MicroBIo Ch. 1: Microbial World

microbes

microorganisms which are life forms too small to be seen by the unaided human eye (through not all microbes are cells; viruses)

Additionally, some microbes can be seen by the naked eye and some multicellular microsopic organism are not microbes i.e. tartegrade)

Microbes are betwen 0.2 um and 1 mm in diameter

pathogens

microbes that cause a disease

culture

collection of cells that have been grown in or on a nutrient medium

medium

liquid or solid nutrient dense mixture that contains all the nutrients required for the growth of a microorganism

growth

increase in the number of cells as a result of cell division

virus

special category of microorganisms, not cells can be 10x smaller than 0.2 um

they are obligated to intracellular parasites that cannot reproduce without a host (are unable to replicate their own DNA solo)

micro euks

microsocpic eukaryotes (type of microbe)

cytoplasmic membrane

seperates the cytoplasm from the outside of the cell. is made of macromoleculse (lipids, proteins, nuclaic acids, and polysaccharids), small organic moleculse (marcro precursors), inorganic ions, and ribosomes

organelle

membrain bound cytoplasmic structures

genome

the full set of genes in a cell

gene

segment of DNA that encodes a protein or an RNA molecule

plasmids

Present in most prokaryotes; small circular DNA segments that are distinct from the chromosome (nonesssential butnuber contain some specal property i.e. antibiotic resistance or unique metabolism)

genome size

Prok: 500-10,000 genes and 0.5-10 million bp

Euk: 20,000-25,000 genes and 3 billion bp long

Size of human microbiome

contains ~39 trilltion microbial cells (mostly bacteria and fungi)

(for reference, the number of body ccells in a human is ~30 trillion)

known human pathogens

ther are ~1,400 know species of human pathogens which makes up only ~1% of the total number of micorbial species

transcription

process by which DNA sequences encode RNA molecules

translation

process by which RNA templates are sued by ribosomes to synthesis proteins

motility

allowance for cells to relocate in response to environmental conditions (typically down through self-propulsion)

differentiation

results in the formation of modifies cells spcialized for growth, dispersal, or survival

intracellular coomunication

cells are “aware” of their neighbors and can respond accordingly

horizontal gene transfer

transffer of genes with neighboring cells, regardless of species ( most prokyroptic cells can do this)

evolution

when genes in a population change in frequency or sequence over time

morphology

cell size and shape

#bacterial cells on earth

estemated 4-6 × 10³⁰

bacterial species in the body

1000+ seperate bacterial species

prokaryotic cell size

between 10- 0.5 um with the smallest being 0.2 um and the largest 600 um

Eukaryotic cell size

5-100 um with the smallest ~0.8um and largest can be many centimeters

viral cell size

20 nm-750 nm in diameter

incantations

folding of one part of the structure within another part of the structure

Prokyryotic morphology

1. coccus

2. rods (bacillus)

3. sprillum

4. spirochete

5. stalk/hyoha (budding and appendaged)

6. Filamentous

(the last 3 are less common, depending on the environment)

domains

all cells fall into one of these; bacteria, archaea, eukarya,

Four main phyla that make up >90% of cultivatd bacteria

Actinobacteria, Firmicutes, Proteobacteria, and Bacteriodetes

There are at least 80 bacteria phyla and 30 major phylogenetic lineages (phyla)

Lecture:

there are 41 accepted major phyla but an estimated 1300

five main phyla of archaea

Euryarchaeota, Crenarchaeota, Thaumarchaeota, Nanoarchaeota, and Korarchaeota.

more than 12 archeal phyla exist

Lecture:

5 known phyla

Kingdoms of Eukarya

6 kingdoms rather than phyla.

major groups:

algae

• photsythetic and primary producers

• live in soil and aquatic environments

• non pathogenic but some CAN produce toxins

fungi

• yeast (unicellular) and mold (multicellular)

• major decomposer

• many plant and some human pathogens

Cyanobacteria

oxygen producing phototrophs

LUCA

last common ancestor from where the three major domains share ~60 genes universally.

extremophiles

miccroorganism that are able to tollerate extreme conditions such as volcanic hot springs, glaciers, ice-covered regions etc.

protozoa

single celled eukaryotic organism. Contain a nucleus and other membrane bound organelles.

They are classified by movement like amoebas (pseudopods), flagellates (flagella), ciliates (cilia), or sporozoans(non-motile adults)

bioremediation

process by which microbes are used to clean up industrial pollution. Transforms toxic pollutants into notoxic forms. this is done through the addition or stimulation of microbes

biofilms

colonies of microbs that can form on any submerged substance. (microbes can grow almost anywhere where liguid water is present)

magnification

capacity of a microscope to enlarge an image

resolution

the ability to distingues two adjacent objects as distinct and separate (up to a specific distance)

differential staining

Stains that render different kinds of cells different colors

Gram Stain

cells are either gram-positive (purple-violet) or gram-negative (pink). the differences arise from differences in the structure of the cell walls of the + and - cells

phase contrast microscopy

relies on the principle that cells differ in refractive index (ability of any material to alter the speed of light) and also differ from their surrounding, generating a dark subject in a light background

dark-feild microscopy

Light is directed from the sides of the specimen and only light that is scattered upon contact reaches the lens. This generates a dark background with a light specimen (gives better resolution that light microscopy

flouresence microscopy

visulizing specimen that fluorescence (naturally or via staining wiht DAPI or other fluorescent stain). Specimin are made to fluoresce by illumination from above with a light of 1 color. filters are used so that only fluorescent light is seen

differential interferance contrast microscopy (DIC)

Used for unstained cells and uses plain polarized light that is passed through a prism to generate 2 distinct beams of light. beams pass thought specimen that differ in refractive index and are combined. beams are not totally in phase but instead inferfere with eachother and give a 3D perspective that enhanes subtle diff in the cell structure. is helpful for visuallizinf internal structures in cells

Confocal Scanning Laser Microscopu (CSL)

computer controlled microscope that couples laser to a fluorescent microscope. Generates a higch contrast, 3D image, that lets the viewer access several planes of focus in a specimen. this is partically useful with thick specimen (ex. biofilm) with multiple layers of cells

Electron microscopy

Uses electrons rather than light and electro magnets in place of lenses. The system opperates in a vacuum where a photograph called an electron micrograph is taken. There are 2 types (transmission and scanning)

Transmission Electron Microscopy (TEM)

Gives high mag and res examination of cels and cell structure (far greater than light microscope). Can even view structures at the molecular level.( resoling power ~ 0.2 nm rather than 0.2 um)

electron cryotomography (cryoET)

Uses TEM to obtain a 3D image of a species. Sample is rapidly frosen at low temps so that they are immobilized in noncrystalline vitreous ice and imaged at low temps (< -150dC). cells are then imaged at various angles to ge ta 3d image

Scanning Electron microscopy (SEM)

optimal 3D imaging of cells for the surface of cells. coats th specimen with a thin film of heavy metal (typically gold). electrons scattered from the metal coating are collected produce an image. Has good depth of feild and can observe fairly large specimen.

black and white but false color is often

aseptic technique

collection of practices that alloe for the preperation and maintenance of sterile (without the presence of living organisms) nutrient media and solutions

pure culture

cultures containing cells from only one type of microorganism

enrichment culture

allow for the isolation from nature of microbes havinf paricular metabolic characteristics

spontaneous generation

the belief that life arose spontaneously from nonliving materials

Koch’s postulates overview

used to definitively link cause and effect in infectous disease. they stress the importance of laboratory cultures of the putative infectious agent followed by introduction of the suspected agent to virgin animals and recovery of the pathogen from diseased or dead animals

Koch’s Postulates

1. pathogen must be present in all infected cases and abscent in asympomatic, healthy individulas

2. a pure culture must be isolated from an infected individual

3. specimen must be used to inoculate an individual, and the indivdual must present as symptomatic or infected

4. original specimine must be recovered from the bodiy of the inculaed individual

pure culture

a population of identical cells, generally originating from the same cell

inorganic substances

compounds without carbon-carbon bonds

chemolithotrophy

any metabolic process in which energy for growth is produced using only inorganic chemical compunds

enrichment media

media used to selectively encourage the growth of specific microorganisms

Robert Koch

anthrax (bacillus anthracis), koch postulates, and pure culture technique

Pittfalls of Koch’s Postulates

Not effective with multipathogenic diseases and d that arise based on concentration or location