Chapter 8.15. Environmental applications of X-ray spectroscopy

Environmental science may be broadly defined as having to do with materials and processes which directly affect the biosphere. These can include natural processes such as soil formation, as well as anthropogenic issues such as climate change and acid mine drainage. In the vast variety of subjects covered by this heading, we find certain themes that recur. For one, `Nature is inhomogeneous at all scales' (Manceau, Tamura et al., 2002). Thus, environmental science needs to be studied at length scales from nanometres to kilometres (Brady & Weil, 1996; Sparks, 2003). For another, the substances of interest are often found in great dilution and always in combination with many others. Thus, an element-specific technique such as XAS can be of great value. Materials in the environment are often poorly crystalline. XAFS allows the study of such materials whereas, for instance, X-ray diffraction (XRD) does not. In some cases, the biological effects of an element may be closely correlated with the valence states in which it is found. For instance, hexavalent chromium is soluble, bioavailable and toxic, while trivalent chromium is much less so. Similarly, arsenite and selenite tend to be more hazardous than arsenate and selenate.

Many and various areas of environmental science have been studied by XAFS, ranging from iron-bearing particles in the ocean to aerosols in the atmosphere, from natural organochlorines in leaf litter to chrome ore-processing residues, and much else. Therefore, we will concentrate on only a few examples to provide a scientist who is unfamiliar with the use of XAFS for environmental work with an idea of how the technique fits in with the science.

There are many reviews of various areas of synchrotron-radiation-related environmental science (see, among others, Kelly et al., 2008; Lombi & Susini, 2009; Manceau, Marcus et al., 2002; Parsons et al., 2002; Sarret et al., 2013; Toner et al., 2014). We cite these few so that the reader can dig more deeply into the subject matter as appropriate for his or her scientific interest.

As has been explained earlier in this volume, XAFS is element-specific, although some elements may interfere with others. Thus, in many cases, very small concentrations of trace elements, down to parts per million, may be studied using fluorescence detection with large-area (submillimetre to millimetre) beams, while even microprobes or nanoprobes are routinely used down to parts per million. Further, it is often found that even if the overall concentration of a sample is small, much of the element of interest may be found in `hotspots' which are sufficiently concentrated to be easily picked up by a microprobe with the quick acquisition of good spectra.

Element specificity implies a certain immunity to chemical complexity. If one is looking at the environment of, say, tellurium, it does not matter how many copper-bearing species the sample contains as long as none of these are hosts to the tellurium. There is nothing special about these two elements that led to their choice in this example.

XAFS is useful when the sample is disordered to any degree. It can be used on single crystals, polycrystals, poorly crystalline nanoparticles such as ferrihydrite or oligomeric iron oxyhydroxides (Toner et al., 2009), or even for liquids and molecular species in solution. XAFS is often the only available technique for structural study of sorbed species, especially if single-crystal surface models are unavailable or inappropriate.

XAFS spectra may be taken either on large (millimetre-scale) regions of the sample or, using a microprobe or nanoprobe, on local spots. Since natural samples are usually inhomogeneous, this property makes XAFS useful in situations in which other methods are incapable of providing spatial resolution.

In many cases, there are a limited number of plausible species or sites for the element of interest. In such cases, it is often not necessary to take data all the way into the EXAFS region. Instead, it is sufficient to take XANES data and use linear combination fitting (LCF) to identify the species present, either in a sample as a whole or at a spot. This method is known as fingerprinting.

The biological effects of some elements, such as arsenic, depend largely on their valence states. In other cases, the redox state of a given element is of interest because of what it implies about the chemistry of the material in which it is found. In these cases, the desired information may be obtained by reading off certain features of the XANES spectrum (Farges & Brown, 1997; Manceau et al., 2012; Prietzel et al., 2007; Wilke et al., 2001, 2005) or by fitting to a limited number of reference spectra that do not necessarily include the actual species present. An example of the use of a limited number of species for references is chemical-state mapping (Marcus, 2010). In this technique, micro X-ray fluorescence or transmission (STXM) maps are taken at a relatively small number of energies chosen to highlight the differences between valence states. The data at each pixel may be considered to be a short, low-resolution XANES spectrum, which is then fitted to a sum of well chosen reference spectra. Fig. 1 shows an example of how this process works. This method allows a rapid survey of the species (usually valence states) found in the scanned region of the sample.

Figure 1 Example of chemical mapping viewed as short XANES. Here, we simulate the process of mapping in a pixel in which the iron happens to be in the form of pyrite, using four energies (7109.1, 7119.4, 7123.0 and 7216.9 eV) and three references: pyrrhotite (Py), siderite (Sd) and ferrihydrite (Fh). The three curves are XANES plots for Py (solid black line), Sd (dashed red line) and Fh (dotted–dashed blue line). The closed symbols are the actual XANES for pyrite, shown only at the energies at which the map was performed, and the open symbols are the best fit using non-negative amounts of the three references (4.6% Fh + 87.8% Py).

We have chosen a few examples based on how well they illustrate certain themes and the use of certain techniques which tend to recur in environmental systems. The choice of which areas to cover is somewhat arbitrary and is biased by the authors' own research. Our first example is the work of Ressler et al. (2000), in which manganese in particulates (from combustion of a fuel additive) collected from the exhaust of 12 car engines was examined by manganese XANES. Principal component analysis (PCA) was used to determine that the data could be analysed as sums of three components, which were then identified using target transformation as Mn₃O₄, MnSO₄·H₂O and Mn₅(PO₄)[PO₃(OH)]₂·4H₂O. EXAFS was then used to corroborate the identifications. This relatively simple example illustrates some useful points about environmental XAFS. For one, non-XAFS information [ESCA (electron spectroscopy for chemical analysis) showing oxygen, phophorus and sulfur in the sample] helped to narrow the list of unknowns. Then, diversity was exploited. While all of the samples had a `family' resemblance, they were different, and the differences could be exploited using statistical analysis. XANES was used as a `fingerprinting' technique in which the reasons for the shapes of the curves, such as valence, were ignored; all that mattered was that the XANES from different components are different and can be added to simulate the XANES of a mixture. Finally, EXAFS was used in combination with XANES to verify structural information. This paper includes a clear explanation of principal component analysis (PCA) and could be read as an introduction to this technique.

X-ray microprobes are commonly used to analyse spatially heterogeneous soils and other natural samples. It has become routine to resin-embed soil, sediment, mine waste or any other sort of inhomogeneous sample, make a polished section of it, perform micro X-ray fluorescence mapping (μXRF), pick some representative spots and perform XAFS on these spots. The elements found in combination with the element of interest (EOI), plus micro X-ray diffraction (μXRD), if available, can yield clues as to what minerals host the EOI. However, caution must be applied. The apparent co-location of a mineral M and an element E does not imply that E is included in or bound to M. For examples of this approach, see, for instance, Manceau, Marcus et al. (2002), Parsons et al. (2002) and Manceau, Tamura et al. (2002). The former reference is a review which lays out the basics as currently understood. Fig. 2 shows a schematic of a similar sampling method as used for the study of iron-bearing particles in the ocean (Toner et al., 2014). Here, particles from a large volume of water are filtered and sections are mapped in μXRF. Particles are chosen for μXAFS analysis. Additionally, the iron in the whole filter could be studied by bulk XAFS. In Manceau, Tamura et al. (2002), nickel in a soil ferromanganese nodule was shown to associate with lithiophorite. EXAFS was performed on the nickel and could be explained with a model in which nickel substituted for manganese in a mixed-layer [MnO₂–Al(OH)₃] lithiophorite. In Kemner et al. (2004), an ∼150 nm-sized X-ray beam was used to identify the locations of bacteria within biofilms and the valence state of chromium within the biofilm relative to the bacteria and their extracellular polymeric matrix.

Figure 2 A typical scheme for the use of micro and macro (`bulk') XAFS in environmental science (example taken from a study of ocean particles; figure modified from Toner et al., 2014).

Another example in which diffraction, mapping of fluorescence and spot XAFS was used is given by Fakra et al. (2018). They collected samples of bacterial biofilm from a selenium-rich area of the Rifle bioremediation site and used a combination of soft X-ray scanning transmission microscopy (STXM) and hard X-ray μXRF, μXANES, μEXAFS and μXRD to speciate the selenium and investigate its relationship to the bacteria which reduced it from selenate to Se⁰. A special cryo-transfer setup was used to enable plunge-freezing in the field followed by cryo-TEM and the X-ray methods, all without thawing. Such care is often required when dealing with samples containing organics, as radiation damage can alter the original speciation in a sample.

Sometimes, data may be acquired sufficiently quickly that a complete, if noisy, XANES spectrum can be acquired at every pixel of a map. This is analogous to an STXM or full-field X-ray microscope stack (Lawrence et al., 2003; Toner et al., 2005). An example of this method in the hard X-ray range is given by Etschmann et al. (2014), who examined copper-laden biosolid waste using a high-speed detection system which allowed data to be taken at >10⁵ pixels and 80 energies. Statistical methods previously developed for use with STXM were used to analyse the set of XANES spectra and identify the species involved and chart their spatial distributions.

Not all environmental work need involve a microprobe or nanoprobe. Even with a microprobe, spot XAFS only yields information on a small and potentially unrepresentative set of positions. However, the species identified in analysing such data may be used as references in fitting bulk-averaged XAFS data to yield a true picture of the abundances of various species. Secondly, one is often interested in deep analysis of species which can be found in spatially uniform samples. For instance, many metals and metalloids of environmental interest are found sorbed to manganese oxides, clays and iron oxyhydroxides (Brown et al., 1999). These materials are often nanocrystalline and hard to analyse on their own, so deciphering the state of sorbed elements on these species is even harder. There has been much work over decades on the structures of nanocrystalline host materials of environmental interest and the sorption or substitutional sites of elements bound to them (Bernier-Latmani et al., 2010; Boyanov et al., 2003, 2011; Grangeon et al., 2012; Kelly et al., 2002; Schlegel & Manceau, 2007; Templeton et al., 2003; Villalobos et al., 2005a,b and many others) as well as nanocrystalline colloidal contaminants such as uranium, silver and zinc (O'Loughlin et al., 2003; Scheckel et al., 2010). Some of this work was performed on laboratory-produced material and some on selected natural samples. It is unnecessary and in some cases impractical to use a microprobe on such samples; bulk beamlines (>0.1 mm beam size) can often provide techniques (X-ray emission and partial fluorescence yield) and liquid-helium temperatures which are hard to achieve with a microprobe. Low temperatures reduce radiation-damage effects and enhance the EXAFS signals, especially from higher shells, due to a reduction of thermal vibrations which cause damping of the EXAFS signal. For example, the complex chemistry of mercury binding via sulfur to organics was elucidated by Manceau et al. (2015) using partial fluorescence yield to pull out features in the XANES at the Hg L₃ edge and correlate them with theoretical predictions. High-energy-resolution fluorescence can also be useful in removing interference from elements other than that of interest which have fluorescence lines near that being measured (see, for example, Kashiwabara et al., 2010). The biogeochemical forms of mercury in fish and bacteria were studied at low temperature by Harris (2003) and Mishra et al. (2011).

To give the reader a more complete idea of the range of environmental science to which XAFS has been applied, we now list, in a very short form, some of the areas which have not been mentioned. No attempt is made here to provide a complete or even a representative set of citations. Citations of references already cited above are not repeated.

Hyperaccumulating (HA) plants: tracing motion and speciation of elements through trophic levels; localization in cell compartments; comparison of speciation in HA versus non-HA plants (Alford et al., 2014; Cappa & Pilon-Smits, 2014; Freeman et al., 2006; Maestri et al., 2010).

Marine minerals and particles: sources of iron; mineralogy of ferromanganese nodules and crusts (Lam & Bishop, 2008; Lam et al., 2012; Marcus et al., 2015; Takahashi et al., 2000, 2007).

Anthropogenically contaminated soils and sediment: speciation; mobility/bioavailability; remediation (Ettler, 2016; Khaokaew et al., 2011; Kim et al., 2004; Manceau et al., 2000; Traina, 1999).

Aerosols: sources (anthropogenic and natural); reactions during transport (Moffet et al., 2008, 2010; Sammut et al., 2008).

Geomicrobiology: sorption and reactions on bacteria (Huang et al., 2011).

Natural organic matter: binding and complexation of metals and arsenic (Hoffmann et al., 2012; Maurer et al., 2010; Mikutta & Kretzschmar, 2011).

Arsenic in soil (Dittmar et al., 2010; Frommer et al., 2011).

During the last 25-plus years, the value of synchrotron-based XAS approaches to investigate complex environmental systems has progressed from being a novel tool to one that many researchers consider a paramount requirement for advancing the field. With future advances in next-generation synchrotron X-ray sources and computational approaches, the potential for higher throughput experiments and multidimensional and dynamic experiments indicates a bright future for environmental applications of XAFS.