, Volume 680, Issue 1, pp 265–284

High resolution mapping of sediment organic matter from acoustic reflectance data

  • Natalia Serpetti
  • Mike Heath
  • Malcolm Rose
  • Ursula Witte
Primary Research Paper


Spatial mapping of the marine environment is challenging when the properties concerned are difficult to measure except by shore-based analysis of discrete samples of material, usually from sparsely distributed sites. This is the case for many seabed sediment properties. We developed an indirect approach to mapping the organic content of coastal sediments from hydro-acoustic reflectance data. The basis was that both organic matter and acoustic reflectance are related to sediment type and grain size composition. Hence there is a collateral relationship between organic matter content and reflectance properties which can be exploited to enable high resolution mapping. We surveyed an area of seabed off the east coast of Scotland using a vessel mounted single beam echosounder with RoxAnn signal processing. Organic carbon, nitrogen and phytoplankton pigment contents were then measured in material from grab and core samples collected at intervals over a year. Relationships between the organic components and hydro–acoustic characteristics were derived by general additive models, and used to construct high resolution maps from the acoustic survey data. Our method is an advance on traditional interpolation techniques sparse spatial data, and represents a generic approach that could be applied to other properties.


Single beam RoxAnn Ground truthing survey Hardness Roughness Total organic carbon (TOC) Total nitrogen (TN) Chlorophyll-a Pheophytin-a Scotland UK 


  1. Arar, E. J. & G. B. Collins, 1997. In vitro Determination of Chlorophyll a and Pheophytin a in Marine and Freshwater Algae by Fluorescence, Method 445.0. National Exposure Research Laboratory, Office of Research and Development, U.S., Environmental Protection Agency, Cincinnati, OH.Google Scholar
  2. Baxter, J. M., I. L. Boyd, M. Cox, L. Cunningham, P. Holmes & C. F. Moffat, 2008. Scotland’s seas: Towards Understanding their State. Chapter 2. Physical Characteristics and Modelling of the Marine Environment (Case Study 2.2 Seabed sediments). Fisheries Research Services, Aberdeen: 28 pp [availble on internet at http://www.scotland.gov.uk/Resource/Doc/218570/0058690.pdf].
  3. Bianchi, T. S., B. Johansson & R. Elmgren, 2000. Breakdown of phytoplankton pigments in Baltic sediments: effects of anoxia and loss of deposit-feeding macrofauna. Journal of Experimental Marine Biology and Ecology 251: 161–183.PubMedCrossRefGoogle Scholar
  4. Burdige, D. J., 2005. Burial of terrestrial organic matter in marine sediments: a re-assessment. Global Biogeochemical Cycles 19: GB4011.CrossRefGoogle Scholar
  5. Boon, A. R. & G. C. A. Duineveld, 1998. Chlorophyll a as a marker for bioturbation and carbon flux in southern and central North Sea sediments. Marine Ecology Progress Series 162: 33–43.CrossRefGoogle Scholar
  6. Caeiro, S., M. H. Costa, P. Goovaerts & F. Martins, 2005. Benthic biotope index for classifying habitats in the Sado estuary: Portugal. Marine Environmental Research 60: 570–593.PubMedCrossRefGoogle Scholar
  7. Calvert, S. E., 1987. Oceanographic controls on the accumulation of organic matter in marine sediments. Geological Society, London, Special Publications 26: 137–151.CrossRefGoogle Scholar
  8. Canfield, D. E., R. Wollast, F. T. Mackenzie & L. Chou, 1993. Organic matter oxidation in marine sediments. In Wollast, R., F. T. Mackenzie & L. Chou (eds), Interactions of C, N, P and S Biogeochemical Cycles and Global Change. Springer, Berlin: 333–363.CrossRefGoogle Scholar
  9. Cawley, G. C. & N. L. C. Talbot, 2010. On over-fitting in model selection and subsequent selection bias in performance evaluation. Journal of Machine Learning Research 11: 2079–2107.Google Scholar
  10. Chivers, R. C., N. C. Emerson & D. Burns, 1990. New acoustic processing for underway surveying. The Hydrographic Journal 56: 9–17.Google Scholar
  11. Chotiros, N. P., A. M. Mautner, A. Løvik, A. Kristensen & O. Bergem, 1997. Acoustic penetration of a silty sand sediment in the 1–10-kHz band. IEEE Journal of Oceanic Engineering 22(4): 604–615.CrossRefGoogle Scholar
  12. Conley, D. J. & R. W. Johnstone, 1995. Biogeochemistry of N, P and Si in Baltic Sea sediments: response to a simulated deposition of a spring bloom. Marine Ecology Progress Series 122: 265–276.CrossRefGoogle Scholar
  13. Creutzberg, F., P. Wapenaar, G. Duineveld & N. Lopez, 1984. Distribution and density of the benthic fauna in the southern North Sea in relation to bottom characteristics and hydrographic conditions. Journal du Conseil International pour l’exploration de la Mer 183: 101–110.Google Scholar
  14. Degraer, S., E. Verfaillie, W. Willems, E. Adriaens, M. Vincx & V. Van Lancker, 2008. Habitat suitability modelling as a mapping tool for macrobenthic communities: an example from the Belgian part of the North Sea. Continental Shelf Research 28: 369–379.CrossRefGoogle Scholar
  15. Ehrenhauss, S., U. Witte, F. Janssen & M. Huettel, 2004. Decomposition of diatoms and nutrient dynamics in permeable North Sea sediments. Continental Shelf Research 24: 721–737.CrossRefGoogle Scholar
  16. Folk, R. L., 1954. The distinction between grain size and mineral composition in sedimentary rock nomenclature. Journal of Geology 62(4): 344–359.CrossRefGoogle Scholar
  17. Furlong, E. T. & R. Carpenter, 1988. Pigment preservation and remineralization in oxic coastal marine sediments. Geochimica et Cosmochimica Acta 52: 87–99.CrossRefGoogle Scholar
  18. Foster-Smith, R. L., C. J. Brown, W. J. Meadows, W. White & D. S. Limpenny, 2004. Mapping seabed biotopes at two spatial scales in the Eastern English Channel. Part 2: comparison of two acoustic ground discrimination systems. Journal of the Marine Biological Association of the United Kingdom 84: 489–500.CrossRefGoogle Scholar
  19. Guisan, A. & N. E. Zimmermann, 2000. Predictive habitat distribution models in ecology. Ecological Modelling 135: 147–186.CrossRefGoogle Scholar
  20. Hamilton, L. J., P. J. Mulhearn & R. Poeckert, 1999. Comparison of RoxAnn and QTC-View acoustic bottom classification system performance for the Cairns area, Great Barrier Reef, Australia. Continental Shelf Research 19: 1577–1597.CrossRefGoogle Scholar
  21. Holtmann, S. E., A. Groenewold, K. H. M. Schrader, J. Asjes, J. A. Craeymeersch, G. C. A. Duineveld, A. J. van Bostelen & J. Van Der Meer, 1996. Atlas of the Zoobenthos of the Dutch Continental Shelf. Ministry of Transport, Public Works and Water Management, Rijswijk, The Netherlands. ISBN 90-369-4301-9.Google Scholar
  22. ICES, 2005. Report of the Working Group on Marine Habitat Mapping (WGMHM), Bremerhaven, Germany, 5–8 April, ICES CM 2005/E:05: 85 pp, unpublished.Google Scholar
  23. Janssen, F., M. Huettel & U. Witte, 2005. Pore-water advection and solute fluxes in permeable marine sediment (II): benthic respiration at three sandy sites with different permeabilities (German Bight, North Sea). Limnology and Oceanography 50(3): 779–792.CrossRefGoogle Scholar
  24. Jenness, M. I. & G. C. A. Duineveld, 1985. Effects of tidal currents on chlorophyll a content of sandy sediments in the southern North Sea. Marine Ecology Progress Series 21: 283–287.CrossRefGoogle Scholar
  25. Jørgensen, B. B., M. Bang & T. H. Blackburn, 1990. Anaerobic mineralization in marine sediments from the Baltic Sea-North Sea transition. Marine Ecology Progress Series 59: 39–54.CrossRefGoogle Scholar
  26. Leavitt, P. R., 1993. A review of factors that regulate carotenoid and chlorophyll deposition and fossil pigment abundance. Journal of Paleolimnology 9: 109–127.CrossRefGoogle Scholar
  27. Lohse, L., J. F. P. Malschaert, C. P. Slomp, W. Helder & W. van Raaphorst, 1995. Sediment-water fluxes of inorganic nitrogen compounds along the transport route of organic matter in the North Sea. Ophelia 41: 173–197.Google Scholar
  28. Lorenzen, C. J., 1967. Determination of chlorophyll and pheopigments: spectroscopic equations. Limnology and Oceanography 12: 343–346.CrossRefGoogle Scholar
  29. McBreen, F., J. G. Wilson, A. S. Y. Mackie & C. N. Aonghusa, 2008. Seabed mapping in the southern Irish Sea: predicting benthic biological communities based on sediment characteristics. Hydrobiologia 606: 93–103.CrossRefGoogle Scholar
  30. Montgomery, D. C. & E. A. Peck, 1992. Introduction to Linear Regression Analysis. Wiley, New York.Google Scholar
  31. Ogrinc, N., G. Fontolan, J. Faganeli & S. Covelli, 2005. Carbon and nitrogen isotope compositions of organic matter in coastal marine sediments (the Gulf of Trieste, N Adriatic Sea): indicators of sources and preservation. Marine Chemistry 95: 163–181.CrossRefGoogle Scholar
  32. Patoine, A. & P. R. Leavitt, 2006. Century-long synchrony of fossil algae in a chain of Canadian prairie lakes. Ecology 87: 1710–1721.PubMedCrossRefGoogle Scholar
  33. Rutgers Van Der Loeff, M. M., 1980. Nutrients in the interstitial waters of the Southern Bight of the North Sea. Netherland of Journal of Sea Research 14: 144–171.CrossRefGoogle Scholar
  34. Serpetti, N., M. R. Heath, E. Armstrong & U. Witte, 2011. Blending single beam RoxAnn and multi-beam swathe QTC hydro-acoustic discrimination techniques for the Stonehaven area, Scotland, UK. Journal of Sea Research 65: 442–455.CrossRefGoogle Scholar
  35. Serpetti, N., M. R. Heath & U. Witte, in preparation. Modelling the main drivers of spatial and temporal variability in sediment metabolism and nutrient fluxes off the north-east coast of Scotland, UK.Google Scholar
  36. Shin, P. K. S., 1982. Multiple discriminant analysis of macrobenthic infaunal assemblages. Journal of Experimental Marine Biology and Ecology 59: 39–50.CrossRefGoogle Scholar
  37. Stephens, M. P., D. C. Kadko, C. R. Smith & M. Latasa, 1997. Chlorophyll-a and pheopigments as tracers of labile organic carbon at the central equatorial Pacific seafloor. Geochimica et Cosmochimica Acta 61(21): 4605–4619.CrossRefGoogle Scholar
  38. Strickland, J. D. H. & T. R. Parsons, 1972. A practical handbook of seawater analysis. Fisheries Research Board of Canada Bulletin 167: 311 pp.Google Scholar
  39. Sun, M.-Y., R. C. Aller & C. Lee, 1991. Early diagenesis of chlorophyll-a in Long Island Sound sediments: a measure of carbon flux and particle reworking. Journal of Marine Research 49: 379–401.CrossRefGoogle Scholar
  40. Sun, M.-Y., C. Lee & R. C. Aller, 1993. Anoxic and oxic degradation of 14C-labelled chloropigments and a 14C-labelled diatom in Long Island Sound sediments. Limnology and Oceanography 38: 1438–1451.CrossRefGoogle Scholar
  41. ThermoQuest FlashEA 1112 Elemental Analyser Operating Manual, 1999. Part Number 317, 08241, 2nd ed, November 1999.Google Scholar
  42. Udden, J. A., 1914. Mechanical composition of clastic sediments. Geological Society of America Bulletin 25: 655–744.Google Scholar
  43. Vanaverbeke, J., T. Gheskiere, M. Steyaert & M. Vincx, 2002. Nematode assemblages from subtidal sandbanks in the Southern Bight of the North Sea: effect of small sedimentological differences. Journal of Sea Research 48: 197–207.CrossRefGoogle Scholar
  44. Verfaillie, E., V. Van Lancker & M. Van Meirvenne, 2006. Multivariate geostatistics for the predictive modelling of the surficial sand distribution in shelf seas. Continental Shelf Research 26: 2454–2468.CrossRefGoogle Scholar
  45. Wentworth, C. K., 1922. A scale of grade and class terms for clastic sediments. The Journal of Geology 30: 377–392.CrossRefGoogle Scholar
  46. Winterwerp, J. C. & W. G. M. van Kesteren, 2004. Introduction to the Physics of Cohesive Sediment in Marine Environment. Elsevier B.V., Amsterdam.Google Scholar
  47. Wollast, R., K. H. Brink & A. R. Robinson, 1998. Evaluation and Comparison of the Global Carbon Cycle in the Coastal Zone and in the Open Ocean. The sea: The Global Coastal Ocean: Processes and Methods. Wiley, New York: 213–252.Google Scholar
  48. Wood, S. N., 2003. Thin plate regression splines. Journal of the Royal Statistical Society, Series B (Statistical Methodology) 65(1): 95–114.CrossRefGoogle Scholar
  49. Young, A., 2007. MESH maps come online. a framework to support seabed habitat mapping. Hydro International 11: 6–9.Google Scholar
  50. Zuur, A. F., E. N. Ieno & C. S. Elphick, 2010. A protocol for data exploration to avoid common statistical problems. Methods in Ecology & Evolution 1: 3–14.CrossRefGoogle Scholar
  51. Zuur, A. F., E. N. Ieno & G. M. Smith, 2007. Analysing Ecological Data. Springer, New York: 467–472.Google Scholar

Copyright information

© Crown Copyright 2011

Authors and Affiliations

  • Natalia Serpetti
    • 1
    • 2
  • Mike Heath
    • 1
    • 3
  • Malcolm Rose
    • 1
  • Ursula Witte
    • 2
  1. 1.Marine Scotland – Science Laboratory AberdeenAberdeenUK
  2. 2.Oceanlab, Institute of Biological and Environmental Sciences, EcologyUniversity of AberdeenNewburghUK
  3. 3.Department of Mathematics and StatisticsUniversity of StrathclydeGlasgowUK

Personalised recommendations