Scientists from the University of Cambridge studied hundreds of tree trunks, dug up by Fenland farmers while ploughing their fields. The team found that most of the ancient wood came from yew trees that populated the area between four and five thousand years ago.

These trees, which are a nuisance when they jam farming equipment during ploughing, contain a treasure trove of perfectly preserved information about what the Fens looked like thousands of years ago.

The Fen yew woodlands suddenly died about 4,200 years ago, when the trees fell into peat and were preserved until today. The researchers hypothesise that a rapid sea level rise in the North Sea flooded the area with salt water, causing the vast woodlands to disappear.

The climate and environmental information these trees contain could be a valuable clue in determining whether this climate event could be related to other events that happened elsewhere in the world at the same time, including a megadrought in the Middle East that may have been a factor in the collapse of ancient Egypt’s Old Kingdom. Their results are reported in the journal Quaternary Science Reviews.

Yew (Taxus baccata) trees are one of the longest-lived species in Europe, and can reach up to 20 metres in height. While these trees are fairly common in Cambridge College gardens and churchyards across southern England, they are absent in the Fens, the low-lying marshy region of eastern England. Much of the Fens was a wetland until it was drained between the 17^th and 19^th centuries using artificial drainage and flood protection. Today, the area is some of the most productive farmland in the UK, thanks to its rich peat soil.

While the area is great for farming and does have its own charms, few people would describe the Fens as spectacular: for the most part, the area is extremely flat and dominated by fields of potatoes, sugar beet, wheat and other crops. But five thousand years ago, the area was a huge forest.

“A common annoyance for Fenland farmers is getting their equipment caught on big pieces of wood buried in the soil, which can often happen when planting potatoes, since they are planted a little deeper than other crops,” said lead author Tatiana Bebchuk, a PhD student from Cambridge’s Department of Geography. “This wood is often pulled up and piled at the edge of fields: it’s a pretty common sight to see these huge piles of logs when driving through the area.”

For farmers, these logs are a nuisance. But for Bebchuk and her colleagues, they are buried treasure. The Cambridge team approached several Fenland farmers and took samples of hundreds of logs that had been dug up and discarded, to find out what secrets they might hold.

“I remember when I first saw this enormous pile of abandoned trees, it was incredible just how many there were,” said Bebchuk. “But when we got them back to lab, we were even more surprised: these trees were so well-preserved, it looked as if they were cut down just yesterday.”

To put current anthropogenic climate change in a long-term context of natural variability, scientists need accurate evidence from the past, and trees are some of the best recorders of past conditions: their annual growth rings contain information about temperature and hydroclimate for every growing season they witnessed. “But the further back in time we go, the less reliable evidence we have, since very old trees and well-preserved wood materials are extremely rare,” said Professor Ulf Büntgen, the senior author of the study.

However, analysis by the Cambridge Tree-Ring Unit (TRU) showed that the yew trees dug up from Fenland fields were very old indeed: some of these ancient trees were 400 years old when they died. The new find provides unique climate information for over a millennium from around 5,200 years ago until about 4,200 years ago, when much of the Fens was a woodland of yew and oak: completely different than it looks today.

“Finding these very old trees in the Fens is completely unexpected — it would be like turning a corner in rural Cambridgeshire and seeing an Egyptian pyramid — you just wouldn’t expect it,” said Bebchuk. “It’s the same with nature — wood rots and decomposes easily, so you just don’t expect a tree that died five or four thousand years ago to last so long.”

Given that most of the Fens are barely above sea level, about 4,200 years ago, a sudden rise in sea level most likely killed the Fen woodlands. The period that the Fen woodlands died coincided with major climatic changes elsewhere in the world: at roughly the same time, a megadrought in China and the Middle East was a possible trigger of the collapse of several civilisations, including Egypt’s Old Kingdom and the Akkadian Empire in Mesopotamia.

“We want to know if there is any link between these climatic events,” said Bebchuk. “Are the megadroughts in Asia and the Middle East possibly related to the rapid sea level rise in northern Europe? Was this a global climate event, or was it a series of unrelated regional changes? We don’t yet know what could have caused these climate events, but these trees could be an important part of solving this detective story.”

“This is such a unique climate and environmental archive that will provide lots of opportunities for future studies, and it’s right from Cambridge’s own backyard,” said Büntgen. “We often travel all over the world to collect ice cores or ancient trees, but it’s really special to find such a unique archive so close to the office.”

Our bodies are, in some ways, like cars — to keep functioning, they need to be checked and repaired regularly. In the case of our bodies, any cells that are damaged or dead need to be replaced to keep organs functioning. This replacement occurs thanks to tissue-resident adult stem cells. In contrast with embryonic stem cells, which can form any cell type in the body, adult stem cells will only form the cell types that are found in the tissue they belong to. But how do tissue-specific stem cells know which cell type to give rise to? Gabriele Colozza, a postdoctoral researcher in the lab of Bon-Kyoung Koo at IMBA — now director at the Center for Genome Engineering, Institute for Basic Science in South Korea — decided to investigate this question using intestinal stem cells.

Intestines — a constant construction site

“In our intestines, cells are exposed to extreme conditions,” Colozza explains. Mechanical wear and tear, but also digestive enzymes and varying pH values all affect intestinal cells. In turn, stem cells in the intestine’s mucosa differentiate to form new intestinal cells. “Damaged cells have to be replaced, but it is a delicate balance between stem cell renewal and differentiation into other cell types: uncontrolled stem cell proliferation may lead to tumor formation; on the other hand, if too many stem cells differentiate, the tissue will be depleted of stem cells and ultimately unable to self-renew.”

This balance is delicately tuned by signaling pathways and feedback loops, which allow cells to communicate with each other. One important pathway is called Wnt. The Wnt pathway is known for its role in embryonic development, and if left unchecked, an overactive Wnt pathway can lead to excessive cell division and the formation of tumors.

Molecular partner identified

A well-known antagonist of Wnt signalling — keeping Wnt in check — is Rnf43, which was originally identified by Bon-Kyoung Koo. Prior to this study, Rnf43 was known to target the Wnt receptor Frizzled and mark it for degradation. “We wanted to know how Rnf43 works, and also what — in turn — controls Rnf43 and helps it to regulate Wnt signalling.” From earlier research, the scientists knew that Rnf43 on its own was not sufficient to break down the Wnt receptor Frizzled, which sits in the plasma membrane. “In our project, we used biochemical assays to identify which proteins interact with Rnf43.” A key partner of Rnf43 turned out to be the protein Daam1.

To understand how Daam1 regulates Rnf43 and affects the tissues it acts in, Colozza turned to intestinal organoids. “We found that Daam1 is required for Rnf43 to be active, so for Rnf43 to regulate Wnt signaling at all. Further work in cells showed Rnf43 needs Daam1 to move the Wnt receptor Frizzled into vesicles called endosomes. From the endosomes, Frizzled is shuttled to the lysosomes where it is degraded, dampening Wnt signaling,” Colozza adds.

Intestinal organoids are three-dimensional cell cultures grown from adult intestinal stem cells, allowing the researchers to mimic the intestinal mucosa. For Colozza, organoids were an opportunity to understand how Rnf43 and Daam1 affect the delicate balance of stem cell renewal and differentiation in the intestine. “We found that when we knock-out Rnf43 or Daam1, the organoids grow into tumor-like structures. These tumor-like organoids keep on growing, even if we withdraw the growth factors they usually depend on, such as R-spondin.”

Switching on Paneth cell formation

When Colozza followed up this result in mouse tissue, the researchers were in for a surprise. “When Rnf43 was missing, the intestines grew tumors — as expected. But when Daam1 was missing, no tumors grew. We were puzzled by this striking difference: how can the loss of factors in the same pathway, that behave similarly in organoids, lead to such different outcomes?”

Looking closely at the intestines, Colozza saw that intestines lacking Rnf43 were full of a specific type of secretory cells, the Paneth cells. Intestines lacking Daam1, on the other hand, contained no extra Paneth cells. Paneth cells secrete growth factors, such as Wnt, that stimulate cell division. “Daam1 is required for the efficient formation of Paneth cells. When Daam1 is active, stem cells differentiate to form Paneth cells. When Daam1 is not active, the stem cells differentiate into another cell type.”

Tumors modify their niche to grow

This link between the molecular results and Paneth cells explains the puzzling difference between intestines and organoids. “In organoid culture, we scientists provide growth factors, so the knockout of both Rnf43 and Daam1 lead to tumor-like organoids. But in the intestine, there is no little scientist providing growth factors. Instead, Paneth cells provide growth factors, like Wnt, and create the right conditions for stem cells to survive and divide. When Paneth cells are lacking — such as when Daam1 is not active to drive cells into becoming Paneth cells — stem cells will not divide much. But when there are too many Paneth cells — such as in intestines lacking Rnf43 — the excessive growth factors can contribute to the formation of tumors.”

Colozza’s and colleagues’ study is the first genetic proof that Daam1, a member of the non-canonical Wnt pathway, is important for specifying Paneth cells, and directly involved in the development of this crucial secretory cell. The results also shed light on the importance of the stem cell niche. “We show that tumor cells modify their microenvironment, and influence their supporting environment so that they can grow better.”

“We have only a good record of the deep ocean for the last ~180 million years,” said David Fike, the Glassberg/Greensfelder Distinguished University Professor of Earth, Environmental, and Planetary Sciences in Arts & Sciences at Washington University in St. Louis. “Everything else is just shallow-water deposits. So it’s really important to understand the bias that might be present when we look at shallow-water deposits.”

One of the ways that scientists like Fike use deposits from the seafloor is to reconstruct timelines of past ecological and environmental change. Researchers are keenly interested in how and when oxygen began to build up in the oceans and atmosphere, making Earth more hospitable to life as we know it.

For decades they have relied on pyrite, the iron-sulfide mineral known as “fool’s gold,” as a sensitive recorder of conditions in the marine environment where it is formed. By measuring the bulk isotopic composition of sulfur in pyrite samples — the relative abundance of sulfur atoms with slightly different mass — scientists have tried to better understand ancient microbial activity and interpret global chemical cycles.

But the outlook for pyrite is not so shiny anymore. In a pair of companion papers published Nov. 24 in the journal Science, Fike and his collaborators show that variations in pyrite sulfur isotopes may not represent the global processes that have made them such popular targets of analysis.

Instead, Fike’s research demonstrates that pyrite responds predominantly to local processes that should not be taken as representative of the whole ocean. A new microanalysis approach developed at Washington University helped the researchers to separate out signals in pyrite that reveal the relative influence of microbes and that of local climate.

For the first study, Fike worked with Roger Bryant, who completed his graduate studies at Washington University, to examine the grain-level distribution of pyrite sulfur isotope compositions in a sample of recent glacial-interglacial sediments. They developed and used a cutting-edge analytical technique with the secondary-ion mass spectrometer (SIMS) in Fike’s laboratory.

“We analyzed every individual pyrite crystal that we could find and got isotopic values for each one,” Fike said. By considering the distribution of results from individual grains, rather than the average (or bulk) results, the scientists showed that it is possible to tease apart the role of the physical properties of the depositional environment, like the sedimentation rate and the porosity of the sediments, from the microbial activity in the seabed.

“We found that even when bulk pyrite sulfur isotopes changed a lot between glacials and interglacials, the minima of our single grain pyrite distributions remained broadly constant,” Bryant said. “This told us that microbial activity did not drive the changes in bulk pyrite sulfur isotopes and refuted one of our major hypotheses.”

“Using this framework, we’re able to go in and look at the separate roles of microbes and sediments in driving the signals,” Fike said. “That to me represents a huge step forward in being able to interpret what is recorded in these signals.”

In the second paper, led by Itay Halevy of the Weizmann Institute of Science and co-authored by Fike and Bryant, the scientists developed and explored a computer model of marine sediments, complete with mathematical representations of the microorganisms that degrade organic matter and turn sulfate into sulfide and the processes that trap that sulfide in pyrite.

“We found that variations in the isotopic composition of pyrite are mostly a function of the depositional environment in which the pyrite formed,” Halevy said. The new model shows that a range of parameters of the sedimentary environment affect the balance between sulfate and sulfide consumption and resupply, and that this balance is the major determinant of the sulfur isotope composition of pyrite.

“The rate of sediment deposition on the seafloor, the proportion of organic matter in that sediment, the proportion of reactive iron particles, the density of packing of the sediment as it settles to the seafloor — all of these properties affect the isotopic composition of pyrite in ways that we can now understand,” he said.

Importantly, none of these properties of the sedimentary environment are strongly linked to the global sulfur cycle, to the oxidation state of the global ocean, or essentially any other property that researchers have traditionally used pyrite sulfur isotopes to reconstruct, the scientists said.

“The really exciting aspect of this new work is that it gives us a predictive model for how we think other pyrite records should behave,” Fike said. “For example, if we can interpret other records — and better understand that they are driven by things like local changes in sedimentation, rather than global parameters about ocean oxygen state or microbial activity — then we can try to use this data to refine our understanding of sea level change in the past.”