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Correlative SIP-FISH-Raman-SEM-NanoSIMS links identity, morphology, biochemistry, and physiology of environmental microbes
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MISIP: a data standard for the reuse and reproducibility of any stable isotope probing-derived nucleic acid sequence and experiment
DNA/RNA-stable isotope probing (SIP) is a powerful tool to link in situ microbial activity to sequencing data. Every SIP dataset captures distinct information about microbial community metabolism, process rates, and population dynamics, offering valuable insights for a wide range of research questions. Data reuse maximizes the information derived from the labor and resource-intensive SIP approaches. Yet, a review of publicly available SIP sequencing metadata showed that critical information necessary for reproducibility and reuse was often missing. Here, we outline the Minimum Information for any Stable Isotope Probing Sequence (MISIP) according to the Minimum Information for any (x) Sequence (MIxS) framework and include examples of MISIP reporting for common SIP experiments. Our objectives are to expand the capacity of MIxS to accommodate SIP-specific metadata and guide SIP users in metadata collection when planning and reporting an experiment. The MISIP standard requires 5 metadata fields—isotope, isotopolog, isotopolog label, labeling approach, and gradient position—and recommends several fields that represent best practices in acquiring and reporting SIP sequencing data (e.g., gradient density and nucleic acid amount). The standard is intended to be used in concert with other MIxS checklists to comprehensively describe the origin of sequence data, such as for marker genes (MISIP-MIMARKS) or metagenomes (MISIP-MIMS), in combination with metadata required by an environmental extension (e.g., soil). The adoption of the proposed data standard will improve the reuse of any sequence derived from a SIP experiment and, by extension, deepen understanding of in situ biogeochemical processes and microbial ecology.
Spectral induced polarization signatures of smoldering remediation enhanced with colloidal activated carbon: An experimental study
Monitoring the remediation of soil and groundwater contaminated by organic compounds remains highly challenging. The spectral induced polarization (SIP) method exhibits significant promise for monitoring changes to the electrical properties of soils that are undergoing remediation. Thermal treatments, such as smoldering combustion, have become established remediation techniques for destroying contaminants. Smoldering combustion is now being supported by colloidal activated carbon (CAC), with CAC able to adsorb contaminants and supplement the fuel source for destroying contaminants. The objective of this study is to investigate the potential of SIP for tracking the smoldering remediation of imitated field soils supplemented with CAC. SIP column experiments were first conducted to assess the response of SIP to varying concentrations of CAC in field soils that contain, or do not contain, organic material (OM). Here these results demonstrate that increasing OM and CAC contents increase both the real and imaginary components of the complex conductivity, with the imaginary conductivity also showing frequency dependence. Next, a suite of smoldering and SIP column experiments was conducted to investigate if SIP can detect changes in imitated field soils of varying OM and CAC contents that have been remediated by smoldering combustion. The SIP results on the examined soils both before and after smoldering show that SIP can detect changes in the real conductivity, and particularly the imaginary conductivity, between different soil compositions and different stages of the remediation process. High resolution scanning electron microscopy (SEM) imaging was performed on all samples to validate the SIP and smoldering experiments, confirming significant reductions in carbon after smoldering. Overall, this study suggests that SIP has potential to detect changes in the electrical properties of field soils due to the addition of remedial fluids like CAC and contaminant destruction by smoldering remediation.
Primary and secondary ice production: interactions and their relative importance
A discrepancy of up to 5 orders of magnitude between ice crystal and ice nucleating particle (INP) number concentrations was found in the measurements, indicating the potentially important role of secondary ice production (SIP) in the clouds. However, the interactions between primary and SIP processes and their relative importance remain unexplored. In this study, we implemented five different ice nucleation schemes as well as physical representations of SIP processes (i.e., droplet shattering during rain freezing, ice-ice collisional break-up, and rime splintering) in the Community Earth System Model version 2 (CESM2). We ran CESM2 in the single column mode for model comparisons with the DOE Atmospheric Radiation Measurement (ARM) Mixed-Phase Arctic Cloud Experiment (M-PACE) observations. We found that the model experiments with aerosol-aware ice nucleation schemes and SIP processes yield the best simulation results for the M-PACE single-layer mixed-phase clouds. We further investigated the relative importance of ice nucleation and SIP to ice number and cloud phase as well as interactions between ice nucleation and SIP in the M-PACE single-layer mixed-phase clouds. Our results show that SIP contributes 80 % to the total ice formation and transforms ~30 % of pure liquid-phase clouds simulated in the model experiments without considering SIP into mixed-phase clouds. The SIP is not only a result of ice crystals produced from ice nucleation, but also competes with the ice nucleation by reducing the number concentrations of cloud droplets and cloud-borne dust INPs. Conversely, strong ice nucleation also suppresses SIP by glaciating mixed-phase clouds and thereby reducing the amount of precipitation particles (rain and graupel).
Solvent Impregnated Polymers Loaded with Liquid-Like Nanoparticle Organic Hybrid Materials for Enhanced Kinetics of Direct Air Capture and Point Source CO 2 Capture
Hybrid CO 2 capture materials, solvent impregnated polymers (SIPs), are developed based on a simple and scalable encapsulation technique to enhance CO 2 capture kinetics of water-lean solvents with high viscosity. Liquid-like nanoparticle organic hybrid materials functionalized with polyethylenimine (NOHM-I-PEI) are incorporated into a shell material and UV-cured to produce gas-permeable solid sorbents with uniform NOHMs loading (NPEI-SIPs). The CO 2 capture kinetics of NPEI-SIPs show a remarkable 50-fold increase compared to that of neat NOHM-I-PEI due to a large increase in the NOHMs-CO 2 interfacial surface area provided by the SIP design. The optimum NOHM-I-PEI loading and sorption temperature are found to be ≈49 wt% and 50 °C, respectively, and NPEI-SIPs exhibit great thermal stability over 20 CO 2 capture/sorbent regeneration temperature swing cycles. The pseudoequilibrium CO 2 loadings of NPEI-SIPs under humid conditions are as high as 3.1 mmol CO 2 g -1 NPEI - SIPs for 15 vol% CO 2 (postcombustion capture) and 1.7 mmol CO 2 g -1 NPEI - SIPs for 400 ppm (direct air capture). Overall, these findings suggest that NPEI-SIPs can effectively capture CO 2 from a wide range of CO 2 concentrations including direct air capture while allowing the flexible design of CO 2 capture reactors by combining the benefits of liquid solvents and solid sorbents.
Synthesis challenges, thermodynamic stability, and growth kinetics of La–Si–P ternary compounds
Although many new compounds have been recently predicted with the help of machine learning, the successful experimental synthesis of these compounds remains challenging. Computational insights about the thermodynamic stability and phase formation kinetics among the ground state and competing metastable phases are highly desirable to rationalize and attempt to overcome synthesis challenges experimentally. In this work, we explore synthetic challenges within ternary La–Si–P compounds through feedback between experimental and computational studies. We discuss the experimental challenges in forming three computationally predicted ternary phases (La 2 SiP, La 5 SiP 3 , and La 2 SiP 3 ). To understand the synthetic challenges, we performed molecular dynamics (MD) simulations using an accurate and efficient artificial neural network machine learning (ANN-ML) interatomic potential. We study the phase stability and formation kinetics of these ternary phases in relation to the reported and synthesized La 2 SiP 4 phase. While the growth of the La 2 SiP 4 phase can be reproduced by our MD simulation, our results indicate that the rapid formation of a Si-substituted LaP crystalline phase is a major barrier to the synthesis of the predicted La 2 SiP, La 5 SiP 3 , and La 2 SiP 3 ternary compounds, agreeing well with experimental observations. Our simulations also suggest that there is a narrow temperature window in which the La 2 SiP 3 phase can be grown from the solid–liquid interface.
On the Role of Airborne Ice Nucleating Particles in Primary and Secondary Ice Formation Processes in Convective Midlatitude Clouds
Abstract Formation of ice in mixed-phase clouds may proceed via primary nucleation and secondary ice production (SIP). Primary nucleation involves the presence of ice nucleating particles (INPs), while SIP follows primary nucleation, resulting in ice crystal number concentrations N ice exceeding the number of INPs. The ice formation pathways in young congestus clouds are not well understood nor are the environmental conditions favorable for the onset of SIP. Coincident airborne measurements of INPs and N ice collected during the Secondary Production of Ice in Cumulus Experiment (SPICULE) campaign over the U.S. central Great Plains are reported for young congestus clouds. Number concentrations of INPs and N ice at temperatures between −10° and −20°C were used to categorize whether SIP was active in each analyzed cloud pass. Observational data suggested that fragmentation of freezing droplets (FFDs) was occurring and the most likely SIP mechanism for ice enhancement during the early stages of the sampled clouds, where higher cloud-base temperatures and stronger updrafts produced conditions favorable for the onset of FFD. Simple model simulations of a congestus cloud were used to compare predictions of N ice from newly implemented SIP mechanisms (including FFD) alongside those from the existing Hallett–Mossop (HM) mechanism. Although predicted N ice , when all SIP mechanisms were active, was in good agreement with observations, the dominant SIP mechanism in the model was predicted to be HM. The rate of heterogeneous freezing in raindrops was likely inhibiting realistic FFD rates in the simulated cloud. These discrepancies between the observations and simulations underscore the need for extended laboratory studies to formulate improved model representations of SIP in convective clouds.
Electrical Responses of Modified Mineral Surfaces as Observed With Spectral Induced Polarization and Atomic Force Microscopy
Abstract Atomic force microscopy (AFM) and spectral induced polarization (SIP) are widely used to investigate the electrical properties of mineral surfaces at vastly different scales of measurement. We compare AFM and SIP measurements made on two different materials (glass beads and silica gel) subjected to etching, deposition of iron oxide particles, and inclusion of calcite grains. We found that the treatments produced qualitatively consistent behaviors in the AFM and SIP data. Direct AFM measurements of surface charge density for silica and calcite surfaces were quantitatively compared to values estimated from the SIP results using a grain polarization model. No statistically significant difference (at a 95% confidence level) was found between the surface charge density of silica estimated by AFM (2.3 ± 6.6 mC/m 2 for glass beads and 1.6 ± 0.1 mC/m 2 for silica gel) versus SIP (5.4 ± 4.4 mC/m 2 for glass beads and 1.6 ± 0.5 mC/m 2 for silica gel). The surface charge density for calcite determined by AFM (43.5 ± 12.9 mC/m 2 ) was approximately 19 times higher than that found for silica. While the charge density of calcite surfaces determined by SIP was also generally higher than that found for silica, different treatments produced significantly different values between 4.7 and 258 mC/m 2 (with a maximum 95% CI of ±8.7 mC/m 2 ). Several possible explanations exist for the range of the observed SIP measurements, including aging of the calcite surfaces. Overall, this study suggests the potential for the complementary use of AFM and SIP measurements to constrain future investigations of polarization mechanisms in porous media.
Spectral induced polarization monitoring of induced calcite precipitation in subsurface sediments
Co-precipitation of contaminants within the crystalline structure of calcite is a promising natural attenuation or remedial technology being considered at contaminated sites. We explore the sensitivity of the spectral induced polarization (SIP) method to induced calcite precipitation in natural sediments as a path forward to non-invasively monitor these sites. We performed time-lapse column experiments using phased (I-IV) injections over 40 days on natural sediments from the Hanford Site (Washington State, USA). In the phased injections, abiotic calcite precipitation was induced and confirmed to have occurred. Previous work in glass beads and homogeneous sand was limited to high frequency detection of calcite, however in this work we observed the development of two polarization mechanisms, one at high frequency (>100 Hz) and one at low frequency (< 100 Hz). Based on the characteristic frequencies from the SIP high and low frequency regimes, characteristic length scales (L) were computed where the adsorption mode of Na+ versus Ca2+ was compared by using diffusion coefficients corresponding to Na+ versus an arithmetically averaged value for Na+ and Ca2+. Using the diffusion coefficient of Na+, the high frequency L was found to correlate well with the size of the calcite crystals. The low frequency L correlated well with the individual natural sediment grain sizes within the columns. During late experimental times (day 36 and 40), the characteristic low frequency in two of the experimental columns shifted to lower frequencies (<0.001 Hz) which may signify SIP sensitivity of the formed calcite with the sediment grains. In field applications, the development of a low frequency polarization length scale to monitor calcite precipitation is promising for field monitoring applications, however further laboratory work needs to be performed to examine the SIP sensitivity of calcite formation in the presence of to natural sediments
Ultra-sensitive isotope probing to quantify activity and substrate assimilation in microbiomes
Abstract Background Stable isotope probing (SIP) approaches are a critical tool in microbiome research to determine associations between species and substrates, as well as the activity of species. The application of these approaches ranges from studying microbial communities important for global biogeochemical cycling to host-microbiota interactions in the intestinal tract. Current SIP approaches, such as DNA-SIP or nanoSIMS allow to analyze incorporation of stable isotopes with high coverage of taxa in a community and at the single cell level, respectively, however they are limited in terms of sensitivity, resolution or throughput. Results Here, we present an ultra-sensitive, high-throughput protein-based stable isotope probing approach (Protein-SIP), which cuts cost for labeled substrates by 50–99% as compared to other SIP and Protein-SIP approaches and thus enables isotope labeling experiments on much larger scales and with higher replication. The approach allows for the determination of isotope incorporation into microbiome members with species level resolution using standard metaproteomics liquid chromatography-tandem mass spectrometry (LC–MS/MS) measurements. At the core of the approach are new algorithms to analyze the data, which have been implemented in an open-source software ( https://sourceforge.net/projects/calis-p/ ). We demonstrate sensitivity, precision and accuracy using bacterial cultures and mock communities with different labeling schemes. Furthermore, we benchmark our approach against two existing Protein-SIP approaches and show that in the low labeling range used our approach is the most sensitive and accurate. Finally, we measure translational activity using 18 O heavy water labeling in a 63-species community derived from human fecal samples grown on media simulating two different diets. Activity could be quantified on average for 27 species per sample, with 9 species showing significantly higher activity on a high protein diet, as compared to a high fiber diet. Surprisingly, among the species with increased activity on high protein were several Bacteroides species known as fiber consumers. Apparently, protein supply is a critical consideration when assessing growth of intestinal microbes on fiber, including fiber-based prebiotics. Conclusions We demonstrate that our Protein-SIP approach allows for the ultra-sensitive (0.01 to 10% label) detection of stable isotopes of elements found in proteins, using standard metaproteomics data.
Impacts of secondary ice production on Arctic mixed-phase clouds based on ARM observations and CAM6 single-column model simulations
For decades, measured ice crystal number concentrations have been found to be orders of magnitude higher than measured ice-nucleating particle number concentrations in moderately cold clouds. This observed discrepancy reveals the existence of secondary ice production (SIP) in addition to the primary ice nucleation. However, the importance of SIP relative to primary ice nucleation remains highly unclear. Furthermore, most weather and climate models do not represent SIP processes well, leading to large biases in simulated cloud properties. This study demonstrates a first attempt to represent different SIP mechanisms (frozen raindrop shattering, ice–ice collisional breakup, and rime splintering) in a global climate model (GCM). The model is run in the single column mode to facilitate comparisons with the Department of Energy (DOE)'s Atmospheric Radiation Measurement (ARM) Mixed-Phase Arctic Cloud Experiment (M-PACE) observations. We show the important role of SIP in four types of clouds during M-PACE (i.e., multilayer, single-layer stratus, transition, and frontal clouds), with the maximum enhancement in ice crystal number concentrations up to 4 orders of magnitude in moderately supercooled clouds. We reveal that SIP is the dominant source of ice crystals near the cloud base for the long-lived Arctic single-layer mixed-phase clouds. The model with SIP improves the occurrence and phase partitioning of the mixed-phase clouds, reverses the vertical distribution pattern of ice number concentrations, and provides a better agreement with observations. The findings of this study highlight the importance of considering SIP in GCMs.
A New Look at the Environmental Conditions Favorable to Secondary Ice Production
This study attempts a new identification of mechanisms of secondary ice production (SIP) based on the observation of small faceted ice crystals (hexagonal plates or columns) with typical sizes smaller than 100µm. Due to their young age, such small ice crystals can be used as tracers for identifying the conditions for SIP. Observations reported here were conducted in oceanic tropical mesoscale convective systems (MCSs) and midlatitude frontal clouds in the temperature range from 0 to −15◦C and heavily seeded by aged ice particles. It was found that in both MCSs and frontal clouds, SIP was observed right above the melting layer and extended to higher altitudes with colder temperatures. The roles of six possible mechanisms to generate the SIP particles are assessed using additional observations. In most observed SIP cases, small secondary ice particles spatially correlated with liquid-phase, vertical updrafts and aged rimed ice particles. However, in many cases, neither graupel nor liquid drops were observed in the SIP regions, and therefore, the conditions for an active Hallett–Mossop process were not met. In many cases, large concentrations of small pristine ice particles were observed right above the melting layer, starting at temperatures as warm as −0.5◦C. It is proposed that the initiation of SIP above the melting layer is stimulated by the recirculation of large liquid drops through the melting layer with convective turbulent updrafts. After re-entering a super cooled environment above the melting layer, they impact with aged ice, freeze, and shatter. The size of the splinters generated during SIP was estimated as 10µm or less. A principal conclusion of this work is that only the freezing drop-shattering mechanism could be clearly supported by the airborne in situ observations.
Characterizing leaf-scale fluorescence with spectral invariants
Sun-induced chlorophyll fluorescence (SIF) is increasingly recognized as a non-destructive probe for tracking terrestrial photosynthesis. Emerging developments in spectral invariants theory provide an innovative and efficient approach for representing SIF radiative transfer processes at the canopy scale. However, modeling leaf-scale fluorescence based on the spectral invariants properties (SIP) remains underexplored. In this study, the spectral invariants theory is employed for the first time to model the leaf-scale total, backward and forward fluorescence (leaf-SIP SIF). The leaf-SIP SIF model separates the leaf-scale radiative transfer process into two distinct components: the wavelength-dependent one associated with leaf biochemical properties, and the wavelength-independent component linked to leaf structural characteristics. The leaf structure-related effects are characterized by two spectrally invariant parameters: the photon recollision probability (p) and the scattering asymmetry parameter (q), which are parameterized using the directly measurable leaf dry matter. Evaluation against field measurements shows that the proposed leaf-SIP SIF model has a good performance, with coefficient of determination (R 2 ) of 0.89, 0.89, 0.90 and root mean squared errors (RMSE) of 1.28, 0.69, 0.74 Wm -2 µm -1 sr -1 , respectively for the total, backward, and forward fluorescence (660–800 nm). The leaf-SIP SIF model with a more concise formulation demonstrates comparable performance with the widely used Fluspect model. Further, the leaf-SIP SIF model provides a simple and efficient approach for simulating leaf-scale fluorescence, with the potential to be integrated into a unified SIP-based model framework for simulating the radiative transfer processes across the soil-leaf-canopy-atmosphere continuum.
Cloud-Resolving ICON Simulations of Secondary Ice Production in Arctic Mixed-Phase Stratocumuli Observed during M-PACE
Field measurements and modeling studies suggest that secondary ice production (SIP) may close the gap between observed Arctic ice nucleating particle (INP) concentrations and ice crystal number concentrations ni. Here, we explore sensitivities with respect to the complexity of different INP parameterizations under the premise that ni is governed by SIP. Idealized, cloud-resolving simulations are performed for the marine cold air outbreak cloud deck sampled during the Mixed-Phase Arctic Cloud Experiment (M-PACE) with the Icosahedral Nonhydrostatic (ICON) model. The impact of the droplet shattering (DS) of raindrops and collisional breakup (BR) in addition to the existing Hallet–Mossop rime splintering mechanism were investigated. Overall, 12 different model experiments (12-h runs) were performed and analyzed. Despite the considerable amount of uncertainty remaining with regard to SIP mechanisms and their process representation in numerical models, we conclude from these experiments that (i) only simulations where DS dominates the SIP signal (potentially amplified by BR) capture observed ice-phase and liquid-phase cloud properties, and (ii) SIP events cluster around the convective outflow region and are structurally linked to mesoscale cloud organization. In addition, interactions with primary nucleation parameterizations of varied complexity were investigated. Here, our simulations show that (i) a stable long-lived mixed-phase cloud (MPC) can be maintained in the absence of primary nucleation once SIP is established, (ii) experiments using a computationally more efficient relaxation-based parameterization of primary nucleation are statistically invariant from simulations considering prognostic INP, and (iii) primary nucleation at cloud-top controls the areal extent of the mixed-phase cloud region, and reduces SIP efficacy via DS due to increased depletion of cloud liquid throughout the entire cloud column.
Sensitivity of Arctic Clouds to Ice Microphysical Processes in the NorESM2 Climate Model
Abstract Ice formation remains one of the most poorly represented microphysical processes in climate models. While primary ice production (PIP) parameterizations are known to have a large influence on the modeled cloud properties, the representation of secondary ice production (SIP) is incomplete and its corresponding impact is therefore largely unquantified. Furthermore, ice aggregation is another important process for the total cloud ice budget, which also remains largely unconstrained. In this study, we examine the impact of PIP, SIP, and ice aggregation on Arctic clouds, using the Norwegian Earth System Model, version 2 (NorESM2). Simulations with both prognostic and diagnostic PIP show that heterogeneous freezing alone cannot reproduce the observed cloud ice content. The implementation of missing SIP mechanisms (collisional breakup, drop shattering, and sublimation breakup) in NorESM2 improves the modeled ice properties, while improvements in liquid content occur only in simulations with prognostic PIP. However, results are sensitive to the description of collisional breakup. This mechanism, which dominates SIP in the examined conditions, is very sensitive to the treatment of the sublimation correction factor, a poorly constrained parameter that is included in the utilized parameterization. Finally, variations in ice aggregation treatment can also significantly impact cloud properties, mainly through their impact on collisional breakup efficiency. Overall, enhancement in ice production through the addition of SIP mechanisms and the reduction in ice aggregation (in line with radar observations of shallow Arctic clouds) result in enhanced cloud cover and decreased TOA radiation biases, compared to satellite measurements, especially during the cold months. Significance Statement Arctic clouds remain a large source of uncertainty in projections of the future climate due to the poor representation of the microphysical processes that govern their life cycle. Ice formation is among the least understood processes. While it is widely recognized that better constraints on primary ice production (PIP) are needed to improve existing parameterizations, we show that secondary ice production (SIP) and ice aggregation can have also a significant impact on ice number concentrations. Constraining ice formation through the addition of missing SIP mechanisms and reducing ice aggregation can improve the representation of the cloud macrophysical properties and enhance total cloud cover in the Arctic region, which in turn contributes to decreased TOA radiation biases in the cold months.