Intro to Microbiology Ch 1

Microbiology

Deals with living/sometimes nonliving things too small to be seen without a microscope

Microbes

Oldest and most dominant form of life on earth, present everywhere that will support life, typically live in complex microbial communities, surround plants and animals, affect human life

Extremophiles

Microbes that inhabit environments characterized by extremes

Robert Hooke

Studied cork, household objects, plants, trees

Cells=”little structures” that seem alive

Cell theory

All living things are composed of cells (Hooke)

Antonie van Leeuwenhoek

Manufactured simple microscopes to study fabrics, rainwater, feces, plaque scraped from teeth

Animalcules: bacteria and protozoa

LUCA

Last universal common ancestor from which cells evolved

60 genes universally present in bacteria, archaea, eukarya

Karyon: eukaryotes

“True nucleus”, come are microbes

Karyon: prokaryotes

No nucleus, all are microbes (bacteria and archaea)

Bacteria

simple, unicellular, prokaryote

Archaea

simple, unicellular, prokaryote, similar to bacteria but often found in extreme environments

Protozoa

unicellular, eukaryote, can be parasite or live as free entity

Fungi

unicellular or multicellular, eukaryote, absorb organic material for nourishment

Algae

unicellular, eukaryote, photosynthesize

Helminths

parasitic worms, not microbes but sometimes microscopic, includes flatworms and roundworks

Viruses

between life/nonlife but not considered alive, composed of DNA/RNA, surrounded by protein coat and membrane, most common microbe

Prions

Simpler than viruses, infectious microbes, composed of only protein (no nucleic acids), not considered alive, abnormal forms of naturally occurring proteins in the brain that cause various neurodegenerative diseases

Nature of microorganisms

Reproduce rapidly, grown fast in large populations in laboratory, analyzed through indirect means

Early earth: anoxic environment

No oxygen but lots of carbon dioxide and nitrogen, hotter than present earth, abiotic synthesis of first biochemical molecules

Early earth: metabolism

Anaerobic fermentation and anaerobic respiration

Evolution of phototrophic microorganisms

Organisms harvest energy from sunlight (3.2-3.5 billion years ago)

Fossilized stromatolites

First evidence for microbial life found 3.5 years ago (likely phototrophic)

Stromatolites

Fossilized microbial mats of layers of filamentous prokaryotes and trapped sediments, contain microfossils that appear similar to modern phototrophic bacteria

Shift from anoxic to oxic environment

Oxygenic phototrophic cyanobacteria appeared 2.8 billion years ago

Great oxidation event

Aerobes emerged, banded iron formations, ozone layer formed

When organelles first appeared

1.8 billion years ago in eukaryotes

Timeline of early earth

Earth formed 4.5 billion years ago

1st microbial cells 3.8-4.3 billion years ago

Louis Pasteur’s swan-necked flask experiments

Used to disprove spontaneous generation, filled flasks with broth and used heat to sterilize, sample exposed to dusk from air showed microbial growth, sample exposed to air without dust showed no microbial growth

Louis Pasteur

Invented pasteurization, developed vaccines for rabies, anthrax, and fowl cholera, helped solidify germ theory of disease

Germ theory of disease

Microbes cause disease (Pasteur, Koch)

Treating disease before germ theory of disease

Trial and error, didn’t know causes of disease, people saw disease as punishment for misdeeds/crimes

First link between microbes and physical/chemical changes in organic material

Discovery that yeasts play a crucial role in fermentation

Oliver Wendell Holmes and Ignaz Semmelweis

Importance of hand washing in preventing disease in hospital settings (couldn’t prove method→scorn from medical community)

Joseph Lister

Surgical infections caused by microbes (deduced from Pasteur’s discoveries), aseptic techniques in surgery like treating wounds with phenol (1867)

Koch’s postulates

Series of logical steps to establish if organism is pathogenic

Koch showed that anthrax was caused by Bacillus anthracis in 1875 and discovered the cause of tuberculosis

Step 1 of Koch’s postulates

Causative agent must be found in every case of disease and absent from healthy hosts

Step 2 of Koch’s postulates

Infectious agent must be isolated and grown outside the host in a laboratory

Step 3 of Koch’s postulates

Experimental susceptible host must get disease when infectious agent is introduced

Step 4 of Koch’s postulates

Same causative agent must be found in diseased experimental host

Pathogens

Microbes that cause disease, minority of microbes (2,000+)

Infectious disease

Pathogens invade susceptible host, cause <5% all deaths where microbial interventions are readily available, cause >33% all deaths where microbial interventions are less readily available

Emerging infectious disease

New/changing disease that is increasing in incidence or has the potential to increase in incidence in the near future

Taxonomic hierarchy

Domain>kingdom>phylum>class>order>family>genus>species>strains

Phylogeny

Taxonomic scheme that represents natural relatedness between groups of living beings

Woese-Fox taxonomy

Based on conserved small subunit ribosomal RNA sequences (ssu 165 rRNA), separated archaea and bacteria and added the domain Eukarya

Universal web of life

Charles Darwin and Ernest Haeckel proposed the kingdoms Plantae and Animalia, Haeckel added Protista and Monera (archaea and bacteria) in 1870

Universal web of life: Whittaker model

Added fungi (1959-195), based on structural similarities and differences

Tree of life based on rRNA gene sequences: Phylogenetic tree

Diagram that depicts the evolutionary history of an organism

Root of universal tree represents point in time when all extant life on earth shared a common ancestor: LUCA (eukarya branched from archaea)

Interdisciplinary biology

All living organisms contain a common set of biological molecules and maintain homeostasis with chemical reactions

Chemical compound

Consists of 2 or more elements in a fixed ratio

Emergent properties

Characteristics different from those of its individual elements

Molecule

2 or more atoms of elements chemically joined together

Atoms

Smallest unit of matter that still retains properties of an element, contain subatomic particles (protons, neutrons, electrons)

Isotope

2 or more atomic forms of an element that differ in number of neutrons

Atomic number and mass

Atomic number: protons and electrons (measured in daltons)

Atomic mass: protons + neutrons (neutrons=mass-number)

Chemical reactions

Forming and breaking chemical bonds

Covalent bond

Strongest, polar or nonpolar, atoms share electrons, cloud surrounds both atoms, can have single double or triple bonds

Electronegativity

Atoms attraction for electrons of covalent bonds

Ionic bond

Neutral, between atoms with opposite charges, strength affected by environment (dry=stronger than aqueous), holds large biological molecules in functional form by weak bonds

Hydrogen bonds

Weakest, between slightly positive and negative atoms, large molecules with many bonds have considerably strength and stability

Endergonic reactions

Reaction absorbs more energy than it releases

Exergonic reactions

Reaction releases more energy than it absorbs

pH scale

0-14, represents concentration of atoms in solution

H atom in bond between water molecules shifts from one molecule to another

Acids

Proton donor, high concentration of free H+ ions in solution

Bases

Proton acceptor, attracted to released OH-, low concentration of free H+ ions in solution

Inorganic compounds

Small and structurally simple molecules that typically lack carbon, ionic bonds

Organic compounds

Contain carbon and hydrogen, structurally complex, carbon chains form basis, covalent bonds

Properties of water

Polar, cohesive, able to moderate temp, expansion upon freezing, good solvent

Properties of water- cohesion

H bonds contribute to transportation of nutrients against gravity in plants

Properties of water- adhesion

Clinging of one substance to another

Properties of water- moderation of temp.

Resists changes because high specific heat

Heat is absorbed when H bonds break, released when H bonds form

Specific heat

Amount of heat absorbed/lost for 1g substance to change temp by 1C

Evaporative cooling

Surface of object becomes cooler during evaporation, result of molecules with high kinetic energy changing from liquid to gas

Properties of water- expansion upon freezing

H bonds in ice are more ordered→low density, floating can insulate water below

Properties of water- versatility as a solvent

Due to polarity of water

Solution: liquid of homogeneous mix of 2 or more substances

Solvent: dissolving agent

Solute: dissolved in solvent to form solution

Biomolecules

Large organic molecules, monomers make up polymers, built on framework of covalently bonded carbon atoms

4 classes: carbohydrates, lipids, proteins, nucleic acids

Dehydration reaction

Occurs when 2 monomers bond through loss of water molecule, facilitated by enzymes

Hydrolysis

Opposite of dehydration reaction, disassembles polymers, facilitated by enzymes

Microbial culture

Method of microbial organisms by letting them reproduce in a culture medium under controlled lab conditions

Culture dependent method

traditional culture/enrichment methods

Culture independent methods

Molecular methods in the absence of laboratory culture, limitations in capturing diversity

Enrichment culture

Begins with collecting samples from appropriate habitat to serve as inoculum (contains organism of interest)

Culture employs highly selective laboratory methods for obtaining microbes from natural samples

Inoculation

Makes it possible to handle and manage microbes in artificial environment and begin to analyze what the samples may contain (intro to test tube)

Enrichment bias

Weed species tend to dominate in the enrichment often to the exclusion of most abundant/ecologically significant organisms in the inoculum

Inoculation

Introduction of inoculum (sample of microbes) into media to culture microbes, can come from clinical specimens obtained from body fluids, anatomical sites, diseased tissues

Agar

Complex polysaccharide added to solid media, not digestible nutrient for most microorganisms, flexible and moldable

Liquefies at 100 C, solidifies at 42 C

Higher solid levels=higher agar levels

Chemical content of media- defined/synthetic

Precisely chemically defined, contain pure organic and inorganic compounds that vary little from one source to another, molecular content is specified by means of exact formula

Chemical content of media- complex/non-synthetic

1 or more components are not chemically defined, contains extracts of animals, plants, yeasts, blood, peptone, soybean digests

Miscellaneous media

General purpose: broad spectrum of complex microbes

Enumeration media: for counting microbes

Assay: test effectiveness of antimicrobial drugs, cosmetics, antiseptics, disinfectants, preservatives

Reducing: ingredients that remove dissolved oxygen from medium to allow growth of anaerobes

Transport: used to maintain and preserve specimens that have to be held for a period of time before clinical analysis

Enriched media

Complex organic substances (serum, blood, hemoglobin, special growth factors for growth of fastidious microbes)

Selective media

Contains 1 or more agents that inhibit growth of certain microbes (select A to inhibit B)

Important in primary isolation of specific types of microorganism from sample containing many different species

Speeds up isolation of desired organisms by suppressing unwanted background organisms and favoring growth of desired ones (agents=antibiotics, salts, dyes, pH)

Differential media

Allows multiple types of organisms to grow but display visible differences in how they grow, variations (size, color, media color, gas bubbles) often come from chemicals in media with which microbes react

Medium can be both selective and differential

Mannitol agar salt: selective bc salt inhibits, differential bc fermentation of sugar mannitol (yellow, non fermented stays red)

Dyes used bc pH indicatorts change color

Incubation

Exposing inoculating medium to optimum growth conditions (hours-days)

Purpose: to promote microbe multiplication and produce actual culture

Outcome: increase in microbes will provide increased quantities needed for further testing

Incubator

Temp-controlled chamber to encourage multiplication of microbes, growth observable without microscope

20-25 C- room temp environmental samples

37 C- human body temp, many pathogens

BSL-1

Low-risk microbes that pose little to no threat of infection in healthy adults, basic teaching lab

BSL-2

Human diseases that pose a moderate health hazard, need PPE (gloves, lab coat, eye protection)

BSL-3

Microbes are indigenous/exotic, can cause serious disease through inhalation, biosafety cabinets

BSL-4

Dangerous/exotic microbes (ebola, Marburg), infections are fatal without treatment, vaccines, HEPA filter, sealed, negative pressure hot zone

Methods of preserving bacterial cultures

Refrigeration (short-term), deep-freezing (placed in suspending liquid frozen at -50 - -90 C, can be thawed/grownyears later), lyphilization/freeze-druing (-54- -72 C, dehydrated in vacuum, can be stored for years and revived via liquid culture media)