Chapter 22: Prokaryotes (Bacteria and Archaea)

prokaryotes

- first organisms on earth- millions of species EVERYWHERE- live on and in other organisms

microbial mats

a multi-layered sheet of prokaryotes that may include (mostly) bacteria and archaea

stromatolites

ancient atmosphere

* anoxic (no molecular oxygen)- only anaerobic organisms
* phototrophs appeared one billion years of formation of Earth
* cyanobacteria evolved from simple phototrophs one billions years later
* ancestral cyanobacteria began "oxygenation" (photosynthesis) of atmosphere

extremophiles

bacteria and archaea that are adapted to grow under extreme conditions

* ex: deep sea vent, heat, dry, cold, or radiation

acidophiles

grow at extreme acid pH (pH 3 or below)

alkaliphiles

grow at basic pH (pH 9 or above)

thermophiles

grow at high temperatures (60-80°C or 140-176°F)

hyperthermophiles

grow at extremely high temperatures (80-122°C or 176-250°F)

psychrophiles

grow at low temperatures (-15-10°C or 5-50°F)

halophiles

grow in high salt concentrations (at least 0.2 M)

osmophiles

live in environments high in sugar as solute

Deinococcus radiodurans

a prokaryote that can tolerate very high doses of ionizing radiation; a polyextremophile

the Dead Sea

a hypersaline basin 10x saltier with 40x more magnesium than sea water and has intense solar radiation- halophilic prokaryotes live here

Robert Koch

discovered the techniques for pure culture, including staining and using growth media

culture medium

contains all the nutrients needed by the target microorganism, can be liquid (broth) or solid

* there should be evidence of microbial growth after incubation time at right temp.

pure culture

a laboratory culture containing a single species of microorganism (can get this from a mixed culture)

blood agar plates

used to diagnose Streptococcus infections

clone

member of a population of genetically identical cells produced from a single cell

Koch's Postulates

1. the microorganism must be found in abundance in all organisms suffering from the disease, but should not be found in healthy organisms
2. the microorganism must be isolated from a diseased organism and grown in pure culture
3. the cultured microorganism should cause disease when introduced into a healthy organism
4. the microorganism must be reisolated from the inoculated, diseased experimental host and identified as being identical to the original specific causative agent

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**can only be fully applied to organisms that can be isolated and cultured**

VBNC

* viable but not culturable
* organisms that cannot be cultured but are not dead
* when prokaryotes respond to environmental stressors by entering dormant state allowing survival

biofilm

* a microbial community held together by gummy-textured matrix
* matrix made of polysaccharides (primarily), proteins, and nucleic acids secreted by the organisms
* typically grow attached to surfaces (everywhere)

exopolysaccharidic (EPS)

anchors organisms in a biofilm to surfaces and protects from damage by antibiotics

prokaryotic cell size

0.1-5.0 µm in diameter

all cells have...

1. plasma membrane
2. cytoplasm
3. double-stranded DNA genome
4. ribosomes

ribosomes

site of protein synthesis

prokaryotes

pro- = before

\-karyon = nucleus

Cocci

* sing. Coccus
* spherical or round

Bacilli

* sing. Bacillus
* rod-shaped

Spirilli

* sing. Spirillum
* spiral-shaped

prokaryote structure

* no membrane-bound organelles
* no nucleus: DNA in nucleoid
* ribosomes "free"
* no microtubules
* almost all have cell wall (prevents cell lysis)
* bacteria: w/ peptidoglycan (PG)
* archaea: w/ other structural polysaccharides (no PG)

prokaryote phylogeny

* universal ancestor gave rise to all 3 domains of life
* archaea and bacteria both prokaryotes, separate from eukaryotes
* archaea believed to give rise to eukarya

domain bacteria

* majority of prokaryotes
* extreme diversity in ecological roles
* some pathogens
* some beneficial
* some symbiotic

proteobacteria

* gram-negative bacteria
* diverse metabolism/nutrition
* includes many N-fixing bacteria
* includes common gastrointestinal pathogens (food poisoning)
* ex: Escherichia coli, Salmonella, Vibrio cholera

chlamydias

* gram-negative bacteria
* all endoparasites (live within animal cells)
* ex: Chlamydia in humans causes STD

Chlamydia trachomatis

* causes eye infection (conjuntivitis) or pneumonia in children of infected women
* cause Pelvic Inflammatory Disease —> leads to infertility
* preventable and curable

spirochetes

* characteristic spiral shape
* many free-living but include disease-causing pathogens
* ex: syphilis (STD), Treponema pallidum, Lyme disease (Borrelia burgdorferi)

cyanobacteria

* plant-like, O2-generating photosynthesis
* some are also N-fixers
* "blooms" of this can make toxins
* ex: Oscillatoria

gram-positive bacteria

* include many decomposers in soil
* include some sources of antibiotics
* include many pathogens
* ex: anthrax, tetanus, staph (Staphylococcus aureus), MRSA infections, strep throat (Streptococcus) and scarlet fever

Domain Archaea

* includes extremophiles & methanogens (produce methane gas)
* many live in "normal" conditions
* no human-disease-causing archaens

methanogens

produce methane (CH4) as by-product of anaerobic respiration

prokaryotic plasma membrane

* thin lipid bilayer (6-8 nm)
* selectively permeable
* structure = phospholipid bilayer with two layers of lipid molecules
* bacterial membrane: fatty acids linked to glycerol
* archaeal membrane: branched isoprene (phytanyl) chains linked to glycerol

gram positive bacteria (staining)

bacteria w/ thick PG layer and stains purple in Gram stain

gram negative bacteria (staining)

bacteria w/ thinner PG layer plus outer lipid bilayer membrane and stains pink in Gram stain

* outer lipopolysaccharide layer often toxic and resists drugs & immune system

capsule/slime layer

* sticky carbs and proteins secreted outside cell wall
* adheres (glues) cells together or to surface
* resists attack from immune system
* holds in moisture

flagellum

(plural: flagella) hair-like structure that extends from the plasma membrane and acts as an organelle of locomotion (motility)

fimbriae

(short pili)

* hair-like protein
* help cells stick to surfaces & each other

sex pilus

(plural: pili)

* pulls two bacteria cells together for DNA transfer (conjugation)
* forms mating bridge

plasmids

* extra tiny DNA rings w/ few genes
* replicate independently
* not "essential" for life, but add diversity
* ex: drug resistance genes

prokaryote reproduction

* asexual
* binary fission
* HGT (transformation, transduction, and conjugation)

binary fission

does not provide an opportunity for genetic recombination or genetic diversity


1. parent cell
2. replication of DNA
3. segregation of DNA
4. cell splitting into two

horizontal gene transfer

a) transformation: DNA fragment from a dead, degraded bacterium and is exchanged for a piece of DNA of the recipient

b) transduction: the transfer of a DNA fragment from one bacterium to another by bacteriophage

c) conjugation: a transfer of DNA from a living donor bacterium to a living recipient bacterium by cell-to-cell contact (sex pilus in Gram-negative)

prokaryote genetic diversity

* high rate of cell division —> many mutations
* one mutation can change phenotype
* mutations (except lethal ones) are passed on
* selection favors best clones
* short generation times —> rapid evolution

endospores

* only in Gram-positive bacteria
* under stress, some bacteria produce endospores (dormant, non-reproductive)
* survive heat, drought for thousands of years
* ex: Bacillus anthracis (causes anthrax), Clostridium tetani (causes tetanus)

macronutrients

nutrients that are needed in large amounts (carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur)

carbon

major element in all macromolecules- carbohydrates, proteins, nucleic acids, lipids, and many other compounds

nitrogen

a component of proteins, nucleic acids, and other cell constituents

hydrogen and oxygen

components of many organic molecules and of water

phosphorus

required by all organisms for the synthesis of nucleotides and phospholipids

sulfur

part of the structure of some amino acids such as cysteine and methionine

micronutrients

nutrients that are required in small amounts

* ex: iron is necessary for the function of the cytochromes involved in electron-transport reactions

photoautotrophs

use energy from sunlight and carbon from carbon dioxide

chemoheterotrophs

obtain both energy and carbon from an organic chemical source

chemolithoautotrophs

obtain their energy from inorganic compounds, and they build their complex molecules from carbon dioxide

photoheterotrophs

obtain their energy from light, but their carbon from organic compounds

nitrogen fixation

gaseous nitrogen is transformed (fixed) into more readily available forms, like ammonia (NH3)

nitrogen-fixing bacteria

bacteria that convert atmospheric nitrogen into ammonia

* ex: Azotobacter (in soil), Rhizobium (in roots of legumes; symbiotic relationship) and cyanobacteria

ammonification

process by which ammonia is released during the decomposition of nitrogen-containing organic compounds

nitrification

conversion of ammonium into nitrite and then the nitrite to nitrate in soils

nitrifying bacteria

perform nitrification

* ex: Nitrobacter, Nitrosomas, and Nitrospira

denitrifying bacteria

reverse the process of nitrification by reducing the nitrate from soils to gaseous compounds such as N2O, NO, and N2

sybiosis

two species living in close relationship

free-living

not living in symbiosis

parasitism

smaller parasite benefits at expense of other species (host)

* ex: anthrax, cholera bacteria

commensalism

one species benefits without any impact (good or bad) on other species

* ex: most bacteria on our skin

mutualism

both species benefit from each other

* ex: Rhizobium in legume roots get sugar & water; provide fixed nitrogen for plant

pathogenic bacteria

* infections produce bacterial poisons
* exotoxins secreted
* produced by both gram-negative and gram-positive bacteria
* ex: tetanus, botulism

exotoxins

toxic substances that bacteria secrete into their environment

endotoxins

* toxic outer membranes of some gram-negative bacteria
* generalized toxic effect
* ex: Salmonella food poisoning

antibiotics

* kill bacteria cells but not eukaryotic cells
* ex: penicillin affects peptidoglycan cell wall
* some antibiotics come from other bacteria

Alexander Fleming

discovered penicillin accidentally

zone of inhibition

the zone where bacteria can't grow around a given antibiotic

human use of prokaryotes

* DNA tech and genetic engineering
* commercial chemical and drug production

food products w/ prokaryotes

yogurt (Lactobacillus bulgaricus), cheese, etc.

produced by fermentation

microbial bioremediation

the use of prokaryotes (or microbial metabolism) to remove pollutants

* some bacteria remove toxic metals
* some transform toxic mercury into nontoxic forms (ex: Pseudomonas aeruginosa convert Hg^+2 into Hg^0)
* help clean up devastating oil spills (Exxon Valdez oil spill 1989)