Micrb 265 lec 10
What is a microbiome?
A microbiome is the collection of microorganisms that exist in a particular environment.
Why are ocean microbiomes important?
Microbes are responsible for nearly all the energy flux in oceans and are major primary producers through photosynthesis and chemosynthesis.
About how abundant are microbes in seawater?
They can be present in the billions per liter of seawater.
Is the ocean microbiome the same everywhere?
No, it varies with location, depth, season, temperature, pH, and other environmental factors.
What kinds of organisms are found in ocean microbiomes?
Viruses, archaea, bacteria, and microbial eukaryotes are all present.
How does pollution affect the ocean microbiome?
Oil spills and microplastics can change the ocean microbiome, including by providing new surfaces for biofilms.
What organisms dominate the soil microbiome?
Bacteria and fungi dominate the soil microbiome.
What major role do soil microbes play in ecosystems?
They recycle organic matter and drive nutrient cycling.
What kinds of dead material do soil microbes break down?
Dead plants, dead animals, and other organic matter.
Which major nutrient cycles are strongly influenced by soil microbes?
Phosphorus, nitrogen, sulfur, and iron cycling.
How do soil microbes affect soil chemistry?
They change pH, ion concentrations, redox states, and nutrient availability.
What are some important metabolic activities of soil microbes?
Nitrogen fixation, fermentation, methanogenesis, hydrogen oxidation, and many redox transformations.
What greenhouse gases are produced in large amounts by soil microbes?
Methane, carbon dioxide, nitric oxide, and nitrous oxide.
Why are soil microbes important in climate change?
They can release major greenhouse gases, especially when environmental conditions change.
Why is permafrost thaw important microbiologically?
When permafrost thaws, trapped organic matter becomes available to microbes, which then degrade it and release more greenhouse gases.
Why are rice fields an important microbiology example?
Rice fields are major sources of methane emissions because flooded soils support methanogens.
About how much of global methane emissions come from rice fields?
About 5 to 10 percent.
Why do flooded rice fields promote methane production?
Flooded soils become low in oxygen, which favors anaerobic metabolism and methanogen growth.
Where does the carbon for methanogenesis in rice fields come from?
Plants photosynthesize and release organic carbon from their roots.
What happens to root-secreted carbon in rice fields?
A consortium of microorganisms degrades it into compounds such as acetate and hydrogen.
Why are acetate and hydrogen important in rice fields?
They are major substrates used by methanogens to produce methane.
What are cable bacteria?
Filamentous, electrically conductive bacteria in the family Desulfobulbaceae that can transport electrons over centimeter distances.
Why are cable bacteria called cable bacteria?
Because their filaments conduct electrons over long distances like biological electrical cables.
When were cable bacteria discovered?
In 2012.
What is the key metabolism of cable bacteria in the rice field example?
They oxidize hydrogen sulfide deep in the soil, transport the electrons upward, and reduce oxygen near the surface.
What electron donor do cable bacteria use in this example?
Hydrogen sulfide.
What final electron acceptor do cable bacteria use in this example?
Oxygen.
What sulfur product do cable bacteria generate from hydrogen sulfide?
Sulfate.
How do cable bacteria reduce methane emissions in rice fields?
They increase sulfate availability, which helps sulfate-reducing bacteria outcompete microbes that would otherwise provide methanogens with food.
How do sulfate-reducing bacteria help suppress methanogenesis?
They outcompete other microbes for organic carbon, so less acetate and hydrogen are produced for methanogens.
What happens to sulfate after sulfate-reducing bacteria use it?
It is reduced back to hydrogen sulfide, which can feed the cycle again.
What is the main ecological effect of adding cable bacteria to rice soils?
Methane emissions drop strongly because methanogens lose access to enough substrate.
By about how much did cable bacteria reduce methane emissions in the rice pot experiment?
By greater than 90 percent.
Are cable bacteria chemoorganotrophs or chemolithotrophs in this example?
Chemolithotrophs.
Why are cable bacteria chemolithotrophs?
Because they use an inorganic electron donor, hydrogen sulfide.
What is the big idea of bioengineering the soil microbiome in the rice example?
Changing microbial interactions can reduce greenhouse gas emissions.
What are animal microbiomes?
The communities of microbes that live in and on animals.
Do all animals have microbiomes?
Yes, all animals have microbiomes.
What kinds of organisms are found in animal microbiomes?
Archaea, bacteria, fungi, and viruses.
Are animal microbiomes identical across animals?
No, they vary widely among different animals and environments.
What is the bobtail squid microbiome example meant to show?
It shows a highly specific, beneficial interaction between an animal and a bacterial symbiont.
What bacterium lives in symbiosis with the bobtail squid?
Aliivibrio fischeri.
What special structure does the bobtail squid have for A. fischeri?
A light organ.
What does A. fischeri provide to the squid?
Bioluminescence.
Why does the bobtail squid use bacterial light?
To match moonlight from above and hide its silhouette from predators below.
What is this anti-silhouette strategy called?
Counter-illumination.
When does A. fischeri produce light?
When cell density is high.
Why is high cell density important for A. fischeri bioluminescence?
Because one cell makes little light, but many cells together make enough light to matter.
Why is bioluminescence regulated instead of always on?
Because producing light is energetically expensive.
What signaling system controls light production in A. fischeri?
Quorum sensing.
What signaling molecule is used by A. fischeri quorum sensing?
AHL, an acyl-homoserine lactone.
What does LuxI do?
LuxI helps produce the AHL autoinducer.
What does LuxR do?
LuxR binds AHL and activates transcription when AHL concentration is high enough.
What is the lux operon?
A set of co-transcribed genes involved in bioluminescence.
What do luxA and luxB encode?
Luciferase.
What do luxC, luxD, and luxE help produce?
Aldehyde substrates used for the light-producing reaction.
What does luciferase do?
It catalyzes the reaction that produces light.
What other molecules are needed for the luciferase reaction?
Oxygen and FMNH2, along with the aldehyde substrate.
What does the squid provide to A. fischeri?
Sugars and amino acids that help the bacteria grow.
Why does A. fischeri benefit from living in the squid?
It gets a nutrient-rich environment to grow in.
Why does the squid benefit from A. fischeri?
It gets controlled bioluminescence for counter-illumination.
Is the squid-A. fischeri interaction mutualism or cooperation?
Cooperation, because both benefit but they can live without each other.
Why is the squid-A. fischeri relationship not strict mutualism in this lecture’s framing?
Because both partners can survive separately even though both benefit when together.
How are baby squid colonized by A. fischeri?
Hatchlings acquire the bacteria from the environment.
Why is specific colonization important for the squid?
The squid wants beneficial light-producing bacteria, not random microbes.
How do A. fischeri reach the light organ?
They use flagella to swim through ducts toward it.
How does the squid help exclude non-motile bacteria?
It flushes the ducts, so only motile bacteria can swim against the flow.
What antimicrobial enzyme does the squid use in the ducts?
Halide peroxidase.
What does halide peroxidase use?
Hydrogen peroxide to oxidize halides.
How does A. fischeri resist this antimicrobial defense?
It has a periplasmic catalase that helps eliminate hydrogen peroxide.
What other antimicrobial molecule does the squid use in the light organ?
Nitric oxide.
How does A. fischeri survive nitric oxide exposure?
It produces nitric-oxide-inactivating enzymes.
What is the main lesson from the squid example?
Microbiome colonization can be highly selective and based on both host defenses and microbial traits.
What is the termite-Trychonympha example meant to show?
Another beneficial symbiosis in which microbes help the host use food it otherwise could not digest well.
What is the human microbiome?
The combined microbes living in and on humans.
Where is the human microbiome found?
On the skin and in places like the mouth, gut, and genital tract.
How has the human microbiome often been identified historically?
By sequencing the 16S rRNA gene.
What is 16S rRNA used for in microbiome studies?
To identify and classify bacteria taxonomically.
Is the human microbiome the same in every person?
No, it is unique to each individual.
When is the human microbiome generally established?
Largely within the first three years of life.
Is the human microbiome stable?
It is generally stable, though it can change with disturbances.
What kinds of disturbances can change the human microbiome?
Antibiotics, infections, and other health or environmental changes.
Does the microbiome always stay changed after a disturbance?
Often it tends to return toward its prior state after the disturbance is removed.
Why is the human microbiome important?
It is required for normal human health.
Do different body sites have different microbiomes?
Yes, different body sites are dominated by different groups of organisms.
What kind of bacteria commonly dominate skin in the lecture example?
Propionibacterium.
What kind of bacteria are common in saliva in the lecture example?
Streptococcus is especially common.
What group commonly dominates the female urogenital tract in the lecture example?
Lactobacillus.
What group commonly dominates the gut in the lecture example?
Bacteroidetes.
Do the most abundant organisms always explain the most important functions?
No, less abundant organisms can also be very important functionally.
What does homeostasis mean in the context of the microbiome?
A relatively stable balanced relationship between host and microbes.
How does the microbiome help resist pathogens?
A stable microbiome can resist colonization by outside microbes.
What did the twin fermented milk study show?
Even after weeks of consuming probiotic organisms, the gut microbiome composition stayed largely unchanged.
What is the main lesson from the probiotic twin study?
The microbiome is often quite stable and not easily displaced.
Does no microbiome composition change mean the probiotic did nothing?
No, it may still have had metabolic effects even if community composition looked stable.
What factors influence a person’s microbiome?
Genetics, environment, diet, and early-life exposures.
How can birth mode affect the initial microbiome?
Vaginally delivered babies initially resemble the mother’s vaginal microbiome more, while C-section babies resemble the mother’s skin microbiome more.
What does the birth-mode example show?
Initial microbiome assembly depends strongly on early environmental exposure.
What is metagenomics?
The study of all genes present in an environmental sample, regardless of which organism they came from.
What is functional genomics in microbiome research?
Looking at what genes are present and what functions the community can perform, rather than just which taxa are there.