Jump to content


This article has been published in the peer-reviewed journal WikiJournal of Science (2024). Click to view the published version.
From Wikipedia, the free encyclopedia

Bioclogging or biological clogging refers to the blockage of pore space in soil by microbial biomass, including active cells and their byproducts such as extracellular polymeric substance (EPS). The microbial biomass obstructs pore spaces, creating an impermeable layer in the soil and significantly reducing water infiltration rates.

Bioclogging occurs under continuous ponded infiltration at various field conditions such as artificial recharge ponds, percolation trenches, irrigation channels, sewage treatment systems, constructed wetlands, landfill liners and natural systems such as riverbeds and soils. It also affects groundwater flow in the aquifer, such as ground source heat pumps, permeable reactive barriers, and microbial enhanced oil recovery. Bioclogging is a significant problem where water infiltration is hampered and countermeasures such as regular drying of the system can reduce the levels of bioclogging. However, bioclogging can also serve beneficial purposes in specific conditions. For instance, bioclogging can be utilized to make an impermeable layer to minimize the rate of infiltration or to enhance soil mechanic properties.

General description[edit]

Change in permeability with time[edit]

Bioclogging is observed as the decrease in the infiltration rate. A decrease in the infiltration rate under ponded infiltration was observed in the 1940s for studying the infiltration of artificial recharge ponds and the water-spreading on agricultural soils. Allison described[1] that when soils are continuously submerged, permeability or saturated hydraulic conductivity changes in 3 key stages:

  1. After initiating field or laboratory tests, the permeability decreases to a minimum. On highly permeable soils this initial decrease is small, or nonexistent, but for relatively impermeable soils, permeability decreases for 10 to 20 days possibly due to physical changes in the structure of the soil.
  2. Permeability increases due to dissolving the entrapped air in soil into the percolating water.
  3. Permeability decreases for 2 to 4 weeks due to the disintegration of aggregates and biological clogging of soil pores with microbial cells and their synthesized products, slimes, or polysaccharides.

This description is based on experiments conducted at that time, and the actual process of bioclogging depends on system conditions, such as nutrient and electron acceptor availability, microbial biofilm formation propensity, initial conditions, etc. In particular, the 3 stages are not necessarily distinct in every field condition of bioclogging; when the second stage is not clear, and permeability just continues to decrease.

Various types of bioclogging[edit]

The change in permeability with time is dependent on the field condition and there are various causes for the change in the hydraulic conductivity,[2] including physical (suspended solids, disintegration of aggregate structure, etc), chemical (dispersion and swelling of clay particles), and biological causes (as listed below). Usually bioclogging means the first of the following, while bioclogging in a broader sense means all of the following.

  1. Bioclogging by microbial cell bodies (such as bacteria,[3][4][5][6] algae[7] and fungus[8][9]) and their synthesized byproducts such as extracellular polymeric substance (EPS)[10] (also referred to as slime), which form biofilm[11][12][13] or microcolony aggregation[14] on soil particles are direct biological causes of the decrease in hydraulic conductivity.
  2. Entrapment of gas bubbles such as methane[15] produced by methane-producing microorganisms clog the soil pore and contributes to decreasing hydraulic conductivity. As gas is also microbial byproduct, it can also be considered to be bioclogging.
  3. Iron bacteria stimulate ferric oxyhydroxide deposition which may cause clogging of soil pores.[16] This is an indirect biological cause of the decrease in hydraulic conductivity.

Bioclogging is mostly observed in saturated conditions, but bioclogging in unsaturated conditions is also studied.[17]

Field observation[edit]

Field problem and countermeasures[edit]

Bioclogging is a significant issue in various environmental and artificial water systems. Here are some specific field problems related to bioclogging and their potential countermeasures.

  1. Bioclogging commonly occurs during continuous ponded infiltration in such places as artificial recharge ponds[18] and percolation trenches.[19] Reduction of infiltration rate due to bioclogging at the infiltrating surface reduces the efficiency of such systems. To minimize the bioclogging effects, pretreatment of the water to reduce suspended solids, nutrients, and organic carbon might be necessary. Regular drying and physical removal of the clogging layer can be an effective countermeasure.
  2. Similarly, septic drain fields are prone to bioclogging primarily due to the continuous flow of nutrient-rich wastewater.[20][21] The organic material causing bioclogging in the septic tank is sometimes called biomat.[22] Pretreatment of water by filtration or reducing the load of the system could delay the failure of the system by bioclogging. Slow sand filter system also suffers from bioclogging.[23] Besides the countermeasures mentioned above, cleaning or backwashing sand may be operated to remove biofilm and recover the permeability of sand.
  3. In river systems, bioclogging can significantly impact aquifer recharge, particularly in dry regions where losing rivers are prevalent.[24] As a result of bioclogging, the connection between surface water and groundwater in riverine systems is affected. The development of a biofilm-induced clogging layer can lead to disconnection, changing the natural water flow patterns between rivers and aquifers.[25]
  4. Bioclogging is also a concern in aquifers, particularly when water is extracted through water wells below the groundwater table.[26] Over months and years of continued operation of water wells, they may show a gradual reduction in performance due to bioclogging or other clogging mechanisms.[27] Bioclogging may also affect the sustainable operation of ground source heat pumps.[28] Common approaches to treating bioclogging include utilizing phosphate, a critical nutrient for iron-bacteria biofilms, and employing chlorine and fungicides to address bacterial issues. Backwashing is a common method to deal with clogging in general, including bioclogging.[28]


In certain environments, bioclogging positively influences hydrological process. Here are some examples.

  1. Bioclogging plays a crucial role in sealing the bottoms of stabilization ponds for dairy farm wastewater treatment.[29] Similarly, irrigation channels for seepage control may be inoculated with algae and bacteria to promote bioclogging for reducing water loss.[30]
  2. Turning to landfill liners, such as compacted clay liners, bioclogging emerges as a beneficial factor. Clay liners are usually used in landfill to minimize pollution from landfill leachate to the surrounding soil environment. The hydraulic conductivity of clay liners becomes lower than the original value due to bioclogging, which is caused by microorganism in the leachate and the pore spaces in the clay.[31][32]
  3. Bioclogging is a common occurrence in constructed wetlands[33] which are engineered for treating various contaminated waters. Notably, in wetlands with subsurface horizontal flow, preferential flow paths avoiding the clogged part can improve the system treatment efficiency.[34]
  4. Biofilm formation plays a crucial role in bioremediation,[35] particularly in treating biodegradable groundwater pollution. A permeable reactive barrier[36] is formed to contain the groundwater flow by bioclogging and also to degrade pollution by microbes.[37] Contaminant flow should be carefully analyzed because a preferential flow path in the barrier may reduce the efficiency of the remediation.[38]
  5. In the extraction of petroleum, enhanced oil recovery techniques are applied to maximize oil extraction from oil fields. The injected water displaces the oil in the reservoir which is transported to recovery wells. As the reservoir is not uniform in permeability, injected water tends to go through a high permeable zone and does not go through the zone where oil remains. In this situation, the bacterial profile modification technique,[39] which injects bacteria into the high permeable zone to promote bioclogging can be employed. It is a type of microbial enhanced oil recovery.
  6. The potential of bioclogging in geotechnical engineering[40] is under exploration, particularly for improving soil mechanical properties. This involves strategies like reducing porosity and hydraulic conductivity, and enhancing shear strength through biocementation, thereby optimizing the soil for construction and environmental applications.[41]

See also[edit]


This article was submitted to WikiJournal of Science for external academic peer review in 2023 (reviewer reports). The updated content was reintegrated into the Wikipedia page under a CC-BY-SA-3.0 license (2024). The version of record as reviewed is: Katsutoshi Seki; et al. (14 February 2024). "Bioclogging" (PDF). WikiJournal of Science. 7 (1): 1. doi:10.15347/WJS/2024.002. ISSN 2470-6345. Wikidata Q116782181.

  1. ^ Allison, L.E. (1947). "Effect of microorganisms on permeability of soil under prolonged submergence". Soil Science. 63 (6): 439–450. Bibcode:1947SoilS..63..439A. doi:10.1097/00010694-194706000-00003. S2CID 97693977.
  2. ^ Baveye, P.; Vandevivere, P.; Hoyle, B.L.; DeLeo, P.C.; de Lozada, D.S. (2006). "Environmental impact and mechanisms of the biological clogging of saturated soils and aquifer materials" (PDF). Critical Reviews in Environmental Science and Technology. 28 (2): 123–191. doi:10.1080/10643389891254197.
  3. ^ Gupta, R.P.; Swartzendruber, D. (1962). "Flow-associated reduction in the hydraulic conductivity of quartz sand". Soil Science Society of America Journal. 26 (1): 6–10. Bibcode:1962SSASJ..26....6G. doi:10.2136/sssaj1962.03615995002600010003x.
  4. ^ Frankenberger, W.T.; Troeh, F.R.; Dumenil, L.C. (1979). "Bacterial effects on hydraulic conductivity of soils". Soil Science Society of America Journal. 43 (2): 333–338. Bibcode:1979SSASJ..43..333F. doi:10.2136/sssaj1979.03615995004300020019x.
  5. ^ Vandevivere, P.; Baveye, P. (1992). "Saturated hydraulic conductivity reduction caused by aerobic bacteria in sand columns" (PDF). Soil Science Society of America Journal. 56 (1): 1–13. Bibcode:1992SSASJ..56....1V. doi:10.2136/sssaj1992.03615995005600010001x.
  6. ^ Xia, L.; Zheng, X.; Shao, H.; Xin, J.; Sun, Z.; Wang, L. (2016). "Effects of bacterial cells and two types of extracellular polymers on bioclogging of sand columns". Journal of Hydrology. 535: 293–300. Bibcode:2016JHyd..535..293X. doi:10.1016/j.jhydrol.2016.01.075.
  7. ^ Gette-Bouvarot, M.; Mermillod-Blondin, F.; Angulo-Jaramillo, R.; Delolme, C.; Lemoine, D.; Lassabatere, L.; Loizeau, S.; Volatier, L. (2014). "Coupling hydraulic and biological measurements highlights the key influence of algal biofilm on infiltration basin performance" (PDF). Ecohydrology. 7 (3): 950–964. Bibcode:2014Ecohy...7..950G. doi:10.1002/eco.1421. S2CID 129758850.
  8. ^ Seki, K.; Miyazaki, T.; Nakano, M. (1996). "Reduction of hydraulic conductivity due to microbial effects" (PDF). Transactions of Japanese Society of Irrigation, Drainage and Reclamation Engineering. 181: 137–144. doi:10.11408/jsidre1965.1996.137.
  9. ^ Seki, K.; Miyazaki, T.; Nakano, M. (1998). "Effect of microorganisms on hydraulic conductivity decrease in infiltration" (PDF). European Journal of Soil Science. 49 (2): 231–236. Bibcode:1998EuJSS..49..231S. doi:10.1046/j.1365-2389.1998.00152.x. S2CID 97173198.
  10. ^ Jiang, Y.; Matsumoto, S. (1995). "Change in microstructure of clogged soil in soil wastewater treatment under prolonged submergence". Soil Science and Plant Nutrition. 41 (2): 207–213. Bibcode:1995SSPN...41..207J. doi:10.1080/00380768.1995.10419577.
  11. ^ Taylor, S.W.; Milly, P.C.D.; Jaffé, P.R. (1990). "Biofilm growth and the related changes in the physical properties of a porous medium: 2. Permeability". Water Resources Research. 26 (9): 2161–2169. Bibcode:1990WRR....26.2161T. doi:10.1029/WR026i009p02161.
  12. ^ Zhao, L.; Zhu, W.; Tong, W. (2009). "Clogging processes caused by biofilm growth and organic particle accumulation in lab-scale vertical flow constructed wetlands" (PDF). Journal of Environmental Sciences. 21 (6): 750–757. Bibcode:2009JEnvS..21..750Z. doi:10.1016/S1001-0742(08)62336-0. PMID 19803078.
  13. ^ Kim, J.; Choi, H.; Pachepsky, Y.A. (2010). "Biofilm morphology as related to the porous media clogging" (PDF). Water Research. 44 (4): 1193–1201. Bibcode:2010WatRe..44.1193K. doi:10.1016/j.watres.2009.05.049. PMID 19604533.
  14. ^ Seki, K.; Miyazaki, T. (2001). "A mathematical model for biological clogging of uniform porous media" (PDF). Water Resources Research. 37 (12): 2995–2999. Bibcode:2001WRR....37.2995S. doi:10.1029/2001WR000395. S2CID 129625309.
  15. ^ Reynolds, W.D.; Brown, D.A.; Mathur, S.P.; Overend, R.P. (1992). "Effect of in-situ gas accumulation on the hydraulic conductivity of peat". Soil Science. 153 (5): 397–408. Bibcode:1992SoilS.153..397R. doi:10.1097/00010694-199205000-00007. S2CID 93225879.
  16. ^ Houot, S.; Berthelin, J. (1992). "Submicroscopic studies of iron deposits occurring in field drains: Formation and evolution". Geoderma. 52 (3–4): 209–222. Bibcode:1992Geode..52..209H. doi:10.1016/0016-7061(92)90037-8.
  17. ^ Volk, E.; Iden, S.C.; Furman, A.; Durner, W.; Rosenzweig, R. (2016). "Biofilm effect on soil hydraulic properties: Experimental investigation using soil-grown real biofilm". Water Resources Research. 52 (8): 5813–5828. Bibcode:2016WRR....52.5813V. doi:10.1002/2016WR018866.
  18. ^ Bouwer, H. (2002). "Artificial recharge of groundwater: hydrogeology and engineering" (PDF). Hydrogeology Journal. 10 (1): 121–142. Bibcode:2002HydJ...10..121B. doi:10.1007/s10040-001-0182-4.
  19. ^ Furumai, H.; Jinadasa, H.K.P.K.; Murakami, M.; Nakajima, F.; Aryal, R.K. (2005). "Model description of storage and infiltration functions of infiltration facilities for urban runoff analysis by a distributed model" (PDF). Water Science and Technology. 52 (5): 53–60. doi:10.2166/wst.2005.0108. PMID 16248180.
  20. ^ Kristiansen, R. (1981). "Sand-filter trenches for purification of septic tank effluent: I. The clogging mechanism and soil physical environment". Journal of Environmental Quality. 10 (3): 353–357. Bibcode:1981JEnvQ..10..353K. doi:10.2134/jeq1981.00472425001000030020x.
  21. ^ Nieć, J.; Spychała, M.; Zawadzki, P. (2016). "New approach to modelling of sand filter clogging by septic tank effluent" (PDF). Journal of Ecological Engineering. 17 (2): 97–107. doi:10.12911/22998993/62296.
  22. ^ "Septic Biomat: defined, properties". InspectAPedia. Retrieved March 22, 2017.
  23. ^ Mauclaire, L.; Schürmann, A.; Thullner, M.; Gammeter, S.; Zeyer, J. (2004). "Slow sand filtration in a water treatment plant: biological parameters responsible for clogging". Journal of Water Supply: Research and Technology-Aqua. 53 (2): 93–108. doi:10.2166/aqua.2004.0009.
  24. ^ Newcomer, M.E.; Hubbard, S.S.; Fleckenstein, J.H.; Maier, U.; Schmidt, C.; Thullner, M.; Ulrich, C.; lipo, N.; Rubin, Y. (2016). "Simulating bioclogging effects on dynamic riverbed permeability and infiltration". Water Resources Research. 52 (4): 2883–2900. Bibcode:2016WRR....52.2883N. doi:10.1002/2015WR018351. S2CID 130425627.
  25. ^ Xian, Y.; Jin, M.; Zhan, H.; Liu, Y. (2019). "Reactive transport of nutrients and bioclogging during dynamic disconnection process of stream and groundwater". Water Resources Research. 55 (5): 3882–3903. Bibcode:2019WRR....55.3882X. doi:10.1029/2019WR024826.
  26. ^ van Beek, C.G.E.M.; van der Kooij, D. (1982). "Sulfate-reducing bacteria in ground water from clogging and non-clogging shallow wells in the netherlands river region". Ground Water. 20 (3): 298–302. Bibcode:1982GrWat..20..298B. doi:10.1111/j.1745-6584.1982.tb01350.x.
  27. ^ "Well remediation and rehabilitation". Groundwater Engineering Limited. Archived from the original on March 22, 2017. Retrieved March 22, 2017.
  28. ^ a b Song, W.; Liu, X.; Zheng, T.; Yang, J. (2020). "A review of recharge and clogging in sandstone aquifer". Geothermics. 87: 101857. Bibcode:2020Geoth..8701857S. doi:10.1016/j.geothermics.2020.101857.
  29. ^ Davis, S.; Fairbanks, W.; Weisheit, H. (1973). "Dairy waste ponds effectively self-sealing". Transactions of the ASAE. 16 (1): 69–71. doi:10.13031/2013.37447.
  30. ^ Ragusa, S.R.; de Zoysa, D.S.; Rengasamy, P. (1994). "The effect of microorganisms, salinity and turbidity on hydraulic conductivity of irrigation channel soil". Irrigation Science. 15 (4): 159–166. Bibcode:1994IrrSc..15..159R. doi:10.1007/BF00193683. S2CID 35184810.
  31. ^ Kamon, M.; Zhang, H.; Katsumi, T. (2002). "Redox effect on the hydraulic conductivity of clay liner" (PDF). Soils and Foundations. 42 (6): 79–91. Bibcode:2002SoFou..42...79K. doi:10.3208/sandf.42.6_79.
  32. ^ Tang, Q.; Wang, H.Y.; Chen, H.; Li, P.; Tang, X.W.; Katsumi, T. (2015). "Long-term hydraulic conductivity of compacted clay permeated with landfill leachates" (PDF). Japanese Geotechnical Society Special Publication. 2 (53): 1845–1848. doi:10.3208/jgssp.CHN-52.
  33. ^ ,Moreira, F.D.; Dias, E.H.O. (2020). "Constructed wetlands applied in rural sanitation: A review". Environmental Research. 190: 110016. Bibcode:2020ER....19010016M. doi:10.1016/j.envres.2020.110016. PMID 32768473.
  34. ^ Suliman, F.; French, H.K.; Haugen, L.E.; Søvik, A.K. (2006). "Change in flow and transport patterns in horizontal subsurface flow constructed wetlands as a result of biological growth". Ecological Engineering. 27 (2): 124–133. Bibcode:2006EcEng..27..124S. doi:10.1016/j.ecoleng.2005.12.007.
  35. ^ Lee, M.D.; Thomas, J.M.; Borden, R.C.; Bedient, P.B.; Ward, C.H.; Wilson, J.T. (1998). "Biorestoration of aquifers contaminated with organic compounds" (PDF). Critical Review in Environmental Control. 18 (1): 29–89. doi:10.1080/10643388809388342.
  36. ^ Naftz, D.; Morrison, S.J.; Fuller, C.C.; Davis, J.A. (2002). Handbook of groundwater remediation using permeable reactive barriers: applications to radionuclides, trace Metals, and nutrients. Cambridge, Massachusetts: Academic Press. ISBN 978-0125135634.
  37. ^ Komlos, J.; Cunningham, A.B; Camper, A.K.; Sharp, R.R. (2004). "Biofilm barriers to contain and degrade dissolved tricholoroethylene". Environmental Progress. 23 (1): 69–77. Bibcode:2004EnvPr..23...69K. doi:10.1002/ep.10003.
  38. ^ Seki, K.; Thullner, M.; Hanada, J.; Miyazaki, T. (2006). "Moderate bioclogging leading to preferential flow paths in biobarriers" (PDF). Ground Water Monitoring & Remediation. 26 (3): 68–76. Bibcode:2006GMRed..26c..68S. doi:10.1111/j.1745-6592.2006.00086.x. S2CID 97009671.
  39. ^ Lappan, R.E.; Fogler, H.S. (1996). "Reduction of porous media permeability from in situ leuconostoc mesenteroides growth and dextran production". Biotechnology and Bioengineering. 50 (1): 6–15. CiteSeerX doi:10.1002/(SICI)1097-0290(19960405)50:1<6::AID-BIT2>3.0.CO;2-L. PMID 18626894. S2CID 803784.
  40. ^ Ivanov, V.; Stabnikov, V. (2017). "Bioclogging and biogrouts". Construction biotechnology: biogeochemistry, microbiology and biotechnology of construction materials and processes. New York: Springer. pp. 139–178. doi:10.1007/978-981-10-1445-1_8. ISBN 978-9811014444.
  41. ^ Ivanov, V.; Chu, J. (2008). "Applications of microorganisms to geotechnical engineering for bioclogging and biocementation of soil in situ". Reviews in Environmental Science and Bio/Technology. 7 (2): 139–153. Bibcode:2008RESBT...7..139I. doi:10.1007/s11157-007-9126-3.