The research team, led by Jyoti Sharma and Michael J. Stout of Louisiana State University Agricultural Center, together with colleagues at Oregon State University and the United States Department of Agriculture, took an unusual approach. Rather than simply adding silicon fertilizer to rice fields, they used a set of rice mutant lines that differ naturally in their ability to take up silicon from the soil. These lines, generated by chemical mutagenesis of the reference variety Nipponbare, carry mutations in OsLsi1, the gene encoding the first silicon influx transporter ever identified in rice roots. By comparing a severely silicon-deficient line, an intermediate line, and lines with near-normal silicon accumulation, the researchers could isolate the effects of the element itself rather than of external supplementation.

The biochemical measurements confirmed that the mutations had the intended effect. The wild-type plants and one mutant line accumulated silicon at roughly 3.5 percent of leaf dry weight, the intermediate mutant reached about 1.9 percent, and the severely deficient line managed only 0.04 percent, a mere five percent of the wild-type level. That difference translated directly into plant performance. Silicon-rich lines produced substantially greater shoot biomass, and when fall armyworm caterpillars were allowed to feed on them for a week, the high-silicon plants lost far less tissue. Most strikingly, two weeks after the attack, the silicon-rich plants had completely compensated for the damage, regrowing to the biomass of uninjured controls, while the silicon-deficient line showed essentially no recovery at all.

The insects noticed the difference too. Fall armyworm larvae reared from hatching to pupation on the low-silicon line gained significantly more weight, developed faster, and emerged as heavier pupae than larvae fed on any of the higher-silicon lines. Short-term feeding assays on excised leaves pointed to the same conclusion: larvae on silicon-poor foliage consumed more food and grew faster, while their digestive efficiency remained unchanged. This detail matters, because it indicates that silicon does not poison the insect’s gut chemistry. Instead, it appears to act as a physical and structural barrier that makes leaves harder and less palatable, reducing how much the caterpillars can eat in the first place.

Perhaps the most surprising result concerned what silicon did not do. The researchers measured the activities of peroxidase, polyphenol oxidase, and trypsin protease inhibitors, three classic defense proteins implicated in rice resistance, as well as the defense hormones jasmonic acid and salicylic acid. Silicon content had no effect on any of these, either before or after herbivore attack. In fact, the low-silicon plants showed higher peroxidase activity and more sustained enzyme induction after injury, suggesting they were mounting a compensatory biochemical defense to make up for what they lacked structurally. Volatile emissions, the chemical signals plants release to attract the natural enemies of herbivores, told a similar story: total emission surged after caterpillar feeding in all lines, but silicon content did not change the strength of that response.

To understand what was happening beneath these biochemical measurements, the team turned to transcriptomics, sequencing the RNA of all four rice lines both before and after fall armyworm feeding. The results were dramatic. When injured plants were compared with uninjured plants of the same genotype, the two high-silicon lines activated roughly 2,700 to 2,800 differentially expressed genes, while the two low-silicon lines mounted a response about forty percent weaker. In other words, silicon-deficient plants were transcriptionally less equipped to respond to attack. Gene ontology analysis revealed a consistent pattern: the low-silicon lines upregulated stress and chemical defense pathways, including phenylpropanoid metabolism and jasmonate signaling, while suppressing genes for growth, photosynthesis, and cell wall construction.

This pattern reflects one of the central tensions in plant biology, the well-known trade-off between growth and defense. Plants cannot maximize both simultaneously, because the resources spent on defensive chemistry are unavailable for building new tissue. The study suggests that silicon changes the economics of this trade-off. Silica deposited in tissues as phytoliths provides a cheap, mineral-based physical defense that does not compete with growth for carbon and nitrogen. Silicon-deficient plants, lacking this low-cost armor, are forced to divert scarce resources into carbon-intensive alternatives such as lignin, which the researchers observed through elevated expression of the lignin biosynthesis gene OsCCR20. The result is a plant that invests heavily in defense yet still ends up vulnerable, because the biochemical defenses it activates are not enough to stop a determined caterpillar.

By integrating whole-genome sequencing with the expression data, the team also identified candidate genes that may underpin silicon-mediated resistance. Genes including the transcription factor OsbHLH024, the silicon transporter OsLsi1 itself, the DNA repair gene OsMSH3, the chloroplast division gene OsARC5, the cytokinin oxidase OsCKX2, and the light-regulated factor OsBBX3 all carried coding mutations and showed altered expression in the susceptible low-silicon line. Quantitative PCR confirmed the sequencing results for most of the genes tested. These candidates offer breeders a molecular toolkit for developing rice varieties that accumulate silicon more efficiently, potentially reducing reliance on insecticides against a pest that has swept across Africa and Asia in recent years and devastates maize, rice, sorghum, and cotton.

The authors propose a conceptual model that captures the full picture. When silicon levels are adequate, rice plants can mount effective constitutive defenses through silica-reinforced tissues while retaining the capacity for compensatory regrowth after damage, achieving a genuine balance between defense and development. When silicon is lacking, plants shift resources toward chemical defense at the expense of growth, yet the defense remains ineffective because the mechanical barrier is absent. The intermediate line in the study was particularly instructive: it achieved fall armyworm resistance similar to the wild type, suggesting that only a threshold amount of silicon is needed for protection, but it paid for that resistance with reduced growth. Only plants with full silicon accumulation managed to have both.

For agriculture, the implications are considerable. Silicon is not classified as an essential plant nutrient, yet this study reinforces a growing body of evidence that it functions as something close to one for grasses, shaping everything from tissue mechanics to gene expression. Silicon fertilization is already practiced in some rice-growing regions, and the new work provides a mechanistic rationale for those practices while pointing toward genetic solutions that could make silicon-rich rice varieties a reality. As the fall armyworm continues its global expansion and pesticide costs climb for smallholder farmers, an element as ordinary as sand may prove to be one of the most powerful tools in the fight to protect the world’s rice harvest.

Subject of Research: Silicon-mediated resistance to the fall armyworm in rice through transcriptional reprogramming of growth and defense

Article Title: Silicon-mediated resistance to Spodoptera frugiperda in rice modulates growth and defense processes via transcriptional reprogramming

Article References: Sharma, J., Chaudhary, C. K., Pruthi, R., Kondi, R. K. R., Gaffke, A., Subudhi, P. K., Tai, T. H., & Stout, M. J. (2026). Silicon-mediated resistance to Spodoptera frugiperda in rice modulates growth and defense processes via transcriptional reprogramming. Plant and Soil. https://doi.org/10.1007/s11104-026-09012-6

Image Credits: AI Generated

DOI: 10.1007/s11104-026-09012-6

Keywords: silicon, rice, fall armyworm, Spodoptera frugiperda, plant defense, transcriptomics, OsLsi1, growth-defense trade-off, phytoliths, jasmonic acid, plant breeding, pest resistance

The research combines three complementary techniques, each filling in a different layer of the story. Sediment coring provided vertical slices through the landscape, revealing the sequence of natural and human-made deposits beneath the site. Electrical resistivity tomography and direct-current resistivity soundings mapped subsurface structures horizontally, tracing buried features without breaking the surface. Finally, phytolith analysis, the study of microscopic silica bodies formed within plant tissues, allowed the researchers to reconstruct which plants grew around the city and how vegetation changed as urbanization took hold. Together, these methods produced a picture of Bubastis that no single approach could deliver: a city whose growth, layout, and even its religious geography were dictated by the shape of the land beneath it.

The most consequential discovery concerns a set of Pleistocene sand mounds known as Geziras. These are relict landforms, remnants of ancient sandy deposits that rise subtly above the surrounding floodplain and, crucially, stay dry during the Nile’s annual inundation. Garbe’s surveys identified several of these mounds across the Bubastis area, and their positions are anything but random. The Temple of Pepi I in the western part of the city stands on one. The palace and the cemetery area in the north occupy others. Residential zones in eastern Bubastis cluster on still more. Even a lost monument may now have a location: an additional mound in the southeastern part of the site can plausibly be linked to the Temple of Hermes, a structure known from ancient writings whose whereabouts had been uncertain. The new evidence supports those textual clues about where the temple once stood.

This pattern reveals a deliberate urban logic. Rather than spreading indiscriminately across the floodplain, the builders of Bubastis selected flood-safe Geziras for their most important and most permanent structures, while leaving the low-lying ground between them for uses that could tolerate, or even benefit from, seasonal flooding. The geomorphology of the Delta was not an obstacle to be overcome but a framework to be exploited. In a landscape where the Nile’s branches shifted course and flood levels fluctuated over the centuries, choosing the right piece of ground was a matter of survival, and the people of Bubastis appear to have understood that from the city’s earliest days.

The coring program also quantified just how intensively different parts of the city were used. In settlement area S1, the researchers documented anthropogenic deposits reaching a thickness of up to 9.5 meters, an extraordinary accumulation of debris, building material, and occupation layers that identifies S1 as the primary living quarter of the city. The thickest deposits date particularly to the Ptolemaic period, from about 332 to 30 BCE, and the Roman period, from about 30 BCE to 200 CE, showing that these late phases of Bubastis’s history were also among its most densely built. By contrast, the surrounding low-lying floodplain areas, especially area S2, show only sparse settlement evidence. These marginal zones were likely given over to agriculture, and they had a distinct advantage for it: a nearby Nile branch, flowing to the north and northeast of the city, regularly deposited nutrient-rich sediments across the floodplain, keeping the fields naturally fertilized.

The phytolith record adds a biological dimension to this reconstruction, tracking vegetation from the end of the last ice age through the city’s decline. During the transition from the Late Pleistocene to the Early Holocene, long before Bubastis existed, the landscape was dominated by grasses, shrubs, and trees, a natural Delta environment shaped by river processes rather than human hands. That changed with the arrival of settlement. From the Old Kingdom onward, spanning roughly 2850 to 2180 BCE, the onset of occupation coincided with a marked increase in cereal-type phytoliths. Crucially, these cereal signatures appear in the nutrient-rich floodplain sediments, providing the earliest evidence for localized cereal cultivation at Bubastis during the Early Old Kingdom. The fields, in other words, were already feeding the city in its formative centuries.

Inside the settlement itself, the phytolith data tell a different story. Elevated proportions of cereal-type phytoliths in anthropogenic deposits across the urban area, and particularly in the main residential zone S1, point to intensive cereal processing and storage taking place within the city walls. Grain was not only grown nearby but handled, threshed, milled, and stockpiled in the residential quarters, a pattern that speaks to the scale of Bubastis’s population and the logistical sophistication required to sustain it. The city was, in a very real sense, an agricultural machine as much as a religious and administrative center, with its food economy woven directly into the fabric of its neighborhoods.

Over time, that arrangement shifted. From the Late Period, beginning around 664 BCE, through Roman times, cultivation practices increasingly moved toward the settlement periphery. As Bubastis expanded and its builders consumed more land, the natural vegetation around the city diminished, and farming was pushed outward to the edges of the urban footprint. This trajectory, from cultivation embedded within and immediately around the early settlement to agriculture relegated to the periphery of a sprawling city, mirrors patterns familiar from urban growth in other ancient and modern contexts, but here it is documented with unusual precision through a combination of sediment chemistry, landform mapping, and plant microfossils.

The broader significance of the work lies in what it says about human adaptability in unstable environments. The Holocene Nile Delta was shaped by a constant interplay of river avulsions, sedimentation, and seasonal flooding, conditions that created fertile opportunities for early civilization while simultaneously driving settlement instability and frequent relocation. Bubastis’s longevity was not an accident of geography but the product of choices: siting temples and palaces on high ground, farming the fertile lows, and adjusting land use as the city and its environment co-evolved. Different geomorphological settings were deliberately selected for specific functions and phases of occupation, a dynamic interplay between nature and human decision-making that unfolded over three thousand years.

The study also refines interpretations of Bubastis’s emergence as a center of religious and administrative power, a status reflected in its extensive temple and palace areas, including the famous Temple of Bastet with its man-made sacred canals identified in earlier geoarchaeological work. Until now, knowledge of the site’s environmental conditions rested on a handful of historical texts and preliminary studies. By delivering the first area-wide reconstruction, the new research demonstrates how strongly the development of an ancient Egyptian urban center depended on regional environmental conditions, and it showcases the value of geoarchaeological methods for reconstructing human-environment interactions across the Delta, where so many settlements rose and fell with the shifting waters of the Nile. For Bubastis, the ground beneath the city was never just a foundation. It was a partner in the city’s survival, and reading that partnership from the sediments is what finally explains how one Delta town outlasted them all.

Subject of Research: Holocene landscape evolution and long-term settlement development at the ancient Egyptian city of Bubastis in the southeastern Nile Delta

Article Title: Holocene landscape evolution and settlement development in the surroundings of the ancient Egyptian city of Bubastis (“Tell Basta”), southeastern Nile Delta

Article References: Garbe, P. (2026). Holocene landscape evolution and settlement development in the surroundings of the ancient Egyptian city of Bubastis (“Tell Basta”), southeastern Nile Delta. E&G Quaternary Science Journal, 75(2), 169-171. https://doi.org/10.5194/egqsj-75-169-2026

Image Credits: AI Generated

DOI: 10.5194/egqsj-75-169-2026

Keywords: Bubastis, Tell Basta, Nile Delta, geoarchaeology, Holocene, Geziras, phytoliths, sediment coring, electrical resistivity tomography, ancient Egypt, urban development, Nile flooding

The fossil, described in a study now in press at Nature’s Scientific Reports, provides the first and oldest record of a capybara in coastal Chile. But its significance extends far beyond adding a rodent to the region’s faunal inventory. If a semiaquatic giant rodent was thriving in the Atacama during the late Miocene, the desert cannot have been the unbroken hyperarid expanse that geologists have long imagined. The finding directly challenges the long-standing characterization of the Atacama as one of the oldest continuously dry regions on the planet, a status it has held in textbooks and review papers for decades. For the research team, led by doctoral student Priscilla Martinez of the University of Arizona Department of Geosciences, the implications were immediately clear and deeply unsettling to conventional wisdom.

The tooth itself emerged from a layer of sediments deposited in a shallow marine environment between roughly 10 and 7 million years ago. The site, known as El Morro, belongs to the fossil-rich Bahía Inglesa Formation, a rock unit that also contains Cerro Ballena, or Whale Hill, famously recognized as the world’s largest concentration of whale fossils. Marine deposits full of whales are one thing; a capybara tooth in the same beds is quite another. Finding a capybara tooth in a marine deposit in what today is one of the driest regions on Earth is, as Martinez put it, just freakish. The oddity of the association underscores how radically the local environment has changed since the late Miocene, when the same coastal setting that entombed whales also supported a large freshwater-dependent mammal.

Capybaras, the largest living rodents, and their close cousins the guinea pigs are native to South America. Today, capybaras thrive east of the Andes in low-elevation wetlands, with their core range roughly tracing the Amazon River basin. Their semiaquatic lifestyle tightly binds them to persistent surface water, wetland vegetation, and the ability to move along riparian corridors beside creeks and rivers. Co-author Barbara Carrapa, a professor of geosciences at the University of Arizona and Martinez’s doctoral advisor, emphasized that there is no other evidence of capybaras in that part of coastal Chile. They are not supposed to be there, she said, which immediately raised two questions for the team: why were they there, and where did they come from?

Geography makes those questions especially thorny. Geologists estimate that long before capybaras appeared in the region roughly 9 million years ago, the Andean mountain chain had already risen into a formidable barrier, in places jutting up to 18,000 feet. That towering wall effectively separates the Atacama Desert from the eastern lowlands that stretch across parts of Venezuela and Colombia down to northeastern Argentina and Uruguay, where the animals live today. Climate compounds the problem. As Martinez noted, the plateau lands of the Central Andes are not only very tall but also extremely arid. If capybaras originated east of the Andes in the foreland region, it is hard to imagine how these short-legged rodents could possibly have crossed such an inhospitable, high-altitude barrier on foot.

The most likely answer, the researchers conclude, is that they did not cross it at all. Instead, the team proposes a dispersal scenario in which capybaras expanded out of their original range by taking advantage of low-elevation wetlands that connected coastal areas in a counterclockwise arc around the northern portion of South America. From today’s Venezuela into Colombia, Ecuador, and Peru, and finally into northern Chile, the animals could have moved along a chain of verdant, water-rich habitats without ever confronting the high Andes. The scenario implies that a continuous or near-continuous corridor of wetland ecosystems hugged the Pacific coast during the late Miocene, a picture starkly at odds with the notion of an ancient, unbroken desert.

Crucially, the capybara tooth is not an isolated anomaly. Co-author Mark Clementz, a paleobiology expert and head of the Department of Geology and Geophysics at the University of Wyoming, pointed out that the same deposits contain multiple lines of evidence indicative of the kind of really wet conditions typically associated with capybaras today. Alongside the rodent remains, the sediments yielded fossils of freshwater fishes and gavials, the fish-eating freshwater crocodilians that require rivers or permanent water bodies to survive. The presence of crocodiles and freshwater fish in the same beds that preserved the capybara paints a coherent ecological picture of rivers, marshes, and wooded waterways rather than barren sand.

Botanical evidence reinforces that reconstruction. The team also unearthed phytoliths, microscopically small accumulations of silica that form inside plant cells and tissues as plants absorb dissolved silica from groundwater through their roots. Because different plant lineages produce characteristically shaped phytoliths, specialists such as co-author Caroline Strömberg, a professor at the University of Washington, can analyze these durable structures to determine what kinds of vegetation once grew at a site. In this case, the phytolith record pointed to palms and other flowering plants, including dicots, none of which would be expected in the Atacama Desert of today. Martinez offered a vivid comparison: think of sunny Southern California full of palm trees. She cautioned that researchers are not sure whether the palms bloomed extensively there, but they were definitely present, a detail that alone rewrites assumptions about the region’s past.

Together, the mammal, reptile, fish, and plant fossils support the idea that there was enough of an ecological community to sustain capybara populations over the long term, as Clementz observed. No other remains of capybaras this old have been found in Chile to date, which makes the single tooth, preserved within a three-foot-thick bed in the middle of a desert, something of a miracle of survival, according to Martinez. The assembly of strange creatures in an unlikely place did not go unnoticed by the local population. Many residents dug for fossils and sold them to collectors, and many of the fossils originally discovered at the location are now lost to science. Fortunately, certain merchants were interested in understanding the specimens better and donated them to local scientists, creating an unusual and invaluable partnership between fossil traders and researchers.

One of the beneficiaries of that collaboration was Carolina Gutstein, the study’s first author, who heads paleontology at the Chilean mining company Fosfatos de Caldera and is a professor at the Universidad Santo Tomás in Santiago. Gutstein has a long history of working with local fossil experts in the area, and those relationships proved essential in tracing and interpreting the material. Clementz added that the findings demonstrate the value of challenging assumptions, in this case the assumption that the Atacama has been an ancient desert for millions upon millions of years. No one really argued with that paradigm, he noted, even in the face of other fossil finds suggesting that conditions were once different. Finding a capybara, an animal that by any measure is not a desert creature, at that location is going to force a serious rethinking of the Atacama’s history.

The implications reach well beyond capybaras and one South American desert. Deserts are extremely sensitive to changes in climate, including year-to-year shifts in monsoon intensity, and understanding how they formed and transformed in the deep past offers a natural experiment that no laboratory can replicate. As Martinez explained, the better scientists understand deserts, the better they can predict how these environments will fare over the long term. And if researchers can reconstruct past climate changes that had nothing to do with humans, they gain a baseline against which to measure how climate may evolve in a world where human influence is now part of the equation. A single fossilized tooth, plucked from a whale-strewn marine bed in the driest place on Earth, has thus opened a window onto a greener, wetter Atacama and a reminder that even the most confident scientific paradigms can be overturned by one small, improbable piece of evidence.

Subject of Research: Late Miocene capybara fossil evidence for a wetter ancient Atacama Desert and transcontinental rodent dispersal

Article Title: Capybaras in the desert? Fossil casts doubt on Atacama as world's oldest continuously dry region

Article References: Capybaras in the desert? Fossil casts doubt on Atacama as world's oldest continuously dry region. (n.d.). Original publication

Image Credits: AI Generated

DOI: Not provided

Keywords: capybara, Atacama Desert, paleontology, Miocene, Chile, fossil tooth, wetlands, Andes, phytoliths, climate history, Scientific Reports, dispersal