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There is no such thing as ‘undisturbed’ soil and sediment sampling: sampler-induced deformation of salt marsh sediments revealed by 3D X-ray computed tomography

  • Sediments, Sec 2 • Physical and Biogeochemical Processes • Research Article
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Abstract

Purpose

Within most environmental contexts, the collection of ‘undisturbed’ samples is widely relied upon in studies of soil and sediments. However, the impact of sampler-induced disturbance is rarely acknowledged, despite the potential significance of modification to sediment structure for the robustness of data interpretation. In this study, 3D computed X-ray microtomography (μCT) is used to evaluate and compare the disturbance imparted by four commonly used sediment sampling methods within a coastal salt marsh.

Materials and methods

Paired sediment core samples from a restored salt marsh at Orplands Farm, Essex, UK, were collected using four common sampling methods (push, cut, hammer and gouge methods). Sampling using two different area-ratio cores resulted in a total of 16 cores that were scanned with μCT to identify and evaluate sediment structural properties of samples that can be attributed to sampling method.

Results and discussion

3D qualitative analysis identifies a suite of sampling disturbance structures including gross-scale changes to sediment integrity and substantial modification of pore space, structure and distribution, independent of sediment strength and stiffness. Quantitative assessment of changes to pore space and sediment density arising from the four sampling methods offers a means of direct comparison between the impact of depth sampling methods. Considerable disturbance to samples results from use of push, hammer and auguring samplers, whilst least disturbance is found in samples recovered by cutting and advanced trimming approaches.

Conclusions

In many environmental studies involving sediment recovery through coring or other depth sampling, there is no such thing as an undisturbed sediment sample. The novel use of μCT scanning of sealed sediment cores has enabled the identification and evaluation of the nature and extent of sample disturbance resulting from four common types of sediment recovery methods. Depth sampling and coring methods remain key tools for understanding sediments and soils, but referring to undisturbed sediment sampling is no longer tenable without supporting evidence.

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References

  • Alaoui A, Lipiec J, Gerke HH (2011) A review of the changes in the soil pore system due to soil deformation: a hydrodynamic perspective. Soil Tillage Res 115-116:1–15

    Google Scholar 

  • Allaire SE, Roulier S, Cessna AJ (2009) Quantifying preferential flow in soils: a review of different techniques. J Hydrol 378:179–204

    Google Scholar 

  • Alley WM (2002) Flow and storage in groundwater systems. Science 296(5575):1985–1990

    CAS  Google Scholar 

  • Araújo-Gomes J, Ramos-Pereira A (2014) The new CutSprof sampling tool and method for micromorphological and microfacies analyses of subsurface salt marsh sediments, Algarve, Portugal. Geo-Mar Lett 35:69–75

    Google Scholar 

  • Baligh MM (1985) Strain path method. J Geotech Eng ASCE 36:1108–1136

    Google Scholar 

  • Baligh MM, Azzouz AS, Chin CT (1987) Disturbances due to “ideal” tube sampling. J Geotech Eng ASCE 113:739–757

    Google Scholar 

  • Ball BC, Batey T, Munkholm LJ (2007) Field assessment of soil structural quality- a development of the Peerlkamp test. Soil Use Mgmt 23:329–337

    Google Scholar 

  • Bendle JM, Palmer AP, Carr SJ (2015) A comparison of micro-CT and thin section analysis of Lateglacial glaciolacustrine varves from Glen Roy, Scotland. Quat Sci Rev 114:61–77

    Google Scholar 

  • Beven K, Germann P (1982) Macropores and water flow in soils. Water Resour Res 18:1311–1325

    Google Scholar 

  • Beven K, Germann P (2013) Macropores and water flow in soils revisited. Water Resour Res 49:3017–3092

    Google Scholar 

  • Black HJ, Dainat M, Köster M, Meyer-Rei L-A (2002) A multiple corer for taking virtually undisturbed samples from shallow water sediments. Estuar Coast Mar Sci 54:45–50

    Google Scholar 

  • Blomqvist S (1991) Quantitative sampling of soft-bottom sediments – problems and solutions. Mar Ecol Prog Ser 72:295–304

    Google Scholar 

  • Brain MJ, Kemp AC, Hawkes AD, Engelhart SE, Vane CH, Cahill N, Hill TD, Donnelly JP, Horton BP (2017) Exploring mechanisms of compaction in salt-marsh sediments using common era relative sea-level reconstructions. Quat Sci Rev 167:96–111

    Google Scholar 

  • Buller AT, McManus J (1979) Sediment sampling and analysis. In: Dyer KR (ed) Estuarine hydrography and sedimentation: a handbook. Cambridge University Press, Cambridge, pp 87–130

    Google Scholar 

  • Bullock P, Federoff N, Jongerious A, Stoops G, Tursina T (1985) Handbook for soil thin section description. Waine Research, Wolverhampton

    Google Scholar 

  • Burt, R (ed) (2009) Soil survey field and laboratory methods manual. Soil Survey Investigations Report No 51, Version 10 US Department of Agriculture, Natural Resources Conservation Service, Nebraska, US Available at ftp://ftp-fc.sc.egov.usda.gov/NSSC/Lab_References/SSIR_51.pdf accessed 29 September 2018

  • Carr SJ (2004) Micro-scale features and structures. In: Evans DJA, Benn DI (eds) A practical guide to the study of glacial sediments. Arnold, London, pp 115–144

    Google Scholar 

  • Clayton CRI (1986) Sample disturbance and BS5930. In: Hawkins AB (ed) Site investigation: assessing BS5930, Geological society, engineering geology special publication no, vol 2. Geological Society, London, pp 33–41

    Google Scholar 

  • Clayton CRI, Matthews MC, Simons NE (1995) Site investigation. Blackwell Science, Oxford

    Google Scholar 

  • Cnudde V, Boone MN (2013) High-resolution X-ray computed tomography in geosciences: a review of the current technology and applications. Earth-Sci Rev 123:1–17

    Google Scholar 

  • Corzo A, Jimenez-Arias JL, Torres E, Garcia-Robledo E, Lara M, Papaspyrou S (2018) Biogeochemical changes at the sediment – water interface during redox transitions in an acidic reservoir : exchange of protons, acidity and electron donors and acceptors. Biogeochemistry 139:241–260

    Google Scholar 

  • Dale J, Cundy AB, Spencer KL, Carr SJ, Croudace IW, Burgess HM, Nash DJ (2019) Sediment structure and physicochemical changes following tidal inundation at a large open coast managed realignment site. Sci Total Environ 660:1419–1432

    CAS  Google Scholar 

  • Deurer M, Grinev D, Young I, Clothier BE, Müller K (2009) The impact of soil carbon management on soil macropore structure: a comparison of two apple orchard systems in New Zealand. Eur J Soil Sci 60:945–955

    CAS  Google Scholar 

  • Doran JW, Mielke LN (1984) A rapid, low-cost method for determination of soil bulk density. Soil Sci Soc Am J 48:717–719

    Google Scholar 

  • Doube M, Kłosowski MM, Arganda-Carreras I, Cordelières FP, Dougherty RP, Jackson JS, Schmid B, Hutchinson JR, Shefelbine SJ (2010) BoneJ: free and extensible bone image analysis in ImageJ. Bone 47(6):1076–1079

    Google Scholar 

  • Emmerson RHC, Manatunge JMA, MacLeod CL, Lester JN (1997) Tidal exchanges between Orplands managed retreat site and the Blackwater Estuary, Essex. J Chart Ins Wat Environ Manage 11:363–372

    CAS  Google Scholar 

  • Environment Canada (1994) Environmental protection series: guidance document on collection and preparation of sediments for physicochemical characterisation and biological testing. Report EPS 1/RM/29. Environment Canada, Ottawa, Canada

  • Fonseca J, O’Sullivan C, Coop MR, Lee PD (2013) Quantifying the evolution of soil fabric during shearing using scalar parameters. Géotechnique 63(10):818–829

    Google Scholar 

  • Frew C (2014) Coring methods. In: Geomorphological Techniques, British Society of Geomorphology 1, 1–10. Available at: http://geomorphology.org.uk/sites/default/files/geom_tech_chapters/4.1.1_Coring.pdf. Accessed 02 March 2018

  • Gardner WS, Mccarthy MJ, Carini SA, Souza AC, Lijun H, Mcneal KS, Puckett MK, Pennington J (2009) Collection of intact sediment cores with overlying water to study nitrogen- and oxygen-dynamics in regions with seasonal hypoxia. Cont Shelf Res 29:2207–2213

    Google Scholar 

  • Gilbert PA (1992) Effect of sampling disturbance on laboratory-measured soil properties. US Army Corps of Engineers Miscellaneous Paper GL-92-35

  • Glew JR, Smol JP (2016) A push corer developed for retrieving high-resolution sediment cores from shallow waters. J Paleolimnol 56:67–71

    Google Scholar 

  • Glew JR, Smol JP, Last WM (2002) Sediment core collection and extrusion. In: Last WM, Smol JP (eds) Tracking environmental change using lake sediments, basin analysis, coring, and chronological techniques developments in paleoenvironmental research. Kluwer Academic Publishers, London, pp 73–105

    Google Scholar 

  • Hight DW (1986) Laboratory testing: assessing BS5930. In: Hawkins AB (ed) Site investigation: assessing bs5930, Geological society, engineering geology special publication no, vol 2. Geological Society, London, pp 43–58

    Google Scholar 

  • Hvorslev MJ (1949) Subsurface exploration and sampling of soils for civil engineering purposes. Waterways Experiment Station, Vicksburg

    Google Scholar 

  • Jahnke RA, Knight LH (1997) A gravity-driven, hydraulically-damped multiple piston corer for sampling fine-grained sediments. Deep-Sea Res Pt I 44:713–718

    CAS  Google Scholar 

  • Johannes A, Weisskopf P, Schulin R, Boivin P (2017) To what extent do physical measurements match with visual evaluation of soil structure? Soil Tillage Res 173:24–32

    Google Scholar 

  • Jones FGW, Thomasson AJ (1976) Bulk density as an indicator of pore space in soils usable by nematodes. Nematologica 2:133–137

    Google Scholar 

  • Kemp RA (1985) Soil micromorphology and the quaternary. QRA technical guide no 2. Cambridge, UK

  • Ketcham RA, Carlson WD (2001) Acquisition, optimisation and interpretation of x-ray tomographic imagery: applications to the geosciences. Comput Geosci 27:381–400

    CAS  Google Scholar 

  • Kettridge N, Binley A (2010) Evaluating the effect of using artificial pore water on the quality of laboratory hydraulic conductivity measurements of peat. Hydrol Process 24:2629–2640

    Google Scholar 

  • Kilfeather AA, van der Meer JJM (2008) Pore size, shape and connectivity in tills and their relationship to deformation processes. Quat Sci Rev 27:250–266

    Google Scholar 

  • Knappett JA, Craig RF (2012) Craig’s soil mechanics, 8th edn. Spon Press, London

    Google Scholar 

  • Kumar S, Anderson SH, Udawatta RP (2010) Agroforestry and grass buffer influences on macropores measured by computed tomography under grazed pasture systems. Soil Sci Soc Am J 74:203–212

    CAS  Google Scholar 

  • Ladd CC, DeGroot DJ (2004) Recommended practice for soft ground site characterisation: Arthur Casagrande lecture. 12th pan-American conference on soil mechanics and geotechnical engineering, Massachusetts Institute of Technology, Cambridge, MA, USA

  • Lane CM, Taffs KH (2002) The LOG corer - a new device for obtaining short cores in soft lacustrine sediments. J Paleolimnol 27:145–150

    Google Scholar 

  • Lanesky DD, Logan BW, Brown RG, Hine AC (1979) A new approach to portable vibracoring underwater and on land. J Sediment Petrol 49:654–657

    Google Scholar 

  • Limaye A (2012) Drishti: a volume exploration and presentation tool. SPIE proceedings, 8506 (developments in x-ray tomography VIII), 85060X

  • Lotter AF, Merkt J, Sturm M (1997) Differential sedimentation versus coring artifacts: a comparison of two widely used piston-coring methods. J Paleolimnol 18:75–85

    Google Scholar 

  • Lowe JJ, Walker MJC (2015) Reconstructing quaternary environments (3rd edition). Routledge, London

    Google Scholar 

  • Luo L, Lin H, Schmidt J (2010a) Quantitative relationships between soil macropore characteristics and preferential flow and transport. Soil Sci Soc Am J 74:1929–1937

    CAS  Google Scholar 

  • Luo L, Lin H, Li S (2010b) Quantification of 3-D soil macropore networks in different soil types and land uses using computed tomography. J Hydrol 393:53–64

    Google Scholar 

  • Menzies J, van der Meer JJM, Domack E, Wellner JS (2010) Micromorphology: as a tool in the detection, analyses and interpretation of (glacial) sediments and man-made materials. Proc Geol Assoc 121:281–292

    Google Scholar 

  • Montagna PA, Baguley JG, Hsiang C, Reuscher MG (2017) Comparison of sampling methods for deep-sea infauna. Limnol Oceanogr Methods 15:166–183

    Google Scholar 

  • Müller K, Katuwal S, Young I, McLeod M, Moldrup P, de Jonge LW, Clothier B (2018) Characterising and linking X-ray CT derived macroporosity parameters to infiltration in soils with contrasting structures. Geoderma 313:82–91

  • Munkholm LJ, Heck RJ, Deen B (2013) Long-term rotation and tillage effects on soil structure and crop yield. Soil Tillage Res 127:85–91

    Google Scholar 

  • Nakashima Y, Komatsubara J (2018) Multifractal analysis of seismically induced soft-sediment deformation structures imaged by x-ray computed tomography. Fractals 26(01):1850018. https://doi.org/10.1142/S0218348X18500184

    Article  Google Scholar 

  • Naveed M, Schjønning P, Keller T, de Jonge LW, Moldrup P, Lamandé M (2016) Quantifying vertical stress transmission and compaction-induced soil structure using sensor mat and X-ray computed tomography. Soil Tillage Res 158:110–122

    Google Scholar 

  • Nuttle WK, Hemond HF (1988) Salt marsh hydrology: implications for biogeochemical fluxes to the atmosphere and estuaries. Glob Biogeochem Cycles 2:91–114

    Google Scholar 

  • Palmer AP, Rose J, Lowe JJ, Walker MJC (2008) Annually laminated Late Pleistocene sediments from Llangorse Lake, South Wales, UK: a chronology for the pattern of ice wastage. Proc Geol Assoc 119:245–258

    Google Scholar 

  • Palmer AP, Rose J, Rasmussen SO (2012) Evidence for phase-locked changes in climate between Scotland and Greenland during GS-1 (Younger Dryas) using micromorphology of glaciolacustrine varves from Glen Roy. Quat Sci Rev 36:114–123

    Google Scholar 

  • Peters JF, Muthuswamy M, Wibowo J, Tordesillas A (2005) Characterization of force chains in granular material. Phys Rev Lett 72:041307

    CAS  Google Scholar 

  • Phillips E, van der Meer JJM, Ferguson A (2011) A new “microstructural mapping” methodology for the identification, analysis and interpretation of polyphase deformation within subglacial sediments. Quat Sci Rev 30:2570–2596

    Google Scholar 

  • Quiggin N (2011) Inspect-X user manual. Nikon Metrology, Hertfordshire

    Google Scholar 

  • Quinton WL, Elliot T, Price JS, Rezanezhad F, Heck R (2009) Measuring physical and hydraulic properties of peat from x-ray tomography. Geoderma 153:269–277

    Google Scholar 

  • Rab MA, Haling RE, Aarons SR, Hannah M, Young IM, Gibson D (2014) Evaluation of X-ray computed tomography for quantifying macroporosity of loamy pasture soils. Geoderma 213:460–470

    Google Scholar 

  • Rabot E, Wiesmeier M, Schlüter S, Vogel HJ (2018) Soil structure as an indicator of soil functions: a review. Geoderma 314:122–137

    Google Scholar 

  • Ray A (2011) CT pro user manual. Nikon Metrology, Hertfordshire

    Google Scholar 

  • Rezanezhad F, Price JS, Quinton WL, Lennartz B, Milojevic T, Van Cappellen P (2016) Structure of peat soils and implications for water storage, flow and solute transport: a review update for geochemists. Chem Geol 429:75–84

    CAS  Google Scholar 

  • Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, Preibisch S, Rueden C, Saalfeld S, Schmid B, Tinevez J, White DJ, Hartenstein V, Eliceira K, Tomancak P, Cardona A (2012) Fiji: an open-source platform for biological-image analysis. Nat Methods 9:676–682

    CAS  Google Scholar 

  • Spencer KL (2017) Sediment sampling and analysis. In: Mitchell S, Uncles R (eds) ECSA practical handbooks on survey and analysis methods, estuarine and coastal hydrography and sedimentology, 2nd edn. Cambridge University Press, Cambridge, pp 153–170

    Google Scholar 

  • Spencer KL, Cundy AB, Croudace IW (2003) Heavy metal distribution and early- diagenesis in salt marsh sediments from the Medway Estuary, Kent, UK. Estuar Coast Shelf Sci 57:43–54

    CAS  Google Scholar 

  • Spencer KL, Cundy AB, Davies-Hearn S, Hughes R, Turner S, MacLeod CL (2008) Physicochemical changes in sediments at Orplands Farm, Essex, UK following 8 years of managed realignment. Estuar Coast Shelf Sci 76:608–619

    Google Scholar 

  • Spencer KL, Carr SJ, Diggens LM, Tempest JA, Morris MA, Harvey GL (2017) The impact of pre-restoration land-use and disturbance on sediment structure, hydrology and the sediment geochemical environment in restored saltmarshes. Sci Total Environ 587–588:47–58

    Google Scholar 

  • Stoops G (2009) Evaluation of Kubiëna’s contribution to micropedology. At the occasion of the seventieth anniversary of his book “Micropedology”. Eurasian Soil Sci 42:693–698

    Google Scholar 

  • Taina IA, Heck RJ, Elliot TR (2008) Application of X-ray computed tomography to soil science: a literature review. Can J Soil Sci 88:1–19

    Google Scholar 

  • Tarplee MFV, van der Meer JJM, Davis GR (2011) The 3D microscopic ‘signature’ of strain within glacial sediments revealed using x-ray computed tomography. Quat Sci Rev 30:3501–3532

    Google Scholar 

  • Tempest JA, Harvey GL, Spencer KL (2015) Modified sediments and subsurface hydrology in natural and recreated salt marshes and implications for delivery of ecosystem services. Hydrol Process 29(10):2346–2357

    Google Scholar 

  • Tseng CL, Alves MC, Crestana S (2018) Quantifying physical and structural soil properties using X-ray microtomography. Geoderma 318:78–87

    Google Scholar 

  • Turberg P, Zeimetz F, Grondin Y, Elandoy C, Buttler A (2014) Characterization of structural disturbances in peats by X-ray CT-based density determinations. Eur J Soil Sci 65:613–624

    Google Scholar 

  • Turner RE, Milan CS, Swenson EM (2006) Recent volumetric changes in salt marsh soils. Estuar Coast Shelf Sci 69:352–359

    Google Scholar 

  • Twiss RJ, Moores EM (1997) Structural Geology. W.H. Freeman and Company, New York

    Google Scholar 

  • van der Meer JJM (1993) Microscopic evidence of subglacial deformation. Quat Sci Rev 12:553–587

    Google Scholar 

  • van der Meer JJM, Menzies J (2011) The micromorphology of unconsolidated sediments. Sediment Geol 238:213–232

    Google Scholar 

  • Viana da Fonseca A, Pineda J (2017) Getting high-quality samples in “sensitive” soils for advanced laboratory tests. Innov Infrastruct Solut 2:34

    Google Scholar 

  • Wright HE (1991) Coring tips. J Paleolimnol 6:37–50

    Google Scholar 

  • Wright HE (1993) Core compression. Limnol Oceanogr 38:699–701

    Google Scholar 

  • Xu J, Wang Y, Yin J, Lin J (2011) New series of corers for taking undisturbed vertical samples of soft bottom sediments. Mar Environ Res 71:312–316

    CAS  Google Scholar 

  • Yang H, Flower RJ (2009) A portable hand-operated sampler for shallow-water surface sediments with special reference to epipelic communities. J Palaeolimn 42:317–324

    Google Scholar 

  • Zhang N, Thompson CEL, Townend IH, Rankin KE, Paterson DM, Manning, AJ (2018) Nondestructive 3D imaging and quantification of hydrated biofilm-sediment aggregates using X-ray microcomputed tomography. Environ Sci Technol 52:13306–13313

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Acknowledgements

The authors would like to thank Kurt Kjaer for permission to use the image visualization shown in Fig. 8. The comments from two anonymous reviewers greatly improved the manuscript and are much appreciated.

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Correspondence to Simon J. Carr.

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Carr, S.J., Diggens, L.M. & Spencer, K.L. There is no such thing as ‘undisturbed’ soil and sediment sampling: sampler-induced deformation of salt marsh sediments revealed by 3D X-ray computed tomography. J Soils Sediments 20, 2960–2976 (2020). https://doi.org/10.1007/s11368-020-02655-7

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