Understanding how soil traps carbon

When carbon molecules from plants enter the soil, they hit a definitive fork in the road.

Either the carbon gets trapped in the soil for days or even years, where it is effectively sequestered from immediately entering the atmosphere. Or it feeds microbes, which then respire carbon dioxide (CO2) into the ever-warming environment.

In a new study, Northwestern University researchers determined the factors that could tip plant-based organic matter in one direction or the other.

By combining laboratory experiments and molecular modeling, researchers examined interactions between organic carbon biomolecules and a type of clay minerals known for trapping organic matter in soil. They found that electrostatic charges, structural features of carbon molecules, surrounding metal nutrients in soil and competition among molecules all play major roles in soil's ability (or inability) to trap carbon.

The new findings could help researchers predict which soil chemistries are most favorable for trapping carbon -- potentially leading to soil-based solutions for slowing human-caused climate change.

The research will be published on Feb. 9 in the Proceedings of the National Academy of Sciences.

"The amount of organic carbon stored in soil is about ten times the amount of carbon in the atmosphere," said Northwestern's Ludmilla Aristilde, the study's senior author. "If this enormous reservoir is perturbed, it would have substantial ripple effects. There are many efforts to keep carbon trapped to prevent it from entering the atmosphere. If we want to do that, then we first must understand the mechanisms at play."

An expert in the dynamics of organics in environmental processes, Aristilde is an associate professor of civil and environmental engineering at Northwestern's McCormick School of Engineering. Jiaxing Wang, a Ph.D. student in Aristilde's laboratory, is the paper's first author. Rebecca Wilson, an undergraduate student at Northwestern, is the paper's second author.

Common clay

Holding 2,500 billion tons of sequestered carbon, soil is one of Earth's largest carbon sinks -- second only to the ocean. But even though soil is all around us, researchers are only just beginning to understand how it locks in carbon to sequester it from the carbon cycle.

To investigate this process, Aristilde and her team looked to smectite clay, a type of clay mineral known to sequester carbon in natural soils. Then, they examined how the clay mineral's surface bonded to ten different biomolecules -- including amino acids, sugars related cellulose and phenolic acids related to lignin -- with varying chemistry and structures.

"We decided to study this clay mineral because it's everywhere," Aristilde said. "Nearly all soils have clay minerals. Also, clays are prevalent in semi-arid and temperate climates -- regions that we know will be affected by climate change."

Opposites attract

Aristilde and her team first looked at interactions between clay minerals and individual biomolecules. Because clay minerals are negatively charged, biomolecules with positively charged components (lysine, histidine and threonine) experienced the strongest binding. But, interestingly, this binding was not solely determined by electrostatic charges. Using 3D computational modeling, the researchers found that the structure of the biomolecules also played a role.

"There are instances where two molecules are both positively charged, yet one has a better interaction with the clay than the other," Aristilde said. "It's because the structural features of the binding are also important. A molecule has to be flexible enough to adopt a structural arrangement that can position itself in a way that aligns its positively charged components with the clay. The lysine, for example, has a long arm with a positive charge that it can use to anchor itself."

A little help from friends

Following this logic, one might assume that negatively charged biomolecules were unable to bind to the clay. But Aristilde and her team discovered that surrounding, natural metal nutrients could intervene. Positively charged metals, such as magnesium and calcium, formed a bridge between the negatively charged biomolecules and clay minerals to create a bond.

"Even with a biomolecule that wouldn't normally bind to the clay, we saw a significant increase in binding when magnesium was there," Aristilde said. "So, natural metal constituents in the soil can facilitate carbon trapping. Although this is a widely reported phenomenon, we shed light on the structures and mechanisms."

Mix and mingle

When studying interactions between individual biomolecules and clay minerals, the researchers found binding was predictable and straightforward. To attain information more closely aligned with real-world environments, Aristilde and her team mixed the different biomolecules together.

"We know different types of biomolecules in the environment exists together," Aristilde said. "So, we also performed experiments with a mixture of biomolecules."

Although the researchers initially thought the biomolecules would compete with one another to interact with the clay, they instead discovered unexpected behaviors. In a surprising twist, even positively charged biomolecules with flexible structures were inhibited from binding to the clay minerals. While they easily bonded to the clay when alone, the biomolecules' urges to bond with one another appears to supersede their attractions to the clay.

"This has not been shown before," Aristilde said. "The energy of attraction between two biomolecules was actually higher than the energy of attraction of a biomolecule to the clay. That led to a decrease in adsorption. It changes the way we think about how molecules compete on the surface. They aren't just competing for binding sites on the surface. They can actually attract each other."

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Researchers extract ancient DNA from a 2,900-year-old clay brick, revealing a time capsule of plant life

Currently housed at the National Museum of Denmark, the clay brick originates from the palace of Neo-Assyrian king Ashurnasirpal II, in the ancient city of Kalhu. Known today as the North-West palace in Nimrud (modern-day northern Iraq), its construction began around 879 BCE. The brick has a cuneiform inscription (written in the now extinct Semitic language Akkadian) stating that it is 'The property of the palace of Ashurnasirpal, king of Assyria.' This makes it possible to date the brick precisely to within a decade (879 BCE to 869 BCE).

During a digitalization project at the Museum in 2020, the group of researchers were able to obtain samples from the inner core of the brick -- meaning that there was a low risk of DNA contamination since the brick was created. The team extracted DNA from the samples by adapting a protocol previously used for other porous materials, such as bone.

After the extracted DNA had been sequenced, the researchers identified 34 distinct taxonomic groups of plants. The plant families with the most abundant sequences were Brassicaceae (cabbage) and Ericaceae (heather). Other represented families were Betulaceae (birch), Lauraceae (laurels), Selineae (umbellifiers) and Triticeae (cultivated grasses).

With the interdisciplinary team comprising assyriologists, archaeologists, biologists, and geneticists, they were able to compare their findings with modern-day botanical records from Iraq as well as ancient Assyrian plant descriptions.

The brick would have been made primarily of mud collected near the local Tigris river, mixed with material such as chaff or straw, or animal dung. It would have been shaped in a mould before being inscribed with cuneiform script, then left in the sun to dry. The fact that the brick was never burned, but left to dry naturally, would have helped to preserve the genetic material trapped within the clay.

Dr Sophie Lund Rasmussen (Wildlife Conservation Research Unit, Department of Biology, University of Oxford), joint first author of the paper, said: 'We were absolutely thrilled to discover that ancient DNA, effectively protected from contamination inside a mass of clay, can successfully be extracted from a 2,900-year-old clay brick. This research project is a perfect example of the importance of interdisciplinary collaboration in science, as the diverse expertise included in this study provided a holistic approach to the investigation of this material and the results it yielded.'

In addition to the fascinating insight this individual brick revealed, the research serves as a proof of concept and method which could be applied to many other archaeological sources of clay from different places and time periods around the world, to identify past flora and fauna. Clay materials are nearly always present in any archaeological site around the world, and their context means they can often be dated with high precision.

This study only described the plant DNA extracted, as these were the most prevalent and best-preserved specimens. However, depending on the sample, all taxa could potentially be identified, including vertebrates and invertebrates. The ability to provide accurate descriptions of ancient biodiversity would be a valuable tool to better understand and quantify present day biodiversity loss, and to gain a deeper understanding of ancient and lost civilisations.

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Climate: Lessons from the latest global warming

56 million years ago, the Earth experienced one of the largest and most rapid climate warming events in its history: the Paleocene-Eocene Thermal Maximum (PETM), which has similarities to current and future warming. This episode saw global temperatures rise by 5-8°C. It was marked by an increase in the seasonality of rainfalls, which led to the movement of large quantities of clay into the ocean, making it uninhabitable for certain living species. This scenario could be repeated today. This is what a team from the University of Geneva (UNIGE) has revealed, thanks to the analysis of sediments taken from the deep waters of the Gulf of Mexico. These results can be found in the journal Geology.

The Paleocene-Eocene Thermal Maximum (PETM), which occurred 56 million years ago, is the largest and most rapid climatic disturbance of the Cenozoic era (65.5 million years ago to the present day). Exceptional both in terms of its amplitude (5-8°C increase) and its suddenness (5,000 years, a very short time on a geological scale), this episode was marked by a warming of temperatures on a global scale. It lasted for about 200 000 years and led to numerous marine and terrestrial extinctions.

It would have been caused by a high concentration of carbon dioxide -- the famous CO2 -- and methane in the atmosphere, two powerful greenhouse gases. As is the case currently, these gases may have been released by several phenomena, certainly in combination: the release of methane hydrates trapped on the seabed, the sudden and significant melting of the permafrost, and the injection of magma into the organic sediments of the western edge of Norway. The origin of these processes is still under debate. The impact of a meteorite and/or the effects of intense volcanic activity in the depths of the North Atlantic could be responsible.

A geological ''archive'' of unprecedented quality

Because of the many similarities between the PETM and the current warming, the geological remains of this period are being closely studied by scientists. A team from the UNIGE is now reporting new elements. ''The objective of our study was to investigate the influence of these climatic changes on sedimentary systems, i.e. on the processes of sediment formation and deposition, and to understand how these changes could have been transmitted from the atmosphere to the depths of the ocean,'' explains Lucas Vimpere, a post-doctoral scholar at the Section of Earth and Environmental Sciences of the UNIGE's Faculty of Science and first author of the study.

The researchers analysed sediments taken from more than 8km deep in the Gulf of Mexico. This basin acts as a giant ''sink'' into which material eroded and transported from the North American continent over millions of years is discharged. ''For reasons of cost and infrastructure, the sediments used to study the PETM are generally taken from shallow marine or continental environments. Thanks to the collaboration of an oil company, we were able to obtain a sample of unprecedented quality, without any alteration'', says the researcher. The 543-metre-long core contains a 180-metre-thick PETM sedimentary record, making it the most complete geological ''archive'' of this period in the world.

More clay on the ocean floor

The UNIGE scientists found that it was composed first of a large layer of clay and then of a layer of sand, a counter-intuitive result. ''At the time of the PETM, we thought that there had been more precipitation, and therefore more erosion, and that large quantities of sand had then been transported first by the fluvial systems into the oceans. However, thanks to our sample, we were able to determine that it was the clays and not the sands that were transported in the first instance'', explains Sébastien Castelltort, full professor at the Earth and Environmental Sciences Section of the UNIGE Faculty of Science, and last author of the study.

This established that the period was not marked by an increase in the annual rate of precipitation but by an increase in its seasonality and intensity. ''This resulted in increased mobility of the river channels -- the deepest areas of a river -- which in turn transported large quantities of fluvial clays deposited on the adjacent alluvial plains to the ocean depths. We can now consider the presence of clay in deep basins as a marker of increased rainfall seasonality,'' says Lucas Vimpere. The phenomenon has led to an increase in ocean turbidity that is harmful to marine life, especially corals.

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