School of Applied Biosciences and Chemistry

Microbiology

BM6/LS6, Kenneth van Driel

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Microbiology in your study career
First year

Course 1 + 2: basic laboratory skills

Course 3: molecular biology and biochemical research of DNA and protein
Course 4: medical diagnostics (microbiology and human biology)

Second year

Course 5: molecular and biochemical research

Course 6: interaction between plant, human and microorganisms

Third and fourth year

Majors: Minor: Internship Graduation

BMLS8: biotechnology Medische microbiologie (NL) project
BMLS9: molecular plant biology Cyto-histopathology (NL)
BMLS10: biomedical research Bio-nanotechnology
Biobased
Drug discovery
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Other
 BM6/LS6
microbiome

(chronic) diseases
genetic diseases
infectious diseases
antibiotics-R bioactive plant
compounds
immune system antibiotics

microbiome

bioactive plant compounds

antibiotics

antibiotics-R
infection
bioactive plant compounds

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Microbiology subjects
Lecture 1-3 Microbial diversity:
• Microbial diversity
• Morphology and structure of microorganisms

Lecture 4-5 Microbial symbiosis:

• The interaction between microorganisms and other organisms

Lecture 6 Infectious diseases and antimicrobial drugs:

• Contamination, infection and spread (pathogenesis)
• Infectious diseases
• Antimicrobial agents to combat infections

Lecture 7 Antimicrobial drugs and antibiotics resistance:

• Resistance to antimicrobial agents
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Assessment: Theme test Tmp
The student can integrate and apply the acquired theoretical knowledge
and practical skills related to plant biology and microbiology in a
theoretical case study/assignment, through experimental design, lab work
and results analysis.

Knowledge 20-30%
Design: 20-30%
Experimenting: 20-30%
Results analysis, data analysis and (Lab)calculations: 20-30%

Theme test Tmp at end of term 3

Resit at the end term 4

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School of Applied Biosciences and Chemistry

Microbial
Diversity part 1

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Microbiology is everywhere!

7 http://www.microbeworld.org/index.php?option=com_jlibrary&view=article&task=download&id=13867,
geraadpleegd 03-02-2016
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9
Before we continue…
Kahoot!

Join at www.kahoot.it or with the Kahoot! App with Game PIN:

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Microbial diversity topics
Bacteria

Archaea

Eukarya
• yeasts and molds (Fungi)
• algae
• protists

Viruses

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Microbial diversity topics for today (part 1)
Bacteria

Archaea

Eukarya (Chapter 18)

• yeasts and molds (Fungi)
• algae
• protists

Viruses (Chapter 8)

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 Bacteria

16 ribosomal protein
sequences from each
organism

Phylogenetic tree of life

Eukarya
Archaea
Hug et al. (2016) A new view of the tree of life.
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Nature Microbiology 1, Article number: 16048
doi:10.1038/nmicrobiol.2016.48
 Bacteria

16 ribosomal protein
sequences from each
viruses??? organism

Phylogenetic tree of life

Eukarya
Archaea
Hug et al. (2016) A new view of the tree of life.
16
Nature Microbiology 1, Article number: 16048
doi:10.1038/nmicrobiol.2016.48
 Bacteria

16 ribosomal protein
sequences from each

X
viruses??? organism

Phylogenetic tree of life

Eukarya
Archaea
Hug et al. (2016) A new view of the tree of life.
17
Nature Microbiology 1, Article number: 16048
doi:10.1038/nmicrobiol.2016.48
Protists

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Protists
Unicellular Eukaryotes (other than yeast and algae)

Very diverse group

Many parasites
• Trichomonas vaginalis – STD
• Trypanosoma brucei – sleeping sickness
• Plasmodium – malaria
• Toxoplasma – toxoplasmosis
• (Minor medical microbiology)

https://imagebank.hematology.org/image/3619/plasmodium-falciparum-
infection--2?type=upload, geraadpleegd 04-09-2018

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Protists
Diatoms
• phototrophic
• phytoplankton
• in marine and fresh waters
• cell wall of silica

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Protists
Diatoms
• phototrophic
• phytoplankton
• in marine and fresh waters
• cell wall of silica

Oomycetes (water molds)

• Phytophtora infestans
• plant pathogens
• potato disease (Irish famine 1845)
• Important for agriculture

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Protists
Amoebozoa
• pseudopodia
• amoeboid movement: https://youtu.be/7pR7TNzJ_pA

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Protists
Amoebozoa
• pseudopodia
• amoeboid movement: https://youtu.be/7pR7TNzJ_pA

Slime molds
• Dictyostelium discoideum: https://youtu.be/vjRPla0BONA
• aggregation, migration, fruiting body formation
• Fig. 17.17 in Madigan et al. (2015) Brock biology of microorganisms

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Fungi

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Fungi (yeasts and molds)
Yeasts are unicellular, grow by cell division

Molds are multicellular, grow filamentous

Eukaryotic micro-organisms with cell wall

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Yeast
Unicellular

Cell division (asexual cycle, mitosis)

Spores (sexual cycle, meiosis)

Examples:
Saccharomyces cerevisiae
Candida albicans (pathogen)

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Filamentous fungi
Mycelium: network of fungal filaments=hyphae

https://www.anbg.gov.au/fungi/images-misc/mycelium/myceliumg.gif, geraadpleegd 11-09-2016

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Filamentous fungi
Mycelium: network of hyphae
Aerial hyphae
Production of spores (asexual)

Brock, Fig 17.19

30 https://www.anbg.gov.au/fungi/images-misc/mycelium/myceliumg.gif, geraadpleegd 11-09-2016
Filamentous fungi
Septation

cell wall staining calcofluor white

31 https://www.anbg.gov.au/fungi/images-misc/mycelium/myceliumg.gif, geraadpleegd 11-09-2016

Filamentous fungi
Septation

septum

cell wall staining calcofluor white

32 https://www.anbg.gov.au/fungi/images-misc/mycelium/myceliumg.gif, geraadpleegd 11-09-2016

 Filamentous fungi
Septal pore complex morphology in the Agaricomycotina
(Basidiomycota) with emphasis on the Cantharellales and
Hymenochaetales.
van Driel KG, Humbel BM, Verkleij AJ, Stalpers J, Müller
WH, Boekhout T.
Mycol Res. 2009 May;113(5):559-76. doi:
10.1016/j.mycres.2008.12.007. Epub 2009 Jan 27.

Laser microdissection of fungal septa as visualised by

scanning electron microscopy.
van Driel KG, Boekhout T, Wösten HA, Verkleij AJ, Müller
WH.
Fungal Genet Biol. 2007 Jun;44(6):466-73. doi:
10.1016/j.fgb.2006.10.006. Epub 2006 Dec 8.

Septal pore cap protein SPC18, isolated from the

basidiomycetous fungus Rhizoctonia solani, also resides in
pore plugs.
van Driel KG, van Peer AF, Grijpstra J, Wösten HA, Verkleij
AJ, Müller WH, Boekhout T.
Eukaryot Cell. 2008 Oct;7(10):1865-73. doi:
10.1128/EC.00125-08. Epub 2008 Aug 29.
septum
The septal pore cap is an organelle that functions in
vegetative growth and mushroom formation of the wood-
rot fungus Schizophyllum commune.
van Peer AF, Wang F, van Driel KG, de Jong JF, van
Donselaar EG, Müller WH, Boekhout T, Lugones LG, cell wall staining calcofluor white
Wösten HA.
Environ Microbiol. 2010 Apr;12(4):833-44. doi:
10.1111/j.1462-2920.2009.02122.x. Epub 2009 Dec 27.
33 https://www.anbg.gov.au/fungi/images-misc/mycelium/myceliumg.gif, geraadpleegd 11-09-2016
Hyphae
Apical growth = fungal tip growth

Spitzenkörper

Formation of septa

Continuous cytosol (coenocytic)

http://faculty.scf.edu/keirlem/BSC_1007_eText_UNIT_3/TEXT_Cellular_Structures/F
34 ungal%20Hypha%20-%20Copy.png, geraadpleegd 11-09-2016
Fungal cell wall

Hardison, S.E. & Brown, G.D. (2012) C-type lectin receptors orchestrate antifungal immunity.
Nature Immunology 13, 817–822 doi:10.1038/ni.2369

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Fungal cell wall

Immunology: PAMPs recognized by PRRs (innate immune system)

36 Hardison, S.E. & Brown, G.D. (2012) C-type lectin receptors orchestrate antifungal immunity.
Nature Immunology 13, 817–822 doi:10.1038/ni.2369
Fungal cell wall
80-90% polysaccharide

chitin: polymer of N-acetylglucosamine (NAG)

beta-glucans, mannan, galactosan, cellulose

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Groups within the Fungi

Phylogeny based on 18S rRNA

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Ascomycetes
Saccharomyces food production, industrial use
Aspergillus food production, industrial use
Penicillium food production, penicillin

Scanning Electron Microscopy images

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Ascomycetes
Ascospores (sexual spores) in ascus

https://atrium.lib.uoguelph.ca/xmlui/bitstream/handle/10214/
5702/Ascobolus_stercoreus_roughened_ascospores.jpg?seque
nce=1&isAllowed=y, geraadpleegd 11-09-2016

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Basidiomycetes
Basidiomycetes
• Agaricus bisporus
• Amanita muscaria

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Basidiomycetes
Basidiospores (sexual spores)
• basidium
• basidiocarp = mushroom

http://media.gettyimages.com/photos/basidiomycota-sem-close-up-of-basidia-a-basidium-is-a-
microscopic-picture-
id128572814?k=6&m=128572814&s=170667a&w=0&h=aG2nXFv5Nau4rMmKYdj2VhZmta-
Lp1hkHcEYf6tbq7Y=, geraadpleegd 01-09-2019

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Basidiomycetes
Basidiospores (sexual spores) Septal pore complex morphology in the Agaricomycotina (Basidiomycota) with
• basidium emphasis on the Cantharellales and Hymenochaetales.
van Driel KG, Humbel BM, Verkleij AJ, Stalpers J, Müller WH, Boekhout T.
• basidiocarp = mushroom Mycol Res. 2009 May;113(5):559-76. doi: 10.1016/j.mycres.2008.12.007. Epub 2009
Jan 27.

Laser microdissection of fungal septa as visualised by scanning electron microscopy.

van Driel KG, Boekhout T, Wösten HA, Verkleij AJ, Müller WH.
Fungal Genet Biol. 2007 Jun;44(6):466-73. doi: 10.1016/j.fgb.2006.10.006. Epub
2006 Dec 8.

Septal pore cap protein SPC18, isolated from the basidiomycetous fungus
Rhizoctonia solani, also resides in pore plugs.
van Driel KG, van Peer AF, Grijpstra J, Wösten HA, Verkleij AJ, Müller WH, Boekhout
T.
Eukaryot Cell. 2008 Oct;7(10):1865-73. doi: 10.1128/EC.00125-08. Epub 2008 Aug
29.

The septal pore cap is an organelle that functions in vegetative growth and
mushroom formation of the wood-rot fungus Schizophyllum commune.
van Peer AF, Wang F, van Driel KG, de Jong JF, van Donselaar EG, Müller WH,
Boekhout T, Lugones LG, Wösten HA.
Environ Microbiol. 2010 Apr;12(4):833-44. doi: 10.1111/j.1462-2920.2009.02122.x.
Epub 2009 Dec 27.

http://media.gettyimages.com/photos/basidiomycota-sem-close-up-of-basidia-a-basidium-is-a-
microscopic-picture-
43 id128572814?k=6&m=128572814&s=170667a&w=0&h=aG2nXFv5Nau4rMmKYdj2VhZmta-
Lp1hkHcEYf6tbq7Y=, geraadpleegd 01-09-2019
Reproduction fungi
Asexual reproduction (mitosis)
1. cell division yeast
2. filamentous growth (cell division)
3. production asexual spores (conidiospores)

Sexual reproduction (meisosis)

• sexual spores (ascospores/basidiospores)

https://figures.boundless-cdn.com/19169/large/figure-24-01-
44 07.jpeg, geraadpleegd 11-09-2016
Importance of fungi
Infectious diseases in human
• Human
• Mainly superficial
• Opportunistic infections
• (minor medical microbiology)

http://www.huidziekten.nl/afbeeldingen/spruw-
2.jpg, http://www.earthdanceorganics.com/wp-
content/uploads/2015/09/mycorrhizae.gif,
http://www.globalspec.com/npapics/38/96117_0
42120085731_ExhibitPic.jpg, geraadpleegd 11-09-
2016

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Importance of fungi
Agriculture and food
• symbiosis with plants
• food production / fermentation
• Plant pathogens

http://www.huidziekten.nl/afbeeldingen/spruw-2.jpg,
http://www.earthdanceorganics.com/wp-content/uploads/2015/09/mycorrhizae.gif,
50 http://www.globalspec.com/npapics/38/96117_042120085731_ExhibitPic.jpg, geraadpleegd
11-09-2016; https://www.forestryimages.org/browse/detail.cfm?imgnum=5390510,
geraadpleegd 01-09-2019
Importance of fungi
Biotechnology
• production of enzymes
• Biofuels
• BMLS8

http://www.huidziekten.nl/afbeeldingen/spruw-
2.jpg, http://www.earthdanceorganics.com/wp-
content/uploads/2015/09/mycorrhizae.gif,
http://www.globalspec.com/npapics/38/96117_0
42120085731_ExhibitPic.jpg, geraadpleegd 11-09-
2016

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 3 Biotech. 2016 Dec; 6(2): 174.
Published online 2016 Aug
19. doi: 10.1007/s13205-016-0485-8

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 Use of (filamentous) fungi in industry
• Aspergillus, Trichoderma, and Fusarium are
commonly used organisms in industry

• Filamentous fungi represent an

enormously important platform for
industrial fermentation mainly due to
their ability to secrete products

• (Filamentous) fungi are used as both

homologous and heterologous gene
Galactofuranose biosynthesis in the
filamentous fungus Aspergillus niger expression hosts

https://www.universiteitleiden.nl/en/research/research-projects/science/ibl-galactofuranose-
53 biosynthesis-in-the-filamentous-fungus-aspergillus-niger
Microbiology today
• Tree of life
- Bacteria
- Eukarya
- Archaea

• Eukaryotic microorganisms
- Protists
- Fungi

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Questions?

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 Questions?

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http://www.oudridderkerk.nl/Data/Sites/1/media/foto/schoolklas/schoolklas-002-800.jpg, geraadpleegd 02-02-2018