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Types of Aquifer Systems. Source: Ritter, Michael E. The Physical Environment: An Introduction to Physical Geology. 1 October 2009. 1 April 2011 <>.

Although, groundwater accounts for 30% of all freshwater on earth and has been used for decades as a source of clean drinking water (Chin 2006), the topic of groundwater or aquifer microbiology is a fairly new concept. Prior to the 1970s, a common assumption in society was that groundwater was the most pristine water and did not contain any microbial populations. This was partially supported by the limitations of sampling methods and culture-based techniques. However, new culture-independent techniques, such as direct extraction, cloning, and community fingerprinting, have allowed researchers to begin to explore microbial communities found in groundwater systems. Despite the recent developments, groundwater microbiology is still a topic that has not been fully explored and therefore only limited information exists. In addition, most current research focuses on microbial diversity and metabolism in contaminated aquifers and not that of pristine aquifer systems.

Physical environment

Aquifers are geological formations that “are characterized by their ability to store and transmit water” (Charbeneau 2000). There are three basic types of aquifers: confined, unconfined, or semi-confined. Confined aquifers are aquifers that are confined above and below by relatively impermeable or impervious material, such as clay. Confined aquifers are usually recharged indirectly through infiltration or directly by underground springs. Unlike confined aquifers, unconfined aquifers are only bounded on the bottom by impermeable material. They are usually shallow, open to the atmosphere, and are often recharged directly and indirectly by rainfall. Finally, semi-confined aquifers, also known as leaky aquifers, are confined by semi-permeable materials.

Many aquifer systems “are hydrologically connected and thus can be considered a continuum ecosystem” (Griebler 2009). The transition zones between the different regions within the aquifer regulate the transfer of nutrients, particles, organisms, and energy within the different regions as well as other connected aquifer systems. However, aquifers are not homogenous and vary significantly from each other in hydrology, chemistry, and geology.

In addition to the heterogeneity of aquifers, aquifers are considered extreme habitats due to their lack of light, low availability of organic carbon and nutrients, and low constant temperatures. As a result, any microorganisms found in aquifer systems are extremophiles that are well-adapted to these extreme conditions.

Microbial communities

Schematic view of aquatic surface and subsurface habitats. Source: Griebler, C. and T. Lueders. "Microbial biodiversity in groundwater ecosystems." Freshwater Biology 54 (2009): 649-677.

According to studies, Bacteria are expected to be the dominant microbes found in aquifer systems, followed by Protozoa, Archaea, and some Fungi. However, some unique faunas could be found in subterranean caves. (USGS 2007)

The microbial communities are expected to consist of heterotrophs and chemolithoautotrophs, who are adapted to living in nutrient-poor and anaerobic conditions, specifically for deep and/or confined aquifers. Therefore, the microbial communities found in aquifers are oligotrophs and k-strategists that grow slowly and have a low tolerance to rapid changes.

Lithoautotrophs are more likely to be more important in deeper aquifer habitats, where oxygen is absent and inorganic electron donors are more likely present than readily-degradable organic carbon. In addition, autotrophic methanogens and acetogens are also likely to be found in relatively greater numbers in deeper aquifer environments. However, it is expected that the distribution of most of these microorganisms is mainly restricted to shallow, unconfined aquifers.

Key Microbe Groups

The main bacteria communities identified in aquifers are members of Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes, all well-known surface heterotrophs. Euryarchaeota and Crenarchaeota were also identified as dominant Archaea found in aquifers. In addition, “Methanogens are a unique functional group within the Archaea” and are of particular interest in anaerobic aquifers.

Some invertebrate communities have also been identified in aquifer habitats between 100 to 1000 species. These communities include microbes from the following phylum: Annelida, Chordata, Cnidaria, Gastrotricha, Mollusca, Nematoda, Nemertina, Platylmintha, Porifera, Tardigrada, and Arthropoda(Gibert 2009).

Microbial processes

Since aquifers are characterized by no light and low organic carbon and nutrient availability, most microbes found in aquifers need to use inorganic electron donors and light-independent chemical reactions as a source of energy. Therefore, as mentioned before, most microbes would be lithoautotrophs. Possible electron donors would be nitrate, manganese, sulfur, iron, and/or sulfate, which would be found in the sediments. However, in shallow, unconfined aquifers, aerobic organoheterotrophs could be present as a result of oxygen being replenished at a faster rate.

Additional abiotic and biotic factors that affect microbial diversity include evolution, biogeography, habitat size, spatial heterogeneity, temporal variability and disturbance, and pollution.

Special Survival Adaptations

As a survival method, most prokaryotes found in aquifers are not free-living but instead attached to sediment particles, rock surfaces, and/or found in thin biofilms. Therefore, it is not shocking to see that the total of number of Bacteria per cm3 of groundwater ranges from 102 to 106 cells compared to 104 to 108 cells per cm3 of sediment; while Protozoa are expected to range from 100 to 105 cells per cm3 of groundwater versus 103 to 108 cells per cm3 of sediment (Griebler 2009).

Sediment surfaces are “geochemically more diverse and offer more ecological niches than ground water” (Griebler 2009). The number of microorganisms found attached to sediments compared to suspended in the groundwater depends on the availability of dissolved organic carbon (DOC) and nutrients, sediment grain size, distribution, and texture. Additional factors that influence microbial populations in aquifers include local hydrogeochemistry, availability of oxidizable substrates, dispersal of microbes from overlying unsaturated zones, and the simple food-web structure in aquifers.

In addition, microbial communities found in the transition zone between surface running waters and the adjacent groundwater systems are expected to contain more diverse and dynamic communities than those located in the aquifer.

Important Biological Interactions

Although not much information exists regarding biological interactions in aquifers, it can be expected that in order for microbial communities to survive, specifically if attached to sediment surfaces, they must participate in the following positive biological interactions: mutualism, symbiosis, synergism, and commensalism.

Current Research

Large programs, such as the US Department of Energy (DOE) Subsurface Science Program (SSP), have pioneered the “first systematic insights into subsurface microbiology” through their research in subsurface microbiology (Griebler 2009). However, most of their current research is focused on subsurface contamination and remediation.

The US Department of Energy (DOE) has founded the Subsurface Microbial Culture Collection (SMCC), which is a database that currently contains greater than 10,000 isolates from subsurface cultures, specifically for Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes (Griebler 2009).

In addition, the annual International Symposium for Subsurface Microbiology focuses on addressing topics related to subsurface microbial life, such as energy metabolism in oligotrophic shallow aquifers and deep terrestrial or marine systems (Griebler 2009).


Charbeneau, Randall J. Groundwater Hydraulics and Pollutant Transport. Long Grove, IL: Waveland Press, Inc., 2000.

Chin, David A. Water-Resources Engineering. 2nd Edition. Upper Saddle River, NJ: Pearson Prentice Hall, 2006.

Gibert, Janine and David C. Culver. "Assessing and Conserving Groundwater Biodiversity: An Introduction." Freshwater Biology 54 (2009): 639-648.

Griebler, C. and T. Lueders. "Microbial biodiversity in groundwater ecosystems." Freshwater Biology 54 (2009): 649-677.

Ritter, Michael E. The Physical Environment: An Introduction to Physical Geology. 1 October 2009. 1 April 2011. <>.

US Geological Survey (USGS). Bacteria and Their Effects on Ground-Water Quality. 21 December 2007. 30 March 2011. <>.

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