Is the earth microbiome regulating our climate?

Gaia 2.0

Here my prediction - we will find in the upcoming decade that the earth microbiome, that vibrant community of tiny organisms, bacteria, fungi, viruses, diatoms, and phytoplankton in our bodies and in our ecosystems, will be key to understanding how the earth regulates its temperature and water circulatory system.

A helpful analogy to think about in this regards, is that the earth’s microbiome is the assembly language layer of earths operating system. In computers, the base level language is the assembly language. Other languages, like C and Java are written on top of it. If we mess up this assembly language, then we make the operating system built on top of it less functional. This operating system is the Earth’s ecosystems, climate, water cycles, and biogeochemical cycles.

Here’s a dialog between an ecologist, a microbiologist, a security guard, a Gaia researcher, and a complexity scientist to explore this paradigm of the “Earth microbiome regulating the climate”. Towards the end, you will find two conjectures I pose as part of this paradigm : The Microbiome Pump Initiator hypotheis which might explains how the microbiome could regulate the biotic pump, and how it could possibly evolutionary evolve. Also there is the Microbial Teleconnection Regulator hypothesis which explains how microbes could coordinate large scale atmospheric circulation and weather.

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Sam the security guard: Microbes are so small. How could they possibly have any impact on climate?

Ching Wu the complexity theorist: Well, carbon dioxide molecules are tiny too, but they have a massive impact on global warming. Scale doesn't always determine influence.

Sam the security guard: Hmm, you are right. Carbon dioxide molecules absorb radiation and so it affects temperature. But how would microbes affect climate?

Emerson the ecologist: There are a variety of ways. Microbes gave us the oxygen we breathe in the first place. Cyanobacteria transformed Earth's atmosphere billions of years ago. Today, marine microbes like phytoplankton still produce over half of our oxygen.

Microbes influence Earth’s biogeochemical cycles - the natural pathways that move key elements like carbon, nitrogen, phosphorus, and sulfur through the air, water, soil, and living organisms. These cycles impact the planet’s climate. Microbes fix nitrogen from the atmosphere so plants can grow, and plants in turn draw down carbon dioxide. In the soil, microbial communities break down organic matter, releasing CO₂ but also helping lock carbon away for centuries. In the oceans, microbial plankton absorb carbon from the atmosphere and send it into the deep sea when they die. These microscopic processes shape the global carbon budget, influence how much heat the Earth traps, and ultimately help determine whether the planet warms or cools.

And we are finding out more and more that microbes - certain bacteria and fungi spores, are playing a large role in seeding cloud formation, which means they are influencing the earth’s temperature (via clouds reflecting of sunlight) and rain.

Giovanni the Gaia researcher: Wouldn’t it then follow that microbes could be regulating the climate?

Emerson the ecologist: Not necessarily. They're influencing climate, yes, but that doesn't mean they're regulating it in a coordinated way. There's a big difference between impact and regulation. Regulation implies systemic feedback or control, and from an evolutionary standpoint, it's not obvious how earth’s microbiome could evolve to regulate something as vast as global climate.

Ching Wu the complexity scientist: Maybe we can get insight into whether the earth microbiome is regulating the climate or not, by first looking at other microbiomes that do regulate things, like the human gut, the soil microbiome, and the lake microbiome. Because in that context, regulation clearly emerges.

The Gut Microbiome

Mary the microbiologist: That's true. The gut microbiome regulates the immune system through several sophisticated mechanisms. First, there's what we call "immune education." Beneficial bacteria train developing immune cells, especially T-cells, to recognize what's normal versus what's dangerous. They do this by presenting molecular patterns that immune cells learn to associate with "friend" rather than "foe."

Second, they produce specific metabolites, like short-chain fatty acids, that directly influence immune cell behavior. These molecules can promote the development of regulatory T-cells, which act like immune system peacekeepers, preventing overreaction to harmless substances.

Sam the security guard: That sounds like it might be regulation. How does that actually work?

Mary the microbiologist: Exactly, it is regulation. The gut microbiome doesn't just influence the immune system; it actively maintains immune homeostasis through multiple feedback mechanisms.

When pathogenic bacteria try to invade, beneficial microbes detect molecular danger signals and respond by releasing antimicrobial compounds while simultaneously sending chemical messages to immune cells to mount an appropriate defense. But here's the key regulatory aspect: when the immune response becomes excessive, certain gut microbes sense the inflammatory environment and counter-regulate by releasing anti-inflammatory molecules.

This creates a dynamic equilibrium. The microbiome continuously monitors immune activity and adjusts its molecular output accordingly. If inflammation is too low, some microbes can stimulate immune vigilance. If it's too high, others dampen the response. It's like a biological thermostat.

What makes this true regulation is the feedback loops: the microbiome responds to immune system states, which in turn respond to microbial signals, creating a self-correcting system that maintains optimal immune function.

Sam the security guard: But how could this evolve? How could something that's not in a species' genes, i.e the microbes, collaborate so intimately with the species?

Mary the microbiologist: That's the fascinating part, it's co-evolution. The host and microbiome evolved together over millions of years. Our immune system didn't evolve in isolation; it evolved in constant interaction with microbial communities. The microbes that were most beneficial to host survival were selected for, and hosts that could best integrate with helpful microbes had survival advantages.

Our genes code for immune receptors that specifically recognize and respond to microbial molecules. We have genetic pathways dedicated to processing microbial metabolites. Our intestinal structure evolved to provide optimal niches for beneficial bacteria. Meanwhile, the microbes evolved molecular mechanisms to communicate with our immune cells and metabolic systems.

It's like two dance partners who've been practicing together for eons, they've learned each other's moves so well that they appear to be one coordinated system. The collaboration is so ancient and fundamental that our biology is essentially incomplete without it. We're not really individual organisms; we're walking ecosystems.

The Soil Microbiome

Ching Wu the complexity scientist: And this kind of regulation happens in soil too, right?

Mary: Exactly. Soil microbes create even more complex regulatory networks with plants. They regulate plant immune systems through sophisticated molecular dialogues. When a plant root encounters beneficial mycorrhizal fungi, the fungi release signaling molecules that essentially tell the plant's immune system "we're allies, not invaders." The plant responds by allowing the fungi to form intimate connections with its root cells, creating a symbiotic network.

But here's where it gets really interesting, these same microbes can flip the switch when pathogens appear. Beneficial bacteria like Pseudomonas and Bacillus species can detect pathogenic fungi or bacteria in the soil and then release compounds that prime the plant's immune system, essentially putting it on high alert. They're like an early warning system.

[Fungi]

The transpiration regulation is equally fascinating. Certain soil bacteria produce metabolites that influence the plant's stomatal behavior, the tiny pores on leaves that control water loss. When soil moisture is low, some microbes release compounds that signal the plant to close its stomata more tightly, conserving water. When conditions are optimal, they can stimulate more transpiration to enhance nutrient uptake.

For example, research by Cecilia M. Joseph and Donald A. Phillips at UC Davis [1] showed that specific microbial metabolites can directly stimulate plant transpiration by affecting the electrical gradients across cell membranes.

There's also feedback in the other direction. Plants release different root exudates depending on their stress levels, and these chemical signals recruit different microbial communities. If a plant is water-stressed, it attracts drought-resistant microbes. If it's under pathogen attack, it recruits microbes with antimicrobial properties. The plant is essentially calling for help, and the soil microbiome responds by reshaping itself to provide exactly what's needed.

Marika Truu's research [3], showing that air humidity changes soil microbiome composition suggests there's even feedback between atmospheric conditions and underground microbial communities. The soil microbiome is responding to atmospheric signals and potentially influencing plant responses to climate conditions.

Here’s where it could get interesting about the role of microbes with climate. Maybe the soil microbes could sense there is temporarily more moisture in the air, and so cause plants to release more transpiration in order to push the air over saturation humidity so that rain will fall.

The Lake Microbiome

Ching Wu the complexity scientist: Does this kind of microbiome regulation happen in lakes too?

[phytoplankton - a photosynthesizing microbe in water bodies]

Mary the microbiologist: Absolutely. Lake microbiomes are remarkable environmental regulators that actively maintain water quality through multiple sophisticated mechanisms. When a toxin enters a lake, the response is incredibly orchestrated.

First, microbes that can metabolize the toxin begin to thrive—they have a new food source. But it's not just random growth. These microbes release chemical signals called autoinducers that communicate with other microbial species, essentially broadcasting "we have a contamination event, and here's how to respond."

The response involves specialized division of labor. Some bacteria focus on breaking down the toxin into smaller, less harmful compounds. Others produce enzymes that neutralize the breakdown products. Still others begin forming biofilms, sticky, structured communities that work like living water treatment plants. These biofilms don't just randomly stick to surfaces; they strategically position themselves in areas with optimal flow patterns to maximize their filtering capacity.

The biofilm creates microenvironments with different oxygen levels, pH conditions, and chemical gradients. Different microbial species occupy different layers, each specialized for specific detoxification processes. The outer layer might specialize in capturing heavy metals, while deeper layers focus on breaking down organic pollutants.

Here's the key regulatory aspect: the microbiome doesn't just react to pollution, it actively maintains baseline water quality. Beneficial bacteria continuously produce compounds that prevent the growth of harmful algae and pathogens. They regulate nutrient cycling, preventing the buildup of excess nitrogen and phosphorus that could trigger harmful algal blooms.

Through quorum sensing, when microbial populations reach certain densities, they coordinate their behavior. If oxygen levels drop, they can signal each other to shift to processes that don't require oxygen. If pH becomes too acidic, they can collectively produce alkaline compounds to buffer the water. They're essentially performing real-time water chemistry regulation.

The most remarkable part is the system's memory. Once a lake microbiome has dealt with a particular type of contamination, it maintains populations of specialized microbes ready to respond if that contamination reoccurs. It's like an environmental immune system with adaptive memory.

[ see my previous article “Bringing our lakes and oceans back to life: how to deal with algae blooms and polluted waters”, about how John Todd figured out how to nurture this lake microbiome to clean up algae blooms and really toxic lakes. He calls the microbiome nature’s biological intelligence.]

Ching Wu: Don’t lakes and wetlands impact how aquifers recharge?

Mary: Yes, and here microbes play a surprising role. There can be sludge and sediment that accumulates at the bottom of lakes and wetlands, rivers too. The microbes can digest this sediment, and impact how much of that water goes into aquifers. And we know that aquifer can then impact the water cycle in profound ways, as it affects how much landscapes get hydrated into dry season via springs, and how much trees can bring up water to create rain in the dry season. So by impacting aquifer recharge, microbes are having a significant impact on the water cycle.

Emerson the ecologist: So when you put it all together, gut, soil, lake, what we see is that microbial communities can regulate complex systems. They're integral components of the system's feedback loops.

There is also a deeper concept here : that of the holobiont. This is the idea that what we traditionally call an "organism" is actually a collective, a host plus all its associated microbes functioning as a single biological unit.

A human isn't just human cells. We're human cells plus trillions of bacterial, fungal, and viral cells that are essential to our survival. The same is true for plants, a tree isn't just plant tissue, it's plant tissue plus mycorrhizal fungi, plus soil bacteria, plus countless other microorganisms that are integral to its function. Even a lake isn't just water, it's water plus its entire microbial ecosystem working together to maintain stability.

The holobiont concept suggests that the boundaries between "self" and "other" are much more fluid than we thought. The regulation we're seeing isn't separate organisms cooperating, it's components of a larger biological system maintaining homeostasis. The gut microbiome regulating immunity, soil microbes managing plant water use, lake microbes maintaining water quality, these aren't examples of cooperation between different entities. They're examples of integrated biological systems regulating themselves.

This could change how we think about evolution. Selection isn't just acting on individual organisms; it's acting on entire holobionts. The most successful combinations of hosts and microbes persist and reproduce together.

Giovanni the Gaia researcher: And if they can regulate a gut, or a lake, or a forest, why not a planet? Maybe Earth itself is a holobiont, with the planet as the host and the global microbiome as the regulating partner. That’s what Gaia theory is about. The Earth's microbiome could then regulate the climate in the same way gut microbes regulate immunity or soil microbes regulate plant health.

Emerson the ecologist: But wait up, there's natural selection driving evolution, but how could these microbes evolve to influence climate? I can see how the gut microbiome and immune system could evolve together over millions of years. They're in constant, intimate contact. The microbes that helped their host survive got passed on, and hosts that could best work with beneficial microbes thrived. It's proximity-driven co-evolution.

But when you're talking about climate regulation, you're talking about microbes on land somehow evolving to influence atmospheric conditions that are physically distant from them. A soil bacterium in the Amazon is separated from the global atmosphere by vast spatial scales. How could there be the kind of direct feedback necessary for co-evolution? The gut microbiome gets immediate feedback from the immune system it's regulating, if it helps the host, it survives. But how would a microbe "know" it's helping stabilize global climate, and how would it be selected for that function when the climate system is so far removed from its immediate environment?

Ching Wu the complexity scientist: But evolution isn't just natural selection, it's also dynamical systems evolution. Think about Daisyworld, James Lovelock's famous model he made to back up his Gaia hypothesis. In Daisyworld, you have a planet with black daisies that absorb heat and white daisies that reflect it. As the sun gets brighter, black daisies heat up their environment, creating conditions that favor white daisies. The white daisies then cool things down, eventually creating conditions that favor black daisies again. Neither daisy is trying to regulate planetary temperature, but the system naturally evolves toward temperature stability through these feedback loops.

The key here is iteration and dynamical systems theory. Systems don't just evolve through direct selection, they evolve toward attractors in the energy landscape. They can be many perturbations over many iterations it finds the attractors. Think of perturbations like wind or fire for dynamical systems, as similar to the mutations of genes in natural selection. Perturbations and mutations are a way of searching phase space for more optimal and efficient solutions.

Heres the key point : microbes can go up and seed clouds every day. They literally become cloud condensation nuclei, which changes temperature and rainfall patterns. This creates a feedback loop because that temperature and rainfall directly affects the soil microbiome and their impact on plants. Which in turn affects transpiration, which affects atmospheric moisture, which affects cloud formation, which affects the microbes that seed those clouds.

It's a feedback loop that can adjust itself through iteration. The system doesn't need conscious intent, it just needs repeated cycles where atmospheric conditions influence microbial communities, which influence plant behavior, which influences atmospheric conditions. Over hundreds of thousands of iterations, this system could evolve toward climate stability through dynamical systems evolution toward the most stable attractor state, which then combines with natural selection to amplify those genes which guide towards these attractor states.

Giovanni: There's an interesting phenomenon trees can influence climate via the water cycle. I wonder if it might suggest an idea for microbes influencing climate. The Amazon rainforest actually calls in the rain by changing large-scale circulation, shifting the rainy season earlier by about two months. Makarieva and Gorshkov have proposed a biotic pump theory where transpiration from the forest condenses to create a partial vacuum that draws in ocean winds. The atmospheric scientist Rong Fu has proposed a similar theory, with a latent heat mechanism instead of the vacuum effect.

Emerson: That biotic pump phenomena is hard to understand from an evolutionary viewpoint. Why would trees of so many different origins all coordinate their transpiration two months earlier? This would actually reduce their individual fitness unless there was a critical mass of trees doing it simultaneously. But the critical mass required is so high that it seems evolutionarily unlikely, how could enough trees of different species coordinate without communication?

Mary: I think I might have an idea for how. It could be to do with the forest microbiome. Forests are connected by vast mycelial networks, fungal threads that link root systems across entire forests. These networks don't just transport nutrients; they carry chemical signals that can coordinate forest-wide responses. They work with the bacteria and other parts of the forest microbiome.

The forest microbiome could be the coordinator. When environmental conditions signal that earlier transpiration would be beneficial, the mycelial network could simultaneously signal trees across vast areas to begin their transpiration response. It's like a forest-wide nervous system, with the microbiome as the information processor.

At the same time the microbiome is coordinating transpiration, it could also be releasing more microbes and fungal spores into the atmosphere to seed the condensation of that transpiration. The forest microbiome isn't just coordinating the pump, it's also providing the condensation nuclei that make the pump work more efficiently.

Emerson: The wet season is normally started by this giant rainband across the arth called the ITCZ, that moves north and south with the season. But the wet season is strted earlier in the Amazon, when the forests divert that ocean moisture. How would the microbes know when to time this.?

Mary: Well we know the soil microbiome can sense humidity, and it has seasonal awareness, so it could learn over the course of millions of years to evolve with the seasons.

Sam: So you're saying the forest microbiome is like the pump initiator? It coordinates the trees to transpire together and then seeds the clouds to make sure that transpiration actually creates rain? We could call it the Microbiome Pump Initiator hypothesis.

Emerson: I'm wondering, do we have an Earth microbiome, or more just a lot of regional microbiomes that are not in large scale coordination?

Ching Wu: There are actually a lot of microbes in the wind. When they land, they affect that regional microbiome. And these microbes blow across oceans to other continents, so they could all be coordinated through this exchange.

This reminds me of a simulation by Tim Lenton called Flask World. He had many flasks, each with their own microbiome, connected by tubes. The various flasks would coordinate with all the other flasks to reach a homeostatic state. Each flask was unique, but there was also emergent coordination across all flasks. Flask world should be a scale invariant model, so you could imagine it working at a much larger continental scale. [2]

So a similar way, the microbiome could coordinate across continents. And when it does this, because soil microbiomes can sense humidity and temperature, it can then adjust its behavior. So it's possible that global winds, temperature via clouds, and rainfall have some coordination via millions of years of iteration.

Sam: So is the Earth microbiome intelligent to some degree? Does it have learning, memory, and the ability to regulate?

Ching Wu: We see in the gut, soil, and lake that the microbiome has emergent intelligence, it communicates and coordinates. If we argue the same evolutionary iteration that lead to those abilities to emerge, could also happen via the everyday microbe-weather interactions, and because there is a continent to continent exchange, then concievably there could be an earth microbiome intelligence.

In complex systems, if a system undergoes many iterations, it evolves over time. There is this concept called a fitness landscape, where a hill is a place of higher fitness. So as you wander around this landscape, you have to go down into a valley, and then come to another hill. Over time, you can find higher and higher hills. So over a million years, this coupled microbe-climate system can evolve to higher hills, higher fitness levels, where they are mich more coordinated.

Mary: Can I get an example of this?

Giovanni: Well we know the soil microbiome can sense temperature. If it gets hotter, it could send signals to the plants to transpire more, to transpire less, or not send signals. When enough plants transpire more, they can create lower clouds, which reflect more sunlight and cool the earth. Now imagine there are mutations or pertubations happening everyday in the soil microbiome, of what signals it sends to the plants based on temperature, or its memory of temperature over past season ( the microbiome has a memory). These signals can then lead to more clouds, less clouds, or no shift. If there is more clouds, and more rain, this can then be beneficial to certain types of microbes in the soil, so those microbes get selected for. Over millions of years of iteration, this combination of dynamical systems evolution coupled with natural selection, could lead to the soil microbiome being able to regulate the temperature for what is most optimal for itself.

Sam: Trees naturally affect how much rain there is downwind by how much they transpire. Would there be any evolutionary reason for trees to regulate their transpiration to best benefit rainfall for ecosystems downwind of it, maybe even 500 miles away.

Ching Wu: Well from a conventional evolutionary viewpoint, they doesn’t seem to be an obvious reason at first glance, why trees in one place should work to get water to ecosystems far away from it. However this microbiome viewpoint gives me an idea.

Microbes are constantly getting blown downwind, and through that they can send signals between ecosystems hundreds of miles apart. Lets call the upwind location X, and the downwind location far away Y. X releases microbes that travel to Y. The soil microbiome at Y can use that as a sign of what is happening at X. Now wind reversals happen once in a while, even if there is a more commonly prevailing wind. That soil microbiome at Y then sends microbes in air, that reach X. Those microbes can impact what the trees do at X. Now we can imagine random mutation of response to each of these microbe signals.

Over millions of iterations, this system begins to find the hills in the fitness landscape, the more energetically favorable states. And a more energetically favorable state could be that when atmospheric humidity gets to a certain point, the trees at X release some extra transpiration, so that Y is more likely to get more rain.

Sam: Does this work across continents too?

Ching Wu: Yes. We know from climate researchers like Roni Avissar and Abigail Swann in a field called teleconnections, that the change in forest on one continent will affect climate on another continent via the forests impacts on jets streams, Hadley cells, El-nino, and Rossby waves, which are cross continental atmospheric phenomena. Now if microbes also blow from continent to continent, over millions of years they could be a cross-continental coordination to influence forest transpiration, which would then influence jet streams, Hadley cells and their ilk. Which means global atmospheric circulation patterns may be being regulated by microbes.

Sam: Wow this is wild. Maybe we can call this the Microbial Teleconnection Regulator hypothesis.

Ching Wu: So the emergent picture is : these nano-size particles gather in large communities inside organisms and different ecological niches, coordinating with their hosts, symbiosising into new functioning wholes; they travel in groups around the globe, and upon reaching new places they pass messages on from where they’ve been, coordinating with their new communities. They seed clouds, and impact global temperature and rainfall, and in so doing provide resources for the communities of nano-size particles below.

Mary: That’s a cool visual.

Giovanni: Isn’t pharmaceuticals and synthetic agriculture fertilizers creating a lot of problems in our environment, and destroying environmental microbiomes.

Mary : Yes indeed it is. As scientists figure out the large role microbes have on our climate I think it will kick off a climate movement to get off our dependence on pharmaceuticals and synthetic agriculture fertilizers.

Ching Wu: It’s time for a cutting edge earth-climate microbiome research programme for microbiologists and climate scientists to coordinate on.

Sam: This picture of the earth microbiome regulating the climate is blowing my mind, its nothing like what I learnt in school.

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References

[1] Joseph, C. M., & Phillips, D. A. (2003). Metabolites from soil bacteria affect plant water relations. Plant Physiology and Biochemistry, 41(2), 189-192

[2] Williams, Hywel TP, and Timothy M. Lenton. "The Flask model: emergence of nutrient‐recycling microbial ecosystems and their disruption by environment‐altering ‘rebel’organisms." Oikos 116, no. 7 (2007): 1087-1105

[3] Truu, M, Tullus, T., Parts, T., & Sellin, A. (2017). Elevated Air Humidity Changes Soil Bacterial Community Structure in the Silver Birch Stand. Frontiers in Microbiology, 8, 557