A novel method for the study of the biophysical interface in soils using nano-scale secondary ion mass spectrometry

Research progress of nano-scale secondary ion mass spectrometry (NanoSIMS) in soil science: Evolution, applications, and challenges

Nano-scale secondary ion mass spectrometry (NanoSIMS) has emerged as a powerful analytical tool for investigating various aspects of soils. In recent decades, the widespread adoption of advanced instrumentation and methods has contributed significantly to our understanding of organic-mineral assemblages. However, few literature reviews have comprehensively summarized NanoSIMS and its evolution, applications, limitations, and integration with other analytical techniques. In this review, we addressed this gap by comprehensively overviewing the development of NanoSIMS as an analytical tool in soils. This review covers studies on soil organic matter (SOM) cycling, soil-root interactions, and the behavior of metals, discussing the capability and limitations related to the distribution, composition, and interactions of various soil components that occur at mineral-organic interfaces. Furthermore, we examine recent advancements in high-resolution imaging and mass spectrometry technologies and their impact on the utilization of NanoSIMS in soils, along with potential new applications such as utilizing multiple ion beams and integrating them with other analytical techniques. The review emphasizes the importance of employing advanced techniques and methods to explore micro-interfaces and provide in situ descriptions of organic-mineral assemblages in future research. The ongoing development and refinement of NanoSIMS may yield new insights and breakthroughs in soil science, deepening our understanding of the intricate relationships between soil components and the processes that govern soil health and fertility.

Gold-FISH enables targeted NanoSIMS analysis of plant-associated bacteria

Bacteria colonize plant roots and engage in reciprocal interactions with their hosts. However, the contribution of individual taxa or groups of bacteria to plant nutrition and fitness is not well characterized due to a lack of in situ evidence of bacterial activity. To address this knowledge gap, we developed an analytical approach that combines the identification and localization of individual bacteria on root surfaces via gold-based in situ hybridization with correlative NanoSIMS imaging of incorporated stable isotopes, indicative of metabolic activity. We incubated Kosakonia strain DS-1-associated, gnotobiotically grown rice plants with 15 N-N2 gas to detect in situ N2 fixation activity. Bacterial cells along the rhizoplane showed heterogeneous patterns of 15 N enrichment, ranging from the natural isotope abundance levels up to 12.07 at% 15 N (average and median of 3.36 and 2.85 at% 15 N, respectively, n = 697 cells). The presented correlative optical and chemical imaging analysis is applicable to a broad range of studies investigating plant-microbe interactions. For example, it enables verification of the in situ metabolic activity of host-associated commercialized strains or plant growth-promoting bacteria, thereby disentangling their role in plant nutrition. Such data facilitate the design of plant-microbe combinations for improvement of crop management.

Correlative Imaging of the Rhizosphere─A Multimethod Workflow for Targeted Mapping of Chemical Gradients

Examining in situ processes in the soil rhizosphere requires spatial information on physical and chemical properties under undisturbed conditions. We developed a correlative imaging workflow for targeted sampling of roots in their three-dimensional (3D) context and assessed the imprint of roots on chemical properties of the root-soil contact zone at micrometer to millimeter scale. Maize (Zea mays) was grown in 15N-labeled soil columns and pulse-labeled with 13CO2 to visualize the spatial distribution of carbon inputs and nitrogen uptake together with the redistribution of other elements. Soil columns were scanned by X-ray computed tomography (X-ray CT) at low resolution (45 μm) to enable image-guided subsampling of specific root segments. Resin-embedded subsamples were then analyzed by X-ray CT at high resolution (10 μm) for their 3D structure and chemical gradients around roots using micro-X-ray fluorescence spectroscopy (μXRF), nanoscale secondary ion mass spectrometry (NanoSIMS), and laser-ablation isotope ratio mass spectrometry (LA-IRMS). Concentration gradients, particularly of calcium and sulfur, with different spatial extents could be identified by μXRF. NanoSIMS and LA-IRMS detected the release of 13C into soil up to a distance of 100 μm from the root surface, whereas 15N accumulated preferentially in the root cells. We conclude that combining targeted sampling of the soil-root system and correlative microscopy opens new avenues for unraveling rhizosphere processes in situ.

Clarifying the evidence for microbial- and plant-derived soil organic matter, and the path toward a more quantitative understanding

Predicting and mitigating changes in soil carbon (C) stocks under global change requires a coherent understanding of the factors regulating soil organic matter (SOM) formation and persistence, including knowledge of the direct sources of SOM (plants vs. microbes). In recent years, conceptual models of SOM formation have emphasized the primacy of microbial-derived organic matter inputs, proposing that microbial physiological traits (e.g., growth efficiency) are dominant controls on SOM quantity. However, recent quantitative studies have challenged this view, suggesting that plants make larger direct contributions to SOM than is currently recognized by this paradigm. In this review, we attempt to reconcile these perspectives by highlighting that variation across estimates of plant- versus microbial-derived SOM may arise in part from methodological limitations. We show that all major methods used to estimate plant versus microbial contributions to SOM have substantial shortcomings, highlighting the uncertainty in our current quantitative estimates. We demonstrate that there is significant overlap in the chemical signatures of compounds produced by microbes, plant roots, and through the extracellular decomposition of plant litter, which introduces uncertainty into the use of common biomarkers for parsing plant- and microbial-derived SOM, especially in the mineral-associated organic matter (MAOM) fraction. Although the studies that we review have contributed to a deeper understanding of microbial contributions to SOM, limitations with current methods constrain quantitative estimates. In light of recent advances, we suggest that now is a critical time to re-evaluate long-standing methods, clearly define their limitations, and develop a strategic plan for improving the quantification of plant- and microbial-derived SOM. From our synthesis, we outline key questions and challenges for future research on the mechanisms of SOM formation and stabilization from plant and microbial pathways.

Advances in Molecular and Microscale Characterization of Soil Organic Matter: Current Limitations and Future Prospects

Soil organic matter (SOM) comprises a continuum of organic materials from granular organic debris to small organic molecules and contains more organic carbon than global vegetation and the atmosphere combined. It has remarkable effects on soil ecological functions and the global carbon cycle as well as the fate of pollutants in the terrestrial ecosystem. Therefore, characterization of SOM is an important topic in soil science, ecology, and environmental science. Chemical complexity and spatial heterogeneity are by far the two biggest challenges to our understanding of SOM. Recent developments in analytical techniques and methods provide the opportunity to reveal SOM composition at the molecular level and to observe its distribution in soils at micro- and nanoscales, which have greatly improved our understanding of SOM. This paper reviews the outstanding advances in SOM characterization regarding these two issues from target and nontarget analyses comprising molecular marker analysis, ultrahigh-resolution mass spectrometry analysis, and in situ microscopic imaging techniques such as synchrotron-based spectromicroscopy, nanoscale secondary ion mass spectrometry, and emerging electron and optical microscopic imaging techniques. However, current techniques and methods remain far from unlocking the unknown properties of SOM. We systematically point out the limitations of the current technologies and outline the future prospects for comprehensive characterization of SOM at the molecular level and micro- and nanoscales, paying particular attention to issues of environmental concern.

NanoSIP: NanoSIMS Applications for Microbial Biology

High-resolution imaging with secondary ion mass spectrometry (nanoSIMS) has become a standard method in systems biology and environmental biogeochemistry and is broadly used to decipher ecophysiological traits of environmental microorganisms, metabolic processes in plant and animal tissues, and cross-kingdom symbioses. When combined with stable isotope-labeling-an approach we refer to as nanoSIP-nanoSIMS imaging offers a distinctive means to quantify net assimilation rates and stoichiometry of individual cell-sized particles in both low- and high-complexity environments. While the majority of nanoSIP studies in environmental and microbial biology have focused on nitrogen and carbon metabolism (using ¹⁵N and ¹³C tracers), multiple advances have pushed the capabilities of this approach in the past decade. The development of a high-brightness oxygen ion source has enabled high-resolution metal analyses that are easier to perform, allowing quantification of metal distribution in cells and environmental particles. New preparation methods, tools for automated data extraction from large data sets, and analytical approaches that push the limits of sensitivity and spatial resolution have allowed for more robust characterization of populations ranging from marine archaea to fungi and viruses. NanoSIMS studies continue to be enhanced by correlation with orthogonal imaging and 'omics approaches; when linked to molecular visualization methods, such as in situ hybridization and antibody labeling, these techniques enable in situ function to be linked to microbial identity and gene expression. Here we present an updated description of the primary materials, methods, and calculations used for nanoSIP, with an emphasis on recent advances in nanoSIMS applications, key methodological steps, and potential pitfalls.

Use of NanoSIMS to Identify the Lower Limits of Metabolic Activity and Growth by Serratia liquefaciens Exposed to Sub-Zero Temperatures

Serratia liquefaciens is a cold-adapted facultative anaerobic astrobiology model organism with the ability to grow at a Martian atmospheric pressure of 7 hPa. Currently there is a lack of data on its limits of growth and metabolic activity at sub-zero temperatures found in potential habitable regions on Mars. Growth curves and nano-scale secondary ion mass spectrometry (NanoSIMS) were used to characterize the growth and metabolic threshold for S. liquefaciens ATCC 27,592 grown at and below 0 °C. Cells were incubated in Spizizen medium containing three stable isotopes substituting their unlabeled counterparts; i.e., ¹³C-glucose, (¹⁵NH₄)₂SO₄, and H₂¹⁸O; at 0, −1.5, −3, −5, −10, or −15 °C. The isotopic ratios of ¹³C/¹²C, ¹⁵N/¹⁴N, and ¹⁸O/¹⁶O and their corresponding fractions were determined for 240 cells. NanoSIMS results revealed that with decreasing temperature the cellular amounts of labeled ions decreased indicating slower metabolic rates for isotope uptake and incorporation. Metabolism was significantly reduced at −1.5 and −3 °C, almost halted at −5 °C, and shut-down completely at or below −10 °C. While growth was observed at 0 °C after 5 days, samples incubated at −1.5 and −3 °C exhibited significantly slower growth rates until growth was detected at 70 days. In contrast, cell densities decreased by at least half an order of magnitude over 70 days in cultures incubated at ≤ −5 °C. Results suggest that S. liquefaciens, if transported to Mars, might be able to metabolize and grow in shallow sub-surface niches at temperatures above −5 °C and might survive—but not grow—at temperatures below −5 °C.

Microbial Identification, High-Resolution Microscopy and Spectrometry of the Rhizosphere in Its Native Spatial Context

During the past decades, several stand-alone and combinatorial methods have been developed to investigate the chemistry (i.e., mapping of elemental, isotopic, and molecular composition) and the role of microbes in soil and rhizosphere. However, none of these approaches are currently applicable to characterize soil-root-microbe interactions simultaneously in their spatial arrangement. Here we present a novel approach that allows for simultaneous microbial identification and chemical analysis of the rhizosphere at micro- to nano-meter spatial resolution. Our approach includes (i) a resin embedding and sectioning method suitable for simultaneous correlative characterization of Zea mays rhizosphere, (ii) an analytical work flow that allows up to six instruments/techniques to be used correlatively, and (iii) data and image correlation. Hydrophilic, immunohistochemistry compatible, low viscosity LR white resin was used to embed the rhizosphere sample. We employed waterjet cutting and avoided polishing the surface to prevent smearing of the sample surface at nanoscale. The quality of embedding was analyzed by Helium Ion Microscopy (HIM). Bacteria in the embedded soil were identified by Catalyzed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH) to avoid interferences from high levels of autofluorescence emitted by soil particles and organic matter. Chemical mapping of the rhizosphere was done by Scanning Electron Microscopy (SEM) with Energy-dispersive X-ray analysis (SEM-EDX), Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS), nano-focused Secondary Ion mass Spectrometry (nanoSIMS), and confocal Raman spectroscopy (μ-Raman). High-resolution correlative characterization by six different techniques followed by image registration shows that this method can meet the demanding requirements of multiple characterization techniques to identify spatial organization of bacteria and chemically map the rhizosphere. Finally, we presented individual and correlative workflows for imaging and image registration to analyze data. We hope this method will be a platform to combine various 2D analytics for an improved understanding of the rhizosphere processes and their ecological significance.

NanoSIMS imaging of extracellular electron transport processes during microbial iron(III) reduction

Microbial iron(III) reduction can have a profound effect on the fate of contaminants in natural and engineered environments. Different mechanisms of extracellular electron transport are used by Geobacter and Shewanella spp. to reduce insoluble Fe(III) minerals. Here we prepared a thin film of iron(III)-(oxyhydr)oxide doped with arsenic, and allowed the mineral coating to be colonised by Geobacter sulfurreducens or Shewanella ANA3 labelled with ¹³C from organic electron donors. This preserved the spatial relationship between metabolically active Fe(III)-reducing bacteria and the iron(III)-(oxyhydr)oxide that they were respiring. NanoSIMS imaging showed cells of G. sulfurreducens were co-located with the iron(III)-(oxyhydr)oxide surface and were significantly more ¹³C-enriched compared to cells located away from the mineral, consistent with Geobacter species requiring direct contact with an extracellular electron acceptor to support growth. There was no such intimate relationship between ¹³C-enriched S. ANA3 and the iron(III)-(oxyhydr)oxide surface, consistent with Shewanella species being able to reduce Fe(III) indirectly using a secreted endogenous mediator. Some differences were observed in the amount of As relative to Fe in the local environment of G. sulfurreducens compared to the bulk mineral, highlighting the usefulness of this type of analysis for probing interactions between microbial cells and Fe-trace metal distributions in biogeochemical experiments.

SERS of cells: What can we learn from cell lysates?

Surface-enhanced Raman spectroscopy (SERS) is a promising and emerging technique to analyze the cellular environment. We developed an alternative, rapid and label-free SERS-based method to get information about the cellular environment by analyzing cells lysates, thus avoiding the need to incorporate nanoparticles into cells. Upon sonicating and filtrating cells, we obtained lysates which, mixed with Au or Ag nanoparticles, yield stable and repeatable SERS spectra, whose overall profile depends on the metal used as substrate, but not on the buffer used for the lysis process. Bands appearing in these spectra were shown to arise mostly from the cytosol and were assigned to adenine, guanine, adenosine and reduced glutathione (GSH). Spectral differences among various cell types also demonstrated that this approach is suitable for cell type identification.

Micro-scale heterogeneity of soil phosphorus depends on soil substrate and depth

Soils comprise various heterogeneously distributed pools of lithogenic, free organic, occluded, adsorbed, and precipitated phosphorus (P) forms, which differ depending on soil forming factors. Small-scale heterogeneity of element distributions recently has received increased attention in soil science due to its influence on soil functions and soil fertility. We investigated the micro-scale distribution of total P and different specific P binding forms in aggregates taken from a high-P clay-rich soil and a low-P sandy soil by combining advanced spectrometric and spectroscopic techniques to introduce new insights on P accessibility and availability in soils. Here we show that soil substrate and soil depth determine micro-scale P heterogeneity in soil aggregates. In P-rich areas of all investigated soil aggregates, P was predominantly co-located with aluminium and iron oxides and hydroxides, which are known to strongly adsorb P. Clay minerals were co-located with P only to a lesser extent. In the low-P topsoil aggregate, the majority of the P was bound organically. Aluminium and iron phosphate predominated in the quartz-rich low-P subsoil aggregate. Sorbed and mineral P phases determined P speciation in the high-P top- and subsoil, and apatite was only detected in the high-P subsoil aggregate. Our results indicate that micro-scale spatial and chemical heterogeneity of P influences P accessibility and bioavailability.

Heavy water and (15) N labelling with NanoSIMS analysis reveals growth rate-dependent metabolic heterogeneity in chemostats

To measure single-cell microbial activity and substrate utilization patterns in environmental systems, we employ a new technique using stable isotope labelling of microbial populations with heavy water (a passive tracer) and (15) N ammonium in combination with multi-isotope imaging mass spectrometry. We demonstrate simultaneous NanoSIMS analysis of hydrogen, carbon and nitrogen at high spatial and mass resolution, and report calibration data linking single-cell isotopic compositions to the corresponding bulk isotopic equivalents for Pseudomonas aeruginosa and Staphylococcus aureus. Our results show that heavy water is capable of quantifying in situ single-cell microbial activities ranging from generational time scales of minutes to years, with only light isotopic incorporation (∼0.1 atom % (2) H). Applying this approach to study the rates of fatty acid biosynthesis by single cells of S. aureus growing at different rates in chemostat culture (∼6 h, 1 day and 2 week generation times), we observe the greatest anabolic activity diversity in the slowest growing populations. By using heavy water to constrain cellular growth activity, we can further infer the relative contributions of ammonium versus amino acid assimilation to the cellular nitrogen pool. The approach described here can be applied to disentangle individual cell activities even in nutritionally complex environments.

Competition between plant and bacterial cells at the microscale regulates the dynamics of nitrogen acquisition in wheat (Triticum aestivum)

The ability of plants to compete effectively for nitrogen (N) resources is critical to plant survival. However, controversy surrounds the importance of organic and inorganic sources of N in plant nutrition because of our poor ability to visualize and understand processes happening at the root-microbial-soil interface. Using high-resolution nano-scale secondary ion mass spectrometry stable isotope imaging (NanoSIMS-SII), we quantified the fate of ¹⁵N over both space and time within the rhizosphere. We pulse-labelled the soil surrounding wheat (Triticum aestivum) roots with either ¹⁵NH₄⁺ or ¹⁵N-glutamate and traced the movement of ¹⁵N over 24 h. Imaging revealed that glutamate was rapidly depleted from the rhizosphere and that most ¹⁵N was captured by rhizobacteria, leading to very high ¹⁵N microbial enrichment. After microbial capture, approximately half of the ¹⁵N-glutamate was rapidly mineralized, leading to the excretion of NH₄⁺, which became available for plant capture. Roots proved to be poor competitors for ¹⁵N-glutamate and took up N mainly as ¹⁵NH₄⁺. Spatial mapping of ¹⁵N revealed differential patterns of ¹⁵N uptake within bacteria and the rapid uptake and redistribution of ¹⁵N within roots. In conclusion, we demonstrate the rapid cycling and transformation of N at the soil-root interface and that wheat capture of organic N is low in comparison to inorganic N under the conditions tested.

A multi-scale approach to determine accurate elemental and isotopic ratios by nano-scale secondary ion mass spectrometry imaging

RATIONALE

Nano-scale secondary ion mass spectrometry (NanoSIMS) is still hampered by a lack of appropriate calibration method for the quantification of elemental and isotopic ratios in heterogeneous materials such as soil samples. The potential of (13)C-(15)N-labeled density fractions of soil to calibrate the C/N, (13)C/(12)C and (15)N/(14)N ratios provided by NanoSIMS was evaluated.

METHODS

The spatial organization of soil particles found at the macro- and micro-scales were compared. The C/N, (13)C/(12)C and (15)N/(14)N ratios measured at the macroscopic scale from different density fractions using an elemental analyzer coupled to an isotope ratio mass spectrometer (EA/IRMS) were compared with the corresponding micro-scale NanoSIMS measurements. When the macro- and micro-scales patterns were similar, macroscopic scale measurements obtained by EA/IRMS and the corresponding NanoSIMS C/N and (15)N/(14)N ratios averaged per fraction were used to obtain correction equations. The correction method using the internal calibration procedure was compared with the traditional one using a single organic standard.

RESULTS

It was demonstrated that the correction method using an internal calibration procedure was applicable for NanoSIMS images acquired on more than 500 µm(2) per fraction and provided more accurate C/N and (15)N/(14)N ratios than the traditional correction method.

CONCLUSIONS

As long as the NanoSIMS sampling was representative of the macroscopic properties, the correction method using an internal calibration procedure allowed better quantification of the isotope tracers and characterization of the C/N ratios. This method not only produced qualitative images, but also accurate quantitative parameters from which ecological interpretations can be derived.

NanoSIMS study of organic matter associated with soil aggregates: advantages, limitations, and combination with STXM

Direct observations of processes occurring at the mineral-organic interface are increasingly seen as relevant for the cycling of both natural soil organic matter and organic contaminants in soils and sediments. Advanced analytical tools with the capability to visualize and characterize organic matter at the submicrometer scale, such as Nano Secondary Ion Mass Spectrometry (NanoSIMS) and Scanning Transmission X-ray Microscopy (STXM) coupled to Near Edge X-ray Absorption Fine Structure Spectroscopy (NEXAFS), may be combined to locate and characterize mineral-associated organic matter. Taking advantage of samples collected from a decadal (15)N litter labeling experiment in a temperate forest, we demonstrate the potential of NanoSIMS to image intact soil particles and to detect spots of isotopic enrichment even at low levels of (15)N application. We show how microsites of isotopic enrichment detected by NanoSIMS can be speciated by STXM-NEXAFS performed on the same particle. Finally, by showing how (15)N enrichment at one microsite could be linked to the presence of microbial metabolites, we emphasize the potential of this combined imaging and spectroscopic approach to link microenvironment with geochemical process and/or location with ecological function.

NanoSIP: NanoSIMS applications for microbial biology

Recent advances in high-resolution imaging secondary ion mass spectrometry (SIMS) (J Biol 5: 20, 2006) have made isotopic tracing at the single-cell level a standard technique for microbial ecology and systems biology; elemental and metal cofactor analyses are also showing significant promise. For example, with the NanoSIMS, metabolic activities of single microbial cells can be tracked by imaging natural isotopic/elemental composition or isotope distribution after stable isotope probing. When linked to molecular visualization methods, such as in situ hybridization and antibody labeling, these techniques enable in situ function to be linked to microbial identity and gene expression. We broadly call this combination of methods nanoSIP, for nanometer-scale stable isotope probing. Here we present the primary materials and methods used for nanoSIP, with an emphasis on key steps and potential pitfalls. Applications to pure cultures, cocultures, and complex communities are discussed.

Identification of diazotrophic microorganisms in marine sediment via fluorescence in situ hybridization coupled to nanoscale secondary ion mass spectrometry (FISH-NanoSIMS)

Growing appreciation for the biogeochemical significance of uncultured microorganisms is changing the focus of environmental microbiology. Techniques designed to investigate microbial metabolism in situ are increasingly popular, from mRNA-targeted fluorescence in situ hybridization (FISH) to the "-omics" revolution, including metagenomics, transcriptomics, and proteomics. Recently, the coupling of FISH with nanometer-scale secondary ion mass spectrometry (NanoSIMS) has taken this movement in a new direction, allowing single-cell metabolic analysis of uncultured microbial phylogenic groups. The main advantage of FISH-NanoSIMS over previous noncultivation-based techniques to probe metabolism is its ability to directly link 16S rRNA phylogenetic identity to metabolic function. In the following chapter, we describe the procedures necessary to identify nitrogen-fixing microbes within marine sediment via FISH-NanoSIMS, using our work on nitrogen fixation by uncultured deep-sea methane-consuming archaea as a case study.

Application of nanoscale secondary ion mass spectrometry to plant cell research

Imaging resource flow in soil-plant systems remains central to understanding plant development and interactions with the environment. Typically, subcellular resolution is required to fully elucidate the compartmentation, behavior, and mode of action of organic compounds and mineral elements within plants. For many situations this has been limited by the poor spatial resolution of imaging techniques and the inability to undertake studies in situ. Here we demonstrate the potential of Nanoscale Secondary Ion Mass Spectrometry (NanoSIMS), which is capable of the quantitative high-resolution spatial imaging of stable isotopes (e.g. (12) C, (13) C, (14) N, (15) N, (16) O, (18) O, (31) P, (34) S) within intact plant-microbial-soil systems. We present examples showing how the approach can be used to investigate competition for (15) N-labeled nitrogen compounds between plant roots and soil microorganisms living in the rhizosphere and the spatial imaging of (31) P in roots. We conclude that NanoSIMS has great potential to elucidate the flow of isotopically-labeled compounds in complex media (e.g. soil) and opens up countless new opportunities for studying plant responses to abiotic stress (e.g. (18) O3, elevated (13) CO2), signal exchange, nutrient flow and plant-microbial interactions.

Single-cell ecophysiology of microbes as revealed by Raman microspectroscopy or secondary ion mass spectrometry imaging

An astonishing diversity of microorganisms thrives on our planet and their activities are fundamental for the functioning of all ecosystems including the human body. Consequently, detailed insights into the functions performed by microorganisms in their natural environment are required to understand human biology and the biology of the world around us and to lay the foundations for targeted manipulation of microbial communities. Isotope-labeling techniques combined with molecular detection tools are frequently used by microbial ecologists to directly link structure and function of microbial communities and to monitor metabolic properties of uncultured microbes at the single-cell level. However, only the recent combination of such techniques with Raman microspectroscopy or secondary ion mass spectrometry enables functional studies of microbes on a single-cell level by using stable isotopes as labels. This review provides an overview of these new techniques and their applications in microbial ecology, which allow us to investigate the ecophysiology of uncultured microbes to an extent that was unimaginable just a few years ago.

Advances in imaging secondary ion mass spectrometry for biological samples

Imaging mass spectrometry combines the power of mass spectrometry to identify complex molecules based on mass with sample imaging. Recent advances in secondary ion mass spectrometry have improved sensitivity and spatial resolution, so that these methods have the potential to bridge between high-resolution structures obtained by X-ray crystallography and cyro-electron microscopy and ultrastructure visualized by conventional light microscopy. Following background information on the method and instrumentation, we address the key issue of sample preparation. Because mass spectrometry is performed in high vacuum, it is essential to preserve the lateral organization of the sample while removing bulk water, and this has been a major barrier for applications to biological systems. Recent applications of imaging mass spectrometry to cell biology, microbial communities, and biosynthetic pathways are summarized briefly, and studies of biological membrane organization are described in greater depth.

Geobiological investigations using secondary ion mass spectrometry: microanalysis of extant and paleo-microbial processes

The application of secondary ion mass spectrometry (SIMS) has tremendous value for the field of geobiology, representing a powerful tool for identifying the specific role of micro-organisms in biogeochemical cycles. In this review, we highlight a number of diverse applications for SIMS and nanoSIMS in geobiological research. SIMS performs isotope and elemental analysis at microscale enabling the investigation of the physiology of individual microbes within complex communities. Additionally, through the study of isotopic or chemical characteristics that are common in both living and ancient microbial communities, SIMS allows for direct comparisons of potential biosignatures derived from extant microbial cells and their fossil equivalents.

Dynamic secondary ion mass spectrometry imaging of microbial populations utilizing C-labelled substrates in pure culture and in soil

We demonstrate that dynamic secondary ion mass spectrometry (SIMS)-based ion microscopy can provide a means of measuring (13)C assimilation into individual bacterial cells grown on (13)C-labelled organic compounds in the laboratory and in field soil. We grew pure cultures of Pseudomonas putida NCIB 9816-4 in minimal media with known mixtures of (12)C- and (13)C-glucose and analysed individual cells via SIMS imaging. Individual cells yielded signals of masses 12, 13, 24, 25, 26 and 27 as negative secondary ions indicating the presence of (12)C(-), (13)C(-), (24)((12)C(2))(-), (25)((12)C(13)C)(-), (26)((12)C(14)N)(-) and (27)((13)C(14)N)(-) ions respectively. We verified that ratios of signals taken from the same cells only changed minimally during a approximately 4.5 min period of primary O(2)(+) beam sputtering by the dynamic SIMS instrument in microscope detection mode. There was a clear relationship between mass 27 and mass 26 signals in Pseudomonas putida cells grown in media containing varying proportions of (12)C- to (13)C-glucose: a standard curve was generated to predict (13)C-enrichment in unknown samples. We then used two strains of Pseudomonas putida able to grow on either all or only a part of a mixture of (13)C-labelled and unlabelled carbon sources to verify that differential (13)C signals measured by SIMS were due to (13)C assimilation into cell biomass. Finally, we made three key observations after applying SIMS ion microscopy to soil samples from a field experiment receiving (12)C- or (13)C-phenol: (i) cells enriched in (13)C were heterogeneously distributed among soil populations; (ii) (13)C-labelled cells were detected in soil that was dosed a single time with (13)C-phenol; and (iii) in soil that received 12 doses of (13)C-phenol, 27% of the cells in the total community were more than 90% (13)C-labelled.

A review of stable isotope techniques for N2O source partitioning in soils: recent progress, remaining challenges and future considerations

Nitrous oxide is produced in soil during several processes, which may occur simultaneously within different micro-sites of the same soil. Stable isotope techniques have a crucial role to play in the attribution of N(2)O emissions to different microbial processes, through estimation (natural abundance, site preference) or quantification (enrichment) of processes based on the (15)N and (18)O signatures of N(2)O determined by isotope ratio mass spectrometry. These approaches have the potential to become even more powerful when linked with recent developments in secondary isotope mass spectrometry, with microbial ecology, and with modelling approaches, enabling sources of N(2)O to be considered at a wide range of scales and related to the underlying microbiology. Such source partitioning of N(2)O is inherently challenging, but is vital to close the N(2)O budget and to better understand controls on the different processes, with a view to developing appropriate management practices for mitigation of N(2)O. In this respect, it is essential that as many of the contributing processes as possible are considered in any study aimed at source attribution, as mitigation strategies for one process may not be appropriate for another. To aid such an approach, here the current state of the art is critically examined, remaining challenges are highlighted, and recommendations are made for future direction.

Visualization, modelling and prediction in soil microbiology

The introduction of new approaches for characterizing microbial communities and imaging soil environments has benefited soil microbiology by providing new ways of detecting and locating microorganisms. Consequently, soil microbiology is poised to progress from simply cataloguing microbial complexity to becoming a systems science. A systems approach will enable the structures of microbial communities to be characterized and will inform how microbial communities affect soil function. Systems approaches require accurate analyses of the spatio-temporal properties of the different microenvironments present in soil. In this Review we advocate the need for the convergence of the experimental and theoretical approaches that are used to characterize and model the development of microbial communities in soils.