Environmental microbiology Flashcards
(36 cards)
what must microbes interact with
-each other and the environment
-Never get a microbe on its own, always present in a community
-We do not fully understand the nature of the interactions
Quorum sensing – just one type of interaction
what is interaction crucial for
microbial cell survival
where is most research taken upon
pure culture
what do individual cells reproduce to form
clonal populations of individual species
-Clonal populations mix and exchange genetic information with members of the same species and members of different species.
Transformation
Transduction
Conjugation
what do species interact to form
communities
what do communities assemble to form
ecosystems
what is the equation for ecosystems
organisms + environment + activities
what diseases can parasitism cause
plant, animal and microbe-microbe diseases
what does predation cause
Nematophagous fungi and Amoebae
what does mutualism cause
-N-fixation in legumes by Rhizobia
-Fungus-plant mycorrhizae
-Human gut microbiome
-Lichen (fungus-alga) symbiosis
what are examples of mixed cultures in nature
-GI tract
-Soil
-Plant roots (mycorrhizae)
-Teeth
what is involved in the traditional strategy for examining bacteria
-Enrichment
-Isolation in pure culture
-Identification= Biochemical tests, Microscopy and DNA sequencing
Relatively slow process
what is involved in the enrichment strategy
- samples include water, soil, human gut contents
-Enrichment medium formulated to support the growth of the desired organisms AND TO ALLOW SMALL NUMBERS TO BE AMPLIFIED
-Isolation medium formulated to support the growth of the desired organisms
what are the limitations to the enrichment strategy
-Many organisms cannot be cultivated so will not appear on the plates yet they may have an important role in the community
-Choice of growth conditions will influence results (bias) e.g. if the plates are incubated aerobically any obligate anaerobes will not be able to grow.
-the selection strategy will always exclude some organisms
what is a disadvantages to cultivation
bias
what does fluorescent staining use (DAPI)
DAPI- 4’,6-diamidino-2-phenylindole
What is the pros of fluorescent staining
-Stains every cell
-Stains dead cells= Excluded by viable cells
-Easy to see
-Every cell has DNA
what does FISH stand for
FISH= Fluorescent In Situ Hybridisation- This technique gives information on population distribution and community organisation
what does fish do
Permeabilize cells so that the DNA probe can enter Allow it to find its matching sequence on rRNA
- short DNA sequence
-complementary to rRNA
-specific sequence (eg. to genus)
-Florescent tag attached
what can we see in a microscope using FISH
-View cells (in situ) under fluorescent microscope, and see what cells fluoresce, showing they have bound the probe
-Fluorescent DNA probe will bind to rRNA gene in the cells only if it exactly matches complementary sequence of rRNA target region
-Many different coloured fluorophores, so can do simultaneous probes for different genera, families….
What are the strengths of FISH
-Information on physical structure of community
-Flexible format= Change probe to change overall analysis
what are the weaknesses of FISH
-Can be subjective interpretation= Same for all microscopy
-No high throughput
what can we detect when we detect DNA sequences
we can detect the species- 16S rRNA sequences most commonly used- Other targets possible
-This strategy can be applied along with some of our more traditional approaches
what is included in enrichment strategy and DNA sequencing (subculture is selected…)
-sample= water, soil and human gut contents
-Enrichment medium formulated to support the growth of the desired organisms AND TO ALLOW SMALL NUMBERS TO BE AMPLIFIED
-Isolation medium formulated to support the growth of the desired organisms
-Subculture the selected organism to obtain a pure culture.
Extract DNA
Sequence 16S rRNA gene
