bioclogging

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{{cite journal |last=Allison |first=L.E. |journal=Soil Science| title=Effect of microorganisms on permeability of soil under prolonged submergence| year=1947| volume=63| issue=6| pages=439–450| doi=10.1097/00010694-194706000-00003|bibcode=1947SoilS..63..439A |s2cid=97693977 }} 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.

The change in permeability with time is dependent on the field condition and there are various causes for the change in the hydraulic conductivity,{{cite journal|last1=Baveye|first1=P.|last2=Vandevivere|first2=P.|last3=Hoyle|first3=B.L.|last4=DeLeo|first4=P.C.|last5=de Lozada|first5=D.S.|year=2006|title=Environmental impact and mechanisms of the biological clogging of saturated soils and aquifer materials|url=https://www.researchgate.net/publication/233057180|format=PDF|journal=Critical Reviews in Environmental Science and Technology|volume=28|issue=2|pages=123–191|doi=10.1080/10643389891254197}} 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,{{cite journal |last1=Gupta |first1=R.P. |last2=Swartzendruber |first2=D. |journal=Soil Science Society of America Journal |title=Flow-associated reduction in the hydraulic conductivity of quartz sand |year=1962| volume=26 | issue=1| pages=6–10 |doi=10.2136/sssaj1962.03615995002600010003x|bibcode=1962SSASJ..26....6G }}{{cite journal |last1=Frankenberger| first1=W.T.| last2=Troeh| first2=F.R.| last3=Dumenil| first3=L.C.| journal=Soil Science Society of America Journal| title=Bacterial effects on hydraulic conductivity of soils| year=1979| volume=43| issue=2| pages=333–338| doi=10.2136/sssaj1979.03615995004300020019x| bibcode=1979SSASJ..43..333F}}{{cite journal|last1=Vandevivere|first1=P.|last2=Baveye|first2=P.|year=1992|title=Saturated hydraulic conductivity reduction caused by aerobic bacteria in sand columns.|url=https://www.researchgate.net/publication/236679936|format=PDF|journal=Soil Science Society of America Journal|volume=56|issue=1|pages=1–13|bibcode=1992SSASJ..56....1V|doi=10.2136/sssaj1992.03615995005600010001x}}{{cite journal |last1=Xia |first1=L. |last2=Zheng |first2=X. |last3=Shao |first3=H. |last4=Xin |first4=J. |last5=Sun |first5=Z. |last6=Wang |first6=L. |journal=Journal of Hydrology |title=Effects of bacterial cells and two types of extracellular polymers on bioclogging of sand columns |year=2016 |volume=535 |pages=293–300 |doi=10.1016/j.jhydrol.2016.01.075|bibcode=2016JHyd..535..293X }} algae{{cite journal|last1=Gette-Bouvarot|first1=M.|last2=Mermillod-Blondin|first2=F.|last3=Angulo-Jaramillo|first3=R.|last4=Delolme|first4=C.|last5=Lemoine|first5=D.|last6=Lassabatere|first6=L.|last7=Loizeau|first7=S.|last8=Volatier|first8=L.|year=2014|title=Coupling hydraulic and biological measurements highlights the key influence of algal biofilm on infiltration basin performance|url=https://www.researchgate.net/publication/264296941|format=PDF|journal=Ecohydrology|volume=7|issue=3|pages=950–964|doi=10.1002/eco.1421|bibcode=2014Ecohy...7..950G |s2cid=129758850}} and fungus{{cite journal|last1=Seki|first1=K.|last2=Miyazaki|first2=T.|last3=Nakano|first3=M.|year=1996|title=Reduction of hydraulic conductivity due to microbial effects.|url=https://www.jstage.jst.go.jp/article/jsidre1965/1996/181/1996_181_137/_pdf|format=PDF|journal=Transactions of Japanese Society of Irrigation, Drainage and Reclamation Engineering|volume=181|pages=137–144|doi=10.11408/jsidre1965.1996.137}}{{cite journal |last1=Seki |first1=K. |last2=Miyazaki |first2=T. | last3=Nakano |first3=M. |journal=European Journal of Soil Science |title=Effect of microorganisms on hydraulic conductivity decrease in infiltration|year=1998 |volume=49 |issue=2 |pages=231–236 |doi=10.1046/j.1365-2389.1998.00152.x |bibcode=1998EuJSS..49..231S |s2cid=97173198 |url=https://github.com/sekika/paper/raw/master/EJSS/Seki-1998-EJSS.pdf }}) and their synthesized byproducts such as extracellular polymeric substance (EPS){{cite journal |last1=Jiang| first1=Y.| last2=Matsumoto| first2=S.| journal=Soil Science and Plant Nutrition| title=Change in microstructure of clogged soil in soil wastewater treatment under prolonged submergence| year=1995| volume=41| issue=2| pages=207–213| doi=10.1080/00380768.1995.10419577| bibcode=1995SSPN...41..207J}} (also referred to as slime), which form biofilm{{cite journal |last1=Taylor |first1=S.W. |last2=Milly |first2=P.C.D.| last3=Jaffé| first3=P.R.| journal=Water Resources Research| title=Biofilm growth and the related changes in the physical properties of a porous medium: 2. Permeability| year=1990| volume=26| issue=9| pages=2161–2169| doi=10.1029/WR026i009p02161|bibcode=1990WRR....26.2161T }}{{cite journal|last1=Zhao|first1=L.|last2=Zhu|first2=W.|last3=Tong|first3=W.|year=2009|title=Clogging processes caused by biofilm growth and organic particle accumulation in lab-scale vertical flow constructed wetlands|url=http://www.jesc.ac.cn/jesc_en/ch/reader/create_pdf.aspx?file_no=2009210608&%3Bflag=1&%3Bjournal_id=jesc_en&origin=publication_detail|format=PDF|journal=Journal of Environmental Sciences|volume=21|issue=6|pages=750–757|doi=10.1016/S1001-0742(08)62336-0|pmid=19803078|bibcode=2009JEnvS..21..750Z }}{{cite journal|last1=Kim|first1=J.|last2=Choi|first2=H.|last3=Pachepsky|first3=Y.A.|year=2010|title=Biofilm morphology as related to the porous media clogging|url=https://www.researchgate.net/publication/26672970|format=PDF|journal=Water Research|volume=44|issue=4|pages=1193–1201|doi=10.1016/j.watres.2009.05.049|pmid=19604533|bibcode=2010WatRe..44.1193K }} or microcolony aggregation{{cite journal |last1=Seki |first1=K. |last2=Miyazaki |first2=T.| journal=Water Resources Research| title=A mathematical model for biological clogging of uniform porous media| year=2001| volume=37| issue=12| pages=2995–2999| doi=10.1029/2001WR000395|bibcode=2001WRR....37.2995S |s2cid=129625309 | url=https://github.com/sekika/paper/raw/master/WRR/Seki-2001-WRR.pdf}} on soil particles are direct biological causes of the decrease in hydraulic conductivity.
2. Entrapment of gas bubbles such as methane{{cite journal |last1=Reynolds |first1=W.D. |last2=Brown |first2=D.A. |last3=Mathur |first3=S.P. |last4=Overend |first4=R.P. |journal=Soil Science |title=Effect of in-situ gas accumulation on the hydraulic conductivity of peat |year=1992 |volume=153 |issue=5 |pages=397–408 |doi=10.1097/00010694-199205000-00007|bibcode=1992SoilS.153..397R |s2cid=93225879 }} 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.{{cite journal |last1=Houot| first1=S.| last2=Berthelin| first2=J.| journal=Geoderma| title=Submicroscopic studies of iron deposits occurring in field drains: Formation and evolution| year=1992| volume=52| issue=3–4| pages=209–222| doi=10.1016/0016-7061(92)90037-8| bibcode=1992Geode..52..209H}} 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.{{cite journal |last1=Volk |first1=E. |last2=Iden |first2=S.C. |last3=Furman |first3=A. |last4=Durner |first4=W. |last5=Rosenzweig |first5=R. |journal=Water Resources Research |title=Biofilm effect on soil hydraulic properties: Experimental investigation using soil-grown real biofilm |year=2016 |volume=52 |issue=8 |pages=5813–5828 |doi=10.1002/2016WR018866|bibcode=2016WRR....52.5813V }}

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{{cite journal |last=Bouwer |first=H. |journal=Hydrogeology Journal |title=Artificial recharge of groundwater: hydrogeology and engineering |year=2002 |volume=10 |issue=1 |pages=121–142 |url=https://link.springer.com/content/pdf/10.1007/s10040-001-0182-4.pdf |doi=10.1007/s10040-001-0182-4 |bibcode=2002HydJ...10..121B}} and percolation trenches.{{cite journal|last1=Furumai|first1=H.|last2=Jinadasa|first2=H.K.P.K.|last3=Murakami|first3=M.|last4=Nakajima|first4=F.|last5=Aryal|first5=R.K.|year=2005|title=Model description of storage and infiltration functions of infiltration facilities for urban runoff analysis by a distributed model|url=https://www.researchgate.net/publication/7518861|format=PDF|journal=Water Science and Technology|volume=52|issue=5|pages=53–60|doi=10.2166/wst.2005.0108|pmid=16248180}} 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.{{cite journal |last=Kristiansen |first=R. | journal=Journal of Environmental Quality |title=Sand-filter trenches for purification of septic tank effluent: I. The clogging mechanism and soil physical environment| year=1981 |volume=10 | issue=3| pages=353–357| doi=10.2134/jeq1981.00472425001000030020x|bibcode=1981JEnvQ..10..353K }}{{cite journal |last1=Nieć| first1=J. |last2=Spychała |first2=M. |last3=Zawadzki |first3=P. |journal=Journal of Ecological Engineering |title=New approach to modelling of sand filter clogging by septic tank effluent |year=2016 | volume=17 |issue=2 |pages=97–107 |doi=10.12911/22998993/62296 |url=http://www.jeeng.net/pdf-62296-4163?filename=NEW%20APPROACH%20TO%20MODELLING.pdf }} The organic material causing bioclogging in the septic tank is sometimes called biomat.{{Cite web|url=http://inspectapedia.com/septic/Septic_Biomat_Formation.php|title=Septic Biomat: defined, properties|publisher=InspectAPedia |accessdate=March 22, 2017}} 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.{{cite journal |last1=Mauclaire |first1=L. |last2=Schürmann |first2=A. |last3=Thullner |first3=M. |last4=Gammeter |first4=S. |last5=Zeyer |first5=J. |journal=Journal of Water Supply: Research and Technology-Aqua |title=Slow sand filtration in a water treatment plant: biological parameters responsible for clogging| year=2004| volume=53 |issue=2 |pages= 93–108 |doi=10.2166/aqua.2004.0009}} 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.{{cite journal |last1=Newcomer |first1=M.E.| last2=Hubbard| first2=S.S.| last3=Fleckenstein| first3=J.H.| last4=Maier| first4=U.| last5=Schmidt| first5=C.| last6=Thullner| first6=M.| last7=Ulrich| first7=C.| last8=lipo| first8=N.| last9=Rubin| first9=Y.| journal=Water Resources Research| title=Simulating bioclogging effects on dynamic riverbed permeability and infiltration| year=2016| volume=52| issue=4| pages=2883–2900| doi=10.1002/2015WR018351|bibcode=2016WRR....52.2883N|s2cid=130425627 }} 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.{{cite journal |last1=Xian |first1=Y.| last2=Jin| first2=M.| last3=Zhan| first3=H.| last4=Liu| first4=Y.| journal=Water Resources Research| title=Reactive transport of nutrients and bioclogging during dynamic disconnection process of stream and groundwater| year=2019| volume=55| issue=5| pages=3882–3903| doi=10.1029/2019WR024826|bibcode=2019WRR....55.3882X }}
4. Bioclogging is also a concern in aquifers, particularly when water is extracted through water wells below the groundwater table.{{cite journal |last1=van Beek |first1=C.G.E.M. |last2=van der Kooij |first2=D. | journal=Ground Water| title=Sulfate-reducing bacteria in ground water from clogging and non-clogging shallow wells in the netherlands river region |year=1982 |volume=20| issue=3| pages=298–302| doi=10.1111/j.1745-6584.1982.tb01350.x|bibcode=1982GrWat..20..298B }} 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.{{Cite web|url=https://www.groundwatereng.com/well-remediation-and-rehabilitation|title=Well remediation and rehabilitation|publisher=Groundwater Engineering Limited|accessdate=March 22, 2017|archive-date=March 22, 2017|archive-url=https://web.archive.org/web/20170322204314/https://www.groundwatereng.com/well-remediation-and-rehabilitation|url-status=dead}} Bioclogging may also affect the sustainable operation of ground source heat pumps.{{cite journal |last1=Song |first1=W. |last2=Liu |first2=X. |last3=Zheng |first3=T. |last4=Yang |first4=J. |journal=Geothermics |title=A review of recharge and clogging in sandstone aquifer |year=2020 |volume =87 |pages=101857 |doi=10.1016/j.geothermics.2020.101857|bibcode=2020Geoth..8701857S }} 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.

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.{{cite journal |last1=Davis | first1=S.| last2=Fairbanks| first2=W.| last3=Weisheit| first3=H.| journal=Transactions of the ASAE| title=Dairy waste ponds effectively self-sealing| year=1973| volume=16| issue=1| pages=69–71| doi=10.13031/2013.37447}} Similarly, irrigation channels for seepage control may be inoculated with algae and bacteria to promote bioclogging for reducing water loss.{{cite journal |last1=Ragusa| first1=S.R.| last2=de Zoysa| first2=D.S.| last3=Rengasamy| first3=P.| journal=Irrigation Science| title=The effect of microorganisms, salinity and turbidity on hydraulic conductivity of irrigation channel soil| year=1994| volume=15| issue=4| pages=159–166| doi=10.1007/BF00193683| bibcode=1994IrrSc..15..159R| s2cid=35184810}}
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.{{cite journal|last1=Kamon|first1=M.|last2=Zhang|first2=H.|last3=Katsumi|first3=T.|year=2002|title=Redox effect on the hydraulic conductivity of clay liner|url=https://www.jstage.jst.go.jp/article/sandf1995/42/6/42_6_79/_pdf|format=PDF|journal=Soils and Foundations|volume=42|issue=6|pages=79–91|doi=10.3208/sandf.42.6_79|bibcode=2002SoFou..42...79K }}{{cite journal|last1=Tang|first1=Q.|last2=Wang|first2=H.Y.|last3=Chen|first3=H.|last4=Li|first4=P.|last5=Tang|first5=X.W.|last6=Katsumi|first6=T.|year=2015|title=Long-term hydraulic conductivity of compacted clay permeated with landfill leachates|url=https://www.jstage.jst.go.jp/article/jgssp/2/53/2_CHN-52/_pdf|format=PDF|journal=Japanese Geotechnical Society Special Publication|volume=2|issue=53|pages=1845–1848|doi=10.3208/jgssp.CHN-52|doi-access=free}}
3. Bioclogging is a common occurrence in constructed wetlands{{cite journal |last1=Moreira |first1=F.D. |last2=Dias |first2=E.H.O. |year=2020 |title=Constructed wetlands applied in rural sanitation: A review |journal=Environmental Research |volume=190 |pages=110016 |bibcode=2020ER....19010016M |doi=10.1016/j.envres.2020.110016 |pmid=32768473}} 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.{{cite journal |last1=Suliman |first1=F. |last2=French |first2=H.K. |last3=Haugen |first3=L.E. |last4=Søvik |first4=A.K. |journal=Ecological Engineering |title=Change in flow and transport patterns in horizontal subsurface flow constructed wetlands as a result of biological growth |year=2006 |volume=27 |issue=2 |pages=124–133 |doi=10.1016/j.ecoleng.2005.12.007|bibcode=2006EcEng..27..124S }}
4. Biofilm formation plays a crucial role in bioremediation,{{cite journal|last1=Lee|first1=M.D.|last2=Thomas|first2=J.M.|last3=Borden|first3=R.C.|last4=Bedient|first4=P.B.|last5=Ward|first5=C.H.|last6=Wilson|first6=J.T.|year=1998|title=Biorestoration of aquifers contaminated with organic compounds|url=https://www.researchgate.net/publication/240520000|format=PDF|journal=Critical Review in Environmental Control|volume=18|issue=1|pages=29–89|doi=10.1080/10643388809388342}} particularly in treating biodegradable groundwater pollution. A permeable reactive barrier{{Cite book |last1=Naftz |first1=D. |last2=Morrison |first2=S.J.| last3=Fuller| first3=C.C.| last4=Davis | first4=J.A. |title=Handbook of groundwater remediation using permeable reactive barriers: applications to radionuclides, trace Metals, and nutrients |year=2002 |publisher=Academic Press |location=Cambridge, Massachusetts|isbn=978-0125135634}} is formed to contain the groundwater flow by bioclogging and also to degrade pollution by microbes.{{cite journal |last1=Komlos| first1=J.| last2=Cunningham| first2=A.B| last3=Camper| first3=A.K.| last4=Sharp| first4=R.R.| journal=Environmental Progress| title=Biofilm barriers to contain and degrade dissolved tricholoroethylene| year=2004| volume=23| issue=1| pages=69–77| doi=10.1002/ep.10003| bibcode=2004EnvPr..23...69K| url=https://scholarworks.montana.edu/xmlui/handle/1/13419}} Contaminant flow should be carefully analyzed because a preferential flow path in the barrier may reduce the efficiency of the remediation.{{cite journal |last1=Seki |first1=K. |last2=Thullner |first2=M. |last3=Hanada |first3=J. |last4=Miyazaki |first4=T. |journal=Ground Water Monitoring & Remediation |title=Moderate bioclogging leading to preferential flow paths in biobarriers|year=2006 |volume=26 |issue=3 |pages=68–76 |doi=10.1111/j.1745-6592.2006.00086.x |bibcode=2006GMRed..26c..68S |s2cid=97009671 |url=https://github.com/sekika/paper/raw/master/GWMR/Seki-2006-GWMR.pdf }}
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,{{cite journal |last1=Lappan |first1=R.E. |last2=Fogler |first2=H.S.| journal=Biotechnology and Bioengineering| title=Reduction of porous media permeability from in situ leuconostoc mesenteroides growth and dextran production | year=1996| volume=50 |issue=1 | pages=6–15 |doi=10.1002/(SICI)1097-0290(19960405)50:1<6::AID-BIT2>3.0.CO;2-L |pmid=18626894 |citeseerx=10.1.1.1017.5978 |s2cid=803784 }} 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{{Cite book |last1=Ivanov |first1=V. |last2=Stabnikov |first2=V.|title=Construction biotechnology: biogeochemistry, microbiology and biotechnology of construction materials and processes |chapter=Bioclogging and biogrouts |pages=139–178| year=2017 |publisher=Springer |location=New York| isbn=978-9811014444|doi=10.1007/978-981-10-1445-1_8}} 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.{{cite journal |last1=Ivanov| first1=V.| last2=Chu| first2=J.| journal=Reviews in Environmental Science and Bio/Technology| title=Applications of microorganisms to geotechnical engineering for bioclogging and biocementation of soil in situ| year=2008| volume=7| issue=2| pages=139–153| doi=10.1007/s11157-007-9126-3| bibcode=2008RESBT...7..139I}}

• Biofilm
• Hydraulic conductivity
• Landfill liner
• Microbial enhanced oil recovery
• Septic tank
• Slow sand filter

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