### **Definitions:** . **Assimilation**: The process by which organisms acquire elements (such as carbon, 1 nitrogen, etc.) to build cellular structures. . **Dissimilation**: The breakdown of organic nutrients to inorganic minerals, usually for energy 2 release. . **Biomass**: The total mass of living organisms in a given area or ecosystem at a particular 3 time. . **Trophic Levels**: The hierarchical levels in an ecosystem, based on how organisms obtain 4 their energy (e.g., producers, primary consumers, secondary consumers). . **Symbiosis**: The intimate relationship between two or more organisms, which may be 5 beneficial or harmful to one or both parties. 6. **Mutualism**: A type of symbiosis in which both organisms benefit. . **Commensalism**: A relationship in which one organism benefits, and the other is 7 unaffected. 8. **Parasitism**: A relationship in which one organism benefits at the expense of the other. 9. **Synergism**: A type of cooperation where both species benefit but could live separately. 0. **Syntrophy**: A relationship where one organism partially digests food, which is further 1 processed by another organism. 1. **Microbial Genome**: The genetic material (DNA or RNA) that defines the characteristics of 1 a microorganism and its ability to fill a particular ecological niche. 2. **Metagenomics**: The analysis of microbial communities' genetic material in their 1 environment to understand their biodiversity and functional potential. 3. **Endosymbiosis**: The symbiotic relationship where one organism lives inside the cells or 1 tissues of another, often leading to co-evolution. 4. **Horizontal Gene Transfer (HGT)**: The transfer of genetic material between organisms in 1 a manner other than through vertical inheritance (parent to offspring). Common in microbes. 5. **Vertical Gene Transfer**: The passing of genetic material from parent to offspring during 1 reproduction. 6. **Biogeochemical Cycles**: Natural processes that recycle nutrients and elements in 1 ecosystems, involving biological, geological, and chemical components. 7. **Microbial Food Web**: The network of interactions between different microbial species in 1 an ecosystem where energy and nutrients are cycled through various trophic levels. --- ### **Drugs and Their Uses:** 1. **Penicillin**: - **Use**: Antibiotic; used to treat bacterial infections by inhibiting bacterial cell wall synthesis. 2. **Tetracycline**: - **Use**: Broad-spectrum antibiotic; inhibits bacterial protein synthesis, effective against a wide variety of bacteria. 3. **Chloramphenicol**: - **Use**: Antibiotic; inhibits protein synthesis in bacteria, used for serious infections like typhoid fever and meningitis. 4. **Sulfonamides**: - **Use**: Antibiotic; inhibits bacterial folic acid synthesis, preventing bacterial growth. 5. **Erythromycin**: - **Use**: Antibiotic; inhibits protein synthesis in bacteria, used for respiratory and skin infections. 6. **Streptomycin**: - **Use**: Antibiotic; inhibits bacterial protein synthesis, effective against tuberculosis and other infections. 7. **Rifampin**: - **Use**: Antibiotic; inhibits bacterial RNA synthesis, used to treat tuberculosis and other infections. 8. **Vancomycin**: - **Use**: Antibiotic; inhibits cell wall synthesis, effective against Gram-positive bacteria, including MRSA. 9. **Isoniazid**: - **Use**: Antibiotic; inhibits mycolic acid synthesis in the cell wall, used to treat tuberculosis. 10. **Amphotericin B**: - **Use**: Antifungal; binds to ergosterol in fungal membranes, used to treat systemic fungal infections. 11. **Acyclovir**: - **Use**: Antiviral; inhibits viral DNA synthesis, used to treat herpes simplex virus (HSV) infections. 12. **Oseltamivir**: - **Use**: Antiviral; inhibits neuraminidase enzyme, used to treat influenza. 13. **Azithromycin**: - **Use**: Antibiotic; a macrolide antibiotic used to treat respiratory, skin, and sexually transmitted infections. 14. **Ciprofloxacin**: - **Use**: Antibiotic; a fluoroquinolone used to treat urinary tract infections, respiratory infections, and more. 15. **Metronidazole**: - **Use**: Antiprotozoal/antibiotic; used to treat protozoal infections and bacterial infections, such as C. difficile. --- ### **Microbes and Their Functions:** 1. **Streptomyces spp.**: - **Function**: Soil-dwelling bacteria; important for the degradation of organic matter and produce many antibiotics like streptomycin. 2. **Rhizobium**: - **Function**: Nitrogen-fixing bacteria; form symbiotic relationships with legumes to convert atmospheric nitrogen into a form usable by plants. 3. **Escherichia coli**: - **Function**: A common bacterium in the human intestine; some strains are harmless while others can cause food poisoning. 4. **Lactobacillus spp.**: - **Function**: Lactic acid bacteria; ferment lactose to produce lactic acid, contributing to the production of yogurt and other dairy products. 5. **Bacillus thuringiensis**: - **Function**: Soil bacterium; produces toxins that are toxic to insects, used as a biological pesticide. 6. **Myxotricha paradoxa**: - **Function**: A ciliate that resides in the guts of termites; has bacterial endosymbionts that help digest cellulose from wood. 7. **Nitrosomonas**: - **Function**: Nitrifying bacteria; oxidize ammonia into nitrites as part of the nitrogen cycle. 8. **Sulfolobus**: - **Function**: Thermophilic archaeon; lives in hot, acidic environments and oxidizes sulfur for energy. 9. **Vibrio cholerae**: - **Function**: Bacterium; causes cholera, a disease characterized by severe diarrhea, by producing cholera toxin. 10. **Pseudomonas aeruginosa**: - **Function**: Opportunistic pathogen; can cause infections in immunocompromised individuals, produces biofilms and has antibiotic resistance. 11. **Saccharomyces cerevisiae**: - **Function**: Yeast; used in baking, brewing, and as a model organism in genetics and cell biology. 12. **Cyanobacteria**: - **Function**: Photosynthetic bacteria; important for carbon fixation and oxygen production in aquatic ecosystems. 13. **Clostridium botulinum**: - **Function**: Anaerobic bacterium; produces botulinum toxin, responsible for botulism, a form of food poisoning. 14. **Archaea (e.g., Methanogens)**: - **Function**: Methanogens produce methane as a byproduct of metabolism, found in anoxic environments like swamps and the guts of ruminants. 15. **Enterococcus spp.**: - **Function**: Normal flora in the human intestines, can cause infections like urinary tract infections and bacteremia in immunocompromised individuals. 16. **Corynebacterium diphtheriae**: - **Function**: Pathogenic bacterium; causes diphtheria, a disease that affects the throat and can lead to difficulty breathing. 17. **Agaricus bisporus**: - **Function**: A species of edible mushroom; used in food production and research in microbiology. 18. **Bordetella pertussis**: - **Function**: Bacterium that causes whooping cough (pertussis), characterized by severe coughing spells. Pili Definition: Pili are hair-like structures on the surface of bacteria that aid in adhesion to surfaces, cells, and other bacteria. They are also involved in genetic transfer through conjugation. ypes of Pili: T Type I Pili: Help bacteria adhere to surfaces and cells. Common in uropathogenic E. coli. Type IV Pili: Involved in motility (twitching) and can assist in DNA transfer during conjugation. Sex Pili: Specialized pili involved in the process of conjugation, which is the exchange of genetic material between bacteria. Phages (Bacteriophages) Definition: Viruses that infect and replicate within bacterial cells. ypes of Phages: T Lytic Phages: Replicate within the host and cause cell lysis to release new phage particles. Lysogenic Phages: Integrate their genetic material into the host genome, becoming a prophage, and replicate with the host until triggered to enter the lytic cycle. Exotoxins Definition: Toxic proteins secreted by bacteria that can damage host cells and tissues. ypes of Exotoxins: T A-B Toxins: Composed of two parts; the A subunit is the active part, and the B subunit binds to the host cell receptor. Example: Diphtheria toxin. Superantigens: Bind to MHC class II molecules and T cell receptors, causing an excessive immune response. Example: Toxic shock syndrome toxin (TSST). Membrane-Damaging Toxins: Directly damage host cell membranes. Example: Hemolysins by Staphylococcus aureus. Enzymatic Toxins: Break down host cell structures and interfere with host biochemical processes. Example: Collagenase by Clostridium perfringens. Toxin Secretion Systems Definition: Systems that bacteria use to produce and/or inject toxins into host cells or the extracellular environment. Types of Toxin Secretion Systems: ype I Secretion System (T1SS): Transport toxins directly into the extracellular space, T bypassing the inner and outer membrane. Example: Hemolysins by E. coli. Type II Secretion System (T2SS): Transports proteins through both the inner and outer membranes. Example: Cholera toxin by Vibrio cholerae. Type III Secretion System (T3SS): A needle-like structure that injects toxins directly into host cells. Example: Salmonella and Yersinia. Type IV Secretion System (T4SS): Transports both proteins and DNA, involved in conjugation and pathogenesis. Example: Agrobacterium tumefaciens. Type VI Secretion System (T6SS): A syringe-like structure used to inject toxic proteins into competing bacteria or host cells. Horizontal Gene Transfer (HGT) Definition: The transfer of genetic material between organisms, not through reproduction, but via other means such as plasmids or bacteriophages. Examples of Horizontal Gene Transfer: Plasmid Transfer: Movement of genetic material via plasmids, often conferring antibiotic resistance. Transposable Elements: DNA sequences that can change their position within the genome, contributing to genetic variation. Bacteriophages: Viruses that can transfer genes between bacteria. Pathogenicity Islands: Large sets of genes transferred as a unit that confer the ability to invade host organisms. Example: E. coli O157:H7. Endosymbionts and Endosymbiosis Definition: Organisms that live inside another organism, often benefiting from the relationship. xamples: E Mitochondria and Chloroplasts: Evolved from bacteria (e.g., Rickettsia and cyanobacteria) and retain features like circular chromosomes, prokaryotic ribosomes, and the ability to reproduce independently. Rhizobium: Bacteria that live in leguminous plant roots, fixing nitrogen in exchange for organic carbon from the plant. Microbial Symbiosis Definition: The interaction between two different species of organisms, often microorganisms and a larger organism, that can have different types of outcomes. ypes of Symbiosis: T Mutualism: Both organisms benefit from the relationship. Example: Lichens (fungus and algae/cyanobacteria) and Rhizobium (in legume roots). Parasitism: One organism benefits at the expense of the other. Example: Plant pathogens like Agrobacterium (induces plant galls). Synergism: Both organisms benefit but can live independently. Example: Colonic bacteria and methanogens in the human gut. Commensalism: One organism benefits while the other is unaffected. Example: Bacteroides in the human gut. yntrophy: A cooperative metabolic relationship where one organism partially digests food for S another. Example: Cellulolytic bacteria and methanogens in the rumen of cattle. Marine Microbiology Definition: The study of microorganisms in the ocean, including plankton and other organisms that form the base of marine food webs. ypes of Marine Microbial Communities: T Plankton: Organisms that float in the ocean's water column. Microplankton (20-200 μm) Nanoplankton (2-20 μm) Picoplankton (0.2-2 μm) Femtoplankton (0.01-0.02 μm) Thermal Vent Communities: Microbes that thrive in extreme conditions, such as sulfur-oxidizing bacteria and methanotrophs. Soil Microbiology Definition: The study of microorganisms in soil, including their roles in nutrient cycling and plant-microbe interactions. ypes of Soil Microbial Communities: T Mycorrhizae: Fungal associations with plant roots that help with nutrient uptake. Ectomycorrhizae: Fungi that colonize the root surface. Endomycorrhizae: Fungi that penetrate plant roots. Nitrogen-Fixing Bacteria: Bacteria that fix nitrogen, such as Rhizobium, which live in plant roots and convert atmospheric nitrogen into a form usable by plants. Decomposers: Fungi and bacteria that break down organic material in the soil. Example: Streptomyces spp. (gives soil its characteristic odor).
