Chapter 1: The microbial world Flashcards
Micro-organism (M)
They are life forms too small to be seen by the human eye
-diverse in function
-Inhabit every environment that supports life
-Many single-celledm some form complex structures and some mulitcellular
-Live in microbial communities
why are M NB
-Oldest forms of life
-Major fraction of Earth’s biomass
-Surround plants and animals
-Affect Human life
In what ways do M impact humans
-food
-industry
-biotechnology
culture
cells grown in/on nutrient medium
Medium
Liquid/solid mixture containing all required nutrients
Growth
Increase in cell number resulting from cell division
Colony
Visible, contains millions/billions of cells
Cell
A living compartment that interacts with the environment and other cells
Factors all cells have
-Cytoplasmic (cell membrane)
-Cytoplasm
-Ribisomes
-Cell wall
which structures distinguish Pro and Eu
Pro
-No organelles
-single circular chromosome
-Plasmid
-Small/compact
Eu
-Linear chromosome
-Much larger
-Organelles
properties of all microbial cells
Structure
-Cytoplasmic mebrane, cytpolasm, genome made of DNA
Metabolism
-Anabolism (build) and Catabolism (break)
Growth
-Proteins are used to convert nutrients into new cells
Evolution
-Chance mutations in DNA cause new cells to have new properties thereby promoting evolution
Properties of only some cells
Differentiation
-Some cells can for, new structures such as spores
Communication
-via chemical messengers
Motility
-Some cells are capable of self-propulsion
Horizonta gene transfer
-Cells can exchange genes with each other via several mechanisms
Morphology
Cell size and shape
Size of Pro
Most are between 0.5 to 10 micro meters
EU size
5 to 100 micro meters
surface area and volume
Advantages to being small is more surface area relative to volume relative to larger cells
-Supports greater nutrient and waste exchange per unit cell volume
-More efficient than larger cells
Cell morphologies (shapes)
-Coccus (circle)
-Rod
-spirillum (spiral)
-Spirochete
-Budding and appendaged
-Filamentous
Fungal cell structure
-Most have hyphae divided into cells by septa
-Pores allow cell-to-cell movement of organelles
-Cell wall contains chitin (fibrous substance consisting of polysaccharides and are major constituent in the exoskeleton of arthropods)
-No chloroplasts (no photosynthesis)
-Multiple vacuoles
Coenocytic fungi
Also known as Non-septate/Aseptate fungi
-Lack septa, continuos cytoplasmic mass with hundreds or thousands of nuclei
Different microbial life
-Bacteria
-Archae
-Eukarya
-Algae
-Fungi
-Protozoa
-Viruses
Bacteria
-Pro
-Usually undifferentiated single cells that are 0.5-10 micrometres long
-80+ phylogenetic lineages
-Cell walls contain peptidoglycan
-Reproduce via binary fission
-Movement achieved using appendages called flagella
-Nutrition derived from organic substances (some can photosynthesise and some can eat inorganic matter)
Archae
-Pro
-12+ phyla
-Associated with extreme environments, extremophiles
-Cell walls lack peptidoglycan
-Lack of known parasites or pathogens of plants and animals
Eukarya
-Plants, animals, fungi
-First were unicellular, and may have appeared 2 billion years ago
-At least 4 kingdoms
-Vary dramatically in size, shape, physiology
Fungi
-Can be uni/multi-cellular
-Cell walls contain chitin
-Reproduce asexually or sexually
-Majority are non-motile
-Nutrition derived from organic substances
Algae
-Not plants
-are able to photosynthesize
-Many conformations
-cell walls contain cellulose
Protozoa/Protists
-Several conformations
-Single celled
-reproduce asexually or sexually
-Movement achieved through the use of appendages called cilia, flagella, pseudopods
-Nutrition derived from organic substances
Viruses
-Obligate parasites that only replicate within host cell
-Not cells
-Do not carry out metabolism; take over infected cells to replicate
-Have small genomes of double-stranded or single-stranded DNA or RNA
-Classified based on structure, genome composition and host specificity (eg. bacteriophages)
History of life
-Atmosphere was anoxic (no O2) and so only anaerobic metabolisms
-first anoxygenic phototrophs
-Cyanobacteria (oxygenic phototrophs)
-Plants and animals
Micro-organisms and agriculture
-Nitrogen-fixing bacteria
-Cellulose-degrading rumen
-gut microbiome: digests complex carbohydrates in humans and synthesizes vitamins and other minerals
M and food
Negative
-Food spoilage and foodborne disease
-harvest, storage, safety and prevention of spoilage influenced by M
Positive
-Improve food safety, preservation
-dairy products
-other food products such as kimchi and pickles
Industrial Microbiology
Use of M for major industries such as pharmaceuticals and brewing
-Biofuels
-Wastewater treatment
-Bioremediation
-Biofilms
Biotechnology
-Genetically-engineered M making high value products in small amounts
Fields of light Microscopy
Brightfield
Fluorescence
Brightfield Microscopy
-Also called light microscopy
-Simplest of all light techniques
-Object illumination is via transmitted white light
Refraction Index
Properties of light are dependent upon the material
Light passing through higher-density material will slow down
Refraction
Change in direction of wave passing from one medium to another
Types of lens used
Converging lens
-Biconvex
Lens abberations
Spherical
Chromatic
Spherical aberration
-Found in optical systems that use elements with spherical surfaces
-Light rays that strike a spherical surface off-center are refracted or reflected more or less than those that strike close to the center
-Manifests as a blurry image
Chromatic abberation
caused by the dispersion of the lens material
-The variation of its refractive index with the wavelength of light
-RI can vary depending on the specific wavelength
Manifests as fringes of colour around the image (mainly green)
Resolving power
The ability to measure the separation of images that are close together
-Determined by the numerical aperture
-As objective increases, numerical aperture increases
Numerical aperature
NA is the ability of the objective to gather light and resolve fine specimen detail at a fixed object distance
-Higher NA = better resolution
NA of air
Theoretical=1
Practical=0.95
NA of oil
Theoretical=1.515
Practical=1.5
Positive staining
Uses basic dyes thats attach to bacteria
Negative staining
Uses negative dyes that are repelled by bacteria and so stain background instead
Nb for observing capsules, shape and size of living bacteria
staining techniques
simple
differentail
complex
simple stains
Made from a single basic dye
Purpose is to highlight the entire organisms so that shape and basic structures are visible
includes crystal violet and safranin
Mordant
Additive that intesifies the stainn by increasing the affinity of stain for biological sample
Gram’s iodine forms complexes with crystal vioelt which causes it to clumo and stay contained by thick layers of peptidoglycan
Differential stains
Different stains react with different kinds of M
used to differentiate between M
Eg. Grams stain
steps of Grams stain
- Application of basic dye crystal violet
- Application of mordant iodine
- Decolourisation using alcohol
- Application of counter stain safranin
Crystal violet stain process (P)
Gram + cellls have thick layers of peptidoglycan in cell wall that retains stain
Gram - cells have thinner pepti that allows stain to wash out during decolourisation
Iodine P
Iodine forms a crystal violet-iodine complex that remains contained within the thick layers of peptidoglycan
Decolorising agent p
Alcohol will remove the crystal violet from some of the cells but not from others
safranin counterstain P
Safranin is a basic red dye
cells are first rinsed with water before stain is applied
Safranin stains the decolourised cells pink and is less noticeable in the cells that contain crystal violet dye
Purpose of knowing gram positive/negatve
+ are more readily killed by cephalosporins and penicillins while - is more resistant to antibiotic treatment
Phase contrast microscopes
Improves image contrast of unstained, live cells
Phase ring amplifies differences in refractive index of cells and surroundings
results in dark cells on light background
Dark-field microscopy
Light reaches specimen from sides
only light scattered by specimen reaches the lens
image appears light on dark background
Better resolution than light microscopes
excellent for observing motility and flagella
Fluoresence Microscopy
Visualise specimens that fluoresce
cells appear to glow due to filters
fluoresce naturally or after fluorescent dye such as DAPI
used in clinical microbiology and M ecology
TEM
Transmission electron microscopy
greater resolving power (0.2nm) than light microscope
enables visualisation of structures on molecular level
speciman must be very thin and stained with high atomic weight substances that scatter electrons and improve contrast
Negative staining allows for direct observation of intact cells/components
CryoET
electron cryotomography: TEM used to obtain #D images
SEM
Scanning electron microscopy
speciman is covered with thin film of heavy metal such as gold
electron beam scans object
scattered e are collected and projected to produce image
magnification range up to 100,000x
only surface visualised
Aseptic technique
Collection of practices that allow preperation and maintenance of sterile media and solutions
Pure culture
cell from single type of M
Enrichment culture
Isolate M having particular metabolic characterisitcs from nature
Louis pasteur discovery
Organisms discriminate between optical isomers
alcoholic fermentation was a biological process
disproved theory of spontaneous generation
Swan-necked flask experiment
germ theory
Discovered by robert Koch
linked microbes to infectious disease
identified anthrax, tb and cholera
developed koch’s postulates
Koch’s postulates
Link cause and effect to infectious disease
Martinus Beijernick
Developed enrichment culture
selectively encourages growth of specific organisms
Sergei Winogradsky
showed specific bacteria linked to specific biochemical transformations
Chemolithtrophy:
showed oxidation of only inorganic compounds to yield energy as chemolithotrophs use carbon from CO2
showed nitrogen fixing and nitrification
Evidence DNA is molecular basis of hereditary
Phylogenetic tree
Made from similarities in rDNA
shows 3 domains
root is LUCA (last common universal ancestor)
Metagenomics
Microbia; genomes/fragments recovered from environmental DNA samples
