Module 1: An introduction to the microbial world (part 1 & 2)

Microbiology

the study of living organisms (microorganisms, microbes) that individually cannot be seen with the naked eye

Extremophiles

microbes able to live in extreme environments → mainly bacteria, arches, some eukaryotes

Pathogens

organisms that cause diseases

Infection Disease

a disease that was caused by a microbe

Normal Microbiota

microbes that live stably on or in the human body

Functions of Normal Microbiota

• aid in digestion of foods

• synthesize essential vitamins needed by our cells

• protection from disease by preventing pathogens from colonizing the body

Pros and Cons of Microbes in Agriculture

• Pros

  • legumes form close association with N2 fixing bacteria

  • microbes colonize disgestive tract of ruminants (Sheep +cows) to help digest cellulose

  • soil microbes decompose plant and animal waste

• Cons

  • causes plant diseases that lead to financial and food loss

Microbial usage in biological control / biocontrol

used to protect plants from plant pathogens and insects.

EX: Bt produces a protein that is toxic to insects at a certain developmental stage (like caterpillars)

Biofouling

unwanted build up of microbes on surfaces exposed to water → leads to clogging of pipes, holding tanks, increased vessel drag

Cellular Microorganisms

mainly single-celled, some multicellular (ex: bacteria, archea, fungi, etc)

Acellular Microorganisms

not composed of cells (ex: viruses)

Most of the diversity of life on our planet is ____

microbial

Prokaryote Cell Structure

• no nucleus

• no membrane-bound organelles

• small

• most have cell wall

Eukaryotic Cell Structure

• Nucleus

• membrane-bound organelles

• large

Characteristics of Bacteria

• single cell prokaryotic organisms

• most are small

• cell walls composed of peptidoglycan

• hetero + autotrophic

• reproduce by binary fission / spores

Cell walls of Bacteria

contains peptidoglycan

Biofilms

caused by bacteria secreting extracellular polysaccharides that are viscous, high MW carbohydrates. They attach to exterior surface of cells as a slime layers and ... [clog something]

Disease(s) associated with Mycobacterium tuberculosis

tuberculosis

Disease(s) associated with Streptococcus pyogenes

strep throat, sepsis, flesh-eating disease

Disease(s) associated with Neisseria meningtidis

meningitis

Archea

• single celled prokaryotes

• many extremophiles

• not disease causing

Fungi

• small, non-motile eukaryotic organisms

• larger than bacteria

• heterotrophic

• break down complex organic polymers → nutrient recycling

• adapt well to environments

Mycology

the study of fungi

Yeasts

• unicellular with oval/spherical shape

• asxual via binary fission or budding

• cell wall contains polysaccharides (glans) and lipids

Molds

• filamentous cells with hypha that grow to form mycelium

• cell wall composed of chitin

mycelium

on a mold, formed from hyphae that grow and aggregate

Septae

on a mold, cross walls within hyphae

Reproduction of Molds

asexually by spores but can be sexual spores

Reproduction of Conidia Mold

produced specialized hyphae called conidiophores

Reproduction of Sporagniospores Molds

produced within a sportangium

Mycosis

diseases caused by fungis

Why are mycoses are difficult to control than diseases caused by bacteria?

said come back to later :(

Fungal-like organisms

eukaryotic microbes that share similar morphology and lifestyle with fungi but belong to distinct phylogenetic lineages

Protozoa

• unicellular, motile eukaryotes found in water

• feed on bacteria + microbes

• can for cysts

Disease associated with Plasmodium Protozoa

malaria

Disease associated with Giardia duodenalis

beaver feaver

Cyst

formed by protozoa as a survival mechanism. Surrounds itself and remain in cyst until consumed by host

Helminths

• multicellular eukaryotic animals

• parasitic with complex life cycles involving multiple hosts

Two main types of Helminths

• Flatworms

• roundworms

Diseases caused by Helminths results when __________

the body is parasitized by the adult or larval stage or helminth

Hygiene Hypothesis

exposure to certain microbes early in life is necessary for development of a healthy immune system

Coccus (cocci)

Rod

Spirillum (Spirilla)

Spirochete

Budding & Appendaged

Flamentous

Single Bacillus

Diplobacilli

Streptobacilli

Coccobacillus

Diplococci

Streptococci

Tetrad

Sarcinae

Staphylococci

Viruses

• Acellular, obligate intracellular parasites

• contains a single type of nucleic acid surrounded by capsid

In viruses, the capsid determines…

the shape of the virus

Bacteriophages

viruses that infect bacteria

the most abundant type of virus

bacteriophage

Phage Therapy

use of bacteriophages as potential therapeutic agents for treating bacterial infectious disease

Microscopy

the use of light or electrons to magnify objects

Magnification

the process of enlarging an object in appearance only

Resolution (resolving power)

the ability to distinguish two points as distinct and separate

Light Microscopy

use of light (photons) to observe a specimen

Types of Light Microscopes

• brightfieqld microscopy

• phase-contrast microscopy

• fluorescence microscopy

• confocal laster scanning microscopy

Electron microscopy

uses elections instead of light to image cells and structures. Electomagnets function as lenses and can be fitted with a camera for taking photographs

Types of election microscopy

• transmission electron microscopy

• scanning electron microscopy

Brightfield microscopy

specimens are visualized due to differences in contrast between specimen and surroundings

Staining in Brightfeild Microscopy

if specimen is not naturally pigmented, can kill cells and distorts structures

Phase-Contrast Microscopy

uses a compound light microscope with special condenser and objectives, results in dark image on a light background (no staining). Used to see living cells

Flourescence microscopy

used to visualize specimens that fluoresce, either naturally or artificially with fluorescent dyes. Used in clinical diagnostic microbiology and microbial ecology for enumerating bacteria

Immunofluorescence

important for rapid detection of pathogens in clinical specimens [STAT+]

Confocal Laser Scanning Microscopy

uses a computerized florescent microscope coupled with a laser source. Computers focus the laser on single layers of the specimen. The images of the layers can then be complied to produced a 3-D image. Uses staining or requires inherent florescence

Electron micrographs

Images taken with an electron microscope fitted with a camera

Transmission electron microscopy (TEM)

much greater resolving power than light microscopes. the specimen in thinly cut and stained and sectioned, electrons pass through specimen and are scattered. Generates 2D image with details of internal structures (cannot use live specimens)

Scanning Electron Microscopy (SEM)

requires the specimen be coated with a thin heavy metal film. An electron beam scans the specimen, scattered electrons are collected and projected to produce a 3D image. Very high magnification and can view surface structures of cells & viruses (cannot be live)

Staining

increases contrast of specimen for brightfieqld microscopy. Contains dyes that bind to specific cellular material

Basic Dyes

are positively charged, bind strongly to negative charged cell components (cell surfaces, nucleic acids)

Steps of Staining cells for microscopic observation

1. spread culture in thin film over slide, dry in air

2. pass slide through flame to heat fix, then flood slide with stain and dry

3. place drop of oil on slide and examine under 100x objective lens

Simple Stain

uses only one dye to stain cells

Differential Stain

used two different coloured dyes (stains and counterstains) to distinguish between different types of bacteria

Special Stain

used to stain specific structures

Gram Stain

used to distinguish bacteria that differ in their cell wall structures (purple = ?, Pink = ?

Steps of Gram Stain

1. Flood the heat fixed smear with crystal violet (primary stain) for 1 min

2. add iodine (mordent) solution for 1 min

3. decolonize with alcohol for 20 sec

4. counterstain with safranin for 1-2 min

Gram Positive Vs Gram Negative

Acid Fast Stain

• a differential stain used to identify bacteria from the genus Mycobacterium.

• It classifies bacteria as either acid-fast or non-acid-fast

How Acid-Fast Stain works

• Mycobacterium spp. have waxy lips in their cell wall called mycotic acids

• the acid-fast stain uses special stain and procedure to stain mycobacterial cells

• once stained, cells resist decolorization by acid-alcohol, and therefore are acid-fast and will appear red. Other bacteria decolourized and are counterstained blue

Steps of Acid-Fast Stain

1. apply carbolfuchsin, heat for 5 min, rinse

2. apply acid-acohol (decolourizer) 2× 15 sec

3. apply methylene blue 1 min (counterstain), rinse

Endospore Stain

a special stain;

• endospores are highly resistant, dormant structures produced by some bacteria. The cannot be stained by any other method

Steps to Endospore Stain

1. apply malachite green (primary stain) heat 5min, then rinse 30 sec

2. apply safranin (counterstain) for 1 min, rinse, then blot dry

3. endospores will appear green, rest of cells as pink