Chapter 23: Microbial Symbioses with Microbes, Plants, and Animals

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Have you ever just stopped and thought about how life on this planet, how it does all the amazing things it does?

You know, you look closer and closer and there are these tiny little partnerships that are the real key.

Like these relationships that are happening all the time, but we just never really think about them.

Welcome to the deep dive.

Today we are going all in on this fascinating world of symbiosis.

We're talking symbiosis between microbes and their hosts.

That's the title of the chapter that we're diving into today.

And basically we want to pull out the coolest, most important stuff about how these microbes are working together.

Now, when we say symbiosis, just to be clear, we're talking about this close relationship between two or more different types of organisms, right?

Yeah, that's it.

And what you start to realize is that these microbial partnerships, they're not just some like odd thing that happens in biology.

They are totally fundamental to how the whole planet works.

Like they drive the big nutrient cycles and even the tiny details of how individual organisms do their thing.

And we're going to be looking at the three main types of symbiosis, mutualistic where both partners benefit,

parasitic where one benefits at the expense of the other and commensalistic where one benefits and the other is kind of just there.

Okay, so let's jump right in.

And I thought it was really interesting how the chapter starts with symbiosis that are happening between microbes themselves, even before we get to like plants and animals.

And the first one that really caught my eye was lichens.

I mean, everyone's seen lichens, right?

That stuff growing on rocks and trees.

But it turns out that's not just one organism.

Right.

A lichen is like a perfect example of mutualism.

Usually it's a partnership between a fungus often from this group called Ascomycetes and a photobiont.

And the photobiont can be a green alga or a cyanobacterium.

So it's either a type of algae or a bacterium that can do photosynthesis, you know, use sunlight to make food.

So the photobiont is the one making the food.

What does the fungus do in this partnership?

Well, think of the fungus as the builder and protector.

It creates this structure called the thallus, which is basically the lichen's body.

That's what gives the lichen its shape and protects the photobiont inside.

The fungus also helps to absorb water and can even release acids that break down rocks, making the minerals in the rock available for both partners.

So it's like a pretty fair trade -off, but the chapter mentions that there's actually more to it than just two organisms, right?

It can get more complex.

Yeah.

It's really cool.

We're learning more and more that a single lichen can actually be like a mini ecosystem.

You can have several different photobionts and there might be other fungi and bacteria hanging out in there too.

So what looks like one simple thing is actually this whole community.

Wow, that's wild.

Okay, moving from dry land to water.

The chapter talks about these things called freshwater consortia.

So again, it's microbes teaming up, but this time it's happening in lakes and ponds.

Yeah, exactly.

These are basically microbial teams in freshwater environments.

And one of the best studied examples is chlorochromatium aggregatum.

So what you have here is these green sulfur bacteria, and they're the phototrophs, meaning they use light for energy, but they can't move on their own.

They're stuck and they attach themselves to these other bacteria that can move, but don't use light for energy.

So that division of labor again, one makes the food and the other gets them around.

Yeah, that's the idea.

The green sulfur bacterium does photosynthesis and the other bacterium acts like a little taxi, moving them to the best spots for light and nutrients.

The thing is, these bacteria are often completely dependent on each other.

They can't live without each other.

And we know that there's this direct flow of nutrients going from the photosynthesizer to the mover.

So it's like this tiny little food truck with its own built -in driver.

And the chapter says that molecular studies are starting to show the details of how their metabolisms are connected, how they evolve together.

Right, like we're looking at their genes and their biochemistry and seeing how their processes are linked up at a molecular level.

And then there's this other crazy mechanism that the chapter talks about.

It's called direct interspecies electron transfer, or DIET.

This is basically where microbes can just like hand off electrons to each other directly.

Oh, that's like a whole electrical grid happening on a microscopic scale.

What kind of microbes do that?

A really good example is these anaerobic methane oxidizing archaea.

We call them ANME archaea.

And they work together with sulfate -reducing bacteria.

They live in environments without oxygen.

So the archaea break down methane and the bacteria use the electrons from that breakdown process.

It's a super efficient way for them to share energy.

I am already getting a sense of how connected this whole microbial world is.

OK, so let's move on to plants now.

The chapter goes into some really important plant microbe symbiosis, starting with those amazing root nodules you find on legumes.

Oh, yeah, root nodules are essential.

I mean, they are a major reason why we have so much food on the planet.

These nodules are like little bumps on the roots of plants like beans and peas and clover.

And they're formed by these bacteria called rhizobia.

Basically, rhizobia are like tiny nitrogen factories that the plant sets up right in its roots.

And nitrogen is so important because even though there's tons of nitrogen in the air, plants can't just use it in that form.

Exactly.

Nitrogen is like a building block for plants, but they need it in a different form.

And that's what rhizobia do.

They can take nitrogen gas from the air and convert it into ammonia, which the plant can actually use.

And in return, the plant gives the bacteria a nice place to live inside the nodule and provides them with sugars for energy.

So it's like the plant builds these tiny little apartments for the bacteria and the bacteria pay their rent in usable nitrogen.

Uh -huh.

Yeah, that's a great way to put it.

And the way those nodules form is pretty incredible.

It's all very specific.

There's this chemical communication going on between the plant and the bacteria using these molecules called nod factors.

The bacteria release the nod factors, and that triggers the plant's root hair to curl around the bacteria.

And eventually they form this little tunnel called an infection thread, which leads into the root and eventually forms the nodule.

And once the bacteria are inside the nodule, they change, right?

They don't just stay the same?

You got it.

Inside the nodule, the rhizobia become what we call bacteroids.

They're basically specialized nitrogen -fixing cells.

And because the enzyme that fixes nitrogen, it's called nitrogenase, is super sensitive to oxygen, the plant has to protect it.

So the plant actually makes this special protein called ligemoglobin, which binds to oxygen and controls the amount of oxygen inside the nodule.

It's crazy how nature comes up with these solutions, and the chapter even mentions that some legumes have nodules on their stems, not just their roots.

Oh yeah, that's right.

Some legumes, like the ones that work with the bacterium Azorazobium colonodens, can actually form nodules on their stems.

It's just another way to get that nitrogen they need so badly.

Speaking of getting nutrients, the chapter talks about mycorrhizae, which is another plant -microbe partnership that I hear a lot about when people talk about healthy soil.

Mycorrhizae are hugely important.

It's basically this team up between plant roots and fungi, and it's super common, like most plants on earth have mycorrhizae.

The main benefit for the plant is that it can absorb way more nutrients from the soil, especially phosphorus and nitrogen, which are often hard for plants to get enough of.

You can almost imagine this network of fungal threads underneath the ground acting like an extension of the plant's roots, reaching out and grabbing nutrients from a much larger area.

So it's like the fungus is giving the plant's roots a huge boost.

Yeah, and the plant gives the fungus sugars in return, the sugars it makes from photosynthesis.

So it's this exchange of resources that both partners need.

The chapter talks about two main types of mycorrhizae, ectomycorrhizae and endomycorrhizae.

What's the difference between those two?

So ectomycorrhizae kind of wrap around the outside of the root and form this network called the heartignet that grows between the root cells.

Endomycorrhizae, on the other hand, they actually go inside the root cells and form these structures called our buscules, which is where the exchange of nutrients happens.

And just like with root nodules, there are specific signaling molecules involved.

The fungi release molecules called mycic factors that help establish the partnership with the plant.

And I remember reading that these fungal networks can actually connect different plants together underground.

It's almost like they're communicating.

Yeah, it's pretty wild.

We know that these mycorrhizal networks can link up multiple trees and other plants, and it's possible that they're not just sharing nutrients, but also signaling molecules.

It's a really active area of research, and we're learning more and more about how plants are connected underground.

OK, so we've seen all these amazing mutualistic relationships, but then the chapter throws in a different example with agrobacterium.

Now this is not a friendly partnership.

No, agrobacterium tumifaciens is definitely a parasite.

It causes this disease in plants called crown gall disease, and it does it in this really interesting way.

The bacterium has this big piece of DNA called a type plasmid, and a part of this plasmid called the tDNA actually gets inserted into the plant's own DNA.

So the tDNA is what causes the problems for the plant.

Exactly.

The tDNA has genes that make the plant grow tumors.

Those are the galls you see, and it also makes the plant produce these weird compounds called opines.

And the opines are basically a special food source that only the agrobacterium can use.

It's like the bacterium is hijacking the plant's cells and making them produce a custom meal.

That's pretty clever in a sneaky kind of way.

And the chapter mentions vir genes, which are also on the type plasmid.

What do those do?

The vir genes are really important for the whole process.

They basically give the bacterium the tools it needs to cause the infection.

They help to cut out the tDNA from the plasmid and get it into the plant cell, where it can then insert itself into the plant's DNA.

Okay, so that's plant -microbe interactions.

Now let's turn our attention to insects.

They have some pretty crazy microbial relationships, too.

They really do.

Insects have this huge diversity of microbial partners that help them in all sorts of ways.

From getting the nutrients they need to defending themselves against predators and parasites.

And the chapter points out that they can get these symbionts in two main ways.

Horizontally, which means picking them up from the environment, and vertically, which means inheriting them from their parents.

And then there's this distinction between primary symbionts and secondary symbionts, right?

Yeah, primary symbionts are like the essential ones.

The insect host can't survive or reproduce without them, and they're usually passed down directly from the parent to the offspring.

They live inside specialized cells in the insect called bacteriocytes, which are often grouped together in an organ called the bacterium.

And one really interesting thing about primary symbionts is that their genomes often get smaller over time.

They lose genes that they don't need anymore because they're getting those functions from the host.

Like the example with Buchnera and aphids.

Yeah, that's a classic example.

Aphids feed on plant sap, which doesn't have all the amino acids they need.

And Buchnera, which is their primary symbiont, has the genes to make those missing amino acids.

So the aphid gets the essential nutrients from its bacterial partner.

And then secondary symbionts are more like optional extras, right?

They can be helpful, but aren't always essential.

That's a good way to think about it.

Secondary symbionts can provide all sorts of benefits, like extra nutrients, protection against heat or other environmental stresses, or defense against enemies.

But the insect can often survive without them, at least under certain conditions.

Speaking of defense, the chapter mentions this really cool example with the rove beetle.

Oh yeah, the rove beetle has this pseudomonas bacterium that makes this really nasty toxin called petarin.

It's like a chemical weapon that the beetle uses to deter predators.

So the beetle basically outsources its defense to its microbial partner.

That's pretty awesome.

And what about bees?

We know they have these complex gut microbiomes, right?

Yeah.

Bees are another great example.

Their gut microbes are super important for their health.

They help to break down pollen, which is their main food source.

And they also protect the bee from harmful bacteria and other pathogens.

And then of course, there are termites.

Their gut symbioses are famous for being super complex, especially when it comes to digesting wood.

Termites are like the ultimate example of how microbes allow animals to eat stuff that they couldn't digest on their own.

Like wood is really hard to break down, but termites have this whole team of microbes in their guts that do the job for them.

And the chapter talks about how there are different types of termites, lower termites and higher termites that have different types of microbes.

So what's the difference between their microbial setups?

Well, lower termites have these protists in their guts that are really good at breaking down cellulose.

Higher termites, on the other hand, they have a more diverse community of bacteria that do the job.

And the termite gut is this really interesting environment.

It's completely anaerobic, which means there's no oxygen.

And the bacteria produce acetate as a byproduct of fermentation, which is the termites main source of energy.

And some of the bacteria can even fix nitrogen, which is an added bonus.

It's like a tiny little bioreactor happening inside the termite.

OK, now let's move on to some other invertebrate symbiosis.

And I have to say, the example with the Hawaiian bobtail squid is just adorable.

I know, right?

It's such a cool partnership.

So the Hawaiian bobtail squid has this special light organ on its underside, and it's home to these bioluminescent bacteria called alivibrio fishery.

The squid gives the bacteria a nice, safe place to live, and in return, the bacteria produce light.

And the light isn't just for fun, right?

It actually helps the squid to camouflage itself.

Yeah, the squid uses the light to basically blend in with the moonlight or starlight coming from above.

It makes it really hard for predators to see the squid's shadow from below.

And the chapter talks about this really cool thing called quorum sensing that controls the light production.

It's basically how the bacteria communicate with each other and only turn on the light when there are enough of them present.

So it's like they have a little bacterial meeting to decide when to turn on the lights.

That's amazing.

OK, from the shallows to the deep, the chapter then takes us to these crazy ecosystems around deep sea hydrothermal vents and cold seeps.

These are some of the most extreme environments on the planet.

There's no sunlight down there, but life still finds a way.

And it's all thanks to symbiosis.

The animals that live down there rely on these special bacteria that can get energy from chemicals like hydrogen sulfide coming from the vents.

And the giant tube worm, Riftia pachyptila, that's one of the most iconic examples, right?

Yeah, giant tube worms are really weird.

They don't even have a mouth or a gut.

They get all their food from the bacteria that live inside them in a special organ called the trophosome.

The bacteria use hydrogen sulfide to make organic compounds, and the worm just absorbs those compounds.

It's like having a built -in food factory.

It blows my mind that there are these whole food webs down there based on bacteria getting energy from chemicals.

And then the chapter goes into entomopathogenic nematodes.

That's quite a name.

Uh -huh, yeah.

These are basically parasitic worms that infect and kill insects.

And they do it with the help of bacteria, either photohabdus or xenohabdus.

The nematode invades the insect, releases the bacteria, and the bacteria produce toxins that kill the insect.

They also release enzymes that digest the insect's tissues, so it's kind of gruesome.

So it's like a tag team of death.

And the last invertebrate symbiosis that the chapter covers is coral reefs.

Ah, coral reefs.

This is another really important one.

Corals have this essential partnership with these tiny algae called symbiodinium.

The algae live inside the coral's tissues and do photosynthesis, providing the coral with food.

And the coral gives the algae a place to live and protection from predators.

And that symbiosis is what makes those incredible coral reef ecosystems possible, right?

Exactly.

The coral gets its energy from the algae, and that energy is what allows the coral to grow and build those amazing reef structures.

But this partnership is really sensitive to things like changes in water temperature.

When the water gets too warm, the coral can expel the algae, and that's what causes coral bleaching.

And when that happens, the whole ecosystem can collapse.

It really highlights how fragile those systems are.

Okay, so for the last part of the chapter, we move into the world of mammals.

And the focus is on herbivores, the plant eaters, and how they rely on microbes to digest all that plant material.

Right.

This is another example of how microbes are absolutely essential for life.

Herbivores, like cows and sheep and horses,

they can't break down cellulose, which is the main component of plant cell walls.

They need microbes to do that for them.

And over millions of years, they've evolved these specialized digestive systems to make it happen.

And the chapter talks about two main types of herbivore digestion,

foregut fermentation and hindgut fermentation.

What's the difference?

So in foregut fermentation, which is what ruminants like cows do, the microbial breakdown of plant material happens in a special part of the stomach called the rumen before the food reaches the true stomach.

In hindgut fermentation, which is what horses and rabbits do, the main site of microbial digestion is in the cecum and the large intestine, which are further down the digestive tract.

Let's focus on the rumen for a minute because that's a really cool example of foregut fermentation.

The rumen is like this amazing microbial ecosystem.

It's warm, it's anaerobic, meaning there's no oxygen, and it has a fairly stable pH.

And it's packed with microbes, bacteria, archaea, protists and fungi, all working together.

They break down cellulose and other complex carbohydrates, and they produce short chain fatty acids, also known as volatile fatty acids, or VFAs.

And those VFAs are what the animal actually uses for energy.

The VFAs are absorbed across the rumen wall and provide the cow with most of its energy.

And not only that, but the microbes also produce vitamins and amino acids, and when the microbes themselves are digested further down the digestive tract, they provide the cow with protein.

So the cow gets energy from the VFAs and protein from the microbes themselves.

It's like having a personal food factory right inside your stomach.

But there's also that downside with methane, right?

Yeah, methane is a byproduct of the fermentation process.

The archaea and the rumen, specifically the methanogens, produce methane, and the cow burps it out.

And methane is a greenhouse gas, so it contributes to climate change.

And the chapter also talks about how changes in the cow's diet can disrupt the balance of the microbes in the rumen, which can lead to problems like acidosis.

And then there's that really cool example with Synergistus jonesi and the Luchina plant, which shows how specific these microbial relationships can be.

Oh yeah, that one's fascinating.

Luchina is a good source of food for livestock in some parts of the world, but it contains this toxin called mimazine.

And in some places, the cows can eat Luchina with no problem because they have this bacterium, Synergistus jonesi, in their rumen that can detoxify mimazine.

But in other places, the cows don't have that bacterium, so they can't eat Luchina without getting sick.

So having the right microbes can make all the difference.

Wow, this deep dive has really shown how important symbiotic relationships are all across the board, from tiny microbes to huge mammals that are shaping ecosystems all over the planet.

They really are.

These partnerships are essential for things like nutrient cycling, defense against enemies, and even just basic survival for so many organisms.

Like we started with lichens, which are these seemingly simple things, but they're actually these complex communities.

And then we went to the DFC, where life depends on these bacteria that can get energy from chemicals.

And then there are all the amazing symbiosis in plants and insects and mammals.

It's incredible how much life on Earth depends on cooperation.

It makes you wonder what other partnerships are out there that we haven't even discovered yet.

Like what other tiny collaborations are happening all around us right under our noses?

That's the big question, isn't it?

And with all the environmental changes happening now, how are those changes affecting these delicate symbiotic relationships?

There's still so much to learn.

Well, I think we can confidently say that we've covered all the major points, theories, findings, and examples from this chapter on symbiosis between microbes and their hosts.

It's been an amazing deep dive.

Thanks for joining us.