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CELS Microbiology > Microbes > Flashcards

Flashcards in Microbes Deck (54):

what 3 things do microbes need to grow

carbon source, energy source and reducing power (electrons)



energy = light, carbon = CO2



energy = chemical compounds, carbon = CO2



energy = light, carbon = organic compounds



energy = chemical compounds, carbon = organic compounds


phases of prokaryote growth in a ‘closed’ batch culture system

Lag phase - time is required to get biosynthetic reactions running. Exponential phase - cells are actively dividing through binary fission and nothing is limiting growth. Stationary phase - resources run out so cells stop multiplying and cryptic growth takes place (when they survive by consuming other dead cells). Death phase - 90% of population dies and waste and toxins accumulate


contradictions to bacteria norms

cooperative feeding, form fruiting body of many cells in unfavourable conditions, contain complex internal organs



an experimental system that simulates real like conditions as closely as possible


enrichment culture

providing temp and chemical conditions in lab that encourage growth of specific organisms


what does winogradsky column require

water, light, sediment, CaCO3 and CaSO4 and cellulose


order of layers of winogradsky column

cyanobacteria, colourless sulfur bacteria, purple sulfur bacteria, green sulfur bacteria, sulfate-reducing bacteria, cellulose degrading



oxygenic, photoautotroph, e- donor = H2O, C source = CO2, acyclic phosphorylation


colourless sulfur bacteria

anoxygenic, chemoautotroph, e- donor = H2S, carbon source = CO2


purple sulfur bacteria

anoxygenic, photoautotroph, e- donor = H2S, carbon source = CO2, cyclic phosphorylating in anoxygenic photosynthesis


green sulfur bacteria

anoxygenic, photoautotroph, e- donor = H2S, carbon source = CO2, cyclic phosphorylating in anoxygenic photosynthesis


sulfate-reducing bacteria

chemoheterotroph, e- donor = sulfate, carbon source = organic carbon, products = H2S and CO2, cause high gradient of H2S at bottom of column


cellulose-degrading bacteria

chemoheterotroph, e- donor = organic carbon, carbon source = glucose/pyruvate, products = acidic so low pH at bottom


what causes high sulfur conc at bottom of column

sulfate reducing bacteria producing sulfur


what causes high O2 conc at top of column

acyclic phosphorylation in oxygenic photosynthesis


how do different layers overcome problem of lack of light

adapt to absorb different wavelengths of light


anoxygenic photosynthesis

photosynthesis without production of of oxygen


oxygenic photosynthesis

photosynthesis with production of oxygen


microbial ecology

study of interrelationships between organisms and their environment


role of heterotrophs in the carbon cycle

heterotrophic microorganisms are the primary biomass recyclers on the planet


primary treatment in water treatment

  1. Purely physical processes
  2. 60% contaminants removed
  3. Waste water is pumped through a sieve to remove indestructibles
  4. Moves into sedimentation tank
    • Sludge at the bottom - incinerated
    • Water - ocean


secondary treatment in water treatment

  • Microbes
  • 95% of contaminants removed- used on top of primary treatment
  • Instead of water being pumped into the ocean straight away, moved through aeration tankà aerobic microbes decompose
  • Liquid then move into settling tanksà flocs (activated sludge) form and then moves back into aeration tank
  • Residual sludgeà anoxic sludge digesterà anaerobic microbes decompose sludge


tertiary treatment of water

  • anything beyond secondary
  • involves chemical treatment e.g. UV, chlorine


objectives of water treatment

  • kill pathogens in water
  • reduce organic, nitrogen and phosphorous load
  • produce a disposable effluent without causing harm to the surrounding environment


biochemical oxygen demand

  • relative amount of dissolved oxygen consumed by microbes to aerobically decompose all organic material in a water sample
  • polluted water has higher BDO than pure water bc more organics present so more O2 required to break down


what is a dead zone + examples

  • When the oxygen concentration in water has fallen so low animals can no longer survive
  • More likely to occur at higher temperatures
  • Dead zone examples: Black sea, Gulf of Mexico


how are microbes useful for production of biofuels

  • Microbes are essential for the production of fuels- they are required to ferment organic products into fuel forms
  • Clostridium magnum is able to metabolise gaseous substrates including H2, CO and CO2


what is remediation

use of microbes to clean up toxic wastes - can repair many environmental problems e.g. oil spills


human microbiome project method

  • Used culture dependent methods of microbial community characterisation (16s and metagenomics) as well as whole genome sequencing of individual bacterial species
  • Emphasis on oral, skin, vagina, gut and nasal/lung


goals of HMP

  1. To develop a reference set of microbial genome sequences and to perform preliminary characterisation of the human microbiome
  2. To explore the relationship between disease and changes in the human microbiome
  3. To develop new technologies and tolls for computational analysis
  4. To establish a resource repository
  5. To study the ethical, legal, and social implications of human microbiome research


HMP findings

  • gut has highest density of microbes
  • strong niche specialisation both within and among individuals
  • at a species/strain level, microbiota of an indivdual is unique
  • community can change but the functions do not change as much
  • Observed variations in both pathways and microbes changed with clinical metadata along ethnic/racial differences

Four types of microbes dominate:

  • Firmicutes
  • Bacteroidetes
  • Actinobacteria
  • Proteobacteria


human gut microflora

  • Bifidobacterium
  • E. Coli
  • Lactobacilli
  • Campylobacter
  • E. Faecaus
  • Clostridium difficile

these are non-pathogenic


effect of microbiota on metabolism

  • When we eat, we feed the microbes and in return they feed us
  • Gut microbes in obese state may have increased capacity to harvest energy= more calories
  • Original gut bacteria linked with obesity research carried out on mice; found that germ-free mice are protected from obesity
  • Therefore, increased obesity/adiposity can be seen as a transmissible trait


what is functional food

Foods that claim to have a health promoting benefit, which is beyond simply nutrition


what is a probiotic + example

  • Probiotics- contain live microorganism culture, and when taken can have a health benefit
  • e.g.  yoghurt contains lactic acid bacteria


what are prebiotics and example

  • Prebiotics - an ingredient that beneficially nourishes the good bacteria already in the large bowel or colon
  • e.g. plant fibre in bananas


fecal transplants: method and risks

  • Method: highly successful treatment for multiple recurrences of Clostridium difficile infection (CDI)
  • risk: Diseases, complications due to procedures, identification of correct donors


describe symbiotic, mutually-dependent relationship between ruminants and microbes

  • The rumen harbours microbes that feed the animal, animal feeds the microbes in the rumen in return- therefore their relationship is symbiotic and mutualistic


importance of rumen microbes in ruminant nutrition

  • Rumen microbes break down food into digestible proteins and vitamins that the animal can absorb


end products of rumen fermentation and use

  • End-products of rumen fermentation= H2 and CO2
  • These are used by methanogens to produce methane


what is syntrophy

  • metabolic interaction between dependent microbial partners
  • e.g. Ruminococcus albus produces H2 and methanogens use H2 - allows fermentation to proceed


importance of methanogens in rumen fermentation

  • important for rumen fermentation as they keep it directed towards short chain volatile fatty acids like acetate
  • without methanogens H2 accumulates and inhibits fermentation (as partial pressure of H2 builds up, oxidation or NADH + H+ is impaired) = animal malnutrition


methane production: problems and solutions

  • Is a greenhouse gas, and contributes massively to global warming
  • Strategies dealing with methane: feed additives, direct fed microbials, enzymes, farm systems, protozoa and phage, animal genetics, vaccination against methanogens, chemical inhibitors (UoO research)


properties of bacterial genome

  1. A single circular chromosome
  2. No nuclear membrane, however the chromosome is restricted to a defined region of the cell known as the nucleoid
  3. Other small circular self-replicating DNA molecules can be found in the cytosol (separate to the main chromosome)- known as plasmids


horizontal gene transfer definition and 3 methods

gene transfer directly from one organism to another (can be same or different species)

  1. transformation
  2. conjugation
  3. transduction



  • Transformation involves uptake of short fragments of naked DNA by naturally transforming bacteria
  • Shown in Griffith’s experiment
  • Plasma and DNA can be transmitted



  • Involves the transfer of DNA material via a sexual pilus to any species, and requires cell to cell contact
  • Only plasmid can be transmitted
  • Anywhere a sexual pili can be attached to, the genes can be transferred to



  • Involves the transfer of DNA from one bacterium to another via bacteriophages
  • Sometimes during the lytic cycle, when the new bacteriophage is assembling, the plasmid inserts into the capsid instead of the bacteriophage DNA
  • DNA and plasmid can be transmitted


key feature of lytic cycle

ends in host cell death


lysogenic cycle

host cell and phage form a lysogenic relationship (formation of prophage)