Showing papers by "Environmental Molecular Sciences Laboratory published in 2022"

Micro-spectroscopic and freezing characterization of ice-nucleating particles collected in the marine boundary layer in the eastern North Atlantic

Abstract: Abstract. Formation of atmospheric ice plays a crucial role in the microphysical evolution of mixed-phase and cirrus clouds and thus climate. How aerosol particles impact ice crystal formation by acting as ice-nucleating particles (INPs) is a subject of intense research activities. To improve understanding of atmospheric INPs, we examined daytime and nighttime particles collected during the Aerosol and Cloud Experiments in the Eastern North Atlantic (ACE-ENA) field campaign conducted in summer 2017. Collected particles, representative of a remote marine environment, were investigated for their propensity to serve as INPs in the immersion freezing (IMF) and deposition ice nucleation (DIN) modes. The particle population was characterized by chemical imaging techniques such as computer-controlled scanning electron microscopy with energy-dispersive X-ray analysis (CCSEM/EDX) and scanning transmission X-ray microscopy with near-edge X-ray absorption fine-structure spectroscopy (STXM/NEXAFS). Four major particle-type classes were identified where internally mixed inorganic–organic particles make up the majority of the analyzed particles. Following ice nucleation experiments, individual INPs were identified and characterized by SEM/EDX. The identified INP types belong to the major particle-type classes consisting of fresh sea salt with organics or processed sea salt containing dust and sulfur with organics. Ice nucleation experiments show IMF events at temperatures as low as 231 K, including the subsaturated regime. DIN events were observed at lower temperatures of 210 to 231 K. IMF and DIN observations were analyzed with regard to activated INP fraction, ice-nucleation active site (INAS) densities, and a water activity-based immersion freezing model (ABIFM) yielding heterogeneous ice nucleation rate coefficients. Observed IMF and DIN events of ice formation and corresponding derived freezing rates demonstrate that the marine boundary layer aerosol particles can serve as INPs under typical mixed-phase and cirrus cloud conditions. The derived IMF and DIN parameterizations allow for implementation in cloud and climate models to evaluate predictive effects of atmospheric ice crystal formation.

MetaboDirect: An Analytical Pipeline for the processing of FTICR-MS-based Metabolomics Data

Abstract: ABSTRACT Background Microbiomes are now recognized as main drivers of ecosystem function ranging from the oceans and soils to humans and bioreactors. However, a grand challenge in microbiome science is to characterize and quantify the chemical currencies of organic matter (i.e. metabolites) that microbes respond to and alter. Critical to this has been the development of Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS), which has drastically increased molecular characterization of complex organic matter samples, but challenges users with hundreds of millions of data points where readily available, user-friendly, and customizable software tools are lacking. Results Here, we build on years of analytical experience with diverse sample types to develop MetaboDirect, an open-source, command-line based pipeline for the analysis, visualization, and presentation of metabolomics data by direct injection FTICR-MS after molecular formula assignment has been performed. When compared to all other available FTICR software, MetaboDirect is superior with respect to its compute time as it only requires a single line of code that launches a fully automated framework for the generation and visualization of a wide range of plots, with minimal coding experience required. Among the tools evaluated, MetaboDirect is also uniquely able to automatically generate biochemical transformation networks ( ab initio ) based on mass differences that provide a comprehensive experimental assessment of metabolite connectives within a given sample or a complex metabolic system, thereby providing important information about the nature of the samples and the set of the microbial reactions or pathways that gave rise to them. Finally, for more experienced users, MetaboDirect allows users to customize plots, outputs, and analyses. Conclusion Application of MetaboDirect to FTICR-MS-based metabolomics datasets from a marine phage-bacterial infection experiment and a Sphagnum leachate microbiome incubation experiment showcase the exploration capabilities of the pipeline that will enable the FTICR-MS research community to evaluate and interpret their data in greater depth and in less time. It will further advance our knowledge of how microbial communities influence and are influenced by the chemical makeup of the surrounding system. Source code and User’s guide of MetaboDirect are freely available through ( https://github.com/Coayala/MetaboDirect ) and ( https://metabodirect.readthedocs.io/en/latest/ ) respectively.

African Smoke Particles Act as Cloud Condensation Nuclei in the Wintertime Tropical North Atlantic Boundary Layer over Barbados

Abstract: Abstract. The number concentration and properties of aerosol particles serving as cloud condensation nuclei (CCN) are important for understanding cloud formation, particularly in the tropical Atlantic marine boundary layer (MBL) where marine cumulus clouds reflect incoming solar radiation and obscure the low-albedo ocean surface. Studies linking aerosol source, composition, and water uptake properties in this region have been conducted primarily during summertime dust transport, despite the region receiving a variety of aerosol particle types throughout the year. In this study, we compare size-resolved aerosol chemical composition data to the hygroscopicity parameter κ derived from size-resolved CCN measurements made during the EUREC4A and ATOMIC campaigns from January to February 2020. We observed unexpected periods of wintertime long-range transport of African smoke and dust to Barbados. During these periods, the accumulation mode aerosol particle and CCN number concentrations as well as the proportions of dust and smoke particles increased while the average κ slightly decreased (κ = 0.45+0.1) from marine background conditions (κ = 0.52+0.08) when the particles were mostly composed of marine organics and sulfate. Size-resolved chemical analysis shows that smoke particles were the major contributor to the accumulation mode aerosol during long-range transport events, indicating that smoke is mainly responsible for the observed increase in CCN number concentrations. Earlier studies conducted at Barbados have mostly focused on the role of dust on CCN, but our results show that aerosol hygroscopicity and CCN number concentrations during wintertime long-range transport events over the tropical North Atlantic are affected by African smoke more than dust. Our findings highlight the importance of African smoke for atmospheric processes and cloud formation over the Caribbean.

Reply on RC1

Abstract: Abstract. Free tropospheric aerosol particles have important but poorly constrained climate effects due to transformations of their physicochemical properties during long-range transport. In this study, we investigate the chemical composition and provide an overview of the phase states of individual particles that have undergone long-range transport over the North Atlantic Ocean in June and July 2014, 2015, and 2017 to the Observatory of Mount Pico (OMP) in the Azores. The OMP is an ideal site for studying long-range-transported free tropospheric particles because local emissions have a negligible influence and contributions from the boundary layer are rare. We used the FLEXible PARTicle Lagrangian particle dispersion model (FLEXPART) to determine the origins and transport trajectories of sampled air masses and found that most of them originated from North America and recirculated over the North Atlantic Ocean. The FLEXPART analysis showed that the sampled air masses were highly aged (average plume age >10 d). Size-resolved chemical compositions of individual particles were probed using computer-controlled scanning electron microscopy with an energy-dispersive X-ray spectrometer (CCSEM-EDX) and scanning transmission X-ray microscopy with near-edge X-ray absorption fine structure spectroscopy (STXM-NEXAFS). CCSEM-EDX results showed that the most abundant particle types were carbonaceous (∼ 29.9 % to 82.0 %), sea salt (∼ 0.3 % to 31.6 %), and sea salt with sulfate (∼ 2.4 % to 31.5 %). We used a tilted stage interfaced within an environmental scanning electron microscope (ESEM) to determine the phase states of individual submicron particles. We found that most particles (∼ 47 % to 99 %) were in the liquid state at the time of collection due to inorganic inclusions. Moreover, we also observed substantial fractions of solid and semisolid particles (∼ 0 % to 30 % and ∼ 1 % to 42 %, respectively) during different transport patterns and events, reflecting the particles' phase-state variability for different atmospheric transport events and sources. Combining phase state measurements with FLEXPART CO tracer analysis, we found that wildfire-influenced plumes can result in particles with a wide range of viscosities after long-range transport in the free troposphere. We also used temperature and RH values extracted from the Global Forecast System (GFS) along the FLEXPART-simulated path to predict the phase state of the particles during transport and found that neglecting internal mixing with inorganics would lead to an overestimation of the viscosity of free tropospheric particles. Our findings warrant future investigation aiming at the quantitative assessment of the influence of internal mixing on the phase states of the individual particles. This study also provides insights into the chemical composition and phase state of free tropospheric particles, which can help models to reduce uncertainties about the effects of ambient aerosol particles on climate.

Reply on RC2

Abstract: Abstract. Free tropospheric aerosol particles have important but poorly constrained climate effects due to transformations of their physicochemical properties during long-range transport. In this study, we investigate the chemical composition and provide an overview of the phase states of individual particles that have undergone long-range transport over the North Atlantic Ocean in June and July 2014, 2015, and 2017 to the Observatory of Mount Pico (OMP) in the Azores. The OMP is an ideal site for studying long-range-transported free tropospheric particles because local emissions have a negligible influence and contributions from the boundary layer are rare. We used the FLEXible PARTicle Lagrangian particle dispersion model (FLEXPART) to determine the origins and transport trajectories of sampled air masses and found that most of them originated from North America and recirculated over the North Atlantic Ocean. The FLEXPART analysis showed that the sampled air masses were highly aged (average plume age >10 d). Size-resolved chemical compositions of individual particles were probed using computer-controlled scanning electron microscopy with an energy-dispersive X-ray spectrometer (CCSEM-EDX) and scanning transmission X-ray microscopy with near-edge X-ray absorption fine structure spectroscopy (STXM-NEXAFS). CCSEM-EDX results showed that the most abundant particle types were carbonaceous (∼ 29.9 % to 82.0 %), sea salt (∼ 0.3 % to 31.6 %), and sea salt with sulfate (∼ 2.4 % to 31.5 %). We used a tilted stage interfaced within an environmental scanning electron microscope (ESEM) to determine the phase states of individual submicron particles. We found that most particles (∼ 47 % to 99 %) were in the liquid state at the time of collection due to inorganic inclusions. Moreover, we also observed substantial fractions of solid and semisolid particles (∼ 0 % to 30 % and ∼ 1 % to 42 %, respectively) during different transport patterns and events, reflecting the particles' phase-state variability for different atmospheric transport events and sources. Combining phase state measurements with FLEXPART CO tracer analysis, we found that wildfire-influenced plumes can result in particles with a wide range of viscosities after long-range transport in the free troposphere. We also used temperature and RH values extracted from the Global Forecast System (GFS) along the FLEXPART-simulated path to predict the phase state of the particles during transport and found that neglecting internal mixing with inorganics would lead to an overestimation of the viscosity of free tropospheric particles. Our findings warrant future investigation aiming at the quantitative assessment of the influence of internal mixing on the phase states of the individual particles. This study also provides insights into the chemical composition and phase state of free tropospheric particles, which can help models to reduce uncertainties about the effects of ambient aerosol particles on climate.

Reviews and syntheses: Use and misuse of peak intensities from high resolution mass spectrometry in organic matter studies: opportunities for robust usage

Abstract: Abstract. Earth’s biogeochemical cycles are intimately tied to the biotic and abiotic processing of organic matter (OM). Spatial and temporal variation in OM chemistry is often studied using high resolution mass spectrometry (HRMS). An increasingly common approach is to use ecological metrics (e.g., within-sample diversity) to summarize high-dimensional HRMS data, notably Fourier transform ion cyclotron resonance MS (FTICR MS). However, problems arise when HRMS peak intensity data are used in a way that is analogous to abundances in ecological analyses (e.g., species abundance distributions). Using peak intensity data in this way requires the assumption that intensities act as direct proxies for concentrations, which is often invalid. Here we discuss theoretical expectations and provide empirical evidence why concentrations do not map to HRMS peak intensities. The theory and data show that comparisons of the same peak across samples (within-peak) may carry information regarding variation in relative concentration, but comparing different peaks (between-peak) within or between samples does not. We further developed a simulation model to study the quantitative implications of both within-peak and between-peak errors that decouple concentration from intensity. These implications are studied in terms of commonly used ecological metrics that quantify different aspects of diversity and functional trait values. We show that despite the poor linkages between concentration and intensity, the ecological metrics often perform well in terms of providing robust qualitative inferences and sometimes quantitatively-accurate estimates of diversity and trait values. We conclude with recommendations for using peak intensities in an informed and robust way for natural organic matter studies. A primary recommendation is the use and extension of the simulation model to provide objective, quantitative guidance on the degree to which conceptual and quantitative inferences can be made for a given analysis of a given dataset. Without objective guidance, researchers that use peak intensities are doing so with unknown levels of uncertainty and bias, potentially leading to spurious scientific outcomes.

Elemental Co-localization of Nutrients, C, Al, and Fe in Soil Minerals with Electron Microscopy and Scatterplot-matrix Analysis

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Micro-spectroscopic and freezing characterization of ice-nucleating particles collected in the marine boundary layer in the Eastern North Atlantic

Abstract: Abstract. Formation of atmospheric ice plays a crucial role in the microphysical evolution of mixed-phase and cirrus clouds and thus climate. How aerosol particles impact ice crystal formation by acting as ice-nucleating particles (INPs) is a subject of intense research activities. To improve understanding of atmospheric INPs, we examined daytime and nighttime particles collected during the Aerosol and Cloud Experiments in the Eastern North Atlantic (ACE-ENA) field campaign conducted in summer 2017. Collected particles, representative of a remote marine environment, were investigated for their propensity to serve as INPs in the immersion freezing (IMF) and deposition ice nucleation (DIN) modes. The particle population was characterized by chemical imaging techniques such as computer-controlled scanning electron microscopy with energy dispersive X-ray analysis (CCSEM/EDX) and scanning transmission X-ray microscopy with near-edge X-ray absorption fine structure spectroscopy (STXM/NEXAFS). Four major particle-type classes were identified where internally mixed inorganic-organic particles make up the majority of the analyzed particles. Following ice nucleation experiments, individual INPs were identified and characterized by SEM/EDX. The identified INP types belong to the major particle-type classes consisting of fresh sea salt with organics or processed sea salt containing dust and sulfur with organics. Ice nucleation experiments show IMF events at temperatures as low as 231 K including the subsaturated regime. DIN events were observed at lower temperatures of 210 to 231 K. IMF and DIN observations were analyzed with regard to activated INP fraction, ice-nucleation active sites (INAS) densities, and water activity-based immersion freezing model (ABIFM) yielding heterogeneous ice nucleation rate coefficients. Observed IMF and DIN events of ice formation and corresponding derived freezing rates demonstrate the marine boundary layer aerosol particles can serve as INPs under typical mixed-phase and cirrus clouds conditions. The derived IMF and DIN parameterizations allow for implementation in cloud and climate models to evaluate predictive effects of atmospheric ice crystal formation.

Physicochemical properties of atmospheric aerosols and their effect on ice cloud formation

Abstract: Atmospheric aerosols play a vital role in the Earth's energy budget-directly by scattering and absorbing solar radiation and indirectly by acting as cloud condensation nuclei and ice-nucleating particles [1, 2]. The cloud formation potential of aerosol is driven by multiple factors, including surface properties, size distribution, composition, mixing state, phase state, and morphology [3]. The interaction of aerosols with clouds alters the aerosol's physicochemical properties. Those properties can also evolve during transport due to atmospheric processing, in turn, affect the aerosol's ice nucleation and cloud formation activities. This thesis presents experimental studies to understand the role of physicochemical properties of aerosol on the formation of ice. To get a detailed understanding of the aerosol effect on ice nucleation, we conducted controlled ice nucleation experiments on a known surface (muscovite mica) with controlled properties (e.g., surface cations) as well as ice nucleation experiments on complex atmospheric particles, which were characterized with multimodal microspectroscopic techniques. The results from controlled experiments suggest that the ice nucleation activity of a surface can be modified by simply changing the surface cations. In contrast, ice nucleation experiments with complex atmospheric particles indicates a more complicated dependence on the physicochemical properties.

Reply on RC3

Abstract: Abstract. Free tropospheric aerosol particles have important but poorly constrained climate effects due to transformations of their physicochemical properties during long-range transport. In this study, we investigate the chemical composition and provide an overview of the phase states of individual particles that have undergone long-range transport over the North Atlantic Ocean in June and July 2014, 2015, and 2017 to the Observatory of Mount Pico (OMP) in the Azores. The OMP is an ideal site for studying long-range-transported free tropospheric particles because local emissions have a negligible influence and contributions from the boundary layer are rare. We used the FLEXible PARTicle Lagrangian particle dispersion model (FLEXPART) to determine the origins and transport trajectories of sampled air masses and found that most of them originated from North America and recirculated over the North Atlantic Ocean. The FLEXPART analysis showed that the sampled air masses were highly aged (average plume age >10 d). Size-resolved chemical compositions of individual particles were probed using computer-controlled scanning electron microscopy with an energy-dispersive X-ray spectrometer (CCSEM-EDX) and scanning transmission X-ray microscopy with near-edge X-ray absorption fine structure spectroscopy (STXM-NEXAFS). CCSEM-EDX results showed that the most abundant particle types were carbonaceous (∼ 29.9 % to 82.0 %), sea salt (∼ 0.3 % to 31.6 %), and sea salt with sulfate (∼ 2.4 % to 31.5 %). We used a tilted stage interfaced within an environmental scanning electron microscope (ESEM) to determine the phase states of individual submicron particles. We found that most particles (∼ 47 % to 99 %) were in the liquid state at the time of collection due to inorganic inclusions. Moreover, we also observed substantial fractions of solid and semisolid particles (∼ 0 % to 30 % and ∼ 1 % to 42 %, respectively) during different transport patterns and events, reflecting the particles' phase-state variability for different atmospheric transport events and sources. Combining phase state measurements with FLEXPART CO tracer analysis, we found that wildfire-influenced plumes can result in particles with a wide range of viscosities after long-range transport in the free troposphere. We also used temperature and RH values extracted from the Global Forecast System (GFS) along the FLEXPART-simulated path to predict the phase state of the particles during transport and found that neglecting internal mixing with inorganics would lead to an overestimation of the viscosity of free tropospheric particles. Our findings warrant future investigation aiming at the quantitative assessment of the influence of internal mixing on the phase states of the individual particles. This study also provides insights into the chemical composition and phase state of free tropospheric particles, which can help models to reduce uncertainties about the effects of ambient aerosol particles on climate.

Overall protocol for MicroPOTS LCMS top down proteomics of kidney tissue sections v1

Abstract: This is the overall workflow for LCMS top down proteomics of kidney functional units from tissue sections using the MicroPOTS platform. The expected outcomes are proteoform identification and quantitation values from selected tissue functional units.

Reply on EC1

Abstract: Free tropospheric aerosol particles have important but poorly constrained climate effects due to transformations of their physicochemical properties during long-range transport. In this study, we investigated the chemical composition and provided an overview of the phase state of individual particles that have been long-range transported over the North Atlantic Ocean in June and July 2014, 2015, and 2017 to the Observatory of Mount Pico (OMP), in the Azores. OMP is an ideal site for studying long-range transported free tropospheric particles with negligible influence from local emissions and rare contributions from the boundary layer. We used the FLEXible PARTicle Lagrangian particle dispersion model (FLEXPART) to determine the origin and transport trajectories of sampled air masses and found that most originated from North America and recirculated over the North Atlantic Ocean. The FLEXPART analysis show that the sampled air masses were highly aged (average plume age > 10 days). Size-resolved chemical compositions of individual particles were probed using computer-controlled scanning electron microscopy with an energy dispersive X-ray spectrometer (CCSEM-EDX) and scanning transmission X-ray microscopy with near-edge X-ray absorption fine structure spectroscopy (STXM-NEXAFS). CCSEM-EDX results show that the most abundant particle types were carbonaceous (~29.9 to 82.0 %), sea salt (~0.3 to 31.6 %), and sea salt with sulfate (~2.4 to 31.5 %). We used a tilted stage interfaced within an Environmental Scanning Electron Microscope (ESEM) to determine the phase state of individual submicron particles. We found that most particles (~47 to 99 %) were in the liquid state at the time of collection due to inorganic inclusions. Moreover, we also observed a substantial fraction of solid and semisolid particles (~0 to 30 % and ~1 to 42 %, respectively) during different transport patterns/events, reflecting the particles' phase state variability for different atmospheric transport events and sources. Combining phase state measurements with FLEXPART CO tracer analysis, we found that wildfire-influenced plumes can result in particles with a wide range of viscosities after long-range transport in the free troposphere. We also used temperature and RH values extracted from the Global Forecast System (GFS) along the FLEXPART simulated path to predict the phase state of the particles during transport and found that neglecting internal mixing with inorganics would overestimate the viscosity of free tropospheric particles. Our findings warrant future investigation on the quantitative assessment of the influence of internal mixing on the phase state of the individual particles. This study also provides insights into the chemical composition and phase state of free tropospheric particles, which can benefit models to reduce uncertainties in ambient aerosol particles' effects on climate.

Overall protocol for MicroPOTS LCMS top down proteomics of pancreas tissue sections v1

Abstract: This is the overall workflow for LCMS top down proteomics of pancreas functional units from tissue sections using the MicroPOTS platform. The expected outcomes are proteoform identification and quantitation values from selected tissue functional units.

Atmospheric particle abundance and sea salt aerosol observations in the springtime Arctic: a focus on blowing snow and leads

Abstract: Abstract. Sea salt aerosols play an important role in the radiation budget and atmospheric composition over the Arctic, where the climate is rapidly changing. Previous observational studies have shown Arctic sea ice leads to be an important source of sea salt aerosols, and modeling efforts have also proposed blowing snow sublimation as a source. In this study, size-resolved atmospheric particle number concentrations and chemical composition were measured at the Arctic coastal tundra site of Utqiaġvik, Alaska during spring (April 3 – May 7, 2016). Blowing snow conditions were observed during 25 % of the five-week study period and were over-predicted by a commonly used blowing snow parameterization based solely on wind speed and temperature. Throughout the study, open leads were present locally. During periods when blowing snow was observed, significant increases in the number concentrations of 0.01–0.06 μm particles (factor of six, on average) and 0.06–0.3 μm particles (67 %, on average), and a significant decrease (82 %, on average) in 1–4 μm particles, were observed, compared to low wind speed periods. These size distribution changes were likely caused by the generation of ultrafine particles from leads and/or blowing snow, with scavenging of supermicron particles by blowing snow. At elevated wind speeds, both submicron and supermicron sodium and chloride mass concentrations were enhanced, consistent with wind-dependent local sea salt aerosol production. At moderate wind speeds below the threshold for blowing snow, as well as during observed blowing snow, individual sea spray aerosol particles were measured. These individual salt particles were enriched in calcium relative to sodium in seawater, due to the binding of this divalent cation with organic matter in the sea surface microlayer and subsequent enrichment during seawater bubble bursting. The chemical composition of the surface snowpack also showed contributions from sea spray aerosol deposition. Overall, these results show the contribution of sea spray aerosol production from leads on both aerosols and the surface snowpack. Therefore, if blowing snow sublimation contributed to the observed sea salt aerosol, the snow being sublimed must have been impacted by sea spray aerosol deposition, rather than upward brine migration through the snowpack. Sea spray aerosol production from leads is expected to increase, with thinning and fracturing of sea ice in the rapidly warming Arctic.