Chapter 14: Metabolic Diversity of Microorganisms

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Welcome back everyone to the Deep Dive.

Today we are going on a journey into, I guess you could call it an unseen world, but one that's absolutely essential for, well for everything really.

We're talking about the incredible metabolic diversity of microbes.

It's really quite amazing when you think about it.

I mean these tiny organisms, they're the ultimate chemists, they're driving all these transformations.

They're just absolutely critical to how our whole biosphere works.

The air we breathe, the cycles that sustain life, it all comes back to the metabolic power of microbes.

And we have a fantastic chapter here on microbial metabolic diversity.

We are going to really dive deep into it and try to pull out all the key principles and I guess really showcase some of the most amazing strategies that these microbes use to make a living.

And our chapter really lays out the foundation, the key principles that underpin this incredible diversity.

So we're going to talk about things like redox reactions, the importance of reducing power, and of course the challenge of maintaining redox balance in a cell.

Okay, so redox reactions.

Can we break that down a little bit because I think for some people that might sound a little bit intimidating.

Yeah, absolutely.

I mean at the simplest level it's all about the movement of electrons.

It's like a tiny electrical current, right?

One molecule loses an electron that's oxidation and another one gains that electron that's reduction.

And this transfer, that's where the energy is.

The bigger the energy difference between where the electron starts and where it ends up, that dictates how much energy the microbe can potentially harness.

And microbes have evolved to use such a wide range of electron donors and acceptors.

I mean they can use organic compounds but also all sorts of inorganic stuff like sulfur, iron, things you wouldn't normally think of as fuel.

Exactly.

And they figured out how to pair these different donors and acceptors in all sorts of creative ways, creating these intricate electron transport chains.

Now the chapter also stresses this idea of reducing power.

Those molecules like NADH and NADPH, they seem really crucial.

Why is that?

These molecules, they're like the cell's little rechargeable batteries, right?

They're packed with electrons ready to be used to power all sorts of reactions, especially those involved in building new molecules.

So it's not just about fueling the cell, it's also about having the right building blocks.

Precisely.

Now for some microbes like chemorganotrophs, which get their energy from organic compounds,

generating this reducing power is sort of a given.

It's just a natural byproduct of their metabolism.

Right, right.

But for others like chemolithotrophs, which use inorganic compounds,

or the phototrophs, which use light energy, getting that reducing power can be a bit more challenging.

It takes extra steps, extra energy.

Now this is where it starts to get really cool.

The chapter introduces these flavin -based electron bifurcating enzymes, and that sounds, well, incredibly complicated.

Yeah, it's pretty amazing.

So imagine an electron stream, right, and it comes to a fork in the road.

Now normally the electrons would just flow down the path of least resistance, but these enzymes, they can split that stream.

Some electrons go down the easy path, releasing energy as they go.

But that released energy, it's used to push other electrons up the more difficult path.

It's like a little energy shuttle, right?

So they're using energy from one reaction to power another reaction that wouldn't normally happen.

Exactly.

It's a way of making those tough uphill reactions actually go forward.

Wow, that's incredibly efficient.

Now the chapter then transitions to talking about how autotrophs, the organisms that can make their own food, bring carbon dioxide into the picture.

And it's not just as a carbon source, it can also be the final electron acceptor.

Right, and that really highlights how intertwined all these processes are.

Carbon dioxide, it's a fundamental building block for life, and it plays this dual role in a lot of these metabolic pathways.

And of course, one of the most important pathways for CO2 fixation is the Calvin cycle.

Exactly.

This is the primary route for oxygenic phototrophs, like plants, algae, and cyanobacteria, but also for many chemolithotrophs that use oxygen.

And the key enzyme here is rubisco.

I mean, you hear so much about it because it's one of the most abundant proteins on earth.

I've always wondered why that is.

I think it really speaks to the sheer scale of the challenge, right?

Capturing all that carbon dioxide from the atmosphere and making it to the rest of life.

It's not necessarily the fastest enzyme, but there's just so much of it that it makes a huge impact.

And some bacteria have even evolved these special compartments called carboxysomes.

Yeah, these are like little micro factories within the cell.

They concentrate the enzymes and substrates of the Calvin cycle, so it runs even more efficiently.

Then we have the reverse citric acid cycle.

So instead of breaking down carbon compounds, they're building them up.

That's right.

It's used by organisms like green sulfur bacteria and many chemolithotrophs that live in environments with low or no oxygen.

They essentially take the standard citric acid cycle and run it backwards using CO2 to synthesize pyruvate, which is a really important building block for all sorts of other molecules.

Now let's move on to this incredible world of phototrophy, where organisms capture light energy to power their metabolism.

And as the chapter highlights, these organisms had a huge impact on the early earth.

Yeah, I mean, oxygenic photosynthesis, which evolved in cyanobacteria, totally transformed our planet.

It's what gave us the oxygen -rich atmosphere we have today, which allowed for the evolution of all those oxygen -breathing organisms, including us.

And at the heart of it all are the pigments, those light harvesting molecules.

We've got the chlorophylls and the bacteriocorophylls, which are structurally similar, but they have these magnesium atoms at their core.

And then there are the cytochromes, which use iron.

Right.

And what's interesting is that even small variations in the structure of these pigments lead to big differences in their absorption spectra, which is the range of wavelengths of light they can capture.

So different phototrophs can actually specialize in capturing different parts of the light spectrum.

Exactly.

And that's what allows them to coexist.

They're not all competing for the exact same wavelengths.

It's a way of dividing up the resources, right?

And these pigments are organized into these intricate photocomplexes within membranes.

You've got the reaction centers where the light energy is converted into chemical energy, and then the antenna pigments, which are like these little light -gathering satellites.

It's an incredibly elegant system.

The antenna pigments capture photons and funnel that energy down to the reaction center.

And the location of these photocomplexes can vary depending on the organism.

In eukaryotes, they're in the phylocoid membranes of chloroplasts, while in anoxygenic bacteria, you might find them in chromatophores or lamellar membranes.

And then there are the chlorizomes, those giant antenna systems found in certain bacteria that live in low -light environments.

Yeah, they're like these super -efficient light collectors, able to capture even the faintest glimmers of light.

So we have this fundamental division in photosynthesis.

Oxygenic, which produces oxygen, and anoxygenic, which doesn't.

And it all boils down to the source of electrons.

Right.

In oxygenic photosynthesis, water is the electron donor, and that's what leads to the other electron donors, like hydrogen sulfide, elemental sulfur, or even hydrogen gas.

It really speaks to their flexibility.

And we shouldn't forget the supporting cast of pigments, like carotenoids and phycobilins.

They help to broaden the range of light that can be harvested and protect the cell from damage.

Carotenoids, you know, they give us those beautiful fall colors, but they also act as antioxidants, quenching those harmful reactive oxygen species that can be generated by light.

And phycobilins, which are often organized into phycobilisms, are particularly good at absorbing longer wavelengths of light, those oranges and reds that penetrate deeper into water.

Okay, let's delve deeper into anoxygenic photosynthesis.

The chapter talks about how the electron flow generates a proton motive force, which then drives ATP synthesis.

And it mentions these two main types of reaction centers, quinone type and iron sulfur type.

What are the key differences between them?

Well, these reaction centers, they're like the heart of the photosynthetic machinery.

When light hits a special pair of bacterioclorical molecules in the reaction center,

it energizes them and they release electrons.

And those electrons then flow down an electron transport chain.

And that flow, that's what generates the proton motive force.

Q -type reaction centers, you find those in purple bacteria, green non -sulfur bacteria, and gemandomonadates, and they use quinones, which are these mobile electron carriers, as part of the chain.

But FES -type reaction centers, which you find in green sulfur bacteria, aceto bacteria, and helio bacteria, they rely more on iron sulfur clusters to move those electrons around.

So they both achieve the same basic goal, but they use different molecular players.

Exactly.

And those differences probably reflect their evolutionary history and the specific environments they're adapted to.

And then we have oxygenic photosynthesis, the process that sustains so much of life on Earth.

And it involves this elegant two -step process called the Z -scheme.

The Z -scheme is all about coordinating two photosystems, PSII and PSI.

It starts with PSII, which uses light energy to split water.

Right.

That releases oxygen, but it also releases electrons and protons.

The electrons then flow through a chain of carriers, building up that proton gradient.

Eventually, they end up at PSI, where they get re -energized by more light.

Okay.

Those high -energy electrons are then used to reduce NADP plus to NADPH.

So you get both ADP and NADPH, the energy currency and the reducing power that the cell needs to build all its components.

And the whole process is happening in the phylocoid membranes of chloroplasts and eukaryotes and in specialized membranes and cyanobacteria.

Right.

The chapter also mentions cyclic electron flow, where electrons cycle around PSI.

That's a way of generating extra ADP without making more NADPH, so the cell can fine tune its energy production.

Now, shifting gears a bit, the chapter moves on to respiratory processes that are defined by the electron donor.

And this is where we meet the chemolysotrophs, those organisms that can get energy from oxidizing inorganic compounds.

And that's pretty amazing when you think about it, right?

I mean, they're getting energy from things like sulfur, iron, nitrogen compounds, things that we wouldn't consider food.

But for them, it's a perfectly good source of electrons.

But the chapter points out that they face this challenge of making NADH, the important reducing agent.

It's not always easy for them to get those electrons to NAD plus side.

Yeah, because sometimes their electron donors have a more positive reduction potential than NAD plus side.

So thermodynamically, it's like pushing a rock uphill.

Right, right.

And to overcome that, they use something called reverse electron flow.

They use some of the energy they get from their electron transport chain to drive those electrons in the opposite direction towards NAD plus side.

So they're willing to pay an energy price to get that crucial reducing power.

Exactly.

It shows you how important NADH is for these organisms.

Now, let's talk about some of the specific groups of chemolysotrophs.

First up, the sulfur oxidizers.

They can use all sorts of reduced sulfur compounds from hydrogen sulfide to elemental sulfur.

And they're found in all sorts of environments.

Yeah, they play a huge role in the sulfur cycle.

And they're often found in places where you have a lot of reduced sulfur, like hydrothermal vents or sulfur springs.

Right.

The chapter explains that the oxidation process usually involves multiple steps.

And sometimes they even store elemental sulfur as an intermediate, either inside or outside the cell.

And this process can make things pretty acidic, right?

Yeah, they produce sulfuric acid as a byproduct.

So they tend to thrive in acidic environments.

In fact, many of them need that acidity to survive.

Interesting.

The chapter mentions this SOX system, which is a set of proteins that helps to oxidize sulfur compounds all the way to sulfate.

Right.

And the electrons from that oxidation, those get fed into the electron transport chain, which is how they generate ATP.

But it's not always a straightforward process.

Some sulfur oxidizers, especially those that store sulfur granules, they might only use part to the SOX system and have other enzymes involved.

Now, let's move on to the iron oxidizers, those iron bacteria.

They get their energy from converting ferrous iron to ferric iron.

And we often see the results of their activity as these reddish brown precipitates.

Yeah, that's ferric hydroxide, which is formed when ferric iron reacts with water.

And it's often found in places like acid mine drainage, where you have a lot of iron and low pH.

The chapter mentions that they don't get a lot of energy from this reaction, especially at acidic pH.

So they have to oxidize a lot of iron to make a living.

Right.

And they've evolved to be acidophiles, meaning they actually thrive in acidic environments.

And the chapter details this model organism, acidithiobacillus ferroxidens, which uses a combination of membrane proteins and electron carriers to transfer electrons from ferrous iron all the way to oxygen.

It's a pretty intricate pathway.

And like many other chemolithotrophs, they rely on reverse electron flow to generate NADH.

Now, onto the nitrogen cycle and those essential players, the nitrifying bacteria.

We've got two main groups here, the ammonia oxidizers and the nitrite oxidizers.

Right.

So the ammonia oxidizers, they take ammonia and convert it to nitrite, which is a two -step process.

First, they use ammonia monoxygenase, or AMO, to convert ammonia to hydroxylamine.

And then they use hydroxylamine oxidoreductase, or HAO, to convert hydroxylamine to nitrite.

And the nitrite oxidizers, they pick up where the ammonia oxidizers leave off.

Exactly.

They take that nitrite and convert it to nitrite.

And both groups are using these reactions to generate a proton mode of force and make ATP, right?

Absolutely.

But again, like many chemolithotrophs, they often need to use reverse electron flow to make enough NADH.

Now, the chapter introduces this fascinating process called anemics, anaerobic ammonia oxidation.

And it seems like it's a really important part of the nitrogen cycle, especially in those oxygen -free environments.

Yeah, it's a more recently discovered pathway, but it's turned out to be quite widespread.

It's carried out by these specialized bacteria that can oxidize ammonium using nitrite as the electron acceptor, and the end product is nitrogen gas.

And they do all this inside a special compartment called the anemoxysome?

Right.

It seems to be a way of protecting the enzymes involved from oxygen, which can be toxic to them.

And they're autotrophs too, right?

Yeah, they fix CO2.

But like many other autotrophs, they need reducing power to do that.

So even though they're using a completely different set of reactions, they face some of the same challenges as the sulfur bacteria and the nitrifying bacteria.

Exactly.

Now, the chapter shifts gears and starts talking about respiratory processes defined by the electron acceptor.

So instead of focusing on what they're using as an electron donor, we're looking at what they're using to accept those electrons at the end of the chain.

And this really opens up a whole new world of possibilities, because microbes have evolved to use a huge diversity of electron acceptors, especially in those environments where oxygen is scarce.

So it's all about being flexible, right?

Finding whatever works.

Exactly.

And it allows them to thrive in places that would be completely off limits to organisms that can only use oxygen.

Let's start with nitrate respiration.

The chapter talks about denitrification and DNRA.

So denitrification, that's the process where nitrate is converted all the way to nitrogen gas.

And it's carried out by a lot of bacteria, both those that can use oxygen and those that can't.

Right.

It's a multi -step process, and it involves a bunch of different enzymes that sequentially reduce nitrate to nitrite, nitric oxide, nitrous oxide, and finally to nitrogen gas.

And it's an important part of the nitrogen cycle, returning nitrogen to the atmosphere.

And it's also used in wastewater treatment to remove excess nitrogen.

Exactly.

Now, DNRA, the similatory nitrate reduction to ammonium, that's a different pathway.

In that case, nitrate is reduced to ammonium, so the nitrogen is kept within the system.

So denitrification releases nitrogen gas, and DNRA keeps it as ammonium.

Right.

And which pathway is favored can depend on a lot of factors, like the availability of different electron donors and the overall environmental conditions.

Now, on to sulfate and sulfur reduction.

This is where we get that characteristic rotten egg smell of hydrogen sulfide.

Yeah, that's the signature of sulfate -reducing bacteria, which are mostly strict anaerobes, so they can't tolerate oxygen.

They're found in all sorts of anoxic environments, like marine sediments, and they play a key role in the sulfur cycle.

And the chapter explains that sulfate is actually a pretty poor electron acceptor, so they have to activate it first using ATP.

Right.

They convert it to APS or PPS, and then they can reduce it to sulfite, and finally to hydrogen sulfide.

And even though it's not the most energetically favorable process, they've evolved all sorts of tricks to make it work, like flavin -based electron bifurcation and efficient ATP synthesis.

The chapter also mentions that some microbes can use other oxidized sulfur compounds as electron acceptors.

Yeah, like elemental sulfur, thiosulfate, and sulfite.

They're all fair game.

Now, this is where things get really interesting.

Metal reduction.

Microbes breathing metals.

Yeah, it sounds kind of crazy, but they can actually use metals,

metalloids, and even minerals as electron acceptors.

And one of the best studied examples is geobacteria sulfurducens.

This bacterium can oxidize organic compounds and transfer those electrons to things like iron III and manganese oxides.

And they do this using these amazing structures called nanowires.

Yeah, these are electrically conductive poly that they extend out from the cell.

They can actually transfer electrons through these nanowires to metal oxides that are far away.

It's like they have these little tiny wires that they use to breathe.

It's an incredible adaptation.

The chapter also talks about

where arsenate is reduced to arsenite.

And this process can actually lead to the formation of minerals.

Wow.

So microbes can not only breathe metals, they can also create minerals.

That's pretty amazing.

And the chapter even mentions some other less common electron acceptors, like organic and halogenated compounds.

And then there's carbon dioxide, which can be used as an electron acceptor in processes like acetogenesis and methanogenesis.

Okay, so let's talk about those C1 compounds, carbon dioxide and methane.

They seem particularly important in those oxygen -free environments.

Yeah, they play a huge role in anaerobic carbon cycling.

And we'll start with acetogenesis, where microbes use CO2 as an electron acceptor and hydrogen gas as the main electron donor to make acetate.

And they use this pathway called the wood -jungle pathway.

Right, exactly.

It's a pretty amazing pathway.

It involves two branches, the methyl branch and the carbonyl branch.

And they come together to form acetyl -CoA.

And it uses some unique coenzymes and enzymes, like tetrahydrofolate and carbon monoxide dehydrogenase.

And even though the energy yield isn't huge, they have these tricks to maximize their ATP production.

Yeah, they use electron -bifurcating hydrogenases and ion pumps to squeeze out as much energy as they can.

Now, on to methanogenesis, the biological production of methane by methanogens.

And they can use CO2, acetate, methanol, all sorts of things.

But it takes a lot of electrons to reduce CO2 all the way to methane.

Right, it takes eight electrons.

And they're added two at a time through this intricate pathway that involves a bunch of unique C1 carriers and coenzymes.

It's like a little assembly line.

Yeah, and each step is catalyzed by a specific enzyme.

The chapter goes into all the details, but the end result is methane.

And the energy conservation of methanogens can be linked to proton or sodium gradients.

And they use different types of ATPases, depending on whether they have cytochromes or not.

Now, we can't talk about methanogenesis without talking about methanotrophy, right?

The consumption of methane.

And it turns out that microbes can eat methane both in the presence and absence of oxygen.

Exactly.

Aerobic methanotrophs, they use oxygen to oxidize methane.

And the first step is usually catalyzed by methane monoxygenase, or MMO.

And there are two forms of MMO, a soluble one and a particular one.

Right.

And the oxidation of methane, it proceeds through a series of intermediates, methanol, formaldehyde, formate, and finally CO2.

And that formaldehyde, it can be used to build biomass.

And then there's anaerobic oxidation of methane, or AOM.

This happens in places like marine sediments, where there's not much oxygen.

Right.

And it often involves a partnership between

anaerobic methanotrophic archaea, or ANME,

and sulfate -reducing bacteria.

And they might be using those manowires again for direct electron transfer.

That's one possibility.

But they could also be using mediated electron transfer, where they exchange small molecules, like hydrogen gas.

It's all about cooperation, right?

Working together to get the job done.

Exactly.

And the chapter mentions this really interesting bacterium called

methylomeribolus oxifera.

It's a denitrifying methanotroph.

So it couples methane oxidation to the reduction of nitrite.

And there's even a possibility that it can generate oxygen internally.

Wow, that's really pushing the boundaries of what we thought microbes could do.

Yeah, it shows you that there's still so much we don't know about the microbial world.

Okay, we're in the final stretch here.

And we're going to talk about fermentation,

those anaerobic pathways that don't rely on external electron acceptors.

Fermentation is all about maintaining redox balance and making ATP through substrate -level phosphorylation.

Right.

So instead of using an electron transport chain, they're using those energy -rich intermediate compounds to directly transfer phosphate to ADP.

Exactly.

And they have to make sure that for every electron they take out of a substrate, they put an electron back into a product that they can excrete.

So they often produce things like acids, alcohols, and hydrogen gas.

And the chapter highlights the incredible diversity of fermentation pathways.

We've got the lactic acid bacteria, the enteric bacteria, the clostridia, and even those heat -loving archaea.

Each group has its own unique set of enzymes and pathways, and they produce a different mix of end products.

But they all share that basic goal of getting energy in the absence of oxygen.

And the chapter even talks about secondary fermentations, where the products of one fermentation become the food for another microbe.

Yeah, it's like a metabolic relay race.

One microbe passes the baton to the next.

And then we have those fermentations that are coupled to ion pumps.

So they're generating ATP by creating ion gradients.

Right.

Cropionogenium modestum, it couples the decarboxylation of a compound to the pumping of sodium ions.

And that sodium gradient can then drive ATP synthesis.

And oxalobacter formidgines, it uses a proton -consuming decarboxylation and an anti -porter system to create a proton gradient.

So they're not using electron transport chains in the traditional sense, but they're still creating those ion gradients that are essential for ATP synthesis.

Exactly.

And it shows you that there are multiple ways to achieve the same goal.

And finally, we have syntrophy, those cooperative interactions between microbes.

They work together to break down compounds that neither of them could handle alone.

And interspecies electron transfer is a key part of that.

Right.

They can transfer electrons directly through physical contact or nanowires.

Or they can do it indirectly by exchanging small molecules like hydrogen gas.

And both partners benefit.

It's a win -win situation.

And last but not least, hydrocarbon metabolism.

Microbes breaking down those compounds made of just carbon and hydrogen.

And they can do it both aerobically and anaerobically.

Aerobic hydrocarbon catabolism, it usually starts with oxygenation, adding oxygen to the molecule.

And then they bring it down further to produce energy and building blocks.

And anaerobic hydrocarbon metabolism, it's a bit trickier because they can't use oxygen to activate those hydrocarbons.

Right.

So they have to use other strategies.

Sure.

Like adding fumarate to an aliphatic hydrocarbon or reducing the aromatic ring in an aromatic hydrocarbon.

So we've gone through this incredible journey through the metabolic landscape of microbes.

It's really amazing how diverse and ingenious they are.

Yeah.

I think the chapter does a great job of highlighting not just the diversity of metabolic strategies, but also the interconnectedness of everything.

How these different pathways are linked together and how they contribute to the overall functioning of the biosphere.

It really makes you appreciate the invisible world all around us and the essential roles that these microbes play in sustaining life on Earth.

Thanks for joining us on the Steep Dive.