Abstract
Purpose
Biogeochemical interfaces, the 3D association of minerals, soil organic matter, and biota, are hotspots of soil processes because they exhibit strong biological, physical, and chemical gradients. Biogeochemical interfaces have thicknesses from nanometers to micrometers and separate bulk immobile phases from mobile liquid or gaseous phases. The aim of this contribution is to review advanced microscopic and spectroscopic characterization techniques that allow for spatially resolved analysis of composition and properties of biogeochemical interfaces or their visualization.
Materials and methods
From the variety of techniques to study biogeochemical interfaces in soil, we focus on X-ray spectromicroscopy, nano-scale secondary ion mass spectrometry, atomic force microscopy, micro-X-ray tomography, and positron emission tomography. Beside an introduction into the respective method, we review published applications and give practical examples.
Results and discussion
The development of terrestrial soils involves the formation of biogeochemical interfaces as the result of the complex 3D interplay of primary and secondary minerals, soil organic matter together with soil biota. X-ray microscopy allows for the visualization of structures down to range of 10–30 nm and for the determination of binding states of elements. Nano-scale secondary ion mass spectrometry is capable of simultaneously analyzing up to seven secondary ion species to give the elemental and isotopic composition down to 50–150 nm. Atomic force microscopy enables to study the topography and mechanical properties (softness, elasticity, plasticity, deformability) of soil particle surfaces down to the nm scale. X-ray micro-tomography has been shown to visualize the interior of materials at the sub-micrometer scale successfully.
Conclusions
Introducing and adapting the discussed methods in soil science has increased the understanding of formation, properties, and functioning of biogeochemical interfaces in soil. A further challenging task is to utilize further promising techniques, e.g., advanced Raman techniques or atomic probe tomography with the highest spatial resolution for 3D compositional information of any microscopy technique.
Similar content being viewed by others
References
Ade H, Kilcoyne A, Tyliszczak T, Hitchcock P, Anderson E, Harteneck B, Rightor E, Mitchell G, Hitchcock A, Warwick T (2003) Scanning transmission X-ray microscopy at a bending magnet beamline at the Advanced Light Source. J Phys 104:3–8
Ahrenholz B, Tölke J, Lehmann P, Peters A, Kaestner A, Krafczyk M, Durner W (2008) Prediction of capillary hysteresis in porous material using lattice Boltzmann methods and comparison to experimental data and a morphological pore network model. Adv Water Res 31:1151–1173
Alvarez-Puebla RA, dos Santos Jr DS, Aroca RF (2007) SERS detection of environmental pollutants in humic acid-gold nanoparticle composite materials. Analyst 132:1210–1214
Attwood D (2000) Soft X-rays and extreme ultraviolet radiation—principles and applications. Cambridge University Press, Cambridge
Bacquart T, Deve G, Ortega R (2010) Direct speciation analysis of arsenic in sub-cellular compartments using micro-X-ray absorption spectroscopy. Environ Res 110:413–416
Bargar JR, Fuller CC, Marcus MA, Brearley AJ, Perez de la Rosa M, Webb SM, Caldwell WA (2009) Structural characterization of terrestrial microbial Mn oxides from Pinal Creek, AZ. Geochim Cosmochim Acta 73:889–910
Bickmore BR, Hochella MF Jr, Bosbach D, Charlet L (1999) Methods for performing atomic force microscopy imaging of clay minerals in aqueous solutions. Clays Clay Miner 47:573–581
Bickmore BR, Bosbach D, Hochella MF Jr, Charlet L, Rufe E (2001) In situ atomic force microscopy study of hectorite and nontronite dissolution: implications for phyllosilicate edge surface structures and dissolution mechanisms. Amer Miner 86:411–423
Bihannic I, Michot LJ, Lartiges BS, Vantelon D, Labille J, Thomas F, Susini J, Salome M, Fayard B (2001) First direct visualization of oriented mesostructures in clay gels by synchrotron-based X-ray fluorescence microscopy. Langmuir 17:4144–4147
Binnig G, Quate CF, Gerber C (1986) Atomic force microscope. Phys Rev Lett 56:930–933
Bosbach D, Charlet L, Bickmore B, Hochella MF Jr (2000) The dissolution of hectorite: in situ, real-time observations using atomic force microscopy. Amer Miner 85:1209–1216
Boxer SG, Kraft ML, Weber PK (2009) Advances in imaging secondary ion mass spectrometry for biological samples. Ann Rev Biophys 38:53–74
Bronick CJ, Lal R (2005) Soil structure and management: a review. Geoderma 124:3–22
Brzoska J-B, Flin F, Lesaffre B, Coléou C, Lamboley P, Delesse J-F, Le Saëc B, Vignoles G (2001) Computation of the surface area of natural snow 3D images from X-ray tomography: two approaches. Image Anal Stereol 20:306–312
Budich C, Neugebauer U, Popp J, Deckert V (2008) Cell wall investigations utilizing tip-enhanced Raman scattering. J Microsc 229:533–539
Butt HJ, Cappella B, Kappl M (2005) Force measurements with the atomic force microscope: technique, interpretation and applications. Surf Sci Rep 59:1–152
Camesano T, Liu Y, Datta M (2007) Measuring bacterial adhesion at environmental interfaces with single-cell and single-molecule techniques. Adv Water Res 30:1470–1491
Cerezo A, Clifton PH, Galtrey MJ, Humphreys CJ, Kelly TF, Larson DJ, Lozano-Perez CS, Marquis EA, Oliver RA, Sha G, Thompson K, Zandbergen M, Alvis RL (2007) Atom probe tomography today. Mater Today 10:36–42
Cialla D, Deckert-Gaudig T, Budich C, Laue M, Möller R, Naumann D, Deckert V, Popp J (2009) Raman to the limit: tip-enhanced Raman spectroscopic investigations of a single tobacco mosaic virus. J Raman Spectrosc 40:240–243
Chen Y, Lo T, Chu Y, Yi J, Liu C, Wang J, Wang C, Chiu C, Hua T, Hwu Y, Shen Q, Yin G, Liang K, Lin H, Je J, Margaritondo G (2008) Full-field hard X-ray microscopy below 30 nm: a challenging nanofabrication achievement. Nanotechnology 19:395302
Chorover J, Kretzschmar R, Garcia-Pichel F, Sparks DL (2007) Soil biogeochemical processes within the critical zone. Elements 3:321–326
Clode PL, Stern RA, Marshall AT (2007) Subcellular imaging of isotopically labeled carbon compounds in a biological sample by ion microprobe (NanoSIMS). Microsc Res Techniq 70:220–229
Clode PL, Kilburn MR, Jones DL, Stockdale EA, Cliff JB III, Herrmann AM, Murphy DV (2009) In situ mapping of nutrient uptake in the rhizosphere using nanoscale secondary ion mass spectrometry. Plant Physiol 151:1751–1757
D’Amore JJ, Al-Abed SR, Scheckel KG, Ryan JA (2005) Methods for speciation of metals in soils: a review. J Environ Qual 34:1707–1745
Deckert-Gaudig T, Deckert V (2010) Tip-enhanced Raman scattering (TERS) and high-resolution bio nano-analysis—a comparison. Phys Chem Chem Phys 12:12040–12049
de Winter DAM, Schneijdenberg CTWM, Lebbink MN, Lich B, Verkleij AJ, Drury MR, Humbel BM (2009) Tomography of insulating biological and geological materials using focused ion beam (FIB) sectioning and low-kV BSE imaging. J Microsc 233:372–383
Diaz J, Ingall E, Benitez-Nelson C, Paterson D, de Jonge MD, McNulty I, Brandes JA (2008) Marine polyphosphate: a key player in geologic phosphorus sequestration. Science 320:652–655
Dong H, Jaisi DP, Kim J, Zhang G (2009) Microbe–clay mineral interactions. Amer Miner 94:1505–1519
Ducker WA, Senden TJ, Pashley RM (1991) Direct measurement of colloidal forces using an atomic force microscope. Nature 353:239–241
Duiker SW, Rhoton FE, Torrent J, Smeck NE, Lal R (2003) Iron (hydr)oxide crystallinity effects on soil aggregation. Soil Sci Soc Am J 67:606–611
Eusterhues K, Wagner FE, Häusler W, Hanzlik M, Knicker H, Totsche KU, Kögel-Knabner I, Schwertmann U (2008) Characterization of ferrihydrite-soil organic matter coprecipitates by X-ray diffraction and Mössbauer spectroscopy. Environ Sci Technol 42:7891–7897
Feser M, Hornberger B, Jacobsen C, De Geronimo G, Rehak P, Hol P, Strueder L (2006) Integrating silicon detector with segmentation for scanning transmission X-ray microscopy. Nucl Instrum Methods Phys Res A 565:841–854
Fischer P, Kim D-H, Chao W, Liddle JA, Anderson EH, Attwood DT (2006) Soft X-ray microscopy of nanomagnetism. Mater Today 9:26–33
Fisher TE, Marszalek PE, Oberhauser AF, Carrion-Vazquez M, Fernandez JM (1999) The micro-mechanics of single molecules studied with atomic force microscopy. J Physiol-London 520:5–14
Flechsig U, Quitmann U, Raabe J, Boege M, Fink R, Ade H (2006) The PolLux microspectroscopy beamline at the Swiss Light Source. AIP Conf Proc 879:505–508
Floss C, Stadermann FJ, Bradley JP, Dai ZR, Bajt S, Graham G, Lea AS (2006) Identification of isotopically primitive interplanetary dust particles: a NanoSIMS isotopic imaging study. Geochim Cosmochim Acta 70:2371–2399
Franz M, Kasperl S (2010) Synchronous artifact reduction in industrial computed tomography. Techn Messen 77:616–623
Giessibl FJ, Quate CF (2006) Exploring the nanoworld with atomic force microscopy. Phys Today 59:44–50
Gleber SC, Thieme J, Chao W, Fischer P (2009) Stereo soft X-ray microscopy and elemental mapping of haematite and clay suspensions. J Microsc 235:199–208
Gross L, Mohn F, Moll N, Liljeroth P, Meyer G (2009) The chemical structure of a molecule resolved by atomic force microscopy. Science 325:1110–1114
Gross L, Mohn F, Moll N, Meyer G, Ebel R, Abdel-Mageed WM, Jaspers M (2010) Organic structure determination using atomic resolution scanning probe microscopy. Nature Chem 765:821–825
Grovenor CRM, Smart KE, Kilburn MR, Shore B, Dilworth JR, Martin B, Hawes C, Rickaby REM (2006) Specimen preparation for NanoSIMS analysis of biological materials. Appl Surf Sci 252:6917–6924
Guerquin-Kern J-L, Wu T-D, Quintana C, Croisy A (2005) Progress in analytical imaging of the cell by dynamic secondary ion mass spectrometry (SIMS microscopy). Biochim Biophys Acta 1724:228–238
Hafida Z, Caron J, Angers DA (2007) Pore occlusion by sugars and lipids as a possible mechanism of aggregate stability in amended soils. Soil Sci Soc Am J 71:1831–1839
Halvorson RA, Vikesland PJ (2010) Surface-enhanced Raman spectroscopy (SERS) for environmental analyses. Environ Sci Technol 44:7749–7755
Henke B, Gullikson E, Davis J (1993) X-ray interactions: photoabsorption, scattering, transmission, and reflection at E = 50–30,000 eV, Z = 1–92. Atom Data Nucl Data Tables 54:181–342
Hering K, Cialla D, Ackermann K, Dörfer D, Möller R, Schneidewind H, Mattheis R, Fritzsche W, Rösch P, Popp J (2008) SERS: a versatile tool in chemical and biochemical diagnostics. Anal Bioanal Chem 390:113–124
Herman G (1980) Image reconstruction from projections. Academic, New York
Herman GT (1979) Correction for beam hardening in computed tomography. Phys Med Biol 24:81–106
Herrmann AM, Ritz K, Nunan N, Clode PL, Pettridge J, Kilburn ML, Murphy DV, O’Donnell AG, Stockdale AE (2007a) Nano-scale secondary ion mass spectrometry—a new analytical tool in biogeochemistry and soil ecology: a review article. Soil Biol Biochem 39:1835–1850
Herrmann AM, Clode PL, Fletcher IR, Nunan N, Stockdale EA, O’Donnell AG, Murphy DV (2007b) A novel method for the study of the biophysical interface in soils using nano-scale secondary ion mass spectrometry. Rapid Commun Mass Sp 21:29–34
Hinsinger P, Plassard C, Jaillard B (2006) Rhizosphere: a new frontier for soil biogeochemistry. J Geochem Explor 88:210–213
Hinsinger P, Glyn Bengough A, Vetterlein D, Young IM (2009) Rhizosphere: biophysics, biogeochemistry and ecological relevance. Plant Soil 321:117–152
Hoppe P (2006) NanoSIMS: a new tool in cosmochemistry. Appl Surf Sci 252:7102–7106
Horcas I, Fernandez R, Gomez-Rodriguez JM, Colchero J, Gomez-Herrero J, Baro AM (2007) WSXM: a software for scanning probe microscopy and a tool for nanotechnology. Rev Sci Instrum 78:013705
Hornberger B, de Jonge MD, Feser M, Hol P, Holzner C, Jacobsen C, Legnini D, Paterson D, Rehak P, Strueder L, Vogt S (2008) Differential phase contrast with a segmented detector in a scanning X-ray microprobe. J Synchrotron Rad 15:355–362
Huber F, Enzmann F, Wenka A, Bouby M, Dentz M, Schäfer T (2011) Tracer and quantum dots migration in a μCT scanned fracture: Experiments and 3D CFD modeling. Environ Sci Technol (in press)
Inoue K, Huang PM (1990) Perturbation of imogolite formation by humic substances. Soil Sci Soc Am J 54:1490–1497
Ireland TR (2004) SIMS measurements of stable isotopes. In: de Groot PA (ed) Handbook of stable isotope analytical techniques. Elsevier, Amsterdam, pp 652–691
Jacobsen C, Flynn G, Wirick S, Zimba C (2000) Soft X-ray spectroscopy from image sequences with sub-100 nm spatial resolution. J Microsc 197:173–184
Jandt KD (1998) Developments and perspectives of scanning probe microscopy (SPM) on organic materials systems. Mater Sci Eng R 21:221–295
Jandt KD (2001) Atomic force microscopy of biomaterials surfaces and interfaces. Surf Sci 491:303–332
Jandt KD (2007) Evolutions, revolutions and trends in biomaterials science—a perspective. Adv Eng Mater 9:1035–1050
Jarvis RM, Brooker A, Goodacre R (2006) Surface-enhanced Raman scattering for the rapid discrimination of bacteria. Faraday Discuss 132:281–292
Kaulich B, Bacescu D, Cocco D, Susini J, David C, DiFabrizio E, Cabrini S, Morrison G, Thieme J, Kiskinova M (2003) Twinmic: a European twin microscope station combining full-field imaging and scanning microscopy. J Phys IV 104:103–107
Kaznatcheev K, Karunakarana C, Lanke U, Urquhar S, Obst M, Hitchcock A (2007) Soft X-ray spectromicroscopy beamline at the CLS: commissioning results. Nucl Instrum Methods Phys Res A 582:96–99
Kelly TF, Miller MK (2007) Invited review article: atom probe tomography. Rev Sci Instrum 78:031101
Kelly TF, Nishikawa O, Panitz JA, Prosa TJ (2009) Prospects for nanobiology with atom-probe tomography. MRS Bull 34:744–749
Kirz J, Jacobsen C, Howells M (1995) Soft-X-ray microscopes and their biological applications. Q Rev Biophys 28:33–130
Kleber M, Johnson MG (2010) Advances in understanding the molecular structure of soil organic matter: implications for interactions in the environment. Adv Agron 106:77–142
Kögel-Knabner I (2002) The macromolecular organic composition of plant and microbial residues as inputs to soil organic matter. Soil Biol Biochem 34:139–162
Kotula PG, Keenan MR, Michael JR (2006) Tomographic spectral imaging with multivariate statistical analysis: comprehensive 3D microanalysis. Microsc Microanals 12:36–48
Krumm M, Kasperl S, Franz M (2008) Reducing non-linear artifacts of multi-material objects in industrial 3D computed tomography. NDT&E Int 41:242–251
Kulenkampff J, Gründig M, Richter M, Enzmann F (2008) Evaluation of positron-emission-tomography for visualization of migration processes in geomaterials. Phys Chem Earth 33:937–942
Kuhlman KR, Martens RL, Kelly TF, Evans ND, Miller MK (2001) Fabrication of specimens of metamorphic magnetite crystals for field ion microscopy and atom probe microanalysis. Ultramicroscopy 89:169–176
Kurek E (2002) Microbial mobilization of metals from soil minerals under aerobic conditions. In: Huang PM, Bollag J-M, Senesi N (eds) Interactions between soil particles and microorganisms. Wiley, Chichester, pp 189–225
Kuwahara Y (2006) In-situ AFM study of smectite dissolution under alkaline conditions at room temperature. Amer Miner 91:1142–1149
Kwong NKKF, Huang PM (1981) Comparison of the influence of tannic acid and selected low-molecular-weight organic acids on precipitation products of aluminum. Geoderma 26:179–193
Lechene C, Hillion F, McMahon G, Benson D, Kleinfeld AM, Kampf JP, Distel D, Luyten Y, Bonventre J, Hentschel D, Park KM, Ito S, Schwartz M, Benichou G, Slodzian G (2006) High-resolution quantitative imaging of mammalian and bacterial cells using stable isotope mass spectrometry. J Biol 5:20
Lehmann J, Liang B, Solomon D, Lerotic M, Luizão F, Kinyangi J, Schäfer T, Wirick S, Jacobsen C (2005) Near-edge X-ray absorption fine structure (NEXAFS) spectroscopy for mapping nano-scale distribution of organic carbon forms in soil: application to black carbon particles. Global Biogeochem Cy 19:GB1013
Lehmann P, Berchtold M, Ahrenholz B, Tölke J, Kaestner A, Krafczyk M, Flühler H, Künsch HR (2008) Impact of geometrical properties on permeability and fluid phase distribution in porous media. Adv Water Res 31:1188–1204
Lešer V, Milani M, Tatti F, Tkalec ŽP, Štrus J, Drobne D (2010) Focused ion beam (FIB)/scanning electron microscopy (SEM) in tissue structural research. Protoplasma 246:41–48
Li T, Wu T-D, Mazéas L, Toffin L, Guerquin-Kern J-L, Leblon G, Bouchez T (2008) Simultaneous analysis of microbial identity and function using NanoSIMS. Environ Microbiol 10:580–588
Lombi E, Sosni J (2009) Synchrotron-based techniques for plant and soil science: opportunities, challenges and future perspectives. Plant Soil 320:1–35
Lozano-Perez S, Schröder M, Yamada T, Terachi T, English CA, Grovenor CRM (2008) Using NanoSIMS to map trace elements in stainless steels from nuclear reactors. Appl Surf Sci 255:1541–1543
Machlin ES, Freilich A, Agrawal DC, Burton JJ, Briant CL (1975) Field-ion microscopy of biomolecules. J Microsc 104:127–168
Macht F, Eusterhues K, Pronk GJ, Totsche KU (2011) Specific surface area, of clay minerals: Comparison between atomic force microscopy measurements and bulk-gas (N2) and -liquid (EGME) adsorption methods. Appl Clay Sci 53:20–26
Masue-Slowey Y, Kocar BD, Bea Jofré SA, Mayer KU, Fendorf S (2011) Transport implications resulting from internal redistribution of arsenic and iron within constructed soil aggregates. Environ Sci Technol 45:582–588
Matyjasik M, Summers S, Manecki M, Inglefield C (2009) The alteration of calcite surface exposed to arctic soil environment—AFM study. Geochim Cosmochim Acta 73:A850
Maurice P, Forsythe J, Hersman L, Sposito G (1996) Application of atomic-force microscopy to studies of microbial interactions with hydrous Fe(III)-oxides. Chem Geol 132:33–43
McCarthy JF, Ilavsky J, Jastrow JD, Mayer LM, Perfect E, Zhuang J (2008) Protection of organic carbon in soil microaggregates via restructuring of aggregate porosity and filling of pores with accumulating organic matter. Geochim Cosmochim Acta 72:4725–4744
McNulty I, Eyberger C, Lai B (2011) The 10th international conference on X-ray Microscopy. AIP Conf Proc 1365
Meakin P, Tartakovsky AM (2009) Modeling and simulation of pore-scale multiphase fluid flow and reactive transport in fractured and porous media. Rev Geophys 47:RG3002
Meganck JA, Kozloff KM, Thornton MM, Broski SM, Goldstein SA (2009) Beam hardening artifacts in micro-computed tomography scanning can be reduced by X-ray beam filtration and the resulting images can be used to accurately measure BMD. Bone 45:1104–1116
Mitrea G, Thieme J, Guttmann P, Heim S, Gleber S (2008) X-ray spectromicroscopy with the scanning transmission X-ray microscope at BESSY II. J Synchrotron Rad 15:26–35
Monga O, Ngom FN, Delerue JF (2009) Representing geometric structures in 3D tomography soil images: application to pore-space modeling. Computat Geosci 33:1140–1161
Monreal CM, Sultan Y, Schnitzer M (2010) Soil organic matter in nano-scale structures of a cultivated Black Chernozem. Geoderma 159:237–242
Mueller CW, Kölbl A, Hoeschen C, Hillion F, Heister K, Herrmann AM, Kögel-Knabner I (2011) Submicron scale imaging of soil organic matter dynamics using NanoSIMS—from single particles to intact aggregates. Org Geochem. doi:10.1016/j.orggeochem.2011.06.003
Musat N, Halm H, Winterholler B, Hoppe P, Peduzzi S, Hillion F, Horreard F, Amann R, Jørgensen BB, Kuypers MMM (2008) A single-cell view on the ecophysiology of anaerobic phototrophic bacteria. P Natl Acad Sci 105:17861–17866
Nagy KL, Cygan RT, Hanchar JM, Sturchio NC (1999) Gibbsite growth kinetics on gibbsite, kaolinite, and muscovite substrates: atomic force microscopy evidence for epitaxy and an assessment of reactive surface area. Geochim Cosmochim Acta 63:2337–2351
Neugebauer U, Schmid U, Baumann K, Ziebuhr W, Kozitskaya S, Deckert V, Schmitt M, Popp J (2007) Towards a detailed understanding of bacterial metabolism—spectroscopic characterization of Staphylococcus epidermidis. Chemphyschem 8:124–137
Nunan N, Wu K, Young IM, Crawford JW, Ritz K (2003) Spatial distribution of bacterial communities and their relationships with the micro-architecture of soil. FEMS Microbiol Ecol 44:203–215
Oades JM (1984) Soil organic matter and structural stability: mechanisms and implications for management. Plant Soil 76:319–337
Omoike A, Chen GL, Van Loon GW, Horton JH (1998) Investigation of the surface properties of solid-phase hydrous aluminum oxide species in simulated wastewater using atomic force microscopy. Langmuir 14:4731–4736
Or D, Smets BF, Wraith JM, Dechesne A, Friedman SP (2007) Physical constraints affecting bacterial habitats and activity in unsaturated porous media—a review. Adv Water Res 30:1505–1527
Petry R, Schmitt M, Popp J (2003) Raman spectroscopy—a prospective tool in the life sciences. Chemphyschem 4:14–30
Pohl R (1967) Einführung in die Physik, 3. Teil—Optik und Atomphysik, 12th edn. Springer, Berlin, p 180
Porter ML, Wildenschild D (2010) Image analysis algorithms for estimating porous media multiphase flow variables from computed microtomography data: a validation study. Computat Geosci 14:15–30
Prietzel J, Thieme J, Eusterhues K, Eichert D (2007) Iron speciation in soils and soil aggregates by synchrotron-based X-ray microspectroscopy (XANES,•-XANES). Eur J Soil Sci 58:1027–1041
Prietzel J, Botzaki A, Tyufekchieva N, Brettholle M, Thieme J, Klysubun W (2011) Sulfur speciation in soil by S K-edge XANES spectroscopy: comparison of spectral deconvolution and linear combination fitting. Environ Sci Technol 45:2878–2886
Quiney HM, Peele AG, Cai Z, Paterson D, Nugent KA (2006) Diffractive imaging of highly focused X-ray fields. Nat Phys 2:101–104
Quitmann C, David C, Nolting F, Pfeiffer F, Stampanoni M (2009) 9th international conference on X-ray microscopy. J Phys: Conf Ser 186
Requena G, Cloetens P, Altendorfer W, Poletti C, Tolnai D, Warchomicka F, Degischer H (2009) Scripta Mater 61:760–763
Richter M, Gründig M, Zieger K, Seese A (2003) Fundamentals of spatial resolved transport in soil columns by positron emission tomography. In: Schulz H-D, Hadeler A (eds) Geochemical processes in soil and groundwater. Wiley-VCH, Weinheim, pp 539–550
Richter M, Gründig M, Zieger K, Seese A, Sabri O (2005) Positron emission tomography for modelling of geochemical transport processes in clay. Radiochim Acta 93:643–651
Sano Y, Shirai K, Takahata N, Hirata T, Sturchio NC (2005) Nano-SIMS analysis of Mg, Sr, Ba and U in natural calcium carbonate. Anal Sci 21:1091–1097
Saunders M, Kong C, Shaw JA, Macey DJ, Clode PL (2009) Characterization of biominerals in the radula teeth of the chiton, Acanthopleura hirtosa. J Struct Biol 167:55–61
Schiffbauer JD, Xiao S (2009) Novel application of focused ion beam electron microscopy (FIB-EM) in preparation and analysis of microfossil ultrastructures: a new view of complexity in early Eukaryotic organisms. Palaios 24:616–626
Schneider G, Guttmann P, Heim S, Rehbein S, Mueller F, Nagashima K, Heymann B, Müller W, McNally J (2010) Three-dimensional cellular ultrastructure resolved by X-ray microscopy. Nat Methods 7:985–988
Schlüter S, Weller U, Vogel H-J (2010) Segmentation of X-ray microtomography images of soil using gradient masks. Computat Geosci 36:1246–1251
Schmid T, Yeo B-S, Leong G, Stadler J, Zenobi R (2009) Performing tip-enhanced Raman spectroscopy in liquids. J Raman Spectrosc 40:1392–1399
Sedlmair J, Gleber S, Peth C, Mann K, Niemeyer J, Thieme J (2011) Characterization of refractory organic substances by NEXAFS using a compact X-ray source. J Soil Sediment, doi:10.10007/s11368-011-0385-9
Seguin V, Gagnon C, Courchesne F (2004) Changes in water extractable metals, pH and organic carbon concentrations at the soil–root interface of forested soils. Plant Soil 260:1–17
Six J, Bossuyt H, Degryse S, Denef K (2004) A history of research on the link between (micro)aggregates, soil biota, and soil organic matter dynamics. Soil Till Res 79:7–31
Solomon D, Lehmann J, Lobe I, Martinez CE, Tveitnes S, Du Preez CC, Amelung W (2005) Sulphur speciation and biogeochemical cycling in long-term arable cropping of subtropical soils: evidence from wet-chemical reduction and S K-edge XANES spectroscopy. Eur J Soil Sci 56:621–634
Smits MM, Bonneville S, Haward S, Leake JR (2008) Ectomycorrhizal weathering, a matter of scale? Mineral Mag 72:131–134
Stöckle RM, Suh YD, Deckert V, Zenobi R (2000) Nanoscale chemical analysis by tip-enhanced Raman spectroscopy. Chem Phys Lett 318:131–136
Stöhr J (1992) NEXAFS spectroscopy. Springer, Berlin
Succi S (2001) The Lattice Boltzmann equation: for fluid dynamics and beyond. Oxford University Press, New York
Sutton SR, Flynn G, Rivers M, Newville M, Eng P (2000) X-ray fluorescence microtomography of individual interplanetary dust particles. Lunar Planet Sci XXXI:CD ROM #1857
Takman P, Stollberg H, Johansson G, Holmberg A, Lindblom M, Hertz H (2007) High-resolution compact X-ray microscopy. J Microsc 226:175–181
Thibault P, Dierolf M, Menzel A, Bunk O, David C, Pfeiffer F (2008) High-resolution scanning X-ray diffraction microscopy. Science 321:379–382
Thieme J, Schneider G, Knoechel C (2003) X-ray tomography of a microhabitat of bacteria and other soil colloids with sub-100 nm resolution. Micron 34:339–344
Thieme J, McNulty I, Vogt S, Paterson D (2007) X-ray spectromicroscopy—a tool for environmental sciences. Environ Sci Technol 41:6885–6889
Thieme J, Sedlmair J, Gleber S-C, Prietzel J, Coates J, Eusterhues K, Abbt-Braun G, Salome M (2010) X-ray spectro-microscopy in soil and environmental sciences. J Synchrotron Radiat 17:149–157
Totsche KU, Rennert T, Gerzabek MH, Kögel-Knabner I, Smalla K, Spiteller M, Vogel H-J (2010) Biogeochemical interfaces in soil: the interdisciplinary challenge for soil science. J Plant Nutr Soil Sci 173:88–99
Turek S (1999) Efficient solvers for incompressible flow problems: an algorithmic and computational approach. Springer, Heidelberg
Van de Casteele E, Van Dyck D, Sijbers J, Raman E (2002) An energy-based beam hardening model in tomography. Phys Med Biol 47:4181–4190
Van de Casteele E, Van Dyck D, Sijbers J, Raman E (2004) A model-based correction method for beam hardening artefacts in X-ray microtomography. J X-ray Sci Technol 12:43–57
Vogel H-J, Weller U, Schlüter S (2010) Quantification of soil structure based on Minkowski functions. Computat Geosci 36:1239–1245
Wagner M (2009) Single-cell ecophysiology of microbes as revealed by Raman microspectroscopy or secondary ion mass spectrometry imaging. Annu Rev Microbiol 63:411–429
Wang Y, Jacobsen C, Maser J, Osanna A (2000) Soft X-ray microscopy with a cryo scanning transmission X-ray microscope: II. Tomography. J Microsc 197:80–93
Warwick T, Franck K, Kortright JB, Meigs G, Moronne M, Myneni S, Rotenberg E, Seal S, Steele WF, Ade H, Garcia A, Cerasari S, Delinger J, Hayakawa S, Hitchcock AP, Tyliszczak T, Kikuma J, Rightor EG, Shin HJ, Tonner BP (1998) A scanning transmission X-ray microscope for materials science spectromicroscopy at the advanced light source. Rev Sci Instrum 69:2964–2973
Weber PK, Graham GA, Teslich NE, Moberly Chan W, Ghosal S, Leighton TJ, Wheeler KE (2010) NanoSIMS imaging of Bacillus spores sectioned by focused ion beam. J Microsc 238:189–199
Whalley WR, Riseley B, Leeds-Harrison PB, Bird NRA, Leech PK, Adderley WP (2005) Structural difference between bulk and rhizosphere soil. Eur J Soil Sci 56:353–360
Wiesemann U, Thieme J, Guttmann P, Frueke R, Rehbein S, Niemann B, Rudolph D, Schmahl G (2003) First results of the new scanning transmission X-ray microscope at BESSY-II. J Phys IV 104:95–98
Wilhein T, Kaulich B, Di Fabrizio E, Romanato F, Cabrini S, Susini J (2001) Differential interference contrast X-ray microscopy with submicron resolution. Appl Phys Lett 78:2082–2084
Wilson GWT, Rice CW, Rillig MC, Springer A, Hartnett DC (2009) Soil aggregation and carbon sequestration are tightly correlated with the abundance of arbuscular mycorrhizal fungi: results from long-term field experiments. Ecol Lett 12:452–461
Wirth R (2009) Focused ion beam (FIB) combined with SEM and TEM: advanced analytical tools for studies of chemical composition, microstructure and crystal structure in geomaterials on a nanometre scale. Chem Geol 261:217–229
Wolter H (1952) Spiegelsysteme fallenden Einfalls als abbildende Optiken für Röntgenstrahlen. Ann Phys 6:94–114
Yeo B-S, Stadler J, Schmid T, Zenobi R, Zhang W (2009) Tip-enhanced Raman spectroscopy—its status, challenges and future directions. Chem Phys Lett 472:1–13
Young IM, Crawford JW (2004) Interactions and self-organisation in the soil–microbe complex. Science 304:1634–1637
Young IM, Crawford JW, Nunan N, Otten W, Spiers A (2008) Microbial distribution in soils: physics and scaling. Adv Agron 100:81–121
Zhang G, Dong H, Jiang H, Kukkadapu RK, Kim J, Eberl D, Xu Z (2009a) Biomineralization associated with microbial reduction of Fe3+ and oxidation of Fe2+ in solid minerals. Amer Miner 94:1049–1058
Zhang WH, Cui X, Martin OJF (2009b) Local field enhancement of an infinite conical metal tip illuminated by a focused beam. J Raman Spectrosc 40:1338–1342
Zhang M, Ginn BR, Dichristina TJ, Stack AG (2010) Adhesion of Shewanella oneidensis MR-1 to iron (oxy)(hydr)oxides: microcolony formation and isotherm. Environ Sci Technol 44:1602–1609
Zhang S, Kent DB, Elbert DC, Shi Z, Davis JA, Veblen DR (2011) Mineralogy, morphology, and textural relationships in coatings on quartz grains in sediments in a quartz-sand aquifer. J Contam Hydrol 124:57–67
Acknowledgments
The authors thank the Deutsche Forschungsgemeinschaft for establishing and continuing the priority program SPP1315 “Biogeochemical Interfaces in Soil”.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Rennert, T., Totsche, K.U., Heister, K. et al. Advanced spectroscopic, microscopic, and tomographic characterization techniques to study biogeochemical interfaces in soil. J Soils Sediments 12, 3–23 (2012). https://doi.org/10.1007/s11368-011-0417-5
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11368-011-0417-5