An evaluation of static ToF-SIMS analysis of environmental organics

Time-of-flight secondary ion mass spectrometry (ToF-SIMS) has been extensively used in surface analysis due to its high mass resolution, sensitivity, and mass spectral imaging capabilities. Static ToF-SIMS has mainly been used for solid material analysis; however, its application in environmental organics is limited. During SIMS spectral analysis, relative mass accuracy and measurement repeatability are key factors for obtaining reliable speciation and acquiring chemical insights of the specimens. Herein, we provide an evaluation of four environmentally relevant organic systems, including glyoxal, pyruvic acid, oil-in-water emulsion, and carbon dioxide (CO2) capture solvent (i.e., N-2-ethoxyethyl-3-morpholinopropan-1-amine, EMMPA), to show the spectral measurement repeatability when using static ToF-SIMS. First, sample preparation is essential in acquiring accurate and reproducible results in ToF-SIMS analysis. The mass spectral results show that characteristic peaks observed can be distinguished with reasonable confidence by comparing the observed mass to charge ratios (m/z) to theoretical ones. The statistical analysis of peak areas indicates that the peak area and/or peak height measurement ratios are satisfactory among replicates. Compared with previous studies, the bismuth cluster primary ion beam, namely Bi3 +, has less fragmentation than Bi+. Therefore, Bi3 + is deemed more suitable for organic analysis using static SIMS. Our results show that ToF-SIMS offers a viable approach to study environmental organics including but not limited to aqueous aerosols, wastewater emulsions, and CO2 capture solvents. It is expected that future studies will expand organic speciation with high fidelity due to the continued advancement of SIMS as a sensitive analysis technique.

Machine Learning Model Construction and Testing: Anticipating Cancer Incidence and Mortality

In recent years, the escalating environmental challenges have contributed to a rising incidence of cancer. The precise anticipation of cancer incidence and mortality rates has emerged as a pivotal focus in scientific inquiry, exerting a profound impact on the formulation of public health policies. This investigation adopts a pioneering machine learning framework to address this critical issue, utilizing a dataset encompassing 72,591 comprehensive records that include essential variables such as age, case count, population size, race, gender, site, and year of diagnosis. Diverse machine learning algorithms, including decision trees, random forests, logistic regression, support vector machines, and neural networks, were employed in this study. The ensuing analysis revealed testing accuracies of 62.17%, 61.92%, 54.53%, 55.72%, and 62.30% for the respective models. This state-of-the-art model not only enhances our understanding of cancer dynamics but also equips researchers and policymakers with the capability of making meticulous projections concerning forthcoming cancer incidence and mortality rates. Considering sustainability, the application of this advanced machine learning framework emphasizes the importance of judiciously utilizing extensive and intricate databases. By doing so, it facilitates a more sustainable approach to healthcare planning, allowing for informed decision-making that takes into account the long-term ecological and societal impacts of cancer-related policies. This integrative perspective underscores the broader commitment to sustainable practices in both health research and public policy formulation.

Metabolic insights from mass spectrometry imaging of biofilms: A perspective from model microorganisms

Biofilms are dense aggregates of bacterial colonies embedded inside a self-produced polymeric matrix. Biofilms have received increasing attention in medical, industrial, and environmental settings due to their enhanced survival. Their characterization using microscopy techniques has revealed the presence of structural and cellular heterogeneity in many bacterial systems. However, these techniques provide limited chemical detail and lack information about the molecules important for bacterial communication and virulence. Mass spectrometry imaging (MSI) bridges the gap by generating spatial chemical information with unmatched chemical detail, making it an irreplaceable analytical platform in the multi-modal imaging of biofilms. In the last two decades, over 30 species of biofilm-forming bacteria have been studied using MSI in different environments. The literature conveys both analytical advancements and an improved understanding of the effects of environmental variables such as host surface characteristics, antibiotics, and other species of microorganisms on biofilms. This review summarizes the insights from frequently studied model microorganisms. We share a detailed list of organism-wide metabolites, commonly observed mass spectral adducts, culture conditions, strains of bacteria, substrate, broad problem definition, and details of the MS instrumentation, such as ionization sources and matrix, to facilitate future studies. We also compared the spatial characteristics of the secretome under different study designs to highlight changes because of various environmental influences. In addition, we highlight the current limitations of MSI in relation to biofilm characterization to enable cross-comparison between experiments. Overall, MSI has emerged to become an important approach for the spatial/chemical characterization of bacterial biofilms and its use will continue to grow as MSI becomes more accessible.

A bibliography study of Shewanella oneidensis biofilm

This study employs a bibliography study method to evaluate 472 papers focused on Shewanella oneidensis biofilms. Biofilms, which are formed when microorganisms adhere to surfaces or interfaces, play a crucial role in various natural, engineered, and medical settings. Within biofilms, microorganisms are enclosed in extracellular polymeric substances (EPS), creating a stable working environment. This characteristic enhances the practicality of biofilm-based systems in natural bioreactors, as they are less susceptible to temperature and pH fluctuations compared to enzyme-based bioprocesses. Shewanella oneidensis, a nonpathogenic bacterium with the ability to transfer electrons, serves as an example of a species isolated from its environment that exhibits extensive biofilm applications. These applications, such as heavy metal removal, offer potential benefits for environmental engineering and human health. This paper presents a comprehensive examination and review of the biology and engineering aspects of Shewanella biofilms, providing valuable insights into their functionality.

Mass Spectral Imaging to Map Plant-Microbe Interactions

Plant-microbe interactions are of rising interest in plant sustainability, biomass production, plant biology, and systems biology. These interactions have been a challenge to detect until recent advancements in mass spectrometry imaging. Plants and microbes interact in four main regions within the plant, the rhizosphere, endosphere, phyllosphere, and spermosphere. This mini review covers the challenges within investigations of plant and microbe interactions. We highlight the importance of sample preparation and comparisons among time-of-flight secondary ion mass spectroscopy (ToF-SIMS), matrix-assisted laser desorption/ionization (MALDI), laser desorption ionization (LDI/LDPI), and desorption electrospray ionization (DESI) techniques used for the analysis of these interactions. Using mass spectral imaging (MSI) to study plants and microbes offers advantages in understanding microbe and host interactions at the molecular level with single-cell and community communication information. More research utilizing MSI has emerged in the past several years. We first introduce the principles of major MSI techniques that have been employed in the research of microorganisms. An overview of proper sample preparation methods is offered as a prerequisite for successful MSI analysis. Traditionally, dried or cryogenically prepared, frozen samples have been used; however, they do not provide a true representation of the bacterial biofilms compared to living cell analysis and chemical imaging. New developments such as microfluidic devices that can be used under a vacuum are highly desirable for the application of MSI techniques, such as ToF-SIMS, because they have a subcellular spatial resolution to map and image plant and microbe interactions, including the potential to elucidate metabolic pathways and cell-to-cell interactions. Promising results due to recent MSI advancements in the past five years are selected and highlighted. The latest developments utilizing machine learning are captured as an important outlook for maximal output using MSI to study microorganisms.

Revealing the Bacterial Quorum-Sensing Effect on the Biofilm Formation of Diatom Cylindrotheca sp. Using Multimodal Imaging

Diatoms contribute to carbon fixation in the oceans by photosynthesis and always form biofouling organized by extracellular polymeric substances (EPS) in the marine environment. Bacteria-produced quorum-sensing signal molecules N-acyl homoserine lactones (AHLs) were found to play an important role in the development of Cylindrotheca sp. in previous studies, but the EPS composition change was unclear. This study used the technology of alcian blue staining and scanning electron microscopy (SEM), confocal laser scanning microscopy (CLSM), and time-of-flight secondary ion mass spectrometry (ToF-SIMS) to directly observe the biofilm formation process. The results showed that AHLs promote the growth rates of diatoms and the EPS secretion of biofilm components. AHLs facilitated the diatom-biofilm formation by a forming process dependent on the length of carbon chains. AHLs increased the biofilm thickness and the fluorescence intensity and then altered the three-dimensional (3D) structures of the diatom-biofilm. In addition, the enhanced EPS content in the diatom-biofilm testified that AHLs aided biofilm formation. This study provides a collection of new experimental evidence of the interaction between bacteria and microalgae in fouling biofilms.

Reducing the matrix effect in mass spectral imaging of biofilms using flow-cell culture

The interactions between soil microorganisms and soil minerals play a crucial role in the formation and evolution of minerals and the stability of soil aggregates. Due to the heterogeneity and diversity of the soil environment, the under-standing of the functions of bacterial biofilms in soil minerals at the microscale is limited. A soil mineral-bacterial biofilm system was used as a model in this study, and it was analyzed by time-of-flight secondary ion mass spectrometry (ToF-SIMS) to acquire molecular level information. Static culture in multi-wells and dynamic flow-cell culture in microfluidics of biofilms were investigated. Our results show that more characteristic molecules of biofilms can be observed in SIMS spectra of the flow-cell culture. In contrast, biofilm signature peaks are buried under the mineral components in SIMS spectra in the static culture case. Spectral overlay was used in peak selection prior to performing Principal component analysis (PCA). Comparisons of the PCA results between the static and flow-cell culture show more pronounced molecular features and higher loadings of organic peaks of the dynamic cultured specimens. For example, fatty acids secreted from bacterial biofilm extracellular polymeric substance are likely to be responsible for biofilm dispersal due to mineral treatment up to 48 h. Such findings suggest that the use of microfluidic cells to dynamically culture biofilms be a more suitable method for reducing the matrix effect arisen from the growth medium and minerals as a perturbation fac-tor for improved spectral and multivariate analysis of complex mass spectral data in ToF-SIMS. These results show that the interaction mechanism between biofilms and soil minerals at the molecular level can be better studied using the flow-cell culture and advanced mass spectral imaging techniques like ToF-SIMS.

Molecular Imaging Reveals Two Distinct Mixing States of PM2.5 Particles Sampled in a Typical Beijing Winter Pollution Case

Mixing states of aerosol particles are crucial for understanding the role of aerosols in influencing air quality and climate. However, a fundamental understanding of the complex mixing states is still lacking because most traditional analysis techniques only reveal bulk chemical and physical properties with limited surface and 3-D information. In this research, 3-D molecular imaging enabled by ToF-SIMS was used to elucidate the mixing states of PM_2.5 samples obtained from a typical Beijing winter haze event. In light pollution cases, a thin organic layer covers separated inorganic particles; while in serious pollution cases, ion exchange and an organic-inorganic mixing surface on large-area particles were observed. The new results provide key 3-D molecular information of mixing states, which is highly potential for reducing uncertainty and bias in representing aerosol-cloud interactions in current Earth System Models and improving the understanding of aerosols on air quality and human health.

Label-free sub-micrometer 3D imaging of ciprofloxacin in native-state biofilms with cryo-time-of-flight secondary ion mass spectrometry

High spatial resolution mass spectrometry imaging has been identified as a key technology needed to improve understanding of the chemical components that influence antibiotic resistance within biofilms, which are communities of micro-organisms that grow attached to a surface. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) offers the unique ability for label-free 3D imaging of organic molecules with sub-micrometer spatial resolution and high sensitivity. Several studies of biofilms have been done with the help of ToF-SIMS, but none of those studies have shown 3D imaging of antibiotics in native-state hydrated biofilms with cell-level resolution. Because ToF-SIMS measurements must be performed in a high-vacuum environment, cryogenic preparation and analysis are necessary to preserve the native biofilm structure and antibiotic spatial distribution during ToF-SIMS measurements. In this study, we have investigated the penetration of the antibiotic ciprofloxacin into Bacillus subtilis biofilms using sub-micrometer resolution 3D imaging cryo-ToF-SIMS. B. subtilis biofilms were exposed to physiologically relevant levels of ciprofloxacin. The treated biofilms were then plunge-frozen in liquid propane and analyzed with ToF-SIMS under cryogenic conditions. Multivariate analysis techniques, including multivariate curve resolution (MCR) and inverse maximum signal factor (iMSF) denoising, were used to aid analysis of the data and facilitate high spatial resolution 3D imaging of the biofilm, providing individually resolved cells and spatially resolved ciprofloxacin intensity at "real world" concentrations.

Molecular identification of wines using in situ liquid SIMS and PCA analysis

Composition analysis in wine is gaining increasing attention because it can provide information about the wine quality, source, and nutrition. In this work, in situ liquid secondary ion mass spectrometry (SIMS) was applied to 14 representative wines, including six wines manufactured by a manufacturer in Washington State, United States, four Cabernet Sauvignon wines, and four Chardonnay wines from other different manufacturers and locations. In situ liquid SIMS has the unique advantage of simultaneously examining both organic and inorganic compositions from liquid samples. Principal component analysis (PCA) of SIMS spectra showed that red and white wines can be clearly differentiated according to their aromatic and oxygen-contained organic species. Furthermore, the identities of different wines, especially the same variety of wines, can be enforced with a combination of both organic and inorganic species. Meanwhile, in situ liquid SIMS is sample-friendly, so liquid samples can be directly analyzed without any prior sample dilution or separation. Taken together, we demonstrate the great potential of in situ liquid SIMS in applications related to the molecular investigation of various liquid samples in food science.

Molecular imaging of plant-microbe interactions on the Brachypodium seed surface

Plant growth-promoting rhizobacteria (PGPR) play a crucial role in biological control and pathogenic defense on and within plant tissues, however the mechanisms by which plants associate with PGPR to elicit such beneficial effects need further study. Here, we present time-of-flight secondary ion mass spectrometry (ToF-SIMS) imaging of Brachypodium distachyon (Brachypodium) seeds with and without exposure to two model PGPR, i.e., Gram-negative Pseudomonas fluorescens SBW25 (P.) and Gram-positive Arthrobacter chlorophenolicus A6 (A.). Delayed image extraction was used to image PGPR-treated seed sections to reveal morphological changes. ToF-SIMS spectral comparison, principal component analysis (PCA), and two-dimensional (2D) imaging show that the selected PGPR have different effects on the host seed surface, resulting in changes in chemical composition and morphology. Metabolite products and biomarkers, such as flavonoids, phenolic compounds, fatty acids, and indole-3-acetic acid (IAA), were identified on the PGPR-treated seed surfaces. These compounds have different distributions on the Brachypodium seed surface for the two PGPR, indicating that the different bacteria elicit distinct responses from the host. Our results illustrate that ToF-SIMS is an effective tool to study plant-microbe interactions and to provide insightful information with submicrometer lateral resolution of the chemical distributions associated with morphological features, potentially offering a new way to study the mechanisms underlying beneficial roles of PGPR.

Three-Dimensional Mass Spectrometric Imaging of Biological Structures Using a Vacuum-Compatible Microfluidic Device

Three-dimensional (3D) molecular imaging of biological structures is important for a wide range of research. In recent decades, secondary-ion mass spectrometry (SIMS) has been recognized as a powerful technique for both two-dimensional and 3D molecular imaging. Sample fixations (e.g., chemical fixation and cryogenic fixation methods) are necessary to adapt biological samples to the vacuum condition in the SIMS chamber, which has been demonstrated to be nontrivial and less controllable, thus limiting the wider application of SIMS on 3D molecular analysis of biological samples. Our group recently developed in situ liquid SIMS that offers great opportunities for the molecular study of various liquids and liquid interfaces. In this work, we demonstrate that a further development of the vacuum-compatible microfluidic device used in in situ liquid SIMS provides a convenient freeze-fixation of biological samples and leads to more controllable and convenient 3D molecular imaging. The special design of this new vacuum-compatible liquid chamber allows an easy determination of sputter rates of ice, which is critical for calibrating the depth scale of frozen biological samples. Sputter yield of a 20 keV Ar₁₈₀₀⁺ ion on ice has been determined as 1500 (±8%) water molecules per Ar₁₈₀₀⁺ ion, consistent with our results from molecular dynamics simulations. Moreover, using the information of ice sputter yield, we successfully conduct 3D molecular imaging of frozen homogenized milk and observe network structures of interesting organic and inorganic species. Taken together, our results will significantly benefit various research fields relying on 3D molecular imaging of biological structures.

In Vivo Molecular Insights into Syntrophic Geobacter Aggregates

Direct interspecies electron transfer (DIET) has been considered as a novel and highly efficient strategy in both natural anaerobic environments and artificial microbial fuel cells. A syntrophic model consisting of Geobacter metallireducens and Geobacter sulfurreducens was studied in this work. We conducted in vivo molecular mapping of the outer surface of the syntrophic community as the interface of nutrients and energy exchange. System for Analysis at the Liquid Vacuum Interface combined with time-of-flight secondary ion mass spectrometry was employed to capture the molecular distribution of syntrophic Geobacter communities in the living and hydrated state. Principal component analysis with selected peaks revealed that syntrophic Geobacter aggregates were well differentiated from other control samples, including syntrophic planktonic cells, pure cultured planktonic cells, and single population biofilms. Our in vivo imaging indicated that a unique molecular surface was formed. Specifically, aromatic amino acids, phosphatidylethanolamine components, and large water clusters were identified as key components that favored the DIET of syntrophic Geobacter aggregates. Moreover, the molecular changes in depths of the Geobacter aggregates were captured using dynamic depth profiling. Our findings shed new light on the interface components supporting electron transfer in syntrophic communities based on in vivo molecular imaging.

Liquid ToF-SIMS revealing the oil, water, and surfactant interface evolution

Bilge water from ships is regarded as a major pollutant in the marine environment. Bilge water exists in a stable oil-in-water (O/W) emulsion form. However, little is known about the O/W liquid-liquid (l-l) interface. Traditional bulk characterization approaches are not capable of capturing the chemical changes at the O/W l-l interface. Although surfactants are deemed essential in droplet formation, their roles in bilge water stabilization have not been fully revealed. We have utilized novel in situ chemical imaging tools including in situ scanning electron microscopy (SEM) and in situ time-of-flight secondary ion mass spectrometry (ToF-SIMS) to study the evolving O/W interface using a NAVY bilge model for the first time. The droplet size distribution (DSD) does not change significantly without the addition of X-100 surfactants under static or rocking conditions. Both the oil components and the water clusters are shown to evolve over time at the O/W droplet interface by in situ liquid SIMS imaging. Of particular interest to droplet stabilization, the contribution of surfactants to the aged bilge droplets becomes more significant as the droplet size increases. The higher mass surfactant component does not appear on the droplet surface immediately while many lower mass surfactants are solvated inside the droplet. We have provided the first three-dimensional images of the evolving O/W interface and demonstrated that in situ surface chemical mapping is powerful enough to reveal the complex and dynamic l-l interface in the liquid state. Our observational insights suggest that surfactants are important in mediating droplet growth and facilitating effective separation of bilge water emulsion.

Detecting Escherichia coli Biofilm Development Stages on Gold and Titanium by Quartz Crystal Microbalance

Bacterial biofilms are responsible for persistent infections and biofouling, raising serious concerns in both medical and industrial processes. These motivations underpin the need to develop methodologies to study the complex biological structures of biofilms and prevent their formation on medical implants, tools, and industrial apparatuses. Here, we report the detailed comparison of Escherichia coli biofilm development stages (adhesion, maturation, and dispersion) on gold and titanium surfaces by monitoring the changes in both frequency and dissipation of a quartz crystal microbalance (QCM) device, a cheap and reliable microgravimetric sensor which allows the real-time and label-free characterization of various stages of biofilm development. Although gold is the most common electrode material used for QCM sensors, the titanium electrode is also readily available for QCM sensors; thus, QCM sensors with different metal electrodes serve as a simple platform to probe how pathogens interact with different metal substrates. The QCM outcomes are further confirmed by atomic force microscopy and crystal violet staining, thus validating the effectiveness of this surface sensitive sensor for microbial biofilm research. Moreover, because QCM technology can easily modify the substrate types and coatings, QCM sensors also provide well-controlled experimental conditions to study antimicrobial surface treatments and eradication procedures, even on mature biofilms.

Understanding Time Dependence on Zinc Metal-Organic Framework Growth Using in Situ Liquid Secondary Ion Mass Spectrometry

The abundance of novel metal-organic framework (MOF) materials continues to increase as more applications are discovered for these highly porous, well-ordered crystalline structures. The simplicity of constituents allows for the design of new MOFs with virtue of functionality and pore topology toward target adsorbates. However, the fundamental understanding of how these frameworks evolve during nucleation and growth is mostly limited to speculation from simulation studies. In this effort, we utilize a unique vacuum compatible system for analysis at the liquid vacuum interface (SALVI) microfluidic interface to analyze the formation and evolution of the benchmark MOF-74 framework using time-of-flight secondary ion mass spectrometry (ToF-SIMS). Principal component analysis of the SIMS mass spectra, together with ex situ electron microscopy, powder X-ray diffractometry, and porosimetry, provides new insights into the structural growth, metal-oxide cluster formation, and aging process of Zn-MOF-74. Samples collected over a range of synthesis times and analyzed closely with in situ ToF-SIMS, transmission electron microscopy, and gas adsorption studies verify the developing pore structure during the aging process.

Correlative surface imaging reveals chemical signatures for bacterial hotspots on plant roots

A universal sample holder allows correlative imaging analysis of plant roots to reveal chemical signatures for bacterial hotspots.

Surface evolution of synthetic bilgewater emulsion

Bilgewater is a regulated shipboard produced waste stream that often contains oil-in-water emulsion. Fundamental knowledge of emulsion surface changes is required for improved wastewater treatment; however, limited information is currently available. We have reported the first surface characterization of synthetic bilgewater emulsions using time-of-flight secondary ion mass spectrometry (ToF-SIMS) coupled with optical microscopy. A Navy standard bilgewater solution consisting of a hydrocarbon and detergent mixture is used as the synthetic bilgewater emulsion model. Both fresh and aged emulsion samples are analyzed to determine their droplet size distributions (DSDs) and surface chemical composition. Our results show that fresh emulsions are largely mono-modal with hydrocarbon fragments as the main surface composition. Aged emulsions are also mono-modal with slightly larger size. Both SIMS spectral comparison and Principal Component Analysis (PCA) show that some surfactant components appear on the fresh emulsion surface while larger molecular weight components appear at the aged bilge droplet surface. Our results indicate that the oil-water interface evolves after emulsion droplet formation. More importantly, surface evolution not only changes the bilgewater DSD, but also alters the surface chemical composition and reactivity.