Evaluation of Conceptual Models of Natural Organic Matter (Humus) From a Consideration of the Chemical and Biochemical Processes of Humification By Robert L. Wershaw Scientific Investigations Report 2004-5121 U.S. Department of the Interior U.S. Geological Survey U.S. Department of the Interior Gale A. Norton, Secretary U.S. Geological Survey Charles G. Groat, Director U.S. Geological Survey, Reston, Virginia: 2004 For sale by U.S. Geological Survey, Information Services Box 25286, Denver Federal Center Denver, CO 80225 For more information about the USGS and its products: Telephone: 1-888-ASK-USGS World Wide Web: http://www.usgs.gov/ Any use of trade, product, or firm names in this publication is for descriptive purposes only and does not imply endorsement by the U.S. Government. iii Contents Abstract.......................................................................................................................................................... 1 Introduction ................................................................................................................................................... 1 Purpose and scope.............................................................................................................................. 2 Degradation reactions of plant tissue ............................................................................................. 2 Degradation pathways of plant tissue components ............................................................................... 3 Enzymatic reactions ............................................................................................................................ 3 Primary metabolites ................................................................................................................... 4 Carbohydrates.................................................................................................................... 4 Lignin ................................................................................................................................. 5 Plant polyesters ................................................................................................................. 6 Aliphatic acids.................................................................................................................... 8 Plant waxes ........................................................................................................................ 8 Amino acids, proteins, and aminosugars .................................................................... 10 Secondary metabolites............................................................................................................ 10 Tannins............................................................................................................................... 10 Terpenes............................................................................................................................ 11 Pyrolytic reactions............................................................................................................................. 12 Cellulose and other polysaccharides.................................................................................... 14 Amino acids ............................................................................................................................... 14 Lignin and other phenolic compounds.................................................................................. 14 Terpenes..................................................................................................................................... 14 Other miscellaneous plant components ............................................................................... 16 Abiotic reactions................................................................................................................................ 16 Photochemical reactions ........................................................................................................ 16 Direct reactions ............................................................................................................... 16 Indirect reactions ............................................................................................................ 16 Radical oxidative degradation................................................................................................ 17 Browning reactions.................................................................................................................. 19 Interactions of degradation products ..................................................................................................... 29 Evaluation of NOM models........................................................................................................................ 31 Humic polymer model ....................................................................................................................... 31 Molecular aggregate models .......................................................................................................... 31 Compartmental model....................................................................................................................... 31 SOM compartments ................................................................................................................. 31 Partially degraded plant material.................................................................................. 32 Microbial biomass ........................................................................................................... 32 Organic coatings on mineral grains ............................................................................. 32 Pyrolytic carbon............................................................................................................... 33 Organic precipitates........................................................................................................ 33 DOM in soil water ............................................................................................................ 34 DOM compartments ................................................................................................................. 34 Summary ...................................................................................................................................................... 35 References .................................................................................................................................................. 35 iv Figures Figure 1. Lignin monomeric units. ........................................................................................................... 5 Figure 2. Lignin degradation pathways. ................................................................................................ 7 Figure 3. Cutin-forming acids. ................................................................................................................. 8 Figure 4. Model cutin monomeric unit according to Kolattukudy (2001). ........................................ 9 Figure 5. Hydrolysable tannin units. ..................................................................................................... 11 Figure 6. Ellagitannin formation. ........................................................................................................... 12 Figure 7. Nonhydrolysable tannins. ..................................................................................................... 13 Figure 8. Pathway for Rhodococcus erythropolis degration of (+)-(4R)-limonene according to van der Werf and others (1999). ............................................................................. 13 Figure 9. Formation of anhydro sugars. ............................................................................................... 15 Figure 10. Proposed mechanisms for photolysis of hydroquinone according to Joschek and Miller (1966) (Scheme I) and Richard and Grabner (1999) (Scheme II). ...... 18 Figure 11. Formation of benzotropolone rings according to Haslam (1998). ................................. 20 Figure 12. Auto-oxidation of pyrogallol (Haslam, 2003). .................................................................... 21 Figure 13. Possible oxidation reactions of thearubigins according to Haslam (2003). ................ 22 Figure 14. Thearubigin units according to Davies and others (1999). ............................................. 23 Figure 15. Formation of anthocyanin pigments (Salas and others, 2003). ...................................... 24 Figure 16. Proanthocyanidin oligomers............................................................................................... 25 Figure 17. Bicyclic and xythylium salt forms of flavene dimers. ..................................................... 26 Figure 18. Effect of pH on the structure anthocyanins. .................................................................... 27 Figure 19. First steps in browning reactions........................................................................................ 28 Evaluation of Conceptual Models of Natural Organic Matter (Humus) From a Consideration of the Chemical and Biochemical Processes of Humification By Robert L. Wershaw Abstract and sorption of hydrophobic organic compounds are depen- dent, to a large extent, on the amount of organic matter in a Natural organic matter (NOM) has been studied