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Water stored underground in cracks and pores, from Natural Resources Canada.[[1]]


Surface water moves downward through unsaturated zones –typically tiny pores and cracks in the soil, sand, or rock, and then reaches a stable water saturated layer named the water table. Groundwater is beneath the water table. Groundwater provide about 0.6 percent of the world’s total water and 20 percent of the available fresh water resources. Microbial organisms play important role in groundwater ecosystem and affect drinking water quality significantly. Microbial contamination of groundwater is a health concern.

Typical aquifer cross-section, from wikipeida.[[2]]

Physical and chemical environment

Substrate and sediment

In the shallow aquifers where generally groundwater is located, typically, there is soil, sand, plant roots, hardpan and low permeability bedrock.


The temperature of groundwater is quite steady because the specific heat capacity of water is high and also because the soil, rock and up layer water protect groundwater from heat changing with the climate [1].


Groundwater is relatively stable compared to surface water. In the aquifer and other porous media, groundwater not only follows gravity, but also follows pressure gradients. The movement of groundwater also depends on the porosity, water content and hydraulic conductivity of aquifer.

groundwater contamination plume, from earth science australia.[[3]]

Chemical environment

The mineral content in the groundwater is usually constant, and could be higher than in the surface water from the same area. Fe2+, Mn2+, H2S, NH4+ CO2 and chlorinated solvents are often presented, concentrations of nitrate and silica could be quite high, but usually no dissolved O2 in the groundwater [2].

Groundwater contamination

Pollutants, such as gasoline, oil, road salts and chemicals seep into groundwater can hurt animals, plants, or humans. Two major contaminate sources are hazardous waste site leaking and landfills. Since groundwater is part of the hydrologic cycle, contaminants released to the groundwater could create a contaminant plume within an aquifer and also can be transferred to the other parts of the cycle [3].



Gram-negative bacteria (such as Pseudomonas, Azotobacter, Neisseria, Maraxella and Acinetobacter) are found extensively in groundwater system. Balkwill (1989) studied the aerobic, chemoheterotrophic bacteria in deep aquifers and other subsurface sediments at a site in South Carolina. They found that 95% of the platable colonies contained nonstreptomycete bacteria, more than 80% of which were gram-negative rods[4]. Gram-positive bacteria are not abundant in groundwater systems; however, the gram-positive bacteria include many important human pathogens such as Micrococcus, Staphylococcus, and Streptococcus [5].


It is estimated that 65% of the water borne disease are caused by enteric viruses[6]. For example, norovirus (also known as Norwalk agent) causes approximately 90% of epidemic non-bacterial outbreaks of gastroenteritis around the world. Infectious hepatitis is the most intensively studied disease that is caused by water borne virus. Virus adsorption to soils and other solids could prolong survival of viruses in the groundwater. Research showed that Viruses originating from wastewater infiltration units are able to migrate horizontally in groundwater for hundreds of meters and vertically as much as 67 meters [7].


Groundwater eukaryotes are comprised of many species, range from single-celled heterotrophic nanoflagellates and fungi to amphipod crustaceans. The location of groundwater eukaryotes might be close to the vadose (unsaturated) zone, the soil or the bottom sediments of surface water [8,9].


Groundwater Archaea have been found throughout depths of several thousand meters. Ammonia-Oxidizing Archaea and methanogenic archaea are two major groups in the groundwater [10].

Microbial processes

Ammonia oxidation

Both bacteria and archaea are able to carry out ammonia oxidation in the groundwater. The ammonia oxidation rate is limited by the available oxygen[10]. Ammonia is oxided into nitrite and nitrate, and then ultimately be removed from the system by reduction to dinitrogen by denitrification.


Denitrification reduce nitrate in the groundwater. Denitrifying bacteria Burkholderia, Bacillus, and Pseudomonas play an important role in groundwater[11].The process removes nitrate which is a major groundwater pollutant, particularly in agricultural regions where nitrate is leached from soils that have been amended with fertilizer or manure. In the groundwater, organic matter is the most common electron donor, but inorganic compounds, such as pyrite (FeS2) and Fe[II]-silicates, may also be used by denitrifying organisms.

Manganese, Iron and sulfate Reduction

Anaerobic conditions are dominant in groundwater. In anaerobic zone, microbial communities could carry out decomposition coupled with Manganese, Iron and sulfate reduction[11]. These processes determined by the redox condition and could affect carbon, Fe and S cycle in the groundwater.


Synthetic halogenated organic compounds in the groundwater could persist for very long time and are recognized as a serious health concern. Dehalogenation removes halogens from organic compounds. Anaerobic dehalogenation reactions can effectively degrade a wide variety of halogenated contaminants in ground water.

Current Research

Groundwater treatment

1. W.W.J.M de Vet et al characterized the microbial populations in groundwater sources and sand filters for drinking water production. They found that both bacteria and archaea, especially Nitrospira, are important in ammonia nitrification. No nitrifying organisms were detected in subsurface aerated groundwater; therefore, the nitrifying capacity is low. Iron-oxidizing bacteria Gallionella ferruginea was detected in subsurface aerated groundwater. It indicted the iron oxidation could be existed and thereby could improve nitrification in groundwater[12].

2. Sven Jechalke et al developed a novel aerated treatment pond for enhanced biodegradation of groundwater contaminants. They use coconut fibre and polypropylene textiles to grow contaminant-degrading biofilms. The results showed that the efficiencies for benzene, MTBE and COD were 99.9%, 38% and 61% respectively. Ammonium degradation rates were low[13].

Groundwater contamination

3. Amitabha Mukhopadhay et al drilled 29 monitoring well across urban Kuwait City and analyzed inorganic and organic constituents including isotopic composition. They found that one well is highly contaminated in terms of total coliform bacteria, fecal coliform bacteria and boron concentration. Another well is significantly contaminated. Three wells might be contaminated, and seven well were not contaminated[14].

Detection of groundwater contamination using microbial community profiles

4. Paula J. Mouser proposed a novel groundwater contamination detection method. They characterized bacteria, archaea and family Geobacteraceae in the contaminated groundwater by using T-RFLP. By knowing the information of microbial communities in the groundwater, they stated that this method is able to detect groundwater contamination[15].


1. Wikipedia, groundwater.

2. Water Treatment Handbook, Degremont, 1991.

3. The Groundwater Fundation.

4. Balkwill DL. Numbers, diversity, and morphological characteristics of aerobic, chemoheterotrophic bacteria in deep subsurface sediments from a site in South Carolina. Geomicrobiology Journal. 1989. Volume 7. Pages: 33-52.

5. Frank Chapelle. Ground-water microbiology and geochemistry. 2000. Wiley; 2 edition.

6. Bruce H. Keswick and Charles P. Gerba. Viruses in groundwater. Environmental Science & Technology. 1980. Volume 14. P.1290-1297.

7. Martin J. Allen. Microbiology of groundwater. Journal WPCF.1978. P.1342-1343.

8. Dan L. Danielopol, Christian Griebler, Amara Gunatilaka and Jos Notenboom. Present state and future prospects for groundwater ecosystems. Environmental Conservation. 2003. Volume 30. P. 104–130.

9. Y.Shi, M.D.Zwolinski, M.E.Schreiber, J.M.Bahr, G.W.Sewell, and W.J.Hickey. Molecular Analysis of Microbial Community Structures in Pristine and Contaminated Aquifers: Field and Laboratory Microcosm Experiments. Applied and Environmental Microbiology. 1999. Volume 65. p. 2143–2150.

10. Paul W. J. J. van der Wielen, Stefan Voost, and Dick van der Kooij. Ammonia-Oxidizing Bacteria and Archaea in Groundwater Treatment and Drinking Water Distribution Systems. Applied and Environmental Microbiology. 2009. Volume75. p.4687–4695.

11. Ann Azadpour-Keeley, Hugh H. Russell, and Guy W. Sewell. Microbial processes affecting monitored natural attenuation of contaminants in the subsurface. EPA/540/S-99/001. 1999.

12. W.W.J.M. de Vet, I.J.T. Dinkla, G. Muyzer, L.C. Rietveld, and M.C.M. van Loosdrecht. Molecular characterization of microbial populations in groundwater sources and sand filters for drinking water production. Water Research. 2009. Volume 43. P. 182–194.

13. Sven Jechalke, Carsten Vogt, Nils Reiche, Alessandro G. Franchini, Helko Borsdorf, Thomas R. Neu, Hans H. Richnow. Aerated treatment pond technology with biofilm promoting mats for the bioremediation of benzene,MTBE and ammonium contaminated groundwater. Water Research. 2010. Volume 44.P.1785-1796.

14. Amitabha Mukhopadhay, Adnan Akber and Eman Al-Awadi. Evaluation of Urban Groundwater Contamination from Sewage Network in Kuwait City. Water Air Soil Pollution. 2011. Volume 216. P.125–139.

15. Paula J. Mouser, Donna M. Rizzo, Gregory K. Druschel, Sergio E. Morales, Nancy Hayden, Patrick O’Grady, and Lori Stevens. Enhanced detection of groundwater contamination from a leaking waste disposal site by microbial community profiles. Water Resources Research. 2010. Volume 46. W12506.

Edited by Liangcheng Yang, a student of Angela Kent at the University of Illinois at Urbana-Champaign.