Wood-eating clams use their feces to dominate their habitat

Deep beneath the waves, tiny clams with shells usually about as big as a pea bore into pieces of sunken wood. The wood is food for them, as well as a home. These rare, scattered, sunken pieces of wood support miniature ecosystems where different wood-boring clam species can live in harmony for years. But in a new paper in Marine Biodiversity, researchers found that one group of wood-boring clams has evolved a unique way to get the wood all for itself: building chimneys made of poop.

"There are two challenges every sea creature has to face: getting pure water in, so you can get oxygen to your gills, and getting rid of your waste. Because nobody wants to live in their poop. But here are these clams living with theirs, and actually thriving," says Janet Voight, Associate Curator of invertebrate zoology at the Field Museum and the study's lead author.

Scientists can put wood on the seafloor, return months or even years later, and recover it with "an amazing array of animals," says Voight; other times wood that has been submerged for the same amount of time comes up so gnawed and bored-through that you can crumble it in your hand. This difference was a mystery, and Voight wanted to know why.

She took stock of the wood-boring clam species present in reports of sunken wood from all over the world, and she noticed a pattern. "There are six main branches in the wood-boring clam family tree, and every woodfall that was bored so heavily it was crushable by hand turned out to have been bored by a species from the same single branch of that family tree," says Voight. She says she was surprised by this finding -- "that's not supposed to happen, you just assume that all wood-boring clam species, which tend to look pretty similar, bore into wood the same way. And yet, here's one group that's doing something totally different."

Scientists had suggested that the extra-chewed-up wood was due to lots of larvae happening to be present nearby, or warmer water temperatures, but it turns out, the very nature of the clams may be responsible. Voight noted all of these extra-efficient, related species have a common trait where the sun don't shine. As the clams dig and move into their boreholes in the wood, they fill the space around them inside the holes with their own feces.

"They don't do it on purpose, their anatomy makes them do it," says Voight. "When these clams bore into wood, their little shell does the boring." Meanwhile, the clams' siphons, tubular appendages for taking in water to get oxygen and expelling waste, stick out behind them. "In most wood-boring clams, these two "in and out" siphons are equal in length and stick out into the water column," says Voight. "But in these related hyper-nasty borers, the siphon for expelling de-oxygenated water and feces is short; it stays inside the borehole in the wood. As a result, says Voight, "they poop in their borehole. They just have to, unless they really, really push." The waste stays right there with the clam, forming a chimney that wraps around the siphon.

That animals would evolve an anatomy that keeps them in such close contact with their own waste, is surprising, says Voight: "It sure isn't very hygienic, and yet they show no evidence of immune problems. They're healthy, they're clearly going to town on the wood. So why did they evolve this way?"

She and her colleagues hypothesized that these fecal chimneys might cue larval settlement: that their free-floating larvae might be able to detect the poop and make their way to it to make a home alongside members of their own species.

But that still leaves the problem: even if a poop chimney serves as a beacon for other members of their species to join them on their wood, how can these individuals survive as more and more larvae settle and the environment becomes filthier and oxygen becomes less available?

"This group of species of clam has been shown in previous studies to be unusually tolerant of low oxygen," says Voight. They also have additional adaptations, like a mucosal lining of their fecal chimneys, and a substance like hemoglobin in their blood that picks up more oxygen; both may reduce the risk of sulfide poisoning from the waste. Taken together, these adaptations allow these speciesto survive in conditions that would make non-related wood-boring clams sick. The end result is more wood for the chimney-producing species to eat, live in, and for their offspring to settle on, unbothered by competitors.

Beyond just solving the mystery of the gross chewed-up wood with an even grosser solution, Voight says that the study illustrates the importance of looking at ecology with an understanding of how different species are related to each other.

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DNA in Viking feces sheds new light on 55,000-year-old relationship between gut companions

Using stool samples from Viking latrines, researchers at the University of Copenhagen have genetically mapped one of the oldest human parasites -- the whipworm. The mapping reflects the parasite's global spread and its interaction with human beings, a delicate relationship that can make us healthier and ill.

Using fossilized eggs in up to 2500-year-old feces from Viking settlements in Denmark and other countries, researchers at the University of Copenhagen's Department of Plant and Environmental Sciences and the Wellcome Sanger Institute (UK) have made the largest and most in-depth genetic analysis of one of the oldest parasites found in humans -- the whipworm.

The study, published in Nature Communications, presents completely new knowledge about the parasite's development and prehistoric dispersal. This knowledge can be applied in efforts to prevent the parasite's drug resistance and its future spread.

The study suggests that human and parasite have developed a delicate interaction over thousands of years, whereby the parasite tries to stay "under the radar" not to be repelled, which allows it more time to infect new people. From other studies, it is known that the whipworm stimulates the human immune system and the gut microbiome, to the mutual benefit of both host and parasite.

While whipworm (Trichuris trichiura) is now rare in industrialized countries, and most often only causes minor problems among healthy individuals, the parasite is estimated to affect 500 million people in developing countries.

"In people who are malnourished or have impaired immune systems, whipworm can lead to serious illness. Our mapping of the whipworm and its genetic development makes it easier to design more effective anti-worm drugs that can be used to prevent the spread of this parasite in the world's poorest regions," says Professor Christian Kapel of UCPH's Department of Plant and Environmental Sciences.

Fossilized latrine poop from Copenhagen and Viborg

Eggs, not worms, made it possible for researchers to examine the genetic material of thousands-of-years-old whipworms. Due to extremely durable chitin in egg capsules, their internal DNA has been well preserved while the eggs have been buried in moist soil.

By examining fossilized stool samples which were previously discovered in the latrines of Viking settlements in Viborg and Copenhagen, the researchers isolated the eggs under a microscope, sieved them from the stool and subjected them to refined genetic analyses that the researchers have been perfecting for years in previous studies.

"We have known for a long time that we could detect parasite eggs up to 9000 years old under a microscope. Lucky for us, the eggs are designed to survive in soil for long periods of time. Under optimal conditions, even the parasite's genetic material can be preserved extremely well. And some of the oldest eggs that we've extracted some DNA from are 5000 years old. It has been quite surprising to fully map the genome of 1000-year-old well-preserved whipworm eggs in this new study," explains Christian Kapel.

The researchers examined archaeological stool samples from several locations. These ancient genetic samples are compared with contemporary samples obtained from people with whipworms from around the world. Doing so has provided researchers with an overview of the worm's genome and its evolution over ten-thousands of years.

"Unsurprisingly, we can see that the whipworm appears to have spread from Africa to the rest of the world along with humans about 55,000 years ago, following the so-called 'out of Africa' hypothesis on human migration," explains Christian Kapel.

Can live unnoticed in the intestine for months

A whipworm can grow five to seven centimeters in length and live unnoticed in the intestine of a healthy individual for several months. During this time, it lays eggs continuously, which are expelled through feces. In people with weakened immune systems, whipworm can cause a wide range of gastrointestinal diseases, malnutrition and even delay childhood development.

Worms are transmitted via the fecal-oral route, meaning that microscopic parasite eggs in soil can spread to drinking water or food, after which they are ingested through the mouth of a new host.

"The eggs lie in the ground and develop for roughly three months. Once matured, eggs can survive in the wild for even longer, as they wait to be consumed by a new host in whose digestive tract they will then hatch. Their entire life cycle is adapted to survive in soil for as long as possible," explains Christian Kapel.

As such, the golden years for these worms in our part of the world were when our toilet and kitchen conditions, as well as personal hygiene, were significantly different than today.

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Prehistoric feces reveal parasites from feasting at Stonehenge

A new analysis of ancient faeces found at the site of a prehistoric village near Stonehenge has uncovered evidence of the eggs of parasitic worms, suggesting the inhabitants feasted on the internal organs of cattle and fed leftovers to their dogs.

Durrington Walls was a Neolithic settlement situated just 2.8km from Stonehenge, and dating from around 2500 BC, when much of the famous stone monument was constructed. It is believed that the site housed the people who built Stonehenge.

A team of archaeologists led by the University of Cambridge investigated nineteen pieces of ancient faeces, or 'coprolite', found at Durrington Walls and preserved for over 4,500 years. Five of the coprolites (26%) -- one human and four dog -- were found to contain the eggs of parasitic worms.

Researchers say it is the earliest evidence for intestinal parasites in the UK where the host species that produced the faeces has also been identified. The findings are published today in the journal Parasitology.

"This is the first time intestinal parasites have been recovered from Neolithic Britain, and to find them in the environment of Stonehenge is really something," said study lead author Dr Piers Mitchell from Cambridge's Department of Archaeology.

"The type of parasites we find are compatible with previous evidence for winter feasting on animals during the building of Stonehenge," he said.

Four of the coprolites, including the human one, contained the eggs of capillariid worms, identified in part by their lemon shape.

While the many types of capillariid around the world infect a wide range of animals, on the rare occasion that a European species infects humans the eggs get lodged in the liver and don't appear in stool.

The evidence of capillariid eggs in human faeces indicates that the person had eaten the raw or undercooked lungs or liver from an already infected animal, resulting in the parasite's eggs passing straight through the body.

During excavations of the main 'midden' -- or dung and refuse heap -- at Durrington Walls, archaeologists uncovered pottery and stone tools along with over 38,000 animal bones. Some 90% of the bones were from pigs, with less than 10% from cows. This is also where the partially mineralised faeces used in the study were found.

"As capillariid worms can infect cattle and other ruminants, it seems that cows may have been the most likely source of the parasite eggs," said Mitchell.

Previous isotopic analyses of cow teeth from Durrington Walls suggest that some cattle were herded almost 100km from Devon or Wales to the site for large-scale feasting. Patterns of butchery previously identified on cattle bones from the site suggest beef was primarily chopped for stewing, and bone marrow was extracted.

"Finding the eggs of capillariid worms in both human and dog coprolites indicates that the people had been eating the internal organs of infected animals, and also fed the leftovers to their dogs," said co-author Evilena Anastasiou, who assisted with the research while at Cambridge.

To determine whether the coprolites excavated from the midden were from human or animal faeces, they were analysed for sterols and bile acids at the National Environment Isotope Facility at the University of Bristol.

One of the coprolites belonging to a dog contained the eggs of fish tapeworm, indicating it had previously eaten raw freshwater fish to become infected. However, no other evidence of fish consumption, such as bones, has been found at the site.

"Durrington Walls was occupied on a largely seasonal basis, mainly in winter periods. The dog probably arrived already infected with the parasite," said Dr Piers Mitchell.

"Isotopic studies of cow bones at the site suggests they came from regions across southern Britain, which was likely also true of the people who lived and worked there."

The dates for Durrington Walls match those for stage two of the construction of Stonehenge, when the world-famous 'trilithons' -- two massive vertical stones supporting a third horizontal stone -- were erected, most likely by the seasonal residents of this nearby settlement.

While Durrington Walls was a place of feasting and habitation, as evidenced by the pottery and vast number of animal bones, Stonehenge itself was not, with little found to suggest people lived or ate there en masse.

Prof Mike Parker Pearson from UCL's Institute of Archaeology, who excavated Durrington Walls between 2005 and 2007, added: "This new evidence tells us something new about the people who came here for winter feasts during the construction of Stonehenge."

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Ancient feces shows people in present-day Austria drank beer and ate blue cheese up to 2,700 years ago

Human feces don't usually stick around for long -- and certainly not for thousands of years. But exceptions to this general rule are found in a few places in the world, including prehistoric salt mines of the Austrian UNESCO World Heritage area Hallstatt-Dachstein/Salzkammergut. Now, researchers who've studied ancient fecal samples (or paleofeces) from these mines have uncovered some surprising evidence: the presence of two fungal species used in the production of blue cheese and beer. The findings appear in the journal Current Biology on October 13.

"Genome-wide analysis indicates that both fungi were involved in food fermentation and provide the first molecular evidence for blue cheese and beer consumption during Iron Age Europe," says Frank Maixner (@FrankMaixner) of the Eurac Research Institute for Mummy Studies in Bolzano, Italy.

"These results shed substantial new light on the life of the prehistoric salt miners in Hallstatt and allow an understanding of ancient culinary practices in general on a whole new level," adds Kerstin Kowarik (@KowarikKerstin) of the Museum of Natural History Vienna. "It is becoming increasingly clear that not only were prehistoric culinary practices sophisticated, but also that complex processed foodstuffs as well as the technique of fermentation have held a prominent role in our early food history."

Earlier studies already had shown the potential for studies of prehistoric paleofeces from salt mines to offer important insights into early human diet and health. In the new study, Maixner, Kowarik, and their colleagues added in-depth microscopic, metagenomic, and proteomic analyses -- to explore the microbes, DNA, and proteins that were present in those poop samples.

These comprehensive studies allowed them to reconstruct the diet of the people who once lived there. They also could get information about the ancient microbes that inhabited their guts. Gut microbes are collectively known as the gut microbiome and are now recognized to have an important role in human health.

Their dietary survey identified bran and glumes of different cereals as one of the most prevalent plant fragments. They report that this highly fibrous, carbohydrate-rich diet was supplemented with proteins from broad beans and occasionally with fruits, nuts, or animal food products.

In keeping with their plant-heavy diet, the ancient miners up to the Baroque period also had gut microbiome structures more like those of modern non-Westernized individuals, whose diets are also mainly composed of unprocessed food, fresh fruits and vegetables. The findings suggest a more recent shift in the Western gut microbiome as eating habits and lifestyles changed.

When the researchers extended their microbial survey to include fungi, that's when they got their biggest surprise: an abundance in one of their Iron Age samples of Penicillium roqueforti and Saccharomyces cerevisiae DNA.

"The Hallstatt miners seem to have intentionally applied food fermentation technologies with microorganisms which are still nowadays used in the food industry," Maixner says.

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Unprecedented preservation of fossil feces from the La Brea Tar Pits

While Rancho La Brea, commonly known as the La Brea Tar Pits, is famous for its thousands of bones of large extinct mammals, big insights are coming from small fossils, thanks to new excavation and chemical techniques.

Today, a team of researchers from La Brea Tar Pits, the University of Oklahoma and the University of California Irvine report the first coprolites -- or fossil feces -- ever discovered in an asphaltic -- or tar pit -- context. These hundreds of fossilized rodent pellets were found during the excavation of a parking garage for the Los Angeles County Museum of Art in Hancock Park in 2016, which had also yielded the more traditional La Brea fossils, such as extinct mammoths, dire wolves and saber-toothed cats.

Alexis Mychajliw, a postdoctoral research associate at OU, is the lead author of the study. The details of the research team's findings were published today in Scientific Reports.

"It's incredible that after more than a century of excavation and study, we are still unearthing new types of fossils from La Brea's treasure trove of deposits," said Emily Lindsey, assistant curator at La Brea Tar Pits. "These tiny finds may lead to big discoveries about the climate and ecosystems of Ice Age Los Angeles."

Researchers were skeptical at first, given the abundance of urban rats in the area.

"We noted the occasional rodent fecal pellet in the processed matrix before, but it was easy to explain it away as modern contamination," said Laura Tewksbury, senior preparator at La Brea Tar Pits.

But, with more and more pellets appearing encased in asphalt, Tewksbury recalled, "We stared at the sheer number of pellets in silence for a minute, before looking at each other and stating, 'There's just no way that much is contamination.'"

Indeed, radiocarbon dates generated at UC Irvine would confirm the pellets were ~50,000 years old.

Rancho La Brea has been associated with the image of big animals getting stuck in "tar pits," or shallow, sticky asphalt pools, with carnivores attracted en masse by struggling herbivore prey. But these coprolites tell a new story of how fossils can be preserved at Rancho La Brea.

"The intact nature and density of the fossils require a taphonomic explanation other than entrapment. The preservation is more likely the result of an asphalt seep overtaking an existing rodent nest," noted Karin Rice, preparator at La Brea Tar Pits.

Using a suite of cutting-edge tools, including stable isotope analysis and scanning electron microscopy, the researchers demonstrated that the fecal pellets were associated with beautifully preserved twigs, leaves, and seeds, apparently as part of an intact nest made by a woodrat. Woodrats -- also known as packrats -- are well-known in the paleontological community for their hoarding behavior that produces massive nests that can be preserved for thousands of years. Slices of plant material from these nests, in turn, represent snapshots of vegetation and climate conditions of the past.

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