Microbes

Question 1

what 3 things do microbes need to grow

Answer 1

carbon source, energy source and reducing power (electrons)

Question 2

photoautotroph

Answer 2

energy = light, carbon = CO2

Question 3

chemoautotroph

Answer 3

energy = chemical compounds, carbon = CO2

Question 4

photoheterotroph

Answer 4

energy = light, carbon = organic compounds

Question 5

chemoheterotroph

Answer 5

energy = chemical compounds, carbon = organic compounds

Question 6

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

Answer 6

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

Question 7

contradictions to bacteria norms

Answer 7

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

Question 8

mesocosm

Answer 8

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

Question 9

enrichment culture

Answer 9

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

Question 10

what does winogradsky column require

Answer 10

water, light, sediment, CaCO3 and CaSO4 and cellulose

Question 11

order of layers of winogradsky column

Answer 11

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

Question 12

cyanobacteria

Answer 12

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

Question 13

colourless sulfur bacteria

Answer 13

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

Question 14

purple sulfur bacteria

Answer 14

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

Question 15

green sulfur bacteria

Answer 15

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

Question 16

sulfate-reducing bacteria

Answer 16

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

Question 17

cellulose-degrading bacteria

Answer 17

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

Question 18

what causes high sulfur conc at bottom of column

Answer 18

sulfate reducing bacteria producing sulfur

Question 19

what causes high O2 conc at top of column

Answer 19

acyclic phosphorylation in oxygenic photosynthesis

Question 20

how do different layers overcome problem of lack of light

Answer 20

adapt to absorb different wavelengths of light

Question 21

anoxygenic photosynthesis

Answer 21

photosynthesis without production of of oxygen

Question 22

oxygenic photosynthesis

Answer 22

photosynthesis with production of oxygen

Question 23

microbial ecology

Answer 23

study of interrelationships between organisms and their environment

Question 24

role of heterotrophs in the carbon cycle

Answer 24

heterotrophic microorganisms are the primary biomass recyclers on the planet

Question 25

primary treatment in water treatment

Answer 25

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

Question 26

secondary treatment in water treatment

Answer 26

* 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

Question 27

tertiary treatment of water

Answer 27

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

Question 28

objectives of water treatment

Answer 28

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

Question 29

biochemical oxygen demand

Answer 29

* 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

Question 30

what is a dead zone + examples

Answer 30

* 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

Question 31

how are microbes useful for production of biofuels

Answer 31

* 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

Question 32

what is remediation

Answer 32

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

Question 33

human microbiome project method

Answer 33

* 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

Question 34

goals of HMP

Answer 34

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

Question 35

HMP findings

Answer 35

* 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

Question 36

human gut microflora

Answer 36

* Bifidobacterium * E. Coli * Lactobacilli * Campylobacter * E. Faecaus * Clostridium difficile these are non-pathogenic

Question 37

effect of microbiota on metabolism

Answer 37

* 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

Question 38

what is functional food

Answer 38

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

Question 39

what is a probiotic + example

Answer 39

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

Question 40

what are prebiotics and example

Answer 40

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

Question 41

fecal transplants: method and risks

Answer 41

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

Question 42

describe symbiotic, mutually-dependent relationship between ruminants and microbes

Answer 42

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

Question 43

importance of rumen microbes in ruminant nutrition

Answer 43

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

Question 44

end products of rumen fermentation and use

Answer 44

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

Question 45

what is syntrophy

Answer 45

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

Question 46

importance of methanogens in rumen fermentation

Answer 46

* 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

Question 47

methane production: problems and solutions

Answer 47

* 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)

Question 48

properties of bacterial genome

Answer 48

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

Question 49

horizontal gene transfer definition and 3 methods

Answer 49

gene transfer directly from one organism to another (can be same or different species) 1. transformation 2. conjugation 3. transduction

Question 50

transformation

Answer 50

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

Question 51

conjugation

Answer 51

* 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

Question 52

transduction

Answer 52

* 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

Question 53

key feature of lytic cycle

Answer 53

ends in host cell death

Question 54

lysogenic cycle

Answer 54

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