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Microbiology

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- The study of microorganisms

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Microorganisms

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- Forms of life too small to be seen with the naked eye - Examples: bacteria, fungi, algae, Protists

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What does the field of microbiology examine?

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- How microbes interact with humans, with food, and how they can be used by humans

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Two Themes of microbiology

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1. Understanding basic life processes (e.g. metabolism, growth,etc.) - Microbes are excellent models for understanding processes in unicellular and multicellular organisms 2. Applying that knowledge to the benefit of humans - Microbes play important roles in medicine, agriculture, industry, and environment

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Why Microorganisms are so important

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- Oldest form of life - Largest mass of living material on earth - Carry out major processes for biogeochemical cycles Ex. Nitrogen cycle - Can live in places unsuitable for other organisms - Other life forms require microbes to survive

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Prokaryotes

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- No membrane-closed organelles, no nucleus - Generally smaller and simpler than eukaryotic cells - Most of these tend to be microorganisms

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Two types of prokaryotes

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- Bacteria and archaea

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Eukaryotes

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- DNA enclosed in a membrane-bound nucleus - Cells are generally larger and more complex - Contain organelles (membrane bound) like golgi

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True Nucleus

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- Membrane Bound

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Genome

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- A cell's full complement of genes - Includes chromosomes and other genetic material in places like mitochondria

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Eukaryotic DNA

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- Linear and found within the nucleus - Associated with proteins that help in folding of the DNA - Usually more than one chromosome - Typically two copies of each chromosome - During cell division, nucleus divides by mitosis - During sexual reproduction, the genome is halved by meiosis

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Prokaryotic DNA

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- Generally have a single, circular DNA molecule called a chromosome - DNA aggregates to form the nucleoid - Prokaryotes also may have small amounts of extrachromosomal DNA called plasmids that confer special properties (e.g. antibiotic resistance)

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Eschericha Coli

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- One of the most extensively studied bacteria - 4.64 million base pairs - 4,300 genes

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Human Cell

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- 1,000X more DNA per cell than E. coli - 7X more genes than E. coli

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Characteristics of living cells

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- Metabolism - Reproduction - Differentiation - Communication - Movement - Evolution

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Metabolism

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- Chemical transformation of nutrients - Breaking down nutrients into smaller parts then taking small parts to build bigger parts

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Reproduction

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- Generation of two cells from one

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Differentation

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- Synthesis of new substances or structures that modify the cell (only in some microbes)

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Communication

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- Generation of, and response to, chemical signals (only in some microbes)

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Movement

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- Via self-propulsion, many forms in microbes

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Evolution

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- Genetic changes in cells that are transferred to offspring - The process of change over time that results in new varieties and species organisms - Change of allele frequency over time - Gradual change in DNA resulting in change over time

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Can bacteria and archaea swap DNA

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- Yes they can

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Microbiology History

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- Earth is 4.6 billion years old - First cells appeared between 3.8 and 3.9 billion years ago (prokaryotes) - The atmosphere was anoxic until - 2 billion - Metabolism were exclusively until evolution of oxygen-producing phototrops - Life was exclusively microbial until 1 billion years ago

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Phylogeny

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- Evolutionary relationships between organisms - Relationships between organisms - Relationships can be deduced by comparing genetic information in the different specimens - Relationships visualized on a phylogenetic tree

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Ribosomal RNA (rRNA)

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- Excellent for determining phylogeny - Very stable does not mutate (usually)

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Domains

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- Comparative rRNA sequencing has defined three distinct lineages of cells 1. Bacteria 2. Archaea 3. Eukarya

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Bacteria Prokaryotic or Eukaryotic?

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Prokaryotic

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Archaea Prokaryotic or Eukaryotic?

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Prokaryotic

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Eukarya Prokaryotic or Eukaryotic?

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Eukaryotic

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Archaea and Bacteria Relationship

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- Not closely related

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Archaea and Eukarya Relationship

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- More closely related to Eukarya than Bacteria

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Evolution and Diversity of Microbial Cells

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- Eukaryotic microorganisms were the ancestors of multicellular organisms - From the last universal common ancestor (LUCA) evolution proceeded to form two domains 1. Bacteria 2. Archaea - Archaea later diverged to form two domains 1. Archea 2. Eukarya

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Microbial Communities

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- The population of interacting assemblages that microorganisms are found in nature

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Habitat

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- The environment in which a microbial population lives in

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Ecosystem

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- Refers to all the living organisms plus physical and chemical constituents of their environment

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Microbial Ecology

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- The study of microbes in their natural habitat - The study of microbial diversity and activity in natural habitats - Example of a microorganism's ecosystem includes the human body

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Microbes and Diversity

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- Microorganisms are the most diverse organisms on the planet, make up the mast majority of diversity on the planet - The product of almost 4 billion years of evolution - Microorganisms differ in size, shape, motility, physiology, pathogenicity, etc. (they evolve quickly) - Microorganisms have exploited every conceivable means of obtaining energy from the environment - There are many many microorganisms we do not know about - We can only culture 1% of known microorganisms

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Microbes and their Environments

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- Microbes 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 Example: Removal of nutrients from the environment and the excretion of waste products

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Types of Environments Microbes can be found in

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- Microbes can be found in almost any environment imaginable - Very hot or very cold - Very acidic or very caustic (basic) - Very salty or very osmotically stressing - Very high pressure

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Extremophiles

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- Bacteria and Archaea that can grow in extremely harsh conditions

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Microorganisms and Humans

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- Can be both beneficial and harmful - Emphasis is typically on harmful microorganisms (infectious disease agents, or pathogens) - Many more microorganisms are beneficial than harmful (mass majority good) - Microorganisms as disease agents - Control of infectious disease during last century

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Reasons why infectious disease is not a main killer of people now

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1. Modern sanitation 2. Modern health standards 3. Vaccines/innoculation

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Microorganisms and Agriculture

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- Many aspects of agriculture depend on microbial activities - No Microbes = No plant life - Positive Impacts: Nitrogen-fixing bacteria: change nitrogen into a form plants can use such as nitrate, nitrite, or ammonia Cellulose-degrading microbes in the rumen Regeneration of nutrients in soil and water - Negative Impacts: Disease in plants and animals

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Nitrogen-fixing bacteria

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- Convert nitrogen into a form that plants and other organisms can use - Forms that is makes includes nitrate, nitrite, and ammonia

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Microorganisms in the human gastrointestinal tract

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- High numbers of microorganisms occur in colon and oral cavity - Not many microbes are in the human stomach due to high acidity (low pH) - There are some microbes in the small intestine - Most microbes live in the large intestine which has a close to neutral pH - There are a lot of microbes present in feces - Positive Impacts: Synthesize vitamins and other nutrients Compete with pathogens for space and resources - Negative Impacts: Can cause disease

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Microorganisms and Food

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- Negative Impacts: Microorganisms can cause food spoilage; for many foods, methods of preservation are needed Can get microbial diseases from consuming infected foods - Positive Impacts: Microbial transformation (typically fermentations) yield Dairy products (e.g. cheeses, yogurt, buttermilk) Other food products (e.g. sauerkraut, pickles, leavened breads, beer) - Active cultures in yogurt are colonies of bacteria

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Discovery of microorganisms =

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- Start of microbiology

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How Microbiology started

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- With the microscope

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Robert Hooke (1635-1703)

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- First to describe microbes - Illustrated fruiting structures of molds

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Antoni van Leeuwenhoek (1632-1723)

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- The first to describe bacteria - Futher progress required development of more powerful microscope - Usually considered the father of microbiology

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Ferdinand Cohn (1828-1898)

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- Founded the field of bacterial classification and discovered bacterial endospores - Classification was based on morphology (i.e. shapes, physical characteristics, etc.)

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Louis Pasteur

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- Discovered that living organisms discriminate between optical isomers - Discovered that alcoholic fermentation was a biologically mediated process (originally thought to be purely chemical) Was important wine is a commodity and can spoil due to contamination from microbes - Disproved Theory of Spontaneous Generation - Led to the development of methods for controlling growth of microorganisms (aseptic technique) - Developed vaccines for anthrax (disease in cattle that can infect humans), fowl cholera (bird cholera), and rabies - Look at notes for details on experiment

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Theory of Spontaneous Generation

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- Life spawns from no life - Redi disproved this for large organisms - Pasteur for microorganisms

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Robert Koch

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- Demonstrated the link between microbes and infectious disease (Germ Theory of Disease) - Identified the causative agents for of anthrax and tuberculosis

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Before Koch what did people believe cause disease?

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- Bad spirits - Bad air - etc.

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Pure Culture

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- Only one microorganism in culture - A culture containing a single kind of organism

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Koch's Postulates

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1. The suspected pathogen must be present in all cases of the disease and absent from healthy animals. 2. The suspected pathogen must be grown in pure culture 3. Cells from a pure culture of the suspected pathogen must cause disease in a healthy animal 4. The suspected pathogen must be reisolated and shown to be the same as the original - All four must be present - Process still used somewhat today

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Koch and the Rise of Pure Cultures

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- Discovered that using solid media provided a simple way to obtain pure cultures (easier than broth) - Observed that masses of cells (called colonies) have different shapes, colors, and sizes - Began with potato slices, but eventually devised a uniform and reproducible nutrient solutions solidified with gelatin and agar

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Colony

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- Collection of cells (a lot of cells)

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How many cells are colonies derived from theoretically

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- One

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Microbial Diversity

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- Field that focuses on nonmedical aspect of microbiology - Large field in microbiology - Roots in the 20th century

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Martinus Beijerinck (1851-1931)

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- Developed enrichment culture technique

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Enrichment Culture Technique

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- Microbes can be isolated from natural samples in a highly selective fashion by manipulating nutrient and incubation conditions - Can be done by using media that enriches specific (target) microorganisms - Example: Nitrogen fixing bacteria

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Sergei Winogradsky (1856-1953)

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- Proposed concept of chemolithotrophy - Demonstrated that specific bacteria are linked to specific biogeochemical transformations (e.g. S and N cycles)

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Chemolithotrophy

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- Oxidation of inorganic compounds linked to energy conservation

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Classical Microbiology Concerns

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- More focused on understanding microbes and processes such as metabolism

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Modern Microbiology Concerns

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- More concerned with things on the molecular and genetic levels - In 20th century, it developed into two distinct directions: applied and basic

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Applied Research

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- Using information from basic research and applying it to produce things such as vaccines - Only as strong as basic research

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Basic Research

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- Foundations of research - Research for the sake of learning

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Molecular Microbiology

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- Fueled by the genomics revolution

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Medical Microbiology

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- Study of infectious diseases

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Imunology

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- Study of immune system

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Agricultural Microbiology

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- Microbes associated with soil

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Industrial Microbiology

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- Production of antibiotics, alcohols, and other chemicals

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Aquatic Microbiology

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- Water, wastewater, and drinking water

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Biotechnology

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- Products of genetically engineered organisms - Example: Insulin from cultured microorganisms

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Microbial Systematics

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- The science of grouping and classifying organisms - Still very hard to define things like species

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Microbial Physiology

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- Study of the nutrients that microbes require for metabolism and growth and the products that microorganisms generate

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Microbial Biochemistry

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- Study of microbial enzymes and chemical reactions

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Mycology

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- Study of fungi

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Parasitology

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- Study of parasites

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Bacterial Genetics

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- Study of heredity and variation in bacteria

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Virology

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- Study of viruses

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Genomics

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- Study of all of the genetic material (DNA) of living cells - Very recent field

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Transciptomics

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- Study of RNA patterns - Tells you what genes are turned off or on depending on certain situations

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Proteomics

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- Study of all the proteins produced by cell(s)

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Metabolomics

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- Study of metabolic expression in cells

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Metagenomics

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- Study of genome of an entire sample - To see what a whole community does

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