Progress 09/01/08 to 08/31/12
Outputs
OUTPUTS: The objective of the proposed project has been to design novel experimental and non-destructive high resolution spectromicroscopic (C, N, Ca, Fe, Al and Si NEXAFS) approaches in collaboration with scientist from USGS, CLS and NSLS that enable us to obtain first-hand process-oriented biogeochemical evidence regarding: (i) the in situ spatial arrangement of minerals, polyvalent metal-ions, organic C functionalities and other architectural features of organo-mineral soil assemblages at the microscopic and sub-microscopic level. Spatial distribution in microaggregates: The methods for the necessary cryo-sectioning had to be adapted as the samples possessed a greater sand content than samples that we had experimented with before. We successfully obtained total elemental contents of C, N, K, Ca, Fe, Si and Al, as well as their functional group chemistry for three full cross-sections of microaggregates. In addition to NEXAFS, we have forged new collaborative arrangements with material scientists and applied physicists to explore extremely novel STEM-EELS (Scanning Transmission Electron Microscopy coupled with Electron Energy Loss Spectroscopy) technology. This affords the possibility to map the functional group chemistry (similar to NEXAFS) with even greater spatial resolution, reaching atomic level. We have measured several sections with this technology and obtained very interesting results at a very high spatial resolution of 1 to 10 nm. Identification of peaks: In order to achieve effective peak identification, a wide range of analytical grade organic reference compounds (amino sugars, amino acids, lipids, nucleobases, etc. and other molecular markers for polyaromatic compounds etc.) organic source materials (plant litter, fungal and bacterial cells, root exudates etc.) have been analyzed and we generated a reference spectral library of organic and inorganic standards that is publically available under http//knb.ecoinformatics.org/knb/metacat/datastar.50.3/knb. Interactions of minerals and organic matter: In batch experiments, we studied the interactions between select minerals and certain forms of organic matter. These were compared to the in-situ measurements in microaggregates of the Merced chronosequence. This project has provided several opportunities for students to engage in high-level research. Karen Heymann (PhD student) was trained on NEXAFS analyses at both the National Synchrotron Light Source (NSLS) at Brookhaven National Laboratory and the Canadian Light Source. In addition we have provided a hands-on training workshop on synchrotron-based spectromicroscopy techniques for minority and less represented participants selected from the University of Pennsylvania and from the University of Massachusetts at the National Synchrotron Light Source. Within the project, a technician (Akio Enders) has been trained on the cryo-sectioning to obtain thin sections for NEXAFS analyses. Motivated by the positive experience through the project, Akio entered an employee degree program to advance to a graduate degree at Cornell University. PARTICIPANTS: Dr Johannes Lehmann, Department of Crop and Soil Sciences, Cornell University: PI, coordination of activities, development of science strategy, reporting. Dr. Dawit Solomon, Department of Crop and Soil Sciences, Cornell University: co-PI, coordination of activities, sampling, development of sampling design and conducting experiments and data analysis, writing of publications. Dr Jennifer Harden, USGS, Menlo Park, CA: collaborator, identification of field sites, data interpretation. Jennifer Harden, collaborator U.S. Geological Survey, USA Dr. Sue Wirick, National Synchrotron Light Source, Brookhaven National Laboratories; Collaborator, involved in data collection at the X1Abeamline, quality control and analysis. Dr. Lisa Miller, National Synchrotron Light Source, Brookhaven National Laboratories; Collaborator, involved in data collection at the U2B beamline, quality control and analysis. Dr. Chithra Karunakaran, Canadian Light Source, Canada Collaborator, involved in data collection at the SM beamline, quality control and analysis. TARGET AUDIENCES: Target audiences include all environmental and soil scientists, as well as ecologists who are engaged in aspects of carbon sequestration in soils and the dynamic processes involved therein and the impact of these processes on climate change. PROJECT MODIFICATIONS: The greatest limitation to our progress was access to beam line and the length of beam time to conduct both the Sr-FTIR and NEXAFS measurements. Because of the demand by an increasing number of scientists globally, available beam time is severely limited at synchrotron facilities for each research group. Although we have excellent relationships and a good track record in utilizing the data that we have collected in the past from these facilities and the fact that our proposals were assessed very favorably each time and we were awarded a generous amount of beam time, the nature of the work and the time required to collect data at micro and nanoscale resolution from a single organomineral assemblage significantly limits the progress that can be made using such approaches. A further delay in our experiments was presented from unforeseeable problems at the beam lines which had forced frequent beam dumping during our measurement time. For these two reasons, the project experienced a delay in data collection. Some of these setbacks were compensated by remote access to the beamline and utilization of random openings of beam time, as well as utilizing other microscope techniques outside synchrotrons.
Impacts
Capturing spatial distribution in microaggregates: We demonstrated the potential of wavelet analysis to investigate nano-scale spatial variation in soil without statistical assumptions that are generally implausible. We found different patterns of scale-dependent variation between the carbon forms, which could be represented by pair-wise wavelet correlations at the different scales, and by principal components analysis of all the correlations at each scale. Aromatic and carboxylic carbon were positively correlated at the coarsest scales, and negatively correlated at the finest scales, suggesting a multiscale pattern in which contrasting forms of carbon are deposited in common clumps, but at finer scales either one or the other form dominates. In contrast phenolic and aliphatic carbon were positively and significantly correlated at all scales, although with weaker correlations at the finer scales, suggesting that their spatial variation has common sources across a range of scales, although the coarse-scale pattern is the dominant one. Identification of peaks: Different standards showed reproducible and unique spectral signatures. The spectra of carbohydrates and amino sugars show resonances between 289.10 and 289.59 eV, whereas amino acids produced a strong signal around 288.70 eV. Spectral features near 285.29 eV were ascribed to ring structure of aromatic amino acids, while spectra between 287.14 and 287.86 eV were attributed to excitations from CH and CH2 groups. Molecular markers for black C exhibit sharp absorption bands between 285.01 and at 285.43 eV. These aromatic carboxylic acids also exhibit broad peaks between 288.35 and 288.48 eV, reflecting carboxyl functional groups bonded to unsaturated C. This investigation provides a more comprehensive NEXAFS spectral library of biogeochemically relevant organic C compounds. Identification and mapping of Micro- and nano-environments of C sequestration in soil: The multi-element STXM-NEXAFS investigation helped us to demonstrated for the first time the potential of synchrotron-based noninvasive STXM-NEXAFS spectroscopy to access biogeochemically relevant elements and acquire spatially defined, multi-element submicron-level information. For example, STXM-NEXAFS identified terminal micro- and nano-organic C repository environments in undisturbed organomineral assemblages, produced multi-element images and fingerprint of physically entrapped particulate black C, non-black C and mineral matter, provided submicron-level multi-element insight about the most likely binding mechanisms in the organomineral interface, provided evidence for a "two-way" direct associative interaction between black C, non-black C and mineral matter, as well as "three-way" indirect molecular-level linkage between black C, non-black C and mineral matter. Organomineral interactions between black C (BC) and mineral surfaces: The work successfully demonstrated that BC-mineral interactions do occur over short reaction times, and that these interactions may result in chemical changes to BC surfaces.
Publications
- Chia CH, Munroe P, Joseph S, Lin Y, Lehmann J, Muller DA, Xin HL and Neves E 2012 Analytical electron microscopy of black carbon and microaggregated mineral matter in Amazonian Dark Earth. Journal of Microscopy 245, 129-139.
- Solomon D, Lehmann, Harden J, Wang J, Kinyangi J, Heymann K, Karunakaran C, Lu Y, Wirick S, and Jacobsen C 2012 Micro- and nano-environments of carbon sequestration: Multi-element STXM-NEXAFS spectromicroscopy assessment of microbial carbon and mineral associations. Chemical Geology 329, 53-73
- Solomon D, Lehmann, Wang J, Kinyangi J, Heymann K, Lu Y, Wirick S, and Jacobsen C 2012 Micro- and nano-environments of carbon sequestration: A multi-element STXM-NEXAFS assessment of black carbon and organomineral associations. Science of the Total Environment 438, 372-388.
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Progress 09/01/10 to 08/31/11
Outputs
OUTPUTS: The objective of the proposed project is to design novel experimental and non-destructive high resolution spectromicroscopic (C, N, Ca, Fe, Al and Si NEXAFS) approaches in collaboration with scientist from USGS, CLS and NSLS that enable us to obtain first-hand process-oriented biogeochemical evidence regarding: (i) the in situ spatial arrangement of minerals, polyvalent metal-ions, organic C functionalities and other architectural features of organo-mineral assemblages at the microscopic and sub-microscopic level, and (ii) element-specific information about local structural and compositional environments of adsorbing atoms and surficial interactions, micro- and nano-scale heterogeneity in spatial allocations and other molecular-level features of organo-mineral assemblages. Spatial distribution in microaggregates: we have made significant progress and collected most of the noninvasive in situ synchrotron-based measurements from the samples. The soft X-ray spectromicroscopic techniques that will help us to identify and map the various micro- and nano-scale physical features such as surficial, organomineral interaction and "bio-exclusion" repository zones from the split-samples collected from the USGS site at the Merced-California chronosequence are measured using both proximal and remote access. Despite the problems encountered in obtaining enough beamtime, we have now recorded excellent multi-element NEXAFS stacks for C K-edge, N K-edge, Ca L3,2-edges, Fe L3,2-edges, Al K-edge and Si K-edge from three ultra-thin sections at the Canadian Light Source in Saskatoon at both 500 nm (from full aggregate cross-section) and 50 nm (from selected hotspots) resolution. In addition to NEXAFS, we have forged new collaborative arrangements with material scientists and applied physicists to explore extremely novel STEM-EELS (Scanning Transmission Electron Microscopy coupled with Electron Energy Loss Spectroscopy) technology. This affords the possibility to map the functional group chemistry (similar to NEXAFS) with even greater spatial resolution, reaching atomic level. Additional studies were conducted on the use of wavelet analysis of soil variation at nanometre- to micrometre-scales to extract more quantitative information and develop a method for soil and environmental scientist to use a more robust spatial quantitative analysis. Identification of peaks: In order to achieve effective peak identification, a wide range of analytical grade organic reference compounds (amino sugars, amino acids, lipids, nucleobases, waxes, suberins, carbohydrates, phenols and other molecular markers for polyaromatic compounds etc.) and organic source materials (plant litter, dissolved organic matter, fungal and bacterial cells, root exudates etc.) have been analyzed in the past and data has been posted at . We started to generate a reference spectral library of organic and inorganic standards. Interactions of minerals and organic matter: in batch experiments, we studied the interactions between select minerals and certain forms of organic matter. These exploratory studies will then be compared to the in-situ measurements in microaggregates of the Merced chronosequence. PARTICIPANTS: Dr Johannes Lehmann, Department of Crop and Soil Sciences, Cornell University: PI, coordination of activities, development of science strategy, reporting. Dr. Dawit Solomon, Department of Crop and Soil Sciences, Cornell University: co-PI, coordination of activities, sampling, development of sampling design and conducting experiments and data analysis, writing of publications. Dr Jennifer Harden, USGS, Menlo Park, CA: collaborator, identification of field sites, data interpretation. Jennifer Harden, collaborator U.S. Geological Survey, USA Dr. Sue Wirick, National Synchrotron Light Source, Brookhaven National Laboratories; Collaborator, involved in data collection at the X1Abeamline, quality control and analysis. Dr. Lisa Miller, National Synchrotron Light Source, Brookhaven National Laboratories; Collaborator, involved in data collection at the U2B beamline, quality control and analysis. Dr. Chithra Karunakaran, Canadian Light Source, Canada Collaborator, involved in data collection at the SM beamline, quality control and analysis. TARGET AUDIENCES: Target audiences include all environmental and soil scientists, as well as ecologists who are engaged in aspects of carbon sequestration in soils and the dynamic processes involved therein and the impact of these processes on climate change. PROJECT MODIFICATIONS: The greatest limitation to our progress is access to beam line and the length of beam time to conduct both the Sr-FTIR and NEXAFS measurements. Because of the demand by an increasing number of scientists globally, available beam time is severely limited at synchrotron facilities for each research group. Although we have excellent relationships and a good track record in utilizing the data that we have collected in the past from these facilities and the fact that our proposals were assessed very favorably each time and we were awarded a generous amount of beam time, the nature of the work and the time required to collect data at micro and nanoscale resolution from a single organomineral assemblage significantly limits the progress that can be made using such approaches. A further delay in our experiments was presented from unforeseeable problems at the beam lines which had forced frequent beam dumping during our measurement time. For these two reasons, the project experienced a delay in data collection. Some of these setbacks were compensated by remote access to the beamline and utilization of random openings of beam time.
Impacts
Outputs generated from peak identification work: we undertook detailed investigation of the carbon (1s) NEXAFS of biogeochemically relevant reference organic compounds to provide a comprehensive systematic overview of spectral signatures and peak positions of major organic molecules that potentially occur in soils as part of organic matter to improve our understanding of the molecular structure and chemistry of this complex organic materials in organo-mineral assemblages. We integrated the conjugated surface and bulk sensitivity potentials of this complementary spectromicroscopic tool to the ensemble of micro-scale physical and chemical characterization techniques to address a broad range of environmental issues related to the impacts of climate change on C sequestration in terrestrial ecosystems. In order to achieve effective peak identification, a wide range of analytical grade organic reference compounds (amino sugars, amino acids, lipids, nucleobases, waxes, suberins, carbohydrates, phenols and other molecular markers for polyaromatic compounds etc.) and organic source materials (plant litter, dissolved organic matter, fungal and bacterial cells, root exudates etc.) have been analyzed. Based on these results, we have built an on-line platform in the form of a spectral library where the data set is now available to the general public. This can be found at http//knb.ecoinformatics.org/knb/metacat/datastar.50.3/knb. Outputs generated from spatial distribution and bulk analysis work: Despite the problems encountered in obtaining sufficient beamtime, we have now recorded excellent multi-element NEXAFS stacks for C K-edge, N K-edge, Ca L3,2-edges, Fe L3,2-edges, Al K-edge and Si K-edge from three ultra-thin sections at the Canadian Light Source in Saskatoon at both 500 nm (from full aggregate cross-section) and 50 nm (from selected hotspots) resolution. Investigations have been conducted on micro- and nano-environments of carbon sequestration - a new concept which we hope will help soil and environmental scientists to investigate the precise mechanism for the interaction between minerals and C in soils and the manner of C sequestration at a nano-level and understand the nanoscale soil carbon sequestration mechanisms relevant for climate change mitigation and agricultural sustainability which is still largely unknown. This data is expected to show the interactions of minerals and organic matter from plant and black carbon in soils. Outputs generated from organomineral interactions between black C (BC) and mineral surfaces work: To observe the effects of minerals on BC surface chemistry, BC-mineral mixtures were made by combining the treated and untreated char with synthetic goethite, pyrophyllite, vermiculite, or kaolinite, or with water only. It was successful in showing that BC-mineral interactions do occur over short reaction times, and that these interactions may result in chemical changes to BC surfaces.
Publications
- Heymann K, Lehmann J, Solomon D, Schmidt MWI, Regier T 2011 C 1s K-edge near-edge X-ray fine structure (NEXAFS) spectroscopy for characterizing the functional group chemistry of black carbon. Organic Geochemistry 42, 1055-1064
- Milne AE, Lehmann J, Solomon D, Lark RM 2011 Wavelet analysis of soil variation at nanometre- to micrometre-scales; an example of organic carbon content in a micro-aggregate. European Journal of Soil Science 62: 617-628.
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Progress 09/01/09 to 08/31/10
Outputs
OUTPUTS: The basic data (with the exception of XRD measurements) were organized and the platform for conducting the experiments and sharing project information with our partner organizations (USGS, BNL and CLS) is already functional. We have conducted an all investigators and collaborators meeting to discuss details about research project, design, method development as planned in the project proposal. We have made significant progress and collected all the noninvasive in situ synchrotron-based FTIR measurements from the samples. The soft X-ray spectromicroscopic techniques that will help us to identify and map the various micro- and nano-scale physical features such as surficial, organomineral interaction and "bio-exclusion" repository zones from the split-samples collected from the USGS site at the Merced-California chronosequence are analyzed measured using both proximal and remote access. Some of the results are either already summarized and published, submitted or under preparation (please see the publication section) in a wide rage of topics that span from speciation and long- and short-term molecular-level dynamics of soil organic sulfur, nano-scale spatial biogeocomplexity of organomineral assemblages using C K-, Ca L2,3- and Fe L2,3-edges NEXAFS spectromicroscopy to micro- and nano-environments of carbon sequestration: Multi-element STXM-NEXAFS spectromicroscopy assessment of microbial carbon and mineral associations in collaboration with scientist from USGS, CLS and NSLS. We have also presented C, N, Al, Si K-edge and Ca and Fe L-edge NEXAFS spectroscopy investigation of micro- and nano- environments of carbon sequestration at the Organic Matter Stabilization and Ecosystem Function Conference in France. We have also continued to prepare clay separates and cryo-microtomed ultrathin sections of microaggregates for standard X-ray crystallography and for C, N, Ca, Fe, Al and Si NEXAFS measurements that will be conducted at the Canadian synchrotron-Light Source and at the National Synchrotron Light Source-Brookhaven National Laboratories. We have taken a detailed investigation on the carbon (1s) NEXAFS spectroscopy of biogeochemically relevant reference organic compounds to provide a comprehensive systematic overview of spectral signatures and peak positions of major organic molecules that potentially occur in soils and built an on-line platform in the form of spectral library where this data set will be available to the general public. Together with the Cornell NanoScale Science and Technology Facility (CNF), we have intensified our effort to address a completely new dimension in soil science involving the nanoscale particles and processes in soils to supplement our investigation since the properties of nanoparticles may differ in important ways from the properties of bulk materials and single atoms or molecules and due to the unusual physical, chemical, and biological properties that can emerge in soils at the nanoscale. Many of these processes are vital to understand for carbon capture and storage in soils for environmental sustainability and mitigating climate change. PARTICIPANTS: Dr Johannes Lehmann, Department of Crop and Soil Sciences, Cornell University: PI, coordination of activities, development of science strategy, reporting. Dr. Dawit Solomon, Department of Crop and Soil Sciences, Cornell University: co-PI, coordination of activities, sampling, development of sampling design and conducting experiments and data analysis, writing of publications. Dr Jennifer Harden, USGS, Menlo Park, CA: collaborator, identification of field sites, data interpretation. Jennifer Harden, collaborator U.S. Geological Survey, USA Dr. Sue Wirick, National Synchrotron Light Source, Brookhaven National Laboratories; Collaborator, involved in data collection at the X1Abeamline, quality control and analysis. Dr. Lisa Miller, National Synchrotron Light Source, Brookhaven National Laboratories; Collaborator, involved in data collection at the U2B beamline, quality control and analysis. Chithra Karunakaran, Canadian Light Source, Canada Collaborator, involved in data collection at the SM beamline, quality control and analysis. TARGET AUDIENCES: Target audiences include all environmental and soil scientists, as well as ecologists who are engage in aspects of carbon sequestration in soils and the dynamic processes involved there in and the impact of these processes in global warming and climate change. PROJECT MODIFICATIONS: The greatest limitation to our progress is access to beamline and the length of beamtime to conduct both the Sr-FTIR and NEXAFS measurements. Because of the demand by a number of scientists from allover the world, there is limited beamtime available at each synchrotron facility for each research group. Although we have excellent relationship and good track record in utilizing the data that we have collected in the past from these facilities and the fact that our proposals were assessed very favorably each time and we were awarded a generous amount of beamtime, the nature of the work and the time required to collect data at a micro and nanoscale resolutions from a single organomineral assemblage significantly limits the progress that can be made using such approaches. A further delay in our experiments was presented from unavoidable problems at the beamlines which will force frequent beam dumping during measurement time. For these two reasons, the project experiences at times delay in data collection and its progress. However, as an alternative solution, we have recently started to use remote access to the STXM and NEXAFS beamline at the Canadian Light Source in collaboration with the beamline scientists, which is helping us to push forward our research agenda and achieve our research objectives.
Impacts
Outputs generated from the data collected from the SR-FTIR and multi-element NEXAFS spectromicroscopy runs provided a significant amount of information about the nano-scale spatial biogeocomplexity of organomineral assemblages, the changes in black carbon chemistry as a result of interaction with clay minerals, the presence of unique micro- and nano-environments of carbon sequestration zones in organomineral assemblages and the interactions microbial carbon and mineral interfaces therein. The standard library enabled us to identify and fingerprint the various micro- and nano-scale physical features such as surficial, organomineral interaction and "bio-exclusion" repository zones for organic matter created as a result of the interplay between mineral particles, organic matter and pore spaces. We have published part of the results of our investigation; and continued to intensify our research effort to investigate the nano particles of silicate, minerals, iron and aluminum oxides and organic materials; and processes in soils to supplement our investigation. We have conducted preliminary experiments and measurements using advanced STEM that have < 1 nm resolution with a conjugated EELS potential for a high resolution imaging, elemental identification and studies of nearest-neighbor bonding at the atomic scale at the organo-mineral interface in soils together with the Cornell nanoscale science and technology facility, a national user facility that supports a broad range of nanoscale science and technology projects. We will explore and obtain atomistic-level understanding the chemical state and control of the electronic properties of interfaces, compositional chemistry and other interactive features of elements, oxide communities such as iron, aluminum, manganese, titanium oxides and other mineral interfaces responsible for binding organic carbon. Model organo-mineral complexes and soil samples will be characterized using various probes of the electronic structure in real-space; and are expected to provide valuable input into developing realistic theoretical models for these novel and exciting systems to address sustainability and climate change mitigation strategies. . This investigation is the first of its type and the unprecedented ability to investigate the different phases present in complex matrices such as soils, separated probably by only an atomically-thin wall, enables the generation of a wealth of new atomic- and nanoscale-level information of organic and oxide communities. Detailed structural information is being generated from the distinctive spectral features of the weathering gradient samples for a number elements (N, Ca, Fe, Al and Si) from the exact same spot where the C measurements were recorded that could be used to build robust peak assignment criteria to exploit the chemical sensitivity of NEXAFS spectroscopy. We will use this understanding to identify the precise mechanisms for carbon sequestration mechanisms in soil for climate change mitigation.
Publications
- Solomon, D., Lehmann, J. Harden, J., Wang, J., Kinyangi, J., Heymann, K., Karunakaran, C., Lu, Y., Wirick, S., Jacobsen, C. 2011. Micro- and nano-environments of carbon sequestration: Multi-element STXM-NEXAFS spectromicroscopy assessment of microbial carbon and mineral associations. Journal of Chemical Geology (under review).
- Solomon, D., Lehmann, J. Harden, J., Wang, J., Kinyangi, J., Heymann, K., Karunakaran, C., Lu, Y., Wirick, S., Jacobsen, C. 2011. Micro- and nano-environments of carbon sequestration: Multi-element STXM-NEXAFS spectromicroscopy assessment of black carbon and mineral associations. Biogeochemistry (under preparation).
- Solomon, D., Lehmann, J., Knoth-de Zurruk, K., Dathe, J., Kinyangi, J., Liang, B., and Machado, S. 2011. Speciation, Long- and Short-term Molecular-level Dynamics of Organic Sulfur Studied by XANES Spectroscopy. Journal of Environmental Quality, doi:10.2134/jeq2010.0061 ; Published online 7 Oct. 2010.
- Solomon, D., Lehmann, J., Heymann, K. and Harden, J. 2010. Nano-scale spatial biogeocomplexity of Organomineral assemblages using C K-, Ca L2,3- and Fe L2,3-edges NEXAFS spectromicroscopy . Canadian Light Source Activity Report, Saskatoon, Canada.
- Heymann, K., Lehmann, J., Solomon, D., Regier, T. 2010. C 1s NEXAFS study of changes in black carbon chemistry as a result of interaction with clay minerals, Canadian Light Source Activity Report, Saskatoon, Canada.
- Lehmann, L. and Solomon, D. 2010. Organic Carbon Chemistry in Soils Observed by Synchrotron-based Spectroscopy. In: Singh, B., and Grafe, M. (Eds.), Synchrotron-Based Techniques in Soils and Sediments, Developments in Soil Science, Volume 34, 2010, Elsevier, The Netherlands Pages 289-312.
- Solomon, D., Lehmann, J., Kinyangi, J., Liang, B., Hanley, K., Heymann, K., Wirick, S. and Jacobsen, C. 2009. Carbon (1s) NEXAFS spectroscopy of biogeochemically relevant organic reference compounds. Soil Science Society of America Journal, 73:1817-1830.
- Solomon, D., Lehmann, J., Kinyangi, J., Pell, A., Riha, S., Theis, J., Solomon, N., Amelung, A., Lobe, I., Machado, S., and Janzen, H. 2009. Anthropogenic and climate influences on biogeochemical dynamics and molecular-level speciation of soil sulfur. Ecological Applications, 19: 989-1002.
- Lehmann, J., Brandes J., Solomon D., Fleckenstein H., Jacobson C., and Thieme J. 2009. Synchrotron-based near-edge X-ray Spectroscopy of NOM in soils and sediments. In: Senesi, N., Xing P. and Huang, P.M. (Eds.), Biophysico-Chemical Processes Involving Natural Nonliving Organic Matter in Environmental Systems IUPAC Series on Biophysico-Chemical Processes in Environmental Systems pp. 723-771.
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Progress 09/01/08 to 08/31/09
Outputs
OUTPUTS: Considerable efforts have been made to organize basic data and developing the enabling platforms for conducting the experiments and sharing project information with our partner organizations (USGS, BNL and CLS). We have also conducted an all investigators and collaborators meeting to discuss details about research project, design, method development as planned in the project proposal. Dr. Solomon and other project personnel have travelled to the USGS site at Menlo Park, CA to visit the chronosequence sites for soil split-sampling and to obtain existing information that will enable better interpretation of the data. We have also made significant progress in developing the right approach for the noninvasive in situ synchrotron-based FTIR and soft X-ray spectromicroscopic techniques, which will help us to identify and map the various micro- and nano-scale physical features such as surficial, organomineral interaction and "bio-exclusion" repository zones for organic matter which are created as a result of the interplay between mineral particles, organic matter and pore spaces in organomineral assemblages from the split-samples collected from the USGS site at obtained from the Merced-California chronosequence, where the underlying substrate ranges in age from 3 up to 3000 kyr. In accordance with the proposed project plan, we have started sample preparation for standard analysis and also prepared ultrathin sections from microaggregates using cryo-microtome and conduct Sr-FTIR and C, N, Ca, Fe, Al and Si NEXAFS analysis measurements on two organomineral samples at the Canadian synchrotron-Light Source and at the National Synchrotron Light Source-Brookhaven National Laboratories. In a second approach, we have made detailed investigation using carbon (1s) NEXAFS spectroscopy of biogeochemically relevant organic reference compounds. This work provides a comprehensive systematic overview of spectral signatures and peak positions of major organic molecules that potentially occur in soils as part of organic matter. The characterization of reference compounds will improve our understanding of the molecular structure and chemistry of complex organic materials in the organomineral assemblages. It will also help integrating the conjugated surface and bulk sensitivity potentials of this complementary spectromicroscopic tool to the ensemble of micro-scale physical and chemical characterization techniques to address a broad range of environmental issues related to the impacts of climate change on C sequestration in terrestrial ecosystems. We have also started building an on-line platform in the form of a spectral library where this data set will be available to the general public. This part of the project progress was presented by "Dawit Solomon, Johannes Lehmann, Jennifer Harden, Sue Wirick and Chithra Karunakaran (2009) Nano-scale biogeochemistry of C, N, Ca, Fe and Si in organo-mineral assemblages" in the form of a poster at the International Symposium on Soil Organic Matter Dynamics: Land Use, Management and Global Change, Colorado Springs, Colorado, USA July 6-9, 2009. PARTICIPANTS: Dr Johannes Lehmann, Department of Crop and Soil Sciences, Cornell University: PI, coordination of activities, development of science strategy, reporting. Dr. Dawit Solomon, Department of Crop and Soil Sciences, Cornell University: co-PI, coordination of activities, sampling, development of sampling design and conducting experiments and data analysis, writing of publications. Dr Jennifer Harden, USGS, Menlo Park, CA: collaborator, identification of field sites, data interpretation. Jennifer Harden, collaborator U.S. Geological Survey, USA Dr. Sue Wirick, National Synchrotron Light Source, Brookhaven National Laboratories; Collaborator, involved in data collection at the X1Abeamline, quality control and analysis. Dr. Lisa Miller, National Synchrotron Light Source, Brookhaven National Laboratories; Collaborator, involved in data collection at the U2B beamline, quality control and analysis. Dr. Chithra Karunakaran, Canadian Light Source, Canada Collaborator, involved in data collection at the SM beamline, quality control and analysis. TARGET AUDIENCES: Target audiences include all environmental and soil scientists, as well as ecologists who are engaged in aspects of carbon sequestration in soils and the dynamic processes involved therein and the impact of these processes on climate change. PROJECT MODIFICATIONS: The greatest limitation to our progress is access to beamline and the length of beamtime to conduct both the Sr-FTIR and NEXAFS measurements. Because of the demand by an increasing number of scientists globally, there is limited beamtime available at synchrotron facilities for each research group. Although we have excellent relationships and a good track record in utilizing the data that we have collected in the past from these facilities and the fact that our proposals were assessed very favorably each time and we were awarded a generous amount of beamtime, the nature of the work and the time required to collect data at micro and nanoscale resolution from a single organomineral assemblage significantly limits the progress that can be made using such approaches. A further delay in our experiments was presented from unforeseeable problems at the beamlines which had forced frequent beam dumping during our measurement time. For these two reasons, the project experienced a delay in data collection.
Impacts
Outputs have generated from both the conceptual models and the data collected in the first two SR-FTIR and NEXAFS runs at the two synchrotron facilities we have acquired a significant amount of information about how to identify and fingerprint the various micro- and nano-scale physical features such as surficial, organomineral interactions and "bio-exclusion" repository zones for organic matter which are created as a result of the interplay between mineral particles, organic matter and pore spaces in organomineral assemblages measured using the first two runs. This will help us to optimize some of our future measurements and collect better quality data. The preliminary spectral library of the reference organic compounds revealed distinct spectral features and peak positions at the C K-edge that are characteristic of the molecular orbitals bonding C atoms. Detailed structural information were also derived from these distinctive spectral features that could be used to build robust peak assignment criteria to exploit the chemical sensitivity of NEXAFS spectroscopy for in situ molecular-level spatial investigation and fingerprinting of complex organic C compounds in organomineral samples. Part of this work was published in a high-ranking journal and generated significant discussion both in the academic but also in the popular press.
Publications
- Dawit Solomon, Johannes Lehmann, James Kinyangi, Biqing Liang, Karen Heymann, Lena Dathe, Kelly Hanley, Sue Wirick, and Chris Jacobsen Carbon (1s) NEXAFS Spectroscopy of Biogeochemically Relevant Reference Organic Compounds Published online 11 September 2009; doi: 10.2136/sssaj2008.0228 Soil Sci Soc Am J 2009 73: 1817-1830
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