MODULE 1 - Microbial Evolution and Ecology Flashcards
what were the first organisms on earth and how did they create the environment which allowed for new forms of life?
anaerobic bacteria because there was no oxygen on earth. When these anaerobes developed the ability to use light to produce oxygen earth began to change from an anaerobic to an aerobic environment. Because of this aerobic organisms began to evolve and proliferate
What is LUCA and what can we assume because of it?
LUCA is the last universal common ancestor, and we can assume that if all life is descended from this, then there will be common biochemistry, architecture and mechanisms between all life e.g. storage of info in DNA, most cells work the same way, most life is made up of proteins etc.
what are the major components of all cells and what are these components made of?
the major components of all cells are membranes, nucleic acids (DNA/RNA), proteins and all these are composed of the same basic materials (CHONSP)
what is CHONSP and why are they the most common elements?
Carbon, Hydrogen, Oxygen, Nitrogen, Sulfur, Phosphorous
Because they form covalent bonds which are strong enough to hold long-term structure but can be broken down so that we can recycle our building blocks and they can also attach to multiple accessories
what is the universal solvent which is required for a chemical reaction to take place?
water hence its importance to all organisms
what are the two essential components for life to occur?
CHONSP and water
what was the Miller-Urey experiment?
simulated life with all the key elements and the right conditions inside a chemostat to make more complex structures proving that its possible for life to form from simple compounds. The experiment succeeded in creating many organic molecules, most essential amino acids and most nucleic acid bases. They concluded that the organic building blocks of life were generated in the probable atmosphere of early earth
why were membranes essential for the development of life?
they enclose and compartmentalise things in environments allowing certain experiments to occur shit loads of times so that a one in a million thing will likely occur in one of a million closed environments where the conditions are perfect
they also allow for gradients to let certain things in and out across the membrane
how were the first membranes formed?
they were likely self-assembled and would have been things like coacervates, micelles and liposomes. These would have been semi-permeable membranes and would persist indefinitely without oxygen or decomposers. These became what is called a protocell (closed environment formed by a membrane)
why might RNA have been the first biological molecule?
central dogma of molecular biology in the modern world suggests info flows from DNA to RNA to protein, however this might not have been the case for the first life forms. DNA is missing an oxygen atom making it more stable and less reactive in an aerobic world. But when the world was anaerobic (when life started) stability wasn’t an issue as there was no oxygen so perhaps RNA was the first molecule as we wouldn’t have had to worry about protecting it from oxygen
what are self-catalytic RNA enzymes?
ribozymes work by folding naturally onto themselves and recognising sequences then catalysing a reaction to cleave themselves
why are self-catalytic RNA enzymes/ribozymes the first step in producing life?
because it is the first time we are able to catalyse a reaction ourselves without letting chance rule it i.e we have reproducibility where the same things can happen over and over and we can expect the same outcome
what is the RNA world hypothesis for the origin of life
heating and cooling of the prebiotic soup leads to formation of more complex structure and eventually generates RNA and liposomes
liposomes and RNA combine with some other shit in the soup to form probionts (predecessor to early life)
so far these are all random reactions but once we have a ribozyme these reactions are reproducible allowing for production of RNA and proteins which allows for the first cells
so the RNA world hypothesis is generally centred around the idea that RNA was the first nucleic acid and was the building block which allowed life to occur
outline how ribozymes are formed
random precursors turn into more complex things like nucleotides which can randomly turn into RNAs which can even more rarely turn into ribozymes
once the world transitioned from a chemical world to a biological one, why did the biological one take over?
once you have life you have reproducibility meaning life can take over as it has a blueprint to allow enzymes to produce nucleotides in the same way
what is the selfish gene hypothesis?
all of life exists because our genes want to survive and so make copies of themselves and everything just came about as a side-effect of this
outline the RNA world hypothesis step by step
RNA forms from inorganic substances (proven by miller-urey)
RNA self-replicates via ribozymes
RNA catalyses protein synthesis
Membrane formation changes internal chemistry allowing new functionality
RNA codes both DNA and protein (DNA becomes master template and proteins catalyse cellular activity)
what was the first organism and where did it live?
it must have been prokaryotic, anaerobic and chemolithotrophic
it possibly consumed iron sulfide and hydrogen sulfide and could have used the resulting hydrogen to drive ATPase by splitting it
why is there so much diversity among microorganisms?
gradients, niches and speciation create lots of different habitats
how do microbes create gradients as they grow and what do these gradients allow for?
anaerobes consuming oxygen create areas with less oxygen where anaerobic or fermenting microorganisms may live (oxygen gradient)
microbes create nutrient gradients by consuming certain nutrients resulting in areas with more or less nutrients
microbes create pH gradients through creating waste products or chemical production through quorum sensing
all these gradients allow for diversity
what experimental evidence is there for evolution?
a single E. coli was inoculated and grown on a glucose limited media so as to create an environment which forces competition so that organisms change for an advantage. Through this they managed to produce three different strains from wildtype, each with differences in maximum specific growth rates and in glucose uptake kinetics
wild type could convert glucose to acetate to glycerol
in the new system the three strains of the same organism specialised in consuming either glucose, acetate or glycerol in order to reduce competition
how do we measure diversity in microbial communities in order to classify organisms?
taxonomy
function
metabolism
what classification systems do we have for microbial diversity?
biological
phenetic
cladistic (phylogenetic)
explain the biological classification system
organisms grouped based on ability to breed so this system doesn’t work for microbes since they don’t need a partner
explain the phenetic classification system
organisms grouped based on overall physical similarity (analogous) with no account of evolutionary history (i.e. only measures the end product)
this system is liable to errors due to convergent evolution
it also is ineffective at classifying microbes as they all very similar physically
what is convergent evolution?
leads to the same phenotypes with no shared recent ancestry e.g. bats, birds and insects all have wings
explain the cladistic (phylogenetic) classification system
most commonly used system
grouping organisms based on evolution from a shared ancestor (clade) as determined from a shared trait. Involves making trees from genetic sequences where more similarity between genomes means two organisms are more closely related. The more mutations accumulated indicates two organisms are more distantly related
the issue with this method is that its liable to ignore useful descriptive traits by being too focused on one evolutionary trait or gene
what is a molecular clock and what is the most commonly used molecular clock?
a gene whose DNA sequence can be used as a comparative temporal measure of evolutionary divergence. We are essentially trying to look at mutations in that gene to see how long the species have been separated from each other. This works because there is usually a linear relationship between time and the number of mutations accumulated
most commonly this is the 16s rRNA gene which encodes the RNA sequences within the small subunit of the ribosome because it is universally conserved in every living organism
what are the four key properties of a molecular clock?
found in all living organisms, maintains its function amongst all living organisms (because you want it to be under the same selection pressure), highly conserved with multiple hyper variable regions (conserved regions used as anchors for alignment and hyper variable regions mutate faster which indicate divergence of a species), sufficient length
why is the 16s rRNA gene called the 18s rRNA gene in eukaryotes?
because it is slightly larger and sediments slightly slower
what did Carl Woese figure out about the domains of life and how?
by looking at different sequences as molecular clocks, he kept finding that all life would be grouped into three groups rather than the previously believed five groups
these groups were eukaryotes, eubacteria (new bacteria) and archaebacteria (old bacteria or the base of the tree which everything evolved from)
how have the 16s observations been validated and what has changed?
observations based on 16s have been validated by other genes, by amino acid sequence and by enzyme structure
RNA polymerase structure however has now shown that archaeological are more closely linked with eukarya rather than bacteria suggesting they are not the old base of the tree but are instead completely different organisms
what is the eocyte hypothesis (two domain hypothesis)?
suggests that eukaryotes branch within the archaea meaning that they are just a sub-group of archaea and there are only two domains of life. it implies that the closest relative to eukaryotes is one or all of the TACK archaea
what evidence do we have for the two domain hypothesis?
TACK archaea and eukaryotes share genes no found in other archaea so our ancestors must be TACK archaea
what is a limitation to phylogenetics?
horizontal gene transfer
what are saprophytic fungi?
decomposers which get nutrition through absorptive nutrition (releasing enzymes which break down something and then they suck up all the nutrients). they convert organic material to fungal biomass, carbon dioxide and small molecules such as organic acids
what are mycorrhizal fungi?
mutualistic fungi which colonise plant roots and help solubilise phosphorus and bring soil nutrients to the plant in exchange for carbon from the plant
what are the two types of mycorrhizal fungi?
ectomycorrhizae - grow on the surface of roots and are commonly associated with trees
endomycorrhizae e.g. arbuscular mycorrhizal fungi - grow within the root cells and commonly associated with grasses, crops, vegetables and shrubs
what is the third group of fungi?
pathogens or parasites which cause reduced production or death when they colonise other organisms
what is the problem with species classification?
there is a long-standing failure of biologists to agree on how we should identify species and how we should define the word ‘species’
differing definitions include; taxonomic rank, a group of organisms capable of interbreeding and producing fertile offspring, and a separately evolving lineage that forms a single gene pool
what do we focus on currently to define a species?
a phenotypic assignment (organisms phenotype) and genome similarities (so kind of a hybrid of what it looks like/what it can do and the evolutionary history when comparing genomes)
what is the definition of a prokaryotic species?
a category that circumscribed a genetically coherent group of individual isolates/strains sharing a high degree of similarity in independent features, comparatively tests under highly standardised conditions
what is a bacterial species defined as?
a genomically coherent group of organisms
what is required for a strain to belong to a new species?
OrthoANI (average nucleotide identity) should be about 95% (meaning if they are divergent by 5% or more they are classified as a new species)
if the above classifies it as a new species and you want to describe it as such, you must carry out additional taxonomic research such as phenotypic characterisations and biochemical tests to show new phenotypes. This is because just cause the gene is there doesn’t mean its being used
it must also have a type strain that is live which anyone can obtain for taxonomic study. It must be a pure culture so it can be used as a benchmark when comparing new species
what is the issue with classification of new bacteria?
it is difficult to quantify differences and define a boundary for a species. This is cause its usually not clusters but a gradient of species making it difficult to decide where to draw the line as a new species
what is the practical definition of a prokaryotic species?
a group of strains that are characterised by a certain degree of phenotypic consistency, showing 70% of DNA-DNA binding and over 97% of 16S ribosomal RNA gene-sequence identity
what three things do all classification systems share?
they are arbitrary (no reason why we draw the line at that certain point, just cause it works with what we’ve done previously)
they are anthropocentric (based off classic microbiology which focused on classifying pathogens but doesn’t fit all microbial diversity)
they are rooted in practical necessity (we just make the best choices we can when it comes to classification cause we don’t know any better systems)
what have bacterial species historically been defined by?
growth characteristics (morphology, gram stain, growth medium) (classic species were generally fast growing pathogens)
disease caused
what is DNA-DNA hybridisation?
involves comparing the genome of two organisms to see how well they hybridise to each other. It is considered phenotypic as well as genotypic because if you compare the genome you should be able to predict what the phenotypes are actually going to be
essentially measures the degree of genetic similarity between complete genomes by measuring the amount of heat required to melt the hydrogen bonds between the base pairs that form the links between the two strands of the double helix of duplex DNA
outline the DNA-DNA hybridisation process?
put genomic DNA in tube and add dye, apply heat and eventually DNA melts and releases dye (so we are looking for when the dye disappears)
you apply a second genome to the same mix and melt it again so that it anneals to the other genome strand. You then get a hybrid genome with one strand from one organism and one from the other
any difference in temperature to melt this hybrid suggests there is a difference in similarity of those genomes
the DNA melting temperatures from both organisms can be graphed to show two peaks (one for one organism and one for the other)
