Microbial Effects

  • Hans-Curt Flemming
  • Martin Strathmann
  • Carlos Felipe Leon Morales
Part of the Environmental Science and Engineering book series (ESE)


Natural sediments are not sterile but inhabited by a large range of microorganisms (Riding and Awramik, 2000) and higher forms of life. As a consequence, these organisms participate in many chemical processes in sediments, in the interaction between sediments and the water phase and in sediment dynamics. In fluvial environments, the interface between the major water body and the sediment, is a very active zone both in physicochemical and biological terms. Especially in highly permeable sediments, the dynamic flux of energy, nutrients, metabolites and particles (including microorganisms) is interdependent with local hydrodynamics (Huettel et al. 2003). Due to their slime matrix, active microbial communities at the water-sediment interface, develop into macroscopic scale structures which modify sediment topography and frictional resistance. These surface alterations have repercussions in fluid flow, shear forces and other physical parameters, especially at the benthic boundary layer. Microbial colonization is not limited to the sediment-liquid interface; equally important on their effect on river sediment hydrodynamics, is their ability to develop at significant sediment depths. At this level, permeability and hydraulic conductivity changes caused by microbial colonization, can have a profound effect on sediment cohesion and sorption/ desorption processes (Leon-Morales et al. this vol.).


Extracellular Polymeric Substance Critical Shear Stress Sediment Stability Suspended Matter Concentration Heavy Metal Transport 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Allison D (2003) The biofilm matrix. Biofouling 19(2):139–150CrossRefGoogle Scholar
  2. Battin TJ, Sengschmitt D (1999) Linking sediment biofilms, hydrodynamics, and river bed clogging: evidence from a large river. Microb Ecol 37:185–196CrossRefGoogle Scholar
  3. Black KS, Tolhurst DJ, Paterson DM, Hagerthey SE (2002) Working with natural cohesive sediments. J Hydraul Eng, pp 2–8Google Scholar
  4. Costerton JW, Lewandowski Z, Caldwell DE, Korber DR, Lappin-Scott HM (1995) Microbial Biofilms. Annual Review of Microbiology 49:711–745CrossRefGoogle Scholar
  5. Costerton JW, Lewandowski Z, Debeer D, Caldwell D, Korber D, James G (1994) Biofilms, the Customized Microniche. Journal of Bacteriology 176(8):2137–2142Google Scholar
  6. Chamberlain AHL (1997) Matrix polymers: the key to biofilm processes. In: Wimpenny J, Handley PS, Gilbert P, Lappin-Scott H, Jones M (eds) Biofilms: Community Interactions and Control., UK, BioLine, pp 41–46Google Scholar
  7. de Brouwer JFC, Wolfstein K, Ruddy GK, Jones TER, Stal LJ (2005) Biogenic Stabilization of Intertidal Sediments: The Importance of Extracellular Polymeric Substances Produced by Benthic Diatoms. DOI 49:501–521Google Scholar
  8. Dade WB, Davis JD, Nichols PD, Nowell ARM, Thistle D, Trexler MB, White DC (1990) Effects of bacterial exopolymer adhesion on the entrainment of sand. Geomicrobiol 8:1–16Google Scholar
  9. Decho AW (1994) Molecular-scale events influencing the macroscale cohesiveness of exopolymers. In: Krumbein WE, Paterson DM, Stal LJ (eds) Biostabilization of sediments, BIS-Verlag, Oldenburg, pp 135–148Google Scholar
  10. Dignac MFU, Rybacki D, Bruchet A, Snidaro D, Scribe P (1998) Chemical description of extracellular polymers: implication on activated sludge floc structure. Wat Sci Tech 38:45–53CrossRefGoogle Scholar
  11. Hemming HC, Leis A (2002) Sorption properties of biofilms. In: Bitton (ed) Encyclopedia of environmental microbiology, Vol. 5. John Wiley & Sons, Inc., New York, pp 2958–2967Google Scholar
  12. Hemming HC, Wingender J (2002) Extracellular polymeric substances (EPS): Structural, ecological and technical aspects. In: Bitton G (ed) Encyclopedia of Environmental Microbiology, vol. 4. John Wiley & Sons, Inc, New York, pp 1223–1231Google Scholar
  13. Hemming HC, Wingender J (2003) The crucial role of extracellullar polymeric substances in biofilms. In: Wuertz S, Bishop P, Wilderer P (eds) Biofilms in wastewater treatment. An interdisciplinary approach., IWA Publishing, London, pp 401Google Scholar
  14. Hemming H-C, Wingender J, Mayer C, Körstgens V, Borchard W (2000a) Cohesiveness in biofilm matrix polymers. In: Lappin-Scott H, Gilbert P, Wilson M, Allison D (eds) Community structure and co-operation in biofilms, SGM symposium 59, Cambridge University Press, pp 87–105Google Scholar
  15. Hemming H-C, Wingender J, Griebe T, Mayer C (2000b) Physico-chemical properties of biofilms. In: Evans LV (ed) Biofilms: recent advances in their study and control, Harwood academic publishersGoogle Scholar
  16. Frølund BG, Nielsen PH (1995) Enzymatic activity in the activated-sludge floc matrix. Appl Microbiol Biotechnol 43:755–761CrossRefGoogle Scholar
  17. Gehrke T, Telegdi J, Thierry D, Sand W (1998) Importance of extracellular polymeric substances from Thiobacillus ferrooxidans for bioleaching. Appl Environ Microbiol 64(7):2743–2747Google Scholar
  18. Hoffman M, Decho AW (1999) Extracellular enzymes within microbial biofilms and the role of the extracellular polymeric matrix. In: Wingender J, Neu TR, Hemming HC (eds) Microbial extracellular polymeric substances. Springer-Verlag, pp 217–230Google Scholar
  19. Huettel M, Røy H, Precht E, Ehrenhauss S (2003) Hydrodynamical impact on biogeochemical processes in aquatic sediments. Hydrobiologia 494:231–236CrossRefGoogle Scholar
  20. Körstgens V, Hemming H-C, Wingender J, Borchard W (2001) Uniaxial compression measurement device for the investigation of the mechanical stability of biofilms. J Microbiol Meth 46:9–16CrossRefGoogle Scholar
  21. Krumbein WE, Paterson DM, Stal LJ (1994) General discussion. In: Krumbein WE, Paterson DM, Stal LJ (eds) Biostabilization of sediments. BIS Oldenburg, pp 433–435Google Scholar
  22. Langley S, Beveridge TJ (1999) Metal binding by Pseudomonas aeruginosa PAO1 is influenced by growth of the cells as a biofilm. Canadian Journal of Microbiology 45(7):616–622CrossRefGoogle Scholar
  23. Leon Morales CF, Leis AP, Strathmann M, Flemming HC (2004) Interactions between laponite and microbial biofilms in porous media: implications for colloid transport and biofilm stability. Water Research 38(16):3614–3626CrossRefGoogle Scholar
  24. Macedo AJ, Kuhlicke U, Neu T, Timmis KN, Abraham W-R (2005) Three stages of a biofilm community developing at the liquid-liquid interface between polychlorinated biphenyls and water. Applied and Environmental Microbiology 71(11):7301–7309CrossRefGoogle Scholar
  25. Madsen KN, Nilsson P, Sundbäck K (1993) The influence of benthic microalgae on the stability of a subtidal sediment. J Exp Mar Biol Ecol 170:159–177CrossRefGoogle Scholar
  26. Mayer C, Moritz R, Kirschner C, Borchard W, Maibaum R, Wingender J, Hemming HC (1999) The role of intermolecular interactions: studies on model systems for bacterial biofilms. Int J Biol Macromol 26(1):3–16CrossRefGoogle Scholar
  27. Neu T (1996) Significance of bacterial surface active compounds in interaction of bacteria with surfaces. Microbiological Reviews 60:151–166Google Scholar
  28. Neu TR, Lawrence JD (1997) Development and structure of microbial biofilms in river water studied by confocal laser scanning microscopy. FEMS Microbiol Ecol 24:11–25CrossRefGoogle Scholar
  29. Paterson DM (1997) Biological mediation of sediment erodibility. In: Burt N, Pareker R, Watts J (eds) Cohesive sediments. Wiley, New York, pp 215–229Google Scholar
  30. Ramsay BR, de Tremblay M, Chavarie C (1988) A method for the quantification of bacterial protein in the presence of Jarosite. Geomicrobiol J 3:171–177CrossRefGoogle Scholar
  31. Riding R, Amrawik SM (2000) Microbial sediments. Springer-Verlag, New York, Heidelberg, 331 ppGoogle Scholar
  32. Sar P, Kazy SK, Asthana RK, Singh SP (1998) Nickel uptake by Pseudomonas aeruginosa: role of modifying factors. Current Microbiology 37:306–311CrossRefGoogle Scholar
  33. Schmitt J, Nivens D, White DC, Hemming H-C (1995) Changes of biofilm properties in response to sorbed substances–an FTIR-ATR study. Water Science and Technology 32(8):149–155CrossRefGoogle Scholar
  34. Schultze-Lam S, Fortin D, Davis BS, Beveridge TJ (1996) Mineralization of bacterial surfaces. Chem Geol 132:171–181CrossRefGoogle Scholar
  35. Skoog DA, West DM, Holler FJ (1996) Fundamentals of analytical chemistry, Saunders college publishingGoogle Scholar
  36. Späth R, Flemming HC, Wuertz S (1998) Sorption properties of biofilms. Water Science and Technology 37(4–5):207–210CrossRefGoogle Scholar
  37. Spiers AJ, Bohannon J, Gehrig SM, Rainey PB (2003) Biofilm formation at the air-liquid interface by the Pseudomonas fluorescens SBW25 wrinkly spreader requires an acetylated form of cellulose. Mol Microbiol 50(1): 15–27CrossRefGoogle Scholar
  38. Stal LJ, de Brouwer JFC (2003) Biofilm formation by benthic diatoms and their influence on the stabilization of interdital mudflats. Ber Forsch.-Zentr., Terramare 12:109–111Google Scholar
  39. Strathmann M, Leon Morales CF, Flemming H-C (2006) Influence of biofilms on colloid mobility in the subsurface. In: Frimmel HE, Flemming H-C, Förstner U (eds) Colloid mobility, Springer-Verlag, Heidelberg, in pressGoogle Scholar
  40. Sutherland IW (1994) Structure-function relationships in microbial exopolysaccharides. Biotech Adv 12:393–448CrossRefGoogle Scholar
  41. Sutherland IW (2001) The biofilm matrix–an immobilized but dynamic microbial environment. Trends in Microbiology 9:222–227CrossRefGoogle Scholar
  42. Tielker D, Hacker S, Loris R, Strathmann M, Wingender J, Wilhelm S, Rosenau F, Jaeger K-E (2005) Pseudomonas aeruginosa lectin LecB is located in the outer membrane and is involved in biofilm formation. Microbiology 151:1313–1323CrossRefGoogle Scholar
  43. Vandevivere P, Kirchman DL (1993) Attachment stimulates exopolysaccharide synthesis by a bacterium. Appl Environ Microbiol 59(10):3280–3286Google Scholar
  44. Vogt M, Flemming HC, Veeman WS (2000) Diffusion in Pseudomonas aeruginosa biofilms: a pulsed field gradient NMR study. J Biotechnol 77(1):137–146CrossRefGoogle Scholar
  45. Wingender J, Jaeger K-E (2002) Extracellular enzymes in biofilms. In: Bitton G (ed) Encyclopedia of Environmental Microbiology, vol. 3. John Wiley & Sons, Inc, New York, pp 1207–1223Google Scholar
  46. Wingender J, Jäger K-E, Flemming H-C (1999) Interactions between extracellular enzymes and polysaccharides. In: Wingender J, Neu T, Flemming H-C (eds) Microbial extracellular polymer substances, Springer-Verlag, Heidelberg, Berlin, pp 231–251Google Scholar
  47. Wingender J, Neu TR, Flemming H-C (1999) What are bacterial extracellular polymeric substances? In: Wingender J, Neu TR, Flemming H-C (eds) Microbial Extracellular Polymeric Substances. Springer Verlag, Berlin, pp 1–19Google Scholar
  48. Yallop ML, de Winder B, Paterson DM, Stal LJ (1994) Comparative structure, primary production and biogenic stabilization of cohesive and non-cohesive marine sediments inhabited by microphyto-benthos. Estuar Coast Shelf Sci 39:565–582CrossRefGoogle Scholar
  49. Yallop ML, Paterson DM, Wellsbury P (2000) Interrelationships between rates of microbial production, exopolymer production, microbial biomass, and sediment stability of intertidal sediments. Microb Ecol 39(2):116–127CrossRefGoogle Scholar


  1. Battin TJ, Sengschmitt D (1999) Linking sediment biofilms, hydrodynamics, and river bed clogging: evidence from a large river. Microb Ecol 37:185–196CrossRefGoogle Scholar
  2. de Brouwer JFC, Ruddy GK, Jones TER, Stal LJ (2002) Sorption of EPS to sediment particles and the effect on the rheology of sediment slurries. Biogeochemistry 61(1):57CrossRefGoogle Scholar
  3. Hemming H-C, Wingender J (2002) Extracellular polymeric substances (EPS): Structural, ecological and technical aspects. In: Bitton G (ed) Encyclopedia of Environmental Microbiology, vol. 4. John Wiley & Sons, Inc., New York, pp 1223–1231Google Scholar
  4. Förstner U (2004) Sediment dynamics and pollutant mobility in rivers: an interdisciplinary approach. Lakes and Reservoirs: Research and Management 9:25–40CrossRefGoogle Scholar
  5. Frølund B, Palmgren R, Keiding K, Nielsen PH (1996) Extraction of extracellular polymers from activated sludge using a cation exchange resin. Water Res 30(8):1749–1758CrossRefGoogle Scholar
  6. Grobe S, Wingender J, Trüper HG (1995) Characterization of mucoid Pseudomonas aeruginosa strains isolated from technical water systems. J Appl Bacteriol 79:94–102Google Scholar
  7. Körstgens V, Flemming H-C, Wingender J, Borchard W (2001) Influence of calcium ions on the mechanical properties of a model biofilm of mucoid Pseudomonas aeruginosa. Wat Sci Tech 43(6):49–57Google Scholar
  8. Leon Morales CF, Leis AP, Strathmann M, Flemming H-C (2004) Interactions between laponite and microbial biofilms in porous media: implications for colloid transport and biofilm stability. Water Res 38(16):3614–3626CrossRefGoogle Scholar
  9. Sutherland T, Grant J, Amos C (1998) The effect of carbohydrate production by the diatom Nitzschia curvilineata on the erodibility of sediment. Limnology Oceanography 43:65–72CrossRefGoogle Scholar
  10. Wingender J, Strathmann M, Rode A, Leis A, Flemming H-C (2001) Isolation and Biochemical Characterization of Extracellular Polymeric Substances from Pseudomonas aeruginosa. Methods Enzymol 336(25):302–314CrossRefGoogle Scholar
  11. Yallop ML, Paterson DM, Wellsbury P (2000) Interrelationships between rates of microbial production, exopolymer production, microbial biomass, and sediment stability in biofilms of intertidal sediments. Microb Ecol 39(2): 116–127CrossRefGoogle Scholar


  1. Bedell JP, Neto M, Pressiat F (2005) Opérations de dragage, pollution potentielle et enjeux environnementaux. Les sédiments du Rhône Grands enjeux, premières réponses. Journée ZABR, Valence, France. 10 juin 2005. ppll3–121Google Scholar
  2. Brohon B, Delolme C, Gourdon R (1999) Qualification of soils through microbial activities measurements: influence of the storage period on INT-reductase, phosphatase and respiration. Chemosphere 38:1973–1984CrossRefGoogle Scholar
  3. Caetano M, Madureira MJ, Vale C (2003) Metal remobilisation during resuspension of anoxic contaminated sediment: short-term laboratory study. Water Air Soil Poll 143:23–40CrossRefGoogle Scholar
  4. Caille N, Tiffreau C, Leyval C, Morel JL (2003) Solubility of metals in an anoxic sediment during prolonged aeration. Sci Total Environ 301:239–250CrossRefGoogle Scholar
  5. Calmano W, Hong J, Forstner U (1993) Binding and mobilization of heavy metals in contaminated sediments affected by pH and redox potential. Water Sci Technol 28:223–235Google Scholar
  6. Carpentier S, Moilleron R, Beltran C, Herve D, Thevenot D (2002) Quality of dredged material in the river Seine basin (France). II. Micropollutants. Sci Total Environ 299:57–72CrossRefGoogle Scholar
  7. Engelen B, Meinken K, von Wintzingerode F, Heuer H, Malkomes H-P, Backhaus H (1998) Monitoring impact of a pesticide treatment on bacterial soil communities by metabolic and genetic fingerprinting in addition to conventional testing procedures. Appl Environ Microbiol 64:2814–2821Google Scholar
  8. Hardy D (2002) Historique National des opérations de curage et perspectives, Ministère de l’écologie et du développement durable, pp l7Google Scholar
  9. McNamara NP, Black HIJ, Beresford NA, Parekh NR (2003) Effects of acute gamma irradiation on chemical, physical and biological properties of soils. Appl Soil Ecol 24:117–132CrossRefGoogle Scholar
  10. Pettine M, Camusso M, Martinotti W, Marchetti R, Passino R, Queirazza G (1994) Soluble and particulate metals in the Po River: Factors affecting concentrations and partitioning. Sci Total Environ 145:243–265CrossRefGoogle Scholar
  11. Poly F (2000) Réponses des communautés bactériennes telluriques à des perturbations chimiques complexes: Activités potentielles et empreintes génétiques, Université Claude Bernard Lyon 1, Lyon, pp 159Google Scholar
  12. Ranjard L, Richaume A, Jocteur-Monrozier L, Nazaret S (1997) Response of soil bacteria to Hg(II) in relation to soil characteristics and cell location. FEMS Microbiol Ecol 24(4):321–331CrossRefGoogle Scholar
  13. Sen TK, Khilar KC (2006) Review on subsurface colloids and colloid-associated contaminant transport in saturated porous media. Advances in Colloid and Interface Science 119:71–96CrossRefGoogle Scholar
  14. Stemmer M, Gerzabek MH, Kandeler E (1998) Organic matter and enzyme activity in particle-size fractions of soils obtained after low-energy sonication. Soil Biol Biochem 30:9–17CrossRefGoogle Scholar
  15. Stephens SR, Alloway BJ, Parker A, Carter JE and Hodson ME (2001) Changes in the leachability of metals from dredged canal sediments during drying and oxidation. Environ Pollut 114:407–413CrossRefGoogle Scholar
  16. Trevors JT (1996) Sterilization and inhibition of microbial activity in soil. J Microbiol Methods 26:53–59CrossRefGoogle Scholar
  17. van Elsas JD, Trevors JT, Wellington EMH (1997) Modern soil microbiology. Marcel Dekker, INC, pp 683Google Scholar
  18. van Rijn J, Tal Y, Schreier HJ (2006) Denitrification in recirculating systems: Theory and applications. Aquacult Eng 34:364–376CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2007

Authors and Affiliations

  • Hans-Curt Flemming
    • 1
  • Martin Strathmann
    • 1
  • Carlos Felipe Leon Morales
    • 1
  1. 1.Aquatic Microbiology, Biofilm CentreUniversity Duisburg-EssenDuisburgGermany

Personalised recommendations