Interactions and Functions of Microorganisms

TABLE OF CONTENTS III. Microbial Diversity and its I. Introduction to Diversity Applications A. Estimates of Biodiversity A. Industry B. Classification of Microbes B. Microbial Geotechnology C. Divisions of Microbiology C. Production of Bacterial D. History of Microbiology Polymers E. Importance of Microbes D. Other Applications II. Classification of Microbes E. Bioprospecting A. Bacteria IV. References B. Fungi V. Appendix C. Protists I. INTRODUCTION TO DIVERSITY A. ESTIMATES OF BIODIVERSITY Table 1. Number of described species from the different kingdoms Kingdom/Major Division Number of Described Species 1,000 4,760 Viruses Monera (Bacteria, Mycoplasma, Cyanophycota) Fungi (Zygomycota, Ascomycota, etc.) 46,983 Algae 26,900 Plantae 248,428 Protozoa 30,800 Animalia (including Arthropoda) 989,761 Chordata (Tunicata, Vertebrata, etc.) 43,852 TOTAL 1,392,485 ● There are currently more than 1 million number of described species across all kingdoms /divisions → Animalia sports the highest number of species ▪ Including Arthropoda (insects) → Estimates of total microbial biodiversity range from 5-30 million species B. CLASSIFICATION OF MICROBES ● There are three domains: → Eubacteria ▪ Have a prokaryotic cell structure → Archaebacteria ▪ Prokaryotes → Eukaryotes ▪ Four kingdoms − Plants, animals, fungi, protists ● ● ● ● ● Molecular Biology → Newer subdivision ● Microbial Ecology ● Applied Microbiology → Deals with microbes which can be helpful in some instances like: ▪ Water treatment ▪ Natural products ▪ Food microbiology ▪ Environmental microbiology D. HISTORY OF MICROBIOLOGY Ancient Knowledge ● Recognition of Immunity → Variolation and protection from infection ▪ Intentional contact with minor form of smallpox → The Myth of the MIlkmaid ▪ Story of Edward Jenner and the milkmaids ▪ Milkmaids who’ve had cowpox seem immune to smallpox. ▪ From here, we get the idea of immunization or vaccination. ● Contagion → Disease can be spread by contact → During the Black Death ▪ A lot of mortality secondary to bubonic plague → Led to exclusion of lepers, burning of plague victims → Catapulting of disease victims into castles during siege ▪ Was done by invading armies to spread disease inside the impenetrable walls of castles in order for the besieged to surrender. History Continued ● Microbiology as a biological science ● Robert Hooke → Discovery of cells, 1665 ● Antony van Leeuwenhoek → Father of Microbiology → Dutch amateur lens grinder → First person to see microbes, late 1600s ● Mid 1800s, microbes were taken more seriously and studied using the scientific method What are microbiologists interested in? Eubacteria and archaebacteria Eukaryotes like fungi and protists Animals like arthropods Viruses C. DIVISIONS OF MICROBIOLOGY By Critter Type ● Bacteriology → Bacteria alone ▪ Gram (+) and Gram (-) ● Virology → Viruses like SARS-CoV-2 ● Mycology → Study of Fungi ● Parasitology → Protozoans (e.g. etiologic agents of malaria, amoeba) → Worms (e.g. helminths) Other Divisions ● Pathogenic Microbiology → Branch of microbiology that studies diseases caused by microbes ● Immunology → Related to microbiology as the immune system is part of this study Figure 1. Von Leeuwenhoek Microscope (circa late 1600s). Retrieved from Roxas, 2022. The Golden Age ● From 1850 to early 20th Century ● Louis Pasteur lays to rest the idea of spontaneous generation → Pasteur shows that fermentation is associated with life → Pasteurization prevents unwanted fermentation ▪ Saved the French wine industry ● Germ Theory of Disease → Sickness is caused by microbes ● Robert Koch → Koch’s Postulates showed how to link a microbe with a disease ▪ If you isolate the microbes from a sick person and grow that in a culture and give it to another susceptible host, that person will have the same disease. ▪ Use of laboratory equipment and techniques like agar and staining Note: Information was directly taken from the trans of Batch 2022. → Review of Koch’s Postulates ▪ The bacteria must be present in every case of the disease. ▪ The bacteria must be isolated from the host with the disease and grown in pure culture. ▪ The specific disease must be reproduced when a pure culture of the bacteria is inoculated into a healthy susceptible host. ▪ The bacteria must be recoverable from the experimentally infected host. ● Ignaz Semmelweis → Father of Handwashing → Showed the importance of handwashing for the prevention of disease ● Joseph Lister → Aseptic surgery ● Paul Ehrlich → Antimicrobials 20th Century ● Advent of Molecular Biology → Use of microbes as model systems for study → Study of DNA and protein synthesis → Development of tools and processes for the use of recombinant DNA ● Applied Microbiology → Food industry → Water and sewage treatment → Bioremediation ● Medicine → Emerging/novel diseases ▪ e.g. COVID-19 → Antibiotic resistance E. IMPORTANCE OF MICROBES ● Major impact on health → Responsible for disease in humans, animals, plants ● Major impact on environment → Major decomposers → Nutrient cycling, elemental cycling ● Microbes are talented → Can live under extreme conditions → May help protect against disease → May help with bioremediation ▪ Eat oil, toxic waste → Can make plastics → Can cause food to spoil, can also make food → Can use light, can also produce light The Communicable Disease Model ● Epidemiologic triangle model of a communicable disease has three main components: ● Environment ● Host (or population) ● Any tilt or disequilibrium in the epidemiologic triangle can lead to communicable disease Table 2. Causative Agents of Notifiable Diseases Notifiable Diseases Agents Acute bloody diarrhea Shigella Acute hemorrhagic fever Dengue, Ebola virus, Marburg virus Acute febrile illness Leptospira interrogans Acute lower respiratory tract S. pneumoniae, Haemophilus infection & pneumonia pneumoniae, Klebsiella pneumoniae Acute watery diarrhea Rotavirus Cholera Vibrio cholerae Dengue hemorrhagic fever Dengue virus Diphtheria Corynebacterium diphtheriae Filariasis Wuchereria bancrofti, Brugia malayi Leprosy Mycobacterium leprae Leptospirosis Leptospira interrogans Malaria Plasmodium falciparum Measles Measles virus Meningococcal infection Neisseria meningitidis Neonatal tetanus & Clostridium tetani non-neonatal tetanus Paralytic shellfish poisoning Toxin-contaminated bivalve shellfish (PSP) and crustaceans Rabies (human) Rabies virus Schistosomiasis Schistosoma japonicum Typhoid fever Salmonella typhi Paratyphoid fever Salmonella paratyphi Viral encephalitis HSV, Japanese encephalitis Viral hepatitis Hepatitis A, B, C Viral meningitis Herpes simplex virus Whooping cough Bordetella pertussis II. CLASSIFICATION OF MICROBES A. BACTERIA ● Size → 0.2 μm - 0.1 mm → Most are 0.5 μm - 2.0 μm ● Shape → Coccus (cocci) → Rod (bacillus, bacilli) → Spiral shapes (spirochetes; spirillum, spirilla) ▪ spirochetes = flexible; spirilla = rigid → Filamentous → Various odd shapes ● Arrangement → Clusters → Tetrads → Sarcina (cocci in cubes of eight) → Pairs → Chains Division of the Eubacteria ● Invented by Hans Christian Gram ● Gram staining is the first step in identifying bacteria → Gram (+)ve: purple → Gram (-)ve: pink/red ● Cell wall architecture → Gram (+)ve: thick peptidoglycan layer in the cell wall (Figure 3) → Gram (-)ve: thin peptidoglycan layer and outer membrane (Figure 4) ● Staining is valuable in bacterial identification Figure 2. The epidemiologic triad model of communicable disease. ● Agent → Element that must be present in order for the diseases to occur → Includes microorganisms such as algae, bacteria, fungi, protozoa, and viruses (see Figure 19 in Appendix) → Can come from air, soil, plants, people, animals, water ▪ Microbes are ubiquitous ● Hyphae → Thread-like structures → Can be partially separated into cells or not at all (coenocytic). ▪ Cytoplasm is continuous throughout hypha. ● Mycelia: a mass of hyphae → Like a bacterial colony ● Some fungi are molds, some are yeasts, → Yeasts: oval, unicellular → Dimorphic: able to grow as either form ▪ Typical of some disease-causing fungi Figure 3. Cell wall architecture of Gram-positive bacteria. (see Appendix for larger image) Figure 4. Cell wall architecture of Gram-negative bacteria. (see Appendix for larger image) EUKARYOTIC MICROBIAL DIVERSITY ● Early attempts at taxonomy on all plants and animals ● Whittaker scheme (late 20th century) → Five kingdoms → Modified by Woese’s work on rRNA ▪ Three domains (one of which is eukaryotes) ● Protista: the grab bag Kingdom → Always recognized as a highly diverse group → In new schemes, split into 7 kingdoms ● Since the application of molecular biology, the taxonomy of all things is constantly changing Eukaryotes vs. Prokaryotes ● Eukaryotes are larger. ● Eukaryotes have membrane-bound organelles. → Examples: Nucleus, mitochondria, membrane systems → Larger size requires functional compartments. Eukaryotic Pathogens ● Fungi ● Protozoa ● Remember: These are all eukaryotes with organelles and many of the same cellular characteristics that humans have. → Makes drug treatment more difficult. B. FUNGI ● Mycology: study of fungi ● Most fungi are saprophytes → Decay nonliving organic matter → Fungi are the king of decomposition ● All fungi are heterotrophs. → Use preformed organic matter → Not autotrophs, not photosynthetic. ● Fungi grow into, through their food. → Release extracellular enzymes, break down polymers into low molecular weight (LMW) compounds for transport ● Often dimorphic → Can exist in 2 forms: ▪ Yeast in body ▪ Mold in culture ● Classification of fungal diseases (mycoses) → Superficial, cutaneous, subcutaneous → Systemic and opportunistic ▪ Systemic: fungi in blood or all over the body ▪ Opportunistic: The usually non-pathogenic fungi can be pathogenic in immunocompromised hosts. → Poisoning and allergies ● Treatment: → Azole drugs, amphotericin B, others Fungi Terminology and Structure Impact of Fungi ● Cause different, wide spectrum of diseases: mycosis (plural: mycoses) → Superficial: on hairs, nails → Cutaneous: involves dermatophytes in skin ▪ Example: athlete’s foot → Subcutaneous: deeper into the skin → Systemic: in deeper tissues, usually via lungs ▪ Involves blood and other parts of the body ▪ Opportunists: serious disease when immune system is depressed ● Antibiotic production → Penicillium, Cephalosporium ● Decomposition; Food industry (soy sauce) Classification of Fungi ● Fungi can be classified based on sexual reproductive structures. → Reproduce both asexually and sexually Deuteromycota ● also known as fungi imperfecti ● No longer a valid classification ● Through morphological and molecular means (e.g. DNA analysis), it is being distributed into the other 3 phyla of fungi. Zygomycota ● Produce zygospores (Figure 5 left) ● Example: Rhizopus ● Fusion of hyphae (haploid) of opposite mating types produces zygospore (diploid). ● Zygospore produces a zygosporangium with haploid spores that are released. ● Asexually, sporangium containing spores (Figure 5 right). Figure 5. A mature zygospore (left) and sporangia (right) of rhizopus. Ascomycota ● Also called sac fungi ● Sexual spores produced inside an ascus (sac). Figure 6. Ascus of ascomycota. ● Asexual spores are called conidiospores or conidia (singular conidium). Figure 7. Conidia or conidiospores . ● Many types of common molds are ascomycetes. → Most molds such as Aspergillus sp. belongs to the family Ascomycota. Basidiomycota ● aka the club fungi or mushrooms ● After extensive growth of hyphae, opposite mating types fuse and above ground mushroom is formed. ● Sexual spores are called basidiospores. → Asexual conidia can also be formed. ● Cryptococcus neoformans → Not seen among immunocompetent individuals, but thrives among immunocompromised hosts (i.e. HIV/AIDS) → Inhalation of spores → Can infect many parts, but has predilection for CNS → Particularly serious in AIDS ● Pneumocystis carinii → Used to be classified under protozoan (Kingdom Protista), but was reclassified as a fungus → Very protozoan like, but is a fungus → Most cases associated with AIDS ▪ AIDS-defining illness − Even if an individual has not been tested for HIV/AIDS, those infected with P. carinii are considered to have the disease already. → Serious lung infections: PCP (P. carinii pneumonia) C. KINGDOM PROTISTA Highly diverse group of organisms Size: 5 μm - 5 mm Defined by what they are not Nutrient/energy acquisition ranges from photosynthesis to predatory to detritivores ● Important in many food webs → Provide link between bacteria and larger organisms ● ● ● ● Figure 8. Examples of basidiomycota (left) and close up of gills (right). Diseases Caused by Fungi Cutaneous and Subcutaneous Mycoses ● Dermatophytes → Various genera → Cause skin and nail diseases → Referred to as Tinea (worm) ▪ Ringlike appearance on scalp. → Cause ringworm, jock itch, athlete’s foot (alipunga), etc. → Attacks only the outer layer of skin ● Sporothrix schenckii → Acquired from soil and plant material → Infects deeper into skin, but not systemic. ▪ May affect the subcutaneous layer ▪ Does not affect the blood and other parts of the body Systemic Mycoses ● Generally acquired by inhalation of spores → Lung infections, may spread beyond into other tissues ● Blastomyces → Causes blastomycosis ● Coccidioides → Causes coccidioidomycosis ● Histoplasma → Causes histoplasmosis → Most common in areas: ▪ Ohio and Mississippi River valleys → Many people are exposed to asymptomatic cases. ▪ Many test positive for exposure Opportunistic Infections ● Usually non-pathogenic in immunocompetent people → Can be pathogenic in immunocompromised people. ● Aspergillus → Causes aspergillosis → Variety of species, very common in soil, plant materials → Serious infections in immunocompromised → Allergies to A. fumigatus → Poisoning from aflatoxin from A. flavus ● Candida → Causes candidiasis → Normal microbiota → Cause of vaginal infections, diaper rash, thrush → Capable of infecting any part of the body → Dangerous in cancer patients, HIV infections, etc. Figure 9. Protist. Protozoal Terminology ● Macronucleus and micronucleus → Two types of nuclei differing in size and function (macro- larger; micro- smaller) ● Cyst → Resting stage similar to a spore with a thick wall and low level of metabolism ● Trophozoite → Stage in life cycle during which the microbe is feeding and growing ● Merozoite → Small cells with a single nuclei produced during schizogony ▪ Large, multinucleated cell undergoes cytokinesis to produce multiple daughter cells (merozoites) Plant-like Protists ● Contain chloroplasts ● Representatives: → Diatoms ▪ Diatomaceous earth = fossilized diatoms: abrasives and slug repellents Figure 10. Diatoms under an electron microscope → Red, brown, yellow algae ▪ Seaweed, source of agar → Dinoflagellates ▪ Neurotoxins and red tide Fungus-like Protists ● Different from true fungi ● Water molds ● Slime molds