Micro- organisms and Microbiology 1 Micro- organisms and Microbiology

I. Introduction and Major Themes of Microbiology 1.1 What Is Microbiology About and Why Is It Important? 1.2 Structure and Activities of Microbial Cells 1.3 Evolution and Diversity of Microbial Cells 1.4 Microorganisms and Their Environments 1.5 The Impact of Microorganisms on Humans

1.1 What Is Microbiology About and Why Is It Important? Microbiology revolves around two different approaches: 1. Understanding basic life processes Microbes are excellent models for understanding cellular processes in unicellular and multicellular organisms 2. Applying that knowledge to the benefit of humans Microbes play important roles in medicine, agriculture, and industry

1.3 Evolution and Diversity of Microbial Cells The first cells First self-replicating entities may not have been cells Last universal common ancestor (LUCA): common ancestral cell from which all cells descended

1.3 Evolution and Diversity of Microbial Cells Life on Earth through the ages (Figure 1.4) Earth is 4.6 billion years old First cells appeared between 3.8 and 3.9 billion years ago The atmosphere was anoxic until ~2 billion years ago Metabolisms were exclusively anaerobic until evolution of oxygen-producing phototrophs Life was exclusively microbial until ~1 billion years ago

Microbial life forms only Mammals Humans Vascular plants Microbial life forms only Shelly invertebrates Origin of Earth (4.6 bya) Present ~20% O2 1 Origin of cellular life bya 4 bya O2 Anoxygenic phototrophic bacteria Algal diversity 2 3 Anoxic Earth bya bya Earth is slowly oxygenated Modern eukaryotes Origin of cyanobacteria Figure 1.4 A summary of life on Earth through time and origin of the cellular domains. Bacteria LUCA Archaea Eukarya 4 3 2 1 bya Figure 1.4 6

1.3 Evolution and Diversity of Microbial Cells The process of change over time that results in new varieties and species of organisms Phylogeny Evolutionary relationships between organisms Relationships can be deduced by comparing genetic information in the different specimens (Figure 1.6a) Ribosomal RNA (rRNA) is excellent for determining phylogeny Relationships visualized on a phylogenetic tree

1.3 Evolution and Diversity of Microbial Cells Comparative rRNA sequencing has defined three distinct lineages of cells called domains: Bacteria (prokaryotic) Archaea (prokaryotic) Eukarya (eukaryotic) Archaea and Bacteria are NOT closely related (Figure 1.6b) Archaea are more closely related to Eukarya than Bacteria (Figure 1.6b)

1.3 Evolution and Diversity of Microbial Cells Eukaryotic microorganisms were the ancestors of multicellular organisms (Figure 1.6b) From the last universal common ancestor (LUCA), evolution proceeded to form two domains (Figure 1.6b) Bacteria Archaea Archaea later diverged to form two domains (Figure 1.6b) Eukarya

Thermodesulfobacterium BACTERIA ARCHAEA EUKARYA Macroorganisms Animals Slime molds Entamoebae Green nonsulfur bacteria Euryarchaeota Fungi Methanosarcina Mitochondrion Methano- bacterium Gram- positive bacteria Extreme halophiles Plants Crenarchaeota Proteobacteria Thermoproteus Ciliates Chloroplast Pyrodictium Thermoplasma Cyanobacteria Thermococcus Flagellates Nitrosopumilus Pyrolobus Green sulfur bacteria Methanopyrus Trichomonads Thermotoga Figure 1.6b Evolutionary relationships and the phylogenetic tree of life. Thermodesulfobacterium Microsporidia Aquifex Diplomonads Figure 1.6b 10

1.4 Microorganisms and Their Environments Microorganisms exist in nature in populations of interacting assemblages called microbial communities (Figure 1.7) The environment in which a microbial population lives is its habitat Ecosystem refers to all living organisms plus physical and chemical constituents of their environment Microbial ecology is the study of microbes in their natural environment

Figure 1.7 Microbial communities. 12

1.4 Microorganisms and Their Environments The diversity in microbial cells is the product of almost 4 billion years of evolution Microorganisms differ in size, shape, motility, physiology, pathogenicity, etc. Microorganisms have exploited every conceivable means of obtaining energy from the environment

1.4 Microorganisms and Their Environments Diversity and abundances of microbes are controlled by resources (nutrients) and environmental conditions (e.g., temp, pH, O2) The activities of microbial communities can affect the chemical and physical properties of their habitats

1.4 Microorganisms and Their Environments Microbes also interact with their physical and chemical environment Ecosystems are greatly influenced (if not controlled) by microbial activities Microorganisms change the chemical and physical properties of their habitats through their activities For example, removal of nutrients from the environment and the excretion of waste products

1.4 Microorganisms and Their Environments The extent of microbial life Microbes are found in almost every environment imaginable Extremophiles are Bacteria and Archaea that can grow in extremely harsh environments Very hot or very cold Very acidic or very caustic Very salty or very osmotically stressing Very high pressure Xenobiology?????

1.4 Microorganisms and Their Environments The extent of microbial life Global estimate is 5 ✕ 1030 cells Most microbial cells are found in oceanic and terrestrial subsurfaces Microbial biomass is significant, and cells are key reservoirs of essential nutrients (e.g., C, P, N)

1.8 Koch, Infectious Disease, and the Rise of Pure Cultures Robert Koch (1843–1910) Demonstrated the link between microbes and infectious diseases Identified causative agents of anthrax and tuberculosis Koch's postulates (Figure 1.20) Developed techniques (solid media) for obtaining pure cultures of microbes, some still in existence today Awarded Nobel Prize for Physiology and Medicine in 1905

KOCH'S POSTULATES Theoretical aspects Experimental aspects Postulates: Laboratory tools: Diseased animal Healthy animal 1. The suspected pathogen must be present in all cases of the disease and absent from healthy animals. Microscopy, staining Red blood cell Observe blood/tissue under the microscope. Red blood cell Suspected pathogen 2. The suspected pathogen must be grown in pure culture. Laboratory cultures Streak agar plate with sample from either a diseased or a healthy animal. No organisms present Colonies of suspected pathogen Inoculate healthy animal with cells of suspected pathogen. 3. Cells from a pure culture of the suspected pathogen must cause disease in a healthy animal. Experimental animals Figure 1.20 Koch’s postulates for proving cause and effect in infectious diseases. Diseased animal Remove blood or tissue sample and observe by microscopy. 4. The suspected pathogen must be reisolated and shown to be the same as the original. Laboratory reisolation and culture Suspected pathogen Laboratory culture Pure culture (must be same organism as before) Figure 1.20 19

1.8 Koch, Infectious Disease, and Pure Cultures Koch and the rise of pure cultures Discovered that using solid media provided a simple way to obtain pure cultures Observed that masses of cells (called colonies) have different shapes, colors, and sizes (Figure 1.21) Began with potato slices, but eventually devised uniform and reproducible nutrient solutions solidified with gelatin and agar (Petri dish-Dr. J. R. Petri)