Chapter 17: Diversity of Archaea

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All right, welcome back to the Deep Dive.

Today we're tackling a domain of life that might not be as familiar as, say, animals or plants, but it's absolutely crucial to, well, pretty much everything.

We're talking archaea.

Yeah, archaea.

And we've got a whole chapter here, a really deep dive into these often overlooked microbes.

So we're going to extract the good stuff, the must -know info about their diversity.

Because they're incredibly diverse.

Oh, absolutely.

And right off the bat, we've got some head scratchers, like they're lipids.

They're linked by ether bonds, not the usual estrobons we see in bacteria and eukaryotes.

Which is a big deal.

It is.

It means these guys can handle some serious heat, some really harsh environments.

And then there's a cell wall situation.

Right, no peptidoglycan, which we always think of with bacteria.

And then the real kicker, their RNA polymerases.

They're way more similar to, like, ours to eukaryotes.

Yeah, that's one of the big clues that points to a, well, a deeper evolutionary connection there.

Definitely.

And we're also going to get into their incredible metabolic flexibility, how they get energy, and the fact that they're the only ones on earth making methane.

Which is a whole other can of worms, but a fascinating one.

Okay, so let's lay the groundwork here.

What are some of those fundamental traits that all archaea share?

All right, so back to those ether -linked lipids.

You can think of them as these super strong bonds,

way more robust than the ester linkages.

And that's what gives their membranes such stability, especially in those crazy environments they like to call home.

Right, like boiling hot springs or super salty lakes, not your average backyard puddle.

Exactly.

And then no peptidoglycan, so their cell walls are built differently.

It's really interesting to see how diverse they are structurally.

So taking a step back in time, what can we glean about the earliest archaea?

What does the genomic evidence say?

Well, it seems like those ancient archaea were real heat lovers, hyperthermophiles.

They probably got their energy by oxidizing hydrogen gas and using carbon dioxide as their carbon source, so carbon fixation.

Like some sort of ancient microscopic photosynthesis almost.

In a way, yeah.

And this actually helps us understand why so many archaea today are found in these extreme environments.

It could be a legacy, a trait passed down for their ancestors.

So how do we make sense of this diversity?

How is the archaeal domain organized?

Okay, so imagine a big family tree.

We've got these major branches called superfolla, and there are four main ones.

Uriarchiota, dpan, taicac, and asgard archaea.

Catchy names.

Right.

And these groupings help us figure out how they're related and what general characteristics they share.

So let's dive into the first one.

Uriarchiota.

This one contains the most well -studied archaea, right?

It does, mostly because we figured out how to grow them in the lab, which makes them much easier to research.

And metabolically, they're all over the place, which makes them really interesting.

Okay.

So within Uriarchiota, we've got those salt -loving halarchia.

Yes.

These guys can handle some seriously salty conditions, at least 1 .5 molar sodium chloride, which is like five to 10 times saltier than the ocean.

Wow.

That's a lot of salt.

It is.

Some of the key players here are halobacterium, halophorax, and natronobacterium.

And here's the thing.

Most of them actually need oxygen to survive.

They're obligate aerobes.

That seems counterintuitive, right?

You think of these extreme environments as being harsh in every way.

You would, wouldn't you?

Yeah.

But they've adapted to these high salt concentrations in incredible ways.

For instance, their cell walls need a ton of sodium ions just to stay intact.

That's wild.

It is.

And then their enzymes, the ones inside their cells doing all the work.

They need super high potassium concentrations to It's this delicate balance to counteract all that external salt.

And doesn't halobacterium have this special trick with light?

Oh, yeah.

It's got this protein called bacteriodopsin, and it actually uses retinol, just like what's in our eyes, to capture light energy.

No way.

It's true.

Basically, bacteriodopsin acts like a pump in the cell membrane.

When light hits it, it pumps protons out of the cell.

Protons.

Those are the positively charged particles, right?

Exactly.

And this pumping action creates this difference in electrical potential, like a battery being charged.

That energy is then used to generate ATP, which is like the fuel cells use.

So they're harnessing light energy, but not like photosynthesis.

It's a totally different mechanism.

So they're like miniature solar panels, basically.

That's incredible.

Now, these salty spots, they're not all the same, are they?

You're right.

Salt is the common denominator, but they could be really different in terms of what other ions are present and how acidic or basic they are, the pH.

So like soda lakes, which are super alkaline on top of being salty.

Exactly.

And haloarchaea thrives in all sorts of these salty niches.

So where are they getting their food in these extreme environments?

Well, they're chemerogonotrophs, which means they break down organic matter for energy.

In many salt lakes, you've got algae like dunalaila that are the primary producers.

They make food from sunlight.

And when those algae die, that's dinner for the haloarchaea.

They feast on the organic carbon compounds left behind.

Okay.

Onto the next group.

Methanogens,

the methane producers.

Yes.

The methanoarchaea.

These guys are the only ones on earth known to produce methane as part of their metabolism.

And that's called methanogenesis, right?

Yep.

And they can't stand oxygen.

They're obligate anaerobes.

So they live in all sorts of places without oxygen.

Like where?

All over.

The guts of animals, especially cows and sheep, where they help break down all that tough plant material.

Ah, so that's where all that methane from cows comes from.

Partially, yeah.

They're also in places like rice paddies, lake sediments, swamps, even the deep ocean and under glaciers.

Under glaciers.

Seriously.

Seriously.

And within the urea archeota, this methane producing ability has popped up in at least eight different orders.

So evolution really hit on something good there.

Definitely.

And there are actually a few different biochemical pathways they use to make methane.

Like what?

Well, there's CO2 reduction, where they use hydrogen gas to convert CO2 into methane.

Sounds straightforward enough.

Then there's methylotrophic methanogenesis, where they eat compounds with methyl groups,

and acetoclastic methanogenesis, where they split acetate into methane and CO2.

So different species have their preferred methods.

Exactly.

It depends on the species and what's available in their environment.

It's also worth noting that they have all sorts of different cell envelope structures.

So all these cow farts and thawing permafrost, that's a lot of methane going into the atmosphere.

It is.

And it's a big concern because methane is a potent greenhouse gas.

Not great for the climate.

No, not at all.

And our agricultural practices and, well, the warming planet itself are creating more and more habitats for these methanogens.

It's kind of like a feedback loop.

It is.

Now, the chapter highlights a couple of interesting methanogens, like methanocaldococcus chinaceae.

Yeah, that one's the star in the archaeal research world.

Why is that?

Well, it was one of the first archaea to have its whole genome sequenced.

So you got a peek under the hood, so to speak.

Exactly.

And what they found was really intriguing.

Its basic genetic processes, like how it copies DNA and makes RNA, are a lot like eukaryotes.

But a lot of its metabolic pathways, how it breaks down and builds molecules, are more like bacteria.

A bit of a hybrid, then.

Yeah, it shows how evolution can mix and match, which is really cool.

And then we've got methanopyrus, the heat champion.

Oh yeah, methanopyrus candelari.

This one holds the record for highest growth temperature, 122 degrees Celsius.

That's like boiling hot.

It is.

And it thrives in these super hot hydrothermal vent environments.

It's got these special lipids in its membrane that help it deal with all that heat.

So tough.

Okay, moving right along within your york iota, we get to the thermoplasma tails.

They like it hot and acidic, right?

They do.

Thermoplasma, ferroplasma, picrophilus, all fans of heat and acid.

A very specific taste.

Right.

And get this, thermoplasma and ferroplasma don't even have cell walls.

How do they hold themselves together?

Well, thermoplasma, for instance, has this unique lipopolysaccharide -like molecule in its membrane that helps it stay stable.

It's found in those self -heating coal refuse piles and acidic soils.

So it's got its own built -in armor.

Exactly.

Ferroplasma gets its energy by oxidizing iron, which actually makes its environment even more acidic.

So they contribute to acid mine drainage.

They do, unfortunately.

It's a serious environmental problem.

And then there's picrophilus.

How acidic is too acidic?

Apparently not acidic enough for this one.

Right.

It grows best at a pH below zero.

Below zero?

That's insane.

It really is.

It does have an S -layer, though, a protein layer on the outside, which probably helps it survive in such harsh conditions.

Okay.

Two more groups within Euryarchiota to cover.

Thermococcalase and archaeoglobulus, both hyperthermophilic.

What sets them apart?

Well, thermococcalase, which include genera, like thermococcus and pyrococcus, can grow at extremely high temperatures and typically use things like proteins or starch for energy and elemental sulfur as an electron acceptor.

So they're like the ultimate recyclers.

In a way, yeah.

Archaeoglobulus, with the main genus archaeoglobus, are also hyperthermophilic, but they get their energy mostly from sulfate reduction.

And archaeoglobus actually has some things in common with methanogens, right?

It does.

It shares some key enzymes and genes with them and can even make a little methane under certain conditions.

So there might be an evolutionary connection there.

It's definitely a possibility.

Then there's ferroglobus, which is similar to archaeoglobus, but loves iron.

Iron, like the metal.

The metal.

It oxidizes ferrous iron for energy and uses nitrate as an electron acceptor.

So even in these crazy hot environments, they found all these different ways to survive.

Exactly.

It's amazing.

Okay.

We've explored the Euryarchiota.

Now we're venturing into the world of those less studied cryptic archaeophila.

The ones that really highlight the power of metagenomics.

Metagenomics being?

Oh, sorry.

Basically studying the genetic material directly from the environment without having to grow the organisms in the lab.

Right.

So we can get a glimpse of what's out there even if we can't see it directly.

Exactly.

And that's how we discovered Thalmarciota.

Which are super abundant, right?

They are, especially in soil and marine environments.

And they're incredibly important for the nitrogen cycle.

Because they're ammonia oxidizers.

Yes.

They convert ammonia into nitrite, which is crucial for plant growth and basically all ecosystems.

So without them, we'd be in trouble.

Big trouble.

Nitrosopumilus and nitrososphera are some of the key players in this group.

And they each have their own specializations, right?

They do.

Nitrosopumilus meridimus is adapted to those super low ammonia concentrations in the open ocean.

While nitrososphera vianensis, the first one isolated from soil, is a bit more flexible and can handle higher ammonia levels.

And they have some unique biochemistry going on too.

Yeah, they've got this unique lipid called Cranearchaeol, which is a great way to detect them in environmental samples.

Like a fingerprint.

Exactly.

And they use a different way of fixing carbon dioxide, the three -hydroxypropionate, four -hydroxybutyric cycle, instead of the Calvin cycle that plants and some bacteria use.

Different strategies for the same goal.

Absolutely.

Okay.

What about Nanoarcheota?

The chapter mentions a hospitable fireball.

What's that all about?

Ah, yes.

Nanoarcheum equitans.

It's the only member of this phylum that we've found so far.

And it's a parasite.

It lives on another archaeon, a Cranearcheota called Ignacoccus hospitalis.

So a parasite within the archaeal domain, that's wild.

And Ignacoccus, that's the hospitable fireball.

It is.

It's a hyperthermophile.

So it lives in these super hot environments.

And it basically provides everything Nanoarcheum needs to survive.

Because Nanoarcheum is so tiny and can't do a lot on its own.

Exactly.

It's got a really reduced genome,

missing a lot of the genes that most organisms need for basic functions.

So it relies heavily on its host.

That's a fascinating example of, like, codependence.

It really is.

And Nanoarcheum is part of a bigger group called the D -Pan superphylum, which has a bunch of other archaea with small cells and reduced genomes.

So maybe a lot of them have these dependent lifestyles.

It's definitely a possibility.

Now for the secret filament, Corarcheota.

Ugh.

Corchaeum cryptophyllum.

This is the only species we've characterized so far.

And it's been a tough one to study because we haven't been able to grow it in pure culture yet.

So we can only grow it with other microbes.

Right.

In these mixed communities.

It's a hyperthermophile, so it likes it hot.

And it's an obligate anaerobic, so no oxygen for this one.

It gets its energy from organic compounds, probably peptides or amino acids.

And why is it so hard to grow on its own?

Well, its genome shows that it's missing a bunch of genes that are normally needed for making essential molecules.

So it probably needs help from its microbial neighbors.

Exactly.

It relies on them for things it can't do itself.

Yeah.

This just shows how important it is to consider these microbial communities, how they interact.

So Corarcheota are part of the TAC superphylum, along with Amarcheota and Crenarcheota.

And the chapter then mentions some other cryptic phyla that are only known from their DNA.

It seems like we're just scratching the surface of archeal diversity.

We really are.

There's so much out there that we're just starting to uncover with these metagenomic techniques, like the Asgard Archaea.

Asgard.

Like from Norse mythology.

Yep.

And these guys are really interesting because their genomes have genes that we thought were only found in eukaryotes.

So like our genes.

Essentially.

And this has led to the idea that Asgard Archaea might be the closest relatives to eukaryotes.

So these microbes could hold clues about how our own cells evolve.

That's the thinking.

The chapter also mentions Agarcheota and Bathyarcheota, which are both part of the TAC superphylum.

We mostly just know their DNA sequences, but some Bathyarcheota might even be able to make methane using a different pathway than the methanogens we talked about earlier.

So even within these cryptic phyla, there's so much metabolic diversity.

It's incredible.

Okay, on to Crenarcheota, the last superphylum.

These are the ones with lots of cultured isolates, especially the ones that like it hot and sulfous.

Right.

They're the heat and sulfur lovers.

Many of them being chemolithotrophic autotrophs too.

Yes.

So they can produce their own food using energy from inorganic compounds.

And they often form the base of the food web in those hot environments.

Exactly.

So where do they hang out?

Mostly in geothermally heated soils and waters, often around volcanoes.

They love sulfur.

Volcanoes.

Not exactly a relaxing vacation spot.

Not for us, maybe.

But for them, it's home.

They mostly rely on anaerobic respiration, using things like hydrogen gas for energy and things like sulfur or nitrate as electron acceptors.

They're not big on fermentation though.

No, not really.

And definitely no photosynthesis.

They're also found in those deep sea hydrothermal vents where the pressure keeps the water super hot, even though it's way below the surface.

So we've got Crenarcheota on land and in the deep sea.

Exactly.

And the chapter breaks them down by habitat, starting with the ones in terrestrial volcanic areas like Sulpholobus and Acidianus.

Tell me about them.

Well, Sulpholobus has this interesting lobed shape and it's pretty metabolically flexible.

It can use sulfur compounds, organic molecules, even iron for energy.

It likes to keep its options open.

It does.

Acidianus can use sulfur both with and without oxygen, so it's adaptable too.

Then there's Thermoproteus and Thermophyllum, which are strict anaerobes that need sulfur for respiration.

And Pyrobaculum, which is interesting because some of them can actually use oxygen, which gives them an advantage in environments where oxygen levels fluctuate.

So even within these hot sulfurous environments, there's diversity in how they get their energy.

Absolutely.

Now onto the submarine Crenarcheota, the ones in those deep sea vents.

Dessulfur Cocales are the big players here.

Yes.

These guys are specifically adapted to those super hot vents.

Pyridictium, for example, grows best above 100 degrees Celsius and it forms these networks of fibers that probably help it stick to surfaces in those turbulent environments.

Smart move.

It is.

And it uses hydrogen gas and elemental sulfur for energy.

Pyrolobosphimari is even more extreme, growing at up to 114 degrees Celsius, and it can only use hydrogen.

A true extremophile.

Definitely.

And then there's Ignecoccus, which we talked about before, the host for Nanoarcheum.

It's got this really unusual cell structure with an outer membrane that has ATPase, the enzyme that makes ATP, and a huge paraplasmic space.

We still don't know exactly what that space is for.

We're still figuring that out.

But it might have to do with its high -temperature lifestyle or its interactions with Nanoarcheum.

And finally, there's Staphylothermus, which forms these clumps of cells and gets its energy by breaking down organic matter.

It likes it a bit cooler,

with an optimal growth temperature of 92 degrees Celsius.

Still pretty hot for us.

Okay, so these Crenarcheota are living right at the edge of what we thought was possible for life.

Which brings us to the final part of the chapter, the discussion of evolution and life at high temperatures.

What are the upper limits?

Well, as we've seen, these hydrothermal vents can get ridiculously hot over 100 degrees Celsius.

Because of the pressure, right?

Exactly.

And the current record holder is methanoporous, which can grow at 122 degrees Celsius in the lab.

It is.

Some scientists think some archaea might be able to grow even hotter.

But there are limits.

Above 150 degrees Celsius, things start to break down, literally.

Like ATP, the energy molecule, wouldn't be stable at those temperatures.

So there are fundamental physical constraints on life.

There are.

So how do these hyperthermophiles manage to survive in such heat?

How do they keep their proteins and DNA from falling apart?

They've got all sorts of tricks.

Their proteins tend to have more hydrophobic amino acids in their core, which helps them fold tighter and resist unfolding at high temperatures.

They also have more ionic bonds, which makes them more stable.

And they have chaperone proteins that help fold proteins correctly and refold any that get messed up by the heat.

So like a protein repair crew?

Exactly.

And the DNA?

They have an enzyme called reverse DNA gyrase that actually twists their DNA in a way that makes it more compact and stable.

They also keep the concentration of certain molecules inside their cells high.

And these molecules help protect the DNA.

And their cell membranes have these special lipids called bifutinol tetraether lipids that form a single, very heat resistant layer.

Even their ribosomal RNAs have a higher G plus C content, which makes them more stable, too.

It's mind blowing how they've adapted to such extreme conditions.

It is.

And the chapter connects these heat loving Archaea to the early history of life on Earth.

What's the link there?

Well, early Earth was a much hotter place.

And many of the most heat tolerant organisms are Archaea, especially those that use hydrogen gas for energy.

Which would have been plentiful back then.

Exactly.

And a lot of them are chemolithotrophs, meaning they get their energy from inorganic compounds, which is probably how early life got its energy, too.

So it's likely that these hyperthermophiles are descendants of some of the earliest life forms on Earth.

It's fascinating to think about how these ancient lineages are still around today, thriving in these extreme environments.

It really is.

So let's recap.

We've covered the unique characteristics of Archaea, those ether -linked lipids, the lack of peptidoglican, the eukaryote -like RNA machinery.

We've explored the four major groups, from the metabolically diverse urea Archaea to the often symbiotic Deepan, the versatile TAC, and the eukaryote -related Asgard Archaea.

We've seen how they've adapted to some of the most extreme environments on Earth, from super -salty lakes to boiling hot springs and deep sea vents.

And we've delved into their diverse metabolisms, from methanogenesis to ammonia oxidation, and how they play critical roles in global nutrient cycles.

And we've seen how studying Archaea can give us clues about the early evolution of life.

We've had those aha moments, like the solar -powered halo bacterium, the mind -boggling acidity tolerance of Procophilus, the heat -champion Methanopyrus, the parasitic nanoarcheum, those eukaryote -like genes in Asgard Archaea, and all those amazing adaptations to extreme heat.

It's been quite a journey.

It has.

And it just shows how much more there is to discover about Archaea.

With all the uncultured Archaea out there, who knows what amazing things we'll find?

Who knows?

That's what makes this field so exciting.

And I think it's safe to say we've covered all the major points from this chapter on Archaeodiversitif.

I think so.

We've gone pretty deep.

We have.

Thanks for joining us on the Deep Dive.