Department of Earth and Planetary Science

Applying full-waveform methods to image small-scale structures of geophysical interest buried within the Earth requires the computation of the seismic wavefield over large distances compared to the target wavelengths. This represents a considerable computational cost when using state-of-the-art numerical integration of the equations of motion in three-dimensional earth models. Box Tomography is a hybrid method that breaks up the wavefield computation into three parts, only one of which needs to be iterated for each model update, significantly saving computational time. To deploy this method in remote regions containing a fluid-solid boundary, one needs to construct artificial sources that confine the seismic wavefield within a small region that straddles this boundary. The difficulty arises from the need to combine the solid-fluid coupling with a hybrid numerical simulation in this region. Here, we report a reconciliation of different displacement potential expressions used for solving the acoustic wave equation and propose a unified framework for hybrid simulations. This represents a significant step towards applying Box Tomography in arbitrary regions inside the Earth, achieving a thousand-fold computational cost reduction compared to standard approaches without compromising accuracy. We also present examples of benchmarks of the hybrid simulations in the case of target regions at the ocean floor and the core-mantle boundary.

We introduce five novel types of Monte Carlo (MC) moves that brings the number of moves of ensemble MC calculations from three to eight. So far such calculations have relied on affine invariant stretch moves that were originally introduced by Christen (2007) [8], walk moves by Goodman and Weare (2010) [16] and quadratic moves by Militzer (2023) [31,32]. Ensemble MC methods have been very popular because they harness information about the fitness landscape from a population of walkers rather than relying on expert knowledge. Here we modified the affine method and employed a simplex of points to set the stretch direction. We adopt the simplex concept to quadratic moves. We also generalize quadratic moves to arbitrary order. Finally, we introduce directed moves that employ the values of the probability density while all other types of moves rely solely on the location of the walkers. We apply all algorithms to the Rosenbrock density in 2 and 20 dimensions and to the ring potential in 12 and 24 dimensions. We evaluate their efficiency by comparing error bars, autocorrelation time, travel time, and the level of cohesion that measures whether any walkers were left behind. Our code is open source.

Rubisco is the primary CO2-fixing enzyme of the biosphere1, yet it has slow kinetics2. The roles of evolution and chemical mechanism in constraining its biochemical function remain debated3,4. Engineering efforts aimed at adjusting the biochemical parameters of rubisco have largely failed5, although recent results indicate that the functional potential of rubisco has a wider scope than previously known6. Here we developed a massively parallel assay, using an engineered Escherichia coli7 in which enzyme activity is coupled to growth, to systematically map the sequence-function landscape of rubisco. Composite assay of more than 99% of single-amino acid mutants versus CO2 concentration enabled inference of enzyme velocity and apparent CO2 affinity parameters for thousands of substitutions. This approach identified many highly conserved positions that tolerate mutation and rare mutations that improve CO2 affinity. These data indicate that non-trivial biochemical changes are readily accessible and that the functional distance between rubiscos from diverse organisms can be traversed, laying the groundwork for further enzyme engineering efforts.

The Red Planet is a magnetic planet. The Martian crust contains strong magnetization from a core dynamo that likely was active during the Noachian period when the surface may have been habitable. The evolution of the dynamo may have played a central role in the evolution of the early atmosphere and the planets transition to the current cold and dry state. However, the nature and history of the dynamo and crustal magnetization are poorly understood given the lack of well-preserved, oriented, ancient samples with geologic context available for laboratory study. Here, we describe how magnetic measurements of returned samples could transform our understanding of six key unknowns about Mars planetary evolution and habitability. Such measurements could i) determine the history of the Martian dynamo fields intensity; ii) determine the history of the Martian dynamo fields direction; iii) test the hypothesis that Mars experienced plate tectonics or true polar wander; iv) constrain the thermal and aqueous alteration history of the samples; v) identify sources of Martian crustal magnetization and vi) characterize sedimentary and magmatic processes on Mars. We discuss how these goals can be achieved using future laboratory analyses of samples acquired by the Perseverance rover.

Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Since its conception, MIBiG has been regularly updated to expand data coverage and remain up to date with innovations in natural product research. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard. In a massive community annotation effort, 267 contributors performed 8304 edits, creating 557 new entries and modifying 590 existing entries, resulting in a new total of 3059 curated entries in MIBiG. Particular attention was paid to ensuring high data quality, with automated data validation using a newly developed custom submission portal prototype, paired with a novel peer-reviewing model. MIBiG 4.0 also takes steps towards a rolling release model and a broader involvement of the scientific community. MIBiG 4.0 is accessible online at https://mibig.secondarymetabolites.org/.

BACKGROUND: Underground research laboratories (URLs) provide a window on the deep biosphere and enable investigation of potential microbial impacts on nuclear waste, CO2 and H2 stored in the subsurface. We carried out the first multi-year study of groundwater microbiomes sampled from defined intervals between 140 and 400 m below the surface of the Horonobe and Mizunami URLs, Japan. RESULTS: We reconstructed draft genomes for > 90% of all organisms detected over a four year period. The Horonobe and Mizunami microbiomes are dissimilar, likely because the Mizunami URL is hosted in granitic rock and the Horonobe URL in sedimentary rock. Despite this, hydrogen metabolism, rubisco-based CO2 fixation, reduction of nitrogen compounds and sulfate reduction are well represented functions in microbiomes from both URLs, although methane metabolism is more prevalent at the organic- and CO2-rich Horonobe URL. High fluid flow zones and proximity to subsurface tunnels select for candidate phyla radiation bacteria in the Mizunami URL. We detected near-identical genotypes for approximately one third of all genomically defined organisms at multiple depths within the Horonobe URL. This cannot be explained by inactivity, as in situ growth was detected for some bacteria, albeit at slow rates. Given the current low hydraulic conductivity and groundwater compositional heterogeneity, ongoing inter-site strain dispersal seems unlikely. Alternatively, the Horonobe URL microbiome homogeneity may be explained by higher groundwater mobility during the last glacial period. Genotypically-defined species closely related to those detected in the URLs were identified in three other subsurface environments in the USA. Thus, dispersal rates between widely separated underground sites may be fast enough relative to mutation rates to have precluded substantial divergence in species composition. Species overlaps between subsurface locations on different continents constrain expectations regarding the scale of global subsurface biodiversity. CONCLUSIONS: Our analyses reveal microbiome stability in the sedimentary rocks and surprising microbial community compositional and genotypic overlap over sites separated by hundreds of meters of rock, potentially explained by dispersal via slow groundwater flow or during a prior hydrological regime. Overall, microbiome and geochemical stability over the study period has important implications for underground storage applications.

A method is presented for high-precision chemical detection that integrates quantum sensing with droplet microfluidics. Using nanodiamonds (ND) with fluorescent nitrogen-vacancy (NV) centers as quantum sensors, rapidly flowing microdroplets containing analyte molecules are analyzed. A noise-suppressed mode of optically detected magnetic resonance is enabled by pairing controllable flow with microwave control of NV electronic spins, to detect analyte-induced signals of a few hundredths of a percent of the ND fluorescence. Using this method, paramagnetic ions in droplets are detected with low limit-of-detection using small analyte volumes, with exceptional measurement stability over >10³ s. In addition, these droplets are used as microconfinement chambers by co-encapsulating ND quantum sensors with various analytes such as single cells, suggesting wide-ranging applications including single-cell metabolomics and real-time intracellular measurements from bioreactors. Important advances are enabled by this work, including portable chemical testing devices, amplification-free chemical assays, and chemical imaging tools for probing reactions within microenvironments.

Cyanobacteria are highly abundant in the marine photic zone and primary drivers of the conversion of inorganic carbon into biomass. To date, all studied cyanobacterial lineages encode carbon fixation machinery relying upon form I Rubiscos within a CO2-concentrating carboxysome. Here, we report that the uncultivated anoxic marine zone (AMZ) IB lineage of Prochlorococcus from pelagic oxygen-deficient zones (ODZs) harbors both form I and form II Rubiscos, the latter of which are typically noncarboxysomal and possess biochemical properties tuned toward low-oxygen environments. We demonstrate that these cyanobacterial form II enzymes are functional in vitro and were likely acquired from proteobacteria. Metagenomic analysis reveals that AMZ IB are essentially restricted to ODZs in the Eastern Pacific, suggesting that form II acquisition may confer an advantage under low-O2 conditions. AMZ IB populations express both forms of Rubisco in situ, with the highest form II expression at depths where oxygen and light are low, possibly as a mechanism to increase the efficiency of photoautotrophy under energy limitation. Our findings expand the diversity of carbon fixation configurations in the microbial world and may have implications for carbon sequestration in natural and engineered systems.

The Voyager spacecraft discovered that the ice giants Uranus and Neptune have nondipolar magnetic fields, defying expectations that a thick interior layer of planetary ices would generate strong dipolar fields. Stanley and Bloxham showed that nondipolar fields emerge if the magnetic field is only generated in a thin outer layer. However, the origin and composition of this dynamo active layer has so far remained elusive. Here, we show with ab initio computer simulations that a mixture of H2O, CH4, and NH3 will phase separate under the pressure-temperature condition in the interiors of Uranus and Neptune, forming a H2O-dominated fluid in the upper mantle and a CH4-NH3 mixture below. We further demonstrate that with increasing pressure, the CH4-NH3 mixture becomes increasingly hydrogen depleted as it assumes the state of a polymeric C-N-H fluid. Since the amount of hydrogen loss increases with pressure, we propose that the C-N-H fluid forms a stably stratified layer. The magnetic fields are primarily generated in an upper layer that is H2O-rich, homogeneous, convective, and electrically conducting. Under these assumptions, we construct ensembles of models for the interiors of Uranus and Neptune with the Concentric MacLaurin Spheroid method. We demonstrate that the phase separation of the solar-type H2O-CH4-NH3 mixture leads to models that match the observed gravity field and to layer thicknesses that are compatible with magnetic field measurements.

High-resolution full waveform seismic tomography of the Earths mantle beneath the south and central Atlantic Ocean brings into focus a series of asthenospheric low shear velocity channels, or fingers on both sides of the southern and central mid-Atlantic ridge (MAR), elongated in the direction of absolute plate motion with a spacing of [Formula: see text]1,800 to 2,000 km, and associated with bands of shallower residual seafloor depth anomalies that suggest channeled flow over thousands of kilometers. Each of the three most clearly resolved fingers on the African side of the MAR corresponds to a separate group of whole mantle plumes rooted in distinct patches at the core-mantle boundary, feeding hotspots, and volcanic lines with distinct isotopic signatures. Plumes of a given group appear to merge at the top of the lower mantle before separating again, suggesting interaction of deep mantle flow with a more vigorous mesoscale circulation in the upper mantle. The corresponding hotspots are generally offset from the location of the deep mantle plume roots. The distinct isotopic signatures of these hotspot groups are also detected in the mid-ocean ridge basalts at the location where the fingers meet the ridge. Meanwhile, at least some of the variability within each plume group could originate in the upper mantle and extended transition zone where plumes in a given group appear to merge and pond. This study also adds to mounting evidence that the African large low shear velocity province is not a uniform, unbroken pile of dense material rising high above the core-mantle boundary, but rather a collection of mantle plumes rooted in patches of distinct composition.