How bacteria, fungi and plants evolved paleo-rain

Bacteria and fungi were here on earth long before plants and animals, laying the groundwork for what followed.

The biologist Lynn Margulis, who made a key discovery on the origin of eukaryotes and the important role of symbiosis in evolution, spent much of her career arguing that bacteria were not merely early life, later superseded by more complex forms. They were, and remain, the foundational layer on which everything else runs, something closer to an operating system than a set of primitive ancestors. Bacteria are everywhere: in soils, in oceans, in the tissues of plants and animals, in the air above continents and the ice of glaciers. They worked their way into the cells of early eukaryotes and became the mitochondria that now power almost all complex life. They thread through the roots of plants, line the guts of animals, and cycle through the atmosphere in quantities we are only now beginning to measure. To understand how Earth’s atmosphere and climate evolved, Margulis argued, you had to understand how microbes co-evolved with them, not as passengers on a physical planet but as active participants shaping its chemistry, its gases, its climate, its conditions for life. The planet and its microbiome, in her view, were not separable things. They had been making each other for billions of years.

The atmosphere we breathe is, in large part, a microbial construction. The Great Oxygenation Event, the transformation of Earth’s atmosphere by photosynthetic bacteria some 2.4 billion years ago, made aerobic life possible and remains the most dramatic single intervention any life form has made on a planetary scale. But the microbial shaping of the atmosphere did not stop there. Nitrogen cycles through denitrifying bacteria in soils; the nitrogen-to-oxygen ratio in the air is the outcome of billions of years of microbial fixation and denitrification running in metabolic counterpoint. Methane, which should not persist in an oxygen-rich atmosphere since it reacts and disappears within a decade, is continuously replenished by methane-producing archaea in ocean sediments, wetlands, and animal guts. Bacteria cycle carbon in and out of the atmosphere, influencing Earth’s temperature across geological time. Each of these processes reflects the same underlying reality that Margulis identified: microbes do not merely inhabit the Earth’s chemical systems, they drive them.

Water is part of the atmosphere too, and here as well, bacteria and fungi, joined eventually by plants, have played a foundational and still underappreciated role.

[Proterozoic Eon]

During the Proterozoic Eon, roughly 2,500 to 541 million years ago, and into the early Ordovician Period, land was almost entirely lifeless to the naked eye. Microbial mats clung to certain wet surfaces, but the continents were bare: rock, wind, and light. When rain fell, it struck mostly unweathered mineral surfaces, pooled briefly, and sheeted off. Without roots or biological structure to interrupt the flow, water followed the nearest gradient to the sea. Very little soaked in.

Without plants, there was no transpiration, no mechanism for recycling water vapor back into the atmosphere from continental surfaces. As a moisture-laden air mass moves inland from the ocean, it loses water each time it rains. Without anything to return that water to the atmosphere, each successive rainfall event has less moisture to work with than the last. This results in exponential decay: heavy rain near the coasts, thinning rapidly as the air mass travels inland, until the continental interior receives almost nothing. The hydrological cycle over land was shallow and simple: ocean evaporation, inland delivery, surface runoff, return to sea.

Geologists reconstructed this ancient hydrology from the rock itself. Evaporites are sedimentary deposits formed when water evaporates and leaves dissolved salts behind, and they are among the most useful witnesses to ancient hydrology. When a lake or shallow sea evaporates completely, it leaves a chemical signature: sequences of gypsum, halite, and other minerals that precipitate in a specific order as salinity increases. Their presence and position tell geologists where standing water existed and how long it stayed. River geomorphology and floodplain sediments extend the picture further. Together they sketch a hydrological map of the ancient world.

Then life began to move onto land, and bacteria and fungi paved the way. After the microbial mats came fungi with their hyphae: threads so thin they could slip into microscopic cracks in rock. Lichens followed, ancient partnerships between fungi and photosynthetic algae or cyanobacteria that dissolve rock with acid and anchor to surfaces nothing else can colonize. These were road-builders, crumbling mineral surfaces into particles, creating the first rough substrate that something else might root in.

The first primitive plants, mosses and liverworts, appeared across damp margins and coastal flats. They had no deep roots, no leaves in the modern sense. They clung close to the ground, vulnerable to drying out. But they were connected, through mycorrhizal partnerships, to fungal networks that extended their reach into the mineral world, scavenging phosphorus, tracing faint films of water, dissolving rock with chemical persistence. In return, the plant fed the fungi carbon captured from sunlight. Energy flowed downward; water and nutrients flowed up. A small, fragile plant became, in effect, a distributed organism, one that threaded itself through the ground so completely that the boundary between plant and fungus lost meaning.

What this consortium was building, slowly, patch by patch, across millions of years, was the soil sponge. A soil with intact fungal networks and microbial communities is structured, porous, biologically active material with a fundamentally different relationship to water than bare rock. Rain that falls on it infiltrates rather than runs off. It is held in pore spaces, made available to roots over days and weeks. The building of the soil sponge enabled more precipitation recycling, allowing water to travel further inland.

. [vascular plants in Devonian period 419-359 million years ago]

The geomorphic signature of this transition is readable in the rock. Sedimentary sequences from the Silurian-Devonian Terrestrial Revolution, the period from roughly 428 to 359 million years ago when vascular plants first spread across coastal lowlands, show the braided, episodic channel patterns of bare-land drainage beginning to give way, first patchily then more broadly, to the finer-grained, more organized deposits that indicate stabilized banks and sustained flow. Evaporite deposition in continental interiors began to shift, becoming less extreme at the margins, consistent with slightly longer water residence times and modest increases in inland rainfall. Early vascular plants, drawing water from soil and releasing it through transpiration, began extending the reach of ocean moisture a little further inland. They were creating precipitation recycling.

Dan Ibarra, while a postdoc at Stanford, modeled this, demonstrating that the evolution of land plants and the expansion of their transpiration flux produced measurable increases in continental interior rainfall consistent with the geological record [Ibarra 2019]. The effect was limited though. Without deep roots or large leaf surfaces, these early plant communities could intercept and return only modest amounts of water to the atmosphere. They slowed the exponential decay of moisture slightly, nudging rain a little further inland, but not all the way to the interior.

The real transformation came in the late Devonian and into the Carboniferous Period, approximately 359 to 299 million years ago, when the first forests spread across the continents. Now Earth had tall trees with deep roots, dense canopies, and vast swampy ecosystems, and with them came more biological control of the water cycle at continental scale.

. [Carboniferous period 359-299 million years ago]

The geomorphic record captures this transition. The shift from braided to meandering river systems, a fingerprint of vegetation stabilizing floodplains and moderating flow, occurs broadly across this interval in multiple continental sequences. Evaporite deposition in continental interiors declined dramatically through the Carboniferous, consistent with rainfall now penetrating far inland, water residence times lengthening substantially, and basins becoming well connected to drainage networks. This was a different order of change from what early vascular plants had produced. Where those earlier communities had only slowed the inland decay of moisture, forests broke it. A single large tree can transpire hundreds of liters of water a day across multiple layers of leaves, returning that water to the atmosphere to fall again further inland. A forest does this across millions of trees simultaneously, passing moisture from canopy to cloud to rain in a relay that can carry ocean water deep into continental interiors that had previously been hydrological dead zones.

Forests help make rain. But forests do not exist in isolation. They grow out of a foundational layer of bacteria and fungi that has been here far longer, and that layer is not merely supporting the forest. It is actively involved in making the rain alongside it.

Over the past half century, a convergence of ideas across biology, ecology, and Earth science has led some portion of scientists to see life not so much as made of individuals but as assemblies, layered systems in which microbes and fungi are not supporting actors but foundational ones. Plants and animals are not separate from this microbial world. They are built within it, and sustained by it.

Lynn Margulis’s work on endosymbiosis showed that the cells of every plant and animal are themselves mergers of once-independent bacteria. The mitochondria that power our cells, and the chloroplasts that enable plants to photosynthesize, were not invented from scratch. They were absorbed. If the most basic units of complex life are already symbiotic, then the idea of a clean, autonomous organism begins to unravel.

In soils, where most terrestrial life begins, the visible world of roots and stems is embedded in a dense, dynamic microbial matrix. Bacteria and fungi break down rock, recycle nutrients, and structure the physical environment in which plants grow. Plants do not simply draw nutrients from this world. They are entangled with it. Through their roots, they trade carbon for minerals, shaping the microbial communities around them even as those communities shape what the plant can access. The forest ecologist Suzanne Simard demonstrated that trees linked by mycorrhizal fungi transfer carbon and nutrients between one another, sometimes sustaining younger or stressed neighbors [Simard 1997, 2004]. A forest viewed this way is not a collection of competing individuals but a connected network, its members linked by flows of matter moving through fungal pathways. Competition and conflict still exist, but the unit of life is larger and more entangled than it appears at first glance.

The biologist Scott Gilbert has helped formalize this thinking through the concept of the holobiont: an organism together with all of its associated microorganisms, functioning as a single ecological and evolutionary unit. A tree is not just tree tissue. It is tree plus fungi plus microbiome, inseparable in practice even if distinguishable in theory.

This reframing matters when we ask who is making the rain. If the unit of life is the holobiont, then transpiration is not simply something a tree does. It is something the assembly does: plant tissue providing the leaf surface and vascular architecture, mycorrhizal fungi regulating how water moves through roots and how stomata respond to moisture stress, bacteria influencing the molecular signals that govern when pores open and close. Mohanned Abdalla, a soil physicist, and Mutez Ali Ahmed, a horticulture researcher measured how arbuscular mycorrhizal fungi affect the transpiration rates of tomatoes under varying moisture conditions [Mohanned 2012]. Robert Augé, Heather Toler, and Arnold Saxton at the University of Tennessee found that these fungi weave themselves into plant roots and exert a controlling influence over stomatal conductance, the process by which a plant opens its leaf pores to breathe and transpire [2015]. University of California Riverside’s Shushu Jiang and collaborators found that bacteria affect transpiration through protein signaling pathways [2013]. These research groups were not asking what this means for rainfall. But the mechanism they identified operates at every scale. Across millions of trees, fungal and bacterial regulation of stomatal behavior shapes the timing and volume of transpiration. Transpiration thus is not a purely botanical process, its also a microbial and fungal one.

[Transmission Electron Microscope picture of Pseudomonas Syringae]

Cloud drops do not form simply because humidity is high enough. They also require a small particle, called an aerosol, on which to nucleate. Meteorologists have tended to focus on inorganic material seeding rain, but microbes and fungal spores can also seed rain. The ability of bacteria to seed rain was first discovered by Gabor Vali and Russell Schnell in the 1970s, then rediscovered by plant pathologist David Sands in the 1980s, as he hung out of biplanes with a Petri dish to capture bacteria from clouds. A particular bacterium, Pseudomonas syringae, had a protein pattern on its surface that helped reorganize water molecules into ice structures. Proteins on the bacterial outer membrane act as physical templates that force water molecules into a crystalline ice lattice at temperatures as warm as -2°C, far warmer than the -15°C typically required for inorganic dust to trigger freezing. The idea that bacteria and fungal spores could seed rain was considered outlandish at first, but as decades passed it has become increasingly mainstream in climate science. Atmospheric scientist Kim Prather, flying collection missions over parts of the United States, found that a third of rain-seeding particles were of biological origin. Christian Pöhlker and colleagues going into remote parts of the Amazon found that bioaerosols, organic matter including fungal spores, bacteria, and forest terpenes that seed rain, were even more prevalent in pristine forest air, where the ratio of biological to inorganic nucleators was far higher than in polluted or degraded regions [2012]. In prehistoric times, before industrial pollution and large-scale deforestation, we can expect that bacteria and fungal spores played a considerably larger role in creating rain than they do today. [For more info see my articles on the science and discovery of bioaerosols Part I, Part II, and Part III]

[Scanning Electron Microscope pictures of fungal spores]

Forests also exhale tiny organic particles of their own. Conifers, broad-leaved trees, and many other plants release volatile organic compounds, terpenes, the molecules responsible for the resinous smell of pine forests, that react in the atmosphere with ozone and hydroxyl radicals to form secondary organic aerosols in the right size range to act as cloud condensation nuclei. Forests continuously manufacture the seeds around which cloud droplets form, chemically altering the atmosphere above them to make rainfall more probable over the very terrain that produced the aerosols.

The microbiologist Cindy Morris has studied the evolution of the bacterial bioaerosol capacities from a deep-time perspective [Morris 2012]. The rise of flowering plants and vast forests created thermal plumes that lifted bacteria high into the atmosphere, while the breakup of Pangaea created new coastlines and the cool, moist mixed-phase clouds that bacteria need to trigger precipitation. In this environment, selection favored ice-nucleating ability as a solution to long-distance dispersal: bacteria that could seed clouds and trigger their own descent via rain were more likely to reach fresh plant hosts. Once on the ground, the moisture from the rain they helped create facilitates a population explosion, often increasing bacterial numbers a thousandfold in 48 hours, while frost from ice nucleation ruptures plant cells to release nutrients. Through this feedback loop, these microbes have co-evolved with land plants to help manufacture the humid, temperate conditions they both require.

A similar logic applies to fungal spores. Spore lineages that are efficient ice nucleators would be selected for, since triggering rain increases the chance of landing on moist, receptive ground where germination is possible. The diversity of spore types in any given air mass is not noise in the system but functional variety, with rain-seeding specialists doing one job and other lineages doing others. Some are optimized for long atmospheric journeys; others for rapid germination once they land; others for establishing mycorrhizal networks quickly in disturbed soil. The ecosystem benefits from both the seeders and the settlers.

The question of how such a system assembled itself points toward selection operating at multiple levels simultaneously. At the level of the individual organism, a bacterium capable of nucleating ice in clouds is more likely to be carried down in precipitation onto a moist plant surface where it can reproduce. A fungal spore that efficiently seeds rain is more likely to land on receptive, wet ground where germination is possible. A mycorrhizal network that regulates transpiration in ways that sustain local humidity is more likely to persist in a living, productive forest than one that allows its host to desiccate. Each organism is selected for traits that incidentally contribute to moisture cycling. No individual needs to intend the larger effect. Cindy Morris has made precisely this argument for ice-nucleating bacteria: their rain-seeding capacity is not an accident but a dispersal strategy, refined by selection over hundreds of millions of years.

But individual selection alone does not fully account for the integration we observe. Group selection, largely dismissed after George Williams’s critiques in the 1960s, has been substantially rehabilitated in recent decades through evolutionist David Sloan Wilson’s multilevel selection framework and through the study of major evolutionary transitions. In ecological systems especially, the community is increasingly recognized as a genuine unit on which selection can act.

A forest-soil community with tightly integrated microbe-fungi-plant relationships, one whose mycorrhizal networks efficiently regulate transpiration, whose bacterial populations actively seed rain, whose fungal spores and terpene aerosols prime the atmosphere above it, will maintain and colonize new territory more successfully than a community lacking that integration. It will draw more moisture inland, sustain productivity through dry periods, recover more quickly from disturbance, and push its margins further into previously arid continental interiors. Selection at the individual level and selection at the community level are not competing explanations here. They are mutually reinforcing. Individual bacteria, spores, and fungal networks are selected for traits that benefit the community water cycle, and communities with more of those traits outcompete and displace those without them.

The deep history of rain on land is a story about what bacteria and fungi made possible, about how they broke the rock and built the soil, how they impacted transpiration and primed the clouds, and how they co-evolved with plants across hundreds of millions of years into communities capable of carrying rain deep into continental interiors that would otherwise receive almost none.

If you are interested in reading more on this topic, see my article “Is the earth microbiome regulating our climate?”

References

Abdalla, Mohanned, and Mutez Ali Ahmed. “Arbuscular mycorrhiza symbiosis enhances water status and soil-plant hydraulic conductance under drought.” Frontiers in Plant Science 12 (2021): 722954.

Augé, Robert M., Heather D. Toler, and Arnold M. Saxton. "Arbuscular mycorrhizal symbiosis alters stomatal conductance of host plants more under drought than under amply watered conditions: a meta-analysis." Mycorrhiza 25, no. 1 (2015): 13-24.

Ibarra, Daniel E., Jeremy K. Caves Rugenstein, Aviv Bachan, Andrés Baresch, Kimberly V. Lau, Dana L. Thomas, Jung-Eun Lee, C. Kevin Boyce, and C. Page Chamberlain. “Modeling the consequences of land plant evolution on silicate weathering.” American Journal of Science 319, no. 1 (2019): 1-43.

Jiang, Shushu, Jian Yao, Ka-Wai Ma, Huanbin Zhou, Jikui Song, Sheng Yang He, and Wenbo Ma. “Bacterial effector activates jasmonate signaling by directly targeting JAZ transcriptional repressors.” PLoS pathogens 9, no. 10 (2013): e1003715.

Morris, Cindy E., Franz Conen, J. Alex Huffman, Vaughan Phillips, Ulrich Pöschl, and David C. Sands. “Bioprecipitation: a feedback cycle linking Earth history, ecosystem dynamics and land use through biological ice nucleators in the atmosphere.” Global change biology 20, no. 2 (2014): 341-351.

Pöhlker, Christopher, Kenia T. Wiedemann, Bärbel Sinha, Manabu Shiraiwa, Sachin S. Gunthe, Mackenzie Smith, Hang Su et al. “Biogenic potassium salt particles as seeds for secondary organic aerosol in the Amazon.” Science 337, no. 6098 (2012): 1075-1078 https://www.science.org/doi/abs/10.1126/science.1223264

DC Sands, VE Langhans, AL Scharen, G de Smet, The association between bacteria and rain and possible resultant meteorological implications. J Hungarian Meteorol Serv 86, 148–152 (1982)

Schnell, Russell C., and Gabor Vali. “Looking back: An account of how ice nucleation by bacteria was discovered (1963 to about mid-1980s). Part II: Broadening the scope.” Bulletin of the American Meteorological Society 105, no. 6 (2024): E1004-E1014. https://journals.ametsoc.org/view/journals/bams/105/6/BAMS-D-23-0115.1.xml

Simard, S., Perry, D., Jones, M. et al. https://www.nature.com/articles/41557 Nature 388, 579–582 (1997). https://doi.org/10.1038/41557

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Vali, Gabor, and Russell C. Schnell. “Looking back: An account of how ice nucleation by bacteria was discovered (1963 to about mid-1980s). Part I: The basics.” Bulletin of the American Meteorological Society 105, no. 4 (2024): E778-E788. https://journals.ametsoc.org/view/journals/bams/105/4/BAMS-D-23-0114.1.xml