Basics of microbiology

Transcription

1 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.

2 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)

3 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

4 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)

5 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 )

6 Microorganisms are the oldest form of life on Earth?

7 Microorganisms are the oldest form of life on Earth Early Earth Present Earth

8 Microorganisms changed the environmental conditions on Earth

9 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

10 Tree of life Three domains of life Eukarya Bacteria Archaea (discovered 1970s)

11 Size, shape and structure of microorganisms

12 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

13 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

14 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 (500 spores/g rock) Deep surface SAF Food Pathogens Insects (pathogen) B. infernus B. pumilus SAFR B. cereus B. anthracis B. thuringiensis Bacterial spores very resistant against many physical and chemical stress factors ubiquitous

15 Size, shape and structure of microorganisms Viruses 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, (November 2006) doi: /nrmicro1527

16 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,

17 Microbial distribution and abundance Where? How many? Garden soil, 1g 2.5 x (25,000,000,000 billion) Milk (raw), 1l 2.5 x 10 9 Air, 1 m Drinking water, 1 ml <100 (non pathogenic) Sea- and freshwater 1.2 x Microorganisms are everywhere. Total (on Earth) (~10 14 kg = 100 billion tons = 1430 billion humans (each 70 kg; currently 7 billion living humans on Earth)) Human skin Human body - Own cells - Microbes

18 Microbial distribution and abundance Up to microorganisms on 1 cm² of skin Up to 100 microorganisms on 1 mm² of skin 1 mm = 1000 µm

19 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.

20 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

21 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.

22 Limits For growth For survival Temperature: -20 C to +113 C -263 C to +150 C Water stress a w a w 1.0 Spores survive in vacuum (10-6 Pa) Salinity: Salt concentration 30 %, salt crystals Salt crystals (endoevaporites) ph: ph = 0-12 ph = Nutrients: High metabolic versatility Lithoautotrophic growth High starvation tolerance not required, better without Oxygen: Aerobic/Anaerobic growth not required, better without Radiation resistance Growth and survival 0- high radiation resistance (<60 Gy/h) 0- high radiation resistance (<5 kgy) Time 20 min up to years x 10 6 a

23 Different metabolic pathways in bacteria

24 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.

25 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

26 The detection of microorganisms Molecular methods Next generation sequencing (NGS) DNA extraction from a sample Amplification of the 16S rrna gene Sequencing Bioinformatic analysis

27 Molecular methods No longer available Most common

28 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

29 Examples for NGS used for Planetary Protection

30 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!

31 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.