microbiology Flashcards
Who came up with the biological species concept ?
Ernest mayr
What is the definition of a species ?
Are populations of organisms that have a high genetic similarity which can transfer genetic material.
What are genes and proteins that are measures of evolutionary change called ?
Chronometers
What methods are there available for genetic comparison ?
16s RNA sequencing
18s RNA sequencing
DNA-DNA hybridisation
What is the threshold for DNA-DNA similarity to be considered a species ?
> 70%
What is the problem with 16s RNA sequencing ?
Molecule being sequenced is on 1500bp in length and the rate of evolutionary change is 1bp every 1 million years. Meaning prokaryotes with 97%similarity may have diverged 50mya.
What is the problem with DNA-DNA similarity ?
DNA-DNA similarity is only a measure of the similarity of the DNA shared between two strains: it does not account for the DNA that is unique to one species or the other
What is the solution to the low resolving power of 16s RNA comparison ?
Whole genome sequecing allowing comparison of every gene.
What is the definition of symbiosis ?
A term used to describe an exclusive and close relationship between 2 species.
What 3 key points define symbiosis ?
- Creates a unique metabolism or structure.
- Selective co-evolution of the two species from generation to generation
- The symbiosis must be maintained through natural selection.
What are the 5 types of symbiosis ?
Mutualistic Commensal Neutral Competitive Parasitic
Give an example of Ectosymbiosis and Endosymbiosis
Outisde the cell way-rumen bacteria
Within cavity-Algae of clams
What type of endosymbiosis occurs in the cell ?
intracellular-Rhizobium
When is the paracium-chlorella symbiosis beneficial ?
When nutrients are low it is beneficial when low light levels it is parasitic.
What does the vertebrate gut biome allow ?
Anaerobic fermentation to occur in rumens allowing digestion of cellulose.
The convoluta-tertrasel symbiosis is an example of intracellular symbiosis what is unique about the green algae?
In symbiosis the green algae have no cell wall but not in symbiosis they are different in structure.
What is produced by the fermentation of cellulose ?
Volatile fatty acids.
What are the 2 layers of tissue that make up a coral and what separates them ?
Endoderm- Contain zooxanthellae
Ectoderm- Contain mucus glands
Separated by mesoglea
What do mucin genes produce and what is the product made of ?
mucus- Glycoprotein (80%oligosaccharide 20% protein core)
How much of the energy produced by zooxanthellae is given to the host coral ?
78% is given to host
45% is used to produce mucus
What did the evolution of surface mucosa do ?
Changed the relationship of eukaryotes and microorganisms forever.
What caused the loss of the acroporids ?
White band disease
why cant kochs postulates be used for coral disease ?
1 Most marine microbes cant be cultured.
2 Diseased and healthy corals are connected by water so cannot collect isolates
3 Coral disease is thought to be caused by multiple agents
4 Difficult to prove symptoms are unique and that the same disease has been created in the lab.
What do polyps use to feed ?
Expand at night and use nematocysts
One of the principles of kochs postulates is that the cultured pathogen should cause disease to a healthy organism. What is wrong with this ?
Some pathogens only infect weakened organisms.
What is the rhizophere ?
Zone of soil around plant roots whereby soil properties are influenced by roots.
What did van luijk observe ?
That grass grew better on non sterile soil in comparison to sterile soil.
What are PGPR ?
Plant-growth promoting rhizobacteria colonise the rhizosphere, the rhizoplane (root surface), or the root itself (within radicular tissues)
What is the main characteristic of an effective PGPR ?
Ability to aggressively colonise plant roots (high competition).
How do PGPR bioferilise ?
The production of stimulatory phytohormones
Lowering of the ethylene level in plant.
Improvement of the plant nutrient status by
liberation of phosphates and micronutrients from insoluble sources by the production of metabolites to lower pH and siderophores.
What pathway do PGPR use to produce auxins ?
Indole 3 pyruvate pathway.
What is tryptophan and what do PGPR do with it ?
Tryptophan is a precursor for auxins and PGPR convert it to indole 3-acetic acid (IAA).
How do PGPR reduce ethylene levels ?
Produce ACC deminase which cleaves the ethylene precursor ACC.
What does ethylene do to plants ?
inhibits root elongation.
What does low levels of IAA do ?
Promotes root elongation.
How do PGPR solubilise phosphates ?
Lower pH of soil via production of metabolites.
Why are siderphores so useful ?
Siderophores bind to iron3 and enters the plant and release the iron3 in the form iron2. Also useful for the prevention of proliferation of pathogens as they out .compete pathogen for nutrients.
What is biocontrol ?
Where the activity of a pathogen is reduced through the agency of another living organism.
PGPR biocontrol how ?
Production of siderophores, by colonising roots thus excluding other microorganisms and through the production of metabolites such as anitbodies and lysozymes.
What is ISR ?
induced systemic resistance- Mediated by rhizobacteria it resembles Systemic acquired resistance.
What induces ISR?
Lipopolysaccaharides and siderophores
Trichoderma harianum is a plant growth promoting fungi what dies it do ?
Improves soil formation and provides fungicides
What are the characteristics of a good PGPB ?
Enhance growth Ability to survive and form a biofilm Ability to colonise roots Ability to compete Safe to environment Tolerant to adverse conditions
What do liquid inoculants contain ?
Mainly water with minerals and organic oils
What is peat used for and what is the problem with this ?
Used as an organic carrier of rhizobia but this causes destruction of peat bogs.
What are cyanobacteria inoculants made from ?
The soil from their habitats
How are synthetic formulations created.
Bacteria encapsulated in polymer. This is placed in a fermenter to provide nutrion until numbers of bacteria is optimal.
What is unique about synthetic formulations ?
The polymer can be designed to release the bacteria at certain times.
If a fungi is dimorphic what does this mean ?
Has a single celled phase (yeast) and a filamentous phase (hyphae)
What are the cross walls in hyphae called ?
septa
How do fungi that have filamentous growth grow ?
Hyphae grow from apical tip and branching occurs behind tip forming a mycelium.
What are animals fungi and protists collectively called ?
Opisthokonts
What are the 2 distinct groups of fungi ?
True fungi- In kingdom fungi
Oomycetes- not in kingdon closely related to brown algae
What are some features of true fungi ?
Use glycogen as storage compound
Haploid nuclei (sometimes multiple)
Cell wall made of chitin and glucans
What is unique about basidiomycota
they are dikaryotic meaning they have 2 haploid nuclei per cell.
How is being dikaryotic maintained ?
Through clamp connections.
How do basdiomycetes reproduce ?
Sexually through production of fruiting bodies
What is the largest group of fungi and what is a good example of one ?
Ascomycetes
Saccaromyces cerevisae
What type of fungi have a motile stage and what makes them motile ?
Chytridiomycota
Have a uniflaggellate zoospore
What class of fungi doesnt have a nucleus but has a globose thalli body ?
Chytridiomycota
What are the two mating types of saccharomyces and what happens when the diploid cell is starved ?
A and alpha can fuse to form a diploid cell. When starved is forms an ascus with 4 ascospores
How do ascomycetes reproduce ?
Asexual-Produce spores called conidea
Sexual- Fruits called ascocarps that contain sac like asci which contain 8 ascospores.
What is a biofilm ?
A coordinated, organised, heterogenous community of bacterial cells surrounded by a self produced polysaccahride matrix.
What is needed for the formation of biofilms ?
Nutrients
moisture
a surface
What are the 4 stages of a biofilm ?
Attachment
Exopolysaccahride production
Maturation
Dispersal
What are the pilli and flagella used for in a biofilm ?
Flagella used for initial attachment and used for movement.
Pilli required for microcolony formation.
How do flagella aid movement ?
Bunch in a counter clockwise motion. Cells moving using a twitching motility
How is a micro colony formed and what happens when critical mass is reached ?
Free living cells attach with flagella and grow and divide into a microcolony. Critical mas leads to expression of genes that causes irreversible attachment.
How is the EPS produced ?
Cells communicate via quorum sensing and when quorum is reached acyl homoserine lactone is produced. Cells then firmly bind to each other and produce EPS matrix.
What is in the EPS ?
polysaccahrides
nucleic acids
lipids
What happens in the maturation stage ?
Cells grow into a 3D complex and things stick to matrix providing nutrients.
Why do biofilms grow in an oscillate like manor ?
This is due to the cells providing ammonia for cells on the outside to grow. When they get hungry production stops and they use it for themselves
What are the 2 methods of dispersal ?
Passive-Fluid sheer, abrasion
Active- Enyzmic dispersal
Give two examples of enzymes used for dispersal ?
Dispersin B hydrolyses sugars in EPS
NucB is a DNAse that breaks up gram negative and positive biofilms.
Why is difficult to remove biofilms ?
They are 500x more resistant than planktonic cells due to quorum sensing, microscale gradients and due to the dormancy of some cells. Antibiotics can not survive the microscale gradient and can not act on dormant cells.
How can biofilms be prevented ?
Block signals that lead to EPS
Interfere with quorum sensing
Induce dispersal
Produce surfaces such as SLIPS
How can biofilms be disrupted ?
surfactants
metal nanoparticles
What does a virus genome encode for ?
Lysozymes, reverse transcriptase
What is a bacterial cell that contains a prophage called ?
lysogen
What is a cryptic virus ?
This is when a prophage has occurred for too long meaning the integrated DNA cannot remove from the host genome
What is the lamda phage receptor ?
Maltose protein
What is the eclipse phase in a virus growth curve ?
A decrease in viruses present due them being attached to bacteria
How was DNA proven to be genetic material ?
Labelled DNA in virus with 32P and the protein with 35S. The bacteria was then infected. The bacteria was blended to remove virus and centrifuged. The DNA from the bacteria formed a pellet. This DNA contained 32P showing integration.
Give 3 benefits of bacteriophage therapy ?
Amplifies inline with infection
Can penetrate deep wounds
Phage can evolve faster than bacteria
Give 3 negative of bacteriophage therapy.
Scepticism of origin
Too specific
Fear of horizontal spread
What RNA enzyme forms a peptide bond during protein synthesis (peptidyl transferase reaction) ?
Ribozyme
What is the term used to describe a ribosome that can self replicate without actually performing self replication ?
Autocatalytic set
What is luca ?
Last universal common ancestor- likely to be a collection of self replicating virus like particles that are contained in non living compartments.
What did the hydrothermal vents provide for Luca ?
A pore to be contained in
Sulphur compounds which have catalytic properties
Temperature of vents would aid formation
Temperature would also allow fatty acids to form bubbles
Phosphates which could form nucleic acids
What does the pore chemistry of the hydrothermal vents allow ?
Proton gradient
How protocells form ?
Self replicating virus system broke away from pore into fatty acid bubble. They then developed a pyrophosphatase enzyme they could use the proton gradient for energy. This processes happened for archaea and eubacteria
Why are bacteria and archaea small ?
Allows them to have a large SA:VOL ratio allowing them to create energy more efficiently
What is a negative of being small ?
limited genome size
How did eukaryotes form ?
Bacteria ended up inside and archaea in an endosymbiosis event. This bacteria formed into the mitochondria.
What is the benefit of mitochondria ?
Solves the energy problem allowing them to get larger thus allowing a bigger genome ?
What happened after the endosymbiosis event ?
The bacteria moved most of its genes to the archaea. Bacterial genes contain alot of transposons which could disrupt archaea genome.
Why dont bacteria have introns ?
Very high competition in bacteria due to vast population size thus negative selection against gene disrupts such as introns.
What is the solution to introns ?
Sex as this recombines genomes that can produce beneficial mutations.
Splicesomes removes introns but transcription translation happens to fast so development of nucleus separated transcription and translation allowing splicesomes to remove all introns.
What does complexity allow for ?
Parasitic DNA to be silenced via methylation
Destroy parasitic DNA via RNA interference
What type of fungi are found in the rumen ?
Chytridiomycota
What pathogen causes bleaching ?
Vibrio shiloi
Explain the lytic cycle.
Virus attaches to receptor and enters the cell.
The DNA circularises and this DNA acts as a template to make more circularised DNA.
This causes late genes to be expressed and causes the circular DNA to package into virus particles which then lyse the cell and release.
What are the oldest fossils on earth ?
Stramatolites (biofilms)
Similar 16s RNA usually means organisms are ?
phenotypically similar
correlation between 16s RNA sequencing and DNA-DNA similarity shows what ?
2 prokaryotes with less than 97% 16s RNA similarity are unlikely to have more than 70% DNA-DNA similarity ?
What does obligate and facultative mean ?
Obligate= Organism cannot survive without symbiosis Facultative= not dependent on symbiosis
What are the 2 products of anaerobic fermentation of cellulose ?
Volatile fatty acids
Methane
What is the most abundant microorganism in the guts of pigs and rodents ?
lactobacillus reuteri
list the 3 types of nitrogen fixing bacteria.
Rhizobia= Legumes in root nodules Frankias= Actinorihizal plant nodules Cyanobacteria= Fungi, liverwarts and do not form nodules
What occurs between aphids and bacteria ?
Bacteria gain all nutrition from cytoplasm of aphid and release amino acids back into the aphid. this is obligate symbiosis
What does the lokiarchaea contain ?
More eukaryotic like genes than any other.
How do mycorrhizal fungi promote plant growth ?
solubilise phosphorus by releasing organic compounds making phosphates available to plants. Increase SA thus increase water up take
How can you detect if microbes can colonise roots ?
GFP gene
DNA probe/pcr
What is a limitation of polymer inoculants ?
Expensive af
Why was DNA selected for storing RNA code?
DNA is stable
Why do archaea and bacteria appear to have evolved independently ?
Have different:
DNA replication strategies
Biochemical pathways
Cell wall membranes
What is the role conjugative plasmid in triparental mating ?
Contains genes for conjugation and mobilisation allowing the GFP plasmid to be moved to the recipient cell
Give examples of 2 bad microbes.
Candida albicans- dimorphic ascomycetes whcih cause thrush in yeast phase and can produce pseudohyphae which can penetrate host tissue and cause invasive diseases.
Aspergillus flavus- Produces the mycotoxin, aflatoxin which harms animals and humans and can cause cancer.
Give 2 examples of good microbes.
Saccharomyces cerevisae- Used for baking, brewing and studying biological processes in humans.
Penicillium rubens- Produced penicillin
