Topic 10: Diversity of Bacteria & Fungi (Part 1) Lecture 19 Flashcards
metagenomics
prokaryotes, can use metagenomics to identify prokaryotic species in soil and even the human gut (called the microbiome)
plasmid
prokaryotes lacks membrane-bound organelles (contains a PLASMID within the nucleotide)
- a small, circular, double-stranded DNA molecule that carries accessory genes separate from those of a bacterial chromosome
peptidoglycan
what bacterial cell walls are composed of
- Structural carbohydrate composed of sugars cross-linked with short polypeptides
capsule
what a cell wall is surrounded by
- Composed of polysaccharides and/ or protein
fimbriae (sing. Fimbria)
Some prokaryotes also have this
• Hairlike projections to anchor to hosts or substrata
Gram Staining
uses crystal violet dye and iodine, and alcohol rinse, and a final stain of red dye
Gram-positive
bacteria have simple cell walls > peptidoglycan
Gram-negative
bacteria have cell walls < peptidoglycan, but more lipopolysaccarhides
Endospores
are types of resistant cells produced by prokaryotes to survive harsh environments
- Bacterial cell replicates its DNA and surrounds it in a super resistant layer
Taxis
movement towards or away from a stimulus
- b/c prokaryotes can move within the environment
flagellum
prokaryotes can use this to move within the environment
binary fission
what prokaryotes reproduce via
- Under optimal conditions can divide every 1-3 hours
• Nutrient and space availability (quorum sensing), self-poisoning, competition limits colony cell
Obligate aerobes
need O2 for cellular respiration (prokaryotes)
Obligate anaerobes
are poisoned by O2
anaerobic respiration
is the process of producing cellular energy without oxygen (or fermentation)
Facultative anaerobes
use O2 when available but will carry out fermentation or anaerobic respiration when oxygen is absent
nitrogen fixation
prokaryotes can also carry out nitrogen fixation -> converting N2 to NH
heterocysts
prokaryotes have specialised cells called heterocysts in photosynthetic
prokaryotes to carry out N-fixation
microbiome
Diverse nutritional modes allow diverse bacteria to inhabit the human gut (called out microbiome) for prokaryotes
extremophiles
Archaea are prokaryotes that inhabit some of the harshest environments (we call these extremophiles)
Halophile
“salt loving”, live in super haline (salty) places
Thermophile
“heat loving”, thermal vents, geysers, volcanic hot springs (think Yellowstone)
Acidophile
“acid loving”, human gut, volcanic features
Methanogen
release methane (many archea also live in moderate environments)
• Found in marshes, cattle guts (cow farts)
• Important decomposers in the environment
heterotrophs
Like animals, fungi are heterotrophs
- an organism that obtains organic food molecules by eating other organisms or substances derived from them
yeasts
The most common fungal body structures are multicellular or single cells (yeasts)
Hyphae (sing. Hypha)
(sing. Hypha) -> tiny tubular filaments surrounding the plasma membrane
- a fungi structure
Mycelium
a mass of hyphae that maximises
SA:volume ratio
- a fungi structure
Fruiting body
reproductive structure
- a fungi structure
Cell walls
composed of chitin (nitrogen-containing polysaccharide)
- a fungi structure
chitin
what fungi cell walls are composed of
- (nitrogen-containing polysaccharide)
septate
divided, allowing large macromolecules to pass between hyphal cells
- 1 of the ways hyphae occur in fungi
coenocytic
(lacking septa) with a continuous cytoplasmic mass
- 1 of the ways hyphae occur in fungi
Mycorrhizae
are specialised fungi that form associations with plants
Ectomycorrhizal
forms sheaths of hyphae around plants roots
- type of mycorrhizal fungi (specialized fungi)
Arbuscular mycorrhizal (endomycorrhizal)
Have branched hyphae called arbuscules that penetrate plant host cells to exchange nutrients
- type of mycorrhizal fungi (specialized fungi)
arbuscules
penetrate plant host cells to exchange nutrients (within the arbuscular mycorrhizal (arbuscules)
spores
what fungi reproduce via
- which can be produced sexually (meiospores) or asexually (mitospores)
meiospores
fungi reproduce via spores, which can be produced sexually (meiospores)
mitospores
fungi reproduce via spores, which can be produced asexually (mitospores)
Haplontic
dominantly haploid stage
Diplontic
dominantly diploid stage
Dikaryotic
“two nuclei”, a transition stage between haplontic and diplontic where plasmogamy (fusion of cytoplasms from parental mycelia) has occurred, but karyogamy (fusion of nuclei, thus completing fertilisation) has not
plasmogamy
(fusion of cytoplasms from parental mycelia) has occurred in the dikaryotic life stage
karyogamy
(fusion of nuclei, thus completing fertilisation) has not occurred in the dikaryotic life stage
heterokaryon
When the fungus is in the dikaryotic stage, we say it is a heterokaryon since its mycelium contains two genetically different nuclei within its cytoplasm
Opisthokonts
Animals, fungi, and protistan relatives form a monophyletic clade called the Opisthokonts (opistho = flagellal position)
nucleariids
Fungi more related to single-celled protistan relatives (nucleariids) than animals proper
Describe Chytrids
• Phylum: Chytridiomycota
• ~1000 species
• Found in LAKES and SOILS, hydrothermal VENTS
• Most are DECOMPOSERS, but SOME are PATHOGENIC
- Batrachochytrium salamandrivorans attacks amphibians and has decimated their populations
• SOME chytrids are MUTUALISTIC
- Live in the guts of sheep to help break down plant matter
• ALL chytrids have flagellated ZOOSPORES (spores that move)
• Have CELL WALLS of CHITIN
zoospores
All chytrids have flagellated zoospores (spores that move)
Describe the Zygomycetes “moulds” basic features.
- Phylum: Zygomycota
- ~1000 species
- Found in SOILS and AIR
- Most are FAST-growing moulds, MICROSCOPIC
Sporangia
produces spores
- in the zygomycetes “moulds”
Zygosporangia
produces the zygote (zygospore)
- in the zygomycetes “moulds”
Describe the Glomeromycetes basic features.
Phylum: Glomeromycota (formerly
Zygomycota)
• ~200 species
• Found in SOILS and AIR
Describe the Ascomycetes “sac fungi” basic features.
Phylum: Ascomycota
• ~65,000 species
• Found in MARINE, FRESHWATER, and TERRESTRIAL HABITATS
• Can be UNICELLULAR YEASTS, or MULTICELLULAR FUNGI
• Saprotrophs, pathogens, mutualists, mycorrhizal
ascocarps
Fruiting body of ascomycetes “sac fungi”
ascospores
Ascomycetes “sac fungi” produces ascospores (sexual) in asci (sing. ascus)
asci (sing. ascus)
Ascomycetes “sac fungi” produces ascospores (sexual) in
ASCI (sing. ascus) - which is a saclike spore capsule located at the tip of a dikaryotic hypha of a sac fungus
Describe Ascomycete life cycle (asexual & sexual stage)
life cycle follows the standard fungal cycle
Asexual Stage:
• Conidiospores are produced in structures
called conidiophores (compare with the
sporangia in Zygomycetes)
• Sexual Stage:
• Ascospores (sexual spore) are produced in
dikaryotic asci contained within ascocarps
• Contain 8 ascospores per ascus
• Conidia may be involved in sexual
reproduction of a – conidiospore meets up
with a + conidiospore
Conidiospores
asexual stage of ascomycete fungi:
- CONIDIOSPORES are produced in structures called conidiophores (compare with the sporangia in Zygomycetes)
- in the asexual stage of Ascomycete
conidiophores
asexual stage of ascomycete fungi:
- conidiospores are produced in structures called CONIDIOPHORES (compare with the sporangia in Zygomycetes)
- in the asexual stage of Ascomycete
Describe Basidiomycetes “club fungi”
Phylum: Basidiomycota
• ~30,000 species
• Contain PUFFBALLS, “MUSHROOMS”, SHELF FUNGI
• Saprotrophs, pathogens (rusts and smuts), mutualists, mycorrhizal
basidiocarps
Fruiting body: basidiocarps containing “gills”
- for the basidiomycetes “club fungi”
basidiospores
Produces BASIDIOCARPS (sexual) in dikaryotic basidia (sing. basidium) contained on the gills
basidia
Produces basidiospores (sexual) in dikaryotic BASIDIA (sing. basidium) contained on the gills
Describe the Basidiomycete life cycle
Basidiomycete life cycle follows the
standard fungal cycle
• Asexual Stage: none or very rare • Sexual Stage: • Basidiospores (sexual spore) are produced in dikaryotic basidia contained within basidiocarps • Contain 4 basidiospores per basidium
Chemotaxis
response to a chemical
Positive chemotaxis
towards a chemical
Negative chemotaxis
away from a chemical
probiotics
We consume probiotics to help establish healthy populations of “good” bacteria
What are the 2 domains of life that prokaryotes span?
bacteria & archaea
What are some of the most extreme habitats on Earth that Prokaryotes live?
• Tailing ponds from mining
• Super salty deserts and lakes (ie Great Salt Lake
in Utah)
• Under glaciers in the Arctic and Antarctic
• Thermal vents surrounding volcanic features
• Human gut (very acidic!)
What is evidence that prokaryotes are the most abundant organisms on the planet?
- 1g of soil can hold more prokaryotes than the number of people who ever lived during Earth’s history
- Can use metagenomics to identify prokaryotic species in soil and even the human gut (called the microbiome)
What are some common characteristics of prokaryotes?
- 0.5 - 5μm in size (exception Thiomargarita namibiensis is 750 μm across!)
- Unicellular
- Lacks membrane-bound organelles (contains a plasmid within the nucleoid)
- Come in three main shapes:
- Coccoid (spherical) – Coccus sp.
- Bacilli (rod-shaped) – Bacillus sp.
- Spiral – Spirillum sp.
What are the 3 main shapes that prokaryotes come in?
- Coccoid (spherical) – Coccus sp
- Bacilli (rod-shaped) – Bacillus sp.
- Spiral – Spirillum sp.
Do prokaryotes have a cell wall? And ALSO explain about the bacterial and archaeal cell walls
• Have a cell wall (yes)
• Bacterial cell walls are composed of peptidoglycan
- Structural carbohydrate composed of sugars cross-linked with short polypeptides
• Archaeal cells walls are composed of other complex sugars and proteins but lack peptidoglycan
What is the capsule composed of? What does it allow? What does it protect?
- Composed of polysaccharides and/ or protein
- Allows adherence to substrata or each other within the colony
- Protects against desiccation and bacteriophages(viruses)
Some prokaryotes also have fimbriae (sing. fimbria)…what does that entail?
Hairlike projections to anchor to hosts or substrata
What is gram staining?And ALSO explain the 2 types.
• Gram Staining uses crystal violet dye and
iodine, and alcohol rinse, and a final stain
of red dye
• Gram-positive bacteria have simple cell walls >
peptidoglycan
• Gram-negative bacteria have cell walls <
peptidoglycan, but more lipopolysaccarhides
Describe how both gram-negative & gram positive FUNCTION.
- Gram-negative bacteria are:
- More toxic due to the lipopolysaccharides
- More protected due to outer lipopolysaccharide layer
- More anti-biotic resistant
- Many antibiotics disrupt the peptidoglycans in the cell….no peptidoglycans, no disruption!
- Some gram-positive strains are also resistant
- “Super bugs” such as Staphylococcus aureus (ie MRSA)
What are the functions of endospores (in prokaryotes)?
- Can survive boiling water
- Need extreme heat and pressure to kill
- Can remain dormant for centuries
How can prokaryotes move within the environment?
- Taxis – movement towards or away from a stimulus
* Can use a flagellum
Describe the different types of taxis
- Chemotaxis -> response to a chemical
* Positive chemotaxis -> towards a chemical
* Negative chemotaxis -> away from a chemical
Compare & contrast flagella in prokaryotes to eukaryotic, bacteria & archea flagella. ALSO what is the structure of the flagella?
- Much thinner than eukaryotic flagella and not covered with an extension of the plasma membrane
- Bacteria and archaea flagella differ in protein composition
- The structure of the flagella across the 3 domains suggest they arose independently -> they are analogous structures!
Describe how prokaryotes reproduce
• Reproduce via binary fission
• Under optimal conditions can divide
every 1-3 hours
• Nutrient and space availability (quorum sensing), self-poisoning, competition limits colony cell
What are the diverse nutritional adaptions allowing Prokaryotes to inhabit diversely harsh environments? Describe all 4 of them
- Obligate aerobes need O2 for cellular respiration
- Obligate anaerobes are poisoned by O2
- Acquire energy from fermentation or anaerobic respiration
- Facultative anaerobes use O2 when available but will carry out fermentation or anaerobic respiration when oxygen is absent
What can prokaryotes also carry out to help adapt to diverse nutritional modes?
- Can also carry out nitrogen fixation -> converting N2 to NH3
- Have specialised cells called heterocysts in photosynthetic prokaryotes to carry out N-fixation
Diverse nutritional modes allow diverse bacteria to inhabit the human gut (called out microbiome). Describe this AND its function
- Contain ~10 trillion bacteria in our guts
- Are MUTUALISTS -> break down food that we cannot
- We can absorb the nutrients they break down in exchange for our blood cells producing anti-microbial compounds to reduce competition and keep only the “good” bacteria
- We consume probiotics to help establish healthy populations of “good” bacteria
Why do we consume probiotics?
to help establish healthy populations of “good” bacteria
Archaea are prokaryotes that inhabit some of the harshest environments. What do we call these?
extremophiles
What are the 3 extremophiles? Describe
- Halophile -> “salt loving”, live in super haline (salty) places
- Thermophile -> “heat loving”, thermal vents, geysers, volcanic hot springs (think Yellowstone)
- Acidophile -> “acid loving”, human gut, volcanic features
Many archaea also live in moderate environments. What is this called?
Methanogen -> release methane
Where are methanogens found? AND why are they important?
- Found in marshes, cattle guts (cow farts)
* Important decomposers in the environment
Describe the basics of fungi. How many, what they look like, where they are found, and what they do etc.
- There are ~ 100,000 species of identified fungi
- Could be up to 1.5 million species!
- Fungi can be single-celled, microscopic, filamentous or macroscopic
- Found in all habitats, both terrestrial and aquatic
- Fungi are the nutrient recyclers within the ecosystem, breaking down decaying organic matter
Like animals, fungi are…
heterotrophs
- an organism that obtains organic food molecules by eating other organisms or substances derived from them
• Animals -> ingestion
• Fungi -> absorption (aka feed via absorption)
How do fungi absorb their food?
- Secrete hydrolytic enzymes into the ENVIRONMENT which breaks down nutrients
- Secrete enzymes to penetrate CELL WALLS of host cells, allowing fungi to get nutrients through parasitism and infection
- Can break down a variety of COMPOUNDS, including lignin and cellulose (which animals cannot digest)
What can fungi be?
can be saprotrophs (decomposers), parasites, pathogens, mutualists
What are the most common fungal body structures?
are multicellular or single cells (yeasts)
What are the several structures that fungi are composed of?
- Hyphae (sing. Hypha)
- Mycelium
- Fruiting body
- Cell walls
What are the 2 forms hyphae can occur in?
- septate (divided, allowing large macromolecules to pass between hyphal cells)
- coenocytic (lacking septa) with a continuous cytoplasmic mass
What is mycorrhizae AND what are the 2 types?
are specialised fungi that form associations with plants
- Ectomycorrhizal
- Arbuscular mycorrhizal (endomycorrhizal)
What does mycorrhizal mycelia do?
increase the surface area and efficiency of absorbing phosphate ions and other minerals in the soil
• More efficient than plant roots
What do plants provide the fungus in exchange?
In exchange, plants provide the fungus ORGANIC NUTRIENTS
Many mycorrhizal fungi look like…
regular “mushrooms”
How do fungi reproduce?
via spores, which can be produced sexually (meiospores) or asexually (mitospores)
Fungi alternate between sexual and asexual cycles in three main life stages:
- Haplontic -> dominantly haploid stage
- Diplontic -> dominantly diploid stage
- Dikaryotic -> “two nuclei”, a transition stage between haplontic and diplontic where plasmogamy (fusion of cytoplasms from parental mycelia) has occurred, but karyogamy (fusion of nuclei, thus completing fertilisation) has not
What do we say when the fungus is in the dikaryotic stage?
When the fungus is in the dikaryotic stage, we say it is a heterokaryon since its mycelium contains two genetically different nuclei within its cytoplasm
What is the evidence or phylogenetics that has suggested fungi originated from a flagellated unicellular aquatic protist ancestor?
- Animals, fungi, and protistan relatives form a monophyletic clade called the Opisthokonts (opistho = flagellal position)
- Fungi more related to single-celled protistan relatives (nucleariids) than animals proper
What do Nucleariids consist of?
of amoebas that feed on algae and bacteria
DNA evidence suggests that animals are more related to another group of…
protists (choanoflagellates) than to either fungi or nucleariids
• We can conclude then that multicellularity evolved independently in animals and fungi
What is the hyphae in the Zygomycetes “moulds”?
• Hyphae are COENOCYTIC with septa ONLY in reproductive hyphae
What is the reproduction features in the Zygomycetes “moulds”?
- Sporangia -> produces spores
* Zygosporangia -> produces the zygote (zygospore)
What is the hyphae in Glomeromycetes “mycorrhizae”?
Hyphae are COENOCYTIC
What is the reproduction features in the Glomeromycetes “mycorrhizae”?
Spores look similar to zygospores
What are most in Glomeromycetes “mycorrhizae”?
Most are arbuscular mycorrhizal
What is a common bread mould within Zygomycetes “moulds”?
Rizopus stolonifer is a common bread mould
About how many plants are associated with Glomeromycetes “mycorrhizae”?
About 80% plants associate with Glomeromycota
What does molecular evidence discern about the Glomeromycetes “mycorrhizae”?
Molecular evidence however has discerned that the Glomeromycota is its own monophyletic clade
What is the hyphae in Ascomycetes “sac fungi”?
Hyphae are septate
What is the reproduction features in Ascomycetes “sac fungi”?
- Fruiting body: ascocarps
* Produces ascospores (sexual) in asci (sing. ascus)
What is the hyphae in Basidiomycetes “club fungi”?
Hyphae are septate
What is the reproduction features in Basidiomycetes “club fungi”?
- Fruiting body: basidiocarps containing “gills”
* Produces basidiospores (sexual) in dikaryotic basidia (sing. basidium) contained on the gills
When conditions are optimal for reproduction in Basidiomycetes “club fungi” can…
ESTABLISH WITHIN HOURS
Some chytrids are MUTUALISTIC which means they…
Live in the guts of sheep to help break down plant matter
What is the reproduction features in chytrids?
ALL chytrids have flagellated ZOOSPORES (spores that move)
