Chapter 28: Biogeochemical Cycles & Microbes in Climate Change

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Today we're looking at something fundamental,

almost invisible, the microbes running our planet's chemistry, and crucially, how the balance they maintain is now tied up with global instability.

The thing that really jumped out at me first was this, well, startling link between climate change and infectious diseases spreading.

It is quite jarring, isn't it?

You think of things like malaria, dengue, even the plague as sort of tropical problems or historical ones, but now they're appearing or getting worse in places like, you know, Wyoming, Idaho, Texas, places you wouldn't expect.

Absolutely.

I saw reports mentioning malaria vectors in Michigan, New York, dengue vectors up near Chicago, even crossing into Europe.

It's a real shift.

And it's not just random.

There is a clear mechanism tied to warming.

Higher temperatures literally expand the habitable zones for these insects, the vectors, but it also does more.

It speeds things up.

Their breeding seasons get longer.

They reproduce faster.

And maybe most importantly, they need to feed more often.

They bite more.

Ah, so more bites mean more chances to transmit disease.

Exactly.

It ramps up the risk significantly for, well, for all of us.

That's the immediate health scare.

But the underlying planetary system, the big picture, you've termed biogeochemical cycling.

What's the mission here getting a handle on this?

Yeah, the mission is really to understand the immense power microbes wield over the elements.

Biogeochemical cycling, it's basically the sum total of everything microbes, physics, and chemistry do to move elements around.

We're talking carbon, nitrogen, sulfur, iron, manganese, cycling between sediments, water, the atmosphere.

The major reservoirs.

Precisely.

And microbes are the key players driving these huge fluxes.

We need to grasp how these cycles normally keep things stable, support life, and critically why our industrial activities are throwing it all out of whack, accelerating climate change.

Okay, let's unpack this.

If microbes are the drivers, there must be rules they follow.

You mentioned redox potential as being fundamental.

That's the core principle, yeah.

Redox potential, or it's simply a measure of how willing a chemical system is to gain or lose electrons.

Think of it like electrical potential, but in a chemical soup.

Okay.

For microbes in the environment, it dictates two absolutely vital things.

One,

which oxidized compounds are around to act as terminal electron acceptors.

That's basically how they breathe without oxygen.

Like using nitrate instead of O2.

Exactly.

And two, what reduced molecules are available to be used as electron donors as their energy source.

Chemolithotrophs rely on this.

So imagine you're a microbe deep down in sediment where there's no oxygen.

How do you decide what to breathe?

It's all about energy efficiency.

Nature follows the path of least resistance, or I guess most energy gain.

If you visualize a core sample, maybe from lake sediment or waterlogged soil, oxygen drops off really fast as you go down.

Right.

Once O2 is gone, microbes switch to anaerobic respiration, and they use the available electron acceptors in a strict order, a hierarchy based on how much energy they get from the reaction.

What's the order?

Oxygen gives the most energy, so it's used first.

Then comes nitrate, NO3.

After that, manganese oxides, like MNIV.

Then iron oxides, FATPEN3.

Then sulfate, SO42.

Only when pretty much all of those are depleted does methanogenesis, making methane, really kick in at the bottom.

It's a clear vertical zonation.

Microbes have found ways to bridge these zones.

The example of cable bacteria was fascinating.

It sounds like science fiction.

It really does.

Cable bacteria are, well, they're amazing.

They are these multicellular filaments, technically delta proteobacteria.

Normally the stuff they eat, sulfide is down in the anoxic zone, but the stuff they breathe, oxygen, is up at the surface.

Big separation.

How do they manage?

They use gliding motility to physically form a long filament, sometimes centimeters long, connecting the two zones.

Cells at the bottom end oxidize sulfide, taking electrons.

Then they pass those electrons, literally cell to cell along the filament, like a biological wire, all the way up to the cells at the top, which use oxygen to get rid of the electrons.

They bridge the redox gap physically.

Incredible biological engineering.

Okay, so if redox is the rule book, carbon must be the main currency, right?

Cycling between organic matter, methane, CO2.

It absolutely is.

Carbon defines life as we know it.

It cycles between its reduced forms, like organic compounds and methane, CH4, and its oxidized forms, mostly CO2, but also CO.

And carbon fixation, turning CO2 into biomass, is the starting point.

It is.

And while we think of plants and trees, we often forget the microbes.

Marine microbes, particularly tiny cyanobacteria like Prochlorococcus and Cynichococcus, are responsible for at least half of all the carbon fixed on earth.

Half.

That's huge.

It is.

And that's not even counting fixation happening in weird places, like deep subsurface environments using processes like anoxygenic photosynthesis or chemosynthesis without lighter oxygen.

Now, the sources also flag methane, CH4.

You mentioned methanogenesis happens way down the redox ladder.

And it's potent stuff.

Very potent.

About 30 times the warming potential of CO2 over the medium term.

And producing it, methanogenesis, is an exclusively anaerobic process.

It involves reducing carbon, like CO2 with hydrogen or acetate, down to CH4.

And here's the kicker.

Only archaea can do it.

No bacteria, no eukaryotes.

Just archaea.

Where does most of it come from?

Major sources globally are things like wetlands, rice paddies, which are artificial wetlands, the digestive tracts of ruminant animals like cows and landfills.

Oh, the cycle has a counterbalance, right?

Methanotrophy.

Thankfully, yes.

Methanotrophy is the consumption, the oxidation of methane.

Keeps a lot of it from reaching the atmosphere.

How does that work?

It can happen aerobically using oxygen.

Certain proteobacteria specialists said this.

Or it can happen anaerobically.

We now know archaea can oxidize methane using other electron acceptors like nitrate, sulfate, or even iron.

It's a crucial sink for methane.

Okay, good time to clarify two key terms you see a lot when discussing carbon cycling.

Mineralization and immobilization.

What's the difference?

Good point.

Mineralization is basically decomposition, breaking down complex organic stuff back into simple inorganic molecules like CO2, ammonia, NH3, methane, CH4.

It releases nutrients back into the environment.

Makes them available again.

Right.

Immobilization is the opposite.

It's when microbes take up those simple inorganic nutrients and incorporate them into their own cells, their biomass.

So the nutrients are locked up, temporarily unavailable for cycling until that microbe dies or gets eaten.

The balance between these two really dictate soil fertility and nutrient flow.

And the speed of mineralization varies wildly.

Lignin, the woody stuff in plants, seems particularly tough to break down.

Oh, lignin is incredibly stable.

It's a complex polymer.

Breaking it down effectively requires oxygen.

Specific fungi and some bacteria like streptomycetes use oxygen dependent enzymes to sort of oxidatively chip away at it.

So in places without oxygen.

Exactly.

In waterlogged anoxic environments like peat bogs or deep sediments, lignin degradation basically grinds to a halt.

That's why peat bogs accumulate massive amounts of carbon over millennia.

It gets locked away.

Okay, let's shift gears to nitrogen.

If carbon was complex, nitrogen seems even more so, cycling through a whole range of oxidation states.

It really is more complex chemically.

Nitrogen can exist in states from MnO3, that's ammonium NH4 plus A, all the way up to plus 5, which is nitrate NO3.

And several steps in between, like N2 gas, 0 nitrous oxide N2O plus 1, nitric oxide NO plus 2, nitrate NO2 plus 3.

This wide range means its role changes dramatically.

Ammonium can only be an electron donor.

Nitrate can only be an electron acceptor.

And things in the middle, like nitrate, can actually be both depending on the conditions and the micro.

The cycle starts with getting nitrogen into a usable form, right?

Nitrogen fixation.

That's the critical input step.

Yes.

Taking inert nitrogen gas N2 from the atmosphere, which makes up almost 80 % of it, but is useless to most life, and reducing it to ammonia, NH3.

This is done only by certain bacteria and archaea, think azotobacter, clostridium, or rhizobium in plant roots.

They possess the special enzyme nitrogenase.

Which is sensitive to oxygen, ironically.

Highly sensitive, yeah.

So they have various strategies to protect it.

But this fixation is what brings new usable nitrogen into the biosphere, often the limiting nutrient for growth.

Once it's fixed, we get into nitrate reduction.

And there are two very different paths here.

Assimilatory and dissimilar.

Yes.

And it's vital to distinguish them.

Assimilatory nitrate reduction is straightforward.

The microbe takes up nitrate, or nitrite, and reduces it just enough to incorporate the nitrogen into its own biomass, amino acids, nucleic acids, etc.

It's using it as a nutrient source.

Right.

Dissimilatory nitrate reduction, on the other hand, is about energy.

The microbe uses nitrate, or other nitrogen oxides, as a terminal electron acceptor for anaerobic respiration, like breathing nitrate instead of oxygen.

This process, often come denitrification when it goes all the way, reduces nitrate completely back to N2 gas.

Does that remove nitrogen from the ecosystem?

It does.

It returns it to the atmosphere.

But, and this is critical for climate change, intermediate gases, like nitrous oxide, N2O, often leak out during this process.

And N2O is a very potent greenhouse gas.

Right.

Now, flipping back to oxidation, turning ammonia back into nitrate, that's nitrification.

Used to be taught as a two -step relay.

That was the classic you, yeah.

Nitrification.

Oxidizing ammonium, NH4 +, all the way to nitrate, NO3.

It's an aerobic process.

For decades, we thought it always required two distinct groups of microbes.

One group, like nitrosomonas, oxidizes ammonium to nitrate, NO2.

Then a second group, like nitrobacter, takes over and oxidizes nitrate to nitrate, a microbial bucket brigade.

But then came chamamix, a shortcut.

Exactly, a game changer.

The discovery of chamamix, which stands for complete ammonia oxidation, revealed that some bacteria, specifically certain species within the genus Nitrosperia, can actually do the whole job themselves.

One organism takes ammonium all the way to nitrate.

It simplifies the process and changes how we think about nitrogen flow in many environments.

Nature loves efficiency.

And speaking of efficiency, there's another major shortcut.

Anamix.

Anamix is fascinating.

Anoxic ammonium oxidation.

It's performed by a unique group of bacteria, the planktomycetes.

They do something really clever.

They took ammonium, NH4 +, as the electron donor, and used nitrate, NO2, as the electron acceptor under anoxic conditions.

And the product?

Nitrogen gas and, two, directly.

It completely bypasses the nitrate step and nitrification demitrification in some ways.

It's incredibly useful in wastewater treatment, for example.

A very efficient way to remove ammonia pollution without needing lots of oxygen for nitrification.

Okay, so we've hit the big ones, carbon and nitrogen.

But the picture isn't complete without touching on others like sulfur and iron, right?

They all interconnect.

Absolutely.

The sulfur cycle, for instance, mirrors nitrogen in some ways with its range of redox states.

A key process is dissimilatory sulfate reduction.

Here, sulfate, SO42, acts as a terminal electron acceptor in anaerobic respiration, mainly by delta proteobacteria like disulfovibrio.

The product is sulfide, H2S.

The rotten egg smell.

That's the one.

Common in marine sediments, marshes.

But sulfur also has this proposed climate connection.

Something about clouds.

Ah, yes.

The DMS hypothesis.

Marine phytoplankton produce a compound called DMSP.

When bacteria in the water metabolize this DMSP, they release dimethyl sulfide, or DMS.

DMS is volatile, goes into the atmosphere, and it's thought that the oxidation products of DMS can act as cloud condensation nuclei tiny particles that water vapor condenses onto to form clouds.

So more DMS could mean more clouds.

That's the idea.

More clouds could mean more sunlight reflected back to space, potentially having a slight cooling effect.

It's a proposed natural feedback loop, a sort of microbial climate regulation.

Still debated how strong it is, though.

Interesting.

And iron.

Seems simple, just rust.

F2 +, and V3 +, C.

Conceptually simple, but environmentally huge.

Oxidized iron F3 +, R is abundant and often acts as a terminal electron acceptor for anaerobic microbes' dissimilatory iron reduction.

They breathe the rust.

Conversely, the reduced form, F2 +, R, which is soluble under acidic conditions, can be used as an energy source, an electron donor, by chemolithotrophs, like acidothiobacillus ferroccidens in acid mine drainage.

They eat iron ions.

Essentially, yes.

Oxidizing F2 +, to Fe3 +, M10.

This microbial iron oxidation likely played a massive role in forming ancient geological deposits, like banded iron formations.

We should also briefly mention mercury,

a chilling example of microbial transformation making something far worse.

Mercury is the poster child for

biotransformation gone wrong, from a human perspective.

Inorganic mercury, maybe from pollution or natural sources, can accumulate in anaerobic sediments.

Certain anaerobic bacteria, including some sulfate reducers like disulfovibrio again, have enzymes that methylate the mercury.

They add a methyl group, CH3.

Creating methyl mercury.

Exactly.

And methyl mercury is volatile, fat soluble, and nasty.

The real danger comes from biomagnification.

It gets into the food chain, and its concentration increases dramatically at each trophic level.

Small fish eat plankton, big fish eat small fish, we eat big fish, and the mercury concentration skyrockets.

Leading to severe neurological damage, like the tragedy in Minamata Bay, Japan.

Precisely.

A direct consequence of microbial metabolism altering a pollutant.

So the big takeaway is that none of these cycles, carbon, nitrogen, sulfur, iron, mercury, work in isolation, do they?

Not at all.

They are deeply intertwined.

Think about chemolithotrophs again, the rock eaters.

To get enough energy to fix just a little bit of CO2 into biomass, they have to oxidize huge quantities of reduced inorganic stuff like ammonium sulfide, or Fe2 plus L.

So they directly link the carbon cycle to the N, S, and phi cycles.

And nutrient limitation links them too.

Absolutely.

Leibig's law of the minimum often applies growth is limited by the essential resource.

Very often, especially in marine systems, that's fixed nitrogen.

So the rate of nitrogen fixation, bringing new nitrogen into the system, can directly control the rate of carbon fixation and overall productivity.

The cycles constrain each other.

Which brings us, inevitably, to the current situation.

Global climate change.

This is essentially biogeochetical cycling thrown out of balance by us.

Fundamentally, yes.

And left be clear on terms, global warming is the observed increase in global temperatures.

Global climate change is the broader pattern changes in wind, precipitation, ocean currents, extreme weather driven by that warming.

The drivers are greenhouse gases, primarily CO2, methane, CH4, and nitrous oxide, and 2O, which trap heat radiating from Earth's surface.

The CO2 numbers are stark.

Pre -industrial levels were around 278 parts per million.

Now we're over 400 ppm, maybe pushing 420.

And climbing.

The main causes are burning fossil fuels, releasing carbon locked away for millions of years in deforestation, removing the trees and plants that act as carbon sinks.

We're putting it into the atmosphere way faster than natural cycles can remove it.

That's the crux of the problem.

The rate of input overwhelms the rate of removal by oceans and terrestrial ecosystems, including microbial processes.

And methane, CH4.

As we said, much more potent per molecule than CO2, roughly 30 times over 100 years.

Its atmospheric concentration has shot up about two and a half times since the pre -industrial era, largely from agriculture, fossil fuel extraction, waste decomposition.

And then there's the nitrogen crisis, driven by fertilizer.

This is huge and maybe less discussed than CO2.

The invention of the Haber -Bosch process allows us to industrially fix massive amounts of nitrogen gas into ammonia, NH4 plus, for fertilizer.

We're now adding as much fixed nitrogen to the land through fertilizer as all natural processes combined.

It's doubled the input.

What does all that extra ammonia do?

Well, some is used by crops, but a lot isn't.

It runs off into rivers and lakes, causing eutrophication algal blooms that deplete oxygen and kill fish.

Or it stays in the soil and fuels microbial processes.

Specifically, nitrification, followed by denitrification.

And denitrification produces N2O.

Exactly.

That excess fertilizer supercharges the microbes, making nitrous oxide N2O.

N2O is incredibly potent, about 280 times the warming potential of CO2.

And it stays in the atmosphere for over a century.

The result being?

We now have the highest atmospheric N2O concentrations in at least 650 ,000 years, based on ice core data.

It's a direct consequence of feeding ourselves through industrial agriculture.

So adding it all up, where does that leave us?

It leaves us with a measurable global average temperature increase of about 0 .8 degrees Celsius since 1880.

But two -thirds of that warming has happened just since 1975.

The acceleration is clear.

Projections for the end of this century, depending on our emissions pathway, range from a further 1 degree C rise to potentially catastrophic rises of up to 6 .4 degrees C, or even more in some scenarios.

And microbes, which historically maintain the balance, are now both impacted by these changes and will be critical players in determining how fast and how far these changes go in the future.

Their feedback loops are crucial.

It really is a profound connection.

So for you listening, the key synthesis seems to be microbial life, governed by fundamental energy rules like redox potential, built and maintained the chemical balance of our planet through these vast elemental cycles.

But our industrial scale, particularly our energy system based on fossil fuels and our food system based on synthetic fertilizers, is completely overloaded the microbial capacity to cycle greenhouse gases like CO2 and N2O, tipping your planet's energy balance.

Which leaves us with a final thought, maybe a challenge.

We've seen how microbes can make things worse, like methylated mercury.

But we also saw examples like dechlorosoma, using human pollutants like perchlorate to breathe while oxidizing iron.

There's immense metabolic diversity out there.

So the question becomes, can we get smarter about harnessing this microbial ingenuity?

Could we perhaps leverage specific chemolithotrophs or other metabolic pathways to help us actively clean up pollution?

Or maybe even find ways to enhance the microbial drawdown of greenhouse gases in soil or oceans.

It's a frontier where microbiology meets planetary engineering.

A fascinating, and perhaps necessary, challenge for the future.

Connecting the very smallest life forms to our very largest planetary problem.

Thank you for walking us through this incredibly important topic.

And to you, our listeners, thank you for joining this deep dive.

Keep exploring the science that connects us all.