week 8 Flashcards
Cornelius Van Niel
-Every molecule in nature can be used as source of carbon or energy by a microorganism
-Microbes found in every environment
Marine and Aquatic microbes, what are primary producers
Oceans + freshwater ecosystems support vast numbers of microbes
Bacteria + algae are primary producers, drivers of entire ecosystem activity
Regions of marine habitat
○ 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
thermocline
after certain depth, temperature becomes constant (around 4 degrees)
Holgar Jannasch discovered what
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
Tara Oceans and Tara Pacific
○ Multi-national projects that collected samples across oceans
§ Findings: in upper ocean layers, temperatures is main determinant of microbiome composition
Mutualism within ocean microbiome-an example
○ 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
Benthos: open ocean floor
○ 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
Soil
* Complex mixture of decaying organic and mineral matter
Levels:
○ 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
microbes found in soil
○ 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
Each particle in soil supports miniature colonies, biofilms, and filaments of bacteria and fungi
○ Humic substances (humus): hold moisture and soil together, product of digestion
○ Bacterial colonies
○ Fungi
○ Fungal filaments
Microbes in rhizosphere helps protect plants from pathogens
○ May fix nitrogen (diazotrophs)
They feed on nutrients provided by the plant in return
Ectomycorrhizae
○ 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
Endomycorrihzae
○ 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
Plant endophytic communities
- 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
- Specialist endophytic relationship is plant roots ad rhizobia, group of specialized bacteria
The Human Microbiome Microbial hitchhikers
○ Majority are bacterial (except for bacteriophage)
○ Most are harmless
Many beneficial to host
The Human Microbiome Microbial invaders on human body
○ We have barriers
○ Non-specific defences
Adaptive and non-adaptive immune defences
commensal organism
non-sterile body sites where microbes are normally found
The consortium of colonizing microbes has been given name human microbiota or microbiome
○ Microbiota: indicates cell consortium
Microbiome: indicates the genetic potential of the consortium
skin microbiome
- 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
mouth microbiome
- 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
- As teeth emerge, other bacteria grows
Nose and oropharynx (back of throat)
- 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
- Nasopharynx populated by Staphylococcus aereus and Staph. Epidermidis
lung microbiome
- 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
- Once thought to be sterile
urogenital tract
- 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
- The urethra contains S. epidermidis and some members of the Enterobacteriaceae
