Fungi set the stage for life on land hundreds of millions of years earlier than thought

From fossils and rare genetic ‘gene-swap’ clues, researchers reconstruct fungi’s deep timeline and reveal how they helped shape early Earth ecosystems.

Okinawa Institute of Science and Technology (OIST) Graduate University

Dickinsonia observed at Nilpena Ediacara National Park, with negative relief — image:
Clear fossil evidence can be found most of the five major groups – here we see a *Dickinsonia* fossil, providing evidence of ancient animal life.
view more
Credit: Citronnel/Wikimedia Commons, copyright CC-BY-SA-4.0

New research published in Nature Ecology & Evolution sheds light on the timelines and pathways of evolution of fungi, finding evidence of their influence on ancient terrestrial ecosystems. The study, led by researchers from the Okinawa Institute of Science and Technology (OIST) and collaborators, indicates the diversification of fungi hundreds of millions of years before the emergence of land plants.

The five paths to a complex world

Professor Gergely J. Szöllősi, author on this study and head of the Model-Based Evolutionary Genomics Unit at OIST explains the foundations of this research. “Complex multicellular life — organisms made of many cooperating cells with specialized jobs — evolved independently in five major groups: animals, land plants, fungi, red algae, and brown algae. On a planet once dominated by single-celled organisms, a revolutionary change occurred not once, but at least five separate times: the evolution of complex multicellular life. Understanding when these groups emerged is fundamental to piecing together the history of life on Earth.”

Emergence here was not simply a matter of cells clumping together; it was the dawn of organisms, where cells took on specialized jobs and were organized into distinct tissues and organs, much like in our own bodies. This evolutionary leap required sophisticated new tools, including highly developed mechanisms for cells to adhere to one another and intricate systems for them to communicate across the organism, and arose independently in each of the five major groups.

The difficulties of dating evolutionary divergence

For most of these groups, the fossil record acts as a geological calendar, providing anchor points in deep time. For example, red algae show up possibly as early as about 1.6 billion years ago (in candidate seaweed-like fossils from India); animals appear by around 600 million years ago (Ediacaran fossils such as the quilted pancake like Dickinsonia); land plants take root roughly 470 million years ago (tiny fossil spores); and brown algae (kelp-like forms) diversified tens to hundreds of millions of years later still. Based on this evidence, a chronological picture of life’s complexity emerges.

There is, however, a notable exception to this fossil-based timeline: fungi. The fungal kingdom has long been an enigma for paleontologists. Their typically soft, filamentous bodies mean they rarely fossilize well. Furthermore, unlike animals or plants, which appear to have a single origin of complex multicellularity, fungi evolved this trait multiple times from diverse unicellular ancestors, making it difficult to pinpoint a single origin event in the sparse fossil record.

Reading the genetic clock

To overcome the gaps in the fungal fossil record, scientists use a "molecular clock." The concept is that genetic mutations accumulate in an organism's DNA at a relatively steady rate over generations, like the ticking of a clock. By comparing the number of genetic differences between two species, researchers can estimate how long ago they diverged from a common ancestor.

However, a molecular clock is uncalibrated; it can reveal relative time but not absolute years. To set the clock, scientists need to calibrate it with "anchor points" from the fossil record. Given the scarcity of fungal fossils, this has always been a major challenge. The OIST-led team addressed this by incorporating a novel source of information: rare gene "swaps" between different fungal lineages, a process known as horizontal gene transfer (HGT).

Prof. Szöllősi explains this concept. “While genes are normally passed down "vertically" from parent to child, HGT is like a gene jumping "sideways" from one species to another. These events provide powerful temporal clues,” he says. “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.”

By identifying 17 such transfers, the team established a series of "older than/younger than" relationships that, alongside fossil records, helped to tighten and constrain the fungal timeline.

A new history for an ancient kingdom

The analysis suggests a common ancestor of living fungi dating to roughly 1.4–0.9 billion years ago—well before land plants. That timing supports a long prelude of fungi–algae interactions that helped set the stage for life on land.

Co-first author on this study, Dr. Lénárd L. Szánthó, emphasizes the importance of these findings. “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.”

This revised timeline fundamentally reframes the story of life's colonization of land. It suggests that for hundreds of millions of years before the first true plants took root, fungi were already present, likely interacting with algae in microbial communities. This long, preparatory phase may have been essential for making Earth's continents habitable. By breaking down rock and cycling nutrients, these ancient fungi could have been the first true ecosystem engineers, creating the first primitive soils and fundamentally altering the terrestrial environment. In this new view, plants did not colonize a barren wasteland, but rather a world that had been prepared for them over eons by the ancient and persistent activity of the fungal kingdom.

About the authors

This work grew from the OIST Model-Based Evolutionary Genomics Unit, co-led by Prof. Gergely J. Szöllősi and Dr. Eduard Ocaña-Pallarès, with Dr. Lénárd L. Szánthó and Zsolt Merényi as first authors. They teamed up with colleagues across Europe, including Professor László G. Nagy’s group, which includes Zsolt Merényi, at the HUN-REN Biological Research Centre in Szeged, Hungary—a team known for fungal evolutionary genomics and the evolution of multicellularity. Further collaborators on this study include Prof. Philip Donoghue, who heads the University of Bristol’s Paleobiology Group, UK, and Prof. Toni Gabaldón, of the Institute for Research in Biomedicine (IRB) and the Barcelona Supercomputing Centre (BSC), Spain, an expert in comparative genomics.

Journal

Nature Ecology & Evolution

DOI

10.1038/s41559-025-02851-z

Method of Research

Data/statistical analysis

Article Title

A timetree of Fungi dated with fossils and horizontal gene transfers

Article Publication Date

1-Oct-2025

Could a fungus provide a blueprint for next-gen hydrogels?

The structural properties in the mycelium of a common soil mold show promise in biomedical applications, such hydrogels and tissue scaffolding

University of Utah

video:
Atul Agrawal, a University of Utah graduate student in mechanical engineering, describes a fungus he grows in his lab. The structural properties of *Marquandomyces*, a common soil mold, show promise in biomedical applications as a hydrogel.
view more
Credit: Brian Maffly, University of Utah

Fungi are vital to natural ecosystems by breaking down dead organic material and cycling it back into the environment as nutrients. But new research from the University of Utah finds one species, Marquandomyces marquandii, a ubiquitous soil mold, shows promise as a potential building block for new biomedical materials.

In recent years, scientists have examined fungal mycelium, the network of root-like threads—or hyphae—that penetrate soils, wood and other nutrient-bearing substrate, in search of materials with structural properties that could be useful for human purposes, particularly construction.

In a series of lab demonstrations, U mechanical engineering researchers show M. marquandii can grow into hydrogels, materials that hold lots of water and mimic the softness and flexibility of human tissues, according to a recent study.

[caption id="attachment_117646" align="alignright" width="501"] Atul Agrawal, Ihsan Elnunu and Steven Naleway, left to right, observe how fungal tissues perform using an instrument that measures materials' tensile, shear, compression and other mechanical properties. Photo credit: Dan Hixson.[/caption]

Unlike other fungi that struggle with water retention and durability, M. marquandii produces thick, multilayered hydrogels that can absorb up to 83% water and bounce back after being stretched or stressed, according to Atul Agrawal, the lead author of the study. These properties make it a good candidate for biomedical uses such as tissue regeneration, scaffolds for growing cells or even flexible, wearable devices.

“What you are seeing here is a hydrogel with multilayers,” said Agrawal, holding a glass flask containing a fungal colony growing in a yellowish liquid medium. “It’s visible to the naked eye, and these multiple layers have different porosity. So the top layer has about 40% porosity, and then there is an alternating bands of 90% porosity and 70% porosity.”

Looking to nature to innovate materials

Agrawal is a Ph.D. candidate at the John and Marcia Price College of Engineering. His paper is the latest to emerge from the lab of senior author Steven Naleway, an associate professor of mechanical engineering who explores biological substances to develop bioinspired materials with structural and medical applications.

Agrawal and Naleway are seeking patent protection for their discoveries about the Marquandomyces fungus.

“This one in particular was able to grow these big, beefy mycelial layers, which is what we are interested in. Mycelium is made primarily out of chitin, which is similar to what's in seashells and insect exoskeletons. It's biocompatible, but also it's this highly spongy tissue,” said Naleway, whose lab is funded by the National Science Foundation. “In theory, you could use it as a template for biomedical applications or you could try to mineralize it and create a bone scaffolding.”

Fungi comprise its own kingdom of organisms, with an estimated 2.2 to 3.8 million species, and just 4% have been characterized by scientists. For decades, scientists have derived from fungi numerous pharmacological substances, from penicillin to LSD. Naleway is among a cohort of engineers now looking to fungal microstructures for potential use in other arenas.

Why fungal mycelia have interesting mechanical properties

In collaboration with U mycologist Bryn Dentinger, Naleway’s lab has produced a string of papers documenting potentially useful structural properties of various species of fungi. One outlined how fungi that grow short hyphae are more stiff than those that grow longer hyphae. Another catalogued the various ways bracket fungi’s high strength-to-weight ratios make them a viable alternative in various applications, including aerospace and agriculture.

The way fungal hyphae grow is the reason why mycelia could have useful structural properties.

“As they grow forward, they lay down these cross walls that then compartmentalize a really long filament into many, many individual cells,” said Dentinger, an associate professor of biology and a curator at the Natural History Museum of Utah. “They will grow forever as long as there's enough nutrition around. There's not a developmental stage where they'll stop. That's a fundamentally different strategy to living in the environment than animals have achieved.”

https://www.youtube.com/shorts/pzS52qySLcc

Fungi evolved multicellularity in ways that are much different than what we see in animals and plants, in which cells differentiate and usually remain in differentiated states.

“In fungi, every cell is capable of differentiating and then reverting to the original state. They're just a lot more malleable and adaptable,” Dentinger said. “So there's a lot that we could exploit from those behaviors that really haven't been explored fully.”

Fortuitous accidents can fuel discovery

Like many discoveries involving fungi, the U hydrogel experiments arose from a happy accident. The group was originally conducting research into what they thought was a hydrocarbon-eating organism commonly called “kerosene fungus,” known to contaminate aviation fuel.

But as their cultures grew the scientists noticed they were behaving unexpectedly, growing in strange layers. Dentinger correctly identifying the mystery fungus as Marquandomyces.

“It highlights the state of mycology because we only have a handle on such a small proportion of the fungi,” Dentinger said. “There's a lot of misidentification around in culture collections and even in herbarium collections. Misidentifying something is just part of the game. And that's really why I am involved with this work with Steven.”

Over the course of the study, the team found these mycelial cultures showed an unusually high degree of hydrophilia, retaining 83% water without losing its shape.

“What was interesting about our research was that the fungus itself created a full-blown structure that was highly organized,” Agrawal said. The Marquandomyces outperformed materials made from more commonly studied fungi, such as Ganoderma and Pleurotus, species that exhibit limitations in water retention, restricting their application in hydrogel-based biomedical systems.

In lab experiments, Agrawal’s team found the material could recover 93% of its shape and strength after repeated stress.

“For it to be able to hold this structure together, this entire mycelium colony is connected together, and what we saw through optical imaging is that within these layers at the site of transition, it's a functionally graded structure,” Agrawal said. “It helps distribute the stress concentration between layers. So when we apply mechanical stress, it distributes that stress evenly and helps with the mechanical performance of these hydrogels.”

C]Steven Naleway, left, and Atul Agrawal examine a fungal culture growing in a liquid medium in Naleway's lab at the University of Utah's College of Engineering.

Credit

Dan Hixson, University of Utah

Atul Agrawal, Ihsan Elnunu and Steven Naleway, left to right, observe how fungal tissues perform using an instrument that measures materials' tensile, shear, compression and other mechanical properties.
Credit
Dan Hixson, University of Utah

#####

The study, “Multilayer, Functionally Graded Organic Living Hydrogels Built by Pure Mycelium,” appeared online Aug. 27 in JOM, The Journal of the Minerals, Metals & Materials Society. It will be published in a special issue of the journal in December. Funding came from the National Science Foundation and the American Chemical Society. Toma Ipsen, an undergraduate in the Dentinger Lab, is a co-author.