The significance of microbial processes in hydrogeology and geochemistry Francis H. Chapelle
Abstract Microbial processes affect the chemical composition of groundwater and the hydraulic properties of aquifers in both contaminated and pristine groundwater systems. The patterns of water-chemistry changes that occur depend upon the relative abundance of electron donors and electron acceptors. In many pristine aquifers, where microbial metabolism is limited by the availability of electron donors (usually organic matter), dissolved inorganic carbon (DIC) accumulates slowly along aquifer flow paths and available electron acceptors are consumed sequentially in the order dissolved oxygen > nitrate > Fe(III) > sulfate > CO2 (methanogenesis). In aquifers contaminated by anthropogenic contaminants, an excess of available organic carbon often exists, and microbial metabolism is limited by the availability of electron acceptors. In addition to changes in groundwater chemistry, the solid matrix of the aquifer is affected by microbial processes. The production of carbon dioxide and organic acids can lead to increased mineral solubility, which can lead to the development of secondary porosity and permeability. Conversely, microbial production of carbonate, ferrous iron, and sulfide can result in the precipitation of secondary calcite or pyrite cements that reduce primary porosity and permeability in groundwater systems. RØsumØ Les processus microbiologiques peuvent affecter la composition chimique de l'eau souterraine et les propriØtØs hydrauliques des nappes aussi bien dans les systmes aquifres polluØs que dans les systmes indemnes de pollution. Les changements de chimisme des eaux qui se produisent dØpendent de l'abondance relative des donneurs et des accepteurs d'Ølectrons. Dans les aquifres non contaminØs, o le mØtabolisme microbien est limitØ par la disponibilitØ des donneurs d'Ølectrons (en gØnØral la matire orgaReceived, January 1999 Revised, July 1999, August 1999 Accepted, October 1999 Francis H. Chapelle US Geological Survey, 720 Gracern Road, Suite 129 Columbia, South Carolina 29210, USA Fax: +1-803-750-6181 e-mail:
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nique), le carbone minØral dissous (CMD) s'accumule lentement le long des axes d'Øcoulement souterrain et les accepteurs d'Ølectrons disponibles sont consommØs de façon sØquentielle, dans l'ordre oxygne dissous > nitrate > fer (III) > sulfate > CO2 (mØthanogense). Dans les aquifres polluØs par des contaminants d'origine humaine, il existe un excs de carbone organique disponible et le mØtabolisme microbien est limitØ par la disponibilitØ des accepteurs d'Ølectrons. En plus des modifications du chimisme des eaux souterraines, la matrice encaissante de l'aquifre est affectØe par des processus microbiens. La production de dioxyde de carbone et d'acides organiques peut conduire à accroître la solubilitØ de minØraux, ce qui peut produire un dØveloppement de la porositØ secondaire et de la permØabilitØ. Inversement, la production microbienne de carbonate, de fer ferreux et de sulfure peut provoquer la prØcipitation de ciments de calcite secondaire ou de pyrite qui rØduisent la porositØ primaire et la permØabilitØ dans les nappes. Resumen Los procesos microbianos afectan la composición química y las propiedades hidrµulicas de los acuíferos, independientemente de su grado de contaminación. Los cambios en la química de las aguas dependen de la abundancia relativa entre donantes y receptores de electrones. En muchos acuíferos no contaminados, donde el metabolismo de los microbios estµ limitado por la disponibilidad de donantes de electrones (normalmente materia orgµnica), el carbono inorgµnico disuelto (CID) se acumula lentamente a lo largo de las líneas de flujo y los receptores de electrones se consumen sucesivamente en el siguiente orden: oxígeno disuelto > nitrato > Fe (III)>sulfato>CO2 (metanogØnesis). En los acuíferos que presentan contaminación antrópica, existe un exceso de carbono orgµnico disponible y entonces el metabolismo de los microbios se encuentra limitado por la disponibilidad de receptores de electrones. Ademµs de los cambios en la química de las aguas, los procesos microbianos afectan tambiØn a la matriz sólida del acuífero; la producción de CO2 y de µcidos orgµnicos puede dar lugar a una mayor solubilidad del mineral, lo que supone un aumento en porosidad secundaria y permeabilidad. Por el contrario, los procesos microbianos pueden dar lugar a la producción de carbonato, Springer-Verlag
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ión ferroso y sulfuro, precipitando calcita o pirita y reduciendo la porosidad primaria y la permeabilidad. Key words microbes ´ microbial processes ´ contamination ´ hydraulic properties
Introduction The fact that microorganisms inhabiting aquifer systems can alter the geochemistry of groundwater has long been known. As early as 1900 it was observed that groundwater associated with petroleum deposits often lacked dissolved sulfate, whereas groundwater not associated with petroleum contained high concentrations of sulfate. It was first suggested that this effect was caused by the metabolism of sulfate-reducing bacteria (Rogers 1917). This hypothesis was confirmed when sulfate-reducing bacteria were isolated from brines associated with petroleum deposits (Bastin 1926). Over the next 40 years, various investigators came to similar conclusions concerning the importance of microorganisms in determining groundwater geochemistry (Cedarstrom 1946; Gurevich 1962). However, not until methods for aseptic sampling of subsurface sediments were developed (Dunlap et al. 1977; Ghiorse and Balkwill 1983; Wilson et al. 1983; Phelps et al. 1989) and comprehensive evaluations of microorganisms present were made (Chapelle et al. 1987, 1988; Fredrickson et al. 1989, 1991) did the effects of microbial metabolism on groundwater geochemistry become widely known. Although microbial processes in pristine aquifers were the first to be systematically studied, by the early 1970s it was also becoming evident that microbial processes were important in the degradation of many common groundwater contaminants. In 1973 microorganisms indigenous to shallow aquifers were first shown to be capable of degrading gasoline compounds (Litchfield and Clark 1973), and soon bioremediation was being utilized to enhance the clean-up of gasolinecontaminated aquifers (Jamison et al. 1975). Since that time, various common chemical contaminants, including chlorinated solvents (McCarty and Semprini 1994; Gossett and Zinder 1996) and explosives (Bradley et al. 1994), have been recognized to be actively biodegraded in groundwater systems. Because of the volumes of these chemicals produced by modern society, and because biodegradation processes may limit the mobility or actively clean up such contamination in the environment, the microbial processes involved in biodegradation have been closely studied in recent years. In addition to affecting the chemistry of groundwater, microbial processes also affect the physical properties of aquifer systems. Geologists have long known that secondary porosity allows the accumulation of petroleum in otherwise non-porous rocks (Moncure et al. 1984). In addition, it has long been Hydrogeology Journal (2000) 8 : 41±46
known that secondary porosity can enhance the waterbearing properties of aquifer systems (Meinzer 1923). However, the processes leading to secondary-porosity development were not well understood. Painstaking isotopic and mass-balance studies showed that decarboxylation of organic matter and other abiotic processes could not account for all of the observed secondary porosity in many systems (Lundergard and Land 1986). The realization that most aquifer systems contain active microorganisms raised the possibility that microbial metabolism could lead to secondary-porosity development in both silicate (Bennett and Siegel 1987) and carbonate (Chapelle et al. 1988) rocks. Subsequent studies have shown that microorganisms can serve to either destroy (McMahon et al. 1992) or enhance (Hiebert and Bennett 1992; McMahon et al. 1995) porosity in aquifer sediments. The central tenet of this paper is that the metabolism and growth of microorganisms present in aquifers affect both the chemical composition of groundwater and the physical properties of aquifers. Whereas the extent of these effects varies widely among aquifers, depending upon rates of microbial metabolism, hydrologic setting, and aquifer mineralogy, the patterns of observed alterations exhibit certain similarities. The purpose of this paper is to describe some common patterns of geochemical alterations observed in aquifer systems and to illustrate them with examples from the literature.
Microbial Alteration of Groundwater Geochemistry The ways in which microbial processes alter the chemical composition of groundwater vary widely. However, two broad categories of water-chemistry patterns are associated with conditions that limit microbial activity in a given aquifer system. Pristine aquifers are often observed to be electron-donor limited. This is to say that microbial metabolism is inherently limited by the availability of organic carbon or other potential electron donors. Many aquifer systems in this category are composed of sediments or rocks tens to hundreds of million years old from which metabolizable organic carbon has been progressively removed over geologic time. The other broad category of aquifers are electron-acceptor limited. In these systems, there is an excess of electron donor available (usually organic carbon but not always) so that microbial metabolism is constrained by the availability of electron acceptors. Examples of this category of aquifers include natural petroleum reservoirs and, importantly, many aquifers that have been chemically contaminated by human activities. In this section, the alteration of groundwater geochemistry in each of these kinds of aquifers is considered.
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Aquifers That Are Electron-Donor Limited The groundwater geochemistry of the Black Creek aquifer in South Carolina, USA, was first described by Foster (1950) and has been extensively studied since that time (Speiran 1987). In addition, the influence of microbial processes on the groundwater chemistry of this aquifer has been described in detail (Chapelle and Lovley 1990; Chapelle and McMahon 1991; McMahon and Chapelle 1991a , 1991b). The Black Creek aquifer is a good example because it exhibits a nearly complete sequence of classic water-chemistry changes commonly observed in regional groundwater systems. In this hydrologic system, groundwater flows from recharge areas near the fall line to discharge areas near the Atlantic Ocean. As groundwater moves along aquifer flow paths, concentrations of dissolved inorganic carbon (DIC) increase from less than 1 mM/L near recharge areas to more than 12 mM/L 150 km downgradient. This DIC is produced by microbial metabolism driving the dissolution of carbonate shell material in the aquifer according to the equation: CaCO3 (carbonate) + CO2 (microbial)cCa2 + + 2HCO3± Because approximately half of the DIC produced comes directly from microbial metabolism (~6 mM), and because it takes approximately 150,000 years for groundwater to travel from the recharge area, it follows that microbial metabolism produces DIC at an overall rate of about 10±4 mM/L of water per year. Thus, even though concentration increases of DIC are large along the aquifer flow path, they reflect very low rates of microbial metabolism (Chapelle and Lovley 1990). The principal reason that rates of microbial metabolism are low in this system is that the aquifer contains very little metabolizable organic carbon. McMahon et al. (1992) show, for example, that Black Creek aquifer sediments contain 0.1±1.0% organic carbon on a dry weight basis. Because of these low rates of microbial metabolism, the amounts of available electron acceptors in the system [oxygen, Fe(III), sulfate, and CO2] are large relative to the abundance of organic carbon. The limited availability of electron donors in this aquifer explains much of the behavior of other solutes in the system. Concentrations of dissolved oxygen drop below detectable levels near the recharge area. Once groundwater becomes anoxic, concentrations of ferrous iron increase, indicating the initiation of active Fe(III) reduction. Downgradient of the high-iron zone, sulfate becomes the principal electron acceptor, with sulfate in groundwater being continuously replenished from high-sulfate water trapped in clay beds that confine the aquifer (Pucci and Owens 1989; Chapelle and McMahon 1991). Not until the very end of the flow path do concentrations of sulfate decrease to the point that the methanogenesis becomes an important process. The defining characteristic of electron donor-limited aquifers is the tendency of microbial electron-accepting processes to proceed from O2 reduction Hydrogeology Journal (2000) 8 : 41±46
r Fe(III) reduction r sulfate reduction r methanogenesis in the direction of groundwater flow, as illustrated by the chemistry of the Black Creek aquifer. This behavior follows directly from the abundance of potential electron acceptors relative to available electron donors.
Aquifers That Are Electron-Acceptor Limited Many ancient sediments have little available organic carbon (or other potential electron donors), but geologic or hydrologic conditions can be such that there is an abundance of available carbon. When the supply of available carbon is very high, microbial metabolism can become limited by the lack of available electron acceptors. Examples of groundwater systems that are electron-acceptor limited include peat aquifers (which are common in northern latitudes), petroleum deposits, and aquifers that have been chemically contaminated by human activities. One of the best documented examples of an electron-acceptor limited aquifer is a shallow aquifer that was contaminated by a crude-oil spill near Bemidji, Minnesota, USA (Baedecker et al. 1993). In 1979, a pipeline burst and spilled about 100,000 gallons of crude oil onto a glacial-outwash aquifer. At the time of the spill, groundwater was saturated with dissolved oxygen (~10 mg/L) due to high rates of atmospheric recharge and low amounts of natural organic carbon present in the aquifer. With the sudden influx of metabolizable carbon, oxygen was rapidly consumed where the oil had accumulated on the water table, and Fe(III)-reducing conditions were established. By 1984, just 5 years after the initial spill, Fe(III) hydroxides present in the aquifer matrix were becoming exhausted near the oil lens and methanogenesis was becoming a significant process. Because of the excess of electron donors available from the oil spill, the water chemistry at Bemidji is characterized by methanogenic conditions, which exist closest to the contaminant source, followed sequentially by sulfate-reducing, Fe(III)-reducing, and oxic conditions. This pattern is exactly opposite to that observed in the Black Creek aquifer, where methanogenesis occurred farthest from the recharge area. Because groundwater at Bemidji contains relatively little sulfate, sulfate reduction is not a major process at this site. This sequence of redox processes is characteristic of groundwater systems that are electronacceptor limited and is often observed in groundwater systems contaminated by petroleum hydrocarbons (Bradley et al. 1998).
Microbial Alteration of Aquifer Properties Microbial processes not only systematically alter the geochemistry of groundwater, but can also alter the hydraulic properties of the aquifers themselves. This is Springer-Verlag
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a topic of special interest to hydrogeologists, because groundwater can only move freely in sediments or rocks that have sufficient effective porosity. This is also a topic of interest in contaminant hydrology, because aquifer porosity can store oily-phase contaminants, making them difficult to remove. As before, it is useful to consider the microbial generation of aquifer porosity and permeability in the context of electron-donor or electron-acceptor limitations.
Aquifers That Are Electron-Donor Limited Groundwater flows in the Black Creek aquifer from recharge areas along the fall line to discharge areas along the Atlantic coast. As discussed previously, the geochemistry of groundwater is significantly altered by microbial processes along this flow path. In addition to altering water chemistry, microbial processes also alter the physical properties of this aquifer. Data from core holes oriented along flow paths indicate a marked lithologic change. In recharge areas near the fall line, secondary intergranular calcite cements are virtually non-existent. At Lake City, South Carolina, which is intermediate between recharge areas and discharge areas, calcite cements are more common. In Myrtle Beach, South Carolina, which is near discharge areas, as much as 50% of the total thickness of the aquifer has been cemented by intergranular calcite cement. This loss of porosity has a significant effect on the hydrology of this aquifer system. The transmissivity of the Black Creek aquifer is so low that groundwater cannot supply municipal water needs for the city of Myrtle Beach. This low transmissivity is due largely to the abundance of intergranular cements that fill primary porosity in this aquifer system. The microbial processes leading to the development of pore-filling cements in the Black Creek aquifer have been investigated in detail (McMahon et al. 1992). This study showed that, whereas sands of the Black Creek aquifer contain relatively little organic carbon, adjacent confining beds contain abundant organic carbon. The fermentation of this confining-bed organic carbon causes the accumulation of organic acids in confining-bed pore water. The diffusive flux of these organic acids to the Black Creek aquifer and the subsequent oxidation of these acids to carbon dioxide lead to a net mass transfer of carbon from confining beds to aquifers. As carbon dioxide reacts with aquifer materials, carbonate and bicarbonate are produced. This process leads to production of secondary porosity in parts of the aquifer. However, as carbonate and bicarbonate accumulate in solution and are transported, groundwater can become oversaturated with respect to calcite, resulting in calcite precipitation in other parts of the aquifer. The contribution of carbon derived from organic material to the pore-filling cements is recorded in the composition of stable carbon isotopes of the cements (McMahon et al. 1992). Primary carbonate shell mateHydrogeology Journal (2000) 8 : 41±46
rial in these sediments has a d13C of about 0 per mil, whereas organic carbon in confining beds has a d13C of about 20 per mil. The pore-filling cements in the aquifer show the signature of isotopically light carbon derived from organic matter. Because this organic matter was oxidized by microbial activity, it follows that microbial activity is driving the production of intergranular cements. This is a particularly well documented example of how microbial processes can alter the hydraulic properties of an aquifer system by destroying primary porosity. Many sedimentary rocks in the geologic record are cemented by secondary calcite cements, and it is likely that these cements also reflect microbial processes operating over long periods of geologic time.
Aquifers That Are Electron-Acceptor Limited The previous example describes how microbial processes in an aquifer that is electron-donor limited can serve to decrease aquifer porosity and permeability by the production of intergranular cements. In aquifers that are electron-acceptor limited, this pattern is often reversed, resulting in the production of secondary porosity. This phenomenon was first studied systematically at the crude-oil spill site in Bemidji, Minnesota (Hiebert and Bennett 1992). These investigators were particularly interested in secondary porosity associated with silicate minerals such as quartz and feldspars. They prepared in situ microcosms by crushing feldspars, sieving them to obtain uniform size, cleaning them with low-power ultrasonification, placing them in porous polyethylene cylinders, and submerging them in wells tapping a petroleum-contaminated aquifer for 14 months. Split samples of material placed into each microcosm were left unreacted to serve as controls. On recovery, the mineral samples were examined with scanning electron microscopy. Results indicate that bacterial cells, exhibiting a variety of morphologies, colonized mineral surfaces and that there was intense etching of the feldspars in particular. Some of this etching was attributed to chemical dissolution due to the relatively high concentrations of organic acids in the groundwater. Other dissolution features were associated with individual cells or colonies of cells. It was observed that cells created a ªreaction zoneº in their immediate vicinity in which organic acids, and possibly exoenzymes produced within the cell, created dissolution ªpitsº and a net increase in secondary porosity. In addition to experimental evidence that microorganisms can produce secondary porosity in aquifers (Hiebert and Bennett 1992), there is field evidence of this phenomenon. It has been shown that quartz grains within a petroleum hydrocarbon-contaminated aquifer (McMahon et al. 1995) exhibit pitting and etching features that are not observed in quartz grains outside the contaminated zone. These investigators also show Springer-Verlag
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that the greatest amount of secondary-porosity development in this aquifer is associated with high concentrations of organic acids. This observation confirms that microbially produced intermediate products such as organic acids are directly involved in the observed porosity development, as was suggested by experimental evidence (Hiebert and Bennett 1992). The production of secondary porosity by microbial activity in aquifers that are electron-acceptor limited has several practical implications. In chemically contaminated aquifers, the production of porosity can lead to the entrapment of oily-phase contaminants, which can serve to complicate the process of aquifer remediation. On the other hand, the production of micropores and the subsequent diffusion of dissolved contaminants into them can serve to restrict the transport of dissolved contaminants (Wood et al. 1990). The most important economic effect of porosity production in these aquifers, however, occurs in petroleum reservoirs. Petrographic examination of rocks from petroleum reservoirs has long indicated that the introduction of hydrocarbons can lead to porosity enhancement (Moncure et al. 1984). This porosity enhancement, in turn, can lead to the accumulation of economically important quantities of petroleum or natural gas. Much of the porosity associated with important petroleum reservoirs is probably a direct result of microbial processes.
Conclusions Microbial processes affect the chemistry of groundwater and the physical properties of aquifers in both pristine and contaminated aquifers. In pristine aquifers, microbial metabolism is often limited by the availability of electron donors, and the slow oxidation of natural sedimentary organic matter leads to the sequential consumption of electron acceptors in the sequence O2±Fe(III)±SO4±CO2. In aquifers contaminated by human activities, microbial metabolism is more often limited by the availability of electron acceptors, and this sequence of electron-acceptor utilization is reversed. Microbial processes in both pristine and contaminated aquifers can lead to either the production or destruction of secondary porosity and permeability. These processes, in turn, affect the water-bearing or oil-bearing properties of aquifers and oil reservoirs. Acknowledgments Preparation of this paper was supported by the Toxic Substances Hydrology Program of the US Geological Survey.
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