Welcome to 10 Cool Papers, a new monthly roundup of recent research from across Carnegie Science. Each month, we'll feature a curated selection of recent papers from across Carnegie Science, chosen by our three division directors and the president. From early-career scientists to established investigators and recent alumni, our community is tackling the biggest questions about life, our planet, and our place in the cosmos.
This first edition spans coral genomic resilience in a warming ocean, new CRISPR tools for studying symbiosis, hidden hydrothermal systems beneath Oregon’s Three Sisters volcanoes, pristine organic material from asteroid Bennu, and galaxies shining just 400 million years after the Big Bang.
Let's dive in!
🦠 Biosphere Sciences & Engineering
1. Editing Symbiosis: CRISPR in a Microscopic Worm
CRISPR-Cas9-based Mutagenesis in the Entomopathogenic Nematode Steinernema hermaphroditum and the Maintenance of Mutant Lines
Publication: Journal of Visualized Experiments
Carnegie Authors: Sally W. Ireri & Mengyi Cao
Carnegie researchers figured out how to reliably edit the DNA of a tiny parasitic worm that lives in partnership with bacteria and infects insects. They used CRISPR to disable a specific muscle gene, which caused the worms to twitch—proof that the editing worked. Because this worm can reproduce as a hermaphrodite, it’s easier to create stable mutant lines that pass genetic changes to future generations. The method they developed can likely be used in other related worm species.
Entomopathogenic nematodes (EPNs) in the genus Steinernema and Heterorhabditis maintain mutualistic interactions with Xenorhabdus and Photorhabdus symbiotic bacteria respectively. Together, these nematode-bacterium pairs infect and kill insect hosts that are primarily larvae from the orders of Lepidoptera and Coleoptera, forming a tractable tripartite system for dissecting the molecular basis of mutualism and parasitism. A key step towards fully utilizing this model is the development of stable and transgenerational genetic tools in EPNs. Here, we demonstrate a reliable CRISPR-Cas9 genome editing platform in the emerging model Steinernema hermaphroditum , a species that is readily maintained in vivo and in vitro, and is highly amenable to gonadal microinjection. Importantly, its hermaphroditic reproduction greatly streamlines the generation and maintenance of homozygous mutant lines. We provide a detailed protocol for efficient, targeted gene disruption using microinjectionbased delivery of Cas9 ribonucleoprotein complexes. As a proof of concept, we modified the conserved muscle-associated gene unc-22, generating a characteristic twitching phenotype that validates targeted mutagenesis in this system. This CRISPR-Cas9 platform opens the door to stable genetic manipulation in S. hermaphroditum , such as transgene expression, and provides a framework that can be extended to additional EPN species of agricultural and ecological importance.
Full Article2. Why Biodiversity Persists
Density Dependence Promotes Species Coexistence and Provides a Unifying Explanation for Distinct Productivity–Diversity Relationships
Publication: Ecology Letters
Carnegie Affiliated Authors: Liang Xu, Emily Zakem & Christopher A. Klausmeier
This study tackles a long-standing ecological question: why do many species manage to coexist instead of one dominating the rest? The researchers show that when species are limited more strongly as they become more common—a process called negative density dependence—it actually helps maintain diversity. Their modeling framework helps explain why biodiversity sometimes increases with productivity and sometimes does not.
Understanding diversity patterns in complex communities, such as microbial consortia, requires a mechanistic framework appropriate for many species. Negative density dependence is often utilised in complex ecosystem models, typically as a density-dependent mortality term for a population, but its full impact on community structure remains unclear. Here, we use mechanistic population models of resource consumption to examine the effects of negative density dependence and develop a tractable framework for understanding diversity patterns in complex systems. To provide mechanistic grounding, we quantify how density-dependent mortality expands coexistence zones along resource gradients in simple communities using graphical analysis. We then derive an analytical formula relating species abundances and coexistence patterns to trait differences among subsets (guilds) of complex communities, in which many species share a resource or predator. Finally, we explain how distinct relationships between productivity and diversity emerge from the resulting mechanistic framework, providing insights into previously unreconciled observed patterns.
Full Article3. Genomic Warning Signs for Coral Reefs
Global Coral Genomic Vulnerability Explains Recent Reef Losses
Publication: Nature Communications
Carnegie Affiliated Authors: Oliver Selmoni, Moises Exposito-Alonso & Phillip A. Cleves
By analyzing the DNA of nearly 600 coral samples from reefs around the world, researchers identified genetic markers associated with heat tolerance. Reefs with fewer heat-adapted corals have experienced greater declines. The findings suggest that while heat-tolerant corals may spread in coming decades, the loss of overall genetic diversity could make future adaptation more difficult.
The dramatic decline of reef-building corals calls for a better understanding of coral adaptation to ocean warming. Here, we characterize genetic diversity of the widespread genus Acropora by building a genomic database of 595 coral samples from different oceanic regions-from the Great Barrier Reef to the Persian Gulf. Through genome-environment associations, we find that different Acropora species show parallel evolutionary signals of heat-adaptation in the same genomic regions, pointing to genes associated with molecular heat shock responses and symbiosis. We then project the present and the predicted future distribution of heat-adapted genotypes across reefs worldwide. Reefs projected with low frequency of heat-adapted genotypes display higher rates of Acropora decline, indicating a potential genomic vulnerability to heat exposure. Our projections also suggest a transition where heat-adapted genotypes will spread at least until 2040. However, this transition will likely involve mass mortality of entire non-adapted populations and a consequent erosion of Acropora genetic diversity. This genetic diversity loss could hinder the capacity of Acropora to adapt to the more extreme heatwaves projected beyond 2040. Genomic vulnerability and genetic diversity loss estimates can be used to reassess which coral reefs are at risk and their conservation.
Full Paper
🪐 Earth & Planets Laboratory
4. Hidden Magma Beneath the Three Sisters
The Magmatic-Hydrothermal System of the Three Sisters Volcanic Cluster, Oregon, Imaged From Field Gravity Measurements
Publication: Journal of Geophysical Research: Solid Earth
Carnegie Author: Hélène Le Mével
Using gravity measurements taken in the field, researchers mapped what’s happening underground beneath Oregon’s Three Sisters volcanoes. They identified low-density regions extending several kilometers below the surface, consistent with hot, water-rich zones and partially molten rock. The work provides a clearer picture of the hidden magmatic and hydrothermal systems beneath this active region.
We calculated the residual Bouguer anomaly and identified three main zones with negative anomalies, ranging from −4 to −8 mGal, located southwest and west of South Sister, within an area that has been uplifting for the past two decades. After inversion, we obtain a 3D density model of the subsurface and identify low-density bodies extending from the surface down to 3 km. We estimate a total of 15 km3 of crustal bodies with density close to 2 g/cm3 that could store up to ~ 5 km3 of water, forming an extensive hydrothermal system beneath the TSVC. We explore the possible combinations of melt compositions and temperatures that could create a bulk density close to our reference crustal density ( 2.5 g/cm3 ) using MELTS thermodynamic simulations. Our results indicate that a magmatic mush with as little as 15 percent partial melt of bulk rhyolitic composition or as much as 52 percent–57 percent partial melt of a bulk dacitic composition could be stored in a magmatic system under TSVC without generating a detectable gravity anomaly. Episodic magma injections at the base of the magmatic system, such as the 1998–2000 intrusion at ~ 6 km depth, would bring heat and gas to the hydrothermal system while maintaining a low melt fraction in the magmatic mush, as imaged at other Cascade volcanoes.
Full Article5. Bennu’s Molecular Time Capsule
Placing Asteroid Bennu's Organic Solids in Molecular and Elemental Context with Those in Aqueously Altered Carbonaceous Chondrites
Publication: Geochimica et Cosmochimica Acta
Carnegie Authors: George D. Cody, Conel M. O’D. Alexander, Dionysis I. Foustoukos & Robert M. Hazen
Scientists analyzed organic material returned from asteroid Bennu and found that it appears to have experienced very little heating over billions of years. The chemistry suggests the asteroid preserved early Solar System material with minimal alteration, helping scientists better understand the temperature and pressure history of this rubble-pile asteroid.
We present the first investigation into the molecular structure of organic solids (insoluble organic matter, IOM) in samples of the carbonaceous asteroid (101955) Bennu returned by the OSIRIS-REx mission. We used 1H and 13C solid-sate nuclear magnetic resonance (ssNMR) to analyze three subsamples of aggregate Bennu material. However, the IOM isolated from two of the three subsamples exhibited substantial magnetic inhomogeneity, due to contaminant magnetic grains. The resulting magnetic interference degraded NMR signals for both 1H and 13C and likely introduced spectral distortions. The third subsample was pretreated with 6 N HCl prior to IOM isolation and exhibited minimal (i.e., typical) magnetic interference. In this subsample’s IOM, we find a very low fraction of aromatic carbon, and a high fraction of aliphatic hydrogen, relative to IOM from Bennu’s closest meteoritic analogs, the petrologic type 1 and 2 carbonaceous chondrites. Elemental analysis–isotope ratio mass spectrometry (EA-IRMS) further reveals a high H/C × 100 atomic values, relative to type 1 and 2 chondritic IOM. These data indicate that Bennu’s organic solids, at least in this aggregate sample, suffered minimal to no molecular evolution from thermal perturbation throughout this material’s long history—starting with accretion of a planetesimal, followed by disruption and gravitational reassembly to form a rubble-pile asteroid, and ultimately migration from the Main Belt to a near-Earth orbit. The state of molecular evolution recorded in IOM places a strong constraint on the magnitude of temperature and pressure derived from impact events that yielded the rubble-pile asteroid Bennu.
Full Article6. What Determines a Planet’s Oceans?
From Underground Oceans to Continents: A Glimpse into the Water Inventory on Rocky Planets Using Host Star Abundances
Publication: The Astrophysical Journal
Carnegie Affiliated Authors: Kiersten M. Boley, Francesca Miozzi*, & Johanna K. Teske
By modeling nearly 700 rocky planets, researchers found that a planet’s internal chemistry—especially the oxidation state of its mantle—and its topography strongly influence how much water ends up on its surface. Some planets may store large amounts of water internally, while flatter worlds are more likely to become flooded.
The amount of surface water is thought to be critical for a planet’s climate stability and thus habitability. However, the probability that a rocky planet may exhibit surface water at any point in its evolution is dependent on multiple factors, such as the initial water mass, geochemical evolution, and interior composition. To date, studies have examined the influence of interior composition on the water inventory of the planet or how surface oceans may be impacted by planet topography individually. Here, we provide the first exploration on the impact of interior composition, topography, and planet radius on the water inventory of rocky planets using a sample of 689 rocky planets with spectroscopically derived stellar abundances from APOGEE and GALAH. We find that the oxidation state of the mantle (FeO content) significantly impacts the mantle water storage capacity and potential for surface flooding. For an FeO ~ 11 wt percent the water storage capacity of a 1 M⊕ is 2 times that of Earth, indicating that the oxidation state may reduce the amount of surface water. We quantify the impact of topography on seafloor pressures, showing that flat topographies are more likely to be flooded for all planet compositions and radii. We also find that Mars-like topographies are more likely to have seafloor pressures that may form high-pressure ice, reducing seafloor weathering. Thus, for the first time, we show that the composition and topography of the mantle influence the water inventory of rocky planets.
Full Article🌌 Observatories
7. Modeling Stellar Streams in a Living Galaxy
Breaking Down the CosmoGEMS: Toward Modeling and Understanding Globular Cluster Stellar Streams in a Fully Cosmological Context
Publication: The Astrophysical Journal
Carnegie Authors: Nondh Panithanpaisal, Ana Bonaca & Newlin C. Weatherford
This new simulation framework models how globular clusters are stretched into stellar streams within a realistically evolving galaxy. By incorporating time-changing gravitational forces, the model produces more accurate stream structures and challenges assumptions used in interpreting observations.
Next-generation surveys are expected to uncover thousands of globular cluster (GC) stellar streams, motivating the need for a theoretical framework that produces realistic GC streams in a fully cosmological, Milky Way─like environment. We present CosmoGEMS, a star-by-star cosmological GC stream framework that self-consistently links small-scale cluster physics with large-scale galactic dynamics. The initial phase-space positions of stream stars are informed by post-processed GC populations within the FIRE cosmological simulation. Escaped stars are orbit-integrated from their time of escape to the present day in a time-evolving galactic potential extracted from the same simulation using a basis function expansion. We explore two example streams on different orbits. One forms a long, thin stream with a velocity dispersion consistent with Milky Way GC streams. However, it exhibits a clump and orbital-phase-dependent misalignments due to the evolving potential. The other stream develops both a thin component and a diffuse, shell-like structure, similar to features observed in streams like Jhelum. These results highlight the power of fully cosmological models in producing realistic stream morphologies and kinematics. Unlike idealized simulations, our models naturally incorporate time-dependent changes in the progenitor's orbit, including orbital plane evolution, which significantly affects stream structure. This challenges common assumptions in stream-finding algorithms and interpretation. CosmoGEMS provides a key step toward connecting future stellar stream observations with the physics of GC evolution and hierarchical galaxy formation in a cosmological context.
Full Article8. Pioneering Panoptic Spectroscopy
Sloan Digital Sky Survey. V. Pioneering Panoptic Spectroscopy
Publication: The Astronomical Journal
Carnegie Author: Juna Kollmeier
SDSS-V is the first all-sky, multiepoch optical-to-infrared spectroscopic survey. Using telescopes in both hemispheres and advanced fiber-positioning systems, the survey is mapping the Milky Way’s chemical and dynamical history while also studying black holes and nearby galaxies.
The Sloan Digital Sky Survey V (SDSS-V) is pioneering panoptic spectroscopy: it is the first all-sky, multiepoch, optical-to-infrared spectroscopic survey. SDSS-V is mapping the sky with multiobject spectroscopy (MOS) at telescopes in both hemispheres (the 2.5 m Sloan Foundation Telescope at Apache Point Observatory and the 100-inch du Pont Telescope at Las Campanas Observatory), where 500 zonal robotic fiber positioners feed light from a wide-field focal plane to an optical (R ~ 2000, 500 fibers) and a near-infrared (R ~ 22,000, 300 fibers) spectrograph. In addition to these MOS capabilities, the survey is pioneering ultra─wide-field (~ 4000 deg2) integral field spectroscopy enabled by a new dedicated facility (LVM-I) at Las Campanas Observatory, where an integral field spectrograph (IFS) with 1801 lenslet-coupled fibers arranged in a 0 .° 5-diameter hexagon feeds multiple R ~ 4000 optical spectrographs that cover 3600─9800 Å. SDSS-V's hardware and multiyear survey strategy are designed to decode the chemodynamical history of the Milky Way and tackle fundamental open issues in stellar physics in its Milky Way Mapper program, trace the growth physics of supermassive black holes in its Black Hole Mapper program, and understand the self-regulation mechanisms and the chemical enrichment of galactic ecosystems at the energy injection scale in its Local Volume Mapper program. The survey is well timed to multiply the scientific output from major all-sky space missions. The SDSS-V MOS programs began robotic operations in 2021; IFS observations began in 2023 with the completion of the LVM-I facility. SDSS-V builds on decades of heritage of SDSS's pioneering advances in data analysis, collaboration spirit, infrastructure, and product deliverables in astronomy.
Full Paper9. Measuring the Ionizing Power of Early Galaxies
The AURORA Survey: Ionizing Photon Production Efficiency with Minimal Nebular Dust Attenuation Systematics
Publication: The Astrophysical Journal
Carnegie Author: Anthony Pahl
Using JWST data, researchers measured how efficiently distant galaxies produce ionizing photons—key to understanding how the early universe became transparent to light. The study improves dust corrections that can significantly affect these measurements, reducing uncertainty in reionization models.
10. A Galaxy from Cosmic Dawn
Star Formation under a Cosmic Microscope: Highly Magnified z = 11 Galaxy behind the Bullet Cluster
Publication: The Astrophysical Journal
Carnegie Author: Andrew Robertson
Astronomers observed a galaxy from when the universe was only about 400 million years old, magnified by gravitational lensing from the Bullet Cluster. The data reveal compact star-forming regions and evidence that most of the galaxy’s stars formed even earlier, offering a rare glimpse into galaxy formation during the era of reionization.
We present measurements of stellar population properties of a newly discovered, spectroscopically confirmed, z=11.10−0.26+0.11, gravitationally lensed galaxy, using JWST NIRSpec PRISM spectroscopy and NIRCam imaging. The arc is highly magnified by the Bullet Cluster (magnification factor μ=14.0−0.3+6.2 ). It contains three star-forming components of which one is barely resolved and two are unresolved, giving intrinsic sizes of ≲10 pc. The clumps also contain ~ 50 percent of the total stellar mass. The galaxy formed the majority of its stars ∼150 Myr ago (by z ~ 14). The spectrum shows a pronounced damping wing, typical for galaxies deep in the reionization era and indicating a neutral intergalactic medium at this line of sight. The intrinsic luminosity of the galaxy is 0.086−0.030+0.008L* (with L* being the characteristic luminosity for this redshift), making it the lowest-luminosity spectroscopically confirmed galaxy at z > 10 discovered to date.
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