Download Study Questions and Answers for Microbial Ecology Lecture 1. What

Study Questions and Answers for Microbial Ecology Lecture
1. What is a biogeochemical cycle? How can prokaryotes influence biogeochemical
cycles?
Biological, geological, and chemical processes that work together to interconvert
an element into various chemical forms (controls the fate of an element), which
influences how an element is transported through the environment. Prokaryotes
carry out metabolic reactions that can alter the fate of an element. Prokaryotes
are the “bio” part of biogeochemical cycle.
2. What is meant by culture-dependent approaches to microbial ecology? How about
culture-independent approaches? Which approach is better?
Culture-dependent approaches rely on growing prokaryotes.
Cultureindependent methods rely on molecular methods to study microbes within their
environments.
3. What is FISH? Is FISH a culture-dependent or independent method?
FISH stands for fluorescent in situ hybridization. It is a culture-independent
technique that is used to visualize certain types of prokaryotes within a sample. A
fluorescent probe is used that targets the 16S rRNA gene of a prok.. The probe
can be specific for one type of microbe like bacteria or archaea. The probe can
be “universal” useful for detecting all prokaryotes. Only the cells with the FISH
probe will fluoresce under the epifluorescent microscope. You can count
prokaryotes using FISH.
4. How does total bacterial counts done with a microscope differ from enumeration by
viable plate counts?
Viable plates will always underestimate the total number bacteria within a
particular sample. This is because we can not meet the nutritional requirements
of ever prok in the sample, this leads to culture bias—only those organisms that
can grow on the particular medium will grow. The other organisms will not. The
fast growers will out-compete the slow growers too. Remember earlier lectures
on this?
5. What are the four approaches to microbial ecology presented in the lecture? Be able
to articulate and give examples for each approach.
Enumeration, microcosm
metagenomics.
studies,
16S
rRNA/functional
gene
analyses,
6. You did PCR for the 16S rRNA gene from 10 soil samples and got a 1500 bp band on
a gel, describe how you could determine the genetic diversity of the DNA in the PCR
tube by clone library and by DGGE. Which method would be faster? Which method
would give you more conclusive results about the types of organisms in the soil
samples?
Clone library: ligate PCR product to a plasmid. Transform into E. coli.
Sequence a bunch of clones. Make phylogenetic tree to determine genetic
diversity. This is very time consuming and not amenable to doing lots of samples
at once.
DGGE: Analyze your PCR product by DGGE. The DNA will separate based on
their GC content. We can easily run all 10 samples on one gel. More bands in a
lane on the gel indicate greater diversity. We still do not know what types of
organisms are in the soil samples unless we cut out bands and sequence them.
DGGE is faster. Clone libraries are time consuming.
Clone library would get you conclusive results about what types of organisms in
the sample.
7. What is metagenomics? Why is this a culture-independent approach used in microbial
ecology studies?
In metagenomics the approach is to determine the sequence of DNA isolated from
an environment. The hope is that you will discover novel organisms and genes
that could not be determined using culture-dependent methods. In metagenomics,
you don’t need to grow any organisms. You just extract the DNA and use highthroughput sequencing facilities to determine the DNA sequence.
8. How does the gut microbiota affect human health? This overlaps with some of
Professor Yildiz’s lecture?
Helps us harvest energy from food; make vitamins; drug and toxin metabolism (this
could actually be harmful); alters immune function both good and bad ways; might
influence cardiac function and behavior; protection from pathogenic bacteria.
9. How does the gut microbiome in animals differ from that of ocean water?
It appears that the microbiome within animals have more genes for catabolic
reactions like carbohydrate and glycan degradation than ocean water. This
makes sense because the environment of a gut has lots of carbs and fiber
compared to ocean water..