Chapter 1 Introduction and motivations

Dissolved organic matter (DOM) plays a central role in the functioning of aquatic ecosystems. For example, characteristics of the DOM pool (quantity and quality) determine underwater light climate (Kirk 1994), the composition of aquatic microbial communities (Foreman and Covert 2003; Kritzberg et al. 2006) and the carbon cycling on local to global scales (J. J. Cole et al. 2007). Chemically, the DOM pool is complex (> 1500 compounds) and analytical methods used to characterize it are relatively complex, time-consuming and costly (Benner 2002; Seitzinger et al. 2005; Jason B Fellman, Hood, and Spencer 2010). This situation called for the development of rapid and cost effective characterization techniques. Because optical properties of DOM can be related to its chemical properties, optical techniques such as fluorescence spectroscopy have been developed and rapidly adopted by the community to characterize the DOM pool in aquatic ecosystems (Paula G Coble et al. 1990; Paula G Coble 1996; McKnight et al. 2001; J B Fellman et al. 2008).

This document aims at providing practical tools that can serve as a starter to those who desire to start working with DOM. R code examples are also provided.

For those that are interested to learn in depth DOM biogeochemistry, there are excellent sources of fundamental information in the following books:

  • Lakowicz (2006)
  • Hansell and Carlson (2014)
  • Findlay and Sinsabaugh (2003)
  • P. Coble et al. (2014)

References

Kirk, John T O. 1994. Light and photosynthesis in aquatic ecosystems. 2nd ed. Cambridge [England] ; New York: Cambridge University Press.

Foreman, C.M., and J.S. Covert. 2003. “Linkages between Dissolved Organic Matter Composition and Bacterial Community Structure.” In Aquatic Ecosystems : Interactivity of Dissolved Organic Matter, 343–62. Elsevier. doi:10.1016/B978-012256371-3/50015-9.

Kritzberg, Emma S, Jonathan J Cole, Michael M Pace, and Wilhelm Granéli. 2006. “Bacterial Growth on Allochthonous Carbon in Humic and Nutrient-enriched Lakes: Results from Whole-Lake 13C Addition Experiments.” Ecosystems 9 (3): 489–99. doi:10.1007/s10021-005-0115-5.

Cole, J J, Y T Prairie, N F Caraco, W H McDowell, L J Tranvik, R G Striegl, C M Duarte, et al. 2007. “Plumbing the Global Carbon Cycle: Integrating Inland Waters into the Terrestrial Carbon Budget.” Ecosystems 10 (1): 172–85. doi:10.1007/s10021-006-9013-8.

Benner, R. 2002. “Chemical composition and reactivity.” In Biogeochemistry of Marine Dissolved Organic Matter, edited by Dennis A Hansell and Craig A Carlson, 59–90. San Diego, CA: Academic Press.

Seitzinger, S P, H Hartnett, R Lauck, M Mazurek, T Minegishi, G Spyres, and R Styles. 2005. “Molecular-level chemical characterization and bioavailability of dissolved organic matter in stream water using electrospray-ionization mass spectrometry.” Limnology and Oceanography 50 (1). Seitzinger, SP Rutgers State Univ, Inst Marine & Coastal Sci, 71 Dudley Rd, New Brunswick, NJ 08901 USA Rutgers State Univ, Inst Marine & Coastal Sci, New Brunswick, NJ 08901 USA: 1–12. doi:10.4319/lo.2005.50.1.0001.

Fellman, Jason B, Eran Hood, and Robert G M Spencer. 2010. “Fluorescence spectroscopy opens new windows into dissolved organic matter dynamics in freshwater ecosystems: A review.” Limnology and Oceanography 55 (6): 2452–62. doi:10.4319/lo.2010.55.6.2452.

Coble, Paula G, Sarah A Green, Neil V Blough, and Robert B Gagosian. 1990. “Characterization of dissolved organic matter in the Black Sea by fluorescence spectroscopy.” Nature 348 (6300). Coble, Pg Univ Washington,Sch Oceanog,Seattle,Wa 98195, USA Univ Washington,Sch Oceanog,Seattle,Wa 98195, USA Woods Hole Oceanog Inst,Woods Hole,Ma 02543: 432–35. doi:10.1038/348432a0.

Coble, Paula G. 1996. “Characterization of marine and terrestrial DOM in seawater using excitation-emission matrix spectroscopy.” Marine Chemistry 51 (4): 325–46. doi:10.1016/0304-4203(95)00062-3.

McKnight, Diane M., Elizabeth W. Boyer, Paul K. Westerhoff, Peter T. Doran, Thomas Kulbe, and Dale T. Andersen. 2001. “Spectrofluorometric characterization of dissolved organic matter for indication of precursor organic material and aromaticity.” Limnology and Oceanography 46 (1). American Society of Limnology; Oceanography: 38–48. doi:10.4319/lo.2001.46.1.0038.

Fellman, J B, D V D’Amore, E Hood, and R D Boone. 2008. “Fluorescence characteristics and biodegradability of dissolved organic matter in forest and wetland soils from coastal temperate watersheds in southeast Alaska.” Biogeochemistry 88 (2): 169–84.

Lakowicz, Joseph R. 2006. Principles of Fluorescence Spectroscopy. Edited by Joseph R. Lakowicz. Boston, MA: Springer-Verlag. doi:10.1007/978-0-387-46312-4.

Hansell, Dennis A., and Craig A. Carlson. 2014. Biogeochemistry of Marine Dissolved Organic Matter. Edited by Dennis A Hansell and Craig A Carlson. 2nd ed. Academic Press.

Findlay, Stuart., and Robert L. Sinsabaugh. 2003. Aquatic ecosystems : interactivity of dissolved organic matter. Academic Press.

Coble, P.G., R.G.M. Spencer, A. Baker, and D.M. Reynolds. 2014. Aquatic Organic Matter Fluorescence. Edited by Paula Coble, Jaimie Lead, Andy Baker, Darren M. Reynolds, and Robert G.M. Spencer. 1st ed. Cambridge: Cambridge University Press. http://ebooks.cambridge.org/ref/id/CBO9781139045452A011 http://amazon.com/o/ASIN/0521764610/.