How Fungi Shaped Our World and Why Their History Matters
Picture Earth 500 million years ago. The land is barren and rocky, with no plants or animals in sight. Life exists only in the oceans. Then, something remarkable happens: plants begin their move onto land. But there's a problem—these pioneering plants lack root systems to absorb nutrients from the tough, rocky surface. How did they survive? They enlisted the help of fungi, organisms with the "magic power" to digest rocks by excreting enzymes and chemicals .
This ancient partnership between plants and fungi triggered one of the most significant transformations in our planet's history. As plants flourished with the help of their fungal partners, they pulled carbon dioxide from the atmosphere, eventually causing a 90% reduction in CO2 levels while enriching the air with oxygen. This dramatic shift created the atmosphere that allowed animals to evolve on land .
"Without fungi, we wouldn't be here," notes evolutionary biologist Toby Kiers .
For centuries, however, the fungal kingdom has been misunderstood and overlooked, often dismissed as mere mushrooms, molds, and maladies. Today, revolutionary science is revealing how fungi predated plants by hundreds of millions of years, engineered Earth's earliest ecosystems, and continue to sustain life as we know it. This is the story of how mycology—the study of fungi—is uncovering the hidden history of our planet's most overlooked kingdom.
The symbiotic relationship between fungi and plants enabled the colonization of land, transforming Earth's atmosphere and paving the way for terrestrial life.
Groundbreaking research shows fungi existed hundreds of millions of years before plants, serving as Earth's first ecosystem engineers.
For most organisms, scientists rely on fossils to piece together evolutionary history. Animals appear in the fossil record around 600 million years ago, followed by land plants approximately 470 million years ago 1 . Fungi, however, have presented a persistent mystery. Their typically soft, filamentous bodies rarely fossilize well, creating enormous gaps in the paleontological record 1 .
To overcome this challenge, an international research team led by the Okinawa Institute of Science and Technology turned to a sophisticated genetic tool: the molecular clock 1 . This technique operates on the principle that genetic mutations accumulate in DNA at a relatively steady rate over generations, similar to the ticking of a clock. By comparing genetic differences between species, researchers can estimate when they diverged from a common ancestor 1 .
The breakthrough came when the team incorporated a novel source of information: horizontal gene transfers (HGT)—rare instances where genes "jump" between different fungal lineages 1 .
"If a gene from lineage A is found to have jumped into lineage B, it establishes a clear rule: the ancestors of lineage A must be older than the descendants of lineage B" 1 .
By identifying 17 such transfers, the team established a series of "older than/younger than" relationships that helped tighten the fungal timeline 1 .
The results, published in 2025 in Nature Ecology & Evolution, were stunning. The analysis revealed that the common ancestor of living fungi dates back roughly 1.4-0.9 billion years ago—well before land plants appeared 1 . This revised timeline fundamentally reframes the story of life's colonization of land.
"Fungi run ecosystems—recycling nutrients, partnering with other organisms, and sometimes causing disease. Pinning down their timeline shows fungi were diversifying long before plants, consistent with early partnerships with algae that likely helped pave the way for terrestrial ecosystems" 1 .
| Time Period | Evolutionary Event | Significance |
|---|---|---|
| 1.4-0.9 billion years ago | Common ancestor of living fungi | Predates plants by hundreds of millions of years |
| 600-800 million years ago | Loss of flagellum, development of branching filaments | Key adaptation to terrestrial environments |
| Around 500 million years ago | Evolution of septate filaments | Allowed for more complex multicellular structures |
| About 300 million years ago | Divergence of Ascomycota and Basidiomycota | Emergence of the two most diverse fungal phyla |
| 130-200 million years ago | Diversification of mushroom fungi | Coincided with rise of flowering plants |
| 60-80 million years ago | Radiation of anaerobic chytrids | Corresponded with spread of grasses and grazing mammals 2 |
Common ancestor of living fungi emerges
Key adaptations for terrestrial life
Plants colonize land with fungal help
Major fungal phyla diverge
Mushroom fungi diversify with flowering plants
While some scientists are looking back through genetic records, others are taking a more direct approach: reviving historical fungal specimens to observe how they've changed. In a groundbreaking 2025 study published in iScience, researchers at the Hebrew University of Jerusalem successfully revived strains of Botrytis cinerea—a widespread plant pathogen that causes gray mold—that had been curated in the National Natural History Collection since the early 1940s 6 .
Why revive 80-year-old fungi? The timing is significant. These specimens were collected before synthetic fertilizers and fungicides became standard in farming, offering a rare glimpse into how industrial agriculture has altered the invisible ecosystems that support global food production 6 .
"These fungi have been quietly evolving in response to everything we've done in agriculture over the past 80 years. By comparing ancient and modern strains, we can measure the biological cost of human intervention—and learn how to do better" 6 .
The research team followed a meticulous process to bring these historical fungi back to life and compare them with modern strains:
Historical strains from the 1940s were carefully revived using specialized growth media
Whole-genome sequencing identified genetic differences accumulated over 80 years
Gene expression patterns compared between historical and modern strains
Infection capabilities measured to assess differences in aggression and specialization
| Characteristic | Historical Strains (1940s) | Modern Strains | Implications |
|---|---|---|---|
| Fungicide Resistance | Minimal resistance | Significant resistance | Shows impact of chemical agriculture |
| Pathogenicity | Less specialized and aggressive | More aggressive | Suggests adaptation to modern monocultures |
| Environmental Adaptation | Different pH tolerance and host specificity | Broader adaptation | Indicates response to changed farm environments |
| Genetic Diversity | Distinct genomic signatures | Modern evolutionary patterns | Reveals directional selection from human activity |
The findings from this fungal "resurrection" experiment were striking. The historical strains showed significant genetic and behavioral differences compared to their modern counterparts 6 . Most notably, they displayed:
This research demonstrates that natural history collections are far more than static repositories of the past. As the researchers noted: "This work shows they are also dynamic resources for modern biology. They allow us to 'rewind' microbial evolution and anticipate future trends in plant disease" 6 . In an era of climate change and pesticide resistance, understanding how pathogens adapted to previous environmental shifts helps scientists design more resilient crop protection strategies and reduce reliance on chemical treatments.
The revolutionary discoveries in mycology rely on sophisticated laboratory tools and techniques. Here are some of the key reagents and methods that enable researchers to extract information from the fungal kingdom:
Uses a bead matrix and lysis buffer to pulverize fungal cells through high-speed agitation. This method is particularly effective with tough fungal structures like Aspergillus hyphae 5 .
Identifies rare gene "swaps" between fungal lineages to establish evolutionary timelines, providing powerful temporal clues when fossil evidence is scarce 1 .
Uses known fossil dates and horizontal gene transfer events to calibrate the rate of genetic mutation, allowing researchers to estimate when different fungal groups diverged 1 .
Special DNA sequences that allow plasmids to replicate independently within fungal cells, enabling genetic manipulation of species like Candida albicans 3 .
Different fungal species present unique challenges for researchers, particularly when it comes to extracting DNA for analysis. A 2005 study systematically compared six DNA extraction methods for recovering fungal DNA from clinical samples and found dramatic differences in effectiveness 5 .
| Extraction Method | Effectiveness with Candida albicans (Yeast) | Effectiveness with Aspergillus fumigatus (Filamentous) | Key Characteristics |
|---|---|---|---|
| Enzymatic Lysis + GNOME Kit |
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Gentle on cells but ineffective with tough structures |
| Bead-Based Methods (FastDNA Kit) |
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Mechanical disruption effective against hyphae |
| MasterPure Yeast Method |
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Balanced performance across fungal types |
| UltraClean Soil Kit |
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Adapted for complex samples like soil |
The study concluded that "the six extraction methods produce markedly differing yields of fungal DNA and thus can significantly affect the results of fungal PCR assays. No single extraction method was optimal for all organisms" 5 . This highlights the importance of matching methodology to the specific fungal species being studied.
The story of fungi is ultimately the story of life on Earth itself. From their humble beginnings over a billion years ago to their quiet reign before plants arrived, fungi have been fundamental architects of our world—breaking down rocks to create soil, partnering with plants to green the continents, and engineering atmospheric changes that made animal life possible 1 .
Today, as we face the interconnected challenges of climate change, agricultural sustainability, and biodiversity loss, understanding fungal history has never been more relevant. Mycorrhizal fungi, which form underground partnerships with plant roots, draw approximately 13 billion tons of carbon from the atmosphere each year—more than a third of annual CO2 emissions from fossil fuels . This natural carbon sequestration system, which began half a billion years ago, continues to operate silently beneath our feet.
The ongoing exploration of the fungal kingdom reminds us that some of nature's most powerful forces are often the least visible. With over 90% of fungal species still unknown to science , the next decade promises even more revolutionary discoveries about these remarkable organisms that have shaped—and continue to sustain—life on our planet.
"They seem to weave their way into everything, and it's almost paradoxical because they're so vast and they underline so many processes that sometimes we don't even notice they're there. It's like not noticing our own breath" .