Download Basics of microbiology

Basics of microbiology
Petra Rettberg, DLR, Germany
This presentation is based on presentations from the
ESA PP course prepared by Petra Rettberg and
Christine Moissl-Eichinger.
PPOSS - microbiology
Eukaryotic cell (all plants and animals)
Study of “Micro-organisms”:
very small organisms
• Microscope
• Single cell organisms (single and clusters,
filaments)
• Yeast, (some) Algae, (some) Fungi, Protozoa,
Viruses
• Mainly: Prokaryotes (Bacteria and Archaea)
• Very diverse and omnipresent
Prokaryotic cell (microorganisms)
The importance of microorganisms
Negative properties - examples
• Human pathogens (infectious diseases, e.g. )
• Animal pathogens
• Plant pathogens
• Food poisoning (production of toxic substances)
• Deterioration of materials (biocorrosion)
• Self-ignition of hay
• ……
The importance of microorganisms
Positive properties - examples
• Destruents in natural nutrient cycles (decay, humus formation)
• Biological wastewater treatment
• Biogas production
• Nitrogen fixation (plant fertilizer)
• Symbiotic Bacteria (gut bacteria, suppression of pathogens, cellulose
degradation)
The importance of microorganisms
Positive properties - examples
• Food production (diary products, alcoholic beverages, soy sauce….)
• Production of antibiotics, vitamins, steroids
• Production of biocatalysts (enzymes)
• Production of organic acids, solvents, hydrogen, ethanol …
• Mining (leaching of iron, copper, uranium…)
•…
Microorganisms are the oldest form of life
on Earth
?
Microorganisms are the oldest form of life
on Earth
http://flickr.com/photo/77516097@N00/514063316
Early Earth
Present Earth
Microorganisms changed the
environmental conditions on Earth
Molecular clock: 16S ribosomal RNA
• Information molecule:
Ribonucleic acid
• Universal
• Same function in all
organisms
• Changes occur constantly
and randomly in time:
history of life can be
traced back… universal
ancestor
Tree of life
Three domains of life
• Eukarya
• Bacteria
• Archaea
(discovered 1970s)
Size, shape and structure of microorganisms
http://www.microbiologyinfo.com/different-size-shape-and-arrangement-of-bacterial-cells/
Size, shape and structure of microorganisms
Bacteria and archaea
Single-celled without nucleus
Size 1 – 5 µm
Different types of cell walls
Some of them motil
https://www.quora.com/What-arethe-various-shapes-of-bacteria
Size, shape and structure of microorganisms
Bacterial spores
• Dormant resistant form
of some bacteria
• Trigger for formation:
Starvation, changes in
the environments
• Can germinate and
replicate again under
suitable conditions
under
Wikipedia
Size, shape and structure of microorganisms
Where
Who
Details
Sky
B. stratosphericus
above 24 km
Soil
B. thermoterrestis
egypt. soil, 55°C
Hay
B. subtilis
the „hay“-Bacillus
Desert
B. sonorensis
Sonoran Desert,
Arizona
Rocks
B. simplex
Deep surface
B. infernus
SAF
B. pumilus SAFR
Food
B. cereus
Pathogens
B. anthracis
Insects
(pathogen)
B. thuringiensis
(500 spores/g rock)
Bacterial spores
• very resistant against
many physical and
chemical stress
factors
• ubiquitous
Size, shape and structure of microorganisms
Viruses 0.02 - 0.3 µm
Host dependent
“Alive”?
Bacteriophages
attached to a
bacterial cell wall,
Graham Beards,
Wikipedia
Sulfolobus spindle-shaped virus 1 from
Prangishvili et al. Nature Reviews Microbiology 4,
837–848 (November 2006) |
doi:10.1038/nrmicro1527
Size, shape and structure of microorganisms
Fungal cells and spores 5 - 20 µm
Compartimentation
Hyphae
Spores formed in special
containments
Sprouting of yeast cells
By Dr. Sahay - Own work, CC BY-SA 3.0,
https://commons.wikimedia.org/w/index.php?curid=28
383655
Microbial distribution and abundance
Where?
How many?
Garden soil, 1g
2.5 x 1010 (25,000,000,000 billion)
Milk (raw), 1l
2.5 x 109
Air, 1 m3
2000
Drinking water, 1 ml
<100 (non pathogenic)
Sea- and freshwater
1.2 x 1029
Total (on Earth)
1030 (~1014 kg = 100 billion tons =
1430 billion humans (each 70 kg;
currently 7 billion living humans on
Earth))
Human skin
1012
Human body
- Own cells
- Microbes
1013
1014-15
Microorganisms
are everywhere.
Microbial distribution and abundance
• Up to 10 000
microorganisms on
1 cm² of skin
• Up to 100
microorganisms on
1 mm² of skin
• 1 mm = 1000 µm
Microbial distribution and abundance
• Microorganisms live almost everywhere on Earth,
in “normal” and “extreme” biotopes
• What is “extreme”? Human perpective!
• An extremophile is an organisms that thrives in physically or
geochemically extreme conditions that are detrimental to
most life on Earth.
Extremophiles
Microorganisms can live
• At high temperatures (hydrothermal vents, hot springs….)
• At cold temperatures (permafrost, sea ice, glaciers …)
• At high pH values (acidic lakes, solfataras, acid mine drainage …)
• At low pH values (alkaline lakes….)
• At hig salt concentrations (evaporation ponds, dead sea …)
• On rocks and in the upper millimeter of porous rocks
Extremophiles
Microorganisms can live
• In nutrient poor environments (deserts, water, cleanrooms)
• In anoxic (oxygen-free) environments (deep sea brines, deep
sediments…)
• At low pressure (lab experiments)
! Each microorganism has its specific requirements for growth.
! Only appriximately 1 % of all microorganisms can be cultivated.
Growth and survival
Limits
For growth
For survival
Temperature:
-20°C to +113°C
 -263°C to +150°C
Water stress
aw  0.7
0  aw  1.0 Spores survive in vacuum
(10-6 Pa)
Salinity:
Salt concentration  30 %, salt crystals
Salt crystals (endoevaporites)
pH:
pH = 0-12
pH = 0 - 12.5
Nutrients:
High metabolic versatility
Lithoautotrophic growth
High starvation tolerance
not required, better without
Oxygen:
Aerobic/Anaerobic growth
not required, better without
Radiation
resistance
0- high radiation resistance (<60 Gy/h)
0- high radiation resistance (<5 kGy)
Time
20 min up to years
 25 - 40 x 106 a
Different metabolic pathways in bacteria
The detection of microorganisms
Cultivation
Propagation of microorganisms in a suitable growth environment called a medium
which
• can be solid or liquid
• may be purely chemical (a chemically defined medium) or
• may contain organic materials (like yeast extract) or
• may consist of living organisms such as fertilized eggs.
Microorganisms growing in or on such a medium form a culture.
Cultivation
A culture is considered a pure culture, if only one type of organism is
present and a mixed culture if populations of different organisms are
present.
colonies from a pure culture
on an agar plate
colonies from a mixed culture
on an agar plate
The detection of microorganisms
Molecular methods
Next generation sequencing (NGS)
• DNA extraction from a sample
• Amplification of the 16S rRNA gene
• Sequencing
• Bioinformatic analysis
Molecular methods
No longer available
Most common
NGS with Illumina
• Amplicons (with adapters) are
applied to flowcell
• Amplification with polymerase: local
clonal DNA colonies (“clusters”)
• Four types of terminator bases
(labelled) are added
• Camera takes a picture
• Dye is removed
• Next terminator bases are added…
• “sequencing by synthesis”
Examples for NGS used for Planetary
Protection
The cleanroom microbiome
• Most contaminants in spacecraft assembly cleanrooms are
human-associated.
• Clean room isolates can be more resistant than comparable
laboratory strains.
• Spore-formers are present as spores.
• A broad diversity of microbes is present, with different
adaptations.
• The contamination is not homogenously distributed.
Microbes are everywhere!
A short summary
• Microorganisms are very small and are not visible by the naked eye.
• Some microorganisms can form spores.
• Bacterial spores are resistant to many physical and chemical stressors.
• They can exist (almost) everywhere.
• They can survive extremely harsh conditions.
• Each microbe has specific requirements... only about 1% of all microbes is
cultivable.
• Different methods to study the uncultivated microbial diversity.