Phytoliths: The Storytelling Stones Inside Plants

Thomas C Hart. American Scientist. Volume 103, Issue 2. Mar/Apr 2015.

Charles Darwin’s voyage aboard the Beagle is legendary in the history of science, and yet one of his notable observations is barely known. Before he glimpsed some of the finches that would bear his name and provide the inspiration for the theory of natural selection, he was one of the first scientists to remark on the uniqueness of microscopic silica bodies called phytoliths. On January 16, 1832, the Beagle stopped at its first port of call, Porto Praya in the Cape Verde islands off the northwest coast of Africa. Darwin, the ever-studious naturalist, noted with a sense of wonder the following in his journal, later published in The Voyage of the Beagle:

Generally the atmosphere is hazy; and this is caused by the falling of impalpably fine dust, which was found to have slightly injured the astronomical instruments. The morning before we anchored at Porto Praya, I collected a little packet of this brown-coloured fine dust, which appeared to have been filtered from the wind by the gauze of the vane at the masthead. Mr. Lyell has also given me four packets of dust which fell on a vessel a few hundred miles northward of these islands. Professor Ehrenberg finds that this dust consists in great part of infusoria with siliceous shields, and of the siliceous tissue of plants. In five little packets which I sent him, he has ascertained no less than sixtyseven different organic forms!

According to Darwin, this dust was a fairly common phenomenon in the region, and created such a haze that ships were rumored to have run aground because of the poor visibility. TTie “siliceous shields” and “siliceous tissues of plants” that Darwin referenced were phytoliths, inorganic silica molds of plant cells and tissues. The term is Greek (phyto means plant, lith means stone). Other names that have been used in the past include opaline silica, plant opal, and opal phytoliths, but the most common is simply phytoliths.

The production of phytoliths is largely under genetic control and begins when a plant’s roots take up monosilicic acid (Si(OH)4) along with water. During this process, called transpiration, plants move water and minerals from the root system throughout the rest of the plant, depositing the monosilicic acid along the way. Some plants can also actively separate the water and leave the monosilicic acid in specific tissues designed for silica accumulation The end result is that the monosilicic acid takes the shape of the surrounding plant tissues, forming microscopic molds.

Phytoliths are produced by taxa in almost every environment throughout the world, including angiosperms (flowering plants), gymnosperms (conifers, cycads, ginko, gnetales), and pteridophytes (ferns). Thus there tend to be large quantities of them in the ground. These microscopic, crystallike structures are composed mostly of silicon dioxide (SiO2), water, and organic carbon, along with some trace elements including aluminum, iron, magnesium, manganese, phosphorous, copper, and nitrogen. Their colors extend from light brown to opaque with most being slightly transparent, and they range in size from 1 to more than 100 micrometers.

Recent studies have suggested that phytoliths might serve protective, structural, and physiological functions. The same genes that regulate the production of lignin, a plant tissue that serves as a defensive mechanism, also regulate phytolith development. High concentrations of phytoliths in plant tissues could make them hard to break down or digest, deterring both herbivores and fungi. In some plant tissues, such as the leaves and stems of rice, phytoliths may also serve a structural function, causing plants to stand more erect and thus allowing for more Sun exposure and photosynthesis. Phytoliths also play an important function in plant physiology because they trap toxic heavy elements, such as manganese and aluminum, which would otherwise be deleterious to the plant. But it can be difficult to say with certainty whether a plant produces phytoliths for these purposes or if they are just a by-product of other processes that are as yet undiscovered.

These structures had no immediate significance to Darwin. Even now it is not fully understood exactly why plants produce phytoliths. But if their biological function is enigmatic, their significance certainly is not. These bodies turn out to be incredibly useful as age markers and as finely engineered biomaterials. As a result, phytoliths are increasingly being applied in such disparate fields as paleontology archaeology, primatology, and forensic science, and are at the forefront of technologies in nanotechnology and environmental science.

A Picture of the Past

Whether or not durability is a key feature of phytoliths in living plants, it certainly is after a plant dies. Phytoliths from plants long decayed can persist in the environment for tens of millions of years and at temperatures up to 1,000 degrees Celsius. Thus phytoliths found during archaeological digs can be important sources of information, particularly in combination with other artifacts. They belong to a class of remains called ecofacts, a class that also includes animal bones; parasites; charred, dried, or waterlogged plant remains; pollen; starch grains; and calcium oxalate crystals. Phytoliths are particularly useful to researchers because their shapes can be unique to a plant at varying levels of specificity, such as the family, genus, species, or subspecies, and even to a plant part.

Under most conditions, phytoliths highlight local vegetation because they chemically bond to the surrounding soil after a plant has decayed. There are some notable exceptions, such as the situation Darwin encountered. In his case, phytoliths landed on the Beagle because they were bound to West African soils that became airborne because of extremely dry and windy conditions. Phytoliths can survive in fossilized feces (called coprolites), plaque (also called dental calculus), and on tooth and artifact surfaces. The ability to distinguish between phytoliths from wild and domesticated taxa (including all of the major food crops) as well as specific plant parts combines to make them a very powerful research tool.

Researchers use phytoliths to better understand plant, animal, and hominin evolution because they survive when most organic matter decays. Indeed, they have even been used to help reconstruct past climates when they have been recovered from lake cores, peat bogs, terrestrial soils, and deep-sea cores from 35 million years ago to the present. Phytoliths provide a complementary source of data because they remain where they were deposited. In contrast, pollen, particularly species that rely on wind as their chief pollinator, is widely dispersed and represents more regional vegetation.

The development of ecosystems dominated by grasses (Poaceae family) during the Mesozoic and Cenozoic (about 70 million years ago) was a pivotal change in Earth’s history and is sometimes referred to as “the Great Transformation.” This period gave rise to the spread of ecosystems such as temperate grasslands, steppes, and both tropical and subtropical savannas. Exactly when this transition occurred has been hotly debated because of its implications for both plant and animal evolution. Caroline Strömberg of the University of Washington and her colleagues recovered phytoliths from coprolites of titanosaurs from the late Cretaceous in India, revealing that these massive herbivores grazed on a broad selection of plants including grasses, conifers, cycads, and dicotyledons such as palm trees. This information suggests that grasses evolved in forested environments before they became widespread and formed large ecosystems. That development explains why animals during this period, such as most of the titanosaur species, did not have teeth specifically designed for grinding tough plant matter, and suggests that some of these animals coevolved with grasses whereas others developed new dentition in response to the newly expanding ecosystems.

Researchers also use phytoliths to reconstruct the diet of other extinct fauna such as the giant ape Gigantopithecus blackii and the American mastodon, Mammut americanum. G. blackii was a ground-dwelling, knuckle-walking ape that roamed the forests of what is now China and Vietnam from about 6 million years ago to about 200,000 years ago. The average male G. blackii is estimated to have been 10 feet tall, weighed at least 1,200 pounds, and was most closely related to the orangutan. Phytoliths attached to the teeth of Gigantopithecus suggests a diverse diet of grasses, such as bamboos, and dicotyledons such as durian or jackfruit. This discovery, led by Dolores Pipemo of the Smithsonian Institution and her colleagues in 1990, was one of the first of its kind to demonstrate that phytoliths are preserved on the surface of the teeth. It also illustrated the role that phytoliths could play in understanding the relationship between primate evolution and diet, because it allowed researchers to start empirically testing hypotheses about eclectic eating and environments of extinct apes.

The American mastodon roamed throughout most of North America from about 1.8 million to 10,000 years before present. This thick-furred mammal was believed to have foraged mostly on forest plants. But the phytoliths contained in the plaque of three mastodons from Kansas dating from 13,890 to 11,500 years before present contradicted this hypothesis and indicated that these animals grazed primarily on grasses with the occasional hackberry and woody plants thrown in for good measure. The grass phytoliths are associated with the Pooid subfamily and, alongside diatoms trapped in the calculus, suggest that these animals grazed in a cool, moist, open environment rather than forest during the late Pleistocene. This study, by Katrina Gobetz of James Madison University and Steven Bozarth of the University of Kansas in 2001, was one of the first to demonstrate that phytoliths could be successfully recovered from plaque.

What Humans Ate

A 2012 study led by Amanda G. Henry of the Max Planck Institute for Evolutionary Anthropology revealed that phytoliths contained in the dental calculus of one of our evolutionary predecessors, Australopithecus sediba (which lived 2 million years before present), indicate that these early bipeds consumed a mixed diet of tropical shade- and water-loving sedges, grasses, fruits, and leaves. Until then, the majority of archaeological evidence used to reconstruct the diet of human evolutionary ancestors (collectively known as hominins) was based on stone tool artifacts, faunal and hominin bones, and chemical analysis of isotopes of carbon and nitrogen.

Phytoliths have also been used to decipher hominin activities. In Peninj, Tanzania, Manuel Dominguez-Rodrigo of the Universidad Complutense in Madrid and his colleagues recovered acacia tree phytoliths embedded on hand axes from 1.7 to 1.5 million years ago, indicating that whomever was using this tool last, most likely Homo erectus, was engaged in some sort of woodworking activity. Those artifacts have not been preserved, but it’s possible that they were carving wooden tools-an activity for which evidence previously had not been found until a million years later.

The plant diet and activities of Neanderthals (Homo neanderthalensis) are another area where phytoliths have proven pivotal. Contrary to the popular belief that Neanderthals consumed mostly meat, the recent work of Henry and Pipemo, along with their colleagues, on the calculus of Neanderthals suggests that they were eating plants such as date palm (of the genus Phoenix) in Iraq as well as roots and tubers in Belgium. At the cave of Tor Faraj in Jordan, phytoliths associated with woody species were recovered at the entrance of the cave, suggesting that the inhabitants used these plants as a windbreak between 69,000 and 49,000 years ago. Inside the cave, date palm and grass seed husk phytoliths were recovered from around a central hearth, implying that this area was used to process plant material. High concentrations of grass phytoliths recovered from the area between the hearth and the back wall of the cave suggest that they were using grass for bedding material. Phytoliths were also used to reconstruct similar Neanderthal and anatomically modem human activity areas at other caves. These studies were the first to provide evidence that Neanderthals engaged in these activities, and could provide some initial clues to their social organization.

Phytolith analysis has been used to uncover the origins and spread of some of the most important modern food crops. Such evidence is particularly valuable in the humid tropics where other plant remains do not preserve well. Piperno and Deborah Pearsall of the University of Missouri discovered that different types of cross-shaped phytoliths were produced in the leaves and cobs of domesticated maize (Zea mays) and its wild progenitor, Teosinte. This discovery, in combination with other evidence, has allowed scientists to pinpoint the domestication of maize to around 8,000 to 9,000 years ago in the Balsas River valley of southwestern Mexico. Similar research techniques have been, and are currently being used, to discover the centers of domestication for rice (Oryza sativa), wheat (Triticum aestivum), barley (Hordeum vulgare), bananas (Musa genus), and banana-related ensete (Ensete genus).

Phytolith analysis can provide a meaningful contribution to archaeological studies even when there is an abundance of artifacts available for identification. For my dissertation at the University of Connecticut, I analyzed phytoliths and microscopic grains of starch recovered from archaeological sediments and human dental calculus from the northern Mesopotamian village of Tell Zeidan, Syria. Tell Zeidan was settled at the confluence of the Euphrates and Balikh rivers in northern Syria from 6,000 to 3,800 bce, right when complex society emerged. The phytoliths recovered from this site, such as those from the fragile leaf tissues from trees and wetland plants, suggests for the first time that the villagers were using nearby wetlands and forests as a source of fuel and construction materials. These data will complement the charred wood and seed fragments found at the site because tree leaves and wetland plants are not normally preserved. The eventual combination of these data will help researchers explore the role of plants and agriculture in the development of one of the earliest complex societies in the world.

For my master’s thesis at the University of Missouri, I examined phytoliths and starch grains recovered from potsherds and soils from medieval Glebe Cottage in Wicken, Northamptonshire, and Durley Cottage, Cambridgeshire, England, and compared these data with recorded crop production patterns for these two sites. The results of this study indicated that although dredge (a mixture of oats and barley) and rye were recorded as the major crops produced by the farmers, the local inhabitants consumed a slightly different diet of wheat, barley, and domesticated legumes. This pattern suggests that, like most villagers in peasant societies around the world, the majority of the food that was grown was traded away, forcing the peasants to eat whatever crops they could grow on their own. Another example of phytoliths contributing useful information to historic period analyses includes reconstructing activity areas of a 17th-century farmhouse and garden near Colonial Williamsburg in the United States. Researchers at this site discovered previously unknown orchards, pastures, and agricultural fields near the farmhouse and realized that the activity areas were far more organized than was previously thought possible at a 17th-century house. Their research demonstrated that the colonists at this particular site had clearly demarcated areas of land use and that they adopted less risky economic strategies than were common in other parts of colonial Virginia.

Carbon-Dating Ancient Ecosystems

To further understand archaeological sites, accurate dating is vital, and here phytoliths can help as well. In lieu of traditional materials such as charred wood, seeds, and bone, phytoliths can be used for radiocarbon dating. Accelerated mass spectrometry (AMS) is a form of radiocarbon dating that uses a very small sample, about the size of a penny, to measure the amount of radioactive carbon-14 and determine the age of an organic sample. In traditional archaeological AMS dating, a single charred seed or wood fragment is processed and represents a single point in time. However, not all archaeological and paleoecological contexts provide suitable samples. Instead, researchers can use the carbon trapped in phytoliths to provide aggregate radiocarbon dates.

The silica in phytoliths protects the trapped carbon from fossilization and weathering processes, as well as the caustic chemicals involved in removing potential contaminants during AMS processing. Thousands of phytoliths from a single soil sample are used and provide a range of dates for that sample rather than a single point in time. This type of analysis is particularly useful for studies where traditional radiocarbon materials are either unavailable, or are contaminated from surrounding bicarbonate materials such as limestone.

The same carbon trapped in phytoliths can also be used to measure the ratio of carbon-12 and carbon-13 isotopes within plant tissues. Plants prefer carbon-12 to carbon-13 when taking in carbon dioxide needed for photosynthesis. Some plants will tolerate much higher levels of carbon-13 and are commonly referred to as C4 plants (the label indicates a type of photosynthetic cycle used in these plants that produces a compound containing four carbons). These plants are drought resistant, enjoy high light intensity, and constitute about half of the world’s grasses. In contrast, other plants (commonly referred to as C3 plants)- such as most of the worlds trees, shrubs, and domesticated grasses- enjoy moderate sunlight and temperatures, plentiful moisture, and will tolerate a much lower level of carbon-13 in their tissues.

Archaeologists and paleoecologists can use this information to reconstruct the general vegetation patterns of a region as well as the environmental conditions in which the plants grew. Oxygen, hydrogen, and aluminum isotopes contained in phytoliths may also prove similarly useful, but further studies are needed to test the feasibility of analyzing them.

Crime Scenes and Nanotech

The majority of phytolith research to date has focused on using the structures to understand various aspects of the past. But the features that make phytoliths so useful for such studies, such as their durability and their taxonomic specificity, are helpful for researchers in modem situations as well.

A recent study by Henry demonstrates the potential for using phytoliths and starch grains to better understand the diet of living primates, one of the most difficult aspects of primate research. Recording an animal’s diet consists of several steps, including observation (which can be especially tricky if the animals run off and eat their food out of view) and fecal examination, often resulting in an incomplete record. Phytoliths, alongside starch grains-contained in feces, soil samples, on primate tools such as chimpanzee nutting stones, and in the dental calculus recovered from tranquilized animals-can provide the missing information. This application of phytolith and starch grain analysis is in its infancy in primatology and could be applied to the study of other extant animal populations.

But to go far afield of diet research, phytoliths can also aid law enforcement. In forensic science, phytoliths fall in the category of trace evidence and forensic botany and have been used to help solve criminal investigations. In one case from Spokane, Washington, phytoliths helped solve a case in which a man was under investigation for arson, embezzlement, and the murder of his son. The suspect’s house had mysteriously burned down while his homeowner’s insurance was safely located at his neighbor’s house, and his son, whom the suspect had reported missing, was found murdered two days later. According to the suspect, as reported in an account by a forensics expert on the case, dirt and damage on his pickup truck came from when he ran his truck off a particular road. However, the phytoliths recovered from the truck were not the same as those from the section of road that the suspect described, but instead matched ones in the soil where his son’s body was found. This evidence was one piece of the puzzle that helped investigators solve how the suspect murdered his son and disposed of the body, leading to his conviction.

On another note, some of the physical properties of phytoliths could make them candidates for use in nanotechnology. As researchers Suresh Neethirajan, Richard Gordon, and Lijun Wang reported in a 2009 paper, phytoliths could be used in nanotechnology directly from plant tissues, or through artificial structures created in a process similar to phytolith production. Most of the preliminary research to date has focused on the former. For example, phytoliths produced in the leaves of the creeping bentgrass (Agrostis palustris) have been shown through thermal infrared imaging to reduce the heat load of the plants, thereby demonstrating their potential for use in protection devices such as thermal cut-off switches, thermal fuses, positive temperature coefficient resistors (which vary their resistance with temperature), and thermocouple devices commonly found in everyday electronic devices and appliances.

Other possible phytolith nanotechnology applications include silicabased pesticides and nanocomposites, and enzyme delivery systems for medicines. Phytolith-based pesticides are created when amorphous nanosilica from melted phytoliths, such as the stem tissues of rice straw, are applied to pests. This silica disrupts the ability of the cuticular lipid of the outside of the insect to retain water, eventually resulting in desiccation and death of the insect. Phytoliths are used to create nanocomposites by melting them down into their most basic structure and shaping them into octasilicate anions, one of the building blocks of nanocomposite structures. The morphology of the melted phytoliths also makes them particularly well suited for carrying organic compounds and encasing enyzmes that are then released in the body during medical treatment.

Researchers in Australia and China also have begun looking into the possibility of using phytoliths as carbon sinks to help reduce the overall levels of carbon dioxide in the atmosphere. When phytoliths form and trap carbon (the same carbon that is used for radiocarbon and stable isotope analysis), they remove it from the atmosphere. This carbon becomes stored in the soil when the plant decays. One of the more common hypotheses regarding carbon sequestration and agriculture is that plants release more carbon back into the atmosphere when they decay than is trapped in the phytoliths. Therefore, decaying crops would not serve as an effective tool against climate change. But Xin Xin Zuo and Hou Yuan Yu of the Chinese Academy of Sciences tested the carbon trapping capabilities of common millet (Panicum miliaceum) and foxtail millet (Setaria itálica) in a dryland agricultural setting and proved this not to be true. According to their calculations, both common and foxtail millet can sequester around 0.020 tons of carbon per hectare. They estimate that, given the current acreage of common millet grown in China, this grain would remove more carbon dioxide from the atmosphere than it gave off, to the tune of 2,370,000 tons of carbon dioxide per year.

Jeff Parr and others in Australia examined carbon bio-sequestration within economic bamboo species and argue that 15,600,000 tons of carbon dioxide would be sequestered in the soil if bamboo were grown exclusively on all of the 22 million hectares of current global bamboo forest. Parr and others use these data to suggest that the current increase in global CO2 emissions would be reduced by about 11 percent if bamboo, or some other plant with high rates of carbon sequestration, were grown on all 4.1 billion hectares of arable land in the world.

It’s obvious that these microscopic structures, created by plants for their own purposes, still have many uses left to explore. Charles Darwin, when he encountered that fine dust aboard the Beagle, could not have imagined how those tiny silica pieces would be so powerful in revealing both our past and present, as well as finding use in future technologies or even potentially shaping our planet. Phytoliths, diminutive and varied as they are, continue to prove their endurance and utility in aggregate. These translucent plant stones have millions of years ahead of them to tell more about their, and our, stories.