Microbiology Summary transcription and translation are in separate places
ribosomes: proteins for protein synthesis
C1: THE MICROBIAL WORLD organelles: cytoplasmic structures
[1.1] M ICROORGANISMS , TINY TITANS OF THE genome: all genes in a cell
EARTH Microorganisms can only be seen when with
gene: a segment that encodes a protein or an
RNA molecule
large colonies (more than 107 individual bacterial
cells). 1 bacteria = 2 micrometer; 40x1012 bacteria transcription: the info on DNA is copied to RNA
habitat: the environment in which a microbial translation: RNA molecule is used to form protein
archaea: chromosomes are differently packed
population lives
microbial communities: interaction between compared to bacteria; replication resembles
eukaryotes; cell wall and cell membrane differs
microbial populations
with bacteria
ecosystem: all the living organisms together with
the physical and chemical components of their Bacteria and archaea are unicellular organisms
environment with special structures: cytoplasmic membrane,
DNA, RNA, ribosomes, proteins.
The metabolic activities of microorganisms
Eukaryotic unicellular organisms resemble
gradually change their ecosystems, both
chemically and physically (example: O2 came into eukaryotes like plants and animals, because of
the air when oxic microbes evolved) their structure
[1.2] STRUCTURE OF MICROBIAL CELLS [1.4] A N INTRODUCTION TO M ICROBIAL LIFE
(1)Bacteria
prokaryote: -pre-nucleus nucleoid: no nucleus
• prokaryotes
with a membrane
-fewer chromosomes s = sedimentation • usually undifferentiated single cells 1–10 μm long
coefficient but vary widely
-no mitochondria
• 30 major phylogenetic lineages, mostly diverse
-no chloroplasts
species with diverse physiologies and ecological
-no endoplasmic reticulum
-ribosome size: (70S) strategies
-(no) organelles (some with (2)Archaea
membrane) • prokaryotes
-cell wall • less morphological diversity than Bacteria
• mostly undifferentiated cells 1–10 μm long
eukaryote: -real-nucleus nucleus: nucleus
• five well-described phyla
with a membrane
• many associated with extreme environments, but
-more chromosomes
not all
-mitochondria
-chloroplasts • lack known parasites or pathogens of plants and
animals
-endoplasmic reticulum
(3)Eukarya
-ribosome size (80S)
-with organelles • plants, animals, fungi
-no/simple cell wall • first were unicellular
• at least six kingdoms
• vary dramatically in size, shape, physiology
(bacteria and archaea)
(4)Viruses
• obligate parasites that only replicate within host
cell
• not cells
• have no metabolism; take over other metabolic
systems to replicate
• have small genomes of double-stranded or
single-stranded DNA or RNA
• very diverse
• classified based on structure, genome
composition, and host specificity
properties of all cells:
1.metabolism: production of building blocks for
making macro-molecules; cells take up nutrients,
transform them, and expel wastes: open system:
genetic: replication, transcription, translation
catalytic: energy, biosynthesis, enzymes
2.growth: nutrients converted to new cell
materials: transcription – translation – DNA
3.evolution: new properties develop (because of
changes in sequence and frequency), best survive
,slow evolution: mother to daughter cell (vertical fermentation: breaking down of a substance;
gene transfer) glucose becomes an alcohol (+CO2) by
fast evolution: spreading genes by plasmids microorganisms
(horizontal gene transfer) sterilization: making something free from bacteria
antibiotic resistance: exchange of DNA/plasmids fermentation without O2: substance > CO2 +
or mutations causes resistance ethanol
▪ properties of some cells: fermentation with O2: substance > CO2 + H2O
1.differentiation: developing new cell structures spontaneous reaction: life arises spontaneously
2.communication: cells interact by chemical from nonliving materials; not the case: cells come
messengers (from the environment) from air or are already present
3.genetic exchange: exchange genes to species - aerobic organism breaths with electron
4.motility: self-propulsion (move themselves) acceptor: O2
- anaerobic organism breaths with electron
[1.5] M ICROORGANISMS AND THE BIOSPHERE : acceptor: NO3-, SO42-, CO2, Fe3+, Mn4+, ….
appearance on earth: OR it is fermentative, meaning that it does not
(1)bacteria respire, but that it uses an internal
(2)anoxygenic phototrophic bacteria; do not metabolite as electron acceptor (e.g. yeasts)
generate O2, there’s no H2O (anoxic world) respiratory chain: electron transport chain:
(3)oxygenic phototrophic bacteria: cyanobacteria; 1- Respiration: the electron acceptor is used to
generate O2 from H2O (also O3 layer formed-> “burn” a compound (compound becomes
earth is protected from UV-light) (oxic world) oxidized);
(4) eukaryotes 2- Electrons are released from the compound
(5) algae 3- Electrons pass via a respiratory chain to the
(6) other organisms terminal electron acceptor (O2);
Microorganisms (especially bacteria and archaea) 4- Respiration leads to energy generation (ATP)
are the oldest form of life on earth (80% of earths 3 ways of electron gain:
time) and they have created the environmental
conditions as they are now: O2 and O3 were
introduced
Some microbes can survive with extreme high or
low temperature, pH, pressure, salt concentrations
Water is most important for microbe activity
Microorganisms constitute the majority of the
biomass on earth and they have created the
environmental conditions as they are now
The number of prokaryotes is 2-3 x 1030 cells and their
total amount of carbon is 450 billion tons C (plants: 560) chemolithoautotrophy: inorganic molecules
large to small biomass: serve as electron donor for respiration,
plants > bacteria > fungi > archaea > protists > chemolithotrophs use C from CO2 (autotrophy)
animals > viruses heterotroph: use nutrients from complex organic
molecules (…)
autotroph: form nutrients from simple inorganic
[1.6] T HE IMPACT OF M ICROORGANISMS ON substances (CO2), but still needs an electron
HUMAN S OCIETY donor (H2) (phototrophs)
microorganisms are crucial in maintaining the
environment (needed for O2 production and [1.7-1.8] LIGHT MICROSCOPY AND THE
closing of cycles); they can have positive/negative
DISCOVERY OF MICROORGANISMS AND
role: pathogens: dangerous microbes for humans
IMPROVING CONTRAST IN LIGHT MICROSCOPY
causing sickness (NOT ALL MICROORGANISMS
ARE PATHOGENS) light microscopy: use photons to make cells visible
antibiotics and resistance: discovery of penicillin; 1)bright-field microscopy: cells have little
antimicrobial agents produced by microorganisms; contrast
can kill/inhibit the growth of other bacteria Improve contrast:
antibiotics consist of (1) targets and (2) resistance • staining (methylene blue, cristal violet, safranin)
mechanisms cell dies
not too often use antibiotics otherwise resistance • differential staining: Gram stain: distinguish
antibiotic use more for animals than humans two groups: gram-positive (purple) and gram-
positive impact: use for agriculture and human negative (pink) cell dies
nutrition (N is fixed; symbiosis (plant + bacteria); • fluorescence: natural (chlorophyll) or stained
antibiotics, fuels, cleaning up pollutants (DAPI; blue); it emits light
(bioremediation) 2)phase contrast: phase-difference amplified
negative impact: waste products (CO2/CH4: 3)dark field: light from the side; not passing the
because of fermentation in cows for nutrition) specimen (surroundings are black)
, [1.9] IMAGING CELLS IN THREE DIMENSIONS Winogradsky: chemolithoautotrophy, micro-
organisms can oxidize inorganic molecules, they
can be used as energy source
[1.10] P ROBING CELL STRUCTURE : ELECTRON
Beijerinck: environment determines the type of
MICROSCOPY microorganisms, so different species can be
Probing cell structure: electron microscopy isolated: enrichment culture; discovered viruses;
electron microscopy: use electrons to make cells everything is everywhere
visible; electromagnets function as lenses;
operates in a vacuum; camera takes a picture
C2: MICROBIAL CELL STRUCTURE AND
[1.13] DISCOVERY OF MICROBIAL DIVERSITY FUNCTION
[1.3] C ELL SIZE AND MORPHOLOGY
morphology: cell shape
Mycoplasma: no cell wall, so no fixed morphology
Major morphologies of prokaryotic cells:
coccus:
spherical/ ovoid
spirillum:
curved or spiral
rod/ bacillus:
[1.15] W OESE AND THE TREE OF LIFE cylindrical
LUCA: last universal common ancestor; then 3 domains for some, the
from the LUCA two domains evolved: bacteria and morphology is
archaea. Then the archaea diverged into archaea dependent on
and eukarya environment
Archaea are discovered by ribosomal RNA and growth
sequences. Trees are based on the nucleotide condition
sequence of rRNA because: Morphology typically does not predict physiology,
- it is present in all life forms ecology, phylogeny, or other properties of a
- it has the same function prokaryotic cell
- it is very conserved (changes little over time by Sometimes selective forces may affect morphology
mutations) • optimization for nutrient uptake or energy
- sequence is long enough conservation
sequencing is used for the taxonomy of • swimming motility in viscous environments
microorganisms and viewing the microbial diversity (helical or spiral-shaped cells)
of ecosystems • gliding motility (filamentous bacteria)
sequencing: (not virus because don’t have rRNA) Pleomorphism: the ability of some micro-
1 isolate DNA from an organism organisms to alter their shape or size in response
2 copy rRNA gene with PCR to environmental conditions
3 sequence DNA (determine the order of Caulobacter crescentus
nucleotides) - Slightly bended rod (‘vibrio’) (crescent)
4 analyze sequence - Very common in surface and saltwater, soil
5 generate phylogenetic tree (diagram that - Swims until it is big enough, then attaches
displays the evolutionary history) (strong), forms a stalk and divides (then detach)
Cultivation-independent methods show most
microbes have not been cultured yet
persons:
Hooke: first description of microorganisms
Leeuwenhoek: discovered protozoa and bacteria
with light microspcope (animalcules)
Woese: discovered that the archaea are a Length of stalk dependent on phosphate
separate group of prokaryotes, based on concentration: less phosphate →longer stalk (more
ribosomal RNA sequences evolutionary proteins so can take up more P). Stalk contains
relationships are verified proteins for P uptake
Fleming: discovered penicillin and lysozyme Most rod-shaped bacteria are between 0.5 and 4.0
Pasteur: discovered fermentation and (an)aerobic μm wide and <15 μm long.
microorganisms, disapproved the spontaneous Size range for prokaryotes: 0.2 μm to >700 μm in
reaction, developed the first rabies vaccine, diameter
developed heat sterilization techniques (swan- Beggiatoa species
necked flask) sulfur chemolithotroph - larger than E.Coli -160 µm
Cohn: filaments - cell volume: 1.000.000 µm3 - 50x160 µm
ribosomes: proteins for protein synthesis
C1: THE MICROBIAL WORLD organelles: cytoplasmic structures
[1.1] M ICROORGANISMS , TINY TITANS OF THE genome: all genes in a cell
EARTH Microorganisms can only be seen when with
gene: a segment that encodes a protein or an
RNA molecule
large colonies (more than 107 individual bacterial
cells). 1 bacteria = 2 micrometer; 40x1012 bacteria transcription: the info on DNA is copied to RNA
habitat: the environment in which a microbial translation: RNA molecule is used to form protein
archaea: chromosomes are differently packed
population lives
microbial communities: interaction between compared to bacteria; replication resembles
eukaryotes; cell wall and cell membrane differs
microbial populations
with bacteria
ecosystem: all the living organisms together with
the physical and chemical components of their Bacteria and archaea are unicellular organisms
environment with special structures: cytoplasmic membrane,
DNA, RNA, ribosomes, proteins.
The metabolic activities of microorganisms
Eukaryotic unicellular organisms resemble
gradually change their ecosystems, both
chemically and physically (example: O2 came into eukaryotes like plants and animals, because of
the air when oxic microbes evolved) their structure
[1.2] STRUCTURE OF MICROBIAL CELLS [1.4] A N INTRODUCTION TO M ICROBIAL LIFE
(1)Bacteria
prokaryote: -pre-nucleus nucleoid: no nucleus
• prokaryotes
with a membrane
-fewer chromosomes s = sedimentation • usually undifferentiated single cells 1–10 μm long
coefficient but vary widely
-no mitochondria
• 30 major phylogenetic lineages, mostly diverse
-no chloroplasts
species with diverse physiologies and ecological
-no endoplasmic reticulum
-ribosome size: (70S) strategies
-(no) organelles (some with (2)Archaea
membrane) • prokaryotes
-cell wall • less morphological diversity than Bacteria
• mostly undifferentiated cells 1–10 μm long
eukaryote: -real-nucleus nucleus: nucleus
• five well-described phyla
with a membrane
• many associated with extreme environments, but
-more chromosomes
not all
-mitochondria
-chloroplasts • lack known parasites or pathogens of plants and
animals
-endoplasmic reticulum
(3)Eukarya
-ribosome size (80S)
-with organelles • plants, animals, fungi
-no/simple cell wall • first were unicellular
• at least six kingdoms
• vary dramatically in size, shape, physiology
(bacteria and archaea)
(4)Viruses
• obligate parasites that only replicate within host
cell
• not cells
• have no metabolism; take over other metabolic
systems to replicate
• have small genomes of double-stranded or
single-stranded DNA or RNA
• very diverse
• classified based on structure, genome
composition, and host specificity
properties of all cells:
1.metabolism: production of building blocks for
making macro-molecules; cells take up nutrients,
transform them, and expel wastes: open system:
genetic: replication, transcription, translation
catalytic: energy, biosynthesis, enzymes
2.growth: nutrients converted to new cell
materials: transcription – translation – DNA
3.evolution: new properties develop (because of
changes in sequence and frequency), best survive
,slow evolution: mother to daughter cell (vertical fermentation: breaking down of a substance;
gene transfer) glucose becomes an alcohol (+CO2) by
fast evolution: spreading genes by plasmids microorganisms
(horizontal gene transfer) sterilization: making something free from bacteria
antibiotic resistance: exchange of DNA/plasmids fermentation without O2: substance > CO2 +
or mutations causes resistance ethanol
▪ properties of some cells: fermentation with O2: substance > CO2 + H2O
1.differentiation: developing new cell structures spontaneous reaction: life arises spontaneously
2.communication: cells interact by chemical from nonliving materials; not the case: cells come
messengers (from the environment) from air or are already present
3.genetic exchange: exchange genes to species - aerobic organism breaths with electron
4.motility: self-propulsion (move themselves) acceptor: O2
- anaerobic organism breaths with electron
[1.5] M ICROORGANISMS AND THE BIOSPHERE : acceptor: NO3-, SO42-, CO2, Fe3+, Mn4+, ….
appearance on earth: OR it is fermentative, meaning that it does not
(1)bacteria respire, but that it uses an internal
(2)anoxygenic phototrophic bacteria; do not metabolite as electron acceptor (e.g. yeasts)
generate O2, there’s no H2O (anoxic world) respiratory chain: electron transport chain:
(3)oxygenic phototrophic bacteria: cyanobacteria; 1- Respiration: the electron acceptor is used to
generate O2 from H2O (also O3 layer formed-> “burn” a compound (compound becomes
earth is protected from UV-light) (oxic world) oxidized);
(4) eukaryotes 2- Electrons are released from the compound
(5) algae 3- Electrons pass via a respiratory chain to the
(6) other organisms terminal electron acceptor (O2);
Microorganisms (especially bacteria and archaea) 4- Respiration leads to energy generation (ATP)
are the oldest form of life on earth (80% of earths 3 ways of electron gain:
time) and they have created the environmental
conditions as they are now: O2 and O3 were
introduced
Some microbes can survive with extreme high or
low temperature, pH, pressure, salt concentrations
Water is most important for microbe activity
Microorganisms constitute the majority of the
biomass on earth and they have created the
environmental conditions as they are now
The number of prokaryotes is 2-3 x 1030 cells and their
total amount of carbon is 450 billion tons C (plants: 560) chemolithoautotrophy: inorganic molecules
large to small biomass: serve as electron donor for respiration,
plants > bacteria > fungi > archaea > protists > chemolithotrophs use C from CO2 (autotrophy)
animals > viruses heterotroph: use nutrients from complex organic
molecules (…)
autotroph: form nutrients from simple inorganic
[1.6] T HE IMPACT OF M ICROORGANISMS ON substances (CO2), but still needs an electron
HUMAN S OCIETY donor (H2) (phototrophs)
microorganisms are crucial in maintaining the
environment (needed for O2 production and [1.7-1.8] LIGHT MICROSCOPY AND THE
closing of cycles); they can have positive/negative
DISCOVERY OF MICROORGANISMS AND
role: pathogens: dangerous microbes for humans
IMPROVING CONTRAST IN LIGHT MICROSCOPY
causing sickness (NOT ALL MICROORGANISMS
ARE PATHOGENS) light microscopy: use photons to make cells visible
antibiotics and resistance: discovery of penicillin; 1)bright-field microscopy: cells have little
antimicrobial agents produced by microorganisms; contrast
can kill/inhibit the growth of other bacteria Improve contrast:
antibiotics consist of (1) targets and (2) resistance • staining (methylene blue, cristal violet, safranin)
mechanisms cell dies
not too often use antibiotics otherwise resistance • differential staining: Gram stain: distinguish
antibiotic use more for animals than humans two groups: gram-positive (purple) and gram-
positive impact: use for agriculture and human negative (pink) cell dies
nutrition (N is fixed; symbiosis (plant + bacteria); • fluorescence: natural (chlorophyll) or stained
antibiotics, fuels, cleaning up pollutants (DAPI; blue); it emits light
(bioremediation) 2)phase contrast: phase-difference amplified
negative impact: waste products (CO2/CH4: 3)dark field: light from the side; not passing the
because of fermentation in cows for nutrition) specimen (surroundings are black)
, [1.9] IMAGING CELLS IN THREE DIMENSIONS Winogradsky: chemolithoautotrophy, micro-
organisms can oxidize inorganic molecules, they
can be used as energy source
[1.10] P ROBING CELL STRUCTURE : ELECTRON
Beijerinck: environment determines the type of
MICROSCOPY microorganisms, so different species can be
Probing cell structure: electron microscopy isolated: enrichment culture; discovered viruses;
electron microscopy: use electrons to make cells everything is everywhere
visible; electromagnets function as lenses;
operates in a vacuum; camera takes a picture
C2: MICROBIAL CELL STRUCTURE AND
[1.13] DISCOVERY OF MICROBIAL DIVERSITY FUNCTION
[1.3] C ELL SIZE AND MORPHOLOGY
morphology: cell shape
Mycoplasma: no cell wall, so no fixed morphology
Major morphologies of prokaryotic cells:
coccus:
spherical/ ovoid
spirillum:
curved or spiral
rod/ bacillus:
[1.15] W OESE AND THE TREE OF LIFE cylindrical
LUCA: last universal common ancestor; then 3 domains for some, the
from the LUCA two domains evolved: bacteria and morphology is
archaea. Then the archaea diverged into archaea dependent on
and eukarya environment
Archaea are discovered by ribosomal RNA and growth
sequences. Trees are based on the nucleotide condition
sequence of rRNA because: Morphology typically does not predict physiology,
- it is present in all life forms ecology, phylogeny, or other properties of a
- it has the same function prokaryotic cell
- it is very conserved (changes little over time by Sometimes selective forces may affect morphology
mutations) • optimization for nutrient uptake or energy
- sequence is long enough conservation
sequencing is used for the taxonomy of • swimming motility in viscous environments
microorganisms and viewing the microbial diversity (helical or spiral-shaped cells)
of ecosystems • gliding motility (filamentous bacteria)
sequencing: (not virus because don’t have rRNA) Pleomorphism: the ability of some micro-
1 isolate DNA from an organism organisms to alter their shape or size in response
2 copy rRNA gene with PCR to environmental conditions
3 sequence DNA (determine the order of Caulobacter crescentus
nucleotides) - Slightly bended rod (‘vibrio’) (crescent)
4 analyze sequence - Very common in surface and saltwater, soil
5 generate phylogenetic tree (diagram that - Swims until it is big enough, then attaches
displays the evolutionary history) (strong), forms a stalk and divides (then detach)
Cultivation-independent methods show most
microbes have not been cultured yet
persons:
Hooke: first description of microorganisms
Leeuwenhoek: discovered protozoa and bacteria
with light microspcope (animalcules)
Woese: discovered that the archaea are a Length of stalk dependent on phosphate
separate group of prokaryotes, based on concentration: less phosphate →longer stalk (more
ribosomal RNA sequences evolutionary proteins so can take up more P). Stalk contains
relationships are verified proteins for P uptake
Fleming: discovered penicillin and lysozyme Most rod-shaped bacteria are between 0.5 and 4.0
Pasteur: discovered fermentation and (an)aerobic μm wide and <15 μm long.
microorganisms, disapproved the spontaneous Size range for prokaryotes: 0.2 μm to >700 μm in
reaction, developed the first rabies vaccine, diameter
developed heat sterilization techniques (swan- Beggiatoa species
necked flask) sulfur chemolithotroph - larger than E.Coli -160 µm
Cohn: filaments - cell volume: 1.000.000 µm3 - 50x160 µm
