Microbes/Fungi Flashcards
How many fungal spores do people inhale per day?
1,000 to 10 billion
What can increase the amount of spores inhaled
Catastrophic flooding or Category 5 hurricane
Are fungi friends to foes?
Both
How can fungi act as friends?
- Terrestrial ecosystem
- Recyclers
- Provide food
- Material for packaging and clothes
- Medicine
- Enzyme
- Model organisms
How can fungi act as foes?
- Crop disease
- Wild-life disease
- Causes allergy and human diseases
What are fungi killing in 2020/2021?
- Frogs
- Crops
- Humans
- COVID
What can plastic-eating fungus help fight?
Plastic waste
What are some global challenges?
-Water crisis
-Energy costs
-Land degradation
-Political conditions
-Climate change
Pest and pathogens
What are the main crops that feed the world?
- Wheat
- Rice
- Maize
- Soya bean
- Potato
What are 5 major threats to global food security?
- Wheat stem rust
- Rice blast
- Corn smut
- Soybean rust
- Potato late blight
How many people could be feed if not for the annual looses of food due to fungi and oomycetes?
600 - 4,000 million people 2000 kCal per day for a year
What do new final pathogens threaten?
Ecosystem resilience
How many ash trees in the died due to fungal pathogen?
150 million
What does Aspergillum niger produce?
Different commercially relevant enzymes
What can white rot fungus Trametes vericolor be modified for?
Biofuel cells
What does studying microbes include?
- Bateriology (Archaea and mycoplasmas)
- Virology (Viroids)
- Phycology (restricted to mycology and oomycetes)
- Protozology
How are microorganisms measures?
In metric units
What are eukaryotic and bacteria microorganisms measured in?
Micrometers and mass
What are virus measured in?
Nano meters
What are atoms and molecules measured in?
Angstroms (A)
What are the different methods involved in microbiology?
- Microscopy
- Sterilisation
- Pure culture methods
- Molecular biology
Who first viewed Giardia lamblia?
Leewenhoek
What did Robert Hook develop?
Compound microscope
What is good about confocal microscopy?
- Specificity
- Resolution
- Live cell imagery
What are autoclaves?
Under high pressure and temperature able to sterilise liquid medium
What are microbiological filters?
Passage through filter causes sterilisations
What can used to sterilise a sample?
Autoclaves
Microbiological filters
What did Koch’s Postulate demonstrate?
The pathogenicity of a microorganism
What leads to microbial diversity?
- Time line
- Origin of life
How many microbes are estimated to be in 2017?
100 billion and 1 trillion
What leads to diversity of microbes?
Adaptation to enviroment
What are the methods of classifying microbial diversity?
- Morphological diversity
- Metabolic diversity
- Ecological diversity
- Genetic diversity
What is taken in to account in terms of classification by morphological diversity?
Features, structures aid of microscopy
What is taken in to account in terms of classification by metabolic diversity?
Biochemical aid of enzymology
What is taken in to account in terms of classification by ecological diversity?
E.g extremophiles
What is taken in to account in terms of classification by genetic diversity?
gene sequences aid of molecular biology, DNA sequencing, genome comparison
What are different shapes of microbes?
- Coccus
- Rod
- Spirillum
- Spirochete
- Hypha
- Stalk
- Filamentous
What is morphological diversity sufficient for?
Distinguishing prokaryotes and eukaryotes
What is morphological diversity insufficient for?
Distinguish microbe types that appear the same
What are different biological difference to determine metabolic diversity?
- Energy source
- Carbon source
What are the different types of energy sources?
Chemotropic
Phototrophs
What are the different types of carbon sources?
- Heterotrophs
- Autotrophs
What is ecological diversity?
Microbes rate of survival in extreme conditions
What are the different types of microbes based on environmental factors?
- Hyperthermophile
- Psychrophile
- Halophile
- Acidophile
- Alkaliphile
- Barophile
What is genetic diversity based on?
DNA sequencing comparing the genome from different microbes
Alterations in genes allows molecular phylogenetic tree
How is ribosomal RNA gene sequencing and phylogeny carried out?
- Pure culture/environmental sample cells lysed and DNA isolated
- Gene-encoding ribosomal RNA is isolated and amplified by PCR
- Amplified rRNA gene is sequenced
- Obtained sequences aligned by computer
- Tree depicts difference in rRNA sequence between organisms analysed
What is the length of line proportional to on a phylogeny tree?
Evolutionary distance
What did Carl Woese do?
rRNA analysis of methanogens and 3 domain of life
Compared bacteria and eukaryotes
What data supports rRNA for 3 domains?
- Transcription - RNA polymerase
- Translation
- Membranes
How does transcription support rRNA for 3 domains?
Bacteria = 4 subunits
Eukarya = 10-12 units
Purification showed 8 or more subunits present in Archaea
How does translation support rRNA for 3 domains?
Sensitivity to inhibitors suggest Archaeal translation is more like Eukarya than bacteria
How does membranes supports rRNA for 3 domains?
Bacteria, eukaryotes - phospholipid bilayer = ester linkage
What are the fundamental difference of archaea membranes?
- Linkage of hydrophobic side chain
- Type of side chain
What does horizontal gene transfer effect?
Phylogenic trees of non-essential genes particularly in prokaryotes
Are fungi plants or animals?
Neither
What are fungi more closely related to animals or plants?
Animals
How are fungi citizens of modern society?
- Ethnically diverse, ancient community
- Manufacturing factory worked, recyclers
- Model organism
- Diseases
When did fungi diverge from other live?
1500 million years ago
When did fungi probably colonise land?
During Cambrian
When did terrestrial fossils become common?
400 million years ago
How did fungi aid the extinction of dinosaurs?
- Meteor struck
- Dust cloud enveloped Earth, fungal bloom
- Iridium peak and layer of fungal spores
- Dinosaurs body temperature lower, subject to infection
How many named species are there of fungi?
140,00
How many species estimated are there of fungi?
1.5 to 5.1 million species
What is the oldest and largest organisms?
Armillaria mella = Honey fungus
How are fungi manufacturing factory workers?
- Enzymes
- Drugs
- Organic acids
- Biofuels
Why are fungi crucial players in our ecosystem?
- 96% of all land plants live in association with fungi
- Major decomposers of organic matter
- Grow in very toxic condition and remove metals and radioisotope from solution
What do fungi teach us?
Principles of how a cell operate
What and why did Paul Nurse receive
Nobel Prize
Used fungus fission yeast investigate the cell cycle
Why do fungi act as serious threats to mankind?
- Rot houses
- Destroy crops
How do fungi act as agents of disease to humans?
Threat to immune-comprimised
Threat less than bacteria and viruses
How do fungi act as agents of disease to plants?
Greater threat than nematodes, bacteria and viruses
Can fungi act as bioterrorism?
Yes
What do bioweapons attack?
Livestock, crops or ecosystem
What are features of a fungal?
- Eukaryotic
- Unicellular growth
- Filamentous growth
- Dimorphic switch
- Heterotrophs
- Secret enzymes
- Fungal wall
- Storage compounds
- Typically haploid
- Produce sexual and sexual spores
- Plastic genomes
- Metabolic flexibility
What factor can cause a dimorphic switch in fungals?
Temperature
Define heterotroph:
An organism which cannot fix carbon from inorganic sources but uses organic carbon for growth
How do fungi obtain nutrients?
Externally digest
What makes up the fungal wall?
Chitin
Glucans
Ergosterol
What do fungi contain in storage compounds?
Mannitol
Trehalose
Glycogen
Why does the genome of fungi plastic?
- Core and dispensable chromosomes
- SNPs
- Effectors
- Retro DNA/transposons
- Emerging new virulent races
What does Opisthokonts mean?
Posterior flagellum
What are considered to be Opisthokonts?
- All true fungi
- Chytrids
- Microscoridia
- Collar-flagellated protists
- Kingdom Animalia
What was the last common ancestor between the fungal and animal kingdom?
Monosiga brevicollis
Describe Monosiga brevicollis features:
Unicellular
Aquatic
Motile
When did fungi diverge from animal kingdom?
800-900 million years ago
What does comparative genomics reveal about the fungal kingdom?
- Fungal genomes lack sequences controlling multicellularity in animals and plants
- Animals, plants and fungi probably diverged at a unicellular grade of organisation
What features do Microsporidia, Cryptomycota, Blastocladiomycota and Chytridiomycota all have in common?
Single-celled
Water living
Motile asexual spoores
Give a summary of fungal evolution:
- 18rRNA sequences
1. Fungi diverged from water moulds (Oomycetes)
2. Formed aseptate filaments
3. Septa
4. Clamp connections in Basidiomycetes
5. Asexual spores
6. Asci - sexual spores
7. Fruiting bodies
8. Holobasidium
9. Mushroom fungi
Fungal Phyla: what is considered higher fungi?
Basidiomycota
Ascomycota
Glomeromycota
Fungal Phyla: what is considered lower fungi?
Zygomycota
Chytridiomycota
Microsporidia
Cryptomucota
Are fungi and microspordia closely-related or not?
Closely related
What are microspordia?
Obligated intracellular pathogens
What do microspordia infect?
Animals and insects
How many microspordia species infect humans?
Causes diarrhoea, eye, muscular, respiratory and genitourinary infections
When was microspordia first described?
1857
Describe the structure of microspordia:
- Smallest of eukaryotes
- Unicellular
- Lack mitochondria, peroxisomes and centrioles
- Prokaryotic features (70S ribosomes/ fused 5.8S/28S rRNAs
- Fungal features: nuclear division, fungal wall
What is phylum 2 of fungal systematics?
Crytomycota
What is the phylum 1 of fungal systematic?
Microspordia
How many species are in crytomycota?
30
What does crytomycota lack?
Lack chitin cell walls present in fungi
What does lack of chin crytomycota cause?
Becomes phagotrophic parasites that feed by engulfing or live inside other cells
How do crytomycota feed?
Taking in nutrients from outside cell
What is the phylum 3 of the fungal systematics?
Chytridiomycota
Where are Chytridiomycota found?
- Aquatic environments living as parasites of algae and planktonic plants
- Soil living as saprotrophs on pollen or parasites on vascular plants
How many species are there in Chytridiomycota?
980-1200 species
How many flagellum are losses from Chytridiomycota during evolution of fungi?
3-4
What is the life cycle of Chytridiomycota?
Thallus becomes sporangium (asexual) and releases zoospores
What are Chytrids important in food webs?
- Zoospores are food sources for phytoplankton
- Decompose organic matter
- Convert inorganic compounds to organic compounds
- Parasites to aquatic plants and animals
- Anaerobic chytrids in rumen and hindguts
What has Chyrtridiomycota causes a massive extinction of?
Species
What are features of Chyrtridiomycota?
Simple microscopic molds within chitin walls and swimming spores
What is the phylum 4 of the fungal systematic?
Zygomycota
How many species are in Zygomycota?
> 1600 species
What are features of Zygomycota?
- Multinucleate mycelium = no septa
- Asexual spres in a sporangium
- Two hyphae fuse to form zygote
How are Zygomycota elecological diverse?
- Saprotropic (soli and dung)
- On mouldy fruit and bread
- Parasitic on insects
What does Zygomycota Mucor spp cause?
Zygomycosis on humans, frogs, cattle and pigs
What is Zygomycota Mucormycosis?
- Infect immune-compromised patients
- Second most common fungal infection in haematological malignancy
- 50 to 90% motility
- Risk increases with diabetes, steroids, other immune-suppressive treatments, high serum iron levels
What is phylum 5 of the fungal systematics?
Glomeromycota
What is coenocytic?
Without division along the length of the filament
How many species are Glomeromycota?
200+
What are Glomeromycota?
Microscopic obligate intracellular mutualistic symbionts of almost all plant roots
What does Glomeromycota form?
Arbuscular mycorrhizal
What are features of Glomeromycota arbuscular mycorrhizal?
- Obligate symbionts formation of arbuscules in plant roots
- Large, multi-nucleate
- Non-septate hyphae
What is considered to be the most sophisticated basal or lower fungi of the fungal systematics?
Glomeromycota
What is phylum 6 of the fungal systematic?
Ascomycota
What is the largest group of the fungi kingdom?
Ascomycota
What are features of Ascomycota?
- Filamentous fungi and some yeasts
- Most licensed fungi
- Spetata hyphae
- Carry sexual spores in sac like structures called ascus
What can Ascomycota be act as?
- Plant pathogens
- Human pathogens
- Drug manufacturers
- Food fungi
- Edible fungi
- Model organisms
What is an ubiquitous human pathogen?
Candida albicans
What is the phylum 7 of the fungal systematic?
Basidiomycota
How many species are Basidiomycota?
50,000
Are Basidiomycota a diverse group?
Yes
How are Basidiomycota a diverse group?
Difference morphologically, ecologically and taxonomically
What are structure of Basidiomycota?
- Septum and dolipores
- Sexual reproduction = basdiospores on basidium
- Asexual reproduction - clamp connection
What is asexual reproduction involving clamp connection?
Allow nuclei to migrate from one cell to another
What are the four different types of lichens?
- Cructose
- Squamulose
- Foliose
- Fruictose
What are crustose lichens?
Crust like and adhere tightly to the surface upon which they grow
What are squamulose lichens?
Composed of scale-like parts
What are foliose lichens?
Leaf-like, composed of flat sheets of loosely bound tissue
What are fruticose lichens?
Composed of free-standing branching tubes
What are lichens?
Mutualistic association between fungus and photosynthetic algal or cyanobacterial pater
How many lichen species are known?
30,000
What does lichen symbiosis nearly always involve?
Ascomycota
Why are lichens important?
- Animal food
- Pollution bioindicators
- Source of using acid (antibiotics)
What is the structure of lichen?
- Upper cortex of fungal hyphae
- Later containing photobiont cells
- Medulla of fungal hyphae
Why are lichens considered resilient?
Dominate life forms in all sorts of unusual environments
Historical perspective of fungal biotechnology:
- 1914:
- 1929:
- 1942:
- 1953:
- 1955:
- 1967:
- 1984:
- 1987:
- 2000s:
- 2017:
- Strain selection/ Koji process
- Fleming and antibiotics
- Tatum and Beadle “one gene, one-enzyme”
- Roper - parasexual analysis
- Backis and Stauffer - initiated mutagenesis in penicillin
- Pirt and Righelato - continuous culture
- Ball - parasexual breeding
- Recombinant DNA/transformation
- Nurse, Cell cycle, genomics
- CRISPR/CAS
What are fungi pioneered for?
Genetic analysis
Why are fungi a major toll for classical genetics?
- Easy growth
- Short life cycle
- Most haploid
- Sexual stage
- Produce asexual spores
Why do fungi serve as a good models for biochemical studies?
- Simple nutrients required
- Can directly correlated with genetic studies
Define heterothallic species:
Sexes that reside in different individuals
What do heterothallic species require to produce sexual spores?
Two compatible homothallic patterns capable of sexual reproduction from a single organisms
Define homothallic species:
Possession, within a single organism, of resources to reproduce sexually
Biologically fungi are:
- Versatile metabolically
- Form hyphae network/mycelium
- Polarised growth
- Ascomycetes or Basidiomycetes or Zygomycte
What must a fungus be able to do for industrial uses?
- Spores easily inoculated into large fermenters
- Grow rapidly and form product in large-scale cultures
- Produce the desired product in relatively short period of time
- Grow in a relatively inexpensive nutrient in bulk quantities
- Not be pathogenic
- Amenable to genetic manipulation
What can fungi be used for?
- Food
- Biological control agents
- Primary metabolites
- Secondary metabolites
- Heterologous hosts for secretion
- Aflotoxins
What is fungal immunosupressant drugs?
Entomopathogenic fungus
What are basic tools for a fungal biotechnologist?
- Good understanding of biology and taxonomy of fungi
- Collection and isolation of samples
- Access to fungal culture collections
- Preservation
What are two different growth kinetics?
- Surface culture
- Submerged culture
What are different types of fungi in fermenters?
- Solid sate
- Submerged liquid
- Batching culturing
- Fed batch
What is solid state fermentation?
- Koji process
- Many years
- Old fashioned
- Cheap
- Effective
What is submerged liquid fermentation?
- Chemostat
- Highly controlled
- Substrates must low
What is batch culture?
All harvest at a particular time
What is continuous culture?
Continuously adding substrate and harvest so never clean chemostat
What gives better improvements of fermentation?
- Strain improvement
- Production improvement
Give examples of therapeutic metabolites (fungal products):
Amino acids, penicillin, cephalosporins, Peptides, cyclosporine, Ergot alkaloids, Lovastatin
What is an example of alfotoxin?
Sclerotia of Claviceps purpurea
What does Clavicepes purpurea?
- Ergotamine
- Ergine
- LSD
What symptoms can Clavicepes purpurea causes?
Sensation of burning, vasoconstriction, limb numbness, cold, gangrene, rotting of fingers, toes, hands
What are organic acids products of fungals?
- Citric acid
- Itaconic acid
- Fumaris acid
What are examples of fungal enzymes?
- A-amylase
- Amyloglucosidase
- Pectinase
- Protease
- Lipase
Where do95% of all fungal enzymes come from?
Aspergillus niger
What is the most abundant organic compound on Earth?
Cellulose
What are examples of cellulose biodegradation?
- Endoglucanases
- Cellobiohydrolases
- B-glucsidase
What is a cellulotyic fungi?
Fermntable sugars, ethanol, paper and pulp industry, textile industry, animal feed, biofuels
What is the second abundant as a renewable carbon source?
Lignin
What does lignin 2 protect?
Cellulose
How does white rot fungi depolymerise lignin?
By lignin and Mn-peroxidases
What organic acid does Aspergillus niger produce?
Citric acid
What percentage of citric acid is used in food industry?
70
What percentage of citric acid is used in pharmaceutical industry?
20
What percentage of citric acid is used on chemical industry/cosmetics?
10
How is citric acid produced?
D-glucose 2x Pyruvate Acetyl-Coa Oxaloacelate -Citrate
What are different types of B-lactam antibiotics nucleus?
- Penicillin nucleus
- Cephalosporin nucleus
- Monobactam nucleus
- Carbapenem nucleus
What size are viroids ssRNAs?
150-400bp
What do viroids cause?
Plant disease
What is the viroid replication mechanism?
Unknown
Does viroid have a protein coat envelope?
No, its naked
What is the average size of a virus?
20-200 nm
Can viruses be naked or enveloped?
Both
How much space does the capsid cover the virus?
60-95%
How much space does the nucleic acid core cover the virus?
5-40%
What do you call a coat and core in a virus?
Nucleocapsid
Does virus contain RNA or DNA?
Both
Does virus contain single stranded or double stranded RNA/DNA?
Both
What are the symptoms of foot and mouth virus?
Mouth sores, debilitation and lamelessness in sheep and clooven hoofed animals
How do you control foot and mouth virus?
Had to kill
What are the symptoms of blue tongue virus?
Lameness/swallowing tongue/death of sheep
What is the vector of blue tongue virus?
Midges
What is the size of a mycoplasmas?
0.1 micrometer
Does mycoplasmas have a small or large genome?
Small
How many genes are in genome of mycoplasmas?
650
What does mycoplasmas lack?
- Enveloped nucleus
- Trye wall
What diseases do mycoplasmas cause?
Plant and animals disease
What is included in the protists?
Algae, protozoa, slime moulds, water moulds/oomycetes
What are example of slime moulds?
Myxomycota
What are features of slime moulds?
- Wall-less
- Cellular
- Acellular
- Brightly coloured
What are different types of water moulds related to oomycota?
- Damping off disease
- Downy mildews
- White rusts
- Late Blight
How helped to the development of discovery of penicillin?
- Alexander Fleming
- Howard Florey
- Ernst Chain
- Norman Heatley
- Charles Fletcher
- Albert Alexander
- Dorothy Hodgkin
How much of B-lactams is the antibiotic market?
+65%