Microbial world + classification + Growth + Metabolism Flashcards
What is microbiology?
- ‘Microbiology’ is derived from the Greek words for small
(micro), life (bios), speech/story (logos)
What is a microorganism?
- A microorganism is a single cell or cluster of cells that can
only be seen with the aid of a microscope
Who is the father of microbiology?
Antonie van Leeuwenhoek (1632-1723)
* ‘father of microbiology’.
* Dutch cloth merchant
What did Louis Pasteur find out?
Louis Pasteur (1822-1895)
* French chemist – founder of ‘medical microbiology’.
Discovered why fermentation sometimes led to formation
of alcohol (wine), and sometimes to acetic acid (vinegar).
Who is Robert Koch
Robert Koch (1843-1910)
* German physician – founder of the ’scientific method of microbiology’.
* Developed the use of solid media (gelatin, later agar) to grow individual
colonies of bacteria.
What is Koch’s Postulates?
Koch’s Postulates: A set of four criteria established to identify causative agent of infection.
Published in 1884:
1) The microbe must be found in all cases but absent
from healthy individuals.
2) The microbe is isolated from the host and grown in
pure culture.
3) When the microbe is introduced to a healthy host
the same disease occurs.
4) The same strain can be reisolated from the newly
diseased host.
Kochs Postulates the problems?
Problems:
* Some bacteria are very difficult to detect isolate.
* Modern molecular microbiology (PCR) needed.
* Pathogen may not have an animal host (e.g., HIV/AIDS)
What are the pathogenic microorganisms?
Pathogenic microorganisms – means causing or capable of causing disease
What are the commensal microorganisms?
Commensal microorganisms – one species benefits while the other is not harmed or helped in any significant way
What are mutualistic microorganisms?
Mutualistic microorganisms – ecological interaction between two species in which both benefit.
➢ Beneficial microbiomes
➢ Human gut: ~1000 species of bacteria
➢ Human skin: ~150 bacterial species with up to 10 million cells per cm2
➢ Bacteria in/on the body outnumber all human cells by a factor of ten.
➢ Flashlight / eyelight fish (Photoblepharon palpebratus). Bioluminescent bacteria
(Vibrio fischeri) live around eyes – attract prey and potential mates.
Do all microorganisms cause disease?
What is chemical recycling?
Chemical recycling
➢ Cyanobacteria use CO2
to make organic compounds such as sugars and provide
O2.
➢ N2 fixing organisms make the building blocks of proteins and nucleic acids.
➢ Fungal degradation of waste.
➢ Bioremediation of waste (bacteria are used in sewage treatment).
What is biotechnology (microbiology)
Biotechnology
➢ Dairy products – cheese, yogurt
➢ Fermentation – alcohol
➢ Enzymes for health and molecular biology
(Taq enzymes for use in PCR)
➢ Recombinant technology – antibiotics,
vitamins, hormones
Different Types of Microorganisms
- Prokaryotes
- no nucleus, no membrane bound organelles, simple cells, 0.2
– 2.0µm in diameter - appeared about 3.5 Billion years ago.
- Eukaryotes
- nucleus, complex cells, membrane bound organelles, 10-
100µm in diameter - appeared about 2 Billion years ago.
- Subcellular
- Viruses (20 – 300nm)
What are Bacteria Archaea examples of?
prokaryotes
What are Fungi Algae Protozoa examples of?
eukaryotes
What are Viruses Viroids Prions examples of?
sub cellular (not really organisms!)
Eukaryotes v. prokaryotes
- Eukaryote
- an organism with a complex cell or cells.
- genetic material is organised into a membrane bound nucleus or nuclei.
- Prokaryotes
- are organisms without a cell nucleus or any other
membrane-bound organelles.
*in most cases unicellular (in rare cases,
multicellular).
What are Eukaryotes
- Eukaryotes comprise animals, plants, fungi, protozoa.
- Mostly multicellular—as well as various other groups that
are collectively classified as protists.
*In contrast, prokaryotes are organisms, such as bacteria
and archaea.
*Eukaryotic cells are generally much larger than
prokaryotes:
- a variety of internal membranes and structures
organelles
* cytoskeleton composed of microtubules,
microfilaments and intermediate filaments (for
organisation and shape)
Eukaryotic cells PROKARYOTIC
CHECK SLIDE FOR DIAGRAMS
What are prokaryotic cells?
*Prokaryotes thrive almost everywhere, including
places too acidic, salty, cold or hot for most other
organisms.
*Due to their ability to adapt to diverse habitats,
prokaryotes are the most abundant organisms on
Earth.
*Prokaryotes are divided into two domains:
bacteria and archaea
How do Structural and functional adaptations
contribute to prokaryotic success
*Earliest life forms (fossils date 3.5 billion yr old)
*Most prokaryotic cells are 0.5-5 µm, much smaller
than the 10-100 µm of many eukaryotic cells
*Prokaryotic cells have a variety of shapes
*The three most common shapes are spheres
(cocci), rods (bacilli), and spirals
What is the Bacterial Taxonomy
Domain: Bacteria (prokaryotic organisms).
Kingdom: Bacteria (though this is sometimes debated).
Phylum: (e.g., Proteobacteria, Firmicutes).
Class: (e.g., Gammaproteobacteria).
Order: (e.g., Enterobacterales).
Family: (e.g., Enterobacteriaceae).
Genus: (e.g., Escherichia).
Species: (e.g., Escherichia coli).
What is light microscopy
⚫ Sample illumination is via transmitted
white light, i.e. illuminated from below and
observed from above
Advantages
-cheap, quick and easy to use.
Limitations
-magnification power is limited, image contrast,
requires sample staining.
What is Light Microscopy: Dark field
⚫ A technique for improving the contrast of
unstained, transparent specimens
⚫ Dark field can dramatically improve image
contrast (especially of transparent objects) while
requiring little equipment setup or sample
preparation
⚫ The technique does suffer from low light
intensity in final image of many biological
samples and continues to be affected by low
apparent resolution
What is Light Microscopy: Phase contrast
⚫ Shows differences in refractive index as a difference in contrast
⚫ Circular annulus in the condenser produces a cone of light
⚫ Cone is superimposed on a similar sized ring within the phaseobjective
⚫ Every objective has a different size ring, so for every objective
another condenser setting has to be chosen
✓ Staining not required
x Halos can form which obscures detail
Key features of microscope (light)
Key features:
1) Resolution
2) Magnification
3) Objectives
4) Illumination
What is resolution
⚫ Resolution = ability to distinguish two very small
and closely-spaced objects as separate entities.
When is resolution the best?
⚫ Resolution is best when the distance separating
the two objects is short.
How is resolution determined?
⚫ Resolution is determined by certain physical
parameters that include the wavelength of light,
and the light-gathering power of the objective
and condenser lenses.
The human eye is best adapted to what light?
⚫ The human eye is best adapted for green
light and our ability to see detail may be
compromised with the use of blue or violet.
⚫ Most manufacturers of microscopes correct
their simplest lenses for green light
What are most microscopes known as? and how is an image magnified?
⚫ Most microscopes are known as compound
microscopes:
⚫ a magnified image of an object is produced by
the objective lens.
⚫ this image is magnified by a second lens
system (the ocular or eyepiece) for viewing.
What is the final magnification of the microscope dependant on?
⚫ Final magnification of the microscope is
dependent on the magnifying power of the
objective times the magnifying power of the
ocular.
Objective magnification powers range from what?
⚫ Objective magnification powers range from 4X to
100X
⚫ Ocular magnification ranges are typically 8X-12X
with 10X being most common
⚫ As a result, a standard microscope will provide
you with a final magnification range of ~40X up
to ~1000X
What does the objective lens contain?
⚫ Each objective lens consists of six or more
pieces of glass that combine to produce a clear
image of an object
⚫ These are needed to provide corrections that
produce image clarity
Why is Illumination important for microscopes?
⚫ Essential factor in producing a good image with
the light microscope is obtaining adequate levels
of light in the specimen or object plane
⚫ It is not only necessary to obtain bright light
around the object, but for optimal imaging, the
light should be uniform across the field of view
The best way to illuminate an image?
⚫ The best way to illuminate the specimen
involves the use of yet another lens system,
known as a condenser
What is epifluorescence microscopy
In epifluorescence microscopy, a parallel beam of light is passed directly upwards through the sample, maximizing the amount of illumination using an excitation filter an emission filter and a dichroic mirror
What is Scanning electron microscopy
⚫ Creates various images by focusing a high
energy beam of electrons onto the surface of a
sample
⚫ Detects signals from the interaction of the
incident electrons with the sample surface
What are The type of signals gathered in an SEM
The type of signals gathered in an SEM vary and
can include
⚫ secondary electrons
⚫ characteristic x-rays
⚫ back scattered electrons
What is microbiology the biology of?
Microbiology is a biology of microorganisms
(tiny organisms visible only under a microscope).
Particular objects of microbiology DIAGRAM
CHECK SLIDES
When was the term bacterium introduced?
Almost certainly, the term “bacterium” was introduced in 1828
by Christian Gottfried Ehrenberg, a famous German naturalist.
The Greek βακτηριον means “small stick”.
Why was studying bacteria important
Studying bacteria played an enormous role in the development of
modern biology, medicine and industry.
A conceptual question:
How do microorganisms appear to life?
2 potential answers:
- self-generation (from non-living matter)
- generation from themselves
What was louis pasteur argument?
The argument of Pasteur against spontaneous generation
1) Sterilising the content of the flask
2) At upright position of the flask no microbial growth occurred.
3) If the liquid reached the flask’s neck with trapped microbes, the microbial growth occurred soon
Area-to-volume ratio is much higher in small cells. What is the result of this?
Area-to-volume ratio is much higher in small cells. As a result, the
exchange of substances is quicker.
Advantages for the smaller cell: metabolism, reproduction and cell
communications occur at higher rate that provides greater chances for survival and evolution.
Living cells contain 4 main classes of compounds which differ them from a
non-living organic matter:
What are they?
Living cells contain 4 main classes of compounds which differ them from a non-living organic matter they are:
Proteins - structural components of the cell, enzymes and
regulators; encoded by genes; synthesised in ribosomes;
Nucleic acids - genetic material (DNA and RNA, substances of heredity);
Lipids - components of cellular membranes, cell wall and
storage granules;
Polysaccharides - components of cell walls and capsule.
Effect of metabolic activities on cells?
Metabolic activities make cells
chemically very complex and diverse.
What is the necessary life functions?
1) Metabolism
2) Reproduction (Growth)
3) Differentiation
4) Communication
5) Movement
6) Evolution
What is metabolism of the cell?
1) Uptake of nutrients from the environment, their transformation within the cell, and elimination of wastes into the environment.
The cell is thus an open system
What is the reproduction of the cell?
Chemicals from the environment are turned into new cells under the direction of pre existing cells
Reproduction is based on :
a) Replication of DNA
2) Equal distribution of replicated DNA into 2 cells after division of the initial cell
What is differentiation of the cell?
Formation of a new cell structure such as a spore, usually as part of a cellular life cycle
Differentiation is not a compulsory property of all microbial cells, but
those species that form spores survive better unfavourable conditions.
What is the communication of the cell?
Cells communicate or interact primarily by means of chemical that are released or taken up.
One of the consequences of cell communications is the quorum
sensing mechanism. It allows a population to sense critical amount
of cells and stop divisions.
What is the movement of the cell?
Living organisms are often capable of self propulsion
Motility is not a compulsory property of all microbes
What is the evolution of a cell?
Cells contain gene and evolve to display new biological properties. Phylogenetic trees show the evolutionary relationship between cells.
What are the Coding functions of a cell?
Coding functions: genetic processes based
on information encoded by DNA
E.g. DNA replication, transcription, RNA, Translation
What are the Machine functions of a cell?
Machine functions: biochemical and physiological processes
based on metabolism.
E.g. 1. Energy: ADP + Pi = ATP
2) Metabolism
3) Enzymes
What are the Two aspects of growth
*increasing size of cells (enlargement of cells)
*increasing number of cells (cell division=replication)
What is Binary fission
1) A parent cell prepares for division by enlarging cell wall, plasma membrane and overall volume. DNA replication then starts.
2) Septum begins to grow inwards as chromosomes move to opposite ends of the cell. Other cytoplasmic components are distributed to the 2 developing cells.
3) The septum is synthesized completely through the cell centre, creating two separate cell chambers
4) At this point, the daughter cells are divided some species separate completely whilst others remain attached forming chains doublets or other cellular arrangements.
What is counting viability
Counting viability of cells
using serial dilutions is a
basic technique in
microbiology.
What is the dilution?: e.g.
10ml of broth culture + 1ml of culture
(10+1): 1 = 11 times
20 ml of broth culture +5ml of culture
(20+5): 5 = 5 times
10ml of broth + 10ml of culture
(10+10):10 = 2 times
For diluting many samples what can be used?
For diluting many simultaneous samples,
saline or water could be used.
What is Haloarcula
a square or rectangular shaped archaeon.
What did Henk Bolhuis and Francisco Rodriguez-Valera do?
Henk Bolhuis and Francisco Rodriguez-Valera taking samples from a
freshly harvested crystalliser pond in Alicante, Spain. From this sample,
‘Haloquadratum walsbyi’ was isolated and cultivated
What does evaporation of sea water result in?
Evaporation of sea water results in crystalliser ponds with:
concentration and precipitation of calcium carbonate, calcium sulphate,
sodium chloride and magnesium chloride.
What happens at the last stage of halite formation
At the last stage of halite formation (before the magnesium chloride is
precipitated), the square bacteria dominate (80% of the total microbial
biomass).
What does the growth medium for H.walsbyi contain?
Growth medium for H. walsbyi contains
up to 2 M of MgCl in addition to 3.3 M of NaCl.
Why is Haloquadratum walsby important
Haloquadratum walsbyi (H. walsbyi), a square-shaped archaeon, is important because its unique morphology and ability to thrive in extremely salty environments provide insights into adaptation strategies in extreme environments, cell shape determination, and the potential for life in similar, harsh conditions on other planets.
Elemental and macromolecular composition of a bacterial cell
Protein = 55
Lipid = 9.1
Polysaccharide = 5
Lipopolysaccharide = 3.4
DNA = 3.1
RNA = 20.5
Numbers = percent of dry weight
Chemistry of life
includes two general, mutually complementary processes – synthesis (= anabolism, energy-consuming process) and breakdown (=catabolism, energy-releasing process)
What makes up metabolism?
Anabolism & catabolism = metabolism
The main features of chemical reactions outside of living cells are
The main features of chemical reactions outside of living cells are:
- they occur spontaneously;
- without particular control;
- wherever and whenever possible;
- usually reactions in the nature are very rapid.
The main features of BIO-chemical reactions (in living cells) are:
- they occur in certain order and in certain compartments of the cell or
the organ; - they are under strict control –due to the presence of regulatory
mechanisms; - they don’t occur at any time;
- biochemical reactions are relatively slow – due to the biological
catalysts (mostly enzymes).
What are nutrients
Nutrients are substances required for metabolism and reproduction of cells
Macronutrients are required in large amounts.
Micronutrients are required in small amounts.
The process of uptake and initial processing of nutrients is called nutrition
How are prokaryotes involved in nutrition?
In contrast to higher organisms, prokaryotes don’t have specialised structures for nutrition.
The whole prokaryotic cell is involved into nutrition all the time during active reproduction.
What happens when nutrition is limited?
When nutrition is limited due to the lack of nutrients, the bacterial growth is
inhibited, and many bacterial species could undergo sporulation, the
temporary state of “conservation”.
Anabolism definition
Anabolism:
the sum of biochemical processes towards the synthesis of cell
constituents from simpler molecules. It requires energy.
Catabolism definition
the sum of biochemical processes leading to breakdown of
complex compounds to simple substances.
It releases energy.
What do Phototrophic organisms do?
Phototrophic organisms
convert solar energy to
chemical energy and
production of ATP.
What is a chemotroph
Chemotrophs oxidise a broad range
of organic and inorganic compounds to
produce ATP.
What does autotroph mean?
Autotrophs – can use inorganic CO2
as a single source of carbon (e.g.
prototrophs and many chemolitotrophs).
What does heterotrophs do?
Heterotrophs – require one or more organic compounds as a source of
carbon (e.g. chemoorganotrophs).
What are the Two major forms of autotrophy:
oxygenic photosynthesis – oxygen (O2) is evolved (in cyanobacteria);
anoxygenic photosynthesis – oxygen is not produced
(purple and green bacteria).
Why are differences in metabolism important?
Differences in metabolism form a basis for structural differences that are integrated in
morphological diversity of organisms.
What makes a basis for metabolic diversity?
Differences in processes of obtaining energy make a basis for metabolic diversity of all
microorganisms, not only bacteria or archaea.
What does catabolism include?
includes fermentation and respiration - two ways of conservation
of energy from organic sources of carbon.
Both processes consist of series of catabolic reactions (breakdown
reactions).
What is fermentation?
Fermentation is an anaerobic catabolism in which an organic
substance serves as a donor and acceptor of electrons and ATP is
produced by substrate-level phosphorylation (from energy-rich
intermediates in the process of fermentable substrate breakdown).
What is respiration?
Respiration is catabolism where organic substance is oxidized by
oxygen (or substitute) as electron acceptor, and ATP is produced by
oxidative phosphorylation.
When do fermentation and respiration occur
Both fermentation and respiration occur after glycolysis.
What is Glycolysis (Embden-Meyerhof-Parnas pathway)
catabolism of glucose to pyruvate. The pyruvate is broken to fermentation products (ethanol + CO2 or lactate).
What is lactic acid fermentation?
Lactic acid fermentation is anaerobic respiration in
Lactobacillus and other bacteria (the same in muscle cells during working hard and fast).
Where does ethanol fermentation occur
Ethanol fermentation occurs in yeasts
What is the citric acid cycle
Citric acid cycle (CAC, also known as Krebs cycle): a way of generation
of ATP (=energy) via respiration after glycolysis.
CAC has bioenergetic and biosynthetic roles.
CAC pruduces important compounds for anabolism (biosynthesis):
a-ketoglutarate and oxalacetate (precursors of a few aminoacids);
succinyl-CoA (precursor for cytochromes, chlorophyll and others).
Nutritional requirements
of microorganisms
Carbon (C) is a major macronutrient for all living cells (~50% of a dry weight). It is a component for all macromolecules. e.g. methane
Nitrogen (N)
is the second most abundant element of the cell (~12% of dry weight).
It is included into proteins, nucleic acids and other cell components.
Nitrogen is available from the nature in organic and, mostly, inorganic
(ammonia NH3 , nitrate NO3- or N2) forms. Most bacteria use ammonia, some use nitrates, and rare bacteria (nitrogen fixing) could use N2 as a single nitrogen source.
What do Free-living aerobic
nitrogen-fixing bacteria do?
These organisms inhabit soil and are
capable of fixing N2
aerobically,
non-symbiotically.
The other essential macronutrients
The other essential macronutrients are:
Phosphorus (P) - needed for nucleic acids and phospholipids);
Sulphur (S) - for amino acids cysteine and methionine; vitamins thiamine, biotin and lipoic acid; also for coenzyme A);
Potassium (K) - required for many enzymes, e.g. for protein synthesis);
Magnesium (Mg) - for stability of ribosomes, membranes and nucleic acids; for activity of many enzymes).
Calcium (Ca) (not essential for many microorganisms) - stabilises cell walls and helps in thermo-resistance of endospores.
Sodium (Na) is required by some microorganisms (e.g. murine microbes) but not all (fresh water microbes can grow without it).
What does Iron do?
plays a role in respiration (it is a component of cytochromes and iron-sulphur
proteins involved in electron transport). It is needed in less amounts than
other macronutrients
How do cells obtain iron?
Cells obtain iron from different insoluble minerals by specialised components
– siderophores.
What are siderophores
Siderophores are different organic compounds (like phenol-derivatives,
peptide-like- or lipid containing compounds) that bind iron and transport it
into cells.
Example of enterobactins
Enterobactins are siderophores of
E. coli and Salmonella
typhimurium.
What are micro nutrients + example?
Micronutrients are needed in trace amounts, as enzyme
components
Boron (B), Chromium (Cr), Cobalt
(Co), Copper (Cu), Iron (Fe),
Manganese (Mn), Molybdenum
(Mo), Nickel (Ni), Selenium (Se),
Tangsten (W), Vanadium (V), Zink (Zn)
Not all of them are needed for all
cells.
What are growth factors?
are organic compounds (vitamins, amino acids, purines
and pyrimidines) needed by some cells in small amounts.
Vitamins are most required growth
factors.
What is culture media
are nutritional mixtures for cultivation of microorganisms in laboratory and
industry.
They can be chemically defined (defined medium) or undefined (complex
medium).
Selective, differential, and enriched media are used for?
Selective, differential, and enriched media are used for the isolation of particular species or for comparative studies of microorganisms.
What is solid media used for?
Solid media (with a gelling agent, usually agar) are useful for isolation and
maintenance of pure microbial cultures. They immobilise cells, allowing
them to grow and form visible, isolated aggregates of cells (colonies)
What is liquid media used for?
Liquid media are used for a rapid and large scale cultivation of pure
microbial cultures.
What do Rhizobial cells do?
Rhizobial cells enter into the root hair via the root hair tip and cause nodule formation.
The rhizobia multiply rapidly first in the plant cells and are transformed then into
swollen, branched bacteroids (less motile but able to fix nitrogen).
Symbiotic nitrogen fixation enhances production of many important crops.
What is bacteria plant symbioses
Bacteria-plant symbioses are close, long-term interactions between bacteria and plants, where both organisms benefit, like nitrogen-fixing bacteria in legumes, or where one benefits at the expense of the other, as in some parasitic interactions
What does leghemoglobin control?
The O2 -binding protein leghemoglobin controls levels of the process in the
nodule.
