From the depths to discovery: a tiny limpet reveals big secrets of the deep sea

Harvard University

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External anatomy (A,B) and digital section to visualize internal anatomy (C,D) of Pectinodonta nautilus

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Credit: Paula Rodríguez-Flores

In the inky depths of the Central Pacific Ocean, nearly 2,400 meters below the surface, scientists have discovered a new species of deep-sea limpet clinging to a sunken log.

During a 2023 expedition aboard the E/V Nautilus, scientists using the remotely operated vehicle Hercules spotted a fragment of sunken wood resting off the remote Johnston Atoll. When they drew closer, they found a thriving community clinging to the timber. Among them was a large population of strange limpets — oval, pale, and thick-shelled, with a distinctive arched profile. It didn’t take long for Paula Rodríguez-Flores, postdoctoral researcher in the Department of Organismic and Evolutionary Biology (OEB) at Harvard who was aboard Nautilus when the wood fragment was collected, to realize they were looking at a new species.

In a new study published in Molluscan Research, researchers in OEB and the Harvard Museum of Comparative Zoology (MCZ) formally describe Pectinodonta nautilus, named in honor of the exploration vessel responsible for its discovery. The team led by Gonzalo Giribet, Professor in OEB and Director of the MCZ, and Postdoctoral Researcher Paula Rodríguez-Flores, used cutting-edge imaging and molecular techniques to fully examine the 79 individuals collected from the 35-centimeter-long piece of wood.

Belonging to a family of mollusks known as Pectinodontidae, P. nautilus is part of a rare group of limpets that make their homes on “wood falls”— sunken tree trunks and branches that drift down from the surface and settle on the seafloor. These decomposing logs become temporary islands of life in an otherwise barren environment, nourishing dense bacterial mats and specialized creatures that feed on them.

“Wood falls are fleeting ecosystems in the deep ocean, and yet they host remarkably specialized fauna,” said Rodríguez-Flores. “Unlike the well-studied ecosystems built around hydrothermal vents and methane seeps, wood falls remain elusive, less studied in their natural setting.” Yet, they are crucial patches of life in the deep ocean, delivering bursts of organic matter into what might otherwise be a biological desert.

Back in the lab with the samples, the team used high-resolution micro-CT scanning and 3D modeling to visualize the limpet’s anatomy without dissection. These limpets are large for their family – some more than three centimeters long – and they continue growing as the wood decays around them. Their off-white shells are sturdy, strongly arched, and unusually smooth. Scanning electron microscopy revealed a faint radial sculpture near the posterior dorsal surface. The smoothness, combined with thick concentric growth lines, set the species apart from its relatives.

Things got even more interesting inside the mouth. Like other wood-dwelling limpets, P. nautilus boasts oversized radular teeth – the chitinous scraping tools that function like conveyor-belt tongues. Each tooth resembles an inverted V studded with around 17 cusps. When compared with relatives like P. mazuae, the new species has nearly double the size in its radular structures, hinting at distinct feeding strategies or evolutionary pressures tied to its isolated nursery log.

DNA sequencing and mitochondrial genome analysis confirmed that P. nautilus represents a distinct lineage within Pectinodonta. Phylogenetic analyses revealed that P. nautilus is most closely linked with species from New Zealand and the Western Pacific, including P. Marinovichi and P. orientalis.

“Our findings suggest this lineage of wood-fall may be far more widespread across the Pacific than previously recognized,” said lead author Gonzalo Giribet, Professor in OEB and Director and Curator of Invertebrates in the MCZ.

The deeper evolutionary tree, however, remains hazy. Mitochondrial arrangements across related families showed intense gene shuffling, making lineage boundaries difficult to pin down. The researchers determined a need for full genome assemblies before confidently rewriting the family history. The findings also indicate that radular morphology, rather than shell shape, may be a more reliable way to distinguish among these cryptic species.

“The discovery underscores how little is known about life in the deep sea,” Rodríguez-Flores said. “Fewer than seven percent of described marine species come from below 1,000 meters, leaving vast stretches of ocean biodiversity unexplored.”

But the presence of individuals of many different sizes – juveniles to well-grown adults – indicates the wood fall supported multiple generations; suggesting that even tiny islands of habitat can sustain deep-sea communities long enough for population turnover and dispersal.

The team, which included Ph.D. candidate Arianna Lord and MCZ Curatorial Associate, Jennifer Winifred Trimble, took on no easy task studying these fragile organism. The team faced challenges in handling the delicate radulae – one disintegrated during cleaning – and in generating complete genome data from the limited tissue available. A shortage of comparative specimens from other oceans also made it difficult to test broader evolutionary and biogeographic patterns.

Still, the researchers say the discovery of Pectinodonta nautilus adds a crucial piece to the puzzle of how life persists in one of Earth’s harshest habitats. They hope to continue examining other deep-sea communities near Johnston Atoll, which have already yielded several new species of crustaceans and corals, including a previously unknown squat lobster species that the Nautilus team named Munidopsis giribeti, in honor of Professor Gonzalo Giribet and his passion and dedication to invertebrates.

“Every deep dive reveals that the ocean still holds countless surprises,” said Rodgríguez-Flores. “We’re only just beginning to understand the hidden biodiversity living on the seafloor.”

External morphology of Pectinodonta nautilus's shell from various angles

Details of the radula, a structure present on gastropods and cephalopods mollusks for feeding. captured by a scanning electron microscope.

Credit

Paula Rodríguez-Flores 

Journal

Molluscan Research

DOI

10.1080/13235818.2025.2578245 

Article Title

A new deep-sea Pectinodonta species (Mollusca, Gastropoda, Patellogastropoda, Pectinodontidae) from a wood fall near Johnston Atoll, Central Pacific

Article Publication Date

5-Nov-2025

 

U of A-led team discovers large ritual constructions by early Mesoamericans

University of Arizona

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University of Arizona archaeologist Takeshi Inomata (left) and archaeologist Melina Garcia excavate a cache of ceremonial artifacts that include mineral pigments associated with cardinal directions. "This is the first case that we've found those pigments associated with each specific direction," Inomata said.

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Credit: Photo by Atasta Flores

In the summer of 2020, an international team led by a University of Arizona archaeologist reported the discovery of the largest monumental construction known today in the Maya area in the state of Tabasco, near Mexico's southeastern border. 

The monument, found at a site called Aguada Fénix, measures nearly a mile long and a quarter-mile wide, ranges from 30 to 50 feet high and dates to 1,000 B.C.

In the five years since that discovery, the team, led by Regents Professor of anthropology Takeshi Inomata and Fred A. Reicker Distinguished Professor of anthropology Daniela Triadan, has pieced together evidence about Aguada Fénix and the nearby area, finding that nearly 500 similar, smaller sites dotted the landscape in southeastern Mexico.

Now, Inomata and his team have unearthed the latest and clearest evidence that Aguada Fénix was a cosmogram – a model to represent the order of the universe, seen at other Maya sites – which could make it among the most significant ceremonial sites for the Maya area. The latest excavation revealed a cross-shaped pit, called a cruciform, that held a cache of ceremonial artifacts, which provide unprecedented information on early Maya rituals.

The new findings were published today in the journal Science Advances. 

The study, Inomata said, is further evidence opposing the long-held belief that Mesoamerican cultures grew gradually, building increasingly larger settlements, such as Tikal in Guatemala and Teotihuacan in central Mexico, whose pyramid monuments are icons for Mesoamerica today. Aguada Fénix predates the heydays of those cities by nearly a thousand years – and is as large or larger than all of them.

"What we are finding is that there was a 'big bang' of construction at the beginning of 1,000 B.C., which really nobody knew about," said Inomata, a researcher in the School of Anthropology, in the College of Social and Behavioral Sciences. "Huge planning and construction really happened at the very beginning."

'This is the first case'

Inomata and his colleagues first found clues of Aguada Fénix in 2017 using lidar, which stands for light detection and ranging. The technique uses lasers from an airplane flown overhead to scan through jungle and forest to create 3D maps of humanmade structures.

The team had already used lidar in 2015 in nearby Guatemala to discover early constructions at the Maya site of Ceibal. Aguada Fénix was arranged similarly to Ceibal, Inomata said.

At Aguada Fénix, the monument's centerline aligns with the rising sun on Oct. 17 and Feb. 24 – a 130-day span that probably represents half of the 260-day cycle of the Mesoamerican ritual calendar, Inomata said, based on analyses by colleagues who are experts on ancient astronomy. This arrangement is similar to other Maya sites that also had ceremonial caches, Inomata said, giving researchers some indication that they might find something similar at Aguada Fénix, on what is now rural ranchland in eastern Tabasco.

The team used radiocarbon to date the cruciform pit and the construction layers above it. Researchers also analyzed sherds of ceramic material that helped date the cruciform.

Their first significant find was several axes made of jade, which researchers recognized from previous excavations as ceremonial.

"That told us that this was really an important ritual place," Inomata said.

As they excavated the cruciform further, the team found ornaments carved from jade that they recognized to represent a crocodile, a bird, and what they believe is a woman giving birth. At the bottom of the pit was a smaller cruciform, where they found mineral pigments – small piles of blue, green and yellowish soil – arranged to correspond to cardinal directions.

"We've known that there are specific colors associated with specific directions, and that's important for all Mesoamerican people, even the Native American people in North America," Inomata said. "But we never had actual pigment placed in this way. This is the first case that we've found those pigments associated with each specific direction. So that was very exciting."

The builders, researchers suspect, arranged the pigments and other materials as an offering, then filled it in with sand and soil. Radiocarbon dating estimates the cache dates to 900-845 B.C. People likely returned to the site for later rituals to leave behind the jade objects.

The study also revealed a network of raised causeways and sunken corridors that Aguada Fénix's builders used to walk to and through the site, as well as canals and a dam to divert water from a nearby laguna. The causeways, corridors and canals followed axes that ran parallel to Aguada Fénix's orientation with the sun and extend as far as six miles away from the settlement's main plateau.

Monumental achievements without a single ruler

While some sites, like Tikal in Guatemala, were presided over by a singularly powerful king, the team has so far found no evidence that Aguada Fénix was constructed under that model. Inomata's theory is that the settlement did have leaders, but rather intellectual ones who made astronomical observations and led the design and planning for the site.

"These leaders didn't have power to force other people," Inomata added. "Most came probably willingly, because this idea of building a cosmogram was really important to them, and so they worked together."

Xanti S. Ceballos Pesina, a doctoral student in the School of Anthropology and a co-author on the study, helped excavate a smaller complex within Aguada Fénix. Ceballos, who grew up in Mexico, has visited numerous Maya sites as an archaeologist.

Looking at Inomata's lidar map of Aguada Fénix, Ceballos said she was still blown away at how extensive Aguada Fénix is, and how it eluded researchers for so long.

"I think it's very cool that new technologies are helping to discover these new types of architectural arrangements," Ceballos said. "And when you see it on the map, it's very impressive that in the Middle Preclassic Period, people with no centralized organization or power were coming together to perform rituals and to build this massive construction."

Inomata said the findings from Aguada Fénix have clear implications about how modern society can evolve.

"People have this idea that certain things happened in the past – that there were kings, and kings built the pyramids, and so in modern times, you need powerful people to achieve big things," he said. "But once you see the actual data from the past, it was not like that. So, we don't need really big social inequality to achieve important things."

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Journal

Science Advances

DOI

10.1126/sciadv.aea2037 

Archaeologists excavating the cruciform, before discovering the cache in the center of the pit.




Inomata and his colleagues first found clues of Aguada Fénix in 2017 using lidar, or light detection and ranging, which uses lasers from an airplane flown overhead to scan through jungle and forest to create 3D maps of humanmade structures.




The team excavated jade axes and ornaments that were likely left later, in return trips to the site, after builders made offerings to the cruciform cache and filled it in.



Mineral pigments in the cruciform cache were arranged to correspond with cardinal directions, according to recorded rituals: Blue azurite to the north, green malachite to the east and yellow ochre with geothite to the south. The western side of the cache included soil and likely other material that began as red and faded over time.



A jade artifact found in the cruciform likely represents a woman giving birth, researchers said.


Credit

Takeshi Inomata/University of Arizona




Xanti S. Ceballos Pesina, a Ph.D. candidate in the University of Arizona School of Anthropology and a co-author on the study, helped excavate a smaller complex within Aguada Fénix. Ceballos, who grew up in Mexico, has visited numerous Maya sites as an archaeologist.


Credit

Courtesy of Xanti S. Ceballos Pesina/University of Arizona

 

Urban fungi show signs of thermal adaptation

Small proof-of-principle study using samples from Baltimore sidewalks suggests fungi developing heat tolerance in city settings

Johns Hopkins Bloomberg School of Public Health

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A new study from researchers at the Johns Hopkins Bloomberg School of Public Health finds that common fungal species may be adapting to higher temperatures in warmer sites within cities compared to cooler sites in the same city.

The findings could signify that urban fungi could one day evolve into disease-causing pathogens. The researchers note that this is a proof-of-principle study, designed to investigate whether fungal species may adapt differently across sites within the same city. While the new findings suggest that they might, the researchers emphasize that more studies, with more samples in different cities, are needed.

Fungi are primarily molds and yeasts that typically can’t survive at warmer temperatures such as the body temperature of people, and only a minuscule subset of fungi can cause diseases. Many scientists worry that the warming climate may be driving fungi to adapt to rising temperatures, opening the door to new fungal pathogens that could survive in humans. One such fungal pathogen, Candida auris, a yeast first isolated from a human patient in 2009, now causes thousands of infections annually in the U.S. alone.

Fungal infections such as C. auris are often multi-drug resistant, with high mortality rates. C. auris has unusual tolerance for higher temperatures. Study senior author Arturo Casadevall, MD, PhD, MS, the Alfred and Jill Sommer Professor and Chair of the Bloomberg School’s Department of Molecular Microbiology and Immunology, and others have argued that C. auris may have acquired this “thermotolerance” only recently, due in part to global warming.

Given cities are at greater risk for extreme heat, the researchers examined urban fungi for signs of heat adaptation. For their study, the researchers gathered samples using taffy-like candy to grab microbes from sidewalks from four different sites in Baltimore—a warm site, an above-average-temperature site, an average-temperature site, and a cool site.

The researchers found that fungal species isolated from relatively warm sites in Baltimore had lighter pigmentation, a trait that prevents overheating and signals possible adaptation to warmer temperatures.

The research team also found that fungal species isolated from warmer sites had greater resistance to heat exposure in a laboratory setting compared to the same species isolated from cooler sites.

The study was published online October 4 in ISME Communications.

“This study opens the door for future research into these adaptations and the identification of urban fungal species that may emerge as potential human pathogens in the near future,” says study first author Daniel Smith, PhD, a postdoctoral student in the Bloomberg School’s Department of Molecular Microbiology and Immunology. Smith is a member of the Casadevall laboratory.

Fungi can develop specific adaptations to help them survive in different climates by producing more heat-absorbing melanin pigmentation when they live in colder latitudes, as the Casadevall laboratory found in a 2018 study.

In the new study, the researchers looked for similar differences in fungal species isolated from warmer versus cooler places, this time within the same city.

Smith selected the four sites based on high-resolution temperature data from the National Oceanic and Atmospheric Administration and confirmed them by measuring dirt and sidewalk temperatures directly at the time of collection. After collection, he cultured the captured fungi and recorded their levels of pigmentation and their abilities to survive brief heat exposure above 55 degrees Celsius/131 degrees Fahrenheit.

The resulting data showed that molds and yeasts from the warmest site had significantly less pigmentation—and absorbed less heat experimentally—compared to molds and yeasts from the coolest site. Many fungal species also were more likely to remain viable after heat exposure if they had been sampled from one or both warm sites compared to cooler sites.

The dozens of species collected for analysis included fungi known to cause diseases. The species with apparent heat adaptations included some that are capable of causing disease in humans. The warmest-site isolate of Rhodotorula mucilaginosa, a common environmental yeast but rare human pathogen was more viable after heat exposure compared to the three isolates of this species from the coolest site. An isolate of another occasionally-pathogenic fungus, Cystobasidium minutum, isolated from a 38.4 Celsius/101 degrees Fahrenheit sidewalk, showed the greatest resistance to experimental heat stress, and was able to grow at 37 degrees Celsius/98.6 degrees Fahrenheit—human body temperature.

The researchers said they expect that the same type of study in other cities would yield similar results—with the caveat that further research is needed. The researchers note that the study has limitations, including variables such as sun exposure, foot traffic, and wildlife.

“These findings are consistent with the idea that high temperatures in an urban environment can induce fungal heat adaptations, thus narrowing the thermal barrier to human infection,” Casadevall says. “These data are preliminary, and we need more and larger studies of this kind to help us understand how fungi are adapting to rising temperatures.”

“Environmental fungi from cool and warm neighborhoods in the heat-island of Baltimore City show differences in thermal susceptibility and pigmentation” was co-authored by Daniel Smith, Madhura Kulkarni, Alexa Bencomo, Tasnim Syakirah Faiez, J. Marie Hardwick, and Arturo Casadevall.

Support for the research was provided in part by the National Institutes of Health (AI162381, AI152078, HL059842, AI168539, AI183596).

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Journal

ISME Communications

DOI

10.1093/ismeco/ycaf177 

Method of Research

Experimental study

Subject of Research

Cells

 

Inexpensive materials transform waste carbon into energy-rich compounds

Washington University in St. Louis

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By Beth Miller

Turning waste carbon into useful products is a vital part of sustainable manufacturing. Recycling carbon dioxide creates carbon monoxide, which through electricity can be converted into energy-rich compounds. However, existing devices for this process use anion exchange membranes that break down over time when exposed to organic materials, making them less effective.

A team of researchers, led by Feng Jiao, the Lauren and Lee Fixel Distinguished Professor in the McKelvey School of Engineering at Washington University in St. Louis, has found that inexpensive and robust materials, porous separators called diaphragms, can be viable alternatives to these membranes in the carbon monoxide conversion process.

After testing various diaphragms, they found that some of them performed as well or better than polymer-based commercial membranes in various operating conditions.

Their findings were published Sept. 26, in Nature Communications. Wanyu Deng, a postdoctoral researcher, and Siyang Xing, a doctoral student, are first authors on the paper.

Diaphragms effectively prevent crossover of cathode and anode gas products and are made of low-cost materials. Jiao’s lab created a diaphragm-based carbon monoxide electrolyzer design. After testing a variety of materials, the electrolyzer cells using Zirfon (a type of diaphragm product containing zirconium dioxide) maintained efficiency for more than 250 hours at 60 degrees Celsius, while the best commercial membranes only lasted within 150 hours. Additionally, a scaled-up Zirfon-based electrolyzer operated steadily for 700 hours.

“These results show that diaphragms can be a scalable and durable solution for carbon monoxide conversion, making the process cheaper and more compatible with renewable energy sources,” said Jiao, who also is director of the Center for Carbon Management and associate director of the National Science Foundation CURB Engineering Research Center.

The team will continue to refine their electrolysis technologies for greater efficiency, as the more affordable and efficient the waste-gas conversion process becomes, the faster manufacturing systems can become circular and sustainable.

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Deng W, Xing S, Maia GWP, Wang Z, Crandall BS, Jiao F. Diaphragm-based carbon monoxide electrolyzers for multicarbon production under alkaline conditions. Nature Communications, Sept. 26. https://doi.org/10.1038/s41467-025-63004-1

This research was supported by the Gates Foundation (INV-051757) and the National Science Foundation (EEC-2330245).

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Journal

Nature Communications