Community structure and hidden phylogenetic diversity of marine fungi in the tropical Indian and western Pacific Oceans
This study utilizes long-read 28S rRNA sequencing of 113 samples from the tropical Indian and western Pacific Oceans to reveal extensive hidden fungal diversity, including three novel candidate phyla, and demonstrates that marine fungal community structure is shaped by distinct vertical stratification and environmental drivers such as longitude, phosphate, and salinity.
Original paper licensed under CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/). This is an AI-generated explanation of a preprint that has not been peer-reviewed. It is not medical advice. Do not make health decisions based on this content. Read full disclaimer
The ocean is often imagined as a blue desert, a vast expanse of water where life is sparse and silent. Yet, beneath the surface, a bustling world of microscopic organisms drives the planet's most essential processes. Among these invisible workers are fungi, a group of life forms that includes mushrooms, molds, and yeasts. While we often think of fungi as things that grow on damp bread or rotting logs on land, they are also critical residents of the sea. They act as nature's recyclers, breaking down dead organic matter and releasing nutrients back into the water, and they serve as parasites that help control populations of other tiny marine creatures. For a long time, scientists believed these marine fungi lived mostly on the ocean floor or on floating wood. However, recent discoveries suggest they are everywhere, drifting in the open water and playing a much larger role in the ocean's health than previously understood. Despite their importance, the full extent of who lives in the ocean and how they are related to one another remains a mystery, largely because the tools used to study them have struggled to see the full picture.
A team of researchers set out to solve this mystery by taking a deep dive into the tropical waters of the Indian and western Pacific Oceans. They collected 113 samples from a wide range of environments, from the sunlit surface waters down to the crushing darkness of the deep ocean, and from the open water to the muddy sediments on the sea floor. To see what was there, they used a powerful new method that reads long stretches of genetic code, allowing them to identify organisms that older, shorter-read methods had missed. Their goal was simple but ambitious: to map out the true diversity of marine fungi in this region, understand how they are distributed, and figure out what environmental factors determine where they live.
The results revealed a world far more complex and diverse than anyone had anticipated. From their samples, the researchers identified nearly 47,000 distinct groups of fungi. While the most common types belonged to well-known families like the Ascomycota and Basidiomycota, the study uncovered a hidden layer of life that had never been seen before. The researchers found three completely new branches on the tree of life, lineages so different from any known fungi that they could not be placed into existing categories. They named these mysterious groups Candidate.Taichumycota, Candidate.Shizhenmycota, and Candidate.Xihemycota. These findings suggest that the ocean is a reservoir of evolutionary history that we have barely begun to explore, and that our current lists of fungal species are missing a significant portion of the story.
The study also showed that these fungi are not randomly scattered; they live in very specific neighborhoods. The researchers discovered a clear vertical pattern, where different types of fungi dominate at different depths. The new, mysterious lineages showed distinct preferences: one group was found only in the surface waters, another was spread throughout the water column but most common near the top, and the third was found everywhere but thrived most in the deep-sea sediments. This separation suggests that as you move deeper into the ocean, the conditions change enough to favor entirely different groups of fungi. The communities living in the deep water and on the sea floor were quite different from those in the surface, indicating that the ocean is structured into distinct ecological zones for these microscopic organisms.
Beyond just who was there, the researchers looked at what these fungi might be doing. By analyzing their genetic makeup, they could predict the roles these organisms play in the ecosystem. The surface waters hosted a mix of fungi with many different jobs, including those that eat dead plants, those that live inside other organisms, and those that act as parasites. In contrast, the deep ocean and the sea floor were dominated by fungi that act as decomposers, breaking down sinking organic matter. This division of labor highlights how the ocean's vertical structure creates different opportunities for life, with the deep sea relying heavily on fungi to recycle the material that falls from above.
Finally, the team investigated what drives these patterns. They found that the mix of fungi in the surface waters is shaped by a combination of geography and the chemistry of the water. The location of a sample, specifically its longitude, was a strong predictor of which fungi were present. Environmental factors also played a major role; the amount of phosphate and the salinity of the water were key drivers of fungal diversity. Interestingly, while these factors explained a portion of the differences between locations, a large amount of variation remained unexplained, suggesting that other complex forces are at work. The study concludes that the tropical Indian and western Pacific Oceans harbor a vast, hidden diversity of fungi, with unique evolutionary lineages and complex ecological roles that are just beginning to be understood. This work reminds us that even in the most studied parts of the ocean, there is still much to discover about the microscopic life that sustains our planet.
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