BIO 101 - General Biology 1 November 2024 PDF

P r o f. S u n d a y B. A k i n d e Department of Microbiology, Faculty of Basic and Applied Sciences, Osun State University, Osogbo, Nigeria Email: [email protected] Phone: 08033798688 BIO 101 Synopsis ▪ Characteristics and classification of living things,...

P r o f. S u n d a y B. A k i n d e Department of Microbiology, Faculty of Basic and Applied Sciences, Osun State University, Osogbo, Nigeria Email: [email protected] Phone: 08033798688 BIO 101 Synopsis ▪ Characteristics and classification of living things, Basic cell types, Prokaryotic and Eukaryotic cells, Cell structure and organization, Functions of cellular organelles; Homeostasis ▪ General characteristics of microorganisms, structure, ecology and reproduction, Distribution of microorganisms in nature ▪ Nutrient and Enzymes, Endocrine system ▪ Reproduction ▪ Digestion and Excretion ▪ Respiration, Growth and Development ▪ Mitosis, Meiosis and Heredity 2 Microbiology Module ▪ Characteristics and classification of living things, Basic cell types, Prokaryotic and Eukaryotic cells, Cell structure and organization, Functions of cellular organelles; Homeostasis ▪ General characteristics of microorganisms, structure, ecology and reproduction, Distribution of microorganisms in nature ▪ Nutrient and Enzymes, Endocrine system ▪ Reproduction ▪ Digestion and Excretion ▪ Respiration, Growth and Development ▪ Mitosis, Meiosis and Heredity 3 Module Lecturers ▪ Prof. Sunday Babatunde AKINDE ▪ Temitope Fasunloye AJANI 4 Module Contents ▪ General Characteristics of Microorganisms. ▪ Structure, Ecology and Reproduction of Microorganisms. ▪ Distribution of Microorganisms in Nature. 5 Introduction – Microbiology World (1/2) ▪ Microbiology - Scientific study of microorganisms. ▪ Examples - Bacteria, Viruses, Fungi, Protozoa, and Algae. ▪ Despite their small size, these organisms play a monumental role in shaping life on Earth. ✓ Drive essential processes such as nutrient cycling, decomposition, and the maintenance of ecosystems. ✓ Contribute to human health, agriculture, and industry. ✓ At the same time, certain microbes pose challenges as pathogens, causing diseases in humans, animals, and plants. 6 Introduction – Microbiology World (2/2) By exploring the microbiological world, we gain insights into the: ✓ fundamental biological processes; ✓ discover solutions to pressing global issues; and ✓ harness the potential of microorganisms for innovative applications in medicine, biotechnology, environmental sustainability, food security, etc. 7 Classification of Microorganisms ▪ The classification of microorganisms involves organizing and categorizing them based on shared characteristics. ▪ This system of classification provides a framework for identifying, studying, and understanding their diversity, relationships, and roles in nature. ▪ Microorganisms are classified into domains, kingdoms, and further subdivisions using morphological, biochemical, genetic, and ecological criteria. 8 Classification Systems in Microbiology (1/4) 1. Early Systems of Classification: Two- Kingdom System (Linnaeus, 1735) 2. Five-Kingdom System (Whittaker, 1969) https://www.nursinghero.com/study-guides/boundless- microbiology/methods-of-classifying-and-identifying- microorganisms 3. Three-Domain System (Woese et al., 1990) 9 Classification Systems in Microbiology (2/4) 1. Early Systems of Classification (Linnaeus, 1735) Classification based on Two-Kingdom System. ✓ Plantae ✓ Animalia ▪ Limitation Failed to account for microorganisms that did not fit neatly into these categories. 10  Classification Systems in Microbiology (3/4) 2. Five-Kingdom System (Whittaker, 1969) Classification based on cellular organization and mode of nutrition: ✓ Monera: Prokaryotes (e.g., bacteria and cyanobacteria). ✓ Protista: Unicellular eukaryotes (e.g., protozoa, algae). ✓ Fungi: Saprophytic eukaryotes (e.g., molds, yeasts). ✓ Plantae: Photosynthetic, multicellular organisms. ✓ Animalia: Multicellular organisms that ingest food. ▪ Limitation Did not account for genetic relationships. 11 Classification Systems in Microbiology (4/4) 3. Three-Domain System (Woese et al., 1990) Classification based on ribosomal RNA (rRNA) gene sequences Bacteria: True prokaryotes (e.g., Escherichia coli). Archaea: Prokaryotes with unique genetic and metabolic traits, often inhabiting extreme environments. Eukarya: Organisms with membrane-bound organelles (includes protists, fungi, plants, and animals). Carl Richard Woese (1928 – 2012) 12  Major Groups of Microorganisms (1/2) Group Domain Characteristics Examples Bacteria Bacteria Prokaryotic, unicellular organisms. Staphylococcus aureus (pathogen), Reproduce by binary fission. Lactobacillus (fermentation). Diverse shapes (e.g., cocci, bacilli, spirilla). Can be autotrophic or heterotrophic. Archaea Archaea Prokaryotic, genetically distinct from bacteria. Methanogens (produce methane), Found in extreme environments (e.g., hot springs, salt lakes). Halophiles (thrive in high salt). Unique cell membrane lipids. Fungi Eukarya Eukaryotic, may be unicellular (yeasts) or multicellular (molds, Saccharomyces cerevisiae (baking mushrooms). yeast), Aspergillus (industrial Heterotrophic, absorb nutrients. enzyme production). Decomposers, pathogens, or used in fermentation. Protists Eukarya Eukaryotic, mostly unicellular, some multicellular (e.g., algae). Amoeba proteus (protozoan), Can be autotrophic (algae) or heterotrophic (protozoa). Chlamydomonas (algae). Diverse locomotion (flagella, cilia, pseudopodia). 13  Major Groups of Microorganisms (2/2) Group Domain Characteristics Examples Viruses Non-cellular Genetic material (DNA or RNA) enclosed in a protein coat. Influenza virus, HIV. Obligate intracellular parasites, replicate only in host cells. Algae Eukarya Photosynthetic eukaryotes. Spirogyra, Chlorella. Found in aquatic environments. Can be unicellular (e.g., diatoms) or multicellular (e.g., seaweeds). Other Non- Non-cellular Viroids: Small, circular RNA molecules infecting plants. Viroids (plant pathogens), Prions Living Entities Prions: Infectious proteins causing neurodegenerative (Creutzfeldt-Jakob disease). Infectious diseases. Agents 14 Significance of Classification 1. Aids in identifying microorganisms and their relationships. 2. Provides insights into microbial evolution and ecology. 3. Facilitates the development of medical, industrial, and environmental applications. 4. Helps in tracking and managing microbial pathogens. 15 General Characteristics of Microorganisms ▪ Microorganisms are a diverse group of microscopic organisms that play critical roles in the environment, human health, and various industries. ▪ This group includes bacteria, archaea, fungi, protozoa, algae, and viruses. ▪ Despite their small size, they exhibit unique characteristics that enable them to thrive in diverse environments. 16 General Characteristics of Microorganisms (1/4) 1. Size and Structure ▪ Microscopic Size: Most microorganisms are too small to be seen with the naked eye, typically ranging from nanometers (e.g., viruses) to micrometers (e.g., bacteria). ▪ Simple Structure: They often lack the complex organ systems found in multicellular organisms. ✓ Prokaryotes (e.g., bacteria, archaea): Lack a nucleus and membrane-bound organelles. ✓ Eukaryotes (e.g., fungi, protozoa, algae): Possess a defined nucleus and organelles. 2. Diversity in Habitat ▪ Microorganisms are ubiquitous, inhabiting extreme environments such as hot springs, deep-sea vents, acidic lakes, and polar ice caps. ▪ They are present in soil, water, air, and even inside other organisms (e.g., gut microbiota in humans). 17 General Characteristics of Microorganisms (2/4) 3. Reproduction ▪ Asexual Reproduction: Common in prokaryotes, involving binary fission, budding, or spore formation. ▪ Sexual Reproduction: Observed in some eukaryotic microorganisms (e.g., fungi), involving genetic recombination. ▪ Rapid Multiplication: Enables them to adapt quickly to environmental changes. 4. Metabolic Versatility ▪ Microorganisms display a wide range of metabolic capabilities: ✓ Autotrophs: Use inorganic substances (e.g., photosynthetic algae and cyanobacteria). ✓ Heterotrophs: Depend on organic materials for nutrition (e.g., fungi, protozoa). ✓ Anaerobes: Survive without oxygen (e.g., certain archaea). ✓ Aerobes: Require oxygen for survival. 18 General Characteristics of Microorganisms (3/4) 5. Genetic Adaptability ▪ Microorganisms can adapt rapidly to environmental pressures through: ✓ Mutation. ✓ Horizontal gene transfer (e.g., conjugation, transformation, transduction). ▪ These adaptations often confer advantages such as antibiotic resistance or enhanced survival in hostile environments. 6. Ecological Roles ▪ Decomposers: Break down organic matter, recycling nutrients in ecosystems. ▪ Producers: Algae and cyanobacteria produce oxygen through photosynthesis. ▪ Symbionts: Form mutualistic relationships with plants, animals, and humans. ▪ Pathogens: Some cause diseases in plants, animals, and humans. 19 General Characteristics of Microorganisms (4/4) 7. Interactions with Humans ▪ Beneficial Roles: ✓ Used in food production (e.g., yeast in bread, bacteria in yogurt). ✓ Essential for biotechnology and pharmaceuticals (e.g., antibiotics, vaccines). ✓ Aid in environmental applications (e.g., bioremediation). ▪ Harmful Roles: ✓ Cause infectious diseases (e.g., tuberculosis, malaria). ✓ Lead to food spoilage. 8. Classification ▪ Microorganisms are classified based on their characteristics: ✓ Prokaryotes: Bacteria and archaea. ✓ Eukaryotes: Fungi, protozoa, algae. ✓ Non-cellular Entities: Viruses, viroids, and prions. 20 Summary of General Characteristics ▪ Microorganisms are ubiquitous and indispensable to life on Earth. ▪ Their diverse characteristics and roles in ecosystems, industries, and health make them a fundamental area of study in microbiology. ▪ Understanding their general traits provides a foundation for exploring their vast potential and addressing the challenges they pose. 21 Structure, Ecology and Reproduction of Microorganisms 22 Structure of Microorganisms ▪ Microorganisms, though microscopic, exhibit diverse structural features that help them survive and thrive in various environments. ▪ Their structures are broadly categorized based on their type (prokaryotic or eukaryotic) and provide insight into their functions, roles, and interactions within ecosystems. 23 General Structures (1/5) 1. Cellular Structures in Prokaryotes Cell Wall: Provides shape and protection. Plasma Membrane: Semi-permeable barrier for transport and metabolic activities. Cytoplasm: Gel-like substance containing enzymes, ribosomes, and DNA. Nucleoid: Region containing circular DNA. Ribosomes (70S): Sites of protein synthesis. Flagella: For motility. Pili/Fimbriae: For attachment and genetic exchange. Capsule/Slime Layer: Protective layers outside the cell wall. Inclusion Bodies: Storage of nutrients like glycogen or sulfur. Endospores: Dormant, resistant structures in some bacteria. 24 General Structures (2/5) 2. Cellular Structures in Eukaryotes Nucleus: Membrane-bound organelle containing DNA. Mitochondria: Site of ATP production. Chloroplasts: Photosynthetic organelles in algae. Endoplasmic Reticulum (ER): o Rough ER: Protein synthesis. o Smooth ER: Lipid synthesis. Golgi Apparatus: Modifies and packages proteins. Lysosomes: Contain digestive enzymes. Cytoskeleton: Provides structural support and aids in transport. Flagella: Long whip-like structures for movement (e.g., in Euglena). Cilia: Short, hair-like structures for movement (e.g., in Paramecium). Pseudopodia: Cytoplasmic extensions for movement and feeding (e.g., in Amoeba). Cell Wall: Found in fungi (chitin) and algae (cellulose). 25 General Structures (1/5) ▪ Comparison of Prokaryotic and Eukaryotic Structures. Feature Prokaryotes Eukaryotes Size 0.1–5 µm 10–100 µm Nucleus No nucleus, nucleoid region True nucleus with nuclear membrane Organelles None Membrane-bound organelles 80S (cytoplasm) and 70S Ribosomes 70S (mitochondria/chloroplasts) Cell Wall Peptidoglycan (bacteria) Cellulose (algae), chitin (fungi) Reproduction Binary fission Mitosis and meiosis 26 General Structures (4/5) 3. Non-Cellular Structures in Viruses Capsid: Protein coat protecting genetic material. Genetic Material: DNA or RNA. Envelope: Lipid layer derived from the host cell (in enveloped viruses). Spikes: Surface proteins used for host attachment. 27 General Structures (5/5) 4. Specialized Structures Viroids: RNA molecules without a protein coat, infect plants. Prions: Misfolded proteins causing diseases like Creutzfeldt-Jakob disease. 28 Structure of Microorganisms (1/3) 29 Structure of Microorganisms (2/3) 30 Structure of Microorganisms (3/3) 31 Significance of Structural Features in Microorganisms ▪ Adaptation: Structural variations help microorganisms adapt to diverse environments. ▪ Pathogenicity: Structures like capsules and flagella enhance the ability to infect hosts. ▪ Biotechnology: Knowledge of structures aids in the development of antibiotics, vaccines, and industrial applications. ▪ Ecological Roles: Structures like chloroplasts and pseudopodia facilitate photosynthesis and nutrient cycling. 32 Ecology of Microorganisms ▪ The ecology of microorganisms is the study of how microorganisms interact with their environment, other organisms, and each other. ▪ These interactions play vital roles in ecosystems by influencing nutrient cycling, energy flow, and the functioning of living organisms. ▪ Microbial ecology spans terrestrial, aquatic, and extreme environments, showcasing the adaptability and diversity of microorganisms.. 33 Microbial Habitats 1. Terrestrial Environments ✓ Soil: A major habitat for microorganisms such as bacteria, fungi, and actinomycetes. ✓ Rhizosphere: The root-soil interface, enriched with nutrients from plants, supporting diverse microbes. ✓ Rocks: Endolithic microorganisms colonize rock surfaces or interiors, surviving harsh conditions. 2. Aquatic Environments ✓ Freshwater: Includes lakes, rivers, and streams; microorganisms such as Cyanobacteria and algae dominate. ✓ Marine: Oceans harbor phytoplankton, bacteria, and archaea contributing to global carbon and nitrogen cycles. ✓ Wetlands: Support anaerobic microbes involved in methane production and organic matter decomposition. 3. Extreme Environments ✓ Hydrothermal Vents: Home to thermophilic archaea and bacteria. ✓ Salt Flats: Support halophilic microorganisms. ✓ Polar Regions: Psychrophilic microbes thrive in sub-zero temperatures. ✓ Acidic/Alkaline Environments: Acidophiles and alkaliphiles adapt to extreme pH levels. 34 Types of Microbial Interactions (1/2) 1. Microbe-Microbe Interactions ✓ Symbiosis: Mutual benefit (e.g., Rhizobium and legumes). ✓ Commensalism: One benefits, the other remains unaffected. ✓ Parasitism: One benefits at the expense of the other (e.g., viruses infecting bacteria). ✓ Competition: Microbes compete for limited resources, such as nutrients. 2. Microbe-Plant Interactions ✓ Nitrogen Fixation: Symbiotic bacteria (Rhizobium, Azotobacter) fix atmospheric nitrogen into usable forms. ✓ Mycorrhizae: Fungi form mutualistic relationships with plant roots, enhancing nutrient absorption. ✓ Pathogenicity: Some microbes cause diseases in plants (e.g., Pseudomonas syringae). 35 Types of Microbial Interactions (2/2) 3. Microbe-Animal Interactions ✓ Gut Microbiota: Microorganisms in the digestive tracts of animals aid in digestion and immunity (e.g., E. coli in humans). ✓ Ruminants: Microbes in the stomach of ruminant animals help digest cellulose. ✓ Pathogens: Microbes can also cause diseases in animals (e.g., Bacillus anthracis causing anthrax). 4. Microbe-Environment Interactions ✓ Decomposition: Microbes break down organic matter, recycling nutrients. ✓ Biogeochemical Cycles: Microbes mediate carbon, nitrogen, sulfur, and phosphorus cycles. ✓ Bioremediation: Microorganisms degrade pollutants and clean up contaminated environments. 36 Microbial Roles in Ecosystems 1. Producers ✓ Photosynthetic microbes such as Cyanobacteria and algae convert sunlight into chemical energy. ✓ Chemolithotrophic bacteria oxidize inorganic compounds to generate energy in the absence of sunlight. 2. Decomposers ✓ Break down organic matter into simpler compounds, recycling nutrients for other organisms. 3. Consumers ✓ Predatory bacteria like Bdellovibrio consume other microorganisms. ✓ Parasitic microorganisms derive nutrients from their hosts. 37 Microbial Communities 1. Biofilms ✓ Complex, surface-attached microbial communities encased in a self-produced matrix. ✓ Found in natural environments (e.g., river rocks), industrial settings (e.g., pipelines), and medical devices. 2. Microbiomes ✓ Entire communities of microorganisms associated with a particular environment or host (e.g., human microbiome). 3. Microbial Succession ✓ Changes in microbial community composition over time, influenced by environmental conditions or disturbances. 38 Adaptations of Microorganisms to Their Environment 1. Metabolic Diversity: Ability to use diverse energy and carbon sources. 2. Survival Mechanisms: ✓ Endospore formation in bacteria like Bacillus. ✓ Production of protective enzymes (e.g., catalase to neutralize reactive oxygen species). 3. Genetic Adaptation: Horizontal gene transfer enhances adaptability to changing environments. 39  Applications of Microbial Ecology 1. Environmental Applications ✓ Bioremediation of polluted sites. ✓ Wastewater treatment. 2. Agriculture ✓ Enhancing soil fertility through nitrogen-fixing bacteria. ✓ Biocontrol agents against pests and pathogens. 3. Public Health ✓ Understanding the role of microbiomes in health and disease. 4. Industry ✓ Microbial production of biofuels, enzymes, and pharmaceuticals. 40 Reproduction of Microorganisms ▪ Microorganisms reproduce through various mechanisms to increase their population and ensure survival. ▪ Their reproductive strategies can be classified as asexual or sexual, depending on the organism and environmental conditions. ▪ Each mode of reproduction is adapted to their structure, physiology, and ecological niche. 41  Modes of Reproduction in Microorganisms Mode of Type Process Examples Reproduction Asexual Binary Fission A single cell divides into two identical daughter cells. Escherichia coli Reproduction Steps: DNA replication → Cell elongation → Septum formation → Separation. Saccharomyces cerevisiae Budding A small outgrowth (bud) forms on the parent cell, grows, and detaches. (yeast) Multicellular organisms break into fragments, each growing into a new Fragmentation Penicillium (fungi) organism. Sporulation Formation of spores that germinate under favorable conditions. Aspergillus (conidiospores), Bacillus, Clostridium Types: Conidiospores (fungi), Endospores (bacteria). (endospores) Plasmodium (parasitic Schizogony Multiple fissions where the nucleus divides several times before cell splits. protozoa) Sexual Transfer of genetic material through direct contact between donor (F+) and Conjugation Escherichia coli Reproduction recipient (F-) cells. Syngamy Fusion of two gametes to form a zygote. Chlamydomonas (algae) Meiosis and Spore Sexual reproduction in fungi involves meiosis to form sexual spores. Rhizopus (zygospores), Formation Types of spores: Zygospores, Ascospores, Basidiospores. Saccharomyces (ascospores), Agaricus (basidiospores) 42  Reproductive Strategies in Specific Microorganisms Microorganism Reproductive Strategies Examples/Details Bacteria - Predominantly reproduce by binary fission. Escherichia coli - Exchange genetic material via horizontal gene transfer mechanisms: - Conjugation: Direct transfer through a pilus. Escherichia coli - Transformation: Uptake of free DNA from the environment. Streptococcus pneumoniae - Transduction: Transfer mediated by bacteriophages. Salmonella Saccharomyces cerevisiae, Fungi - Asexual reproduction via budding or sporulation. Aspergillus Rhizopus (zygospores), - Sexual reproduction involves plasmogamy, karyogamy, and meiosis to form spores. Agaricus (basidiospores) Protozoa - Asexual reproduction includes binary fission and schizogony. Plasmodium (schizogony) - Sexual reproduction includes syngamy and conjugation (e.g., ciliates like Paramecium). Paramecium Viruses - Do not reproduce independently; replicate by hijacking host cell machinery. - Steps of replication: (1) Attachment to host cell. (2) Entry of genetic material. (3) Influenza virus, HIV Replication of viral components. (4) Assembly of new virions. (5) Release from host cell. Algae - Asexual reproduction through binary fission, fragmentation, or spore formation. Chlamydomonas, Spirogyra - Sexual reproduction involves gametes that fuse to form a zygote. Chlamydomonas 43 Factors Influencing Microbial Reproduction 1. Nutrient Availability: Sufficient nutrients enhance growth and reproduction. 2. Temperature: Optimal temperature promotes enzymatic activities. 3. pH: Most microorganisms prefer neutral pH, though extremophiles adapt otherwise. 4. Moisture: Essential for metabolic processes and reproduction. 5. Oxygen: Aerobes and anaerobes reproduce differently depending on oxygen availability. 6. Light: Critical for photosynthetic microorganisms like algae. 44 Distribution of Microorganisms in Nature ▪ Microorganisms are ubiquitous in nature, meaning they exist in almost every environment, from the deepest oceans to the highest mountains, and even within other organisms. ▪ Their diversity and adaptability allow them to thrive in extreme conditions where other life forms may not survive. ▪ This distribution plays a crucial role in ecological balance, nutrient cycling, and the survival of all life forms on Earth. 45  Microbial Distribution in Different Environments (1/3) Environment Type Subcategory Microbial Characteristics Examples Terrestrial Rhizobium in rhizosphere Soil Rich in diverse microorganisms (bacteria, fungi, actinomycetes). Environments fixes nitrogen. Microbes play roles in nutrient cycling, decomposition, and plant growth. Microorganisms exist in rocks and deep subsurface layers, Subsurface Endolithic microbes metabolizing inorganic compounds. Desiccation-tolerant microbes like cyanobacteria survive on Arid Regions Cyanobacteria surfaces with minimal water. Aquatic Includes rivers, lakes, and ponds. Dominated by cyanobacteria Freshwater Cyanobacteria, algae Environments and algae, contributing to oxygen production and food chains. Oceans harbor diverse microbes like phytoplankton, bacteria, Phytoplankton, Marine and archaea. Extremophiles thrive in deep-sea vents. extremophiles Support anaerobic microbes that produce methane and Wetlands Methanogens decompose organic material. Atmospheric Microorganisms, including fungal spores and bacteria, are Bioaerosols Environments found in the atmosphere. Influence cloud formation. Fungal spores, bacteria 46 Microbial Distribution in Different Environments (2/3) Environment Type Subcategory Microbial Characteristics Examples Host-Associated Endophytic and rhizospheric microbes aid in nutrient Mycorrhizal fungi, Plants Environments uptake and pathogen resistance. Azotobacter Microbes inhabit the gastrointestinal tract, skin, and Gut microbiota in Animals mucosal surfaces, aiding in digestion, immunity, and humans protection. Human microbiome includes bacteria, fungi, and viruses Humans found on skin, in the mouth, and throughout the Skin and gut microbiota digestive tract. 47  Microbial Distribution in Different Environments (3/3) Environment Type Subcategory Microbial Characteristics Examples Extreme Thermal Springs Thermophiles thrive in high-temperature waters. Thermus aquaticus Environments Polar Regions Psychrophiles inhabit glaciers and permafrost. Psychrophiles Acidophiles live in acidic waters; alkaliphiles thrive in soda Acidophiles, Acidic/Alkaline lakes. alkaliphiles Barophilic microbes withstand immense pressures at oceanic Deep Sea Barophiles depths. 48 Conclusion ▪ The study of microorganisms offers a window into the unseen world that governs much of life on Earth. ▪ By understanding their characteristics, distribution, ecology, and reproduction, we unlock endless possibilities for advancing: ✓ science, ✓ improving human well-being, and ✓ ensuring ecological sustainability. 49