The ultimate microscope, directed at a cell, would reveal the dynamics of all the cell's components with atomic resolution. In contrast to their real-world counterparts, computational microscopes are ...currently on the brink of meeting this challenge. In this perspective, we show how an integrative approach can be employed to model an entire cell, the minimal cell, JCVI-syn3A, at full complexity. This step opens the way to interrogate the cell's spatio-temporal evolution with molecular dynamics simulations, an approach that can be extended to other cell types in the near future.
Surface-enhanced Raman spectroscopy (SERS) of species bound to environmentally relevant oxide nanoparticles is largely limited to organic molecules structurally related to catechol that facilitate a ...chemical enhancement of the Raman signal. Here, we report that magnetite (Fe3O4) nanoparticles provide a SERS signal from oxalic acid and cysteine via an electric field enhancement. Magnetite thus likely provides an oxide substrate for SERS study of any adsorbed organic molecule. This substrate combines benefits from both metal-based and chemical SERS by providing an oxide surface for studies of environmentally and catalytically relevant detailed chemical bonding information with fewer restrictions of molecular structure or binding mechanisms. Therefore, the magnetite-based SERS demonstrated here provides a new approach to establishing the surface interactions of environmentally relevant organic ligands and mineral surfaces.
Visualizing hydrated interfaces is of widespread interest across the physical sciences and is a particularly acute need for layered minerals, whose properties are governed by the structure of the ...electric double layer (EDL) where mineral and solution meet. Here, we show that cryo electron microscopy and tomography enable direct imaging of the EDL at montmorillonite interfaces in monovalent electrolytes with ångstrom resolution over micron length scales. A learning-based multiple-scattering reconstruction method for cryo electron tomography reveals ions bound asymmetrically on opposite sides of curved, exfoliated layers. We observe conserved ion-density asymmetry across stacks of interacting layers in cryo electron microscopy that is associated with configurations of inner- and outer-sphere ion-water-mineral complexes that we term complexation waves. Coherent X-ray scattering confirms that complexation waves propagate at room-temperature via a competition between ion dehydration and charge interactions that are coupled across opposing sides of a layer, driving dynamic transitions between stacked and aggregated states via layer exfoliation.
Ecological theory posits that dispersal among habitat patches links local communities and is a key “regional” process that maintains biological diversity. However, manipulations required to ...experimentally test regional processes are infeasible for most systems, and thus more work is needed to detect the scales at which regional processes manifest and their overall effect on diversity. In a Californian grassland, a hotspot for global biodiversity, we used a seed vacuum to increase dispersal at spatial scales varying from1mto 10 km while maintaining a realistic spatial structure of species pools and environmental conditions. We found that dispersal limitation has a profound influence on diversity; species richness increased with the spatial scale of seed mixing, doubling in plots that received seed from large (≥5 km) compared with small (≤5 m) scales. This increase in diversity corresponded to an increase in how well species distributions were explained by environmental conditions, from modest at small scales (R² = 0.34) to strong at large scales (R² = 0.52). Responses to the spatial scale of seed mixing were nonlinear, with no differences below 5 m or above 5 km. Nonlinearities were explained by homogeneity of environmental conditions below 5 m and by a lack of additional variation in the species pool above 5 km. Our approach of manipulating natural communities at different spatial scales reveals (i) nonlinear transitions in the importance of environmental sorting and dispersal, and (ii) the negative effects of dispersal limitation on local diversity, consistent with previous research suggesting that large numbers of species are headed toward regional extinction.
Iron oxide nanoparticles are present throughout the Earth and undergo mineral phase transformations that affect their stability and reactivity. The formation of the iron oxide hematite from a 2-line ...ferrihydrite (2lnFh) precursor requires both phase transformation and growth. Whether phase transformation occurs before or after substantial particle growth, and by which mechanisms particles grow, remain unclear. We conducted time-resolved studies employing X-ray diffraction, room temperature and cryogenic transmission electron microscopy, preferential dissolution by oxalate buffer, and low temperature SQuID magnetometry to investigate the kinetics and mechanism of hematite formation from 2lnFh. A novel form of magnetic measurement was found to be exquisitely sensitive to the presence of hematite, detecting its formation at far lower concentrations than possible with X-ray diffraction. These results indicate that small hematite domains were present even in as-prepared 2lnFh suspensions as a side-product of 2lnFh synthesis and that the hematite domains increased in size and crystallinity with aging time at elevated temperatures. Second-order kinetics reveals that the hematite growth is consistent with a particle-mediated growth mechanism, possibly oriented attachment.
Changing temperature can substantially shift ecological communities by altering the strength and stability of trophic interactions. Because many ecological rates are constrained by temperature, new ...approaches are required to understand how simultaneous changes in multiple rates alter the relative performance of species and their trophic interactions. We develop an energetic approach to identify the relationship between biomass fluxes and standing biomass across trophic levels. Our approach links ecological rates and trophic dynamics to measure temperature‐dependent changes to the strength of trophic interactions and determine how these changes alter food web stability. It accomplishes this by using biomass as a common energetic currency and isolating three temperature‐dependent processes that are common to all consumer–resource interactions: biomass accumulation of the resource, resource consumption and consumer mortality. Using this framework, we clarify when and how temperature alters consumer to resource biomass ratios, equilibrium resilience, consumer variability, extinction risk and transient vs. equilibrium dynamics. Finally, we characterise key asymmetries in species responses to temperature that produce these distinct dynamic behaviours and identify when they are likely to emerge. Overall, our framework provides a mechanistic and more unified understanding of the temperature dependence of trophic dynamics in terms of ecological rates, biomass ratios and stability.
Fractures are integral to the hydrology and geochemistry of watersheds, but our understanding of fracture dynamics is very limited because of the challenge of monitoring the subsurface. Here we ...provide evidence that long-term, high-frequency measurements of the river concentration of the ultra-trace element thorium (Th) can provide a signature of bedrock fracture processes spanning neighboring watersheds in Colorado. River Th concentrations show abrupt (subdaily) excursions and biexponential decay with approximately 1-day and 1-week time constants, concentration patterns that are distinct from all other solutes except beryllium and arsenic. The patterns are uncorrelated with daily precipitation records or seasonal trends in atmospheric deposition. Groundwater Th analyses are consistent with bedrock release and dilution upon mixing with river water. Most Th excursions have no seismic signatures that are detectable 50 km from the site, suggesting the Th concentrations can reveal aseismic fracture or fault events. We find, however, a weak statistical correlation between Th and seismic motion caused by distant earthquakes, possibly the first chemical signature of dynamic earthquake triggering, a phenomenon previously identified only through geophysical methods.
A fundamental goal of ecology is to understand what controls the distribution and abundance of species. Both environmental niches and trade-offs among species in dispersal and competitive ability ...have traditionally been cited as determinants of plant community composition. More recently, neutral models have shown that communities of species with identical life-history characteristics and no adaptation to environmental niches can form spatial distribution patterns similar to those found in nature, so long as the species have a limited dispersal distance. If there is a strong correlation between geographic distance and change in environmental conditions, however, such spatial patterns can arise through either neutral or niche-based processes. To test these competing theories, we developed a sampling design that decoupled distance and environment in the understory plant communities of an old-growth, temperate forest. We found strong evidence of niche-structuring but almost no support for neutral predictions. Dispersal limitation acted in conjunction with environmental gradients to determine species' distributions, and both functional and phylogenetic constraints appear to contribute to the niche differentiation that structures community assembly. Our results indicate that testing a neutral hypothesis without accounting for environmental gradients will at best cause unexplained variation in plant distributions and may well provide misleading support for neutrality because of a correlation between geographic distance and environment.
The photoreductive dissolution of Mn(IV) oxide minerals in sunlit aquatic environments couples the Mn cycle to the oxidation of organic matter and fate of trace elements associated with Mn oxides, ...but the intrinsic rate and mechanism of mineral dissolution in the absence of organic electron donors is unknown. We investigated the photoreduction of δ-MnO ₂ nanosheets at pH 6.5 with Na or Ca as the interlayer cation under 400-nm light irradiation and quantified the yield and timescales of Mn(III) production. Our study of transient intermediate states using time-resolved optical and X-ray absorption spectroscopy showed key roles for chemically distinct Mn(III) species. The reaction pathway involves ( i ) formation of Jahn–Teller distorted Mn(III) sites in the octahedral sheet within 0.6 ps of photoexcitation; ( ii ) Mn(III) migration into the interlayer within 600 ps; and ( iii ) increased nanosheet stacking. We propose that irreversible Mn reduction is coupled to hole-scavenging by surface water molecules or hydroxyl groups, with associated radical formation. This work demonstrates the importance of direct MnO ₂ photoreduction in environmental processes and provides a framework to test new hypotheses regarding the role of organic molecules and metal species in photochemical reactions with Mn oxide phases. The timescales for the production and evolution of Mn(III) species and a catalytic role for interlayer Ca ²⁺ identified here from spectroscopic measurements can also guide the design of efficient Mn-based catalysts for water oxidation.
Significance The photoreductive dissolution of Mn oxides governs the biogeochemical cycle of Mn and the fate of organic and inorganic species associated with Mn oxides in the euphotic zones of marine and freshwater systems. Mn oxide minerals also have garnered interest as water oxidation catalysts inspired by the Mn ₄CaO ₄ cluster of photosystem II. However, the mechanism of water oxidation by MnO ₂ and the rate limiting steps for this reaction are unknown. In this study, we couple flow-through experiments and ultrafast pump–probe optical and X-ray absorption spectroscopy to develop a photoreduction model that includes the mechanism and timescales for the initial electron transfer steps in the oxidation of water by MnO ₂.
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