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

Soil organic matter dynamics mediated by arbuscular mycorrhizal fungi - an updated conceptual framework

Arbuscular mycorrhizal (AM) fungi play an important role in soil organic matter (SOM) formation and stabilization. Previous studies have emphasized organic compounds produced by AM fungi as persistent binding agents for aggregate formation and SOM storage. This concept overlooks the multiple biogeochemical processes mediated by AM fungal activities, which drive SOM generation, reprocessing, reorganization, and stabilization. Here, we propose an updated conceptual framework to facilitate a mechanistic understanding of the role of AM fungi in SOM dynamics. In this framework, four pathways for AM fungi-mediated SOM dynamics are included: 'Generating', AM fungal exudates and biomass serve as key sources of SOM chemodiversity; 'Reprocessing', hyphosphere microorganisms drive SOM decomposition and resynthesis; 'Reorganizing', AM fungi mediate soil physical changes and influence SOM transport, redistribution, transformation, and storage; and 'Stabilizing', AM fungi drive mineral weathering and organo-mineral interactions for SOM stabilization. Moreover, we discuss the AM fungal role in SOM dynamics at different scales, especially when translating results from small scales to complex larger scales. We believe that working with this conceptual framework can allow a better understanding of AM fungal role in SOM dynamics, therefore facilitating the development of mycorrhiza-based technologies toward soil health and global change mitigation.

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.

Nitrogen-Rich Organic Matter Formation and Stabilization in Iron Ore Tailings: A Submicrometer Investigation

Organic matter (OM) formation and stabilization are critical processes in the eco-engineered pedogenesis of Fe ore tailings, but the underlying mechanisms are unclear. The present 12 month microcosm study has adopted nanoscale secondary ion mass spectrometry (NanoSIMS) and synchrotron-based scanning transmission X-ray microscopy (STXM) techniques to investigate OM formation, molecular signature, and stabilization in tailings at micro- and nanometer scales. In this system, microbial processing of exogenous isotopically labeled OM demonstrated that 13C labeled glucose and 13C/15N labeled plant biomass were decomposed, regenerated, and associated with Fe-rich minerals in a heterogeneous pattern in tailings. Particularly, when tailings were amended with plant biomass, the 15N-rich microbially derived OM was generated and bound to minerals to form an internal organo-mineral association, facilitating further OM stabilization. The organo-mineral associations were primarily underpinned by interactions of carboxyl, amide, aromatic, and/or aliphatic groups with weathered mineral products derived from biotite-like minerals in fresh tailings (i.e., with Fe2+ and Fe3+) or with Fe3+ oxyhydroxides in aged tailings. The study revealed microbial OM generation and subsequent organo-mineral association in Fe ore tailings at the submicrometer scale during early stages of eco-engineered pedogenesis, providing a basis for the development of microbial based technologies toward tailings' ecological rehabilitation.

Interactions between organic matter and Fe oxides at soil micro-interfaces: Quantification, associations, and influencing factors

Iron (Fe) oxides are widely recognized to prevent the degradation of organic matter (OM) in environments, thereby promoting the persistence of organic carbon (OC) in soils. Thus, discerning the association mechanisms of Fe oxides and OC interactions is key to effectively influencing the dynamics and extent of organic C cycling in soils. Previous studies have focused on i) quantifying Fe oxide-bound organic carbon (Fe-OC) in individual environments, ii) investigating the distribution and adsorption capacity of Fe-OC, and iii) assessing the redox cycling and transformation of Fe-OC. Furthermore, the widespread application of high-tech instrumentation and methods has greatly contributed to a better understanding of the mechanism of organic mineral assemblages in the past few decades. However, few literature reviews have comprehensively summarized Fe-OC distributions, associations, and characteristics in soil-plant systems. Here, studies investigating the Fe-OC contents among different environments are reviewed. In addition, the mechanisms and processes related to OM transformation dynamics occurring at mineral-organic interfaces are also described. Recent studies have highlighted that diverse interactions occur between Fe oxides and OC, with organic compounds adhering to Fe oxides due to their huge specific surfaces area and active reaction sites. Moreover, we also review methods for understanding Fe-OC interactions at micro-interfaces. Lastly, developmental prospects for understanding coupled Fe-OC geochemical processes in soil environments at molecular- and nano-scales are outlined. The summary suggests that combined advanced techniques and methods should be used in future research to explore micro-interfaces and in situ descriptions of organic mineral assemblages. This review also suggests that future studies need to consider the functional and spatial complexity that is typical of soil/sediment environments where Fe-OC interactions occur.

Spatial heterogeneity of particulate organic matter for the sorption of ciprofloxacin at the microstructure scale

Particulate organic matter (POM) is a major antibiotic sorbent of the active soil organic carbon pool. Until now, the spatial heterogeneity of POM for ciprofloxacin (CFC) sorption at the microstructure scale has not been quantified. To our knowledge, this is the first study that combines a batch sorption experiment, NanoSIMS, and a ¹³C isotopic tracer to expound the distribution characteristics of CFC and the dominant sorption components of POM. Four POMs separated from soils (wetland, oil waste field, and farmlands) were utilized to study the sorption mechanisms using batch experiments. POM separated from the wetland was utilized for further study at the microstructure scale. The results revealed that the POM had a great CFC sorption capacity ranging from 65.20 mg g^-1 to 77.51 mg g^-1. Both the kinetics and NanoSIMS results showed that the sorption mechanisms included surface distribution and intra-particle diffusion. The microstructural distribution characteristics exhibited a marginal accumulation tendency and a surface accumulation effect. A combination of the NanoSIMS with the pH and salinity results explained that CFC adsorption was dominated by the organic components of POM. Overall, the present study demonstrates that the characteristics and organic components of the POM played a decisive role in the CFC-POM interactions. This study provides the first evidence of the vector potential of CFC rereleased into the environment during the POM turnover process.

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.

Characterizing Natural Organic Matter Transformations by Microbial Communities in Terrestrial Subsurface Ecosystems: A Critical Review of Analytical Techniques and Challenges

Determining the mechanisms, traits, and pathways that regulate microbial transformation of natural organic matter (NOM) is critical to informing our understanding of the microbial impacts on the global carbon cycle. The capillary fringe of subsurface soils is a highly dynamic environment that remains poorly understood. Characterization of organo-mineral chemistry combined with a nuanced understanding of microbial community composition and function is necessary to understand microbial impacts on NOM speciation in the capillary fringe. We present a critical review of the popular analytical and omics techniques used for characterizing complex carbon transformation by microbial communities and focus on how complementary information obtained from the different techniques enable us to connect chemical signatures with microbial genes and pathways. This holistic approach offers a way forward for the comprehensive characterization of the formation, transformation, and mineralization of terrestrial NOM as influenced by microbial communities.

Tungsten distribution and vertical migration in soils near a typical abandoned tungsten smelter

As an emerging contaminant, tungsten's distribution and speciation in soils are far from understood. In this study, two soil profiles near a typical abandoned tungsten smelter in Hunan Province, China were collected and investigated, to ascertain the binding and association of tungsten with different soil components and subsequently to understand its mobility. The data showed that past tungsten smelting activities resulted in elevated concentrations of both tungsten and arsenic in the soil profiles, both of which ranged from dozens of to a few hundred mg/kg. Nano-scale secondary ion mass spectrometry (NanoSIMS) was employed to quantify the distribution and association of tungsten with various other elements. Combined with sequential extraction and mineralogical analysis, the data from NanoSIMS showed that aluminosilicates including kaolinite and illite were the most important mineral hosts for tungsten, whereas arsenic was predominantly bound to iron (oxyhydr)oxides. Additional data from ¹³C nuclear magnetic resonance and X-ray photoelectron spectroscopy revealed that soil organic matter retained tungsten in deep soils (>70 cm) by binding tungsten through carboxyls on aromatic rings. Compared to arsenic, tungsten migrated deeper in the soil profiles, suggesting its higher mobility and potential risk to groundwater quality.

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.

Bridging Microbial Functional Traits With Localized Process Rates at Soil Interfaces

In this review, we introduce microbially-mediated soil processes, players, their functional traits, and their links to processes at biogeochemical interfaces [e.g., rhizosphere, detritusphere, (bio)-pores, and aggregate surfaces]. A conceptual view emphasizes the central role of the rhizosphere in interactions with other biogeochemical interfaces, considering biotic and abiotic dynamic drivers. We discuss the applicability of three groups of traits based on microbial physiology, activity state, and genomic functional traits to reflect microbial growth in soil. The sensitivity and credibility of modern molecular approaches to estimate microbial-specific growth rates require further development. A link between functional traits determined by physiological (e.g., respiration, biomarkers) and genomic (e.g., genome size, number of ribosomal gene copies per genome, expression of catabolic versus biosynthetic genes) approaches is strongly affected by environmental conditions such as carbon, nutrient availability, and ecosystem type. Therefore, we address the role of soil physico-chemical conditions and trophic interactions as drivers of microbially-mediated soil processes at relevant scales for process localization. The strengths and weaknesses of current approaches (destructive, non-destructive, and predictive) for assessing process localization and the corresponding estimates of process rates are linked to the challenges for modeling microbially-mediated processes in heterogeneous soil microhabitats. Finally, we introduce a conceptual self-regulatory mechanism based on the flexible structure of active microbial communities. Microbial taxa best suited to each successional stage of substrate decomposition become dominant and alter the community structure. The rates of decomposition of organic compounds, therefore, are dependent on the functional traits of dominant taxa and microbial strategies, which are selected and driven by the local environment.

Molecular Determination of Organic Adsorption Sites on Smectite during Fe Redox Processes Using ToF-SIMS Analysis

Turnover of soil organic carbon (SOC) is strongly affected by a balance between mineral protection and microbial degradation. However, the mechanisms controlling the heterogeneous and preferential adsorption of different types of SOC remain elusive. In this work, the heterogeneous adsorption of humic substances (HSs) and microbial carbon (MC) on a clay mineral (nontronite NAu-2) during microbial-mediated Fe redox cycling was determined using time-of-flight secondary ion mass spectrometry (ToF-SIMS). The results revealed that HSs pre-adsorbed on NAu-2 would partially inhibit structural modification of NAu-2 by microbial Fe(III) reduction, thus retarding the subsequent adsorption of MC. In contrast, NAu-2 without precoated HSs adsorbed a significant amount of MC from microbial polysaccharides as a result of Fe(III) reduction. This was attributed to the deposition of a thin Al-rich layer on the clay surface, which provided active sites for MC adsorption. This study provides direct and detailed molecular evidence for the first time to explain the preferential adsorption of MC over HSs on the surface of clay minerals in iron redox processes, which could be critical for the preservation of MC in soil. The results also indicate that ToF-SIMS is a unique tool for understanding complex organic-mineral-microbe interactions.

A bidirectional scanning method for scanning transmission X-ray microscopy

Scanning mode is a key factor for the comprehensive performance, including imaging efficiency, of scanning transmission X-ray microscopy (STXM). Herein is presented a bidirectional scanning method designed for STXM with an S-shaped moving track. In this method, artificially designed ramp waves are generated by a piezo-stage controller to control the two-dimensional scanning of the sample. The sample position information is measured using laser interferometric sensors and sent to a field-programmable gate array (FPGA) board which also acquires the X-ray signals simultaneously from the detector. Since the data recorded by the FPGA contain the real position of each scanned point, the influence of the backlash caused by the back-turning movement on the STXM image can be eliminated. By employing an adapted post-processing program, a re-meshed high-resolution STXM image can be obtained. This S-track bidirectional scanning method in fly-scan mode has been implemented on the STXM endstation at the Shanghai Synchrotron Radiation Facility (SSRF), and successfully resolved the ∼30 nm interval between the innermost strips of a Siemens star. This work removes the limitation on bidirectional scanning caused by motor backlash and vibration, and significantly improves the efficiency of STXM experiments.

Denitrifying pathways dominate nitrous oxide emissions from managed grassland during drought and rewetting

Nitrous oxide is a powerful greenhouse gas whose atmospheric growth rate has accelerated over the past decade. Most anthropogenic N2O emissions result from soil N fertilization, which is converted to N2O via oxic nitrification and anoxic denitrification pathways. Drought-affected soils are expected to be well oxygenated; however, using high-resolution isotopic measurements, we found that denitrifying pathways dominated N2O emissions during a severe drought applied to managed grassland. This was due to a reversible, drought-induced enrichment in nitrogen-bearing organic matter on soil microaggregates and suggested a strong role for chemo- or codenitrification. Throughout rewetting, denitrification dominated emissions, despite high variability in fluxes. Total N2O flux and denitrification contribution were significantly higher during rewetting than for control plots at the same soil moisture range. The observed feedbacks between precipitation changes induced by climate change and N2O emission pathways are sufficient to account for the accelerating N2O growth rate observed over the past decade.

Intrinsic enzyme-like activity of magnetite particles is enhanced by cultivation with Trichoderma guizhouense

Fungal-mineral interactions can produce large amounts of biogenic nano-size (~ 1-100 nm) minerals, yet their influence on fungal physiology and growth remains largely unexplored. Using Trichoderma guizhouense NJAU4742 and magnetite (Mt) as a model fungus and mineral system, we have shown for the first time that biogenic Mt nanoparticles formed during fungal-mineral cultivation exhibit intrinsic peroxidase-like activity. Specifically, the average peroxidase-like activity of Mt nanoparticles after 72 h cultivation was ~ 2.4 times higher than that of the original Mt. Evidence from high resolution X-ray photoelectron spectroscopy analyses indicated that the unique properties of magnetite nanoparticles largely stemmed from their high proportion of surface non-lattice oxygen, through occupying surface oxygen-vacant sites, rather than Fe redox chemistry, which challenges conventional Fenton reaction theories that assume iron to be the sole redox-active centre. Nanoscale secondary ion mass spectrometry with a resolution down to 50 nm demonstrated that a thin (< 1 μm) oxygen-film was present on the surface of fungal hyphae. Furthermore, synchrotron radiation-based micro-FTIR spectra revealed that surface oxygen groups corresponded mainly to organic OH, mineral OH and carbonyl groups. Together, these findings highlight an important, but unrecognized, catalytic activity of mineral nanoparticles produced by fungal-mineral interactions and contribute substantially to our understanding of mineral nanoparticles in natural ecosystems.

Calcareous organic matter coatings sequester siderophores in alkaline soils

Although most studies of organic matter (OM) stabilization in soils have focused on adsorption to aluminosilicate and iron-oxide minerals due to their strong interactions with organic nucleophiles, stabilization within alkaline soils has been empirically correlated with exchangeable Ca. Yet the extent of competing processes within natural soils remains unclear because of inadequate characterization of soil mineralogy and OM distribution within the soil in relation to minerals, particularly in C poor alkaline soils. In this study, we employed bulk and surface-sensitive spectroscopic methods including X-ray diffraction, ⁵⁷Fe-Mössbauer, and X-ray photoemission spectroscopy (XPS), and transmission electron microscopy (TEM) methods to investigate the minerology and soil organic C and N distribution on individual fine particles within an alkaline soil. Microscopy and XPS analyses demonstrated preferential sorption of Ca-containing OM onto surfaces of Fe-oxides and calcite. This result was unexpected given that the bulk combined amounts of quartz and Fe-containing feldspars of the soil constitute ~90% of total minerals and the surface atomic composition was largely Fe and Al (>10% combined) compared to Ca (4.2%). Soil sorption experiments were conducted with two siderophores, pyoverdine and enterobactin, to evaluate the adsorption of organic molecules with functional groups that strongly and preferentially bind Fe. A greater fraction of pyoverdine was adsorbed compared to enterobactin, which is smaller, less polar, and has a lower aqueous solubility. Using NanoSIMS to map the distribution of isotopically-labeled siderophores, we observed correlations with Ca and Fe, along with strong isotopic dilution with native C, indicating associations with OM coatings rather than with bare mineral surfaces. We propose a mechanism of adsorption by which organics aggregate within alkaline soils via cation bridging, favoring the stabilization of larger molecules with a greater number of nucleophilic functional groups.

Sorption of oxytetracycline in particulate organic matter in soils and sediments: Roles of pH, ionic strength and temperature

Particulate organic matter (POM) is a fraction of organic matter with dissimilar properties in different soils. POM isolated from soils and sediments (wetland, oil waste field, farmlands and aquaculture pond sediment) was used to study its sorption behavior on the antibiotic oxytetracycline (OTC). Impacts of solution pH, ionic strength and temperature on the OTC sorption were studied. The sorption rates of OTC in POM from wetland (POM-w) and farmland (POM-f1, POM-f2) were rapid during the first 3 h and gradually decreased with reaction time until reaching the equilibrium. Linear sorption occurred from 3 to 12 h in POM from oil waste field land (POM-o) and aquaculture pond sediment (POM-a). The organic carbon normalized partition coefficient (k_oc) varied from 215.0 to 4493.6 L kg^-1, and it was nearly 10× higher for the POM-w, POM-f1 and POM-f2 than in the POM-o and POM-a. Sorption of OTC by POM exhibited strong pH dependence. Ionic factors affected OTC sorption in POM-f1, POM-f2 and POM-a. The sorption capacity declined >50% in a solution with Ca²⁺ compared to other ions with similar ionic strength. Sorption thermodynamics showed an entropy increasing and endothermic progress during the OTC sorption in POM, implying a spontaneous sorption process. Several mechanisms were involved in OTC sorption in POM, including hydrogen bonding, cation exchange, hydrophobic partitioning and surface complexation.

Nitrogen fertilization modifies organic transformations and coatings on soil biogeochemical interfaces through microbial polysaccharides synthesis

The soil-water interfaces (SWI) in soil pores are hotspots for organic matter (OM) transformation. However, due to the heterogeneous and opaque nature of soil microenvironment, direct and continuous tracing of interfacial reactions, such as OM transformations and formation of organo-mineral associations, are rare. To investigate these processes, a new soil microarray technology (SoilChips) was developed and used. Homogeneous 800-μm-diameter SoilChips were constructed by depositing a dispersed Oxisol A horizon suspension on a patterned glass. Dissolved organic matter from the original soil was added on the SoilChips to mimic SWI processes. The effects of ammonium fertilization (90 mg N kg^-1 soil) on chemical composition of SWIs were evaluated via X-ray photoelectron spectroscopy. Over 21 days, ammonium addition increased OM coatings at SWIs and modified the OM chemical structure with more alcoholic- and carboxylic-C compared to the unfertilized control. Molecular modeling of OM composition at SWIs showed that N fertilization mainly facilitated the microbial production of glucans. We demonstrated that N availability modifies the specific OM molecular processing and its immobilization on SWIs, thereby providing a direct insight into biogeochemical transformation of OM at micro-scale.

Soil Organic Matter and Phosphate Sorption on Natural and Synthetic Fe Oxides under in Situ Conditions

Iron (Fe) oxides in soils are strong sorbents for environmentally important compounds like soil organic matter (SOM) or phosphate, while sorption under field conditions is still poorly understood. We installed polyvinyl chloride plastic bars which have been coated either with synthetic Fe or manganese (Mn) oxides for 30 days in a redoximorphic soil. A previous study revealed the formation of newly formed ("natural") Fe oxides along the Mn oxide coatings. This enables us to differentiate between sorption occurring onto the surfaces of synthetic versus natural Fe oxides. After removal of the bars, they were analyzed by nanoscale secondary ion mass spectrometry (NanoSIMS) to study the distribution of Fe (⁵⁶Fe¹⁶O^-), SOM (¹²C¹⁴N^-), and phosphorus (³¹P¹⁶O₂^-) at the microscale. Image analysis of individual Fe oxide particles revealed a close association of Fe, SOM, and P resulting in coverage values up to 71%. Furthermore, ion ratios between sorbent (⁵⁶Fe¹⁶O^-) and sorbate (¹²C¹⁴N^- and ³¹P¹⁶O₂^-) were smaller along the natural oxides when compared with those for synthetic Fe oxides. We conclude that both natural and synthetic Fe oxides rapidly sequester SOM and P (i.e., within 30 days) but that newly, natural formed Fe oxides sorbe more SOM and P than synthetic Fe oxides.

Monitoring Soil Surface Mineralogy at Different Moisture Conditions Using Visible Near-Infrared Spectroscopy Data

The soil minerals determine essential soil properties such as the cation exchange capacity, texture, structure, and their capacity to form bonds with organic matter. Any alteration of these organo-mineral interactions due to the soil moisture variations needs attention. Visible near-infrared imaging spectroscopy is capable of assessing spectral soil constituents that are responsible for the organo-mineral interactions. In this study, we hypothesized that the alterations of the surface soil mineralogy occur due to the moisture variations. For eight weeks, under laboratory conditions, imaging spectroscopy data were collected on a 72 h basis for three Silty Loam soils varying in the organic matter (no, low and high) placed at the drying-field capacity, field capacity and waterlogging-field capacity treatments. Using the Spectral Information Divergence image classifier, the image area occupied by the Mg-clinochlore, goethite, quartz coated 50% by goethite, hematite dimorphous with maghemite was detected and quantified (percentage). Our results showed these minerals behaved differently, depending on the soil type and soil treatment. While for the soils with organic matter, the mineralogical alterations were evident at the field capacity state, for the one with no organic matter, these changes were insignificant. Using imaging spectroscopy data on the Silty Loam soil, we showed that the surface mineralogy changes over time due to the moisture conditions.

Soil aggregates as biogeochemical reactors: Not a way forward in the research on soil-atmosphere exchange of greenhouse gases

The goal of this comment is to show that the "aggregate reactor" framework recently proposed in an article published in this journal is severely limited by two kinds of indeterminacy. The first is related to the size of aggregates, which is not defined precisely. The second issue is with the impossibility to replicate boundary conditions that are identical to what chunks of soils would have experienced in their natural state. We suggest that the study of GHG release in undisturbed soil samples is a better way to proceed forward.

Soil Aggregate Microbial Communities: Towards Understanding Microbiome Interactions at Biologically Relevant Scales

Soils contain a tangle of minerals, water, nutrients, gases, plant roots, decaying organic matter, and microorganisms which work together to cycle nutrients and support terrestrial plant growth. Most soil microorganisms live in periodically interconnected communities closely associated with soil aggregates, i.e., small (<2 mm), strongly bound clusters of minerals and organic carbon that persist through mechanical disruptions and wetting events. Their spatial structure is important for biogeochemical cycling, and we cannot reliably predict soil biological activities and variability by studying bulk soils alone. To fully understand the biogeochemical processes at work in soils, it is necessary to understand the micrometer-scale interactions that occur between soil particles and their microbial inhabitants. Here, we review the current state of knowledge regarding soil aggregate microbial communities and identify areas of opportunity to study soil ecosystems at a scale relevant to individual cells. We present a framework for understanding aggregate communities as "microbial villages" that are periodically connected through wetting events, allowing for the transfer of genetic material, metabolites, and viruses. We describe both top-down (whole community) and bottom-up (reductionist) strategies for studying these communities. Understanding this requires combining "model system" approaches (e.g., developing mock community artificial aggregates), field observations of natural communities, and broader study of community interactions to include understudied community members, like viruses. Initial studies suggest that aggregate-based approaches are a critical next step for developing a predictive understanding of how geochemical and community interactions govern microbial community structure and nutrient cycling in soil.

Emergent Properties of Microbial Activity in Heterogeneous Soil Microenvironments: Different Research Approaches Are Slowly Converging, Yet Major Challenges Remain

Over the last 60 years, soil microbiologists have accumulated a wealth of experimental data showing that the bulk, macroscopic parameters (e.g., granulometry, pH, soil organic matter, and biomass contents) commonly used to characterize soils provide insufficient information to describe quantitatively the activity of soil microorganisms and some of its outcomes, like the emission of greenhouse gasses. Clearly, new, more appropriate macroscopic parameters are needed, which reflect better the spatial heterogeneity of soils at the microscale (i.e., the pore scale) that is commensurate with the habitat of many microorganisms. For a long time, spectroscopic and microscopic tools were lacking to quantify processes at that scale, but major technological advances over the last 15 years have made suitable equipment available to researchers. In this context, the objective of the present article is to review progress achieved to date in the significant research program that has ensued. This program can be rationalized as a sequence of steps, namely the quantification and modeling of the physical-, (bio)chemical-, and microbiological properties of soils, the integration of these different perspectives into a unified theory, its upscaling to the macroscopic scale, and, eventually, the development of new approaches to measure macroscopic soil characteristics. At this stage, significant progress has been achieved on the physical front, and to a lesser extent on the (bio)chemical one as well, both in terms of experiments and modeling. With regard to the microbial aspects, although a lot of work has been devoted to the modeling of bacterial and fungal activity in soils at the pore scale, the appropriateness of model assumptions cannot be readily assessed because of the scarcity of relevant experimental data. For significant progress to be made, it is crucial to make sure that research on the microbial components of soil systems does not keep lagging behind the work on the physical and (bio)chemical characteristics. Concerning the subsequent steps in the program, very little integration of the various disciplinary perspectives has occurred so far, and, as a result, researchers have not yet been able to tackle the scaling up to the macroscopic level. Many challenges, some of them daunting, remain on the path ahead. Fortunately, a number of these challenges may be resolved by brand new measuring equipment that will become commercially available in the very near future.

Rapid soil formation after glacial retreat shaped by spatial patterns of organic matter accrual in microaggregates

Global change contributes to the retreat of glaciers at unprecedented rates. The deglaciation facilitates biogeochemical processes on glacial deposits with initiating soil formation as an important driver of evolving ecosystems. The underlying mechanisms of soil formation and the association of soil organic matter (SOM) with mineral particles remain unclear, although further insights are critical to understand carbon sequestration in soils. We investigated the microspatial arrangement of SOM coatings at intact soil microaggregate structures during various stages of ecosystem development from 15 to >700 years after deglaciation in the proglacial environment of the Damma glacier (Switzerland). The functionally important clay-sized fraction (<2 μm) was separated into two density fractions with different amounts of organo-mineral associations: light (1.6-2.2 g/cm³ ) and heavy (>2.2 g/cm³ ). To quantify how SOM extends across the surface of mineral particles (coverage) and whether SOM coatings are distributed in fragmented or connected patterns (connectivity), we developed an image analysis protocol based on nanoscale secondary ion mass spectrometry (NanoSIMS). We classified SOM and mineral areas depending on the ¹⁶ O^- , ¹² C^- , and ¹² C¹⁴ N^- distributions. With increasing time after glacial retreat, the microspatial coverage and connectivity of SOM increased rapidly. The rapid soil formation led to a succession of patchy distributed to more connected SOM coatings on soil microaggregates. The maximum coverage of 55% at >700 years suggests direct evidence for SOM sequestration being decoupled from the mineral surface, as it was not completely masked by SOM and retained its functionality as an ion exchange site. The chemical composition of SOM coatings showed a rapid change toward a higher CN:C ratio already at 75 years after glacial retreat, which was associated with microbial succession patterns reflecting high N assimilation. Our results demonstrate that rapid SOM sequestration drives the microspatial succession of SOM coatings in soils, a process that can stabilize SOM for the long term.

Nitrogen-rich microbial products provide new organo-mineral associations for the stabilization of soil organic matter

Understanding the cycling of C and N in soils is important for maintaining soil fertility while also decreasing greenhouse gas emissions, but much remains unknown about how organic matter (OM) is stabilized in soils. We used nano-scale secondary ion mass spectrometry (NanoSIMS) to investigate the changes in C and N in a Vertisol and an Alfisol incubated for 365 days with ¹³ C and ¹⁵ N pulse labeled lucerne (Medicago sativa L.) to discriminate new inputs of OM from the existing soil OM. We found that almost all OM within the free stable microaggregates of the soil was associated with mineral particles, emphasizing the importance of organo-mineral interactions for the stabilization of C. Of particular importance, it was also found that ¹⁵ N-rich microbial products originating from decomposition often sorbed directly to mineral surfaces not previously associated with OM. Thus, we have shown that N-rich microbial products preferentially attach to distinct areas of mineral surfaces compared to C-dominated moieties, demonstrating the ability of soils to store additional OM in newly formed organo-mineral associations on previously OM-free mineral surfaces. Furthermore, differences in ¹⁵ N enrichment were observed between the Vertisol and Alfisol presumably due to differences in mineralogy (smectite-dominated compared to kaolinite-dominated), demonstrating the importance of mineralogy in regulating the sorption of microbial products. Overall, our findings have important implications for the fundamental understanding of OM cycling in soils, including the immobilization and storage of N-rich compounds derived from microbial decomposition and subsequent N mineralization to sustain plant growth.

Source dynamics of radiocesium-contaminated particulate matter deposited in an agricultural water reservoir after the Fukushima nuclear accident

The Fukushima nuclear accident in Japan resulted in the deposition of radiocesium over forested and rural landscapes northwest of the power plant. Although there have been several investigations into the dynamics of contaminated river sediment, less attention has been paid to the sources of deposited particulate matter in dams and reservoirs. In the Fukushima Prefecture, there are 10 significant dams and over a 1000 reservoirs for both agricultural and surface water management. These reservoirs may have trapped a significant volume of radiocesium-contaminated sediment. Therefore, characterizing the sources of contaminated particulate matter is important for the ongoing management of contamination in the region. Accordingly, the composition of particulate matter deposited in the Mano Dam reservoir, approximately 40km northwest of the power plant, was investigated with the analyses and modelling of carbon and nitrogen stable isotope ratios (δ¹³C and δ¹⁵N), total organic carbon (TOC) and total nitrogen (TN) concentrations. Four sediment cores, with lengths ranging 29-41cm, were sampled in the Mano Dam. Source samples from 46 forest soils, 28 cultivated soils and 25 subsoils were used to determine the source contributions of particulate matter. Carbon and nitrogen parameters were analyzed on all samples and a concentration-dependent distribution modelling approach was used to apportion source contributions. Three of the four cores sampled in the Mano Dam reservoir had distinct radiocesium peaks representative of the initial post-accident wash-off phase. Cultivated sources were responsible for 48±7% of the deposited fine particulate matter whereas forests were modelled to contribute 27±6% and subsoil sources 25±4%. Ongoing decontamination of cultivated sources in the Fukushima region should result in a decrease of contaminated matter deposition in reservoirs.

Organic matter identifies the nano-mechanical properties of native soil aggregates

Localized variations at the nanoscale in soil aggregates and in the spatial organisation of soil organic matter (SOM) are critical to understanding the factors involved in soil composition and turnover. However soil nanoscience has been hampered by the lack of suitable methods to determine soil biophysical properties at nanometre spatial resolution with minimal sample preparation. Here we introduce for the first time an Atomic Force Microscopy (AFM)-based Quantitative Nano-Mechanical mapping (QNM) approach that allows the characterisation of the role of SOM in controlling surface nano-mechanical properties of soil aggregates. SOM coverage resulted in an increased roughness and surface variability of soil, as well as in decreased stiffness and adhesive properties. The latter also correlates with nano- to macro-wettability features as determined by contact angle measurements and Water Drop Penetration Time (WDPT) testing. AFM thus represents an ideal quantitative tool to complement existing techniques within the emerging field of soil nanoscience.

Dynamics of soil biogeochemical gas emissions shaped by remolded aggregate sizes and carbon configurations under hydration cycles

Changes in soil hydration status affect microbial community dynamics and shape key biogeochemical processes. Evidence suggests that local anoxic conditions may persist and support anaerobic microbial activity in soil aggregates (or in similar hot spots) long after the bulk soil becomes aerated. To facilitate systematic studies of interactions among environmental factors with biogeochemical emissions of CO₂ , N₂ O and CH₄ from soil aggregates, we remolded silt soil aggregates to different sizes and incorporated carbon at different configurations (core, mixed, no addition). Assemblies of remolded soil aggregates of three sizes (18, 12, and 6 mm) and equal volumetric proportions were embedded in sand columns at four distinct layers. The water table level in each column varied periodically while obtaining measurements of soil GHG emissions for the different aggregate carbon configurations. Experimental results illustrate that methane production required prolonged inundation and highly anoxic conditions for inducing measurable fluxes. The onset of unsaturated conditions (lowering water table) resulted in a decrease in CH₄ emissions while temporarily increasing N₂ O fluxes. Interestingly, N₂ O fluxes were about 80% higher form aggregates with carbon placement in center (anoxic) core compared to mixed carbon within aggregates. The fluxes of CO₂ were comparable for both scenarios of carbon sources. These experimental results highlight the importance of hydration dynamics in activating different GHG production and affecting various transport mechanisms about 80% of total methane emissions during lowering water table level are attributed to physical storage (rather than production), whereas CO₂ emissions (~80%) are attributed to biological activity. A biophysical model for microbial activity within soil aggregates and profiles provides a means for results interpretation and prediction of trends within natural soils under a wide range of conditions.

Advances in Scanning Transmission X-Ray Microscopy for Elucidating Soil Biogeochemical Processes at the Submicron Scale

Organic matter, minerals, and microorganisms are spatially associated in complex organo-mineral assemblages within soils. A mechanistic understanding of processes occurring within organo-mineral assemblages requires noninvasive techniques that minimize any disturbance to the physical and chemical integrity of the sample. Synchrotron-based soft (50-2200 eV) X-ray spectromicroscopic techniques, including scanning transmission X-ray microscopy (STXM), transmission X-ray microscopy (TXM), X-ray photoemission electron microscopy (X-PEEM), and scanning photoelectron microscopy (SPEM), coupled with microspectroscopy (e.g., near-edge X-ray absorption fine structure; NEXAFS) allow for determining the spatial association and speciation of most elements found in soils while maintaining sample integrity. This review highlights application of the four spectromicroscopic techniques mentioned above to soil biogeochemical research, with particular emphasis on STXM-NEXAFS, which has contributed to the greatest set of advancements in the understanding of soil organo-mineral interactions, including mineral control on organic carbon cycling and the mechanisms of biomineral formation.

Exploring the interactions and binding sites between Cd and functional groups in soil using two-dimensional correlation spectroscopy and synchrotron radiation based spectromicroscopies

Understanding how heavy metals bind and interact in soils is essential for predicting their distributions, reactions and fates in the environment. Here we propose a novel strategy, i.e., combining two-dimensional correlation spectroscopy (2D COS) and synchrotron radiation based spectromicroscopies, for identifying heavy metal binding to functional groups in soils. The results showed that although long-term (23 yrs) organic fertilization treatment caused the accumulation of Cd (over 3 times) in soils when compared to no fertilization and chemical fertilization treatments, it significantly (p<0.05) reduced the Cd concentration in wheat grain. The 2D COS analyses demonstrated that soil functional groups controlling Cd binding were modified by fertilization treatments, providing implications for the reduced bioavailability of heavy metals in organic fertilized soils. Furthermore, correlative micro X-ray fluorescence spectromicroscopy, electron probe micro-analyzer mapping, and synchrotron-radiation-based FTIR spectromicroscopy analysis showed that Cd, minerals, and organic functional groups were heterogeneously distributed at the micro-scale in soil colloids. Only minerals, rather than organic groups, had a similar distribution pattern with Cd. Together, this strategy has a potential to explore the interactions and binding sites among heavy metals, minerals and organic components in soil.

Dynamics of PAHs and derived organic compounds in a soil-plant mesocosm spiked with 13C-phenanthrene

Polycyclic Aromatic Hydrocarbons (PAHs) are ubiquitous and persistent soil pollutants. Their fate and the influence of the plant rhizosphere on their dynamics has been extensively studied, but studies mainly focused on their dissipation rate. We conducted a plant-soil mesocosm experiment to study the fate and distribution of PAHs or derived compounds in the extractable fraction, the residual soil, the shoot biomass and the root biomass. The experiment was conducted for 21 days using ryegrass and a forest soil spiked with ¹³C-labeled phenanthrene (PHE), using combined IRMS and NanoSIMS for analyses. Almost 90% of the initial extractable PHE content was dissipated within 3 weeks, but no rhizospheric effect was highlighted on PHE dissipation. More than 40% of ¹³C-PHE was still in the soil at the end of the experiment, but not as PHE or PAH-derived compounds. Therefore it was under the form of new compounds (metabolites) and/or had been incorporated into the microbial biomass. About 0.36% of the initial ¹³C-PHE was recovered in the root and shoot tissues, representing similar ¹³C enrichment (E¹³C) as in the soil (E¹³C ≈ 0.04 at.%). Using NanoSIMS, ¹³C was also localized at the microscale in the roots and their close environment. Global ¹³C enrichment confirmed the results obtained by IRMS. Some hotspots of ¹³C enrichment were found, with a high ³²S/¹²C¹⁴N ratio. Comparing the ratios, sizes and shapes of these hotspots suggested that they could be bacteria.

Do forests represent a long-term source of contaminated particulate matter in the Fukushima Prefecture?

The Fukushima Daiichi Nuclear Power Plant (FDNPP) accident resulted in radiocesium fallout contaminating coastal catchments of the Fukushima Prefecture. As the decontamination effort progresses, the potential downstream migration of radiocesium contaminated particulate matter from forests, which cover over 65% of the most contaminated region, requires investigation. Carbon and nitrogen elemental concentrations and stable isotope ratios are thus used to model the relative contributions of forest, cultivated and subsoil sources to deposited particulate matter in three contaminated coastal catchments. Samples were taken from the main identified sources: cultivated (n = 28), forest (n = 46), and subsoils (n = 25). Deposited particulate matter (n = 82) was sampled during four fieldwork campaigns from November 2012 to November 2014. A distribution modelling approach quantified relative source contributions with multiple combinations of element parameters (carbon only, nitrogen only, and four parameters) for two particle size fractions (<63 μm and <2 mm). Although there was significant particle size enrichment for the particulate matter parameters, these differences only resulted in a 6% (SD 3%) mean difference in relative source contributions. Further, the three different modelling approaches only resulted in a 4% (SD 3%) difference between relative source contributions. For each particulate matter sample, six models (i.e. <63 μm and <2 mm from the three modelling approaches) were used to incorporate a broader definition of potential uncertainty into model results. Forest sources were modelled to contribute 17% (SD 10%) of particulate matter indicating they present a long term potential source of radiocesium contaminated material in fallout impacted catchments. Subsoils contributed 45% (SD 26%) of particulate matter and cultivated sources contributed 38% (SD 19%). The reservoir of radiocesium in forested landscapes in the Fukushima region represents a potential long-term source of particulate contaminated matter that will require diligent management for the foreseeable future.

Toward a Predictive Understanding of Earth's Microbiomes to Address 21st Century Challenges

Microorganisms have shaped our planet and its inhabitants for over 3.5 billion years. Humankind has had a profound influence on the biosphere, manifested as global climate and land use changes, and extensive urbanization in response to a growing population. The challenges we face to supply food, energy, and clean water while maintaining and improving the health of our population and ecosystems are significant. Given the extensive influence of microorganisms across our biosphere, we propose that a coordinated, cross-disciplinary effort is required to understand, predict, and harness microbiome function. From the parallelization of gene function testing to precision manipulation of genes, communities, and model ecosystems and development of novel analytical and simulation approaches, we outline strategies to move microbiome research into an era of causality. These efforts will improve prediction of ecosystem response and enable the development of new, responsible, microbiome-based solutions to significant challenges of our time.

Distribution and Speciation of Cu in the Root Border Cells of Rice by STXM Combined with NEXAFS

Root border cells (RBCs) serve plants in their initial line of defense against stress from the presence of heavy metals in the soil. In this research, light microscopy and synchrotron-based scanning transmission X-ray microscopy (STXM) combined with near edge X-ray absorption fine structure spectroscopy (NEXAFS) with a nanoscale spatial resolution were used to investigate the effects of copper (Cu) upon the RBCs, as well as its distribution and speciation within the RBCs of rice (Oryza sativa L.) under aeroponic culture. The results indicated that with increasing exposure time and concentration, the attached RBCs were surrounded by a thick mucilage layer which changed in form from an ellipse into a strip in response to Cu ion stress. Copper was present as Cu(II), which accumulated not only in the cell wall but also in the cytoplasm. To our knowledge, this is the first time that STXM has been used in combination with NEXAFS to provide new insight into the distribution and speciation of metal elements in isolated plant cells.

In situ visualisation and characterisation of the capacity of highly reactive minerals to preserve soil organic matter (SOM) in colloids at submicron scale

Mineral-organo associations (MOAs) are a mixture of identifiable biopolymers associated with highly reactive minerals and microorganisms. However, the in situ characterization and correlation between soil organic matter (SOM) and highly reactive Al and Fe minerals are still unclear for the lack of technologies, particularly in the long-term agricultural soil colloids at submicron scale. We combined several novel techniques, including nano-scale secondary ion mass spectrometry (NanoSIMS), X-ray absorption near edge structure (XANES) and confocal laser scanning microscopy (CLSM) to characterise the capacity of highly reactive Al and Fe minerals to preserve SOM in Ferralic Cambisol in south China. Our results demonstrated that: (1) highly reactive minerals were strongly related to SOM preservation, while SOM had a more significant line correlation with the highly reactive Al minerals than the highly reactive Fe minerals, according to the regions of interest correlation analyses using NanoSIMS; (2) allophane and ferrihydrite were the potential mineral species to determine the SOM preservation capability, which was evaluated by the X-ray photoelectron spectroscopy (XPS) and Fe K-edge XANES spectroscopy techniques; and (3) soil organic biopolymers with dominant compounds, such as proteins, polysaccharides and lipids, were distributed at the rough and clustered surface of MOAs with high chemical and spatial heterogeneity according to the CLSM observation. Our results also promoted the understanding of the roles played by the highly reactive Al and Fe minerals in the spatial distribution of soil organic biopolymers and SOM sequestration.

Advancements in the application of NanoSIMS and Raman microspectroscopy to investigate the activity of microbial cells in soils

The combined approach of incubating environmental samples with stable isotope-labeled substrates followed by single-cell analyses through high-resolution secondary ion mass spectrometry (NanoSIMS) or Raman microspectroscopy provides insights into the in situ function of microorganisms. This approach has found limited application in soils presumably due to the dispersal of microbial cells in a large background of particles. We developed a pipeline for the efficient preparation of cell extracts from soils for subsequent single-cell methods by combining cell detachment with separation of cells and soil particles followed by cell concentration. The procedure was evaluated by examining its influence on cell recoveries and microbial community composition across two soils. This approach generated a cell fraction with considerably reduced soil particle load and of sufficient small size to allow single-cell analysis by NanoSIMS, as shown when detecting active N2-fixing and cellulose-responsive microorganisms via (15)N2 and (13)C-UL-cellulose incubations, respectively. The same procedure was also applicable for Raman microspectroscopic analyses of soil microorganisms, assessed via microcosm incubations with a (13)C-labeled carbon source and deuterium oxide (D2O, a general activity marker). The described sample preparation procedure enables single-cell analysis of soil microorganisms using NanoSIMS and Raman microspectroscopy, but should also facilitate single-cell sorting and sequencing.

Fe biomineralization mirrors individual metabolic activity in a nitrate-dependent Fe(II)-oxidizer

Microbial biomineralization sometimes leads to periplasmic encrustation, which is predicted to enhance microorganism preservation in the fossil record. Mineral precipitation within the periplasm is, however, thought to induce death, as a result of permeability loss preventing nutrient and waste transit across the cell wall. This hypothesis had, however, never been investigated down to the single cell level. Here, we cultured the nitrate reducing Fe(II) oxidizing bacteria Acidovorax sp. strain BoFeN1 that have been previously shown to promote the precipitation of a diversity of Fe minerals (lepidocrocite, goethite, Fe phosphate) encrusting the periplasm. We investigated the connection of Fe biomineralization with carbon assimilation at the single cell level, using a combination of electron microscopy and Nano-Secondary Ion Mass Spectrometry. Our analyses revealed strong individual heterogeneities of Fe biomineralization. Noteworthy, a small proportion of cells remaining free of any precipitate persisted even at advanced stages of biomineralization. Using pulse chase experiments with (13)C-acetate, we provide evidence of individual phenotypic heterogeneities of carbon assimilation, correlated with the level of Fe biomineralization. Whereas non- and moderately encrusted cells were able to assimilate acetate, higher levels of periplasmic encrustation prevented any carbon incorporation. Carbon assimilation only depended on the level of Fe encrustation and not on the nature of Fe minerals precipitated in the cell wall. Carbon assimilation decreased exponentially with increasing cell-associated Fe content. Persistence of a small proportion of non-mineralized and metabolically active cells might constitute a survival strategy in highly ferruginous environments. Eventually, our results suggest that periplasmic Fe biomineralization may provide a signature of individual metabolic status, which could be looked for in the fossil record and in modern environmental samples.

Submicron structures provide preferential spots for carbon and nitrogen sequestration in soils

The sequestration of carbon and nitrogen by clay-sized particles in soils is well established, and clay content or mineral surface area has been used to estimate the sequestration potential of soils. Here, via incubation of a sieved (<2 mm) topsoil with labelled litter, we find that only some of the clay-sized surfaces bind organic matter (OM). Surprisingly, <19% of the visible mineral areas show an OM attachment. OM is preferentially associated with organo-mineral clusters with rough surfaces. By combining nano-scale secondary ion mass spectrometry and isotopic tracing, we distinguish between new labelled and pre-existing OM and show that new OM is preferentially attached to already present organo-mineral clusters. These results, which provide evidence that only a limited proportion of the clay-sized surfaces contribute to OM sequestration, revolutionize our view of carbon sequestration in soils and the widely used carbon saturation estimates.

Clay-sized particles bind organic matter and sequester carbon and nitrogen in soils, yet extent and localization of organic matter coverage remain unclear. Using NanoSIMS, Vogel et al. chemically image soils at ultra-high resolution and show that only particles with rough surfaces react with organic matter.

Advanced techniques for in situ analysis of the biofilm matrix (structure, composition, dynamics) by means of laser scanning microscopy

The extracellular constituents in bioaggregates and biofilms can be imaged four dimensionally by using laser scanning microscopy. In this protocol we provide guidance on how to examine the various extracellular compartments in between microbial cells and communities associated with interfaces. The current options for fluorescence staining of matrix compounds and extracellular microhabitats are presented. Furthermore, practical aspects are discussed and useful notes are added. The chapter ends with a brief introduction to other approaches for EPS analysis and an outlook for future needs.

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.