Summary microbiology
Driessen
1. The microbial world
Microbes are the oldest form of life. They make up 15% of the earth's biomass. There are
30
2𝑥10 microbial cells on earth. They contribute to the global mass of carbon, nitrogen, and
phosphorus.
A cell is a living compartment that interacts with the environment and other cells. All cells
have in common:
- Cytoplasmic (cell) membrane: barrier that separates the inside of the cell from the
outside environment
- Cytoplasm: aqueous mixture of macromolecules, small organics, ions, and
ribosomes inside cell
- Ribosomes: protein-synthesizing structures
- Cell wall: present in some microbes; confers structural strength.
Genes, genomes, nucleus, and nucleoid
Eukaryotic DNA contains linear chromosomes within the nucleus. Prokaryotic DNA are
generally single circular chromosomes that aggregate to form the nucleoid region. They may
also have plasmids.
History of life on earth
The earth is 4.6 billion years old. The first cells appeared between 3.8 and 4.3 billion years
ago. The atmosphere was anoxic until 2.6 billion years ago. The first anoxygenic
phototrophs came 3.6 years ago and plants & animals 0.5 billion years ago.
,Extremophiles
Microbes on human society
Microbes can be beneficial and harmful to humans. They are important for agriculture and
nutrition. They are used for production of biofuels and biogas.
Tree of life
rRNA made it possible to build the first tree of life. Carl Woese realized that rRNA sequences
could be used to infer evolutionary relationships. Archaea diverged from Eukarya.
Cultivation-independent methods show that microbes are omnipresent.
Terms
Culture: cells grown in/on nutrient medium.
Medium: liquid/solid mixture containing all required nutrients.
Metabolism: chemical transformation of nutrients.
LUCA: last universal common ancestor.
Ecosystems: all living organisms plus physical and chemical constituents of their
environment.
Industrial microbiology: use of microbes for major industries such as pharmaceuticals and
brewing.
Biotechnology: genetically engineered microbes making high-value products in small
amounts.
Bioremediation: cleaning up pollutants.
Metagenomics: microbial genomes/fragments can be recovered from environmental DNA
samples.
, 2. Build of the prokaryotic cell
Morphology
Morphology of microbes does not predict physiology, ecology, phylogeny, or other properties
of a prokaryotic cell. There are however selective forces determining morphology. E.g.
optimization nutrient uptake, swimming motility, gliding motility. The sizes of prokaryotes are
between 0.2 um to >600 um. Most cultured rod-shaped bacteria are between 0.5 and 10 um
wide. Eukaryotes are bigger, 5 to 100 um in diameter.
There are advantages to being small. The surface to volume ratio is higher and there are
more mutations (faster evolution). There are limits of cell size. Under 0.15 um is unlikely.
There are however smaller ultramicrobacteria that are supported by other bacteria for the
missing functions.
The cytoplasmic membrane
The cytoplasmic membrane is a series of layered structures surrounding the cytoplasm and
governing interactions with the environment. The main function is the selective permeability.
Bacterial cytoplasmic membrane:
- Phospholipid bilayer containing embedded proteins.
- Phospholipids contain both hydrophobic and hydrophilic elements.
- 8-10 nm wide and sometimes strengthened with hopanoids.
- Has integral and peripheral membrane proteins.
Archaeal cytoplasmic membrane:
- ether linkages in phospholipids of Archaea in contrast to Bacteria and Eukarya that
have ester linkages in phospholipids.
- Archaeal lipids have isoprenes instead of fatty acids.
- Major lipids are phosphoglycerol diethers with phytanyl 𝐶20 side chains and
diphosphoglycerol tetraethers with biphytanyl 𝐶40 side chains.
- Many different isoprenoid chains including some ring structures (e.g., crenarchaeol).
Transporting Nutrients into the Cell
There are multiple types of transport systems. In active transport systems solutes are
against the concentration gradient. The 3 mechanisms are:
- Simple transport, with transmembrane transport proteins.
- Group translocation, a series of proteins modify the substrate during transport.
- ABC system, three components are used.
Driessen
1. The microbial world
Microbes are the oldest form of life. They make up 15% of the earth's biomass. There are
30
2𝑥10 microbial cells on earth. They contribute to the global mass of carbon, nitrogen, and
phosphorus.
A cell is a living compartment that interacts with the environment and other cells. All cells
have in common:
- Cytoplasmic (cell) membrane: barrier that separates the inside of the cell from the
outside environment
- Cytoplasm: aqueous mixture of macromolecules, small organics, ions, and
ribosomes inside cell
- Ribosomes: protein-synthesizing structures
- Cell wall: present in some microbes; confers structural strength.
Genes, genomes, nucleus, and nucleoid
Eukaryotic DNA contains linear chromosomes within the nucleus. Prokaryotic DNA are
generally single circular chromosomes that aggregate to form the nucleoid region. They may
also have plasmids.
History of life on earth
The earth is 4.6 billion years old. The first cells appeared between 3.8 and 4.3 billion years
ago. The atmosphere was anoxic until 2.6 billion years ago. The first anoxygenic
phototrophs came 3.6 years ago and plants & animals 0.5 billion years ago.
,Extremophiles
Microbes on human society
Microbes can be beneficial and harmful to humans. They are important for agriculture and
nutrition. They are used for production of biofuels and biogas.
Tree of life
rRNA made it possible to build the first tree of life. Carl Woese realized that rRNA sequences
could be used to infer evolutionary relationships. Archaea diverged from Eukarya.
Cultivation-independent methods show that microbes are omnipresent.
Terms
Culture: cells grown in/on nutrient medium.
Medium: liquid/solid mixture containing all required nutrients.
Metabolism: chemical transformation of nutrients.
LUCA: last universal common ancestor.
Ecosystems: all living organisms plus physical and chemical constituents of their
environment.
Industrial microbiology: use of microbes for major industries such as pharmaceuticals and
brewing.
Biotechnology: genetically engineered microbes making high-value products in small
amounts.
Bioremediation: cleaning up pollutants.
Metagenomics: microbial genomes/fragments can be recovered from environmental DNA
samples.
, 2. Build of the prokaryotic cell
Morphology
Morphology of microbes does not predict physiology, ecology, phylogeny, or other properties
of a prokaryotic cell. There are however selective forces determining morphology. E.g.
optimization nutrient uptake, swimming motility, gliding motility. The sizes of prokaryotes are
between 0.2 um to >600 um. Most cultured rod-shaped bacteria are between 0.5 and 10 um
wide. Eukaryotes are bigger, 5 to 100 um in diameter.
There are advantages to being small. The surface to volume ratio is higher and there are
more mutations (faster evolution). There are limits of cell size. Under 0.15 um is unlikely.
There are however smaller ultramicrobacteria that are supported by other bacteria for the
missing functions.
The cytoplasmic membrane
The cytoplasmic membrane is a series of layered structures surrounding the cytoplasm and
governing interactions with the environment. The main function is the selective permeability.
Bacterial cytoplasmic membrane:
- Phospholipid bilayer containing embedded proteins.
- Phospholipids contain both hydrophobic and hydrophilic elements.
- 8-10 nm wide and sometimes strengthened with hopanoids.
- Has integral and peripheral membrane proteins.
Archaeal cytoplasmic membrane:
- ether linkages in phospholipids of Archaea in contrast to Bacteria and Eukarya that
have ester linkages in phospholipids.
- Archaeal lipids have isoprenes instead of fatty acids.
- Major lipids are phosphoglycerol diethers with phytanyl 𝐶20 side chains and
diphosphoglycerol tetraethers with biphytanyl 𝐶40 side chains.
- Many different isoprenoid chains including some ring structures (e.g., crenarchaeol).
Transporting Nutrients into the Cell
There are multiple types of transport systems. In active transport systems solutes are
against the concentration gradient. The 3 mechanisms are:
- Simple transport, with transmembrane transport proteins.
- Group translocation, a series of proteins modify the substrate during transport.
- ABC system, three components are used.
