In a new account of exquisitely preserved microfossils, researchers at UC Santa Barbara and McGill University revealed that eukaryotic organisms had already evolved into a diverse array of forms even 1.64 billion years ago. The paper, published in the journal Papers in Paleontology, recounts an assemblage of eukaryotic fossils from an era early in the group’s evolutionary history. The authors describe four new taxa, as well as evidence of several advanced characteristics already present in these early eukaryotes.

“These are among the oldest eukaryotes that have ever been discovered,” explained lead author Leigh Anne Riedman, an assistant researcher in UCSB’s Department of Earth Science. “Yet, even in these first records we’re seeing a lot of diversity.”

Eukarya forms one of the major domains of life, encompassing the plant, animal and fungi clades, as well as all other groups whose cells have a membrane-bound nucleus, like protists and seaweeds. Many scientists had thought early eukaryotes were all fairly similar during the late Paleoproterozoic, and that diversification took place around 800 million years ago. But Riedman and her co-authors found fossils of a delightfully diverse, and complex, cast of characters in rock nearly twice as old.

Scientists knew from previous studies that eukaryotes had evolved by this time, but their diversity in this era was poorly understood. So Riedman headed to the Outback in late 2019. Within one week, she had collected about 430 samples from eight cores drilled by a prospecting company; they now reside in the library of the Northern Territory Geological Survey. The two cores used for this study spanned roughly 500 meters of stratigraphy, or 133 million years, with around 15 million years of significant deposition.

Riedman returned to the United States with shale and mudstone: remnants of an ancient coastal ecosystem that alternated between shallow, subtidal mudflats and coastal lagoons. A dip in hydrofluoric acid dissolved the matrix rock, concentrating the precious microfossils which she then analyzed under the microscope.

“We were hoping to find species with interesting and different characteristics to their cell walls,” Riedman said. She hoped that these features could shed light on what was happening within the cells during this time period. Reaching any conclusions about the cellular interior would require a great deal of sleuthing, though, since the fossils preserve only the exterior of the cells.

The researchers were surprised by the diversity and complexity preserved in these fossils. They recorded 26 taxa, including 10 previously undescribed species. The team found indirect evidence of cytoskeletons, as well as platy structures that suggest the presence of internal vesicles in which the plates were formed — perhaps ancestral to Golgi bodies, present in modern eukaryotic cells. Other microbes had cell walls made of bound fibers, similarly suggestive of the presence of a complex cytoskeleton.

The authors also found cells with a tiny trapdoor, evidence of a degree of sophistication. Some microbes can form a cyst to wait out unfavorable environmental conditions. In order to emerge, they need to be able to etch an opening in their protective shell. Making this door is a specialized process. “If you’re going to produce an enzyme that dissolves your cell wall, you need to be really careful about how you use that enzyme,” Riedman said. “So in one of the earliest records of eukaryotes, we’re seeing some pretty impressive levels of complexity.”

Many people in the field had thought this ability emerged later, and the evidence for it in this assemblage further emphasizes how diverse and advanced eukaryotes were even at this early juncture. “The assumption has always been that this is around the time that eukaryotes appeared. And now we think that people just haven’t explored older rocks,” said co-author Susannah Porter, an Earth science professor at UC Santa Barbara.

This paper is part of a larger project investigating early eukaryote evolution. Riedman and Porter want to know in what environments early eukaryotes were diversifying, why they were there, when they migrated to other places, and what adaptations they needed in order to fill those new niches.

A big part of this effort involves understanding when different characteristics of eukaryotes first arose. For instance, the authors are quite interested to learn whether these organisms were adapted to oxygenated or anoxic environments. The former would suggest that they had an aerobic metabolism, and possibly mitochondria. Every modern eukaryote that’s been found descends from ancestors that possessed mitochondria. This suggests that eukaryotes acquired the organelle very early on, and that it provided a significant advantage.

Riedman and Porter are currently working on a fresh account of eukaryote diversity through time. They’ve also collected even older samples from Western Australia and Minnesota. Meanwhile, their geochemist collaborators at McGill are spearheading a study on oxygen levels and preferred eukaryote habitats, aspects that could shed light on their evolution.

“These results are a directive to go look for older material, older eukaryotes, because this is clearly not the beginning of eukaryotes on Earth,” Riedman said.

The value of wide beaches and dunes

Beaches and dunes are vital to society. They protect us from flooding, are an important source for our drinking water, and are an important habitat for numerous plant and animal species. They are also indispensable when we spend a day at the beach or walk through the dunes. When beaches and dunes are given enough space, they can fulfill all these functions. But, if dune areas become too narrow, natural flood protection, drinking water extraction and biodiversity are threatened. Yet beaches and dunes are increasingly squeezed by infrastructure on the one hand and rising sea levels on the other, write researchers from the Netherlands Institute for Sea Research, University of Groningen, Utrecht University, TU Delft and the Dutch Forestry Commission in the leading journal Nature Communications.

A quarter million measurements

To map this coastal squeeze, the researchers combined measurement data from previous work of TU Delft with Open Street Map data. They then measured the straight-line distance from the coastline to the nearest paved road or building. They took this measurement every kilometer, along all the sandy beaches in the world, yielding a total of 235,469 measurements.

Less than 400 meters

These measurements showed that human infrastructure is generally located very close to the sea. On average, the first building or paved road is found at 390 meters from the sea. In the densely populated Netherlands this is even at 210 meters, and in France the space is even tighter with 30 meters from the sea. Of all continents, Europe appears to have the most trapped beaches and dunes with an average distance of 130 meters, while Oceania is the least squeezed with an average distance of 2.8 km.

Rising sea levels

In the future, coastal squeeze is likely to increase worldwide. Rising sea levels will further narrow the space between buildings and the sea. In a natural situation, beaches and dunes would migrate inland, but buildings and roads impede this process. Therefore, researchers expect that 23 to 30 percent of beaches and dunes will be washed away or drowned by 2100.

Protection

Hopeful is the important role of nature protection. The researchers found that, when dune areas have a protected status, buildings and roads are found to be four times more distant than in unprotected areas. However, currently only 16% of the world’s sandy coasts are protected. The researchers therefore emphasize that it is important to better protect beaches and dunes.

“When people restrict the amount of food that they eat, they typically think it might affect their digestive tract or fat buildup, but not necessarily about how it affects the brain,” said Kenneth Wilson, Ph.D., Buck postdoc and first author of the study, published online on January 11, 2024 in Nature Communications. “As it turns out, this is a gene that is important in the brain.”

The team additionally demonstrated a detailed cellular mechanism of how dietary restriction can delay aging and slow the progression of neurodegenerative diseases. The work, done in fruit flies and human cells, also identifies potential therapeutic targets to slow aging and age-related neurodegenerative diseases.

“We found a neuron-specific response that mediates the neuroprotection of dietary restriction,” said Buck Professor Pankaj Kapahi , Ph.D., co-senior author of the study. “Strategies such as intermittent fasting or caloric restriction, which limit nutrients, may enhance levels of this gene to mediate its protective effects.”

“The gene is an important brain resilience factor protecting against aging and neurological diseases,” said Buck Professor Lisa Ellerby, Ph.D., co-senior author of the study.

Understanding variability in response to dietary restriction

Members of the team have previously shown mechanisms that improve lifespan and healthspan with dietary restriction, but there is so much variability in response to reduced calories across individuals and different tissues that it is clear there are many yet to be discovered processes in play. This project was started to understand why different people respond to diets in different ways.

The team began by scanning about 200 strains of flies with different genetic backgrounds. The flies were raised with two different diets, either with a normal diet or with dietary restriction, which was only 10% of normal nutrition. Researchers identified five genes which had specific variants that significantly affected longevity under dietary restriction. Of those, two had counterparts in human genetics.

The team chose one gene to explore thoroughly, called “mustard” (mtd) in fruit flies and “Oxidation Resistance 1” (OXR1) in humans and mice. The gene protects cells from oxidative damage, but the mechanism for how this gene functions was unclear. The loss of OXR1 in humans results in severe neurological defects and premature death. In mice, extra OXR1 improves survival in a model of amyotrophic lateral sclerosis (ALS).

The link between brain aging, neurodegeneration and lifespan

To figure out how a gene that is active in neurons affects overall lifespan, the team did a series of in-depth tests. They found that OXR1 affects a complex called the retromer, which is a set of proteins necessary for recycling cellular proteins and lipids. “The retromer is an important mechanism in neurons because it determines the fate of all proteins that are brought into the cell,” said Wilson. Retromer dysfunction has been associated with age-related neurodegenerative diseases that are protected by dietary restriction, specifically Alzheimer’s and Parkinson’s diseases.

Overall, their results told the story of how dietary restriction slows brain aging by the action of mtd/OXR1 in maintaining the retromer. “This work shows that the retromer pathway, which is involved in reusing cellular proteins, has a key role in protecting neurons when nutrients are limited,” said Kapahi. The team found that mtd/OXR1 preserves retromer function and is necessary for neuronal function, healthy brain aging, and lifespan extension seen with dietary restriction.

“Diet is influencing this gene. By eating less, you are actually enhancing this mechanism of proteins being sorted properly in your cells, because your cells are enhancing the expression of OXR1,” said Wilson.

The team also found that boosting mtd in flies caused them to live longer, leading researchers to speculate that in humans excess expression of OXR1 might help extend lifespan. “Our next step is to identify specific compounds that increase the levels of OXR1 during aging to delay brain aging,” said Ellerby.

“Hopefully from this we can get more of an idea of why our brains degenerate in the first place,” said Wilson.

“Diet impacts all the processes in your body,” he said. “I think this work supports efforts to follow a healthy diet, because what you eat is going to affect more than you know.”

Kapahi is founder and a member of the scientific advisory board at Juvify Bio. The other authors have no conflicts of interest.