Skip to main content Accessibility help
  • Print publication year: 2014
  • Online publication date: June 2014

4 - Sampling Design for Organic Matter Fluorescence Analysis

from Part II - Instrumentation and Sampling


Ahad, J.M.E., Ganeshram, R.S., Spencer, R.G.M., Uher, G., Gulliver, P., and Bryant, C.L. (2006). Evidence for anthropogenic 14C-enrichment in estuarine waters adjacent to the North Sea. Geophys. Res. Lett., 33, L08608, doi:10.1029/2006GL025991.
Andersen, D.O., Alberts, J.J., and Takacs, M. (2000). Nature of natural organic matter (NOM) in acidified and limed surface waters. Water Res., 34(1), 266–278.
Astoreca, R., Rousseau, V., and Lancelot, C. (2009). Coloured dissolved organic matter (CDOM) in Southern North Sea waters: Optical characterization and possible origin. Estuar., Coast. Shelf Sci., 85, 633–640.
Aufdenkampe, A.K., Mayorga, E., Hedges, J.I., Llerena, C., Quay, P.D., Gudeman, J., Krusche, A.V., and Richey, J.E. (2007). Organic matter in the Peruvian headwaters of the Amazon: Compositional evolution from the Andes to the lowland Amazon mainstem. Org. Geochem., 38, 337–364.
Baker, A. (2001). Fluorescence excitation–emission matrix characterization of some sewage impacted rivers. Environ. Sci. Technol., 35(5), 948–953.
Baker, A. (2002). Fluorescence excitation-emission matrix characterization of river waters impacted by a tissue mill effluent. Environ., Sci. Technol., 36(7), 1377–1382.
Baker, A. and Inverarity, R. (2004). Protein-like fluorescence intensity as a possible tool for determining river water quality. Hydrol. Process., 18(15), 2927–2945.
Baker, A., Elliott, S., and Lead, J.R. (2007). Effects of filtration and pH perturbation on freshwater organic matter fluorescence. Chemosphere, 67, 2035–2043.
Belzile, C., Roesler, C.S., Christensen, J.P., Shakhova, N., and Semiletov, I. (2006). Fluorescence measured using the WETStar DOM fluorometer as a proxy for dissolved matter absorption. Estuar., Coast. Shelf Sci., 67, 441–449.
Benner, R. and Hedges, J.I. (1993). A test of the accuracy of freshwater DOC measurements by high-temperature catalytic oxidation and UV-promoted persulfate oxidation. Mar. Chem., 41, 161–165.
Blough, N.V., Zafiriou, O.C., and Bonilla, J. (1993). Optical absorption spectra of waters from the Orinoco River outflow: Terrestrial input of colored organic matter to the Caribbean. J. Geophys. Res., 98(C2), 2271–2278.
Bouillon, S., Abril, G., Borges, A.V., Dehairs, F., Govers, G., Hughes, H.J., Merckx, R., Meysman, F.J.R., Nyunja, J., Osburn, C., and Middelburg, J.J. (2009). Distribution, origin and cycling of carbon in the Tana River (Kenya): A dry season basin-scale survey from headwaters to the delta. Biogeosciences, 6(11), 2475–2493.
Chen, R.F. and Gardner, G.B. (2004). High-resolution measurements of chromophoric dissolved organic matter in the Mississippi and Atchafalaya River plume regions. Mar. Chem., 89(1–4), 103–125.
Chen, W., Westerhoff, P., Leenheer, J.A., and Booksh, K. (2003). Fluorescence excitation-emission matrix regional integration to quantify spectra for dissolved organic matter. Environ. Sci. Technol., 37, 5701–5710.
Coble, P.G., Del Castillo, C.E., and Avril, B. (1998). Distribution and optical properties of CDOM in the Arabian Sea during the 1995 Southwest Monsoon. Deep-Sea Res. Pt. II, 45(10–11), 2195–2223.
Conmy, R.N., Coble, P.G., Cannizzaro, J.P., and Heil, C.A. (2009). Influence of extreme storm events on West Florida Shelf CDOM distributions. J. Geophys. Res-Biogeosci., 114, G00F04, doi:10.1029/2009JG000981.
Cory, R.M., McKnight, D.M., Chin, Y.P., Miller, P., and Jaros, C.L. (2007). Chemical characteristics of fulvic acids from Arctic surface waters: Microbial contributions and photochemical transformations. J. Geophys. Res.-Biogeosci., 112, doi:10.1029/2006JG000343.
Cory, R.M., Miller, M.P., McKnight, D.M., Guerard, J.J., and Miller, P.L. (2010). Effect of instrument-specific response on the analysis of fulvic acid fluorescence spectra. Limnol. Oceanogr. Methods, 8, 67–78.
Del Castillo, C.E., Coble, P.G., Conmy, R.N., Muller-Karger, F.E., Vanderbloemen, L., and Vargo, G.A. (2001). Multispectral in situ measurements of organic matter and chlorophyll fluorescence in seawater: Documenting the intrusion of the Mississippi River in the West Florida Shelf. Limnol. Oceanogr., 46(7), 1836–1843.
Del Vecchio, R. and Blough, N.V. (2002). Photobleaching of chromophoric dissolved organic matter in natural waters: Kinetics and modeling. Mar. Chem., 78(4): 231–253.
Fellman, J.B., D’Amore, D.V., and Hood, E. (2008). An evaluation of freezing as a preservation technique for analyzing dissolved organic C, N, and P in surface water samples. Sci. Tot. Environ., 392, 305–312.
Fellman, J.B., Hood, E., Edwards, R.T., and D’Amore, D.V. (2009). Changes in the concentration, biodegradability, and fluorescent properties of dissolved organic matter during stormflows in coastal temperate watersheds. J. Geophys. Res. Biogeosci., 114, G01021, doi:10.1029/2008JG000790.
Ferrari, G.M., Dowell, M.D., Grossi, S., and Targa, C. (1996). Relationship between the optical properties of chromophoric dissolved organic matter and total concentration of dissolved organic carbon in the southern Baltic Sea region. Mar. Chem., 55, 299–316.
Fu, P., Wu, F., Liu, C., Wang, F., Li, W., Yue, L., and Guo, Q. (2007). Fluorescence characterization of dissolved organic matter in an urban river and its complexation with Hg(II). Appl. Geochemis., 22, 1668–1679.
Gao, L., Fan, D., Li, D., and Cai, J. (2010). Fluorescence characteristics of chromophoric dissolved organic matter in shallow water along the Zhejiang coasts, southeast China. Mar. Environ. Res., 69, 187–197.
Gardolinski, P.C.F.C., Hanrahan, G., Achterberg, E.P., Gledhill, M., Tappin, A.D., House, W.A., and Worsfold, P.J. (2001). Comparison of sample storage protocols for the determination of nutrients in natural waters. Water Res., 35(15), 3670–3678.
Helms, J.R., Stubbins, A., Ritchie, J.D., Minor, E.C., Kieber, D.J., and Mopper, K. (2008). Absorption spectral slopes and slope ratios as indicators of molecular weight, source, and photobleaching of chromophoric dissolved organic matter. Limnol. Oceanogr., 53(3), 955–969.
Hiriart-Baer, V.P., Diep, N., and Smith, R.E.H. (2008). Dissolved organic matter in the Great Lakes: Role and nature of allochthonous material. J. Great Lakes Res., 34, 383–394.
Hood, E., Fellman, J.B., Spencer, R.G.M., Hernes, P.J., Edwards, R., D’Amore, D.V., and Scott, D. (2009). Glaciers as a source of ancient and labile organic matter to the marine environment. Nature, 462, 1044–1048.
Hudson, N., Baker, A., Reynolds, D.M., Carliell-Marquet, C., and Ward, D. (2009). Changes in freshwater organic matter fluorescence intensity with freezing/thawing and dehydration/ rehydration. J. Geophys. Res. Biogeosci., 114, G00F08, doi:10.1029/2008JG000915.
Hur, J., Jung, N.C., and Shin, J.K. (2007). Spectroscopic distribution of dissolved organic matter in a dam reservoir impacted by turbid storm runoff. Environ. Monit. Assess., 133, 5367.
Jaffe, R., McKnight, D., Maie, N., Cory, R., McDowell, W.H., and Campbell, J.R. (2008). Spatial and temporal variations in DOM composition in ecosystems: The importance of long-term monitoring of optical properties. J. Geophys. Res. Biogeosci., 113, G04032, doi:10.1029/2008JG000683.
Kaplan, L.A. (1992). Comparison of high-temperature and persulfate oxidation methods for determination of dissolved organic carbon in freshwaters. Limnol. Oceanogr., 37(5), 1119–1125.
Kattner, G. (1999). Storage of dissolved inorganic nutrients in seawater: Poisoning with mercuric chloride. Mar. Chem., 67, 61–66.
Kirkwood, D.S. (1992). Stability of solutions of nutrient salts during storage. Mar. Chem., 38, 151–164.
Kratzer, S., Bowers, D., and Tett, P.B. (2000). Seasonal changes in colour ratios and optically active constituents in the optical Case-2 waters of the Menai Strait, North Wales. Int. J. Remote Sens., 21(11), 2225–2246.
Kremling, K. and Brugmann, L. (1999). 2. Filtration and storage. In K. Grashoff, K. Kremling, and M. Ehrhardt, (Eds.), Methods of Seawater Analysis, 3rd ed. Berlin, Germany: Wiley-TCH.
Lane, S.L., Flanagan, S., and Wilde, F.D. (2003). Selection of equipment for water sampling (ver. 2.0): U.S. Geological Survey Techniques of Water-Resources Investigations, book 9, chapter A2, March. Retrieved from (Accessed December 1, 2009).
Lapworth, D.J., Gooddy, D.C., Allen, D., and Old, G.H. (2009). Understanding groundwater, surface water, and hyporheic zone biogeochemical processes in a Chalk catchment using fluorescence properties of dissolved and colloidal organic matter. J. Geophys. Res. Biogeosci., 114, G00F02, doi:10.1029/2009JG000921.
Lead, J.R. and Wilkinson, K.J. (2006). Natural aquatic colloids: current knowledge and future trends. Environ. Chem., 3, 159–171.
McKnight, D.M., Boyer, E.W., Westerhoff, P.K., Doran, P.T., Kulbe, T., and Andersen, D.T. (2001). Spectrofluorometric characterization of aquatic fulvic acids for determination of precursor organic material and general structural properties. Limnol. Oceanogr., 46, 38–48.
Mitchell, B.G., Bricaud, A., Carder, K., Cleveland, J., Feraari, G.M., Gould, R., Kahru, M., Kishino, M., Maske, H., Moisan, T., Moore, L., Nelson, N., Phinney, D., Reynolds, R.A., Sosik, H., Stramski, D., Tassan, S., Trees, C., Weidemann, A., Wieland, J.D., and Vodacek, A. (2000). Determination of spectral absorption coefficients of particles, dissolved material and phytoplankton for discrete water samples. In G.S. Fargion and J.L. Mueller (Eds.), Ocean Optics Protocols for Satellite Ocean Color Sensor Validation, Revision 2 (pp. 125–153). NASA/TM-2000–209966. Greenbelt, MD: NASA Goddard Space Flight Center.
Mobed, J.J., Hemmingsen, S.L., Autry, J.L., and McGown, L.B. (1996). Fluorescence characterisation of IHSS humic substances: Total luminescence spectra with absorbance correction. Environ. Sci. Technol., 30(10), 3061–3066
Moran, M.A., Sheldon, W.M., and Zepp, R.G. (2000). Carbon loss and optical property changes during long-term photochemical and biological degradation of estuarine dissolved organic matter. Limnol. Oceanogr., 45, 1254–1264.
Murphy, K.R., Stedmon, C.A., Waite, T.D., and Ruiz, G.M. (2008). Distinguishing between terrestrial and autochthonous organic matter sources in marine environments using fluorescence spectroscopy. Mar. Chem., 108, 40–58.
Murphy, K.R., Butler, K.D., Spencer, R.G.M., Stedmon, C.A., Boheme, J.R., and Aiken, G.R. (2010). Measurement of dissolved organic matter fluorescence in aquatic environments: An intercalibration study. Environ. Sci. Technol., 44, 9405–9412.
Newson, M., Baker, A., and Mounsey, S. (2001). The potential role of freshwater luminescence measurements in exploring runoff pathways in upland catchments. Hydrol. Process., 15(6), 989–1002.
Osburn, C.L., Morris, D.P., Thorn, K.A., and Moeller, R.E. (2001). Chemical and optical changes in freshwater dissolved organic matter exposed to solar radiation. Biogeochemistry, 54(3), 251–278.
Osburn, C.L., Retamal, L., and Vincent, W.F. (2009). Photoreactivity of chromophoric dissolved organic matter transported by the Mackenzie River to the Beaufort Sea. Mar. Chem., 115(1–2), 10–20.
Otero, M., Mendonca, A., Valega, M., Santos, E.B.H., Pereira, E., Esteves, V.I., and Duarte, A. (2007). Fluorescence and DOC contents of estuarine pore waters from colonized and non-colonized sediments: Effects of sampling preservation. Chemosphere, 67, 211–220.
Patel- Sorrentino, N., Mounier, S., and Benaim, J.Y. (2002). Excitation-emission fluorescence matrix to study pH influence on organic matter fluorescence in the Amazon basin rivers. Water Res., 36, 2571–2581.
Peiris, R.H., Halle, C., Budman, H., Moresoli, C., Peldszus, S., Huck, P.M., and Legge, R.L. (2010). Identifying fouling events in a membrane-based drinking water treatment process using principal component analysis of fluorescence excitation-emission matrices. Water Res., 44, 185–194.
Reynolds, D.M. and Ahmad, S.R. (1995). The effect of metal ions on the fluorescence of sewage water. Water Res., 29(9), 2214–2216.
Rosenstock, B. and Simon, M. (1993). Use of dissolved combined and free amino acids by planktonic bacteria in Lake Constance. Limnol. Oceanogr., 38(7), 1521–1531.
Saraceno, J.F., Pellerin, B.A., Downing, B.D., Boss, E., Bachand, P.A.M., and Bergamaschi, B.A. (2009). High frequency in situ optical measurements during a storm event: Assessing relationships between dissolved organic matter, sediment concentrations, and hydrologic processes. J. Geophys. Res. Biogeosci., 114, G00F09, doi:10.1029/2009JG000989.
Seredynska-Sobecka, B., Baker, A., and Lead, J.R. (2007). Characterisation of colloidal and particulate organic carbon in freshwaters by thermal fluorescence quenching. Water Res., 41(14), 3069–3076.
Sharp, J.H., Benner, R., Bennett, L., Carlson, C.A., Fitzwater, S.E., Peltzer, E.T., and Tupas, L.M. (1995). Analyses of dissolved organic carbon in seawater – The JGOFS EQPAC methods comparison. Mar. Chem., 48(2), 91–108.
Sharp, J.H., Beuregard, A.Y., Burdige, D., Cauwet, G., Curless, S.E., Lauck, R., Nagel, K., Ogawa, H., Parker, A.E., Primm, O., Pujo-Pay, A., Savidge, W.B., Seitzinger, S., Spyres, G., and Styles, R. (2004). A direct instrument comparison for measurement of total dissolved nitrogen in seawater. Mar. Chem., 84(3–4), 181–193.
Spencer, R.G.M., Pellerin, B.A., Bergamaschi, B.A., Downing, B.D., Kraus, T.E.C., Smart, D.R., Dahlgren, R.A., and Hernes, P.J. (2007a). Diurnal variability in riverine dissolved organic matter composition determined by in situ optical measurement in the San Joaquin River (California, USA). Hydrol. Process., 21, 3181–3189.
Spencer, R.G.M., Baker, A., Ahad, J.M.E., Cowie, G.L., Ganeshram, R., Upstill-Goddard, R.C., and Uher, G. (2007b). Discriminatory classification of natural and anthropogenic waters in two U.K. estuaries. Sci. Tot. Environ., 373, 305–323.
Spencer, R.G.M., Bolton, L., and Baker, A. (2007c). Freeze/thaw and pH effects on freshwater dissolved organic matter fluorescence and absorbance properties from a number of UK locations. Water Res., 41, 2941–2950.
Spencer, R.G.M., Stubbins, A., Hernes, P.J., Baker, A., Mopper, K., Aufdenkampe, A.K., Dyda, R.Y., Mwamba, V.L., Mangangu, A.M., Wabakanghanzi, J.N., and Six, J. (2009). Photochemical degradation of dissolved organic matter and dissolved lignin phenols from the Congo River. J. Geophys. Res. Biogeosci., 114, G03010, doi:10.1029/2009JG000968.
Spencer, R.G.M., Hernes, P.J., Ruf, R., Baker, A., Dyda, R.Y., Stubbins, A., and Six, J. (2010). Temporal controls on dissolved organic matter and lignin biogeochemistry in a pristine tropical river, Democratic Republic of Congo. J. Geophys. Res.Biogeosciences, doi:10.1029/2009JG001180.
Stedmon, C.A., Markager, S., and Bro, R. (2003). Tracing dissolved organic matter in aquatic environments using a new approach to fluorescence spectroscopy. Mar. Chem., 82, 239–254.
Stedmon, C.A. and Markager, S. (2005). Tracing the production and degradation of autochthonous fractions of dissolved organic matter by fluorescence analysis. Limnol.Oceanogr., 50(5), 1415–1426.
Stubbins, A., Spencer, R.G.M., Chen, H., Hatcher, P.G., Mopper, K., Hernes, P.J., Mwamba, V.L., Mangangu, A.M., Wabakanghanzi, J.N., and Six, J. (2010). Illuminated darkness: Molecular signatures of Congo River dissolved organic matter and its photochemical alteration as revealed by ultrahigh precision mass spectrometry. Limnol. Oceanogr., 55(4), 1467–1477.
Tam, S.-C. and Sposito, G. (1993). Fluorescence spectroscopy of aqueous pine litter extracts: effects of humification and aluminium complexation. Eur. J. Soil Sci., 44(3), 513–524.
Tiltstone, G.H., Moore, G.F., Sorensen, K., Rottgers, R., Jorgensen, P.V., Vicente, V.M., and Ruddick, K.G. (2002). Regional validation of MERIS chlorophyll products in North Sea coastal waters. REVAMP Inter-calibration report. Retrieved from
Tupas, L.M., Popp, B.N., and Karl, D.M. (1994). Dissolved organic carbon in oligotrophic waters: experiments on sample preservation, storage and analysis. Mar. Chem., 45, 207–216.
Tzortziou, M., Osburn, C.L., and Neale, P.J. (2007). Photobleaching of dissolved organic material from a tidal marsh-estuarine system of the Chesapeake Bay. Photochem. Photobiol., 83(4), 782–792.
U.S. Geological Survey (2006). Collection of water samples (ver. 2.0): U.S. Geological Survey Techniques of Water-Resources Investigations, book 9, chapter A4. September. Retrieved from (Accessed December 1, 2009).
Walker, S.A., Amon, R.M.W., Stedmon, C., Duan, S.W., and Louchouarn, P. (2009). The use of PARAFAC modeling to trace terrestrial dissolved organic matter and fingerprint water masses in coastal Canadian Arctic surface waters. J. Geophys. Res.-Biogeosci., 114, G00F06, doi:10.1029/2009JG000990.
Westerhoff, P., Chen, W., and Esparza, M. (2001). Fluorescence analysis of a standard fulvic acid and tertiary treated wastewater. J. Environ. Qual., 30, 2037–2046.
Wickland K.P., Neff J.C., and Aiken G.R. (2007). DOC in Alaskan boreal forests: sources, chemical characteristics, and biodegradability. Ecosystems, 10, 1323–1340.
Wiebinga, C.J. and de Baar, H.J.W. (1998). Determination of the distribution of dissolved organic carbon in the Indian sector of the Southern Ocean. Mar. Chem., 61, 185–201.
Yamashita, Y. and Jaffe, R. (2008). Characterizing the interactions between trace metals and dissolved organic matter using excitation-emission matrix and parallel factor analysis. Environ. Sci. Technol., 42, 7374–7379.
Yamashita, Y., Maie, N., Briceno, H., and Jaffe, R. (2010a). Optical characterization of dissolved organic matter in tropical rivers of the Guayana Shield, Venezuela. Journal of Geophysical Research-Biogeosciences, 115, G00F10, doi:10.1029/2009JG000987.
Yamashita, Y., Cory, R.M., Nishioka, J., Kuma, K., Tanoue, E., and Jaffe, R. (2010b). Fluorescence characteristics of dissolved organic matter in the deep waters of the Okhotsk Sea and the northwestern North Pacific Ocea. Deep-Sea Res. Pt. II, 57, 1478–1485.