Microbial Diversity Lecture PDF

○ Eukaryotes OUTLINE # Four (4) Kingdoms Plants, animals,...

○ Eukaryotes OUTLINE # Four (4) Kingdoms Plants, animals, fungi, protists MICROBIAL DIVERSITY I. INTRODUCTION TO DIVERSITY 1 WHAT ARE MICROBIOLOGISTS INTERESTED IN? A. Estimates of Biodiversity Eubacteria and archaebacteria B. Classification of Microbes Eukaryotes like fungi and protists C. Divisions of Microbiology Animals like arthropods D. History of Microbiology Viruses E. Importance of Microbes II. INTRODUCTION TO DIVERSITY 3 DIVISIONS OF MICROBIOLOGY A. Bacteria B. Fungi C. Protists BY CRITTER TYPE III. MICROBIAL DIVERSITY AND ITS 6 Bacteriology APPLICATIONS ○ Bacteria alone A. Industry Gram (+) and Gram (-) B. Microbial Geotechnology Virology C. Production of Bacterial Polymers ○ Viruses like SARS-COV-2 D. Other Applications Mycology E. Bioprospecting ○ Study of Fungi IV. REVIEW QUESTIONS 8 Parasitology V. APPENDICES ○ Protozoans (e.g. etiologic agents of malaria, amoeba) ○ Worms (e.g. helminths) OTHER DIVISIONS SOURCE Roxas, E. (2024). Microbial Diversity [Lecture]. Pathogenic Microbiology ○ Branch of microbiology that studies diseases caused by Note: Yellow text indicates additional information from the lecture microbes Immunology INTRODUCTION TO DIVERSITY ○ Related to microbiology as the immune system is part of this study ESTIMATES OF BIODIVERSITY Molecular Biology ○ Newer subdivision Table 1. Number of described species from the different kingdoms ○ Hastens the diagnosis of microorganisms Number of Microbial Ecology Kingdom /Major Division Described Species ○ Focuses on the importance of the environment and its Viruses 1,000 relationship with microorganisms Applied Microbiology Monera (Bacteria, Mycoplasma, 4,760 ○ Deals with microbes which can be helpful in some Cyanophycota) instances like: Water treatment Fungi (Zygomycota, Ascomycota, etc.) 46,983 Natural products Algae 26,900 Food microbiology Environmental microbiology Plantae 248,428 Protozoa 30,800 HISTORY OF MICROBIOLOGY Animalia (including Arthropoda) 989,761 ANCIENT KNOWLEDGE Chordata (Tunicata, Vertebrata, etc.) 43,852 Recognition of Immunity ○ Variolation and protection from infection TOTAL 1,392,485 Intentional contact with minor form of smallpox There are currently more than 1 million number of described ○ The Myth of the MIlkmaid species across all kingdoms /divisions Story of Edward Jenner and the milkmaids ○ Animalia sports the highest number of species Milkmaids who’ve had cowpox seem immune to Including Arthropoda (insects) smallpox. ○ Estimates of total microbial biodiversity range from 5-30 From here, we get the idea of immunization or million species vaccination. Contagion CLASSIFICATION OF MICROBES ○ Disease can be spread by contact There are three (3) domains: ○ During the Black Death ○ Eubacteria A lot of mortality secondary to bubonic plague Have a prokaryotic cell structure ○ Led to exclusion of lepers, burning of plague victims ○ Archaebacteria ○ Catapulting of disease victims into castles during siege Prokaryotes Was done by invading armies to spread disease inside the impenetrable walls of castles in order for the besieged to surrender. PH153: Microbial Diversity BSPH2025 Aguila, Decio, De Guzman, L., Estilloso 1  HISTORY CONTINUED 20TH CENTURY MICROBIOLOGY Microbiology as a biological science Advent of Molecular Biology Robert Hooke ○ Use of microbes as model systems for study ○ Discovery of cells, 1665 ○ Study of DNA and protein synthesis Antony van Leeuwenhoek ○ Development of tools and processes for the use of ○ Father of Microbiology recombinant DNA ○ Dutch amateur lens grinder Applied Microbiology ○ First person to see microbes, late 1600s ○ Food industry Also the time where he introduced the microscope ○ Water and sewage treatment (see Figure 1) ○ Bioremediation Mid 1800s, microbes were taken more seriously and studied Medicine using the scientific method ○ Emerging/novel diseases e.g. COVID-19 ○ Antibiotic resistance 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 adapt and transform into antimicrobial-resistant pathogens ○ Can live under extreme conditions ○ May help protect against disease ○ May help with bioremediation Eat oil, toxic waste Figure 1. Von Leeuwenhoek Microscope (circa late 1600s). Retrieved ○ Can make plastics from Roxas, 2022. ○ Can cause food to spoil, can also make food ○ Can use light, can also produce light THE GOLDEN AGE From 1850 to early 20th Century THE COMMUNICABLE DISEASE MODEL Louis Pasteur lays to rest the idea of spontaneous Epidemiologic triangle model of a communicable disease generation has three main components: ○ Pasteur shows that fermentation is associated with life ○ Pasteurization prevents unwanted fermentation Saved the French wine industry Germ Theory of Disease ○ Sicknesses are 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 REVIEW OF KOCH’S POSTULATES Information was directly taken from the trans of Batch 2022. ○ The bacteria must be present in every case of the disease Figure 2. The epidemiologic triad model of communicable disease. ○ The bacteria must be isolated from the host with the disease and grown in pure culture Agent ○ The specific disease must be reproduced when a pure ○ Element that must be present in order for the diseases to culture of the bacteria is inoculated into a healthy occur susceptible host ○ Includes microorganisms such as algae, bacteria, fungi, ○ The bacteria must be recoverable from the protozoa, and viruses (see Figure A-2). experimentally infected host. ○ Can come from air, soil, plants, people, animals, water Microbes are ubiquitous Environment Ignaz Semmelweis ○ Facilitate or prevent the transmission of the agent ○ Father of Handwashing Host (or population) ○ Showed the importance of handwashing for the ○ Even with the presence of the agent and an environment prevention of disease that facilitates transmission, a communicable disease will Joseph Lister not occur if the host is not susceptible ○ Aseptic surgery Any break or disruption in the equilibrium between the Paul Ehrlich population, infectious agent, and the environment can lead to ○ Antimicrobials communicable disease PH153: Microbial Diversity BSPH2025 Aguila, Decio, De Guzman, L., Estilloso 2 Table 2. Causative Agents of Notifiable Diseases ○ Gram (-)ve: thin peptidoglycan layer and outer Notifiable Diseases Agents membrane Only Gram (-)ve has lipopolysaccharide Acute bloody diarrhea Shigella Staining is valuable in bacterial identification Acute hemorrhagic fever Dengue, Ebola virus, Marburg virus ○ Mode of treatment start to differ based on stain 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 Figure 3. Cell wall architecture of Gram-positive and Gram-negative Paralytic shellfish poisoning Toxin-contaminated bivalve shellfish bacteria. (PSP) and crustaceans Rabies (human) Rabies virus EUKARYOTIC MICROBIAL DIVERSITY Schistosomiasis Schistosoma japonicum Early attempts at taxonomy: on all plants and animals Whittaker scheme (late 20th century) Typhoid fever Salmonella typhi ○ Five kingdoms Paratyphoid fever Salmonella paratyphi ○ Modified by Woese’s work on rRNA Viral encephalitis HSV, Japanese encephalitis Three domains (one of which is eukaryotes) Protista: the grab bag Kingdom Viral hepatitis Hepatitis A, B, C ○ Always recognized as a highly diverse group Viral meningitis Herpes simplex virus ○ In new schemes, split into 7 kingdoms Whooping cough Bordetella pertussis Since the application of molecular biology, the taxonomy of all things is constantly changing Notifiable diseases are reported to the Department of Health EUKARYOTES VS. PROKARYOTES ○ Channels of Reporting Rural Health Officer - Rural Health Unit Eukaryotes are larger. Provincial Health Officer - Provincial Health Office Eukaryotes have membrane-bound organelles. City Health Officer - City Health ○ Nucleus, mitochondria, membrane systems ○ Larger size requires functional compartments. INTRODUCTION TO DIVERSITY EUKARYOTIC PATHOGENS BACTERIA Fungi Protozoa Size Remember: These are all eukaryotes with organelles and ○ 0.2 μm - 0.1 mm many of the same cellular characteristics that humans ○ Most are 0.5 μm - 2.0 μm have. Shape ○ Makes drug treatment more difficult ○ Coccus (cocci) ○ Rod (bacillus, bacilli) FUNGI ○ Spiral shapes (spirochetes; spirillum, spirilla) Spirochetes = flexible; spirilla = rigid Mycology: study of fungi Examples: Leptospira, Treponema, Borrelia Most fungi are saprophytes ○ Filamentous ○ Decay nonliving organic matter ○ Various odd shapes ○ Fungi are the king of decomposition Arrangement All fungi are heterotrophs. ○ Clusters ○ Use preformed organic matter ○ Tetrads ○ Not autotrophs, not photosynthetic. ○ Sarcina (cocci in cubes of eight) Fungi grow into, through their food. ○ Pairs ○ Release extracellular enzymes, break down polymers ○ Chains into low molecular weight (LMW) compounds for transport DIVISION OF THE EUBACTERIA Often dimorphic ○ Can exist in 2 forms: Invented by Hans Christian Gram Yeast in body Gram staining is the first step in identifying bacteria Mold in culture ○ Gram (+)ve: purple ○ Gram (-)ve: pink/red Cell wall architecture ○ Gram (+)ve: thick peptidoglycan layer in the cell wall PH153: Microbial Diversity BSPH2025 Aguila, Decio, De Guzman, L., Estilloso 3  Classification of fungal diseases (mycoses) ○ Superficial, cutaneous, subcutaneous ○ Systemic and opportunistic Systemic: fungi in blood or all over the body Opportunistic: usually non-pathogenic fungi that can be pathogenic in immunocompromised hosts ○ Poisoning and allergies Treatment: ○ Azole drugs, amphotericin B, others FUNGI TERMINOLOGY AND STRUCTURE Hyphae ○ Thread-like structures Figure 5. Ascus of ascomycota. ○ Can be partially separated into cells or not at all (coenocytic). Asexual spores are called conidiospores or conidia Cytoplasm is continuous throughout hypha. (singular conidium). 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 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 Figure 6. Conidia or conidiospores ○ Subcutaneous: deeper into the skin ○ Systemic: in deeper tissues, usually via lungs Many types of common molds are ascomycetes. Involves blood and other parts of the body ○ Most molds such as Aspergillus sp. belongs to the family ○ Opportunists: serious disease when immune system is Ascomycota. depressed Antibiotic production BASIDIOMYCOTA ○ Penicillium, Cephalosporium aka the club fungi or mushrooms Decomposition; Food industry (soy sauce) After extensive growth of hyphae, opposite mating types fuse and above ground mushroom is formed. CLASSIFICATION OF FUNGI Sexual spores are called basidiospores. Fungi can be classified based on sexual reproductive ○ Asexual conidia can also be formed. 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 Figure 7. Examples of basidiomycota (left) and close up of gills (right). Produce zygospores (Figure 4 left) Example: Rhizopus DISEASES CAUSED BY FUNGI Fusion of hyphae (haploid) of opposite mating types produces zygospore (diploid). CUTANEOUS AND SUBCUTANEOUS MYCOSES Zygospore produces a zygosporangium with haploid spores Dermatophytes that are released. ○ various genera Asexually, sporangium containing spores (Figure 4 right). ○ 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 Figure 4. A mature zygospore (left) and sporangia (right) of rhizopus SYSTEMIC MYCOSES Endemic mycoses: endemic in some regions ASCOMYCOTA Generally acquired by inhalation of spores Also called sac fungi ○ Lung infections, may spread beyond into other tissues Sexual spores produced inside an ascus (sac). Blastomyces ○ Causes blastomycosis PH153: Microbial Diversity BSPH2025 Aguila, Decio, De Guzman, L., Estilloso 4  Coccidioides PLANT-LIKE PROTISTS ○ Causes coccidioidomycosis Contain chloroplasts Histoplasma Representatives: ○ Causes histoplasmosis ○ Diatoms ○ Most common in areas: Ohio and Mississippi River Diatomaceous earth = fossilized diatoms: abrasives valleys and slug repellents ○ Many people are exposed to asymptomatic cases: ○ Red, brown, yellow algae positive for exposure Seaweed, source of agar Paracoccidioides ○ Dinoflagellates ○ Causes paracoccidioidomycosis Neurotoxins and red tide OPPORTUNISTIC INFECTIONS Usually non-pathogenic in immunocompetent people ○ Can be pathogenic in immunocompromised people. Aspergillus ○ Purely mold ○ 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 ○ Dimorphic Figure 8. Diatoms viewed under microscope ○ Causes candidiasis ○ Normal microbiota FUNGUS-LIKE PROTISTS ○ Cause of vaginal infections, diaper rash, thrush Different from true fungi ○ Capable of infecting any part of the body Water molds ○ Dangerous in cancer patients, HIV infections, etc. Slime molds Cryptococcus neoformans ○ Purely yeast ○ 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 ○ Currently P. jiroveci ○ Used to be classified under 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 Figure 9. Slime molds on a decaying trunk HIV/AIDS, those infected with P. carinii are considered to have the disease already. ANIMAL-LIKE PROTISTS Serious lung infections: PCP (P. carinii pneumonia) Capable of ingesting their food Found among many different groups KINGDOM PROTISTA ○ Not good for taxonomy 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 PROTOZOAL TERMINOLOGY Macronucleus and micronucleus ○ Two types of nuclei differing in size and function (macro- Figure 10. Paramecium, an animal-like protist larger; micro- smaller) Cyst PROTOZOANS ○ Resting stage similar to a spore with a thick wall and low level of metabolism Unicellular eukaryotes Trophozoite Lack a cell wall ○ Stage in life cycle during which the microbe is feeding Require moist environments (water, damp soil, etc.) and growing Great amounts of diversity based on: Merozoite ○ Locomotion: float, cilia, flagella, pseudopodia ○ Small cells with a single nuclei produced during ○ Nutrition: chemoheterotrophs, photoautotrophs schizogony (seen in malaria infection) ○ Simple to complex life cycles, reproduction Large, multinucleated cell undergoes cytokinesis to ○ Different cell organelles, some lack mitochondria produce multiple daughter cells (merozoites) Cell ultrastructure and molecular analysis becoming the main methods used for classification ○ Suggests that several kingdoms would be appropriate PH153: Microbial Diversity BSPH2025 Aguila, Decio, De Guzman, L., Estilloso 5 CLASSIFICATION OF PROTOZOA Protozoa Classification Alveolates ciliates, apicomplexans, dinoflagellates Amoebae shelled and unshelled Euglenozoa amoebae, euglenoids, kinetoplastids Archaezoa diplomonadida, parabasalia Animal-like group responsible for human diseases protozoa Old groupings: ○ Ciliates ○ Amoebae ○ Flagellates ○ Sporozoans (apicomplexans) Figure 12. Benefits of probiotics Typically have life cycles ○ Simple: like vegetative and cyst ○ Complex: like protozoans have MICROBIAL DIVERSITY AND ITS APPLICATIONS Uses of microorganisms in the industry ○ Essential to many processes Nitrogen cycle: nitrogen is recycled in the ecosystem Decomposition of animal and plant waste ○ Increasingly important to industry Food production Water treatment\ FERMENTATION Chemical conversion of carbohydrates into alcohols or acids Occurs when oxygen supplies are LIMITED → ANAEROBIC RESPIRATION Examples of foods produced using fermentation: cheese, yogurt, butter, beer, wine, bread ○ Saccharomyces cerevisiae (baker’s yeast or brewer’s yeast) Figure 13. Distribution of intestinal microflora Most common yeast used in the preparation of beer Beer: made from barley, wheat, or rye grain → ○ Live bacteria in probiotic yogurts are thought to restore germinated to convert starch to sugar (e.g. maltose) the natural microbe population of the gut (flora), which can be depleted by antibiotics. BIOFUELS Rapidly developing area of research Aims: ○ reduce the use of fossil fuels and greenhouse gas emissions ○ decrease pollution and waste management problems Anaerobic microorganisms can convert biomass (e.g. manure or crop residues) into useful energy sources, through landfill power plants, for example. Fermentation process that produces: carbon dioxide (CO2) Figure 11. Saccharomyces cerevisiae and methane (CH4). ○ Wine is also produced by fermentation Grapes are crushed to release sugars Yeast is then added for fermentation and conversion of sugars into alcohol ○ For sparkling wines, the carbon dioxide produced by the fermentation process is trapped to create bubbles PROBIOTICS Live microorganisms that can protect the host, prevent disease, and provide a health benefit to the host Example: ○ Antibiotics can kill off normal intestinal flora, and the administration of probiotic bacteria can replenish the flora to normal levels. Figure 14. Biofuels life cycle PH153: Microbial Diversity BSPH2025 Aguila, Decio, De Guzman, L., Estilloso 6  Aims to improve the mechanical properties of soil so that it BIOFUELS LIFE CYCLE will be more suitable for construction or environmental directly lifted from B2024 Trans purposes. Two notable applications: bioclogging and biocementation. 1. Feedstock - biomass feedstocks such as food crops (sugar, starch, oil), palm, rapeseed, soy, beets and BIOCLOGGING cereals (corn, wheat, etc). 2. Transportation - usually done via trucks, rails, ships, and Production of pore-filling materials through microbial means barges. → reduced porosity and hydraulic conductivity of soil ○ Pipelines are being explored as a more efficient means of transporting fuel across land to major HYDRAULIC CONDUCTIVITY markets. the ability of the fluid to pass through the pores and 3. Biorefinery - sustainable process for the production of fractured rocks (Saravanan et al., 2019). biofuels and other bio-products from biomass feedstock using different conversion technologies 4. Processing and conversion - refers to conversion of BIOCEMENTATION biomass into liquid fuels, called biofuels. Generation of particle-binding materials through microbial processes in situ → increased shear strength of soil MAJOR CONVERSION PROCESSES OF BIOMASS The most suitable microorganisms for soil bioclogging or biocementation are (Ivanov & Chu, 2008): Direct combustion to produce heat ○ facultative anaerobic and microaerophilic bacteria (burning) ○ anaerobic fermenting bacteria, anaerobic respiring bacteria, and obligate aerobic bacteria may also be Thermochemical to produce solid, gaseous, suitable for use in geotechnical engineering. conversion and liquid fuels. Chemical conversion to produce liquid fuels PRODUCTION OF BACTERIAL EXOPOLYMERS Production of bacterial exopolymers in situ can be used to Biological conversion to produce liquid and modify soil properties. gaseous fuels Application: enhancing oil recovery or soil bioremediation (Stewart & Fogler, 2001) 5. Distribution - Distributed from the point of production to Oligotrophic bacteria from genus Caulobacter: groups of fuel terminals and wholesalers by truck, train, barge or microorganisms that produce insoluble extracellular sometimes shipped by pipeline. polysaccharides to bind the soil particles and fill in the 6. End user - Biofuel is used to generate power in backup soil pores. systems where emission matters most. ○ This includes facilities such as schools, hospitals and OTHER APPLICATIONS other forms located in residential areas. Molecular basis of microbial genetics Genetic engineering in plants, animals and microorganisms Mutation and mutant selection Genetic exchange BIOGAS Cloning The ‘biogas’ produced can be used: (1) as fuel or (2) in the Emerging techniques generation of electricity. Transgenesis: emerging applications; Scientists are developing processes that exploit Rapid analytical techniques, principles and applications in photosynthetic bacteria or algae. the food industry; ○ These microorganisms can capture sunlight to produce Practical applications of genetic technology in the food new biomass that can be turned into alternative sources industry of energy. Enzyme production Phage resistant cheese starters and enzyme production DNA probes Immunochemical assays Enzyme immunoassays Biosensors Novel techniques Cultivation of microorganisms, animal plant cells in industrial situations Engineering, biochemical, and chemical considerations in fermentation technologies Products and processes: microbial products, mammalian products, antibiotics, vitamins and amino acids, enzymes, organic acids; Food fermentations and waste utilization Regulatory, food safety and ethical issues related to applications of biotechnology Figure 15. Outline of biogas power generation and heat supply system BIOPROSPECTING (Roxas, 2022) “Maximizing plants in the environment” MICROBIAL GEOTECHNOLOGY Bioprospecting of plants entails the search for economically valuable biochemical resources from the flora wealth of a New branch of geotechnical engineering country. Deals with applications of microbiological methods to Such initiatives hold the promise of new medicines and geological materials used in engineering. biodegradable pesticides that can be a source of income for developing countries, thus providing incentives to conserve biodiversity. PH153: Microbial Diversity BSPH2025 Aguila, Decio, De Guzman, L., Estilloso 7  d. Both statements are incorrect. THREAT TO MEDICINAL FLORA OF PAKISTAN 8. Which of the following statements about fungi is true? Crude medicinal plant material is worth more than Rs. 150M a. Fungi are often dimorphic and exist as yeast in culture (US $2.3M) per year. and mold in the body. ○ Most of these plants are obtained from the wild. b. Fungi are capable of producing substances such as Pakistan exports large quantities of crude plant at very cheap amphotericin B that can be used as antibiotics. prices in the international market (worth US $6M), in the c. Fungi can cause systemic diseases in deeper tissues, entire business chain, gatherers receive the least money and and even opportunistic diseases when the host immune are forced to collect more and more plant material to survive, system is compromised so Pakistan receives a paltry return from its natural flora d. Fungi can also cause superficial diseases involving wealth. dermatophytes in the skin, such as athlete's foot. 9. This classification of fungi produces zygospores. REVIEW QUESTIONS a. Ascomycota b. Basidiomycota c. Deuteromycota 1. Robert Hooke coined the term 'cell'. Louis Pasteur d. Zygomycota articulated the theory of spontaneous generation. a. Only the first statement is correct. 10. Sexual spores of the Ascomycota are produced inside b. Only the second statement is correct. a(n) ________. Their asexual spores are called _________ or c. Both statements are correct. _________. d. Both statements are incorrect. a. Hyphae; zygospores; sporangium b. Ascus, basidiospores; basidiosporangia 2. Which of the following pairs of words is/are correctly c. Ascus; conidiospores; conidia matched? d. Hyphae; ascospores; ascosporium I. HSV : Viral encephalitis II. Corynebacterium diphtheriae : Diphtheria 11. These fungi are the etiologic agents of skin and nail III. Shigella : Acute watery diarrhea diseases such as ringworm, jock itch, and athlete’s foot. a. I a. Dermatophytes b. I and II b. Blastomyces c. I, II and III c. Coccidioides d. None of the above d. Sporothrix 3. The following pair of words are correctly matched, 12. The following fungi are usual etiologic agents of EXCEPT: opportunistic infections EXCEPT: a. Antony van Leeuwenhoek: Father of Microbiology a. Candida b. Edward Jenner: developed smallpox vaccine b. Aspergillus c. Joseph Lister: developed antimicrobials c. Cryptococcus neoformans d. Ignaz Semmelweis: Father of Handwashing d. Histoplasma 4. Gram-positive organisms are stained either purple or 13. Bioclogging is the production of pore-filling materials blue, while gram-negative organisms are either pink or red through microbial means so that porosity and hydraulic in color. Gram-positive cell walls contain a thick layer of conductivity of soil can be increased. Meanwhile, peptidoglycan, while Gram-negative cell walls do not have biocementation is the generation of particle-binding a peptidoglycan layer. materials through microbial means so that shear strength a. Only the first statement is correct. of soil can be increased. b. Only the second statement is correct. a. Only the first statement is correct c. Both statements are correct. b. Only the second statement is correct. d. Both statements are incorrect. c. Both statements are correct. d. Both statements are incorrect. 5. Which of the following causative agents and notifiable diseases are incorrectly paired? 14. The following types of microorganisms are suitable for a. Filariasis: Wuchereria bancrofti use in geotechnical engineering, EXCEPT: b. Leprosy: Leptospira interrogans a. Anaerobic fermenting bacteria c. Neonatal tetanus: Clostridium tetani b. Facultative anaerobic bacteria d. Malaria: Plasmodium falciparum c. Microaerophilic bacteria d. Obligate aerobic bacteria 6. Which of the following statements about eukaryotes and e. None of the above prokaryotes is/are true? a. Fungi are eukaryotic pathogens. 15. Which of the following microorganisms is utilized in the b. Protozoa and bacteria are prokaryotic pathogens. production of bacterial polymers to enhance oil recovery c. Eukaryotes are membrane-bound and are larger than or bioremediation? prokaryotes. a. Ruminococci d. Both A and C. b. Bifidobacteria c. Caulobacter 7. All fungi are heterotrophs that metabolize organic d. Saccharomyces cerevisiae matter, and most of them are saprophytes that decay nonliving organic matter. They do this by releasing 16. This deals with application of microbiological methods intracellular enzymes that break down polymers into low to improve mechanical properties of soil to increase its molecular weight compounds for transport. suitability for construction or environmental purposes. a. Only the first statement is correct. a. Microbial geotechnology b. Only the second statement is correct. b. Bioclogging c. Both statements are correct. c. Biocementation PH153: Microbial Diversity BSPH2025 Aguila, Decio, De Guzman, L., Estilloso 8  d. Biorefinery a. Giardia lamblia b. Trichomonas vaginalis 17. This entails the search for economically valuable c. Entamoeba histolytica chemical resources from the flora of the country to find d. Acanthamoeba new medicines. a. Bioremediation 27. All of the following organisms are protists EXCEPT: b. Biosensing a. Euglena c. Biological conversion b. Paramecium d. Bioprospecting c. Algae d. Cyanobacteria 18. Which of the following microorganisms is usually utilized in the fermentation of maltose to alcohol in beer 28. This fungus can cause food poisoning caused by its toxin that production? is mainly found in plant materials or agricultural products. a. Ruminococci a. Aspergillus flavus b. Bifidobacteria b. Candida albicans c. Caulobacter c. Cryptococcus neoformans d. Saccharomyces cerevisiae d. Histoplasma 19. The following applications of microorganisms utilize the Match the following causative agent to its associated fermentation process, EXCEPT: disease a. Wine production b. Biofuel production 29. Brugia malayi A. Rabies c. Biogas production 30. Herpes simplex virus B. Whooping cough d. Bacterial exopolymer production 31. Bordetella pertussis C. Acute watery diarrhea e. Two of the choices 32. Lyssavirus D. Acute hemorrhagic fever f. None of the above 33. Rotavirus E. Viral encephalitis 34. Ebola virus F. Filariasis 20. ______ is the resting stage of a protist similar to a spore with a thick wall and a low level of metabolism. ______ is a 35. What distinguishes spirochetes from spirilla in terms of their stage where the protist is actively feeding and growing. shape? a. Merozoite; cyst a. Spirochetes are rigid, while spirilla are flexible. b. Blastocyst; trophozoite b. Spirochetes are flexible, while spirilla are rigid. c. Cyst; trophozoite c. Spirochetes are always filamentous, while spirilla are d. Merozoite; trophozoite never filamentous. d. Spirochetes have a spherical shape, while spirilla are 21. Fermentation is the chemical conversion of carbon to rod-shaped. alcohols and acids using yeasts, bacteria, or a combination thereof. It is a type of aerobic respiration. 36. Which of the following statements is true about the Whittaker a. Only the first statement is correct. scheme of taxonomy compared to Woese’s modifications? b. Only the second statement is correct. a. The Whittaker scheme was based on rRNA analysis, c. Both statements are correct. while Woese’s work introduced five kingdoms. d. Both statements are incorrect. b. Woese’s modifications led to the establishment of the three-domain system, including eukaryotes. 22. Representatives of plant-like protists include the c. The Whittaker scheme identified seven kingdoms, while following EXCEPT: Woese’s work simplified it to five. a. Dinoflagellates d. The Whittaker scheme and Woese’s modifications both b. Red, brown, yellow algae introduced the concept of eukaryotes as a separate c. Diatoms domain. d. Slime molds 37. Which fungal pathogen is associated with serious infections 23. Aspergillus sp. : Ascomycota; Rhizopus : _________ in immunocompromised individuals and has a predilection for the a. Deuteromycota central nervous system? b. Basidiomycota a. Aspergillus c. Zygomycota b. Candida d. Ascomycota c. Cryptococcus neoformans d. Pneumocystis jiroveci 24. The following statements describe protozoans EXCEPT? a. Unicellular prokaryotes 38. In biofuels, which of the following microorganisms is/are b. Cell wall present involved in the conversion of biomass into useful energy c. Require moist environments sources? d. Classification based on cell ultrastructure and molecular a. Anaerobic analysis b. Aerobic e. Two of the choices are correct. c. Microaerophilic f. None of the above d. All of the above 25. Mycelia are thread-like structures. A mass of mycelium 39. Exploitation of photosynthetic bacteria or algae is mostly is called a hyphae. involved in what application of microorganisms? a. Only the first statement is correct. a. Biogas b. Only the second statement is correct. b. Microbial geotechnology c. Both statements are correct. c. Biofuels d. Both statements are incorrect. d. Bioprospecting 26. The following organisms both have cyst and trophozoite life 40. The following are benefits of probiotics EXCEPT: stages in their life cycles EXCEPT: a. It improves stool concentration. PH153: Microbial Diversity BSPH2025 Aguila, Decio, De Guzman, L., Estilloso 9  b. It aids digestion. 16. A Bioclogging and biocementation → applications of c. It can be ingested as food products. microbial geotechnology. d. None of the above. Biorefinery is a phase in the biofuel life cycle. True or False: 17. D 41. The Gram staining technique differentiates bacteria based on 18. D Fermentation: conversion of starch to sugar the presence of lipopolysaccharides in Gram-positive bacteria. Saccharomyces cerevisiae (baker’s yeast) is used in 42. Zygomycota fungi produce zygospores through the fusion of fermentation haploid hyphae from the same mating type. 43. Candida species are exclusively yeast forms and do not 19. D Wine production: fermentation using yeast exhibit a mold form under any conditions. Biogas and biofuel production: methane fermentation. 44. Euglenozoa is a group of protozoa that includes amoebae, Bacterial exopolymer production: biofilm production. euglenoids, and kinetoplastids. 45. A merozoite is a large, multinucleated cell that undergoes 20. C cytokinesis to produce multiple daughter cells. 46. In the context of fungal classification, the term 21. D Carbon → carbohydrates; aerobic → anaerobic "Deuteromycota" refers to fungi that reproduce exclusively through asexual means. 22. D Slime molds are fungus-like protists 47. In the production of wine, yeast is added after grapes are crushed to convert sugars into alcohol. 23. C 48. Slime molds are classified as fungi due to their role in decomposing organic matter. 24. E Unicellular prokaryotes → Unicellular eukaryotes; cell 49. Biocementation involves the creation of pore-filling materials wall present → cell wall absent to reduce soil porosity and hydraulic conductivity. 50. Biogas production involves the use of photosynthetic bacteria to convert sunlight into energy, which can then be used as fuel. 25. D Hyphae - Thread-like structures; Mycelia: a mass of hyphae ANSWER KEY: 26. B 1. A. Articulated → lays to rest or disprove 27. D 2. B. Shigella : Acute bloody diarrhea Rotavirus : Acute watery diarrhea 28. A 3. C. Joseph Lister: founder of Aseptic surgery Paul Ehrlich: developed antimicrobials 29. F 4. A. Do not have a peptidoglycan layer → have a thin 30. E peptidoglycan layer and outer membrane 31. B 5. B. Leprosy → Mycobacterium leprae Leptospirosis → Leptospira interrogans 32. A 6. D. Protozoans are eukaryotic pathogens 33. C 7. A. Intracellular enzymes → Extracellular enzymes 34. D 8. C. A. Exist as mold in culture and yeast in the body. 35. B B. Amphotericin B: Treatment against fungal infections; Penicillium and Cephalosporium: Antibiotics produced by fungi 36. B D. Superficial diseases → Cutaneous diseases 37. C 9. D 38. A 10. C 39. A 11. A 40. A (It improves bowel movement, not stool 12. D. Histoplasma is an etiologic agent of systemic concentration.) mycoses 41. False (Lipopolysaccharides are found in Gram-negative 13. B Bioclogging: reduce porosity and hydraulic bacteria) conductivity 42. False (Zygospores are produced by the fusion of 14. E All are suitable for geotechnical engineering based on haploid hyphae from opposite mating types.) Ivanov & Chu (2008) 43. False (Candida can exhibit both yeast and mold forms, 15. C Ruminococci and Bifidobacteria → intestinal showing dimorphism.) microflora Saccharomyces cerevisiae (baker’s yeast) is used in 44. True fermentation 45. False (A merozoite is a small cell produced during PH153: Microbial Diversity BSPH2025 Aguila, Decio, De Guzman, L., Estilloso 10  schizogony, not a large, multinucleated cell.) 46. True 47. True 48. False (Slime molds are classified as fungus-like protists, not true fungi.) 49. False (Biocementation involves the generation of particle-binding materials to increase soil shear strength, not reduce porosity.) 50. False (Biogas production typically involves anaerobic microorganisms breaking down organic matter, not photosynthetic bacteria.) PH153: Microbial Diversity BSPH2025 Aguila, Decio, De Guzman, L., Estilloso 11  APPENDICES Figure A-1. Parts of a Paramecium Figure A-2. Examples of microorganisms as agents of infection (Bacteria - 3,4,5,7,8; Virus - 2,6,9; 1 - Protozoa). PH153: Microbial Diversity BSPH2025 Aguila, Decio, De Guzman, L., Estilloso 12