Zhao Hao

The mechanics of fracture healing in calcite remain poorly constrained yet are fundamental to managing fluid transport in geothermal reservoirs and hydrocarbon systems. Here, we apply microfocused synchrotron Laue X-ray diffraction and infrared spectroscopy to investigate subcritical crack healing in a 1 mm-thick calcite crystal subjected to controlled loading in a double-torsion device. Over a 44-hour period following load removal, we map the evolution of residual strain fields surrounding the crack tip and observe a progressive increase in compressive strain perpendicular to the crack plane accompanied by infrared spectroscopic signatures that reveal enhanced accumulation of water at the healed interface. The correlation between strain evolution and surface chemistry suggests that spontaneous crack healing in calcite is driven by dynamic anelastic relaxation coupled with irreversible fluid-mineral interactions. These findings offer insight into time-dependent crack closure processes in carbonates and highlight the role of chemically-mediated plasticity in subsurface fracture evolution.

Inelastic x-ray scattering spectroscopy (IXS) is a modern synchrotron based vibrational spectroscopy, which measures transitions in the terahertz vibrations. This paper presents the first IXS on a metallo-enzyme derived sample, namely, the iron-molybdenum cofactor (FeMoco) of nitrogenase. We have also measured the corresponding far infrared absorption spectrum (far IR spectrum) of FeMoco and compared these data to previously published nuclear resonant vibrational spectra (NRVS) of FeMoco and far infrared spectra of the model Mo–dioxo–homocitrate complex K2[MoO2(R,S-H2homocitrate)2]·2H2O. Although NRVS offers several clear advantages, IXS can probe vibrations not involving iron motion and is still sensitive to heavier elements. This provides a useful method to study molybdenum vibrations, such as the ν(Mo–O) mode at 530 cm−1 in FeMoco, which is observable by IXS but not by NRVS. The comparison of the vibrational frequencies of FeMoco with those of the Mo-complex supports an earlier proposal that the homocitrate ligand in FeMoco is protonated. This work, which introduces IXS to bioinorganic chemistry, concludes by examining both the opportunities and the challenges of applying IXS to other biologically relevant systems.

Exposure of matter to high-energy heavy ions induces defects along the ion trajectories through electronic and nuclear energy loss processes. Defects, including color centers, can recombine or form along latent damage tracks in semiconductors. Latent tracks in diamond were only recently observed. Here we report on color center formation in nitrogen-doped diamond along the latent tracks of 1 GeV gold and uranium ions. We optically observe direct formation of single vacancy related color centers (GR1-centers) along the tracks. Mobile vacancies can form NV-centers with native nitrogen atoms during thermal annealing. Molecular dynamics simulations show that isolated vacancies and vacancy clusters form through electronic stopping processes along ion trajectories. Moreover, by using 1 GeV Au ions with a dilute fluence, we create individually isolated quasi-1D chains of NV-centers, which appear as isolated bright luminescence strings and present competitive electron spin properties compared to a background of NV-centers. Such spin textures can be building blocks for applications in quantum sensing and computing.

Recent evidence suggests that, similar to larger organisms, dispersal is a key driver of microbiome assembly; however, our understanding of the rates and taxonomic composition of microbial dispersal in natural environments is limited. Here, we characterized the rate and composition of bacteria dispersing into surface soil via three dispersal routes (from the air above the vegetation, from nearby vegetation and leaf litter near the soil surface, and from the bulk soil and litter below the top layer). We then quantified the impact of those routes on microbial community composition and functioning in the topmost litter layer. The bacterial dispersal rate onto the surface layer was low (7900 cells/cm²/day) relative to the abundance of the resident community. While bacteria dispersed through all three routes at the same rate, only dispersal from above and near the soil surface impacted microbiome composition, suggesting that the composition, not rate, of dispersal influenced community assembly. Dispersal also impacted microbiome functioning. When exposed to dispersal, leaf litter decomposed faster than when dispersal was excluded, although neither decomposition rate nor litter chemistry differed by route. Overall, we conclude that the dispersal routes transport distinct bacterial communities that differentially influence the composition of the surface soil microbiome.

The perennial native switchgrass adapts better than other plant species do to marginal soils with low plant-available nutrients, including those with low phosphorus (P) content. Switchgrass roots and their associated microorganisms can alter the pools of available P throughout the whole soil profile making predictions of P availability in situ challenging. Plant P homeostasis makes monitoring of P limitation via measurements of plant P content alone difficult to interpret. To address these challenges, we developed a machine-learning model trained with high accuracy using the leaf tissue chemical profile, rather than P content. By applying this learned model in field trials across two sites with contrasting extractable soil P, we observed that actual plant available P in soil was more similar than expected, suggesting that adaptations occurred to alleviate the apparent P constraint. These adaptations come at a metabolic cost to the plant that have consequences for feedstock chemical components and quality. We observed that other biochemical signatures of P limitation, such as decreased cellulose-to-lignin ratios, were apparent, indicating re-allocation of carbon resources may have contributed to increased P acquisition. Plant P allocation strategies also differed across sites, and these differences were correlated with the subsequent year’s biomass yields.

This study investigates the isolated decomposition of spruce and lodgepole conifer needles to enhance our understanding of how needle litter impacts near-surface terrestrial biogeochemical processes. Harvested needles were exported to a subalpine meadow to enable a discrete analysis of the decomposition processes over 2 years. Initial chemistry revealed the lodgepole needles to be less recalcitrant with a lower carbon to nitrogen (C:N) ratio. Total C and N fundamentally shifted within needle species over time with decreased C:N ratios for spruce and increased ratios for lodgepole. Differences in chemistry correlated with CO₂production and soil microbial communities. The most pronounced trends were associated with lodgepole needles in comparison to the spruce and needle-free controls. Increased organic carbon and nitrogen concentrations associated with needle presence in soil extractions further corroborate the results with clear biogeochemical signatures in association with needle chemistry. Interestingly, no clear differentiation was observed as a function of bark beetle impacted spruce needles vs those derived from healthy spruce trees despite initial differences in needle chemistry. These results reveal that the inherent chemistry associated with tree species has a greater impact on soil biogeochemical signatures during isolated needle decomposition. By extension, biogeochemical shifts associated with bark beetle infestation are likely driven more by changes such as the cessation of rhizospheric processes than by needle litter decomposition.

Beneficial microbial associations enhance the fitness of most living organisms, and wood-feeding insects offer some of the most striking examples of this. Odontotaenius disjunctus is a wood-feeding beetle that possesses a digestive tract with four main compartments, each of which contains well-differentiated microbial populations, suggesting that anatomical properties and separation of these compartments may enhance energy extraction from woody biomass. Here, using integrated chemical analyses, we demonstrate that lignocellulose deconstruction and fermentation occur sequentially across compartments, and that selection for microbial groups and their metabolic pathways is facilitated by gut anatomical features. Metaproteogenomics showed that higher oxygen concentration in the midgut drives lignocellulose depolymerization, while a thicker gut wall in the anterior hindgut reduces oxygen diffusion and favours hydrogen accumulation, facilitating fermentation, homoacetogenesis and nitrogen fixation. We demonstrate that depolymerization continues in the posterior hindgut, and that the beetle excretes an energy- and nutrient-rich product on which its offspring subsist and develop. Our results show that the establishment of beneficial microbial partners within a host requires both the acquisition of the microorganisms and the formation of specific habitats within the host to promote key microbial metabolic functions. Together, gut anatomical properties and microbial functional assembly enable lignocellulose deconstruction and colony subsistence on an extremely nutrient-poor diet.

Like all higher organisms, plants have evolved in the context of a microbial world, shaping both their evolution and their contemporary ecology. Interactions between plant roots and soil microorganisms are critical for plant fitness in natural environments. Given this co-evolution and the pivotal importance of plant–microbial interactions, it has been hypothesized, and a growing body of literature suggests, that plants may regulate the composition of their rhizosphere to promote the growth of microorganisms that improve plant fitness in a given ecosystem. Here, using a combination of comparative genomics and exometabolomics, we show that pre-programmed developmental processes in plants (Avena barbata) result in consistent patterns in the chemical composition of root exudates. This chemical succession in the rhizosphere interacts with microbial metabolite substrate preferences that are predictable from genome sequences. Specifically, we observed a preference by rhizosphere bacteria for consumption of aromatic organic acids exuded by plants (nicotinic, shikimic, salicylic, cinnamic and indole-3-acetic). The combination of these plant exudation traits and microbial substrate uptake traits interact to yield the patterns of microbial community assembly observed in the rhizosphere of an annual grass. This discovery provides a mechanistic underpinning for the process of rhizosphere microbial community assembly and provides an attractive direction for the manipulation of the rhizosphere microbiome for beneficial outcomes.

The organic and mineralogical heterogeneity in shale at micrometer and nanometer spatial scales contributes to the quality of gas reserves, gas flow mechanisms and gas production. Here, we demonstrate two molecular imaging approaches based on infrared spectroscopy to obtain mineral and kerogen information at these mesoscale spatial resolutions in large-sized shale rock samples. The first method is a modified microscopic attenuated total reflectance measurement that utilizes a large germanium hemisphere combined with a focal plane array detector to rapidly capture chemical images of shale rock surfaces spanning hundreds of micrometers with micrometer spatial resolution. The second method, synchrotron infrared nano-spectroscopy, utilizes a metallic atomic force microscope tip to obtain chemical images of micrometer dimensions but with nanometer spatial resolution. This chemically “deconvoluted” imaging at the nano-pore scale is then used to build a machine learning model to generate a molecular distribution map across scales with a spatial span of 1000 times, which enables high-throughput geochemical characterization in greater details across the nano-pore and micro-grain scales and allows us to identify co-localization of mineral phases with chemically distinct organics and even with gas phase sorbents. This characterization is fundamental to understand mineral and organic compositions affecting the behavior of shales.

Climate model projections for tropical regions show clear perturbation of precipitation patterns leading to increased frequency and severity of drought in some regions. Previous work has shown declining soil moisture to be a strong driver of changes in microbial trait distribution, however the feedback of any shift in functional potential on ecosystem properties related to carbon cycling are poorly understood. Here we show that drought-induced changes in microbial functional diversity and activity shape, and are in turn shaped by, the composition of dissolved and soil-associated carbon. We also demonstrate that a shift in microbial functional traits that favor the production of hygroscopic compounds alter the efflux of carbon dioxide following soil rewetting. Under drought the composition of the dissolved organic carbon pool changed in a manner consistent with a microbial metabolic response. We hypothesize that this microbial ecophysiological response to changing soil moisture elevates the intracellular carbon demand stimulating extracellular enzyme production, that prompts the observed decline in more complex carbon compounds (e.g., cellulose and lignin). Furthermore, a metabolic response to drought appeared to condition (biologically and physically) the soil, notably through the production of polysaccharides, particularly in experimental plots that had been pre-exposed to a short-term drought. This hysteretic response, in addition to an observed drought-related decline in phosphorus concentration, may have been responsible for a comparatively modest CO2 efflux following wet-up in drought plots relative to control plots.