week 8

Question 1

Cornelius Van Niel

Answer 1

-Every molecule in nature can be used as source of carbon or energy by a microorganism
-Microbes found in every environment

Question 2

Marine and Aquatic microbes, what are primary producers

Answer 2

Oceans + freshwater ecosystems support vast numbers of microbes

Bacteria + algae are primary producers, drivers of entire ecosystem activity

Question 3

Regions of marine habitat

Answer 3

○ Pelagic zone: into ocean
○ Coastal Shelf: where land meets ocean
○ Neuston: surface of ocean, very small (highest [microbe])
○ Euphotic zone: middle area of ocean closer to coast to where light can penetrate
○ Aphotic zone: where light cannot penetrate
Benthos: depth of the sea

Question 4

thermocline

Answer 4

after certain depth, temperature becomes constant (around 4 degrees)

Question 5

Holgar Jannasch discovered what

Answer 5

unculturable marine bacteria
○ Could see more ocean microbes under microscopes than on plates
○ Ocean microbes are oligotrophic (hard to culture)
○ Demonstrated that decomposition of material in depths of ocean takes up to 100x longer than on land

Question 6

Tara Oceans and Tara Pacific

Answer 6

○ Multi-national projects that collected samples across oceans
§ Findings: in upper ocean layers, temperatures is main determinant of microbiome composition

Question 7

Mutualism within ocean microbiome-an example

Answer 7

○ Prochlorococcus most abundant bacterial genus on Earth, proved hard to culture
○ Reason: formed symbiotic relationship with helper bacterium called Alteromonas
§ Produces catalase, helps remove H2O2 (toxic by-product of Prochlorococcus photosynthesis)
§ Prochlorococcus lost ability to make its own catalase
○ High CO2 concentrations may harm this symbiosis by reducing the efficiency of the catalase

Question 8

Benthos: open ocean floor

Answer 8

○ Extreme pressure (barophiles), cold (psychrophiles), and nutrient depletion (oligotrophs)
○ These microbes have slow metabolic rates and high concentrations of heavy metal resistance genes

Hydrothermal vent system: fissure in earth allowing heated material to meet water

Question 9

Soil
* Complex mixture of decaying organic and mineral matter
Levels:

Answer 9

○ Organic horizon: organic matter decomposing
○ Aerated horizon: decomposed organic particles
○ Eluviated Horizon: insoluble particles leached by rainwater
○ B horizon: clay and minerals
○ Water table: water pooled
○ Water-saturated horizon: organic matter, clay, minerals leached
○ Bedrock

Question 10

microbes found in soil

Answer 10

○ Fungi, actinomycetes, slime molds found above A horizon
○ Fungi (mycorrhizae), aerobic bacterial biofilms and bacteria filaments found above water tables
○ Prokaryotic domain (chemolithotrophs, anaerobic heterotrophs) found in water-saturated
Edoliths (methanogens and chemolithotrophs) found in bedrock

Question 11

Each particle in soil supports miniature colonies, biofilms, and filaments of bacteria and fungi

Answer 11

○ Humic substances (humus): hold moisture and soil together, product of digestion
○ Bacterial colonies
○ Fungi
○ Fungal filaments

Question 12

Microbes in rhizosphere helps protect plants from pathogens

Answer 12

○ May fix nitrogen (diazotrophs)
They feed on nutrients provided by the plant in return

Question 13

Ectomycorrhizae

Answer 13

○ Ecto-outside
○ Colonize the rhizoplane
○ Form a thick, protective mantle around the root
○ Extend outwards to absorb nutrients
○ Allows plants that are distant to each other to connect
Good for agriculture because in crops they help take up more nutrients

Question 14

Endomycorrihzae

Answer 14

○ Endo-inside
○ Fungi invade root cells, forming arbuscules
○ Grows inside plant cells
○ Are dependent on their host
○ Lack sexual cycles
○ Exist entirely underground
Relatively small number of endomycorrhizae species, but are extremely important to ecosystem

Question 15

Plant endophytic communities

Answer 15

• Endophytes grow within plant tissues
  ○ Can be bacterial or fungal
  
  • Specialist endophytic relationship is plant roots ad rhizobia, group of specialized bacteria
    ○ Elaborate partnership where bacterial cells adapt to life within nodules to forma. Nitrogen fixing organ for the host plant
    Nodules are pink-leghemoglobin

Question 16

The Human Microbiome Microbial hitchhikers

Answer 16

○ Majority are bacterial (except for bacteriophage)
○ Most are harmless
Many beneficial to host

Question 17

The Human Microbiome Microbial invaders on human body

Answer 17

○ We have barriers
○ Non-specific defences
Adaptive and non-adaptive immune defences

Question 18

commensal organism

Answer 18

non-sterile body sites where microbes are normally found

Question 19

The consortium of colonizing microbes has been given name human microbiota or microbiome

Answer 19

○ Microbiota: indicates cell consortium
Microbiome: indicates the genetic potential of the consortium

Question 20

skin microbiome

Answer 20

• Difficult to colonize (dry, acidic, protective oils)
  
  • Constantly renewed, multiple layers
  • More microbe sin moist areas (ears, armpits etc.)
  • Mostly gram + bacteria
    ○ More resistant to salt and dryness
    ○ Staphylococcus epidermidis
    ○ Cutibacterium acnes
    § Degrades skin oils
    § Inflames sebaceous glands

Question 21

mouth microbiome

Answer 21

• Infant’s mouth colonized by
  ○ Non-pathogenic Neisseria ssp. (gram-negative cocci)
  ○ Streptococcus (gram + cocci), Lactobacillus ssp. (gram positive rods)
  
  • As teeth emerge, other bacteria grows
    ○ E.g. Prevotella and Fusobacterium ssp.: between gums and teeth
    ○ E.g. Streptococcus mutans: tooth enamel Different strains of streptococcus mutans do not exist at the same time
    ○ Many oral bacteria are strict anaerobes- they make biofilms where anaerobes are, which exclude oxygen from mixing populations of cells, and this causes plaque on teeth
  • Oral and respiratory tract are most common infection site for humans
    ○ Breathing in air (non-sterile)
    Eating and drinking

Question 22

Nose and oropharynx (back of throat)

Answer 22

• Nostrils and nasopharynx dominated by Bacillota and Actinomycetota
  ○ Usually one species or genus dominate another
  
  • Nasopharynx populated by Staphylococcus aereus and Staph. Epidermidis
    ○ Some S. epidermis strains are better at keeping us healthy
    Oropharynx-similar composition of microbes to saliva

Question 23

lung microbiome

Answer 23

• Approx surface area of 75m2
  
  • Once thought to be sterile
    ○ Community of microbes present
    ○ Mainly anaerobes (microbes in lungs are resisting in forms of biofilms)
    ○ Only recently appreciated because healthy lungs analyzations are not ethically okay to be put under trial, only harmed lungs were examined
  • Microbiota in diseases such as COPD, cystic fibrosis + asthma seems to be distinct for each condition and different to that of a healthy lung
    The mucocilliatory escalator (tiny hairs) constantly sweeps inhaled particles up towards throat

Question 24

urogenital tract

Answer 24

• The kidneys and urinary bladder are normally sterile
  
  • The urethra contains S. epidermidis and some members of the Enterobacteriaceae
    ○ Can cause UTIs
  • Composition of the vaginal microbiota changes with menstrual cycle
    ○ Rare example of a microbial community where diversity in the community is not considered a good thing
  • Acidic secretions favours Lactobacillus spp. (producing lactic acid, perpetuating environment), more likely to resist attacks of STIs and viruses from acidic environment
    Lactobacillus spp. Presence appears to protect from STIs and improve reproductive success

Question 25

stomach microbiome

Answer 25

• Has low pH (highly acidic)
  
  • Few microbes survive
  • Helicobacter pylori
    ○ Survives at pH 1
    ○ Has flagella
    ○ Has low tolerance to acidity, but has enzyme that converts urea to ammonia, so surrounding it becomes neutral
    ○ Burrows into protective mucus
    ○ Can cause gastric ulcers
  • Decreased stomach acidity-hypochlorydia
    ○ Caused by malnourishment
    ○ Also caused deliberately Ex through PPI use
    Can lead to intestinal disease (stomach acid is key defensive barrier)

Question 26

intestine microbiome

Answer 26

• Lower intestine contains 10 9 -10 11 per gm of feces
  ○ 1000 anaerobes: 1 facultative anaerobe
  
  • Most important microbial ecosystem in human body lives in colon
  • Does as much metabolic work as liver
    Most human microbiome research focuses on gut microbiome