Samenvatting Microbiology
Inhoudsopgave
HC1: introductie ......................................................................................................................................................................... 4
Relevance of microbes .................................................................................................................................................................... 4
Cells ................................................................................................................................................................................................ 4
Ecology ........................................................................................................................................................................................... 4
Evolution......................................................................................................................................................................................... 5
Impact on humans.......................................................................................................................................................................... 5
History of microbiology .................................................................................................................................................................. 5
HC2: Microbial cell structure ...................................................................................................................................................... 6
Cell morphology and size................................................................................................................................................................ 6
The cytoplasmic membrane ........................................................................................................................................................... 6
Prokaryotic cell wall ....................................................................................................................................................................... 7
The outer membrane ...................................................................................................................................................................... 8
Cell walls of Archaea ...................................................................................................................................................................... 9
Cell surface structures and inclusions ............................................................................................................................................. 9
Microbial locomotion (=bewegen) ............................................................................................................................................ 11
Flagella and swimming ................................................................................................................................................................ 11
Gliding .......................................................................................................................................................................................... 12
Taxis .............................................................................................................................................................................................. 13
HC3 + 4 + 5: Microbial growth................................................................................................................................................... 14
Bacterial Cell Division ................................................................................................................................................................... 14
Cell Growth and Binary Fission ................................................................................................................................................ 14
Fts Proteins and Cell Division .................................................................................................................................................. 14
MreB and Determinants of Cell Morphology .......................................................................................................................... 14
Population Growth ....................................................................................................................................................................... 15
The Concept of Exponential Growth ....................................................................................................................................... 15
The Mathematics of Exponential Growth ................................................................................................................................ 15
The Microbial Growth Cycle .................................................................................................................................................... 15
Continuous Culture: The Chemostat ....................................................................................................................................... 15
Measuring Microbial Growth ....................................................................................................................................................... 16
Microscopic Counts ................................................................................................................................................................. 16
Viable Counts........................................................................................................................................................................... 16
Turbidimetric Methods ............................................................................................................................................................ 16
Temperature and Microbial Growth ............................................................................................................................................. 17
Effect of Temperature on Growth ............................................................................................................................................ 17
Microbial Life in the Cold ......................................................................................................................................................... 17
Microbial Life at High Temperatures ....................................................................................................................................... 17
Other Environmental Factors Affecting Growth ........................................................................................................................... 18
Acidity and Alkalinity ............................................................................................................................................................... 18
Osmotic Effects on Microbial Growth ...................................................................................................................................... 18
Oxygen and Microorganisms ................................................................................................................................................... 18
Toxic Forms of Oxygen ............................................................................................................................................................. 18
Nutrition and culture of microorganisms ..................................................................................................................................... 19
, Nutrition and Cell Chemistry ................................................................................................................................................... 19
Culture Media .......................................................................................................................................................................... 20
Laboratory Culture .................................................................................................................................................................. 20
HC6+7: Metabolism of microorganisms .................................................................................................................................... 21
Energetics and catalysis ............................................................................................................................................................... 21
Oxidoreduction ............................................................................................................................................................................. 21
Energy storage ............................................................................................................................................................................. 21
Metabolic diversity of microorganisms ........................................................................................................................................ 22
Aerobic respiration .................................................................................................................................................................. 22
Anaerobic respiration .............................................................................................................................................................. 22
Fermentation ........................................................................................................................................................................... 23
Chemolithotrophy ................................................................................................................................................................... 25
Phototrophy ............................................................................................................................................................................ 26
HC8: Diversity of bacteria ......................................................................................................................................................... 28
Proteobacteria.............................................................................................................................................................................. 28
Proteobacteria (α) ................................................................................................................................................................... 28
Proteobacteria (β) ................................................................................................................................................................... 28
Proteobacteria (γ) .................................................................................................................................................................... 29
Proteobacteria (δ) ................................................................................................................................................................... 29
Proteobacteria (ε) .................................................................................................................................................................... 29
Firmicutes ..................................................................................................................................................................................... 30
Actinobacteria ......................................................................................................................................................................... 31
Bacteroidetes ............................................................................................................................................................................... 31
Tenericutes ................................................................................................................................................................................... 32
Chlamydiae ................................................................................................................................................................................... 32
Planctomycetes ............................................................................................................................................................................ 32
Verrucomicrobia ........................................................................................................................................................................... 32
Thermotogae ................................................................................................................................................................................ 32
Aquificae....................................................................................................................................................................................... 33
Deinococci .................................................................................................................................................................................... 33
Spirochaetes ................................................................................................................................................................................. 33
Anderen ........................................................................................................................................................................................ 33
HC9: Major Microbial Habitats and Diversity ............................................................................................................................ 34
Microbial Ecology ......................................................................................................................................................................... 34
General Ecological Concepts.................................................................................................................................................... 34
Ecosystem Service: Biogeochemistry and Nutrient Cycles ...................................................................................................... 34
The Microbial Environment .......................................................................................................................................................... 34
Environments and Microenvironments ................................................................................................................................... 34
Surfaces and Biofilms .............................................................................................................................................................. 35
Microbial Mats ........................................................................................................................................................................ 36
Terrestrial Environments............................................................................................................................................................... 36
Soils ......................................................................................................................................................................................... 36
The Subsurface ........................................................................................................................................................................ 36
Aquatic Environments .................................................................................................................................................................. 36
Freshwaters ............................................................................................................................................................................. 36
Coastal and Ocean Waters: Phototrophic Microorganisms ..................................................................................................... 37
Pelagic Bacteria, Archaea, and Viruses ................................................................................................................................... 37
Terrestrial VS aquatic ............................................................................................................................................................... 37
The Deep Sea and Deep-Sea Sediments .................................................................................................................................. 37
Hydrothermal Vents ................................................................................................................................................................ 38
,HC10: Nutrient Cycles, Biodegradation, and Bioremediation .................................................................................................... 39
Nutrient Cycles ............................................................................................................................................................................. 39
The Carbon Cycle ..................................................................................................................................................................... 39
Syntrophy and Methanogenesis .............................................................................................................................................. 39
The Nitrogen Cycle .................................................................................................................................................................. 39
The Sulfur Cycle ....................................................................................................................................................................... 39
The Iron Cycle .......................................................................................................................................................................... 39
Microbial Symbioses ................................................................................................................................................................. 39
Plants as Microbial Habitats ........................................................................................................................................................ 39
The Legume–Root Nodule Symbiosis ...................................................................................................................................... 39
Agrobacterium and Crown Gall Disease .................................................................................................................................. 40
Mammals as Microbial Habitats .................................................................................................................................................. 41
The Rumen and Ruminant Animals ......................................................................................................................................... 41
Insects as Microbial Habitats ....................................................................................................................................................... 42
Heritable Symbionts of Insects ................................................................................................................................................ 42
Termites ................................................................................................................................................................................... 43
Aquatic Invertebrates as Microbial Habitats ................................................................................................................................ 43
Hawaiian Bobtail Squid ............................................................................................................................................................ 43
Marine Invertebrates at Hydrothermal Vents and Gas Seeps ................................................................................................. 44
HC11: Viruses ........................................................................................................................................................................... 45
Virus types .................................................................................................................................................................................... 45
Structure of viruses ....................................................................................................................................................................... 45
Ecology ......................................................................................................................................................................................... 46
Human virome .............................................................................................................................................................................. 48
Viroids and prions......................................................................................................................................................................... 49
HC12 + 13: Microbial diseases .................................................................................................................................................. 51
Principles of epidemiology ........................................................................................................................................................... 51
Person-to-person diseases (25) .................................................................................................................................................... 51
Vectorborne diseases.................................................................................................................................................................... 52
Soilborne diseases ........................................................................................................................................................................ 52
Waterborne diseases .................................................................................................................................................................... 52
Foodborne diseases ...................................................................................................................................................................... 52
HC14: Microbes in industry ...................................................................................................................................................... 53
Bioleaching ................................................................................................................................................................................... 53
Bioremediation ............................................................................................................................................................................. 53
Wastewater treatment ................................................................................................................................................................. 54
Other ............................................................................................................................................................................................ 56
,HC1: introductie
Relevance of microbes
Microbe = onzichtbaar voor het blote oog ➔ Bacteriën, virussen, gisten, protisten & fungi
• Groeit snel & is makkelijk te manipuleren ➔ goede modellen
o Medicijnen, voedsel, industrie, biochemie…
• Kunnen leven in meest extreme condities
Cells
• Kolonies hebben verschillende densiteiten met miljoenen prokaryote cellen
• Veel microben morfologisch gelijk, maar metabolisch zeer verschillend
Opbouw prokaryoot VS eukaryoot:
• Prokaryoot: bacteriën & archea
• Eukaryoot: fungi, gist, protisten & algen
• Genoom bepaald de mogelijkheid tot adaptatie
o Circulair chromosoom/plasmiden/…
o Virussen < prokaryoten < eukaryoten
o Hangt ook af van levensstijl ➔ als ze een host nodig hebben
is het genoom kleiner
o Door genetische uitwisseling evolueren microben snel
(resistentie opbouwen)
o Adaptatie naar
▪ Bewegen (flagellen)
▪ Differentiatie (sporen)
▪ Communicatie
Ecology
Ecosysteem = alle levende organismes + chemische & fysische aspecten
• Voorbeeld: gletsjer
Invloed van de omgeving op microben:
• pH
• Nutriënten
• Temperatuur
• Vochtigheid
• O2
• Druk
Invloed van microben op omgeving:
• Bacterial blooms (bv: cyanobacteriën) (ze groeien zo snel dat ze zichtbaar worden en water
vertroebelen)
• Decompositie ➔ anders zaten we nu op meters hoog, dood materiaal
,Evolution
• Microben fossiliseren niet ➔ moeilijk te onderzoeken
• Aangepast aan alle mogelijke habitats, want tijd genoeg om te
adapteren
• Zitten vooral in aard-/oceaanbodems en oppervlaktes
Impact on humans
Kan voordelen/nadelen hebben (meer voordelige micro-organismen dan
nadelige)
• Menselijke ziektes veel door microben ➔ oplossing = antibiotica & vaccinatie
• Agricultuur
o +: stikstoffixerende bacteriën, cellulose afbraak in maag, regeneratie van nutriënten in
bodem & water
o -: ziektes in dieren & planten
• Voedsel
o +: fermentatie (yoghurt, kaas, bier, brood, …)
o -: vervallen ➔ schimmelen…
• Industrie
o Energie, antibiotica, ontmijnen, wastewater treatment, …
• Genetic engeneering
o Antibiotica, enzymen, chemicaliën, insuline, …
History of microbiology
• Ontstaan toen de microscoop werd uitgevonden (17e eeuw) & met die evolutie meegegaan
• Vruchtstructuren van schimmels en endosporen van bacteriën werden ontdekt
• Louis Pasteur heeft de theorie van spontane generatie weerlegd, microben verschijnen niet out of
the blue, en zijn dus te kweken en te controleren
• Pasteur’s swan-necked flask experiment:
• Koch’s Postulates (link tussen oorzaak en effect van de besmetting):
, HC2: Microbial cell structure
Cell morphology and size
Algemene vormen:
• Coccus (rond/ovaal)
• Rod (cylinder)
• Spirillum
Ongewone vormen:
• Spirochetes
• Appendaged (lijken op fungi hyfen, maar veel kleiner)
• Filamentous (heel lang)
Vorm is niet zo informatief ➔ wel voor voedingsopname en zwemmogelijkheden
Grootte:
• Prokaryoten: 0.5 – 4 µm
• Eukaryoten: 10 ➔ 200 µm
• Upper limit ➔ anders kan het metabolisme niet onderhouden worden
• Lower limit ➔ alle componenten moeten erin kunnen ➔ pathogenen kunnen wel kleiner
zijn aangezien die dingen kunnen krijgen van hun host
• Voordeel aan klein zijn: meer celoppervlakte tov volume ➔ hogere voedingsopname per
unit celvolume ➔ sneller groeien
The cytoplasmic membrane
Omschrijving:
• Cytoplasma scheiden van omgeving
• Doorlaatbaar maar selectief
o Concentratie van specifieke metabolieten bepalen
o Excretie van afvalproducten
• Opbouw:
o Fosfolipiden dubbellaag:
▪ Hydrofoob(vetzuren) + hydrofiel
o Eiwitten in membraan:
▪ Functie: substraat transport/energieopbrengst
o Membraanversterkers:
▪ Kationen binden aan – ladingen van fosfolipiden
▪ Planaire structuur zorgt voor stabiliteit
• Verschillen:
o Archea bevatten ether linken met fosfolipiden, isoprene staarten en bi-
/monolaag
o Esterbindingen zijn bacteriën of eukaryoten, net zoals vetzuurstaarten
en een bilaag
• Functie doorlaatbaarheid:
o Hoe kleiner, minder geladen en meer hydrofoob, hoe makkelijker het
erdoor kan gaan
o Transporters nodig:
▪ Tegen concentratigradient werken ➔ energie nodig
▪ Aquaporinen ➔ waterdiffusie
▪ Bidirectioneel transport
▪ …
o Verschillende types transport:
▪ Simpel transport: proton motive force (proton zoals
lactose bindt en activeert een conformatieverandering
