Synchrotron‐Based Near‐Edge X‐Ray Spectroscopy of Natural Organic Matter in Soils and Sediments

Lehmann, Johannes; Solomon, Daniel; Brandes, Jay; Fleckenstein, H.; Jacobson, Carl E.; Thieme, Jürgen

doi:10.1002/9780470494950.ch17

Cited by 35 publications

(39 citation statements)

References 170 publications

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“…[5,6] For example, although near-edge X-ray fine structure spectroscopy (NEXAFS) essentially meets the first four criteria (at least for particulate matter) the technique requires access to a synchrotron X-ray beam line. [125] In the short term HPLC possibly offers the best approach for the routine analysis of organic P in aquatic samples. Several liquid chromatographic approaches have been used to determine organic P in aquatic samples including reverse-phase, ionpairing, ion-exchange and size exclusion chromatography.…”

Section: Synthesismentioning

confidence: 99%

Organic phosphorus in the aquatic environment

Baldwin¹

2013

Environ. Chem.

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Environmental context. Organic phosphorus can be one of the major fractions of phosphorus in many aquatic ecosystems. This paper discusses the distribution, cycling and ecological significance of five major classes of organic P in the aquatic environment and discusses several principles to guide organic P research into the future.Abstract. Organic phosphorus can be one of the major fractions of phosphorus in many aquatic ecosystems. Unfortunately, in many studies the 'organic' P fraction is operationally defined. However, there are an increasing number of studies where the organic P species have been structurally characterised -in part because of the adoption of 31 P NMR spectroscopic techniques. There are five classes of organic P species that have been specifically identified in the aquatic environment -nucleic acids, other nucleotides, inositol phosphates, phospholipids and phosphonates. This paper explores the identification, quantification, biogeochemical cycling and ecological significance of these organic P compounds. Based on this analysis, the paper then identifies a number of principles which could guide the research of organic P into the future. There is an ongoing need to develop methods for quickly and accurately identifying and quantifying organic P species in the environment. The types of ecosystems in which organic P dynamics are studied needs to be expanded; flowing waters, floodplains and small wetlands are currently all under-represented in the literature. While enzymatic hydrolysis is an important transformation pathway for the breakdown of organic P, more effort needs to be directed towards studying other potential transformation pathways. Similarly effort should be directed to estimating the rates of transformations, not simply reporting on the concentrations. And finally, further work is needed in elucidating other roles of organic P in the environment other than simply a source of P to aquatic organisms.

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Section: Synthesismentioning

confidence: 99%

Organic phosphorus in the aquatic environment

Baldwin¹

2013

Environ. Chem.

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“…Soft X‐ray spectromicroscopic techniques are capable of inducing beam damage on organic matter‐containing samples, as mentioned for electron microscopies (Lehmann et al, 2009; Schäfer et al, 2009; Gianoncelli et al, 2015). Electrons from TEM and soft X‐rays from STXM may induce similar damage to spectral chemistry at the same critical dose (defined as the dose that increments a specific spectroscopic feature by 63%) (Wang et al, 2009a).…”

Section: Soft X‐ray Spectromicroscopymentioning

confidence: 99%

“…Careful experimentation involving soft X‐ray spectromicroscopy‐microspectroscopy extends beyond minimizing beam damage to the general optimization of sample preparation in alignment with analytical goals. Bulk spectroscopic analyses refer to characterization of the entire homogenous material, whereas surface‐sensitive spectroscopic analyses generally characterize the outer ∼10 nm of the sample surface (Lehmann et al, 2009). For instance, bulk C NEXAFS may be achieved through transmission mode, in which X‐rays are transmitted through the entire sample or by fluorescence yield, which has an X‐ray penetration depth of ∼100 nm for C 1s excitation (Lehmann et al, 2009).…”

Section: Soft X‐ray Spectromicroscopymentioning

confidence: 99%

“…Bulk spectroscopic analyses refer to characterization of the entire homogenous material, whereas surface‐sensitive spectroscopic analyses generally characterize the outer ∼10 nm of the sample surface (Lehmann et al, 2009). For instance, bulk C NEXAFS may be achieved through transmission mode, in which X‐rays are transmitted through the entire sample or by fluorescence yield, which has an X‐ray penetration depth of ∼100 nm for C 1s excitation (Lehmann et al, 2009). Surface‐sensitive C NEXAFS can be achieved by total electron yield measurement.…”

Section: Soft X‐ray Spectromicroscopymentioning

confidence: 99%

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

et al. 2017

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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.

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“…Additional less intense spectral features occurred at 288.6 eV and at 287.4 eV and were interpreted as carboxylic and aliphatic C, assigned to polysaccharide and most likely saturated lipids, respectively (Lehmann et al, 2009). Additional less intense spectral features occurred at 288.6 eV and at 287.4 eV and were interpreted as carboxylic and aliphatic C, assigned to polysaccharide and most likely saturated lipids, respectively (Lehmann et al, 2009).…”

Section: Distribution Of Organic and Inorganic Carbon As A Function Omentioning

confidence: 99%

Limited influence of Si on the preservation of Fe mineral‐encrusted microbial cells during experimental diagenesis

et al. 2015

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The reconstruction of the history of microbial life since its emergence on early Earth is impaired by the difficulty to prove the biogenicity of putative microfossils in the rock record. While most of the oldest rocks on Earth have been exposed to different grades of diagenetic alterations, little is known about how the remains of micro-organisms evolve when exposed to pressure (P) and temperature (T) conditions typical of diagenesis. Using spectroscopy and microscopy, we compared morphological, mineralogical, and chemical biosignatures exhibited by Fe mineral-encrusted cells of the bacterium Acidovorax sp. BoFeN1 after long-term incubation under ambient conditions and after experimental diagenesis. We also evaluated the effects of Si on the preservation of microbial cells during the whole process. At ambient conditions, Si affected the morphology but not the identity (goethite) of Fe minerals that formed around cells. Fe-encrusted cells were morphologically well preserved after 1 week at 250 °C-140 MPa and after 16 weeks at 170 °C-120 MPa in the presence or in the absence of Si. Some goethite transformed to hematite and magnetite at 250 °C-140 MPa, but in the presence of Si more goethite was preserved. Proteins-the most abundant cellular components-were preserved over several months at ambient conditions but disappeared after incubations at high temperature and pressure conditions, both in the presence and in the absence of Si. Other organic compounds, such as lipids and extracellular polysaccharides seemed well preserved after exposure to diagenetic conditions. This study provides insights about the composition and potential preservation of microfossils that could have formed in Fe- and Si-rich Precambrian oceans.

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Synchrotron‐Based Near‐Edge X‐Ray Spectroscopy of Natural Organic Matter in Soils and Sediments

Cited by 35 publications

References 170 publications

Organic phosphorus in the aquatic environment

Organic phosphorus in the aquatic environment

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

Limited influence of Si on the preservation of Fe mineral‐encrusted microbial cells during experimental diagenesis

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