Crustal Geophysics and Geochemistry Science Center

Integrated Methods Development Project

Geochemical Methods - Biogeochemical Methods

Subtask Objectives

Development of carbon-rich mature soils over exposed metal-mine waste piles to mitigate acid generation is a component of some remediation strategies. Microbes can have a pronounced effect on movement of CO2 in and out of soils, and thus the carbon content of the soil. Several factors, especially microbial activity, can cause the carbon to remain stored in soils, be released back into the atmosphere, or react with certain minerals to form carbonates. The role of mine wastes as sinks for CO2, especially in the form of carbonate minerals, has not been thoroughly studied. This subtask will investigate the role of microbes in the earliest stages of metal-mine waste soil formation.

This research will study microbial factors that affect the flux of CO2 (production versus removal) in soils that have developed naturally or have been engineered on metal-mine waste piles. The primary goal is to determine microbial factors that are most important in soil CO2 movement, and in doing so, how these factors might be altered to enhance soil development on mine wastes, how to better-define the long-term interaction of microbes, carbon, and mine waste minerals, and to develop a process model of soil formation in metal-mine wastes. Much interest in the carbon cycle has appeared in recent years with respect to global change issues. This subtask will give the Minerals Program the capability to examine some detailed interactions of microbes and geologic media in the carbon cycle. In addition, this capability should prove useful if future funding for research on the carbon cycle is increased.

Tools are being developed to couple the quantification of microbial groups with a sequence -based analyses of community composition and diversity. The methods developed under this task will be applied to several projects the broad theme of studies of microbial groups whose metabolic activities control the mobility or reactivity of major or trace elements of concern. An additional initative is the testing and application kitbased techniques for the determination of aquatic, sediment, and plant toxicity indicators for scarce, technologically-important metals such as Te, In, Ga, and Li in environmentally relevant forms.

In developing these coupled quantification/community description methods, our objectives are to describe the dynamic role of microbial populations in sequestering and mobilizing elements of concern at specific sites or under specific conditions, and to be able to model the processes by which microbes carry out these functions.

Planned Work

Additional experiments focusing on the flux of CO2 in mine waste materials will be undertaken and completed. Some of these experiments will be run at higher pH (>6.0) to see if this enhances the sequestration of CO2 in the solid (mineral and organic) reservoirs by way of increasing the sizes of the different carbon reservoirs. This requires major changes in the reaction vessel setup and will likely change the types of microbes that become dominant in the process of CO2 sequestration and "soil" formation. Results at the low pH values attained by letting the system stabilize on its own have shown very slow CO2 uptake by the system. This slow uptake probably reflects the equally slow process of carbon assimilation by the lithotrophic microbes at low pH.

Work this year continues on three fronts: (1) submitting one of the two products listed in planning stage, (2) testing automatied ribosomal intergenic spacer analysis (ARISA) for microbial diversity assessment, and (3) testing, validating, and troubleshooting kit based aquatic, sediment, and plant toxicity tests as applied to scarce, technologically-important metals such as Ga, Li, In, and Te.



  • Foster, A.L., Ashley, R.P., Ona-Nguema, G., Brown, Jr., G.E., Luber, E., White, III, R., and Tufano, K., 2010, Microbially-mediated arsenic cycling at the Lava Cap Mine Superfund Site, Nevada County, CA: Geological Society of America Abstracts with Programs, Vol. 42, No. 5, p. 500.
  • Foster, A.L., Ona-Nguema, G., and Brown, Jr., G.E., 2008, Role of microbes in attenuation and mobilization of arsenic at the Lava Cap Mine Superfund site, Nevada County, CA: The 236th American Chemical Society National Meeting, Philadelphia, PA, August 17-21, 2008.


  • Foster, A L., Munk, L., Koski, R.A., Shanks, III, W.C., and Stillings, L.L., 2008, Relationships between microbial communities and environmental parameters at sites impacted by mining of volcanogenic massive sulfide deposits, Prince William Sound, Alaska: Applied Geochemistry 23 (2), pp. 279-307.
  • Yager, D.B., Stanton, M.R., Choate, L.M., and Burchell, Alison, 2009, Acid neutralizing capacity and leachate results for igneous rocks, with associated carbon contents of derived soils, Animas River AML site, Silverton, Colorado, in Barnhisel, R.I., ed., 2009 National Meeting of the American Society of Reclamation, Billings, MT, Revitalizing the Environment: Proven Solutions and Innovative Approaches, ASMR, Lexington, KY, pp. 1662-1697.


  • Andrea Foster, 2008, Development and Application of Denaturing High Performance Liquid Chromatography (DHPLC) Methods for the Analysis of Microbial Community Composition: U.S. Geological Survey Workshop.

Contact Information

Andrea Foster
Bldg. 15, McKelvey Building 345 Middllefield Road Mail Stop 901
Menlo Park, CA 94025-3561
Phone: 650-329-5437
Email: Andrea Foster

Mark Stanton
Box 25046 MS 964 Denver Federal Center
Denver, CO 80225-0046
Phone: 303-236-1924
Email: Mark Stanton

Douglas Yager
Box 25046 MS 973 Denver Federal Center
Denver, CO 80225-0046
Phone: 303-236-2487
Email: Douglas Yager

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