4 This diagram illustrates the process of using siRNA or miRNA in a eukaryotic cell to silence genes involved in the pathogenesis of various diseases. (credit: modification of work by National Center for Biotechnology Information)


Figure 7.14 A black smoker at the bottom of the ocean belches hot, chemical-rich water, and heats the surrounding waters. Sea vents provide an extreme environment that is nonetheless teeming with macroscopic life (the red tubeworms) supported by an abundant microbial ecosystem. (credit: NOAA)


Figure 7.12 The curves show the approximate pH ranges for the growth of the different classes of pH-specific prokaryotes. Each curve has an optimal pH and extreme pH values at which growth is much reduced. Most bacteria are neutrophiles and grow best at near-neutral pH (center curve). Acidophiles have optimal growth at pH values near 3 and alkaliphiles have optimal growth at pH values above 9.


Figure 7.9 Anaerobic environments are still common on earth. They include environments like (a) a bog where undisturbed dense sediments are virtually devoid of oxygen, and (b) the rumen (the first compartment of a cow’s stomach), which provides an oxygen-free incubator for methanogens and other obligate anaerobic bacteria. (credit a: modification of work by National Park Service; credit b: modification of work by US Department of Agriculture)


Figure 7.10 Diagram of bacterial cell distribution in thioglycolate tubes.


Figure 7.2 (a) The electron micrograph depicts two cells of Salmonella typhimurium after a binary fission event. (b) Binary fission in bacteria starts with the replication of DNA as the cell elongates. A division septum forms in the center of the cell. Two daughter cells of similar size form and separate, each receiving a copy of the original chromosome. (credit a: modification of work by Centers for Disease Control and Prevention)


Figure 7.3 FtsZ proteins assemble to form a Z ring that is anchored to the plasma membrane. The Z ring pinches the cell envelope to separate the cytoplasm of the new cells.


Figure 7.5 The growth curve of a bacterial culture is represented by the logarithm of the number of live cells plotted as a function of time. The graph can be divided into four phases according to the slope, each of which matches events in the cell. The four phases are lag, log, stationary, and death.


Figure 7.6 Both graphs illustrate population growth during the log phase for a bacterial sample with an initial population of one cell and a doubling time of 1 hour. (a) When plotted on an arithmetic scale, the growth rate resembles a curve. (b) When plotted on a semilogarithmic scale (meaning the values on the y-axis are logarithmic), the growth rate appears linear.


Figure 7.8 Stages in the formation and life cycle of a biofilm. (credit: modification of work by Public Library of Science and American Society for Microbiology)


Figure 6.2 MALDI-TOF methods are now routinely used for diagnostic procedures in clinical microbiology laboratories. This technology is able to rapidly identify some microorganisms that cannot be readily identified by more traditional methods. (credit “MALDI plate photo”: modification of work by Chen Q, Liu T, Chen G; credit “graphs”: modification of work by Bailes J, Vidal L, Ivanov DA, Soloviev M)


Figure 6.3 Fatty acid methyl ester (FAME) analysis in bacterial identification results in a chromatogram unique to each bacterium. Each peak in the gas chromatogram corresponds to a particular fatty acid methyl ester and its height is proportional to the amount present in the cell. (credit “culture”: modification of work by the Centers for Disease Control and Prevention; credit “graph”: modification of work by Zhang P. and Liu P.)


Figure 5.10 Endogenous normal prion protein (PrPc) is converted into the disease-causing form (PrPsc) when it encounters this variant form of the protein. PrPsc may arise spontaneously in brain tissue, especially if a mutant form of the protein is present, or it may originate from misfolded prions consumed in food that eventually find their way into brain tissue. (credit b: modification of work by USDA)


Figure 5.11 Creutzfeldt-Jakob disease (CJD) is a fatal disease that causes degeneration of neural tissue. (a) These brain scans compare a normal brain to one with CJD. (b) Compared to a normal brain, the brain tissue of a CJD patient is full of sponge-like lesions, which result from abnormal formations of prion protein. (credit a (right): modification of work by Dr. Laughlin Dawes; credit b (top): modification of work by Suzanne Wakim; credit b (bottom): modification of work by Centers for Disease Control and Prevention)


Figure 5.7 In influenza virus infection, viral glycoproteins attach the virus to a host epithelial cell. As a result, the virus is engulfed. Viral RNA and viral proteins are made and assembled into new virions that are released by budding.


Figure 5.8 (a) Varicella-zoster, the virus that causes chickenpox, has an enveloped icosahedral capsid visible in this transmission electron micrograph. Its double-stranded DNA genome becomes incorporated in the host DNA. (b) After a period of latency, the virus can reactivate in the form of shingles, usually manifesting as a painful, localized rash on one side of the body. (credit a: modification of work by Erskine Palmer and B.G. Partin—scale-bar data from Matt Russell; credit b: modification of work by Rosmarie Voegtli)


Figure 5.9 The one-step multiplication curve for a bacteriophage population follows three steps: 1) inoculation, during which the virions attach to host cells; 2) eclipse, during which entry of the viral genome occurs; and 3) burst, when sufficient numbers of new virions are produced and emerge from the host cell. The burst size is the maximum number of virions produced per bacterium.


Figure 5.2 (a) Tobacco mosaic virus (TMV) viewed with transmission electron microscope. (b) Plants infected with tobacco mosaic disease (TMD), caused by TMV. (credit a: modification of work by USDA Agricultural Research Service—scale-bar data from Matt Russell; credit b: modification of work by USDA Forest Service, Department of Plant Pathology Archive North Carolina State University)


Figure 5.4 The size of a virus is small relative to the size of most bacterial and eukaryotic cells and their organelles.


Figure 5.5 (a) The naked atadenovirus uses spikes made of glycoproteins from its capsid to bind to host cells. (b) The enveloped human immunodeficiency virus uses spikes made of glycoproteins embedded in its envelope to bind to host cells (credit a “micrograph”: modification of work by NIAID; credit b “micrograph”: modification of work by Centers for Disease Control and Prevention)


Figure 5.6 Viral capsids can be (a) helical, (b) polyhedral, or (c) have a complex shape. (credit a “micrograph”: modification of work by USDA ARS; credit b “micrograph”: modification of work by U.S. Department of Energy)


Figure 4.14 Multicellular fungi (molds) form hyphae, which may be septate or nonseptate. Unicellular fungi (yeasts) cells form pseudohyphae from individual yeast cells.


Figure 4.15 These images show asexually produced spores. (a) This brightfield micrograph shows the release of spores from a sporangium at the end of a hypha called a sporangiophore. The organism is a Mucor sp. fungus, a mold often found indoors. (b) Sporangia grow at the ends of stalks, which appear as the white fuzz seen on this bread mold, Rhizopus stolonifer. The tips of bread mold are the dark, spore-containing sporangia. (credit a: modification of work by Centers for Disease Control and Prevention; credit b right: modification of work by “Andrew”/Flickr)


Figure 4.17 Table showing the groups of fungi of particular importance for human health. (Credit “Ascomycota”: modification of work by Dr. Lucille Georg, Centers for Disease Control and Prevention; credit “Microsporidia”: modification of work by Centers for Disease Control and Prevention)


Figure 4.16 (a) This brightfield micrograph shows ascospores being released from asci in the fungus Talaromyces flavus var. flavus. (b) This electron micrograph shows the conidia (spores) borne on the conidiophore of Aspergillus, a type of toxic fungus found mostly in soil and plants. (c) This brightfield micrograph shows the yeast Candida albicans, the causative agent of candidiasis and thrush. (credit a, b, c: modification of work by Centers for Disease Control and Prevention)


Figure 4.11 A micrograph of the nematode Enterobius vermicularis, also known as the pinworm. (credit: modification of work by Centers for Disease Control and Prevention)


Figure 4.12 (a) The oral sucker is visible on the anterior end of this liver fluke, Opisthorchis viverrini. (b) This micrograph shows the scolex of the cestode Taenia solium, also known as the pork tapeworm. The visible suckers and hooks allow the worm to attach itself to the inner wall of the intestine. (credit a: modification of work by Sripa B, Kaewkes S, Sithithaworn P, Mairiang E, Laha T, and Smout M; credit b: modification of work by Centers for Disease Control and Prevention)


Figure 4.3 (a) Paramecium spp. have hair-like appendages called cilia for locomotion. (b) Amoeba spp. use lobe- like pseudopodia to anchor the cell to a solid surface and pull forward. (c) Euglena spp. use a whip-like structure called a flagellum to propel the cell.


Figure 4.4 This tree shows a proposed classification of the domain Eukarya based on evolutionary relationships. Currently, the domain Eukarya is divided into six supergroups. Within each supergroup are multiple kingdoms. Dotted lines indicate suggested evolutionary relationships that remain under debate. The subgroups with members of clinical relevance have a start next to them.


Figure 4.7 (a) Apicomplexans are parasitic protists. They have a characteristic apical complex that enables them to infect host cells. (b) A colorized electron microscope image of a Plasmodium sporozoite. (credit b: modification of work by Ute Frevert)


Figure 4.8 This specimen of the ciliate Balantidium coli is a trophozoite form isolated from the gut of a primate. B. coli is the only ciliate capable of parasitizing humans. (credit: modification of work by Kouassi RYW, McGraw SW, Yao PK, Abou-Bacar A, Brunet J, Pesson B, Bonfoh B, N’goran EK & Candolfi E)


Figure 4.10 (a) This illustration of a Euglena shows the characteristic structures, such as the stigma and flagellum. (b) The pellicle, under the cell membrane, gives the cell its distinctive shape and is visible in this image as delicate parallel striations over the surface of the entire cell (especially visible over the grey contractile vacuole). (credit a: modification of work by Claudio Miklos; credit b: modification of work by David Shykind)


Figure 1.11 Common bacterial shapes. Note how coccobacillus is a combination of spherical (coccus) and rod- shaped (bacillus). (credit “Coccus”: modification of work by Janice Haney Carr, Centers for Disease Control and Prevention; credit “Coccobacillus”: modification of work by Janice Carr, Centers for Disease Control and Prevention; credit “Spirochete”: Centers for Disease Control and Prevention)


Figure 1.12 Some archaea live in extreme environments, such as the Morning Glory pool, a hot spring in Yellowstone National Park. The color differences in the pool result from the different communities of microbes that are able to thrive at various water temperatures.


Figure 1.13 Assorted diatoms, a kind of algae, live in annual sea ice in McMurdo Sound, Antarctica. Diatoms range in size from 2 μm to 200 μm and are visualized here using light microscopy. (credit: modification of work by National Oceanic and Atmospheric Administration)


Figure 1.15 Candida albicans is a unicellular fungus, or yeast. It is the causative agent of vaginal yeast infections as well as oral thrush, a yeast infection of the mouth that commonly afflicts infants. C. albicans has a morphology similar to that of coccus bacteria; however, yeast is a eukaryotic organism (note the nuclei) and is much larger. (credit: modification of work by Centers for Disease Control and Prevention)


Figure 1.16 Large colonies of microscopic fungi can often be observed with the naked eye, as seen on the surface of these moldy oranges.


Figure 1.17 (a) The beef tapeworm, Taenia saginata, infects both cattle and humans. T. saginata eggs are microscopic (around 50 µm), but adult worms like the one shown here can reach 4–10 m, taking up residence in the digestive system. (b) An adult guinea worm, Dracunculus medinensis, is removed through a lesion in the patient’s skin by winding it around a matchstick. (credit a, b: modification of work by Centers for Disease Control and Prevention)


Figure 1.18 (a) Members of the Coronavirus family can cause respiratory infections like the common cold, severe acute respiratory syndrome (SARS), and Middle East respiratory syndrome (MERS). Here they are viewed under a transmission electron microscope (TEM). (b) Ebolavirus, a member of the Filovirus family, as visualized using a TEM. (credit a: modification of work by Centers for Disease Control and Prevention; credit b: modification of work by Thomas W. Geisbert)


Figure 1.6 Swedish botanist, zoologist, and physician Carolus Linnaeus developed a new system for categorizing plants and animals. In this 1853 portrait by Hendrik Hollander, Linnaeus is holding a twinflower, named Linnaea borealis in his honor.


Figure 1.7 Ernst Haeckel’s rendering of the tree of life, from his 1866 book General Morphology of Organisms, contained three kingdoms: Plantae, Protista, and Animalia. He later added a fourth kingdom, Monera, for unicellular organisms lacking a nucleus.


Figure 1.8 This timeline shows how the shape of the tree of life has changed over the centuries. Even today, the taxonomy of living organisms is continually being reevaluated and refined with advances in technology.


Figure 1.9 Woese and Fox’s phylogenetic tree contains three domains: Bacteria, Archaea, and Eukarya. Domains Archaea and Bacteria contain all prokaryotic organisms, and Eukarya contains all eukaryotic organisms. (credit: modification of work by Eric Gaba)


Figure 1.2 A microscopic view of Saccharomyces cerevisiae, the yeast responsible for making bread rise (left). Yeast is a microorganism. Its cells metabolize the carbohydrates in flour (middle) and produce carbon dioxide, which causes the bread to rise (right). (credit middle: modification of work by Janus Sandsgaard; credit right: modification of work by “MDreibelbis”/Flickr)


Figure 1.3 (a) The Cloaca Maxima, or “Greatest Sewer” (shown in red), ran through ancient Rome. It was an engineering marvel that carried waste away from the city and into the river Tiber. (b) These ancient latrines emptied into the Cloaca Maxima.


Figure 1.4 (a) Hippocrates, the “father of Western medicine,” believed that diseases had natural, not supernatural, causes. (b) The historian Thucydides observed that survivors of the Athenian plague were subsequently immune to the infection. (c) Marcus Terentius Varro proposed that disease could be caused by “certain minute creatures . . . which cannot be seen by the eye.” (credit c: modification of work by Alessandro Antonelli)


Figure 1.5 (a) Louis Pasteur (1822–1895) is credited with numerous innovations that advanced the fields of microbiology and immunology. (b) Robert Koch (1843–1910) identified the specific microbes that cause anthrax, cholera, and tuberculosis.


Figure 2.10 A typical prokaryotic cell contains a cell membrane, chromosomal DNA that is concentrated in a nucleoid, ribosomes, and a cell wall. Some prokaryotic cells may also possess flagella, pili, fimbriae, and capsules.


Figure 2.11 (credit “Coccus” micrograph: modification of work by Janice Haney Carr, Centers for Disease Control and Prevention; credit “Coccobacillus” micrograph: modification of work by Janice Carr, Centers for Disease Control and Prevention; credit “Spirochete” micrograph: modification of work by Centers for Disease Control and Prevention.


Figure 2.12 The nucleoid region (the area enclosed by the green dashed line) is a condensed area of DNA found within prokaryotic cells. Because of the density of the area, it does not readily stain and appears lighter in color when viewed with a transmission electron microscope.


Figure 2.13 Prokaryotic ribosomes (70S) are composed of two subunits: the 30S (small subunit) and the 50S (large subunit), each of which are composed of protein and rRNA components.


Figure 2.14 (a) Sporulation begins following asymmetric cell division. The forespore becomes surrounded by a double layer of membrane, a cortex, and a protein spore coat, before being released as a mature endospore upon disintegration of the mother cell. (b) An electron micrograph of a Carboxydothermus hydrogenoformans endospore. These Bacillus spp. cells are undergoing sporulation. The endospores have been visualized using Malachite Green spore stain. (credit b: modification of work by Jonathan Eisen)


Figure 2.15 The bacterial plasma membrane is a phospholipid bilayer with a variety of embedded proteins that perform various functions for the cell. Note the presence of glycoproteins and glycolipids, whose carbohydrate components extend out from the surface of the cell. The abundance and arrangement of these proteins and lipids can vary greatly between species.


Figure 2.16 Peptidoglycan is composed of polymers of alternating NAM and NAG subunits, which are cross-linked by peptide bridges linking NAM subunits from various glycan chains. This provides the cell wall with tensile strength in two dimensions.


Figure 2.17 Bacteria contain two common cell wall structural types. Gram-positive cell walls are structurally simple, containing a thick layer of peptidoglycan with embedded teichoic acid external to the plasma membrane.[footnote]B. Zuber et al. “Granular Layer in the Periplasmic Space of Gram-Positive Bacteria and Fine Structures of Enterococcus gallinarum and Streptococcus gordonii Septa Revealed by Cryo-Electron Microscopy of Vitreous Sections.” Journal of Bacteriology 188 no. 18 (2006):6652–6660[/footnote] Gram- negative cell walls are structurally more complex, containing three layers: the inner membrane, a thin layer of peptidoglycan, and an outer membrane containing lipopolysaccharide. (credit: modification of work by “Franciscosp2”/Wikimedia Commons)


Figure 2.19 (a) Capsules are a type of glycocalyx composed of an organized layer of polysaccharides. (b) A capsule stain of Pseudomonas aeruginosa, a bacterial pathogen capable of causing many different types of infections in humans. (credit b: modification of work by American Society for Microbiology)


Figure 2.20 Bacteria may produce two different types of protein appendages that aid in surface attachment. Fimbriae typically are more numerous and shorter, whereas pili (shown here) are longer and less numerous per cell. (credit: modification of work by American Society for Microbiology)


Figure 2.21 The basic structure of a bacterial flagellum consists of a basal body, hook, and filament. The basal body composition and arrangement differ between gram-positive and gram-negative bacteria. (credit: modification of work by “LadyofHats”/Mariana Ruiz Villareal)


Figure 2.5 Robert Hooke (1635–1703) was the first to describe cells based upon his microscopic observations of cork. This illustration was published in his work Micrographia.


Figure 2.6 According to the endosymbiotic theory, mitochondria and chloroplasts are each derived from the uptake of bacteria. These bacteria established a symbiotic relationship with their host cell that eventually led to the bacteria evolving into mitochondria and chloroplasts.


Figure 2.7 Ignaz Semmelweis (1818–1865) was a proponent of the importance of handwashing to prevent transfer of disease between patients by physicians.


Figure 2.4 (a) French scientist Louis Pasteur, who definitively refuted the long-disputed theory of spontaneous generation. (b) The unique swan-neck feature of the flasks used in Pasteur ’s experiment allowed air to enter the flask but prevented the entry of bacterial and fungal spores. (c) Pasteur’s experiment consisted of two parts. In the first part, the broth in the flask was boiled to sterilize it. When this broth was cooled, it remained free of contamination. In the second part of the experiment, the flask was boiled and then the neck was broken off. The broth in this flask became contaminated. (credit b: modification of work by “Wellcome Images”/Wikimedia Commons)


Figure 2.8 (a) Joseph Lister developed procedures for the proper care of surgical wounds and the sterilization of surgical equipment. (b) Robert Koch established a protocol to determine the cause of infectious disease. Both scientists contributed significantly to the acceptance of the germ theory of disease.


Figure 2.2 Francesco Redi’s experimental setup consisted of an open container, a container sealed with a cork top, and a container covered in mesh that let in air but not flies. Maggots only appeared on the meat in the open container. However, maggots were also found on the gauze of the gauze-covered container.


Figure 2.3 (a) Francesco Redi, who demonstrated that maggots were the offspring of flies, not products of spontaneous generation. (b) John Needham, who argued that microbes arose spontaneously in broth from a “life force.” (c) Lazzaro Spallanzani, whose experiments with broth aimed to disprove those of Needham.


Figure 3.2 (a) Some prokaryotes, called halophiles, can thrive in extremely salty environments such as the Dead Sea, pictured here. (b) The archaeon Halobacterium salinarum, shown here in an electron micrograph, is a halophile that lives in the Dead Sea. (credit a: modification of work by Jullen Menichini; credit b: modification of work by NASA)


Figure 3.3 (a) Nitrogen-fixing bacteria such as Rhizobium live in the root nodules of legumes such as clover. (b) This micrograph of the root nodule shows bacteroids (bacterium-like cells or modified bacterial cells) within the plant cells. The bacteroids are visible as darker ovals within the larger plant cell. (credit a: modification of work by USDA)


DD-transpeptidase catalytic mechanism


The structural similarity between (A)  D -Ala- D -Ala terminus of peptidoglycan terminus and (B) penicillins. Transpeptidases misrecognize penicillins for the TPase catalytic reaction.


Bacillus subtilis  mass-swarming outwards on a gel substrate from the mother colony visible at the top middle


A Gram stain of the quorum-sensing  Streptococcus pneumoniae . The dark purple signifies gram-positive bacteria.


When  Anthony Fauci  became director of the  NIAID , he drew a map of the world for presentation at a congressional hearing that showed a single notable emerging infectious disease threat: HIV. Since then, he has continually updated the map, now showing the emergence of numerous infectious disease threats to illustrate the experiences of his years in office as well as highlighting certain infections that had emerged before HIV. [ 1 ]


Throughout the 20th century until 1980, with the exception of the 1918 Spanish flu pandemic, the death rate from infectious diseases in the United States was steadily decreasing.  However, because of the AIDS epidemic, the death rate from infectious diseases increased by 58% between 1980 and 1992.


A representation of the  endosymbiotic theory


An overview of the endosymbiosis theory of eukaryote origin (symbiogenesis).


Diagram of cospeciation, where parasites or endosymbionts speciate or branch alongside their hosts. This process is more common in hosts with primary endosymbionts.


Pea aphids are commonly infested by parasitic wasps. Their secondary endosymbionts attack the infesting parasitoid wasp larvae promoting the survival of both the aphid host and its endosymbionts.


Population numbers as a function of Hamming distance  d  and mutation rate (1-Q). The horizontal axis  d   is the Hamming distance of the molecular sequences from the master sequence. The vertical axis is the logarithm of population for any sequence at that distance divided by total population (thus the division of  n d  by the binomial coefficient). The total number of digits per sequence is L=100, and the master sequence has a selective advantage of a=1.05.


The population of the master sequence as a fraction of the total population ( n ) as a function of overall mutation rate (1-Q). The total number of digits per sequence is L=100, and the master sequence has a selective advantage of a=1.05. The "phase transition" is seen to occur at roughly 1-Q=0.05.


Comparison of typical phage (bacteriophage) infection and transduction ( A ) with typical GTA (gene transfer agent) production and transduction ( B ).


Methods for detecting gene transfer agents.  ( A ) Method used by Marrs in 1974.  ( B ) Cell-free extract method.


Typical prophage and GTA gene clusters.


Schematic diagram of phylogenetic relationships between known bacterial gene transfer agents.


The evolutionary forces that act on bacterial gene transfer agent and the cells that produce it.


Typical steps in the production of bacterial gene transfer agents. ( 1 ) Transcription and translation of the GTA genes. ( 2 ) Assembly of GTA structural proteins into empty heads and unattached tails. ( 3 ) Packaging of 'headful' segments of DNA into heads and attachment of tails. ( 4 ) Lysis of the cell.


Genetic transduction by bacterial gene transfer agents. ( 1 ) GTA particles encounter a suitable recipient cell.  ( 2 ) Particles attach to cell and inject their DNA, and cellular proteins translocate the DNA across the inner membrane. ( 3 ) DNA is degraded if it cannot recombine with the recipient genome. ( 4 ) DNA with similar sequences to the recipient genome undergoes recombination.


Regulation diagram for RcGTA, the Rhodobacter capsulatus gene transfer agent


Tree of life showing vertical and horizontal gene transfers


A speciation event produces  orthologs  of a gene in the two daughter species. A horizontal gene transfer event from one species to another adds a  xenolog  of the gene to the receiving genome.


1: Donor bacterium   2: Bacterium who will receive the gene   3: The red portion represents the gene that will be transferred.   Transformation in bacteria happens in a certain environment.


1: Donor bacterium cell (F+ cell)   2: Bacterium that receives the plasmid (F- cell)   3: Plasmid that will be moved to the other bacterium   4: Pilus and T4SS.   Conjugation in bacteria using a sex pilus; then the bacterium that received the plasmid can go give it to other bacteria as well.


E. coli  cells going through conjugation and sharing genetic information. F-pilus is reaching towards other cell.


Before it is transformed, a bacterium is susceptible to antibiotics. A plasmid can be inserted when the bacteria is under stress, and be incorporated into the bacterial DNA creating antibiotic resistance. When the plasmids are prepared they are inserted into the bacterial cell by either making pores in the plasma membrane with temperature extremes and chemical treatments, or making it semi permeable through the process of  electrophoresis , in which electric currents create the holes in the membrane. After conditions return to normal the holes in the membrane close and the  plasmids  are trapped inside the bacteria where they become part of the genetic material and their genes are expressed by the bacteria.


Oil in the sea.


Divergent Pathways for the Aerobic Degradation of Toluene [ 10 ]


Anaerobic Degradation of Toluene [ 10 ]


Involvement of biosurfactant (rhamnolipid) produced by  Pseudomonas sp  in the uptake of hydrocarbons. [ 18 ]


Overview of the biotic section of the global carbon cycle principally related to the metabolism of hydrocarbons.


The great plate count anomaly. Counts of cells obtained via cultivation are orders of magnitude lower than those directly observed under the microscope. This is because microbiologists are able to cultivate only a minority of naturally occurring microbes using current laboratory techniques, depending on the environment. [ 1 ]


Louis Pasteur


Quorum sensing of gram-negative cell


Gram-positive bacteria quorum sensing


Extent of sea ice coverage throughout the year over Arctic and Antarctic.


Frost flowers growing on sea ice in the Arctic.


The microbial loop is a marine trophic pathway in which microbes re-incorporate dissolved organic carbon into the food chain and remineralize nutrients.


Time-line of  paleoviruses  in the human lineage [ 17 ]


Phylogenetic tree showing the relationships of  morbilliviruses  of different species [ 23 ]


The equations are the mathematical expression of the major concepts implied by quasispecies theory. The first equation describes the change of concentration of molecule i as a function of replication parameters, and its production from other molecules of the same ensemble. The second equation is the error threshold relationship, indicating the maximum amount of information (ʋ max ) and the maximum average error rate p max  (p = 1- q; q is the copying fidelity) for maintenance of genetic information. Terms are defined in the box on the right. Below, an evolving mutant spectrum (with mutations represented as symbols on the genomes), with an invariant consensus sequence. [ 9 ]  Adapted from. [ 10 ]


Flow of conceptual derivations of quasispecies theory for viral populations, and some biological consequences.


Upon isolation from an infected host (middle boxes), a virus sample may be adapted to cultured cells and subjected to large population or  bottleneck transfers  (left box), or be adapted to a different host  in vivo  (right box). Relevant adaptive mutations are highlighted with colored symbols.


Illustration of bottleneck of different severity, defined by the different circles inserted in the entire population (large rectangle) and the outer rectangles. Symbols represent mutant classes.


This visualization of "survival of the flattest" in evolutionary biology. [ 118 ]


The  coccolithophore   Gephyrocapsa oceanica  may become an important  carbon sink  as  the acidity of the ocean increases . [ 1 ]


Two scientists prepare samples of soil mixed with oil to test a microbe's ability to clean up contaminated soil.


Paleoarchean  (3.35-3.46 billion years old) stromatolite from Western Australia.


The colors of  Grand Prismatic Spring  in  Yellowstone National Park  are due to mats of  thermophilic   bacteria . [ 26 ]


Blood Falls, 2006


Blood Falls, at the toe of  Taylor Glacier ,  2013


A schematic cross-section of Blood Falls showing how subglacial microbial communities have survived in cold, darkness, and absence of oxygen for a million years in brine water below  Taylor Glacier .


Environments in which subsurface life has been found [ 1 ]


Photograph of the sunken  Alvin  taken in 1969


Schematic of an expedition aboard the Japanese drilling ship  D/V  Chikyū [ 1 ]


Researcher sampling fluid from a deep mine [ 1 ]


The PUSH50 device keeps deep-sea samples at high pressure. [ 1 ]


Schematic of the  Sumatra Trench  and the associated  island arcs  and  back-arc regions


The purplish rod-shaped cells, a few microns long, are " Candidatus  Desulforudis audaxviator ". [ 1 ]


The bright colors of  Grand Prismatic Spring  and  Yellowstone National Park , are produced by  thermophiles , a type of extremophile.


Diversity of extreme environments on Earth   [ 4 ]


Microscopic image from the hypersaline  Lake Tyrrell  (salinity> 20% w/v), in which the eukaryotic  chlorophyte ,  Dunaliella salina , can be tentatively identified.  Dunaliella salina  is grown commercially for the carotenoid,  β-carotene , which is widely used as a natural food colorant as well as a precursor to vitamin A. Alongside is the haloarchaeon,  Haloquadratum walsbyi , which has flat square-shaped cells with gas vesicles that allow flotation to the surface, most likely to acquire oxygen.


This is a before and after picture of a cleanup project of the  Little Conemaugh River [ 55 ]


Magnified cells of bacterium GFAJ-1 grown in medium containing arsenate


Wolfe-Simon at Mono Lake, 2010


Tufa  formations along the shore of  Mono Lake


Scanning electron micrograph  of GFAJ-1 cells grown in defined minimal medium supplemented with 1.5 mM phosphate


Structure of poly-β-hydroxybutyrate


Structures found on meteorite fragment  Allan Hills 84001


Desulfovibrio vulgaris  is the best-studied sulfate-reducing microorganism species; the bar in the upper right is 0.5  micrometre  long.


Sludge from a pond; the black color is due to metal sulfides that result from the action of sulfate-reducing microorganisms.


Overview of the three key enzymatic steps of the dissimilatory sulfate reduction pathway. Enzymes:  sat  and  atps  respectively stand for sulfate adenylyltransferase and ATP sulfurylase (EC 2.7.7.4);  apr  and  aps  are both used to adenosine-5'-phosphosulfate reductase (EC 1.8.4.8); and  dsr  is the dissimilatory (bi)sulfite reductase (EC 1.8.99.5);


Contamination on an agar plate


96 pinner used to perform spot assays with yeast, fungal or bacterial cells


An agar plate being viewed in an electronic  colony counter


Example of a workup algorithm of possible bacterial infection in cases with no specifically requested targets (non-bacteria, mycobacteria etc.), with most common situations and agents seen in a New England community hospital setting. Different agar plates are used for different specimen sources, as seen in the upper left quadrant.


Red blood cells  on an agar plate are used to diagnose  infection . On the left is a positive  Staphylococcus  infection, on the right a positive  Streptococcus  culture.


Hemolyses of  Streptococcus  spp.  (left) α-hemolysis ( S. mitis ); (middle) β-hemolysis ( S. pyogenes ); (right) γ-hemolysis (= nonhemolytic,  S. salivarius )


Four types of agar plate demonstrating differential growth depending on bacterial  metabolism


the yeast  Candida albicans  growing both as yeast cells and  filamentous cells  on YPD agar


A bacterial lawn used in antibiotic resistance testing.


Staphylococcus aureus  biofilm on an indwelling  catheter


Probable  cyanobacteria  in the vertical section of a silicified biofilm from the Lower Cretaceous. Very shallow hypersaline environment of the  Urgonian   carbonate platform  of Provence, south eastern France.


Biofilm of golden  hydrophobic   bacteria ; ceiling of Golden Dome Cave, a  lava tube  in  Lava Beds National Monument [ 20 ]


Mature biofilm structure   [ 25 ]  Biofilm is characterised by heterogenous environment and the presence of a variety of subpopulations. A biofilm structure is composed of metabolically active (both resistant and tolerant) and non-active cells (viable but not culturable cells and persisters) as well as polymer matrix consisting of polysaccharide, extracellular DNA and proteins. Biofilm growth is associated with an escalated level of mutations and  horizontal gene transfer  which is promoted in due to the packed and dense structure. Bacteria in biofilms communicate by  quorum sensing , which activates genes participating in virulence factors production. [ 25 ] [ 26 ]


Five stages of biofilm development   [ 28 ]  (1) Initial attachment, (2) Irreversible attachment, (3) Maturation I, (4) Maturation II, and (5) Dispersion. Each stage of development in the diagram is paired with a  photomicrograph  of a developing  P. aeruginosa  biofilm. All photomicrographs are shown to the same scale.


Biofilm dispersal


Scanning electron micrograph of mixed-culture biofilm, demonstrating in detail a spatially heterogeneous arrangement of bacterial cells and extracellular polymeric substances.


Mats of bacterial biofilm color the hot springs in  Yellowstone National Park . The longest raised mat area is about half a meter long.


Thermophilic bacteria in the outflow of  Mickey Hot Springs ,  Oregon , approximately 20 mm thick.


A biofilm from the  Dead Sea


Transmission electron micrograph showing bacteria Escherichia coli that form extensive biofilms using a network of conjugative F-pili. Source: Jonasz Patkowski


Aeromonas veronii  biovar  sobria   Gram stain  on microscope slide


Colonial morphology of various specimens of  Pseudomonas aeruginosa , including mucoid types


Some terms used to describe colonial morphology


A colony of  Brandt's cormorants  in  Point Lobos , California


A breeding colony of  northern gannets  on the  Heligoland  archipelago in the  North Sea .


The pelagic  Marrus orthocanna  is a colonial  siphonophore  assembled from two types of  zooids


A dilution made with bacteria and  peptoned  water is placed in an  Agar plate  ( Agar plate count  for food samples or  Trypticase soy agar  for clinic samples) and spread over the plate by tipping in the pattern shown.


A solution of bacteria at an unknown concentration is often  serially diluted  in order to obtain at least one plate with a countable number of bacteria. In this figure, the "x10" plate is suitable for counting.


The traditional way of enumerating CFUs with a "click-counter" and a pen. When the colonies are too numerous, it is common practice to count CFUs only on a fraction of the dish.


An automated colony counter using image processing.


Figure 1. Alternative Electron Transport Chain to move electrons to outer membrane of  Geobacter Sulfurreducens .


Figure 2. Proposed methods of exoelectrogen electron transport: Direct Transfer, Transfer through Electron Shuttle, Transfer through Conductive Biofilm, Transfer through Conductive Pili.


Extracellular polymeric substance matrix formation in a  biofilm


Succinoglycan from  Sinorhizobium meliloti


Two strains of  Zoogloea resiniphila . The tube on the left shows typical floc formations in an otherwise clear culture of a bacterium,  Zoogloea resiniphila , isolated from an activated sludge wastewater treatment reactor. In the tube on the right, planktonic growth by a floc-impaired mutant results in a turbid appearance.


Photomicrograph of the microflora Streptococcus pyogenes bacteria, 900x mag.


Hemolyses of  Streptococcus  spp. (left) α-hemolysis ( S. mitis ); (middle) β-hemolysis ( S. pyogenes ); (right) γ-hemolysis (non-hemolytic,  S. salivarius )


The aquatic microbial loop is a marine trophic pathway which incorporates  dissolved organic carbon  into the food chain.


Soil carbon cycle through the microbial loop   [ 10 ]


Microbial cultures on solid and liquid media


A culture of  Bacillus anthracis


Liquid cultures of the  cyanobacterium   Synechococcus  PCC 7002


Example of a workup algorithm of possible bacterial infection in cases with no specifically requested targets (non-bacteria, mycobacteria etc.), with most common situations and agents seen in a New England setting. The grey box near top left shows a  Venn diagram  of what culture media are routinely used for various sources or purposes.


Motile and non-motile bacteria can be differentiated along the stab lines. Motile bacteria (left) will grow out from the stab line while non-motile bacteria (right) are present only along the stab line.


Broth dilution assay. The MIC is determined by examining tubes containing the microbe and a  dilution series  of antimicrobial agent for turbidity.


Etest. After the required incubation period, when an even lawn of growth is distinctly visible, the MIC value is read where the pointed end of the inhibition ellipse intersects the side of the strip.


E. Coli/Coliform Petrifilms


Plastic spreader


EC Petrifilm which has tested positive for coliforms


Individual coliform colony from previous picture


The plant aerial surface, mostly occupied by leaves, is inhabited by diverse microorganisms, forming the phyllosphere


A leaf from a healthy  Arabidopsis  plant (left) and a leaf from a dysbiosis mutant plant (right) [ 33 ]


{A} The  heatmap  on the left illustrates how the composition of  operational taxonomic units  (OTUs) in the manuka phyllosphere and associated soil communities differed significantly. No core soil microbiome was detected. (B) The chart on the right shows how OTUs in phyllosphere and associated soil communities differed in relative abundances. [ 11 ]


Depiction of the human body and bacteria that predominate


Scanning electron microscope  image of  Staphylococcus epidermidis  one of roughly a thousand  bacteria  species present on  human skin . Though usually not  pathogenic , it can cause  skin infections  and even life-threatening illnesses in those that are  immunocompromised .


Ecology of the 20 sites on the skin studied in the Human Microbiome Project


Social motility of  African trypanosomiasis


Swarming motility of  Pseudomonas aeruginosa .


The Wistar rat, which was the first developed rat model strain


Line of T175 cell culture flasks containing red cell culture medium


Airing  futons  (of both the quilt and mattress variety) in Japan. Note  specialized railing clips


Figure 1: Wenzel model


Figure 2: Schematic of grafting density.


Figure 3: Biocide release over time


Overview of cycle between autotrophs and  heterotrophs .  Photosynthesis  is the main means by which plants, algae and many bacteria produce organic compounds and oxygen from carbon dioxide and water ( green arrow ).


Flowchart to determine if a species is autotroph, heterotroph, or a subtype


Green fronds of a  maidenhair fern , a photoautotroph


Foton-12 capsule on display


Experiment BIOPAN-5 part of the Foton-M2 mission


A  black smoker  vent in the  Atlantic Ocean , providing energy and nutrients for chemotrophs


Earthworms  are soil-dwelling detritivores.


Two  Adonis blue  butterflies lap at a small lump of feces lying on a rock.


Fungi are the primary  decomposers  in most environments, illustrated here  Mycena interrupta . Only fungi produce the enzymes necessary to decompose  lignin , a chemically complex substance found in wood.


A decaying tree trunk in Canada's  boreal forest . Decaying wood fills an important ecological niche, providing habitat and shelter, and returning important nutrients to the soil after undergoing decomposition.


Detritivore nutrient cycling model


Transmission electron microscope image of a cross section through a soybean ( Glycine max )  root nodule . The nitrogen fixing bacteria, and fungi  Bradyrhizobium japonicum , infects the roots and establishes a symbiosis. This high magnification image shows part of a cell with single bacteroid (bacterium-like cell or modified bacterial cell) within their  symbiosomes . In this image, you can also see  endoplasmic reticulum ,  Golgi apparatus  and cell wall.


Plant-endophytic bacteria interactions   [ 6 ]  Abbreviations: polyhydroxyalkanoates (PHA), volatile organic compounds (VOC), reactive oxygen species (ROS), reactive nitrogen species (RNS), type III secretion system (T3SS), type VI secretion system (T6SS), hemagglutinins (HA), small RNAs (sRNAs), copper-micro RNAs (Cu-miRNAs), lipopolysaccharide (LPS), arabinogalactan proteins (AGPs), microbe-associated molecular patterns (MAMPs), jasmonic acid (JA), ethylene (ET), salicylic acid (SA). The arrows pointing upwards indicate an increase, while the ones pointing downwards indicate a decrease in the expression levels.


Location of the astrobiology EXPOSE-E and EXPOSE-R facilities on the  International Space Station


Colonies of  Bacillus subtilis  grown on a culture dish in a  molecular biology  laboratory.


Ultraviolet radiation harm the  DNA  molecules of living organisms in different ways. In one common damage event, adjacent  thymine  bases bond with each other, instead of across the "ladder". This " thymine dimer " makes a bulge, and the distorted DNA molecule does not function properly.


Acarospora


Tobacco seeds ( Nicotiana tabacum )


Types of  ionizing radiation  - gamma rays are represented by wavy lines, charged particles and neutrons by straight lines. The small circles show where ionization processes occur.


Chemical structure of 2'-fucosyllactose consisting of lactose and fucose subunits


The different types of organisms involved in biological weathering of the Earth's crust and a timescale for their evolution. [ 2 ]


Anaerobic  bacteria  can be identified by growing them in test tubes of  thioglycollate broth :   1:  Obligate aerobes  need oxygen because they cannot ferment or respire anaerobically. They gather at the top of the tube where the oxygen concentration is highest.   2:  Obligate anaerobes  are poisoned by oxygen, so they gather at the bottom of the tube where the oxygen concentration is lowest.   3:  Facultative anaerobes  can grow with or without oxygen because they can metabolise energy aerobically or anaerobically. They gather mostly at the top because aerobic respiration generates more ATP than either fermentation or anaerobic respiration.   4:  Microaerophiles  need oxygen because they cannot ferment or respire anaerobically. However, they are poisoned by high concentrations of oxygen. They gather in the upper part of the test tube but not the very top.   5:  Aerotolerant organisms  do not require oxygen as they metabolise energy anaerobically. Unlike obligate anaerobes however, they are not poisoned by oxygen. They can be found evenly spread throughout the test tube.


Fungi are a major group of osmotrophic organisms since Fungi degrade biomass.


Photoheterotrophs are ubiquitous in marine ecosystems. Notably, bacteria and archaea may use proteorhodopsin as a supplementary, light-driven energy source.


Flowchart to determine if a species is  autotroph ,  heterotroph , or a subtype


Terrestrial and aquatic phototrophs: plants grow on a fallen log floating in algae-rich water


Flowchart to determine if a species is autotroph,  heterotroph , or a subtype


The  lichen   Xanthoria elegans  can continue to  photosynthesize  at −24 °C. [ 1 ]


Snow surface with  snow algae   Chlamydomonas nivalis .


Psychrophilic  algae  can tolerate cold temperatures, like this  Chlamydomonas  green algae growing on snow in  Antarctica .


Antarctic  diatom  algae covering the underwater surface of broken  sea ice  in the  Ross Sea .


The wingless midge ( Chironomidae )  Belgica antarctica .


Many microbial rhodopsins, such as this  bacteriorhodopsin , are ion pumps that convert light to chemical energy.


A  cluster  of  Escherichia coli   bacteria  magnified 10,000 times


Mahavira  postulated the existence of microscopic creatures in the  6th century BC .


The mausoleum of  Akshamsaddin , who mentioned microorganisms in his book Maddat ul-Hayat in the 15th century, in Bolu, Turkiye.


Antonie van Leeuwenhoek  was the first to study microscopic organisms.


Lazzaro Spallanzani  showed that boiling a broth stopped it from decaying.


Louis Pasteur  showed that Spallanzani's findings held even if air could enter through a filter that kept particles out.


Robert Koch  showed that microorganisms caused  disease .


Carl Woese 's 1990  phylogenetic tree  based on  rRNA  data shows the domains of  Bacteria ,  Archaea , and  Eukaryota . All are microorganisms except some eukaryote groups.